diff --git a/.gitignore b/.gitignore
index a110f14c6e77ce9a8f80ee9f71b36315b6edfc6e..6c8603940a54ec0ace3ed0582fc786da328c81d9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,6 +13,9 @@ bin/*.prj
bin/*.txt
segmentationData/
+# Ignore segmentation help function used in compiled LEVER versions.
+CompiledSegHelp.m
+
#ignore thumbnails created by windows
Thumbs.db
#Ignore files build by Visual Studio
@@ -58,3 +61,12 @@ src/MATLAB/*.csv
src/MATLAB/filmstrip/*/*
src/MATLAB/*.exe
bin64/*.exe
+*.ipdb
+*.iobj
+*.exp
+*.tlog
+*.idb
+*.opendb
+src/c/Output/TrackerMex/Debug_x64/
+src/c/Output/TrackerMex/Release_x64/
+src/c/trackerMex.mexw64
diff --git a/src/gnu gpl v3.txt b/LICENSE
similarity index 100%
rename from src/gnu gpl v3.txt
rename to LICENSE
diff --git a/bin64/LEVER_SegAndTrackFolders.exe b/bin64/LEVER_SegAndTrackFolders.exe
index 1d9f15730b67a1dc6f68cc25a76dd4fc5471f4b4..59b002c7389308f269cd3415c3c5fbb0a80cf299 100644
Binary files a/bin64/LEVER_SegAndTrackFolders.exe and b/bin64/LEVER_SegAndTrackFolders.exe differ
diff --git a/bin64/LEVer.exe b/bin64/LEVer.exe
index fc1b01a469a5d4ec7664a39cabc50e9a44b7fd2d..e8d5b9d9561db81d894b43758ebd9937a07bce62 100644
Binary files a/bin64/LEVer.exe and b/bin64/LEVer.exe differ
diff --git a/bin64/MTC.exe b/bin64/MTC.exe
deleted file mode 100644
index 041116cabb278981321a8cd7f5978cd015dc6819..0000000000000000000000000000000000000000
Binary files a/bin64/MTC.exe and /dev/null differ
diff --git a/bin64/Segmentor.exe b/bin64/Segmentor.exe
index 6f743777da97bf502da52284a6acce4d84ea218d..a79c01b79d1a5e6138f0c41f584d167ac68e1170 100644
Binary files a/bin64/Segmentor.exe and b/bin64/Segmentor.exe differ
diff --git a/src/MATLAB/+Helper/.gitignore b/src/MATLAB/+Dev/.gitignore
similarity index 100%
rename from src/MATLAB/+Helper/.gitignore
rename to src/MATLAB/+Dev/.gitignore
diff --git a/src/MATLAB/+Dev/BuildDependencyGraph.m b/src/MATLAB/+Dev/BuildDependencyGraph.m
new file mode 100644
index 0000000000000000000000000000000000000000..517cc444a11fedbf72eb5dafee55511f88c9e7a0
--- /dev/null
+++ b/src/MATLAB/+Dev/BuildDependencyGraph.m
@@ -0,0 +1,108 @@
+function graphStruct = BuildDependencyGraph(chkPath, bRecurseExternal)
+ if ( ~exist('chkPath','var') || isempty(chkPath) )
+ chkPath = pwd();
+ end
+
+ if ( ~exist('bRecurseExternal','var'))
+ bRecurseExternal = true;
+ end
+
+ %% Make sure we get back to our current dir even on error.
+ oldDir = cd(chkPath);
+ cleanupObj = onCleanup(@()(cd(oldDir)));
+
+ %%
+ filenames = getAllFiles(chkPath);
+
+ %% Initialize sparse matrix assuming a fanout of about 10x
+ n = length(filenames);
+ graphStruct = struct('nodes',{filenames}, 'graph',{sparse([],[],[],n,n,10*n)});
+
+ graphStruct = recursiveGetDeps(chkPath, graphStruct, filenames, bRecurseExternal);
+ graphStruct = sortNodes(chkPath,graphStruct);
+end
+
+function graphStruct = sortNodes(localPath, graphStruct)
+ bLocal = strncmp(localPath,graphStruct.nodes, length(localPath));
+ localIdx = find(bLocal);
+ externalIdx = find(~bLocal);
+
+ %% Sort lexicographically, but all local functions are first.
+ [~,localSrt] = sort(graphStruct.nodes(bLocal));
+ [~,externalSrt] = sort(graphStruct.nodes(~bLocal));
+
+ srtIdx = [localIdx(localSrt); externalIdx(externalSrt)];
+
+ graphStruct.nodes = graphStruct.nodes(srtIdx);
+ graphStruct.graph = graphStruct.graph(srtIdx,:);
+ graphStruct.graph = graphStruct.graph(:,srtIdx);
+end
+
+function graphStruct = recursiveGetDeps(localPath,graphStruct, checkNames, bRecurseExternal)
+ if ( isempty(checkNames) )
+ return;
+ end
+
+ newEntries = {};
+
+ matRoot = matlabroot();
+ % Get single-link dependencies
+ for i=1:length(checkNames)
+ [fList,pList] = matlab.codetools.requiredFilesAndProducts(checkNames{i}, 'toponly');
+ toolboxes = arrayfun(@(x)(fullfile(matRoot,'toolbox',x.Name)),pList, 'UniformOutput',false);
+
+ selfIdx = find(strcmp(checkNames{i},fList));
+ if ( isempty(selfIdx) )
+ selfIdx = 1;
+ fList = [checkNames(i) fList];
+ end
+
+ newNodes = [fList.'; toolboxes.'];
+ newGraph = createCallGraph(selfIdx, newNodes);
+ newStruct = struct('nodes',{newNodes},'graph',{newGraph});
+
+ [graphStruct,addedNodes] = Dev.MergeGraphStruct(graphStruct, newStruct);
+ newEntries = [newEntries; addedNodes];
+ end
+
+ % Don't recurse through external dependencies
+ bMatlab = strncmp(matRoot,newEntries, length(matRoot));
+ newEntries = newEntries(~bMatlab);
+ if ( ~bRecurseExternal )
+ bNewLocal = strncmp(localPath,newEntries, length(localPath));
+ newEntries = newEntries(bNewLocal);
+ end
+
+ graphStruct = recursiveGetDeps(localPath,graphStruct, newEntries, bRecurseExternal);
+end
+
+function callGraph = createCallGraph(callerIdx,newNodes)
+ jIdx = setdiff(1:length(newNodes),callerIdx);
+ iIdx = repmat(callerIdx,1,length(jIdx));
+
+ callGraph = sparse(iIdx,jIdx, ones(1,length(jIdx)), length(newNodes),length(newNodes), length(jIdx));
+end
+
+function fullNames = getAllFiles(dirName)
+ matlabFiles = what(dirName);
+
+ funcFileNames = vertcat(matlabFiles.m);
+ funcFileNames = [funcFileNames; vertcat(matlabFiles.mex)];
+
+ fullNames = cellfun(@(x)(fullfile(dirName,x)), funcFileNames, 'UniformOutput',false);
+
+ for i=1:length(matlabFiles.packages)
+ pkgFullNames = getAllFiles(fullfile(dirName, ['+' matlabFiles.packages{i}]));
+ fullNames = [fullNames; pkgFullNames];
+ end
+
+ for i=1:length(matlabFiles.classes)
+ classDir = fullfile(dirName, ['@' matlabFiles.classes{i}]);
+ if ( ~exist(classDir,'dir') )
+ continue;
+ end
+
+ classFullNames = getAllFiles(classDir);
+ fullNames = [fullNames; classFullNames];
+ end
+end
diff --git a/src/MATLAB/+Dev/BuildToolboxMap.m b/src/MATLAB/+Dev/BuildToolboxMap.m
new file mode 100644
index 0000000000000000000000000000000000000000..b1f67fcbe607c9174cad82fe06653a3148cdfc9d
--- /dev/null
+++ b/src/MATLAB/+Dev/BuildToolboxMap.m
@@ -0,0 +1,27 @@
+function toolboxMap = BuildToolboxMap()
+ toolboxRoot = toolboxdir('');
+ toolboxMap = containers.Map('keyType','char', 'valueType','any');
+
+ % Ignore fixPoint, because
+ toolboxList = dir(toolboxRoot);
+
+ bInvalidName = arrayfun(@(x)(strcmp(x.name,'.') || strcmp(x.name,'..') || strcmp(x.name,'fixpoint')), toolboxList);
+ bValidDir = ~bInvalidName & (vertcat(toolboxList.isdir) > 0);
+ toolboxList = toolboxList(bValidDir);
+
+ % Always add local/shared directory to matlab
+ toolboxMap('MATLAB') = {fullfile(toolboxRoot,'local');fullfile(toolboxRoot,'shared')};
+
+ for i=1:length(toolboxList)
+ verStruct = ver(toolboxList(i).name);
+ if ( isempty(verStruct) )
+ continue;
+ end
+
+ if ( isKey(toolboxMap,verStruct.Name) )
+ toolboxMap(verStruct.Name) = [toolboxMap(verStruct.Name); {fullfile(toolboxRoot,toolboxList(i).name)}];
+ else
+ toolboxMap(verStruct.Name) = {fullfile(toolboxRoot,toolboxList(i).name)};
+ end
+ end
+end
diff --git a/src/MATLAB/+Dev/CheckMEXSynch.m b/src/MATLAB/+Dev/CheckMEXSynch.m
deleted file mode 100644
index cd8c746a9a0879d5c87f0875fa987cd7c6627f81..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Dev/CheckMEXSynch.m
+++ /dev/null
@@ -1,22 +0,0 @@
-function CheckMEXSynch(checkGraph)
- [checkOut checkIn] = mexDijkstra('debugAllEdges');
-
- checkOut = sortrows(checkOut);
- checkIn = sortrows(checkIn);
-
- if ( any(checkOut(:) ~= checkIn(:)) )
- error('In/Out MEX Edges are out of synch.');
- end
-
- if ( exist('checkGraph','var') )
- [rcm, ccm] = find(checkGraph > 0);
- graphInd = sub2ind(size(checkGraph), rcm, ccm);
- checkMAT = [rcm ccm full(checkGraph(graphInd))];
-
- checkMAT = sortrows(checkMAT);
-
- if ( any(checkOut(:) ~= checkMAT(:)) )
- error('MEX Edges out of synch with Matlab.');
- end
- end
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Dev/CompileLEVer.m b/src/MATLAB/+Dev/CompileLEVer.m
index ac233f2413fec459038423cdbee6b36fab4542ab..344049255a25240e914bf86d1787cbcecda012de 100644
--- a/src/MATLAB/+Dev/CompileLEVer.m
+++ b/src/MATLAB/+Dev/CompileLEVer.m
@@ -2,10 +2,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -25,35 +25,18 @@
function CompileLEVer(forceVersion)
totalTime = tic();
-
- % Try to set up git for the build, give a warning about checking the
- % fallback file if we can't find git.
- bFoundGit = Dev.SetupGit();
- if ( ~bFoundGit )
- questionStr = sprintf('%s\n%s','Cannot find git you should verify the fallback file version info before building.','Are you sure you wish to continue with the build?');
- result = questdlg(questionStr,'Build Warning','Yes','No','No');
- if ( strcmpi(result,'No') )
- return;
- end
- end
-
- % Give a messagebox warning if there are uncommitted changes.
- % Note: even committed changes may not have been pushed to server.
- [status,result] = system('git status --porcelain');
- if ( status == 0 && (length(result) > 1) )
- questionStr = sprintf('%s\n%s','There are uncommitted changes in your working directory','Are you sure you wish to continue with the build?');
- result = questdlg(questionStr,'Build Warning','Yes','No','No');
- if ( strcmpi(result,'No') )
- return;
- end
- end
-
- if ( ~exist('forceVersion', 'var') )
- Dev.MakeVersion();
- else
- Dev.MakeVersion(0, forceVersion);
+
+ if ( ~exist('forceVersion','var') )
+ forceVersion = '';
end
+
+ %% General compiler setup: Deals with version updates and pulls external dependencies
+ initStruct = Dev.InitCompiler('LEVER',forceVersion);
+
+ %% Build FrameSegmentor help information into a function for use in compiled LEVER
+ Dev.MakeSegHelp();
+ %% Setup visual studio for MEX compilation
[vsStruct comparch] = setupCompileTools();
bindir = '..\..\bin';
@@ -65,11 +48,15 @@ function CompileLEVer(forceVersion)
mkdir(bindir);
end
+ %% Compile all MEX files
outputFiles = {};
newOutput = compileMEX('mexMAT', vsStruct);
outputFiles = [outputFiles; {newOutput}];
+ newOutput = compileMEX('Tracker', vsStruct);
+ outputFiles = [outputFiles; {newOutput}];
+
newOutput = compileMEX('mexDijkstra', vsStruct);
outputFiles = [outputFiles; {newOutput}];
@@ -82,49 +69,18 @@ function CompileLEVer(forceVersion)
newOutput = compileMEX('mexHashData', vsStruct);
outputFiles = [outputFiles; {newOutput}];
-
- newOutput = compileEXE('MTC', vsStruct, bindir);
- outputFiles = [outputFiles; {newOutput}];
-
- [toolboxStruct externalStruct] = Dev.GetExternalDependencies();
- if ( ~isempty(externalStruct.deps) )
- fprintf('ERROR: Some local functions have external dependencies\n');
- for i=1:length(externalStruct.deps)
- fprintf('[%d] %s\n', i, externalStruct.deps{i});
- for j=1:length(externalStruct.funcs{i})
- if ( ~isempty(externalStruct.callers{i}{j}) )
- for k=1:length(externalStruct.callers{i}{j})
- localName = Dev.GetLocalName(externalStruct.callers{i}{j}{k});
- fprintf(' %s calls: %s\n', localName, externalStruct.funcs{i}{j});
- end
- end
- end
- fprintf('------\n');
- end
-
-% error('External dependencies cannot be packaged in a MATLAB executable');
- questionStr = sprintf('%s\n%s','Possible external dependencies were found in project, you should verify all these functions are local before continuing the build.','Are you sure you wish to continue?');
- result = questdlg(questionStr,'External Dependency Warning','Continue','Cancel','Cancel');
- if ( strcmpi(result,'Cancel') )
- return;
- end
- end
-
- % temporarily remove any startup scripts that would normally be run by matlabrc
- enableStartupScripts(false);
+ %% Compile LEVER, Segmentor, and batch LEVER_SegAndTrackFolders.
addImgs = {'+UI\backFrame.png'; '+UI\forwardFrame.png'; '+UI\pause.png';'+UI\play.png';'+UI\stop.png'};
- newOutput = compileMATLAB('LEVer', bindir, addImgs, toolboxStruct.deps);
+ newOutput = compileMATLAB('LEVer', bindir, addImgs, initStruct.toolboxList);
outputFiles = [outputFiles; {newOutput}];
- newOutput = compileMATLAB('LEVER_SegAndTrackFolders', bindir, {}, toolboxStruct.deps);
+ newOutput = compileMATLAB('LEVER_SegAndTrackFolders', bindir, {}, initStruct.toolboxList);
outputFiles = [outputFiles; {newOutput}];
- newOutput = compileMATLAB('Segmentor', bindir, {}, toolboxStruct.deps);
+ newOutput = compileMATLAB('Segmentor', bindir, {}, initStruct.toolboxList);
outputFiles = [outputFiles; {newOutput}];
- enableStartupScripts(true);
-
fprintf('\n');
% mcrfile = mcrinstaller();
@@ -133,16 +89,16 @@ function CompileLEVer(forceVersion)
bIsEXE = cellfun(@(x)(~isempty(x)), strfind(lower(outputFiles), '.exe'));
exeOutputs = outputFiles(bIsEXE);
- verSuffix = Helper.GetVersion('file');
- zip(fullfile(bindir,['LEVer' verSuffix '.zip']), [exeOutputs; {'*.bat'}], bindir);
+% verSuffix = Dev.GetVersion('file');
+% zip(fullfile(bindir,['LEVer' verSuffix '.zip']), [exeOutputs; {'*.bat'}], bindir);
toc(totalTime)
end
function [vsStruct comparch] = setupCompileTools()
- vsStruct.vstoolroot = getenv('VS100COMNTOOLS');
+ vsStruct.vstoolroot = getenv('VS140COMNTOOLS');
if ( isempty(vsStruct.vstoolroot) )
- error('Cannot compile MTC and mexMAT without Visual Studio 2010');
+ error('Cannot compile MEX files without Visual Studio 2015');
end
setenv('MATLAB_DIR', matlabroot());
@@ -152,12 +108,8 @@ function [vsStruct comparch] = setupCompileTools()
vsStruct.buildbits = '64';
vsStruct.buildenv = fullfile(vsStruct.vstoolroot,'..','..','vc','bin','amd64','vcvars64.bat');
vsStruct.buildplatform = 'x64';
- elseif ( strcmpi(comparch,'win32') )
- vsStruct.buildbits = '32';
- vsStruct.buildenv = fullfile(vsStruct.vstoolroot,'..','..','vc','bin','vcvars32.bat');
- vsStruct.buildplatform = 'win32';
else
- error('Only windows 32/64-bit builds are currently supported');
+ error('Only windows 64-bit builds are currently supported');
end
system(['"' vsStruct.buildenv '"' ]);
@@ -208,8 +160,8 @@ function outputFile = compileMATLAB(projectName, bindir, extrasList, toolboxList
end
extrasList = vertcat({'LEVER_logo.tif';
'+Segmentation\FrameSegmentor_*.m';
- '+Helper\GetVersion.m';
- '+Helper\VersionInfo.m'}, extrasList);
+ '+Dev\GetVersion.m';
+ '+Dev\VersionInfo.m'}, extrasList);
extraCommand = '';
if ( ~isempty(extrasList) )
@@ -237,45 +189,3 @@ function outputFile = compileMATLAB(projectName, bindir, extrasList, toolboxList
fprintf('Done (%f sec)\n', toc(compileTime));
end
-
-function enableStartupScripts(bEnable)
- searchPrefix = '';
- renamePrefix = 'disabled_';
- if ( bEnable )
- searchPrefix = 'disabled_';
- renamePrefix = '';
- end
-
- searchName = [searchPrefix 'startup.m'];
- newName = [renamePrefix 'startup.m'];
-
- startupScripts = findFilesInPath(searchName, userpath);
- for i=1:length(startupScripts)
- scriptPath = fileparts(startupScripts{i});
- movefile(startupScripts{i}, fullfile(scriptPath,newName));
- end
-end
-
-function fullNames = findFilesInPath(filename, searchPaths)
- fullNames = {};
-
- chkPaths = [];
- while ( ~isempty(searchPaths) )
- [newPath remainder] = strtok(searchPaths, pathsep);
- if ( isempty(newPath) )
- searchPaths = remainder;
- continue;
- end
-
- chkPaths = [chkPaths; {newPath}];
- searchPaths = remainder;
- end
-
- for i=1:length(chkPaths)
- chkFullPath = fullfile(chkPaths{i}, filename);
- if ( exist(chkFullPath, 'file') )
- fullNames = [fullNames; {chkFullPath}];
- end
- end
-end
-
diff --git a/src/MATLAB/+Dev/DataHash.m b/src/MATLAB/+Dev/DataHash.m
deleted file mode 100644
index 31a2986956a96398d1bd91678b18a318819eb11b..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Dev/DataHash.m
+++ /dev/null
@@ -1,408 +0,0 @@
-function Hash = DataHash(Data, Opt)
-% DATAHASH - Checksum for Matlab array of any type
-% This function creates a hash value for an input of any type. The type and
-% dimensions of the input are considered as default, such that UINT8([0,0]) and
-% UINT16(0) have different hash values. Nested STRUCTs and CELLs are parsed
-% recursively.
-%
-% Hash = DataHash(Data, Opt)
-% INPUT:
-% Data: Array of these built-in types:
-% (U)INT8/16/32/64, SINGLE, DOUBLE, (real or complex)
-% CHAR, LOGICAL, CELL (nested), STRUCT (scalar or array, nested),
-% function_handle.
-% Opt: Struct to specify the hashing algorithm and the output format.
-% Opt and all its fields are optional.
-% Opt.Method: String, known methods for Java 1.6 (Matlab 2009a):
-% 'SHA-1', 'SHA-256', 'SHA-384', 'SHA-512', 'MD2', 'MD5'.
-% Known methods for Java 1.3 (Matlab 6.5):
-% 'MD5', 'SHA-1'.
-% Default: 'MD5'.
-% Opt.Format: String specifying the output format:
-% 'hex', 'HEX': Lower/uppercase hexadecimal string.
-% 'double', 'uint8': Numerical vector.
-% 'base64': Base64 encoded string, only printable
-% ASCII characters, 33% shorter than 'hex'.
-% Default: 'hex'.
-% Opt.Input: Type of the input as string, not case-sensitive:
-% 'array': The contents, type and size of the input [Data] are
-% considered for the creation of the hash. Nested CELLs
-% and STRUCT arrays are parsed recursively. Empty arrays of
-% different type reply different hashs.
-% 'file': [Data] is treated as file name and the hash is calculated
-% for the files contents.
-% 'bin': [Data] is a numerical, LOGICAL or CHAR array. Only the
-% binary contents of the array is considered, such that
-% e.g. empty arrays of different type reply the same hash.
-% Default: 'array'.
-%
-% OUTPUT:
-% Hash: String, DOUBLE or UINT8 vector. The length depends on the hashing
-% method.
-%
-% EXAMPLES:
-% % Default: MD5, hex:
-% DataHash([]) % 7de5637fd217d0e44e0082f4d79b3e73
-% % MD5, Base64:
-% Opt.Format = 'base64';
-% Opt.Method = 'MD5';
-% DataHash(int32(1:10), Opt) % bKdecqzUpOrL4oxzk+cfyg
-% % SHA-1, Base64:
-% S.a = uint8([]);
-% S.b = {{1:10}, struct('q', uint64(415))};
-% Opt.Method = 'SHA-1';
-% DataHash(S, Opt) % ZMe4eUAp0G9TDrvSW0/Qc0gQ9/A
-% % SHA-1 of binary values:
-% Opt.Method = 'SHA-1';
-% Opt.Input = 'bin';
-% DataHash(1:8, Opt) % 826cf9d3a5d74bbe415e97d4cecf03f445f69225
-%
-% NOTE:
-% Function handles and user-defined objects cannot be converted uniquely:
-% - The subfunction ConvertFuncHandle uses the built-in function FUNCTIONS,
-% but the replied struct can depend on the Matlab version.
-% - It is tried to convert objects to UINT8 streams in the subfunction
-% ConvertObject. A conversion by STRUCT() might be more appropriate.
-% Adjust these subfunctions on demand.
-%
-% MATLAB CHARs have 16 bits! In consequence the string 'hello' is treated as
-% UINT16('hello') for the binary input method.
-%
-% DataHash uses James Tursa's smart and fast TYPECASTX, if it is installed:
-% http://www.mathworks.com/matlabcentral/fileexchange/17476
-% As fallback the built-in TYPECAST is used automatically, but for large
-% inputs this can be more than 10 times slower.
-% For Matlab 6.5 installing typecastx is obligatory to run DataHash.
-%
-% Tested: Matlab 6.5, 7.7, 7.8, WinXP, Java: 1.3.1_01, 1.6.0_04.
-% Author: Jan Simon, Heidelberg, (C) 2011 matlab.THISYEAR(a)nMINUSsimon.de
-%
-% See also: TYPECAST, CAST.
-% FEX:
-% Michael Kleder, "Compute Hash", no structs and cells:
-% http://www.mathworks.com/matlabcentral/fileexchange/8944
-% Tim, "Serialize/Deserialize", converts structs and cells to a byte stream:
-% http://www.mathworks.com/matlabcentral/fileexchange/29457
-% Jan Simon, "CalcMD5", MD5 only, faster C-mex, no structs and cells:
-% http://www.mathworks.com/matlabcentral/fileexchange/25921
-
-% $JRev: R-j V:010 Sum:q3tnsDSkI19o Date:09-Sep-2011 13:32:19 $
-% $License: BSD (use/copy/change/redistribute on own risk, mention the author) $
-% $File: Tools\GLFile\DataHash.m $
-% History:
-% 001: 01-May-2011 21:52, First version.
-% 007: 10-Jun-2011 10:38, [Opt.Input], binary data, complex values considered.
-
-% Main function: ===============================================================
-% Java is needed:
-if ~usejava('jvm')
- error(['JSimon:', mfilename, ':NoJava'], ...
- '*** %s: Java is required.', mfilename);
-end
-
-% typecastx creates a shared data copy instead of the deep copy as Matlab's
-% TYPECAST - for a [1000x1000] DOUBLE array this is 100 times faster!
-persistent usetypecastx
-if isempty(usetypecastx)
- usetypecastx = ~isempty(which('typecastx')); % Run the slow WHICH once only
-end
-
-% Default options: -------------------------------------------------------------
-Method = 'MD5';
-OutFormat = 'hex';
-isFile = false;
-isBin = false;
-
-% Check number and type of inputs: ---------------------------------------------
-nArg = nargin;
-if nArg == 2
- if isa(Opt, 'struct') == 0 % Bad type of 2nd input:
- error(['JSimon:', mfilename, ':BadInput2'], ...
- '*** %s: 2nd input [Opt] must be a struct.', mfilename);
- end
-
- % Specify hash algorithm:
- if isfield(Opt, 'Method')
- Method = upper(Opt.Method);
- end
-
- % Specify output format:
- if isfield(Opt, 'Format')
- OutFormat = Opt.Format;
- end
-
- % Check if the Input type is specified - default: 'array':
- if isfield(Opt, 'Input')
- if strcmpi(Opt.Input, 'File')
- isFile = true;
- if ischar(Data) == 0
- error(['JSimon:', mfilename, ':CannotOpen'], ...
- '*** %s: 1st input is not a file name', mfilename);
- end
-
- if exist(Data, 'file') ~= 2
- error(['JSimon:', mfilename, ':FileNotFound'], ...
- '*** %s: File not found: %s.', mfilename, Data);
- end
-
- elseif strncmpi(Opt.Input, 'bin', 3) % Accept 'binary'
- isBin = true;
- if (isnumeric(Data) || ischar(Data) || islogical(Data)) == 0
- error(['JSimon:', mfilename, ':BadDataType'], ...
- '*** %s: 1st input is not numeric, CHAR or LOGICAL.', mfilename);
- end
- end
- end
-
-elseif nArg ~= 1 % Bad number of arguments:
- error(['JSimon:', mfilename, ':BadNInput'], ...
- '*** %s: 1 or 2 inputs required.', mfilename);
-end
-
-% Create the engine: -----------------------------------------------------------
-try
- Engine = java.security.MessageDigest.getInstance(Method);
-catch
- error(['JSimon:', mfilename, ':BadInput2'], ...
- '*** %s: Invalid algorithm: [%s].', mfilename, Method);
-end
-
-% Create the hash value: -------------------------------------------------------
-if isFile
- % Read the file and calculate the hash:
- FID = fopen(Data, 'r');
- if FID < 0
- error(['JSimon:', mfilename, ':CannotOpen'], ...
- '*** %s: Cannot open file: %s.', mfilename, Data);
- end
- Data = fread(FID, Inf, '*uint8');
- fclose(FID);
-
- Engine.update(Data);
- if usetypecastx
- Hash = typecastx(Engine.digest, 'uint8');
- else
- Hash = typecast(Engine.digest, 'uint8');
- end
-
-elseif isBin % Contents of an elementary array:
- if usetypecastx % Faster typecastx:
- if isreal(Data)
- Engine.update(typecastx(Data(:), 'uint8'));
- else
- Engine.update(typecastx(real(Data(:)), 'uint8'));
- Engine.update(typecastx(imag(Data(:)), 'uint8'));
- end
- Hash = typecastx(Engine.digest, 'uint8');
-
- else % Matlab's TYPECAST is less elegant:
- if isnumeric(Data)
- if isreal(Data)
- Engine.update(typecast(Data(:), 'uint8'));
- else
- Engine.update(typecast(real(Data(:)), 'uint8'));
- Engine.update(typecast(imag(Data(:)), 'uint8'));
- end
- elseif islogical(Data) % TYPECAST cannot handle LOGICAL
- Engine.update(typecast(uint8(Data(:)), 'uint8'));
- elseif ischar(Data) % TYPECAST cannot handle CHAR
- Engine.update(typecast(uint16(Data(:)), 'uint8'));
- Engine.update(typecast(Data(:), 'uint8'));
- end
- Hash = typecast(Engine.digest, 'uint8');
- end
-
-elseif usetypecastx % Faster typecastx:
- Engine = CoreHash_(Data, Engine);
- Hash = typecastx(Engine.digest, 'uint8');
-
-else % Slower built-in TYPECAST:
- Engine = CoreHash(Data, Engine);
- Hash = typecast(Engine.digest, 'uint8');
-end
-
-% Convert hash specific output format: -----------------------------------------
-switch OutFormat
- case 'hex'
- Hash = sprintf('%.2x', double(Hash));
- case 'HEX'
- Hash = sprintf('%.2X', double(Hash));
- case 'double'
- Hash = double(reshape(Hash, 1, []));
- case 'uint8'
- Hash = reshape(Hash, 1, []);
- case 'base64'
- Hash = fBase64_enc(double(Hash));
- otherwise
- error(['JSimon:', mfilename, ':BadOutFormat'], ...
- '*** %s: [Opt.Format] must be: HEX, hex, uint8, double, base64.', ...
- mfilename);
-end
-
-% return;
-
-% ******************************************************************************
-function Engine = CoreHash_(Data, Engine)
-% This mothod uses the faster typecastx version.
-
-% Consider the type and dimensions of the array to distinguish arrays with the
-% same data, but different shape: [0 x 0] and [0 x 1], [1,2] and [1;2],
-% DOUBLE(0) and SINGLE([0,0]):
-Engine.update([uint8(class(Data)), typecastx(size(Data), 'uint8')]);
-
-if isstruct(Data) % Hash for all array elements and fields:
- F = sort(fieldnames(Data)); % Ignore order of fields
- Engine = CoreHash_(F, Engine); % Catch the fieldnames
-
- for iS = 1:numel(Data) % Loop over elements of struct array
- for iField = 1:length(F) % Loop over fields
- Engine = CoreHash_(Data(iS).(F{iField}), Engine);
- end
- end
-
-elseif iscell(Data) % Get hash for all cell elements:
- for iS = 1:numel(Data)
- Engine = CoreHash_(Data{iS}, Engine);
- end
-
-elseif isnumeric(Data) || islogical(Data) || ischar(Data)
- if isempty(Data) == 0
- if isreal(Data) % TRUE for LOGICAL and CHAR also:
- Engine.update(typecastx(Data(:), 'uint8'));
- else % typecastx accepts complex input:
- Engine.update(typecastx(real(Data(:)), 'uint8'));
- Engine.update(typecastx(imag(Data(:)), 'uint8'));
- end
- end
-
-elseif isa(Data, 'function_handle')
- Engine = CoreHash(ConvertFuncHandle(Data), Engine);
-
-else % Most likely this is a user-defined object:
- try
- Engine = CoreHash(ConvertObject(Data), Engine);
- catch
- warning(['JSimon:', mfilename, ':BadDataType'], ...
- ['Type of variable not considered: ', class(Data)]);
- end
-end
-
-% return;
-
-% ******************************************************************************
-function Engine = CoreHash(Data, Engine)
-% This methods uses the slower TYPECAST of Matlab
-% See CoreHash_ for comments.
-
-Engine.update([uint8(class(Data)), typecast(size(Data), 'uint8')]);
-
-if isstruct(Data) % Hash for all array elements and fields:
- F = sort(fieldnames(Data)); % Ignore order of fields
- Engine = CoreHash(F, Engine); % Catch the fieldnames
- for iS = 1:numel(Data) % Loop over elements of struct array
- for iField = 1:length(F) % Loop over fields
- Engine = CoreHash(Data(iS).(F{iField}), Engine);
- end
- end
-elseif iscell(Data) % Get hash for all cell elements:
- for iS = 1:numel(Data)
- Engine = CoreHash(Data{iS}, Engine);
- end
-elseif isempty(Data)
-elseif isnumeric(Data)
- if ( issparse(Data) )
- chkIdx = find(Data);
- if ( isempty(chkIdx) )
- return;
- end
- Engine.update(typecast(chkIdx, 'uint8'));
- if isreal(Data)
- Engine.update(typecast(full(Data(chkIdx)), 'uint8'));
- else
- Engine.update(typecast(full(real(Data(chkIdx))), 'uint8'));
- Engine.update(typecast(full(imag(Data(chkIdx))), 'uint8'));
- end
-
- else
- if isreal(Data)
- Engine.update(typecast(Data(:), 'uint8'));
- else
- Engine.update(typecast(real(Data(:)), 'uint8'));
- Engine.update(typecast(imag(Data(:)), 'uint8'));
- end
- end
-elseif islogical(Data) % TYPECAST cannot handle LOGICAL
- Engine.update(typecast(uint8(Data(:)), 'uint8'));
-elseif ischar(Data) % TYPECAST cannot handle CHAR
- Engine.update(typecast(uint16(Data(:)), 'uint8'));
-elseif isa(Data, 'function_handle')
- Engine = CoreHash(ConvertFuncHandle(Data), Engine);
-else % Most likely a user-defined object:
- try
- Engine = CoreHash(ConvertObject(Data), Engine);
- catch
- warning(['JSimon:', mfilename, ':BadDataType'], ...
- ['Type of variable not considered: ', class(Data)]);
- end
-end
-
-% return;
-
-% ******************************************************************************
-function FuncKey = ConvertFuncHandle(FuncH)
-% The subfunction ConvertFuncHandle converts function_handles to a struct
-% using the Matlab function FUNCTIONS. The output of this function changes
-% with the Matlab version, such that DataHash(@sin) replies different hashes
-% under Matlab 6.5 and 2009a.
-% An alternative is using the function name and name of the file for
-% function_handles, but this is not unique for nested or anonymous functions.
-% If the MATLABROOT is removed from the file's path, at least the hash of
-% Matlab's toolbox functions is (usually!) not influenced by the version.
-% Finally I'm in doubt if there is a unique method to hash function handles.
-% Please adjust the subfunction ConvertFuncHandles to your needs.
-
-% The Matlab version influences the conversion by FUNCTIONS:
-% 1. The format of the struct replied FUNCTIONS is not fixed,
-% 2. The full paths of toolbox function e.g. for @mean differ.
-FuncKey = functions(FuncH);
-
-% ALTERNATIVE: Use name and path. The <matlabroot> part of the toolbox functions
-% is replaced such that the hash for @mean does not depend on the Matlab
-% version.
-% Drawbacks: Anonymous functions, nested functions...
-% funcStruct = functions(FuncH);
-% funcfile = strrep(funcStruct.file, matlabroot, '<MATLAB>');
-% FuncKey = uint8([funcStruct.function, ' ', funcfile]);
-
-% Finally I'm afraid there is no unique method to get a hash for a function
-% handle. Please adjust this conversion to your needs.
-
-% return;
-
-% ******************************************************************************
-function DataBin = ConvertObject(DataObj)
-% Convert a user-defined object to a binary stream. There cannot be a unique
-% solution, so this part is left for the user...
-
-% Perhaps a direct conversion is implemented:
-DataBin = uint8(DataObj);
-
-% Or perhaps this is better:
-% DataBin = struct(DataObj);
-
-% return;
-
-% ******************************************************************************
-function Out = fBase64_enc(In)
-% Encode numeric vector of UINT8 values to base64 string.
-
-Pool = [65:90, 97:122, 48:57, 43, 47]; % [0:9, a:z, A:Z, +, /]
-v8 = [128; 64; 32; 16; 8; 4; 2; 1];
-v6 = [32, 16, 8, 4, 2, 1];
-
-In = reshape(In, 1, []);
-X = rem(floor(In(ones(8, 1), :) ./ v8(:, ones(length(In), 1))), 2);
-Y = reshape([X(:); zeros(6 - rem(numel(X), 6), 1)], 6, []);
-Out = char(Pool(1 + v6 * Y));
-
-% return;
diff --git a/src/MATLAB/+Dev/FrameSegHelp.m b/src/MATLAB/+Dev/FrameSegHelp.m
new file mode 100644
index 0000000000000000000000000000000000000000..a81a70cef27a2978c46691347c2bfc58a9908724
--- /dev/null
+++ b/src/MATLAB/+Dev/FrameSegHelp.m
@@ -0,0 +1,95 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function helpStruct = FrameSegHelp(funcName)
+ helpStruct = [];
+
+ SupportedTypes = Load.GetSupportedCellTypes();
+ segInfo = [SupportedTypes.segRoutine];
+
+ segFuncs = arrayfun(@(x)(char(x.func)), segInfo, 'UniformOutput',false);
+ funcIdx = find(strcmp(segFuncs, funcName));
+ if ( isempty(funcIdx) )
+ return;
+ end
+
+ if ( isdeployed() )
+ helpStruct = Dev.CompiledSegHelp(funcName);
+ return;
+ end
+
+ chkInfo = segInfo(funcIdx);
+ chkName = char(chkInfo.func);
+
+ helpStruct.func = chkName;
+ helpStruct.summary = '';
+ helpStruct.paramHelp = cell(length(chkInfo.params),1);
+
+ helpString = help(chkName);
+ if ( isempty(helpString) )
+ helpString = chkName;
+ end
+
+ %% Get a segmentation summary from function help.
+ tokMatch = regexp(helpString,'^\s*FrameSegmentor_*\w*\s*-\s*(.+?)^\s*$', 'once','tokens','lineanchors');
+ if ( isempty(tokMatch) )
+ helpLines = strsplit(helpString,'\n');
+ funcSummary = escapeString(strtrim(helpLines{1}));
+ else
+ funcSummary = escapeString(tokMatch{1});
+ end
+
+ %% Get parameter help if available in function documentation.
+ helpStruct.summary = funcSummary;
+ for i=1:length(chkInfo.params)
+ paramName = chkInfo.params(i).name;
+
+ helpStruct.paramHelp{i} = '';
+ tokMatch = regexp(helpString,['^\s*(' paramName '.+?)^\s*$'], 'once','tokens','lineanchors');
+ if ( ~isempty(tokMatch) )
+ helpStruct.paramHelp{i} = escapeString(tokMatch{1});
+ end
+ end
+end
+
+% Escape inStr so that safeStr will reproduce inStr when passed as a format string to sprintf()
+function safeStr = escapeString(inStr)
+ escStr = {'%%','\\','\a','\b','\f','\n','\r','\t','\v'};
+ escChars = num2cell(sprintf([escStr{:}]));
+
+ escStr = [{''''''},escStr];
+ escChars = [{''''},escChars];
+
+ escMap = containers.Map(escChars,escStr);
+
+ safeStr = '';
+ for i=1:length(inStr)
+ nextChar = inStr(i);
+ if ( isKey(escMap,nextChar) )
+ nextChar = escMap(nextChar);
+ end
+
+ safeStr = [safeStr nextChar];
+ end
+end
diff --git a/src/MATLAB/+Dev/GetCommitInfo.m b/src/MATLAB/+Dev/GetCommitInfo.m
new file mode 100644
index 0000000000000000000000000000000000000000..cdfc4bbf7e354d40848a01ca698b25ccc50636f3
--- /dev/null
+++ b/src/MATLAB/+Dev/GetCommitInfo.m
@@ -0,0 +1,15 @@
+% [repoName,commitHash] = GetCommitInfo(inPath)
+%
+
+function [repoName,commitHash] = GetCommitInfo(inPath)
+ remoteUrl = Dev.GitRemote(inPath,'origin');
+
+ repoName = '';
+
+ tokMatch = regexp(remoteUrl,'\w+@[\w\-.]+:[\w\-.]+/([\w\-]+\.git)', 'tokens','once');
+ if ( ~isempty(tokMatch) )
+ repoName = tokMatch{1};
+ end
+
+ commitHash = Dev.GitCommitHash(inPath);
+end
diff --git a/src/MATLAB/+Dev/GetCoreHashList.m b/src/MATLAB/+Dev/GetCoreHashList.m
index bfc98cfaa3023fd414fb229d90635c0f7a1caaf5..7e9d004c41cadc20c9f611fcafb3318cb9fc6d33 100644
--- a/src/MATLAB/+Dev/GetCoreHashList.m
+++ b/src/MATLAB/+Dev/GetCoreHashList.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function hashList = GetCoreHashList()
global CellHulls CellTracks CellFamilies HashedCells CellPhenotypes Costs GraphEdits
diff --git a/src/MATLAB/+Dev/GetExternalDependencies.m b/src/MATLAB/+Dev/GetExternalDependencies.m
deleted file mode 100644
index 96bc7bcd55af3e3641c38e332bbe68c7bc265f1d..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Dev/GetExternalDependencies.m
+++ /dev/null
@@ -1,283 +0,0 @@
-function [toolboxStruct externalStruct calledNames callGraph] = GetExternalDependencies(chkPath)
- if ( ~exist('chkPath', 'var') )
- chkPath = pwd();
- end
-
- [localNames localFileNames] = getLocalNames(chkPath);
- [fullNames calledFrom] = recursiveGetDeps(localFileNames);
-
- bIsLocal = cellfun(@(x)(~isempty(strfind(x,chkPath))), fullNames);
- localNodeList = find(bIsLocal);
-
- [toolboxes toolboxMap] = getMatlabToolboxes(fullNames);
- toolboxFuncs = transpose(arrayfun(@(x)(fullNames(toolboxMap == x)), 1:length(toolboxes), 'UniformOutput',0));
-
- bIsMatlab = (toolboxMap > 0);
- [externalDeps externalMap] = getOtherDeps(fullNames, bIsMatlab, bIsLocal);
- externalFuncs = transpose(arrayfun(@(x)(fullNames(externalMap == x)), 1:length(externalDeps), 'UniformOutput',0));
-
- fullGraph = createCallGraph(calledFrom);
- bIsCalled = findCalledNodes(localNodeList, fullGraph);
-
- toolboxCallers = getToolboxCallers(localNodeList, toolboxes, toolboxMap, fullGraph, fullNames);
- externalCallers = getToolboxCallers(localNodeList, externalDeps, externalMap, fullGraph, fullNames);
-
-% calledNames = fullNames(bIsCalled);
-% callGraph = fullGraph(bIsCalled,bIsCalled);
- callToolboxMap = toolboxMap(bIsCalled);
- callExternalMap = externalMap(bIsCalled);
-
-% [squashNames squashGraph squashMap] = squashToolboxNodes(calledNames, callGraph, toolboxes, callToolboxMap);
-
-% usedToolboxes = unique(callToolboxMap(callToolboxMap>0));
-% toolboxes = toolboxes(usedToolboxes);
-% toolboxFuncs = toolboxFuncs(usedToolboxes);
-% toolboxCallers = toolboxCallers(usedToolboxes);
-
- usedExternal = unique(callExternalMap(callExternalMap>0));
- externalDeps = externalDeps(usedExternal);
- externalFuncs = externalFuncs(usedExternal);
- externalCallers = externalCallers(usedExternal);
-
- toolboxStruct = struct('deps', {toolboxes}, 'funcs', {toolboxFuncs}, 'callers',{toolboxCallers});
- externalStruct = struct('deps', {externalDeps}, 'funcs', {externalFuncs}, 'callers',{externalCallers});
-end
-
-function [toolboxes toolboxMap] = getMatlabToolboxes(funcNames)
- bIsMatlab = strncmpi(matlabroot, funcNames, length(matlabroot));
- matlabIdx = find(bIsMatlab);
- matlabNames = funcNames(bIsMatlab);
-
- % Add default matlab dependencies first, these will always be used
- toolboxes = {'matlab';'local';'shared'};
- toolboxMap = zeros(length(funcNames),1);
- for i=1:length(matlabNames)
- toolboxPattern = '(?<=^.+[\\/]toolbox[\\/])[^\\/]+';
- matchToolbox = regexp(matlabNames{i}, toolboxPattern, 'match', 'once');
- if ( isempty(matchToolbox) )
- continue;
- end
-
- if ( any(strcmpi(matchToolbox,toolboxes)) )
- toolboxMap(matlabIdx(i)) = find(strcmpi(matchToolbox,toolboxes));
- continue;
- end
-
- toolboxes = [toolboxes; {matchToolbox}];
- toolboxMap(matlabIdx(i)) = length(toolboxes);
- end
-end
-
-function [externalDeps externalMap] = getOtherDeps(funcNames, bIsMatlab, bIsLocal)
- externalMap = zeros(length(funcNames),1);
- externalDeps = {};
-
- bExternal = (~bIsMatlab & ~bIsLocal);
- externalFuncs = funcNames(bExternal);
-
- tokenRemains = externalFuncs;
- tokenDelims = filesep;
-
- pred = [];
- bLeaves = false(0,0);
-
- pathNodes = {};
- nodeMap = ((1:length(externalFuncs)).');
- sharedPred = zeros(length(externalFuncs),1);
-
- depth = 1;
- nextPred = zeros(length(externalFuncs),1);
- bEmpty = false;
- while ( ~all(bEmpty) )
- [tokenNodes tokenRemains] = strtok(tokenRemains, tokenDelims);
-
- bEmpty = cellfun(@(x)(isempty(x)), tokenNodes);
-
- tokenNodes = tokenNodes(~bEmpty);
- tokenRemains = tokenRemains(~bEmpty);
-
- nextPred = nextPred(~bEmpty);
- nodeMap = nodeMap(~bEmpty);
-
- [newNodes ia ic] = unique(tokenNodes);
-
- bEmptyLeaf = cellfun(@(x)(isempty(x)), tokenRemains);
- bNewLeaves = bEmptyLeaf(ia);
-
- pred = [pred; nextPred(ia)];
-
- % As soon as we hit a leaf node, update shared predecessor for all
- % nodes. This will be condsidered the toolbox path.
- leafPreds = unique(nextPred(ia(bNewLeaves)));
- [bShared setPred] = ismember(nextPred, leafPreds);
-
- bUpdateShared = (sharedPred(nodeMap) == 0) & bShared;
- sharedPred(nodeMap(bUpdateShared)) = leafPreds(setPred(bUpdateShared));
-
- nextPred = ic + length(pathNodes);
-
- bLeaves = [bLeaves; bNewLeaves];
- pathNodes = [pathNodes; newNodes];
-
- depth = depth + 1;
- end
-
- [sharedPath ia ic] = unique(sharedPred);
- externalDeps = cell(length(sharedPath),1);
- for i=1:length(sharedPath)
- curIdx = sharedPath(i);
- while ( curIdx ~= 0 )
- externalDeps{i} = fullfile(pathNodes{curIdx}, externalDeps{i});
- curIdx = pred(curIdx);
- end
- end
-
- externalMap(bExternal) = ic;
-end
-
-function toolboxCallers = getToolboxCallers(localNodes, toolboxes, toolboxMap, fullGraph, fullNames)
- toolboxCallers = cell(length(toolboxes),1);
- for i=1:length(toolboxes)
- bInToolbox = (toolboxMap == i);
- [callerIdx funcIdx] = find(fullGraph(:,bInToolbox));
- toolboxCallers{i} = cell(max(funcIdx),1);
- for j=1:length(funcIdx)
- if ( ~ismember(callerIdx(j),localNodes) )
- continue;
- end
-
- toolboxCallers{i}{funcIdx(j)} = [toolboxCallers{i}{funcIdx(j)}; fullNames(callerIdx(j))];
- end
- end
-end
-
-function callGraph = createCallGraph(calledFrom)
- numEdges = cellfun(@(x)(length(x)), calledFrom);
- calledIdx = arrayfun(@(x,y)(y*ones(1,x)), numEdges, ((1:length(calledFrom)).'), 'UniformOutput',0);
-
- jIdx = ([calledIdx{:}]);
- iIdx = ([calledFrom{:}]);
-
- callGraph = sparse(iIdx,jIdx, ones(1,sum(numEdges)), length(calledFrom),length(calledFrom), sum(numEdges));
-end
-
-function bIsCalled = findCalledNodes(localFuncIdx, callGraph)
- bIsCalled = false(size(callGraph,1),1);
- bIsCalled(localFuncIdx) = 1;
-
- for i=1:length(localFuncIdx)
- [d pred] = matlab_bgl.dijkstra_sp(callGraph, localFuncIdx(i));
-
- bHasPath = ~isinf(d);
- bIsCalled = (bIsCalled | bHasPath);
- end
-end
-
-function [squashNames squashGraph squashMap] = squashToolboxNodes(funcNames, callGraph, toolboxes, toolboxMap)
- squashNames = funcNames;
- squashMap = toolboxMap;
- squashGraph = callGraph;
-
- for i=1:length(toolboxes)
- bInToolbox = (squashMap == i);
-
- tempRows = any(squashGraph(bInToolbox,:),1);
- squashRows = [tempRows(~bInToolbox) any(tempRows(bInToolbox))];
-
- tempCols = any(squashGraph(:,bInToolbox),2);
- squashCols = tempCols(~bInToolbox);
-
- squashGraph = [squashGraph(~bInToolbox,~bInToolbox) squashCols; squashRows];
-
- squashNames = [squashNames(~bInToolbox); toolboxes(i)];
- squashMap = [squashMap(~bInToolbox); i];
- end
-end
-
-function [deplist calledFrom] = recursiveGetDeps(checkNames, bFollowToolboxes, deplist, calledFrom)
- if ( ~exist('calledFrom','var') )
- calledFrom = {};
- end
-
- if ( ~exist('deplist','var') )
- deplist = {};
- end
-
- if ( ~exist('bFollowToolboxes','var') )
- bFollowToolboxes = 0;
- end
-
- if ( isempty(checkNames) )
- return;
- end
-
- % Get single-link dependencies
- try
- [newdeps, builtins, classes, prob_files, prob_sym, eval_strings, newCalledFrom, java_classes] = depfun(checkNames, '-toponly', '-quiet');
- catch excp
- newdeps = cell(0,1);
- newCalledFrom = cell(0,1);
- end
- [deplist calledFrom newEntries] = mergeLists(deplist, calledFrom, newdeps, newCalledFrom);
-
- % Remove any matlab toolbox entries from being recursively followed
- if ( ~bFollowToolboxes )
- bIsToolbox = strncmpi(matlabroot, newEntries, length(matlabroot));
- newEntries = newEntries(~bIsToolbox);
- end
-
- [deplist calledFrom] = recursiveGetDeps(newEntries, bFollowToolboxes, deplist, calledFrom);
-
-end
-
-function [deplist calledFrom newEntries] = mergeLists(deplist, calledFrom, newdeps, newCalledFrom)
- oldIdx = cellfun(@(x)(find(strcmpi(x,deplist))), newdeps, 'UniformOutput',0);
- bNew = cellfun(@(x)(isempty(x)), oldIdx);
-
- newEntries = newdeps(bNew);
-
- idxMap = zeros(1,length(newdeps));
- idxMap(~bNew) = [oldIdx{~bNew}];
- idxMap(bNew) = (1:length(newEntries)) + length(deplist);
-
- deplist = [deplist; newEntries];
- calledFrom = [calledFrom; cell(length(newEntries),1)];
-
- calledFrom(idxMap) = cellfun(@(x,y)(unique([x idxMap(y)])), calledFrom(idxMap), newCalledFrom, 'UniformOutput',0);
-end
-
-function [checkNames fullNames] = getLocalNames(dirName, packageString)
- if ( ~exist('packageString','var') )
- packageString = '';
- end
-
- matlabFiles = what(dirName);
-
- funcFileNames = vertcat(matlabFiles.m);
- funcFileNames = [funcFileNames; vertcat(matlabFiles.mex)];
-
- checkNames = cellfun(@splitFName, funcFileNames, 'UniformOutput',0);
- checkNames = cellfun(@(x)([packageString x]), checkNames, 'UniformOutput',0);
- fullNames = cellfun(@(x)(fullfile(dirName,x)), funcFileNames, 'UniformOutput',0);
-
- for i=1:length(matlabFiles.packages)
- nextPackageString = makePackageString(packageString, matlabFiles.packages{i});
- [pckgCheckNames pckgFullNames] = getLocalNames(fullfile(dirName, ['+' matlabFiles.packages{i}]), nextPackageString);
-
- checkNames = [checkNames; pckgCheckNames];
- fullNames = [fullNames; pckgFullNames];
- end
-end
-
-function packageString = makePackageString(packageString, nextPackage)
- if ( isempty(packageString) )
- packageString = [nextPackage '.'];
- return;
- end
-
- packageString = [packageString nextPackage '.'];
-end
-
-function name = splitFName(fileName)
- [path, name] = fileparts(fileName);
-end
diff --git a/src/MATLAB/+Dev/GetLocalName.m b/src/MATLAB/+Dev/GetLocalName.m
deleted file mode 100644
index edb1e31b4bc720b1f7b71bc26345adc632a246d8..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Dev/GetLocalName.m
+++ /dev/null
@@ -1,17 +0,0 @@
-function localName = GetLocalName(fullName, chkPath)
- if ( ~exist('chkPath', 'var') )
- chkPath = pwd();
- end
-
- localName = [];
- partialPath = fullName;
- while ( ~isempty(partialPath) && ~strcmpi(chkPath,partialPath) )
- [partialPath callPart] = fileparts(partialPath);
-
- if ( callPart(1) == '+' )
- localName = [callPart(2:end) '.' localName];
- else
- localName = fullfile(callPart, localName);
- end
- end
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Dev/GetVersion.m b/src/MATLAB/+Dev/GetVersion.m
new file mode 100644
index 0000000000000000000000000000000000000000..e563019b7f900a6f58297480871853d1d86796fd
--- /dev/null
+++ b/src/MATLAB/+Dev/GetVersion.m
@@ -0,0 +1,59 @@
+% version = GetVersion(command)
+% Get a version string or number depending on the command argument. This
+% m-file serves as a single repository for all version-related information.
+%
+% Note: Uses autogenerated version information in +Dev\VersionInfo.m
+
+function versionStr = GetVersion(command)
+ versionStr = [];
+
+ verInfo = Dev.LoadVersion();
+
+ if ( ~exist('command','var') )
+ command = 'string';
+ end
+
+ % Get rid of slashes in branch names
+ cleanBranch = strrep(verInfo.branchName, '/', '_');
+ cleanBranch = strrep(cleanBranch, '\', '_');
+
+ primaryHash = '';
+ matchTok = regexp(verInfo.commitHash{1},'.*:\s*(\w+)','tokens','once');
+ if ( ~isempty(matchTok) )
+ primaryHash = matchTok{1};
+ end
+
+ if ( strcmpi(command, 'string') || strcmpi(command, 'versionString') )
+ versionStr = [num2str(verInfo.majorVersion) '.' num2str(verInfo.minorVersion) ' ' cleanBranch];
+ return;
+ end
+
+ if ( strcmpi(command, 'buildString') )
+ versionStr = [verInfo.buildNumber '/' verInfo.buildMachine];
+ return;
+ end
+
+ if ( strcmpi(command, 'primaryHash') )
+ versionStr = primaryHash;
+ return
+ end
+
+ if ( strcmpi(command, 'buildHashes') )
+ versionStr = verInfo.commitHash;
+ return
+ end
+
+ if ( strcmpi(command, 'fullString') )
+ versionStr = [verInfo.name ' v' num2str(verInfo.majorVersion) '.' num2str(verInfo.minorVersion) ' ' verInfo.buildNumber '/' verInfo.buildMachine ' ' cleanBranch ' ' primaryHash];
+ return;
+ end
+
+ if ( strcmpi(command, 'file') )
+ minorStr = num2str(verInfo.minorVersion);
+ minorStr = strrep(minorStr, '.', '_');
+ versionStr = [num2str(verInfo.majorVersion) minorStr '_' cleanBranch];
+ return;
+ end
+
+end
+
diff --git a/src/MATLAB/+Dev/GitCommitHash.m b/src/MATLAB/+Dev/GitCommitHash.m
new file mode 100644
index 0000000000000000000000000000000000000000..3548ce2344b3b9837be6440a1db0a9e64ac45246
--- /dev/null
+++ b/src/MATLAB/+Dev/GitCommitHash.m
@@ -0,0 +1,16 @@
+function commitHash = GitCommitHash(inPath)
+ bGit = Dev.SetupGit();
+ if ( ~bGit )
+ return;
+ end
+
+ oldDir = cd(inPath);
+ cleanupObj = onCleanup(@()(cd(oldDir)));
+
+ [status,hashOut] = system('git rev-parse HEAD');
+ if ( status ~= 0 )
+ return;
+ end
+
+ commitHash = strtrim(hashOut);
+end
diff --git a/src/MATLAB/+Dev/GitRemote.m b/src/MATLAB/+Dev/GitRemote.m
new file mode 100644
index 0000000000000000000000000000000000000000..fae8a87be8ac2859aceb2d211cfba370d7573a6a
--- /dev/null
+++ b/src/MATLAB/+Dev/GitRemote.m
@@ -0,0 +1,18 @@
+function remoteURL = GitRemote(inPath,remoteName)
+ remoteURL = '';
+
+ bGit = Dev.SetupGit();
+ if ( ~bGit )
+ return;
+ end
+
+ oldDir = cd(inPath);
+ cleanupObj = onCleanup(@()(cd(oldDir)));
+
+ [status,urlOut] = system(['git remote get-url ' remoteName]);
+ if ( status ~= 0 )
+ return;
+ end
+
+ remoteURL = strtrim(urlOut);
+end
diff --git a/src/MATLAB/+Dev/GitStatus.m b/src/MATLAB/+Dev/GitStatus.m
new file mode 100644
index 0000000000000000000000000000000000000000..90f0693283146a3e3a542455480a64b3d7be004f
--- /dev/null
+++ b/src/MATLAB/+Dev/GitStatus.m
@@ -0,0 +1,67 @@
+function changeLines = GitStatus(chkPath,chkFiles)
+ changeLines = {};
+
+ if ( ~exist('chkFiles','var') )
+ chkFiles = {};
+ end
+
+ bGit = Dev.SetupGit();
+ if ( ~bGit )
+ return;
+ end
+
+ oldDir = cd(chkPath);
+ cleanupObj = onCleanup(@()(cd(oldDir)));
+
+ [status,res] = system('git status -uall --porcelain');
+ if ( status ~= 0 )
+ return;
+ end
+
+ statusLines = strsplit(res,'\n').';
+
+ bValid = cellfun(@(x)(~isempty(x)),statusLines);
+ statusLines = statusLines(bValid);
+
+ changeTypes = cellfun(@(x)(8*changeMap(x(1)) + changeMap(x(2))), statusLines);
+ changeFiles = cellfun(@(x)(x(4:end)), statusLines, 'UniformOutput',false);
+
+ if ( isempty(chkFiles) )
+ changeLines = changeFiles(changeTypes > 0);
+ return;
+ end
+
+ changeLines = {};
+
+ regexpFiles = regexptranslate('escape', strrep(chkFiles, '\','/'));
+ for i=1:length(changeFiles)
+ matchStarts = regexp(changeFiles{i},regexpFiles, 'start','once');
+ bMatched = cellfun(@(x)(~isempty(x)), matchStarts);
+
+ if ( any(bMatched) )
+ changeLines = [changeLines; changeFiles(i)];
+ end
+ end
+
+ extCell = arrayfun(@(x)([ '.\' x.ext '|']), mexext('all'), 'UniformOutput',false);
+ extStr = [extCell{:}];
+ bMexFiles = cellfun(@(x)(~isempty(x)), regexp(chkFiles,extStr(1:end-1),'once'));
+ if ( any(bMexFiles) )
+ matchStarts = regexp(changeFiles,'^src/c/', 'start','once');
+ bMatched = cellfun(@(x)(~isempty(x)), matchStarts);
+
+ cFiles = changeFiles(bMatched);
+ for i=1:length(cFiles)
+ changeLines = [changeLines; {'Possible MEX dependency - ' cFiles{i}}];
+ end
+ end
+end
+
+function change = changeMap(c)
+ changeList = ['?','M','A','D'];
+
+ change = find(c == changeList);
+ if ( isempty(change) )
+ change = 0;
+ end
+end
diff --git a/src/MATLAB/+Dev/InitCompiler.m b/src/MATLAB/+Dev/InitCompiler.m
new file mode 100644
index 0000000000000000000000000000000000000000..2a96f76da37295dd174aa6e37fd1775539051bf9
--- /dev/null
+++ b/src/MATLAB/+Dev/InitCompiler.m
@@ -0,0 +1,134 @@
+function initStruct = InitCompiler(productName,forceVersion)
+ if ( ~exist('forceVersion','var') )
+ forceVersion = '';
+ end
+
+ rootDir = pwd();
+
+ initStruct = [];
+
+ %% Build dependency graph for current directory
+ depGraph = Dev.BuildDependencyGraph(rootDir,true);
+
+ %% Get list of matlab toolbox dependencies
+ toolboxRoot = toolboxdir('');
+ bMatlab = strncmp(toolboxRoot,depGraph.nodes, length(toolboxRoot));
+
+ toolboxNodes = depGraph.nodes(bMatlab);
+ toolboxList = Dev.LoadToolboxes(toolboxNodes);
+
+ %% Remove matlab paths/dependencies
+ depGraph.nodes = depGraph.nodes(~bMatlab);
+ depGraph.graph = depGraph.graph(~bMatlab,~bMatlab);
+
+ %% Get rootPaths and local subdirectories for dependencies
+ [rootPaths,rootNames,localPaths] = Dev.SplitDependencyNames(depGraph.nodes);
+
+ %% Verify no uncommited changes on dependencies
+ changeString = {};
+ [chkPaths,ia,ic] = unique(rootPaths);
+ chkNames = rootNames(ia);
+ for i=1:length(chkPaths)
+ bInPath = (ic == i);
+ changeLines = Dev.GitStatus(chkPaths{i},localPaths(bInPath));
+
+ if ( ~isempty(changeLines) )
+ changeString = [changeString; {[chkNames{i} ' (' chkPaths{i} '):']}];
+ for j=1:length(changeLines)
+ changeString = [changeString; {[' ' changeLines{j}]}];
+ end
+ end
+ end
+
+ if ( ~isempty(changeString) )
+ message = sprintf('The following dependencies have uncommitted changes, are you sure you wish to continue?\n\n');
+ for i=1:length(changeString)
+ message = [message sprintf('%s\n',changeString{i})];
+ end
+
+ answer = questdlg(message, 'Uncommitted changes!', 'Continue','Cancel', 'Cancel');
+ if ( strcmpi(answer,'Cancel') )
+ initStruct = [];
+ return;
+ end
+ end
+
+ %% Make full version string and fallback version file
+ Dev.MakeVersion(productName,forceVersion,chkPaths);
+
+ %% Copy the external dependencies to local paths
+ bExternal = ~strncmp(rootDir,rootPaths,length(rootDir));
+ externalPaths = rootPaths(bExternal);
+ externalDeps = localPaths(bExternal);
+
+ copyPaths = {};
+ for i=1:length(externalPaths)
+ localDir = fileparts(externalDeps{i});
+ if ( ~exist(fullfile(rootDir,localDir),'dir') )
+ mkdir(fullfile(rootDir,localDir));
+ end
+
+ copyPaths = [copyPaths; fullfile(rootDir,externalDeps{i})];
+ copyfile(fullfile(externalPaths{i},externalDeps{i}), fullfile(rootDir,externalDeps{i}));
+ end
+
+ initStruct.toolboxList = toolboxList;
+ initStruct.cleanupObj = onCleanup(@()(compilerCleanup(copyPaths)));
+
+ % temporarily remove any startup scripts that would normally be run by matlabrc
+ enableStartupScripts(false);
+end
+
+function compilerCleanup(copyPaths)
+ % Remove all copied dependencies
+ for i=1:length(copyPaths)
+ if ( exist(copyPaths{i},'file') )
+ delete(copyPaths{i});
+ end
+ end
+
+ % Re-enable any disabled startup scripts
+ enableStartupScripts(true);
+end
+
+function enableStartupScripts(bEnable)
+ searchPrefix = '';
+ renamePrefix = 'disabled_';
+ if ( bEnable )
+ searchPrefix = 'disabled_';
+ renamePrefix = '';
+ end
+
+ searchName = [searchPrefix 'startup.m'];
+ newName = [renamePrefix 'startup.m'];
+
+ startupScripts = findFilesInPath(searchName, userpath);
+ for i=1:length(startupScripts)
+ scriptPath = fileparts(startupScripts{i});
+ movefile(startupScripts{i}, fullfile(scriptPath,newName));
+ end
+end
+
+function fullNames = findFilesInPath(filename, searchPaths)
+ fullNames = {};
+
+ chkPaths = [];
+ while ( ~isempty(searchPaths) )
+ [newPath remainder] = strtok(searchPaths, pathsep);
+ if ( isempty(newPath) )
+ searchPaths = remainder;
+ continue;
+ end
+
+ chkPaths = [chkPaths; {newPath}];
+ searchPaths = remainder;
+ end
+
+ for i=1:length(chkPaths)
+ chkFullPath = fullfile(chkPaths{i}, filename);
+ if ( exist(chkFullPath, 'file') )
+ fullNames = [fullNames; {chkFullPath}];
+ end
+ end
+end
+
diff --git a/src/MATLAB/+Dev/LoadToolboxes.m b/src/MATLAB/+Dev/LoadToolboxes.m
new file mode 100644
index 0000000000000000000000000000000000000000..5f93c35aff9dfce6dfde80b07b7da5f306709a32
--- /dev/null
+++ b/src/MATLAB/+Dev/LoadToolboxes.m
@@ -0,0 +1,15 @@
+function toolboxPaths = LoadToolboxes(toolboxNodes)
+ toolboxMap = Dev.BuildToolboxMap();
+
+ toolboxRoot = toolboxdir('');
+ toolboxNames = cellfun(@(x)(x(length(toolboxRoot)+2:end)), toolboxNodes, 'UniformOutput',false);
+
+ toolboxPaths = {};
+ for i=1:length(toolboxNames)
+ if ( ~isKey(toolboxMap,toolboxNames{i}) )
+ continue;
+ end
+
+ toolboxPaths = [toolboxPaths; toolboxMap(toolboxNames{i})];
+ end
+end
diff --git a/src/MATLAB/+Dev/LoadVersion.m b/src/MATLAB/+Dev/LoadVersion.m
new file mode 100644
index 0000000000000000000000000000000000000000..e9a39d08dd39d0c0665ebcfa7d7695c924ef481f
--- /dev/null
+++ b/src/MATLAB/+Dev/LoadVersion.m
@@ -0,0 +1,82 @@
+function verInfo = LoadVersion()
+ %% Use compiled VersionInfo function when deployed
+ if ( isdeployed )
+ verInfo = Dev.VersionInfo();
+ return;
+ end
+
+ %% Try to load version tag and branch using git
+ bFoundGit = Dev.SetupGit();
+ verInfo = [];
+ if ( bFoundGit )
+ chkVerInfo = gitVersionInfo();
+ end
+
+ %% Use fallback file for name (set by Dev.MakeVersion)
+ fallbackFile = 'version.json';
+
+ fallbackVerInfo = loadFallbackInfo(fallbackFile);
+ if ( isempty(fallbackVerInfo) )
+ fprintf('WARNING: Invalid fallback file, unable to load version information.\n');
+ return;
+ end
+
+ if ( isempty(chkVerInfo) )
+ fprintf('WARNING: Could not find git directory, using fallback %s\n', fallbackFile);
+ chkVerInfo = fallbackVerInfo;
+ end
+
+ % Always use the name from fallback file
+ chkVerInfo.name = fallbackVerInfo.name;
+
+ verInfo = chkVerInfo;
+end
+
+%% Read fallback json version file
+function verInfo = loadFallbackInfo(fallbackFile)
+ verInfo = [];
+
+ fid = fopen(fallbackFile);
+ if ( fid <= 0 )
+ return;
+ end
+
+ jsonVer = fread(fid, '*char').';
+ fclose(fid);
+
+ verInfo = Utils.ParseJSON(jsonVer);
+end
+
+%% Use git tags to get version information
+function verInfo = gitVersionInfo()
+ verInfo = [];
+
+ [verStatus,verString] = system('git describe --tags --match v[0-9]*.[0-9]* --abbrev=0');
+ [branchStatus,branchString] = system('git rev-parse --abbrev-ref HEAD');
+
+ [majorVer,minorVer] = Dev.ParseVerTag(verString);
+
+ if ( verStatus ~= 0 || isempty(majorVer) || isempty(minorVer) )
+ fprintf('WARNING: There was an error retrieving tag from git:\n %s\n', verString);
+ return;
+ end
+
+ branchName = strtrim(branchString);
+ if ( branchStatus ~= 0 )
+ fprintf('WARNING: There was an error retrieving branch name from git:\n %s\n', branchName);
+ return;
+ end
+
+ [repoName,commitHash] = Dev.GetCommitInfo(pwd());
+ commitString = [repoName ' : ' commitHash];
+
+ %% VersionInfo default structure
+ verInfo = struct(...
+ 'name',{repoName},...
+ 'majorVersion',{majorVer},...
+ 'minorVersion',{minorVer+1},...
+ 'branchName',{branchName},...
+ 'buildNumber',{'UNKNOWN'},...
+ 'buildMachine',{'UNKNOWN'},...
+ 'commitHash',{{commitString}});
+end
diff --git a/src/MATLAB/+Dev/MakeSegHelp.m b/src/MATLAB/+Dev/MakeSegHelp.m
new file mode 100644
index 0000000000000000000000000000000000000000..a79fae0e572645236de0545d60063046f5501f54
--- /dev/null
+++ b/src/MATLAB/+Dev/MakeSegHelp.m
@@ -0,0 +1,89 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function MakeSegHelp()
+ funcPrefix = {
+ '% helpStruct = CompiledSegHelp(funcName)'
+ '% Return a cached segmentation function help string.'
+ '%'
+ '% Note: This file is autogenerated by build script DO NOT MODIFY!!'
+ ''
+ 'function helpStruct = CompiledSegHelp(funcName)'
+ ' helpStruct = [];'
+ ' funcStructs = struct(''func'',{}, ''summary'',{}, ''paramHelp'',{});'};
+
+ helpTemplate = struct(...
+ 'func', {' funcStructs(%d).func = ''%s'';'},...
+ 'summary',{' funcStructs(%d).summary = ''%s'';'},...
+ 'param',{' funcStructs(%d).paramHelp = {%s};'});
+
+ funcPostfix = {
+ ' segFuncs = {funcStructs.func};'
+ ' funcIdx = find(strcmp(segFuncs,funcName));'
+ ' if ( isempty(funcIdx) )'
+ ' return;'
+ ' end'
+ ' '
+ ' helpStruct = funcStructs(funcIdx);'
+ 'end'};
+
+ SupportedTypes = Load.GetSupportedCellTypes();
+ segInfo = [SupportedTypes.segRoutine];
+ segFuncs = arrayfun(@(x)(char(x.func)), segInfo, 'UniformOutput',false);
+
+ helpStruct = [];
+ for i=1:length(segFuncs)
+ newStruct = Dev.FrameSegHelp(segFuncs{i});
+ if ( isempty(newStruct) )
+ error('Unrecognized segmentation algorithm!');
+ end
+
+ helpStruct = [helpStruct; newStruct];
+ end
+
+ fid = fopen(fullfile('+Dev','CompiledSegHelp.m'),'w');
+ %%
+ for i=1:length(funcPrefix)
+ fprintf(fid, '%s\n', funcPrefix{i});
+ end
+ fprintf(fid, '\n');
+
+ %%
+ for i=1:length(helpStruct)
+ paramString = '';
+ for j=1:length(helpStruct(i).paramHelp)
+ paramString = [paramString sprintf('\n ''%s'';', helpStruct(i).paramHelp{j})];
+ end
+
+ fprintf(fid, [helpTemplate.func '\n'], i, helpStruct(i).func);
+ fprintf(fid, [helpTemplate.summary '\n'], i, helpStruct(i).summary);
+ fprintf(fid, [helpTemplate.param '\n\n'], i, paramString);
+ end
+
+ %%
+ for i=1:length(funcPostfix)
+ fprintf(fid, '%s\n', funcPostfix{i});
+ end
+ fclose(fid);
+end
diff --git a/src/MATLAB/+Dev/MakeVersion.m b/src/MATLAB/+Dev/MakeVersion.m
index af3171388c0fc6b0665654e8f765f31f17a1b25b..4c91fd3699249b5c4a8ba7d88fa671ac331a8a11 100644
--- a/src/MATLAB/+Dev/MakeVersion.m
+++ b/src/MATLAB/+Dev/MakeVersion.m
@@ -1,7 +1,8 @@
-function verInfo = MakeVersion(bTransientUpdate, forceVersion)
+function verInfo = MakeVersion(productName, forceVersion, dependencyPaths)
+ %% Template for the Dev.VersionInfo command
funcString = {
'%% versionInfo = VersionInfo()'
'%% Return the version info structure'
@@ -9,76 +10,48 @@ function verInfo = MakeVersion(bTransientUpdate, forceVersion)
'%% Note: This file is autogenerated by build script DO NOT MODIFY!!'
''
'function versionInfo = VersionInfo()'
- ' versionInfo = struct(...'
- ' ''majorVersion'',{%d},...'
- ' ''minorVersion'',{%d},...'
- ' ''branchName'',{''%s''},...'
- ' ''buildNumber'',{''%s''},...'
- ' ''buildMachine'',{''%s''},...'
- ' ''commitHash'',{''%s''});'
- ' end'};
-
- if ( ~exist('bTransientUpdate', 'var') )
- bTransientUpdate = 0;
- end
+ ' jsonVer = ''%s'';'
+ ' '
+ ' versionInfo = Utils.ParseJSON(jsonVer);'
+ 'end'};
if ( ~exist('forceVersion', 'var') )
- forceVersion = [];
- end
-
- verInfo = struct(...
- 'majorVersion',{0},...
- 'minorVersion',{0},...
- 'branchName',{'UNKNOWN'},...
- 'buildNumber',{'UNKNOWN'},...
- 'buildMachine',{'UNKNOWN'},...
- 'commitHash',{''});
-
-
- fallbackFile = 'version.txt';
-
- bFoundGit = Dev.SetupGit();
- if ( ~bFoundGit )
- fprintf('WARNING: Could not find git directory, falling back to %s\n', fallbackFile);
+ forceVersion = '';
end
- [verTag branchName] = gitVersionAndBranch(bFoundGit, fallbackFile);
-
- if ( ~isempty(forceVersion) && ischar(forceVersion) )
- verTag = ['v' forceVersion];
+ if ( ~exist('dependencyPaths', 'var') )
+ dependencyPaths = {};
end
- % Get version info from git tag
- if ( ~isempty(verTag) )
- verTag = strtrim(verTag);
- numTok = regexp(verTag, '[Vv](\d+)\.(\d+(?:\.\d+)?).*', 'tokens', 'once');
- if ( length(numTok) >= 2 )
- verInfo.majorVersion = str2double(numTok{1});
- verInfo.minorVersion = str2double(numTok{2});
- end
- end
+ fallbackFile = 'version.json';
- % Increment version if we're getting it from tag/fallback
- if ( isempty(forceVersion) )
- verInfo.minorVersion = verInfo.minorVersion + 1;
+ %% Load version info from git tags
+ verInfo = Dev.LoadVersion();
+ if ( isempty(verInfo) )
+ error('Unable to load git version information');
end
- % Try to get a branch name
- [status,branchName] = system('git rev-parse --abbrev-ref HEAD');
- if ( ~isempty(branchName) )
- verInfo.branchName = strtrim(branchName);
- end
+ % Force name to be the passed in product name
+ verInfo.name = productName;
- [status commitHash] = system('git rev-parse HEAD');
- if ( ~isempty(commitHash) )
- verInfo.commitHash = strtrim(commitHash);
+ %% If we are forcing a specific version number
+ if ( ~isempty(forceVersion) )
+ verString = ['v' forceVersion];
+
+ [majorVer,minorVer] = Dev.ParseVerTag(verString);
+ if ( isempty(majorVer) )
+ error('Invalid version string %s', verString);
+ end
+
+ verInfo.majorVersion = majorVer;
+ verInfo.minorVersion = minorVer;
end
- % Get a timestamp build-number
+ %% Get a timestamp build-number
c = clock();
verInfo.buildNumber = sprintf('%d.%02d.%02d.%02d', c(1), c(2), c(3), c(4));
- % Get machine ID
+ %% Get machine ID
[status,buildMachine] = system('hostname');
if ( status ~= 0 )
fprintf('WARNING: There was an error retrieving hostname:\n %s\n', buildMachine);
@@ -86,82 +59,49 @@ function verInfo = MakeVersion(bTransientUpdate, forceVersion)
verInfo.buildMachine = strtrim(buildMachine);
end
- if ( ~bTransientUpdate )
- if ( ~bFoundGit )
- error('Unable to use git to build version string for build.');
- end
-
- % Concatenate the template function lines into one giant string
- templateString = [];
- for i=1:length(funcString)
- templateString = [templateString funcString{i} '\n'];
- end
-
- % Now insert all our arguments into the template and write to a file.
- fid = fopen('+Helper\VersionInfo.m', 'wt');
- if ( fid <= 0 )
- error('Unable to open +Helper\VersionInfo.m for writing');
- end
-
- fprintf(fid, templateString, verInfo.majorVersion, verInfo.minorVersion, verInfo.branchName, verInfo.buildNumber, verInfo.buildMachine, verInfo.commitHash);
-
- fclose(fid);
-
- % Update fallback file if we used git to retrieve version info.
- fid = fopen(fallbackFile, 'wt');
- if ( fid < 0 )
- return;
- end
-
- fprintf(fid, '%s\n', verTag);
- fprintf(fid, '%s\n', branchName);
-
- fclose(fid);
- end
-end
-
-function [verTag branchName commitHash] = gitVersionAndBranch(bUseGit, fallbackFile)
- verTag = '';
- branchName = '';
- commitHash = '';
+ %% Make sure local path is not in the list
+ localPath = pwd();
+ bHasLocal = strcmp(localPath,dependencyPaths);
+ dependencyPaths = dependencyPaths(~bHasLocal);
- if ( bUseGit )
- [verStatus,verTag] = system('git describe --tags --match v[0-9]*.[0-9]* --abbrev=0');
- [branchStatus,branchName] = system('git rev-parse --abbrev-ref HEAD');
- [hashStatus,commitHash] = system('git rev-parse HEAD');
-
- if ( verStatus ~= 0 )
- fprintf('WARNING: There was an error retrieving tag from git:\n %s\n', verTag);
- verTag = '';
- end
-
- if ( branchStatus ~= 0 )
- fprintf('WARNING: There was an error retrieving branch name from git:\n %s\n', branchName);
- branchName = '';
- end
-
- if ( hashStatus ~= 0 )
- fprintf('WARNING: There was an error retrieving commit hash from git:\n %s\n', commitHash);
- commitHash = '';
- end
-
- return;
+ %% Add all other dependent commit hashes to list
+ hashStrings = cell(length(dependencyPaths),1);
+ for i=1:length(dependencyPaths)
+ [repoName,commitHash] = Dev.GetCommitInfo(dependencyPaths{i});
+ hashStrings{i} = [repoName ' : ' commitHash];
end
- if ( ~exist(fallbackFile, 'file') )
- fprintf('ERROR: There is no fallback version.txt file!\n');
- return;
- end
+ verInfo.commitHash = [verInfo.commitHash; hashStrings];
- fid = fopen(fallbackFile, 'rt');
+ %% Create +Dev/VersionInfo.m for use in compiled files
+ % Concatenate the template function lines into one giant string
+ templateString = [];
+ for i=1:length(funcString)
+ templateString = [templateString funcString{i} '\n'];
+ end
+
+ % Now insert all our arguments into the template and write to a file.
+ if ( ~exist('+Dev','dir') )
+ mkdir('+Dev');
+ end
- if ( fid < 0 )
+ fid = fopen(fullfile('+Dev','VersionInfo.m'), 'wt');
+ if ( fid <= 0 )
+ error('Unable to open +Dev/VersionInfo.m for writing');
+ end
+
+ jsonVer = Utils.CreateJSON(verInfo,false);
+ fprintf(fid, templateString, jsonVer);
+
+ fclose(fid);
+
+ %% Update fallback file if we used git to retrieve version info.
+ jsonStr = Utils.CreateJSON(verInfo);
+ fid = fopen(fallbackFile, 'wt');
+ if ( fid <= 0 )
return;
end
-
- verTag = fgetl(fid);
- branchName = fgetl(fid);
- commitHash = fgetl(fid);
-
+
+ fprintf(fid, '%s\n', jsonStr);
fclose(fid);
end
diff --git a/src/MATLAB/+Dev/MergeGraphStruct.m b/src/MATLAB/+Dev/MergeGraphStruct.m
new file mode 100644
index 0000000000000000000000000000000000000000..c8dcab1c81d9c9dea391115a403cf66f7cca8c30
--- /dev/null
+++ b/src/MATLAB/+Dev/MergeGraphStruct.m
@@ -0,0 +1,18 @@
+function [graphStruct,newNodes] = MergeGraphStruct(graphStruct, newStruct)
+ oldIdx = cellfun(@(x)(find(strcmp(x,graphStruct.nodes),1,'first')), newStruct.nodes, 'UniformOutput',0);
+ bNew = cellfun(@(x)(isempty(x)), oldIdx);
+
+ newNodes = newStruct.nodes(bNew);
+
+ p = length(newNodes);
+ [m,n] = size(graphStruct.graph);
+
+ idxMap = zeros(1,length(newStruct.nodes));
+ idxMap(~bNew) = [oldIdx{~bNew}];
+ idxMap(bNew) = (1:p) + n;
+
+ graphStruct.nodes = [graphStruct.nodes; newNodes];
+ graphStruct.graph = [graphStruct.graph zeros(n,p); zeros(p,n+p)];
+
+ graphStruct.graph(idxMap,idxMap) = (graphStruct.graph(idxMap,idxMap) | newStruct.graph);
+end
\ No newline at end of file
diff --git a/src/MATLAB/+Dev/ParseVerTag.m b/src/MATLAB/+Dev/ParseVerTag.m
new file mode 100644
index 0000000000000000000000000000000000000000..278ecaa61b879af28761ec7d4c6b4c2fd95031d0
--- /dev/null
+++ b/src/MATLAB/+Dev/ParseVerTag.m
@@ -0,0 +1,15 @@
+% [majorVer,minorVer] = ParseVerTag(verString)
+%
+
+function [majorVer,minorVer] = ParseVerTag(verString)
+ majorVer = [];
+ minorVer = [];
+
+ verString = strtrim(verString);
+
+ numTok = regexp(verString, '[Vv](\d+)\.(\d+(?:\.\d+)?).*', 'tokens', 'once');
+ if ( length(numTok) >= 2 )
+ majorVer = str2double(numTok{1});
+ minorVer = str2double(numTok{2});
+ end
+end
diff --git a/src/MATLAB/+Dev/PrintIntegrityErrors.m b/src/MATLAB/+Dev/PrintIntegrityErrors.m
index f511f62f3bcbbe6c52a7046676a25be5b7b0c3b8..1580608e2d7207e3b1d9979ec3aebe9e6080b946 100644
--- a/src/MATLAB/+Dev/PrintIntegrityErrors.m
+++ b/src/MATLAB/+Dev/PrintIntegrityErrors.m
@@ -1,6 +1,30 @@
% PrintIntegrityErrors(errs, filename)
% Prints integrity errors to filename (or stdout if no name specified)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function PrintIntegrityErrors(errs, fid)
if ( isempty(errs) )
diff --git a/src/MATLAB/+Dev/ReplayActionsFile.m b/src/MATLAB/+Dev/ReplayActionsFile.m
index 6df25993fde817a4e3e775a5c0efbcb63d29ee73..11d2b4861ac265db4e6e4a4b6dc71d9e142bb07d 100644
--- a/src/MATLAB/+Dev/ReplayActionsFile.m
+++ b/src/MATLAB/+Dev/ReplayActionsFile.m
@@ -1,5 +1,29 @@
% ReplayActionsFile(filename)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function ReplayActionsFile(filename)
loadStruct = load(filename, 'ReplayEditActions');
diff --git a/src/MATLAB/+Dev/ReplayEditAction.m b/src/MATLAB/+Dev/ReplayEditAction.m
index ff62a9222e017bd31c1b5f1f293189b29846f004..deab54970cbaeebb4f8b63e0ddc233987779cd9a 100644
--- a/src/MATLAB/+Dev/ReplayEditAction.m
+++ b/src/MATLAB/+Dev/ReplayEditAction.m
@@ -2,6 +2,30 @@
%
% ReplayEditAction attempts to replay an action from an editaction list.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [bErr chkHash varargout] = ReplayEditAction(actPtr, varargin)
varargout = cell(1,max(0,nargout-2));
diff --git a/src/MATLAB/+Dev/SetupGit.m b/src/MATLAB/+Dev/SetupGit.m
index 86d9a197e937a810d5dcd3c3453c0100488e9974..aece550b17f59bdfd74b87a7b3614ed789303da7 100644
--- a/src/MATLAB/+Dev/SetupGit.m
+++ b/src/MATLAB/+Dev/SetupGit.m
@@ -30,9 +30,10 @@ function gitPath = findGitPath()
gitPath = '';
comparch = computer('arch');
- progFilesPath = 'C:\Program Files (x86)';
+ progFilesPath64 = 'C:\Program Files';
if ( strcmpi(comparch,'win64') )
progFilesPath = getenv('ProgramFiles(x86)');
+ progFilesPath64 = getenv('ProgramFiles');
elseif ( strcmpi(comparch,'win32') )
progFilesPath = getenv('ProgramFiles');
else
@@ -40,7 +41,9 @@ function gitPath = findGitPath()
end
tryPaths = {fullfile(progFilesPath, 'Git');
+ fullfile(progFilesPath64, 'Git');
fullfile(progFilesPath, 'msysgit');
+ fullfile(progFilesPath64, 'msysgit');
'C:\Git';
'C:\msysgit'};
diff --git a/src/MATLAB/+Dev/SplitDependencyNames.m b/src/MATLAB/+Dev/SplitDependencyNames.m
new file mode 100644
index 0000000000000000000000000000000000000000..6cf65d26a984843f085c59872b023989e11b83e6
--- /dev/null
+++ b/src/MATLAB/+Dev/SplitDependencyNames.m
@@ -0,0 +1,61 @@
+function [rootPath,rootName,localPath] = SplitDependencyNames(depList)
+ rootPath = cell(length(depList),1);
+ rootName = cell(length(depList),1);
+ localPath = cell(length(depList),1);
+
+ dropPostfix = {'src/MATLAB'};
+ localMatches = '^private$|^\+.+$|^@.+$|^.+\.(m|mexw64|mexw32|fig)$';
+
+ for i=1:length(depList)
+ qualPath = splitQualifiedPath(depList{i});
+
+ bLocalPath = cellfun(@(x)(~isempty(x)),regexp(qualPath,localMatches, 'start','once'));
+ endRoot = find(diff(bLocalPath),1,'last');
+ if ( isempty(endRoot) )
+ % This shouldn't happen if matlab toolboxes are handled first.
+ continue;
+ end
+
+ chkPath = qualPath(1:endRoot);
+ for j=1:size(dropPostfix,1)
+ chkPostfix = strsplit(dropPostfix{j},'/');
+ cmpIdx = length(chkPath)-length(chkPostfix) + 1;
+ bDropMatch = strcmp(chkPostfix,chkPath(cmpIdx:end));
+
+ if ( all(bDropMatch) )
+ chkPath = chkPath(1:(cmpIdx-1));
+ break;
+ end
+ end
+
+ rootName{i} = chkPath{end};
+ rootPath{i} = fullfile(qualPath{1:endRoot});
+ localPath{i} = fullfile(qualPath{(endRoot+1):end});
+ end
+end
+
+function qualPath = splitQualifiedPath(inPath)
+ chkPath = strrep(inPath, '\','/');
+
+ qualPath = {};
+ splitRoot = regexp(chkPath,'^(/{1,2}.+?|.+?:)/(.*?)$','tokens','once');
+ if ( ~isempty(splitRoot) )
+ qualPath = splitRoot(1);
+ chkPath = splitRoot{2};
+ end
+
+ splitPath = strsplit(chkPath,'/');
+ while ( ~isempty(splitPath) )
+ popPath = splitPath{1};
+ splitPath = splitPath(2:end);
+
+ if ( strcmp('.',popPath) )
+ continue;
+ elseif ( strcmp('..',popPath) )
+ qualPath = qualPath(1:end-1);
+ continue;
+ end
+
+ qualPath = [qualPath {popPath}];
+ end
+end
diff --git a/src/MATLAB/+Dev/UnitTestMexDijkstra.m b/src/MATLAB/+Dev/UnitTestMexDijkstra.m
deleted file mode 100644
index 9891d1c90b44a11ba1cf5a266d8581331db01f85..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Dev/UnitTestMexDijkstra.m
+++ /dev/null
@@ -1,54 +0,0 @@
-function UnitTestMexDijkstra(costGraph, numIters)
-
- UI.Progressbar(0);
- % Test single edge removal
- mexDijkstra('initGraph', costGraph);
- numIters = min(numIters, nnz(costGraph));
- testCostGraph = costGraph;
- for i=1:numIters
- [rcm, ccm] = find(testCostGraph > 0);
-% graphInd = sub2ind(size(testCostGraph), rcm, ccm);
-
- rndidx = randi(length(rcm),1);
- testCostGraph(rcm(rndidx),ccm(rndidx)) = 0;
-
- mexDijkstra('removeEdges', rcm(rndidx),ccm(rndidx));
- UI.Progressbar((i/numIters) / 3);
- end
- Dev.CheckMEXSynch(testCostGraph);
-
- % Test out edge removal
- mexDijkstra('initGraph', costGraph);
- testCostGraph = costGraph;
- for i=1:numIters
- [rcm, ccm] = find(testCostGraph > 0);
-% graphInd = sub2ind(size(testCostGraph), rcm, ccm);
-
- if ( isempty(rcm) )
- break;
- end
-
- rndidx = randi(length(rcm),1);
- testCostGraph(rcm(rndidx),:) = 0;
-
- mexDijkstra('removeEdges', rcm(rndidx),[]);
- UI.Progressbar((i/numIters) / 3 + 1/3);
- end
- Dev.CheckMEXSynch(testCostGraph);
-
- % Test in edge removal
- mexDijkstra('initGraph', costGraph);
- testCostGraph = costGraph;
- for i=1:numIters
- [rcm, ccm] = find(testCostGraph > 0);
-% graphInd = sub2ind(size(testCostGraph), rcm, ccm);
-
- rndidx = randi(length(rcm),1);
- testCostGraph(:,ccm(rndidx)) = 0;
-
- mexDijkstra('removeEdges', [],ccm(rndidx));
- UI.Progressbar((i/numIters) / 3 + 2/3);
- end
- Dev.CheckMEXSynch(testCostGraph);
- UI.Progressbar(1);
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Dev/VerifyCachedCostMatrix.m b/src/MATLAB/+Dev/VerifyCachedCostMatrix.m
deleted file mode 100644
index e5bf68d65123c7e5b264043db16446906ad17414..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Dev/VerifyCachedCostMatrix.m
+++ /dev/null
@@ -1,51 +0,0 @@
-% err = VerifyCachedCostMatrix()
-% Compares CachedCostMatrix to what would be generated by old GetCostMatrix
-% code.
-
-function err = VerifyCachedCostMatrix()
- global Costs GraphEdits CellHulls CachedCostMatrix
- err = [];
-
- costMatrix = Costs;
- % bRemovedEdges = (GraphEdits < 0);
- % costMatrix(bRemovedEdges) = 0;
- %
- % bSetEdges = (GraphEdits > 0);
- % bSetRows = any(bSetEdges, 2);
- % bSetCols = any(bSetEdges, 1);
- %
- % costMatrix(bSetRows,:) = 0;
- % costMatrix(:,bSetCols) = 0;
- % costMatrix(bSetEdges) = GraphEdits(bSetEdges)*eps;
-
- % Vectorized/binary indexed implementation of this code is commented
- % out above because we cannot use more than 46K square elements in a
- % matrix in 32-bit matlab.
- [r,c] = find(GraphEdits < 0);
- for i=1:length(r)
- costMatrix(r(i),c(i)) = 0;
- end
-
- % Remove all edges to/from deleted hulls
- % This may end up being super slow, however it stops other graph code
- % from always having to check for deleted hulls (in general) by making
- % them unreachable.
- r = find([CellHulls.deleted]);
- for i=1:length(r)
- costMatrix(r(i),:) = 0;
- costMatrix(:,r(i)) = 0;
- end
-
- [r,c] = find(GraphEdits > 0);
- for i=1:length(r)
- costMatrix(r(i),:) = 0;
- costMatrix(:,c(i)) = 0;
- end
- for i=1:length(r)
- costMatrix(r(i),c(i)) = GraphEdits(r(i),c(i))*eps;
- end
-
- [r,c] = find(costMatrix ~= CachedCostMatrix);
-
- err = [r c];
-end
diff --git a/src/MATLAB/+Dev/WriteFrozenErrorCounts.m b/src/MATLAB/+Dev/WriteFrozenErrorCounts.m
index 6e31a72de847b92f178d0e37a74f46dea81b8272..5251dd6de9c015d806d00a6f60ae8f29928b6c8d 100644
--- a/src/MATLAB/+Dev/WriteFrozenErrorCounts.m
+++ b/src/MATLAB/+Dev/WriteFrozenErrorCounts.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function WriteFrozenErrorCounts(rootDir)
flist = dir(fullfile(rootDir,'*.mat'));
@@ -41,7 +65,7 @@ function [datasetName, frozenTrees, hullCount, trackCount, missingCount, userSeg
return;
end
- datasetName = CONSTANTS.datasetName;
+ datasetName = Metadata.GetDatasetName();
for i=1:length(frozenTrees)
[hullIDs missingHulls] = Families.GetAllHulls(frozenTrees(i));
diff --git a/src/MATLAB/+Dev/WriteGraphDOT.m b/src/MATLAB/+Dev/WriteGraphDOT.m
deleted file mode 100644
index f6364ca82cd2d780d7a02b59ee2d3f34a95f19df..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Dev/WriteGraphDOT.m
+++ /dev/null
@@ -1,69 +0,0 @@
-function WriteGraphDOT(callGraph, fullFuncList)
- fullNames = cellfun(@(x)(strrep(x, '\', '\\')), fullFuncList, 'UniformOutput',0);
-
-% toolboxes = {};
-% toolboxMap = zeros(1,length(fullFuncList));
-% for i=1:length(fullFuncList)
-% toolboxPattern = '(?<=^.+[\\/]toolbox[\\/])[^\\/]+';
-% matchToolbox = regexp(fullFuncList{i}, toolboxPattern, 'match', 'once');
-% if ( isempty(matchToolbox) )
-% continue;
-% end
-%
-% if ( any(strcmpi(matchToolbox,toolboxes)) )
-% toolboxMap(i) = find(strcmpi(matchToolbox,toolboxes));
-% continue;
-% end
-%
-% toolboxMap(i) = length(toolboxes) + 1;
-% toolboxes = [toolboxes; {matchToolbox}];
-% end
-
- % Write a DOT file representing call graph
- fid = fopen('adjmat.dot','w');
- % fprintf(fid,'digraph G {\ncenter = 1;\nsize="10,10";\n');
- fprintf(fid, 'digraph G \n{\n');
- fprintf(fid, 'rankdir=LR\n');
- fprintf(fid, 'node [shape=box]\n');
-
- bUsedNodes = false(1,length(fullFuncList));
-% for i=1:length(toolboxes)
-% bInToolbox = (toolboxMap == i);
-% tbGraph = callGraph(bInToolbox,bInToolbox);
-% subNodes = find(bInToolbox);
-%
-% fprintf(fid, 'subgraph ["%s"]\n{\n', toolboxes{i});
-%
-% for j=1:length(subNodes)
-% [funcPath shortName] = fileparts(fullFuncList{subNodes(j)});
-% fprintf(fid, '%d[label="%s"]; ', subNodes(j), shortName);
-% end
-%
-% fprintf(fid, '\n');
-%
-% [r c] = find(tbGraph);
-% for j=1:length(r)
-% fprintf(fid, '%d -> %d; ', subNodes(r(j)), subNodes(c(j)));
-% end
-%
-% fprintf(fid, '\n}\n');
-%
-% bUsedNodes(bInToolbox) = 1;
-% callGraph(bInToolbox,bInToolbox) = 0;
-% end
-
- remainingNodes = find(~bUsedNodes);
- for i=1:length(remainingNodes)
- [funcPath shortName] = fileparts(fullFuncList{remainingNodes(i)});
- fprintf(fid, '%d[label="%s"]; ', remainingNodes(i), shortName);
- end
-
- fprintf(fid, '\n');
- [r c] = find(callGraph);
- for i=1:length(r)
- fprintf(fid, '%d -> %d; ', r(i), c(i));
- end
-
- fprintf(fid, '\n}');
- fclose(fid);
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Dev/hemetoSegTesting.m b/src/MATLAB/+Dev/hemetoSegTesting.m
deleted file mode 100644
index 247d61e062e0bda91d3e360e9951b2a2036a8669..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Dev/hemetoSegTesting.m
+++ /dev/null
@@ -1,103 +0,0 @@
-orgImg = imread('C:\Users\Eric\Pictures\Pos18\Pos18\Doc_0008_2_Position18.tif_Files_cropped\120608ML_p018_t00637_w0.tif');
-gry = mat2gray(orgImg);
-thGry = graythresh(gry);
-bwGry = im2bw(gry,thGry);
-se=strel('disk',2);
-gd=imdilate(gry,se);
-ge=imerode(gry,se);
-ig=gd-ge;
-
-thIg = graythresh(ig);
-bwig=im2bw(ig,thIg);
-
-% gry_ig=bwGry-bwig;
-% gry_ig(:)=max(gry_ig(:),0);
-% ds = bwdist(bwig);
-
-bw = bwGry &~ bwig;
-bw2 = +bwGry;
-bw2 = bw2-ig;
-
-bw3 = imfill(bw,'holes');
-% bw3 = imopen(bw3,se);
-
-[bwR bwC] = find(bwGry);
-imagesc(gry);colormap gray, hold on
-plot(bwC,bwR,'sb');
-
-CC = bwconncomp(bw3,8);
-stats = regionprops(CC, 'Area', 'Centroid', 'Eccentricity','MinorAxisLength');
-idx = find([stats.Area] > 100);
-for i=1:length(idx)
- id = sprintf('%d',idx(i));
- text(stats(idx(i)).Centroid(1),stats(idx(i)).Centroid(2),id);
-end
-
-cell = 166;
-pixels = CC.PixelIdxList{cell};
-[r c] = ind2sub(size(orgImg), pixels);
-points = [];
-for i=1:length(pixels)
-% for j=1:stats(cell).MinorAxisLength*bw2(pixels(i))
-% z = ceil(j/2);
-% if (mod(j,2))
-% z = -z;
-% end
- points = [points;[r(i) c(i) i]];
-% end
-end
-
-[B I]=unique(points,'rows');
-
-clstr = 4;
-opt = statset('MaxIter',400);
-obj = gmdistribution.fit([points(:,1) points(:,2)],clstr,'Options',opt,'Replicates',15);
-kIdx = cluster(obj, [points(:,1) points(:,2)]);
-
-[kIdxK m] = kmeans([points(:,1) points(:,2)],clstr,'Replicates',15);
-
-hulls = [];
-for i=1:clstr
- hulls(i).pixels = [];
-end
-
-for i=1:length(I)
- hulls(kIdx(I(i))).pixels = [hulls(kIdx(I(i))).pixels; points(I(i),:)];
-end
-
-hullsK = [];
-for i=1:clstr
- hullsK(i).pixels = [];
-end
-
-for i=1:length(I)
- hullsK(kIdxK(I(i))).pixels = [hullsK(kIdxK(I(i))).pixels; points(I(i),:)];
-end
-
-% for i=1:4
-% hulls(i).pixels = [r(kIdx==i) c(kIdx==i)];
-% end
-
-%imagesc(gry); colormap gray, hold on
-
-plot(hulls(1).pixels(:,2),hulls(1).pixels(:,1),'.r');
-plot(hulls(2).pixels(:,2),hulls(2).pixels(:,1),'.g');
-plot(hulls(3).pixels(:,2),hulls(3).pixels(:,1),'.b');
-plot(hulls(4).pixels(:,2),hulls(4).pixels(:,1),'.c');
-plot(hulls(5).pixels(:,2),hulls(5).pixels(:,1),'om');
-plot(hulls(6).pixels(:,2),hulls(6).pixels(:,1),'.y');
-plot(hulls(7).pixels(:,2),hulls(7).pixels(:,1),'.k');
-
-plot(hullsK(1).pixels(:,2),hullsK(1).pixels(:,1),'.r');
-plot(hullsK(2).pixels(:,2),hullsK(2).pixels(:,1),'.g');
-plot(hullsK(3).pixels(:,2),hullsK(3).pixels(:,1),'.b');
-plot(hullsK(4).pixels(:,2),hullsK(4).pixels(:,1),'.c');
-plot(hullsK(5).pixels(:,2),hullsK(5).pixels(:,1),'.m');
-plot(hullsK(6).pixels(:,2),hullsK(6).pixels(:,1),'.y');
-plot(hullsK(7).pixels(:,2),hullsK(7).pixels(:,1),'.k');
-
-plot(m(1,2),m(1,1),'sk','MarkerFaceColor','k');
-plot(m(2,2),m(2,1),'sk','MarkerFaceColor','k');
-plot(m(3,2),m(3,1),'sk','MarkerFaceColor','k');
-plot(m(4,2),m(4,1),'sk','MarkerFaceColor','k');
-plot(m(5,2),m(5,1),'sk','MarkerFaceColor','k');
diff --git a/src/MATLAB/+Dev/testMexDijkstra.m b/src/MATLAB/+Dev/testMexDijkstra.m
deleted file mode 100644
index 1163126ebf2dabbe7c2f4f19d67a2c00e374dfca..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Dev/testMexDijkstra.m
+++ /dev/null
@@ -1,143 +0,0 @@
-function testMexDijkstra()
- global CellHulls
-
- clear mex
-
- tic;
- costMatrix = Tracker.GetCostMatrix();
- mexDijkstra('initGraph', costMatrix);
-
- maxFrameExt = 19;
-
- UI.Progressbar(0);
- for i=1:length(CellHulls)
-% [pathExt pathCost] = dijkstraSearch(i, costMatrix, @checkExtension, maxFrameExt);
- [testPaths testCosts] = mexDijkstra('checkExtension', i, maxFrameExt+1);
-
-% [pathCost srtidx] = sort(pathCost);
-% pathExt = pathExt(srtidx);
-%
-% [testCosts srtidx] = sort(testCosts);
-% testPaths = testPaths(srtidx);
-%
-% if ( length(pathExt) ~= length(testPaths) )
-% error(['Unequal paths at i=' num2str(i) ' (lengths mismatched)']);
-% end
-%
-% for j=1:length(pathExt)
-% if ( testCosts(j) ~= pathCost(j) )
-% error(['Unequal paths at i=' num2str(i) ' (' num2str(j) '-th cost mismatced)']);
-% end
-% end
-%
-% for j=1:length(pathExt)
-% if ( testPaths{j}(end) ~= pathExt{j}(end) )
-% error(['Unequal paths at i=' num2str(i) ' (' num2str(j) '-th endHull mismatced)']);
-% end
-% end
-
- UI.Progressbar(i / length(CellHulls));
- end
-
- toc
-
- disp('SWEETNESS!');
-end
-
-function bGoodExt = checkExtension(startHull, endHull, path)
- global CellTracks CellHulls
-
- bGoodExt = false;
-
- trackID = Hulls.GetTrackID(endHull);
- bGoodTime = (CellTracks(trackID).startTime == CellHulls(endHull).time);
- if ( ~bGoodTime )
- return;
- end
-
- parentID = CellTracks(trackID).parentTrack;
- if ( ~isempty(parentID) )
- nzParent = CellTracks(parentID).hulls(find(CellTracks(parentID).hulls,1,'last'));
- [costMatrix bPathHulls bNextHulls] = Tracker.GetCostSubmatrix(nzParent, 1:length(CellHulls));
- nxtHulls = find(bNextHulls);
- [dump minidx] = min(costMatrix);
- if ( nxtHulls(minidx) == endHull )
- return;
- end
- end
-
- bGoodExt = true;
-end
-
-function [paths pathCosts] = dijkstraSearch(startHull, costGraph, acceptFunc, maxExt)
- paths = {};
- pathCosts = [];
-
- bestCosts = sparse([],[],[],1,size(costGraph,1),round(0.01*size(costGraph,1)));
- bestPaths = cell(1,size(costGraph,1));
-
- bestPaths{startHull} = startHull;
-
- termHulls = [];
-
- trvList = [];
- trvHull = startHull;
- while ( true )
-
- nextHulls = find(costGraph(trvHull,:));
- nextPathCosts = costGraph(trvHull,nextHulls) + bestCosts(trvHull);
-
-% % Don't even bother putting paths that are higher cost in the list
-% bestChk = bestCosts(nextHulls);
-% bestChk(bestChk == 0) = Inf;
-% bKeepNext = (min([nextPathCosts;bestChk],[],1) == nextPathCosts);
-% nextHulls = nextHulls(bKeepNext);
-% nextPathCosts = nextPathCosts(bKeepNext);
-
- trvList = [trvList; nextPathCosts' trvHull*ones(length(nextHulls),1) nextHulls'];
- bestChk = full(bestCosts(trvList(:,3)));
- bestChk(bestChk == 0) = Inf;
- bKeepNext = (min([trvList(:,1)';bestChk],[],1) == trvList(:,1)');
- trvList = trvList(bKeepNext,:);
-
-% trvList = sortrows([trvList; nextPathCosts' trvHull*ones(length(nextHulls),1) nextHulls'],1);
- trvList = sortrows(trvList,1);
-
- while ( size(trvList,1) > 0 )
- if ( length(bestPaths{trvList(1,2)}) > maxExt )
- trvList = trvList(2:end,:);
- continue;
- end
-
- if ( (bestCosts(trvList(1,3))==0) )
- bestCosts(trvList(1,3)) = trvList(1,1);
- bestPaths{trvList(1,3)} = [bestPaths{trvList(1,2)} trvList(1,3)];
- elseif ( (bestCosts(trvList(1,3)) > trvList(1,1)) )
- error('This should never happen!');
- end
-
- % Is the next traversal a terminal node?
- if ( acceptFunc(startHull, trvList(1,3),[bestPaths{trvList(1,2)} trvList(1,3)]) )
- termHulls = union(termHulls,trvList(1,3));
- trvList = trvList(2:end,:);
- continue;
- end
-
- break;
- end
-
- if ( isempty(trvList) )
- break;
- end
-
- trvHull = trvList(1,3);
- trvList = trvList(2:end,:);
- end
-
- paths = cell(1,length(termHulls));
- pathCosts = zeros(1,length(termHulls));
- for i=1:length(termHulls)
- paths{i} = bestPaths{termHulls(i)};
- pathCosts(i) = bestCosts(termHulls(i));
- end
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Editor/AddHull.m b/src/MATLAB/+Editor/AddHull.m
index 958a536ae0f606e8a588cf149f4d16a69a68ecbb..7105b241fca11b970a195274a3c55db8014553c5 100644
--- a/src/MATLAB/+Editor/AddHull.m
+++ b/src/MATLAB/+Editor/AddHull.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Editor/AddMitosisAction.m b/src/MATLAB/+Editor/AddMitosisAction.m
index af3a288b1479a3ac6534e6bae86f8de9d5bae39d..cafe0a38ae53454e2c3d8ab8505030358b25e70f 100644
--- a/src/MATLAB/+Editor/AddMitosisAction.m
+++ b/src/MATLAB/+Editor/AddMitosisAction.m
@@ -5,6 +5,30 @@
% leftChild is non-empty also change its label to the parent track before
% adding the mitosis.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = AddMitosisAction(parentTrack, leftChild, siblingTrack, time)
global CellTracks
diff --git a/src/MATLAB/+Editor/AddNewCell.m b/src/MATLAB/+Editor/AddNewCell.m
index 44304e7a10b856dca570e41992841d7df46af579..8784ff6bc3ad01f69b81bc46a5d7b8a80e892176 100644
--- a/src/MATLAB/+Editor/AddNewCell.m
+++ b/src/MATLAB/+Editor/AddNewCell.m
@@ -5,6 +5,30 @@
% find a segmentation result, add a singple point segmentation at
% clickPoint
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [historyAction newTrack] = AddNewCell(clickPoint, time)
newTrack = Segmentation.AddNewSegmentHull(clickPoint, time);
diff --git a/src/MATLAB/+Editor/AddPhenotype.m b/src/MATLAB/+Editor/AddPhenotype.m
index eceeb6de346a8c60ab707a350e2ef7df0f2814ef..c8b8d1643e91dd0fa9fef5d5134635eecfb25672 100644
--- a/src/MATLAB/+Editor/AddPhenotype.m
+++ b/src/MATLAB/+Editor/AddPhenotype.m
@@ -5,6 +5,30 @@
% NOTE: this is one of the few edit actions that does not directly affect
% undo stack it will always be followed by a ContextSetPhenotype action.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [historyAction phenoID] = AddPhenotype(description)
global CellPhenotypes Colors
diff --git a/src/MATLAB/+Editor/ChangeLabelAction.m b/src/MATLAB/+Editor/ChangeLabelAction.m
index 74dc6879f6d111288ff20b6919f72bf6cf930f56..21aed091fb444cb8e7d808fa4c3fc9f87cdf0ef1 100644
--- a/src/MATLAB/+Editor/ChangeLabelAction.m
+++ b/src/MATLAB/+Editor/ChangeLabelAction.m
@@ -3,6 +3,30 @@
%
% Changes trackID to newTrackID beginning at time.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = ChangeLabelAction(trackID, newTrackID, time)
%TODO: This edit graph update may need to more complicated to truly
%capture user edit intentions.
diff --git a/src/MATLAB/+Editor/ChangeParent.m b/src/MATLAB/+Editor/ChangeParent.m
index 546d7a57ad10be6d7298475ef52abc25eea8775c..a6a59029226e1c1ef9bcc403613a018bce74939d 100644
--- a/src/MATLAB/+Editor/ChangeParent.m
+++ b/src/MATLAB/+Editor/ChangeParent.m
@@ -5,6 +5,30 @@
% Context Swap Labels
% Toggle lock on family ID
% Maria Enokian
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function historyAction = ChangeParent(familyID,trackID,newTrackID, time)
% Initialized variables
global CellFamilies CellTracks Figures
diff --git a/src/MATLAB/+Editor/ContextAddAllToExtendedFamily.m b/src/MATLAB/+Editor/ContextAddAllToExtendedFamily.m
new file mode 100755
index 0000000000000000000000000000000000000000..80180899a68ca25a4d3a0c33ba3b2091a95e0a69
--- /dev/null
+++ b/src/MATLAB/+Editor/ContextAddAllToExtendedFamily.m
@@ -0,0 +1,34 @@
+% ContextAddAllToExtendedFamily.m - Context menu callback function for adding
+% all tracks on a frame to an extended family
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function ContextAddAllToExtendedFamily(time)
+ global Figures
+
+ Families.MultiTreeAllTracks(time);
+
+ UI.DrawTree(Figures.tree.familyID);
+ UI.DrawCells();
+end
diff --git a/src/MATLAB/+Editor/ContextAddMitosis.m b/src/MATLAB/+Editor/ContextAddMitosis.m
index d0279d3b3bcb8c807e348af1cbe91b39205d9b93..a299ef5318ea6ff97720b16421c45211609dad38 100644
--- a/src/MATLAB/+Editor/ContextAddMitosis.m
+++ b/src/MATLAB/+Editor/ContextAddMitosis.m
@@ -1,5 +1,29 @@
% ContextAddMitosis(trackID, siblingTrack, time)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
% ChangeLog:
% EW 6/8/12 created
function ContextAddMitosis(trackID, siblingTrack, time, localLabels, revLocalLabels)
diff --git a/src/MATLAB/+Editor/ContextAddToExtendedFamily.m b/src/MATLAB/+Editor/ContextAddToExtendedFamily.m
index 6900ff7dc674e7a25ac71846fe02eb8e64a24bc9..7427628621981964e7820e658262bb48604f16fd 100755
--- a/src/MATLAB/+Editor/ContextAddToExtendedFamily.m
+++ b/src/MATLAB/+Editor/ContextAddToExtendedFamily.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -24,22 +24,26 @@
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-function ContextAddToExtendedFamily(trackID)
+function ContextAddToExtendedFamily(hullIDs)
global CellFamilies CellTracks Figures
- familyID = CellTracks(trackID).familyID;
-
- if ~isempty(CellFamilies(familyID).extFamily)
- xfam = CellFamilies(familyID).extFamily;
- if length(xfam) > 1
- warn = sprintf('Track %d is already in an extended family', trackID);
- warndlg(warn);
- return;
+ trackIDs = Hulls.GetTrackID(hullIDs);
+ familyIDs = [CellTracks(trackIDs).familyID];
+
+ for i=1:length(familyIDs)
+ familyID = familyIDs(i);
+ if ~isempty(CellFamilies(familyID).extFamily)
+ xfam = CellFamilies(familyID).extFamily;
+ if length(xfam) > 1
+ warn = sprintf('Track %d is already in an extended family', trackID);
+ warndlg(warn);
+ return;
+ end
end
end
[localLabels, revLocalLabels] = UI.GetLocalTreeLabels(Figures.tree.familyID);
- answer = inputdlg('Enter cell label of family to join','Join Family',1,{UI.TrackToLocal(localLabels, trackID)});
+ answer = inputdlg('Enter cell label of family to join','Join Family',1,{num2str(CellFamilies(Figures.tree.familyID).tracks(1))});
if(isempty(answer)),return,end;
newTrackIDLocal = answer{1};
@@ -57,14 +61,14 @@ function ContextAddToExtendedFamily(trackID)
return
end
- if ( newTrackID == trackID )
- warn = sprintf('Track %s is the current track.', newTrackIDLocal);
+ if ( ismember(newTrackID, trackIDs) )
+ warn = sprintf('Track %s is one of the selected track(s).', newTrackIDLocal);
warndlg(warn);
return;
end
newFamilyID = CellTracks(newTrackID).familyID;
- newExtFamily = union(CellFamilies(newFamilyID).extFamily, [familyID newFamilyID]);
+ newExtFamily = union(CellFamilies(newFamilyID).extFamily, [familyIDs newFamilyID]);
[CellFamilies(newExtFamily).extFamily] = deal(newExtFamily);
UI.DrawTree(Figures.tree.familyID);
diff --git a/src/MATLAB/+Editor/ContextChangeLabel.m b/src/MATLAB/+Editor/ContextChangeLabel.m
index bee4e4c8fb28e1d0323440089a95e3fc56047115..89d142130f72d16a781b4b644f1b1cdef5c8bc08 100644
--- a/src/MATLAB/+Editor/ContextChangeLabel.m
+++ b/src/MATLAB/+Editor/ContextChangeLabel.m
@@ -5,10 +5,10 @@
% EW 6/8/12 reviewed
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Editor/ContextChangeParent.m b/src/MATLAB/+Editor/ContextChangeParent.m
index a94023a08d0cbb50c548c4e2ca4b8ae3e994d59f..14b2d26f18e9fd2af88dc5fd8fefdb3ac7a8ea85 100644
--- a/src/MATLAB/+Editor/ContextChangeParent.m
+++ b/src/MATLAB/+Editor/ContextChangeParent.m
@@ -1,6 +1,30 @@
% ContextChangeParent.m - Allows user to correct the parents during the
% mitosis stage, and fix the tree.
% Maria Enokian
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function ContextChangeParent(familyID,time,trackID)
global CellTracks
global Figures
diff --git a/src/MATLAB/+Editor/ContextProperties.m b/src/MATLAB/+Editor/ContextProperties.m
index 954f0eea7c67fd3695189208e05e9a47a46f355a..c171da84e1512c1133b31960ce495d7e81ba3dc8 100644
--- a/src/MATLAB/+Editor/ContextProperties.m
+++ b/src/MATLAB/+Editor/ContextProperties.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Editor/ContextRemoveAllFromExtendedFamily.m b/src/MATLAB/+Editor/ContextRemoveAllFromExtendedFamily.m
new file mode 100755
index 0000000000000000000000000000000000000000..e2adbcba68309c51c74be1e8de162b065f0ce5b5
--- /dev/null
+++ b/src/MATLAB/+Editor/ContextRemoveAllFromExtendedFamily.m
@@ -0,0 +1,34 @@
+% ContextAddAllToExtendedFamily.m - Context menu callback function for adding
+% all tracks on a frame to an extended family
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function ContextRemoveAllFromExtendedFamily()
+ global Figures CellFamilies
+
+ [CellFamilies(:).extFamily] = deal([]);
+
+ UI.DrawTree(Figures.tree.familyID);
+ UI.DrawCells();
+end
diff --git a/src/MATLAB/+Editor/ContextRemoveFromExtendedFamily.m b/src/MATLAB/+Editor/ContextRemoveFromExtendedFamily.m
index 862a765e3b5d3d79b412fa2af23df7cc951b3a3e..c5f25fca2c43b4fc5b54519f35a38995ae5bbf88 100755
--- a/src/MATLAB/+Editor/ContextRemoveFromExtendedFamily.m
+++ b/src/MATLAB/+Editor/ContextRemoveFromExtendedFamily.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Editor/ContextRemoveFromTree.m b/src/MATLAB/+Editor/ContextRemoveFromTree.m
index 05374a0323cdb30b680e8b255d7d81975d3c82f4..cbae7dc4638694c3984b9cc34178fd83e65129a0 100644
--- a/src/MATLAB/+Editor/ContextRemoveFromTree.m
+++ b/src/MATLAB/+Editor/ContextRemoveFromTree.m
@@ -5,10 +5,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Editor/ContextSetPhenotype.m b/src/MATLAB/+Editor/ContextSetPhenotype.m
index a291f7b8a1705807bdeb72ec85f058956d09607a..e72f1d5aaee3db6574d4c9bf326c2b6016993d15 100644
--- a/src/MATLAB/+Editor/ContextSetPhenotype.m
+++ b/src/MATLAB/+Editor/ContextSetPhenotype.m
@@ -4,6 +4,30 @@
% Sets or clears the phenotype specified for the given hull. If the
% phenotype is "dead" there is also some special handling to drop children.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = ContextSetPhenotype(hullID, phenotype, bActive)
global CellPhenotypes
diff --git a/src/MATLAB/+Editor/ContextSwapLabels.m b/src/MATLAB/+Editor/ContextSwapLabels.m
index 08a8fa41afce8969f15b7323bc418ae8184d38f0..bf20fb9faeaa120a3f4293cade8a48d286a04af0 100644
--- a/src/MATLAB/+Editor/ContextSwapLabels.m
+++ b/src/MATLAB/+Editor/ContextSwapLabels.m
@@ -3,6 +3,30 @@
%
% Swap tracking for tracks A and B beginning at specified time.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = ContextSwapLabels(trackA, trackB, time)
Tracker.GraphEditSetEdge(trackA, trackB, time);
diff --git a/src/MATLAB/+Editor/CreateMitosisAction.m b/src/MATLAB/+Editor/CreateMitosisAction.m
index e1efde9d25a604ba0373f8165a6eeee19372def9..7de7a66d85c3790ef1e2d555dea75ded522fc9ab 100644
--- a/src/MATLAB/+Editor/CreateMitosisAction.m
+++ b/src/MATLAB/+Editor/CreateMitosisAction.m
@@ -3,6 +3,30 @@
%
% Create user identified mitosis events and add to current tree.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = CreateMitosisAction(trackID, dirFlag, time, linePoints)
global CellTracks
@@ -49,11 +73,11 @@ function historyAction = CreateMitosisAction(trackID, dirFlag, time, linePoints)
end
function newPoints = clipToImage(linePoints)
- global CONSTANTS
-
newPoints = linePoints;
- newPoints(:,1) = min(newPoints(:,1), repmat(CONSTANTS.imageSize(2),size(linePoints,1),1));
- newPoints(:,2) = min(newPoints(:,2), repmat(CONSTANTS.imageSize(1),size(linePoints,1),1));
+
+ xyImageDims = Metadata.GetDimensions('xy');
+ newPoints(:,1) = min(newPoints(:,1), repmat(xyImageDims(1),size(linePoints,1),1));
+ newPoints(:,2) = min(newPoints(:,2), repmat(xyImageDims(2),size(linePoints,1),1));
newPoints(:,1) = max(newPoints(:,1), repmat(1,size(linePoints,1),1));
newPoints(:,2) = max(newPoints(:,2), repmat(1,size(linePoints,1),1));
diff --git a/src/MATLAB/+Editor/DeleteCells.m b/src/MATLAB/+Editor/DeleteCells.m
index a6a9275d2b227e32ea79a610937e2ce6e89f8192..579d05258151904f080f36109623c0f27ad35d26 100644
--- a/src/MATLAB/+Editor/DeleteCells.m
+++ b/src/MATLAB/+Editor/DeleteCells.m
@@ -4,10 +4,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Editor/DropReplayableSubtask.m b/src/MATLAB/+Editor/DropReplayableSubtask.m
index 64f677f3302f74ba0e08fc50c73c74003c699be1..53611b454be04e48e1e8b17a94f1979ea9eab387 100644
--- a/src/MATLAB/+Editor/DropReplayableSubtask.m
+++ b/src/MATLAB/+Editor/DropReplayableSubtask.m
@@ -9,6 +9,30 @@
% The tasklabel should match the task that was added, the labels are only
% an error checking device.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = DropReplayableSubtask(taskLabel)
global TaskStack
diff --git a/src/MATLAB/+Editor/History.m b/src/MATLAB/+Editor/History.m
index f3d16bdf55f4632a9f2ed27451bfd2ff38057bd1..0ff96b9ef6acd1acdf4d96f1b2522c6efc66d660 100644
--- a/src/MATLAB/+Editor/History.m
+++ b/src/MATLAB/+Editor/History.m
@@ -15,23 +15,23 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-%
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
-%
+%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
-%
+%
% You should have received a copy of the GNU General Public License
-% along with LEVer in file "gnu gpl v3.txt". If not, see
+% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -160,16 +160,17 @@ function setMenus()
end
if (isfield(Figures.cells,'menuHandles') && isfield(Figures.cells.menuHandles,'saveMenu'))
+ datasetName = Metadata.GetDatasetName();
if ( Editor.StackedHistory.IsSaved() )
set(Figures.cells.menuHandles.saveMenu,'Enable','off');
set(Figures.tree.menuHandles.saveMenu,'Enable','off');
- set(Figures.cells.handle,'Name',[CONSTANTS.datasetName ' Image Data']);
- set(Figures.tree.handle,'Name',[CONSTANTS.datasetName ' Image Data']);
+ set(Figures.cells.handle,'Name',[datasetName ' Image Data']);
+ set(Figures.tree.handle,'Name',[datasetName ' Lineage Data']);
else
set(Figures.cells.menuHandles.saveMenu,'Enable','on');
set(Figures.tree.menuHandles.saveMenu,'Enable','on');
- set(Figures.cells.handle,'Name',[CONSTANTS.datasetName ' Image Data *']);
- set(Figures.tree.handle,'Name',[CONSTANTS.datasetName ' Image Data *']);
+ set(Figures.cells.handle,'Name',[datasetName ' Image Data *']);
+ set(Figures.tree.handle,'Name',[datasetName ' Lineage Data *']);
end
end
end %setMenu
diff --git a/src/MATLAB/+Editor/InitHistory.m b/src/MATLAB/+Editor/InitHistory.m
index fb70431b29b7ca4b560a7eb3c517eb3ac9804cec..366760f75384e726906649e4c56975273161d212 100644
--- a/src/MATLAB/+Editor/InitHistory.m
+++ b/src/MATLAB/+Editor/InitHistory.m
@@ -3,6 +3,30 @@
%
% Tells the replay code that history has been reinitialized (on open).
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = InitHistory()
historyAction = 'Init';
end
diff --git a/src/MATLAB/+Editor/LearnFromEdits.m b/src/MATLAB/+Editor/LearnFromEdits.m
index 5c14f529d87bc04c265494df2bd67dffac995260..390d3573edff874c0fa665fd4b9d72f9c2114e9f 100644
--- a/src/MATLAB/+Editor/LearnFromEdits.m
+++ b/src/MATLAB/+Editor/LearnFromEdits.m
@@ -3,6 +3,30 @@
%
% Propagate segmentation edits forward.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = LearnFromEdits()
global SegmentationEdits
diff --git a/src/MATLAB/+Editor/LockedAddMitosisAction.m b/src/MATLAB/+Editor/LockedAddMitosisAction.m
index 11951ac5b6e88727442a5278675882cc547f28dc..6c5e097e221e6256911e32f2b52229a4cb30af38 100644
--- a/src/MATLAB/+Editor/LockedAddMitosisAction.m
+++ b/src/MATLAB/+Editor/LockedAddMitosisAction.m
@@ -5,6 +5,30 @@
% leftChild is non-empty also change its label to the parent track before
% adding the mitosis. Try to minimize locked tree structure changes
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = LockedAddMitosisAction(parentTrack, leftChildTrack, siblingTrack, time)
global CellTracks
diff --git a/src/MATLAB/+Editor/LockedChangeLabelAction.m b/src/MATLAB/+Editor/LockedChangeLabelAction.m
index 10c6378733f96d737ad4da9ab646a86d5bb78401..3e9b6efa57d6de05b5d4d09d92ad1e49a76d3855 100644
--- a/src/MATLAB/+Editor/LockedChangeLabelAction.m
+++ b/src/MATLAB/+Editor/LockedChangeLabelAction.m
@@ -4,6 +4,30 @@
% Changes hull at time from trackID to newTrackID. Tries to preserve tree
% structure.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = LockedChangeLabelAction(trackID, newTrackID, time)
Tracker.GraphEditSetEdge(newTrackID,trackID,time,false);
Tracks.LockedChangeLabel(trackID,newTrackID,time);
diff --git a/src/MATLAB/+Editor/LogEdit.m b/src/MATLAB/+Editor/LogEdit.m
index aa48e935e8b380589abccc422e847d3d7a2ec2f1..852f7fe861f22ebd84e45af316197238a6addb97 100644
--- a/src/MATLAB/+Editor/LogEdit.m
+++ b/src/MATLAB/+Editor/LogEdit.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function LogEdit(actionStr, inputIDs, outputIDs, bUserEdit)
global EditList
diff --git a/src/MATLAB/+Editor/MergeCellsAction.m b/src/MATLAB/+Editor/MergeCellsAction.m
index f12cf60a768f602c2c988cb4cabd36317dd66669..911ec921eed0198562a958af5ad02994f33d9ad5 100644
--- a/src/MATLAB/+Editor/MergeCellsAction.m
+++ b/src/MATLAB/+Editor/MergeCellsAction.m
@@ -3,6 +3,30 @@
%
% Attempt to merge oversegmented cells.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [historyAction deletedCells replaceCell] = MergeCellsAction(selectedHulls, selectedTree)
global SegmentationEdits
diff --git a/src/MATLAB/+Editor/MitosisEditInitializeAction.m b/src/MATLAB/+Editor/MitosisEditInitializeAction.m
index c139554d0132b4fdd339a4d965ad4cd7d7ff876a..c51d5dc117a574eb0aeba3273e0c91c345de775e 100644
--- a/src/MATLAB/+Editor/MitosisEditInitializeAction.m
+++ b/src/MATLAB/+Editor/MitosisEditInitializeAction.m
@@ -3,6 +3,30 @@
%
% Initialize mitosis editing state
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = MitosisEditInitializeAction(treeID, endTime)
global CellFamilies
diff --git a/src/MATLAB/+Editor/MitosisHullPhenotypeAction.m b/src/MATLAB/+Editor/MitosisHullPhenotypeAction.m
index 8aea85b38b6bf6a7c4b51d3c9904c3fdc1070113..9ee53c05e329607c384f09193a7b68a0328d9a5a 100644
--- a/src/MATLAB/+Editor/MitosisHullPhenotypeAction.m
+++ b/src/MATLAB/+Editor/MitosisHullPhenotypeAction.m
@@ -1,6 +1,30 @@
% [historyAction newTrack] = MitosisHullPhenotypeAction()
% Edit Action:
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [historyAction hullID] = MitosisHullPhenotypeAction(clickPoint, time, trackID)
hullID = Hulls.FindHull(time, clickPoint);
diff --git a/src/MATLAB/+Editor/OriginAction.m b/src/MATLAB/+Editor/OriginAction.m
index 645f560339bdf02aaf5c1547c8e93d5f4241b20e..eeaa2bac75c3980656c24886a812479647e0e9a0 100644
--- a/src/MATLAB/+Editor/OriginAction.m
+++ b/src/MATLAB/+Editor/OriginAction.m
@@ -4,6 +4,30 @@
% This initial action creates a hash of several core data structures to
% allow verification that a run of edits starts from the correct data.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [historyAction coreHash bInitialSeg] = OriginAction(bInitialSeg)
historyAction = '';
coreHash = Dev.GetCoreHashList();
diff --git a/src/MATLAB/+Editor/Redo.m b/src/MATLAB/+Editor/Redo.m
index 86e0c73153057b0b9c88bf5fb3fb27e27776b286..53d5e7a845449fdc374100295a144aac09afbbf9 100644
--- a/src/MATLAB/+Editor/Redo.m
+++ b/src/MATLAB/+Editor/Redo.m
@@ -4,6 +4,30 @@
% This is purely a placeholder to tell the replay action code that a redo
% was performed.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = Redo()
historyAction = 'Redo';
end
diff --git a/src/MATLAB/+Editor/RemoveTrackHulls.m b/src/MATLAB/+Editor/RemoveTrackHulls.m
index e398ad51387a9b8069ad65c0c7fd91741b752f2f..8cbc373cd63c1381f54695a165368e605a1e87c3 100644
--- a/src/MATLAB/+Editor/RemoveTrackHulls.m
+++ b/src/MATLAB/+Editor/RemoveTrackHulls.m
@@ -5,10 +5,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Editor/ReplayableEditAction.m b/src/MATLAB/+Editor/ReplayableEditAction.m
index b092f75f086de5932091b2f16cc2660113d8b3c5..bcfeeb0511dc3d5eaab2a46a75f6fe61bd7fab47 100644
--- a/src/MATLAB/+Editor/ReplayableEditAction.m
+++ b/src/MATLAB/+Editor/ReplayableEditAction.m
@@ -14,6 +14,30 @@
% Regardless of success, the action and all arguments are added to the end
% of the replay list.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [bErr varargout] = ReplayableEditAction(actPtr, varargin)
global ReplayEditActions
diff --git a/src/MATLAB/+Editor/ResegBackAction.m b/src/MATLAB/+Editor/ResegBackAction.m
index da567bc54b29669d711f1ddc162d6d101acf0481..60d41b45d3c0be4a2850cfc378fac3d2192be950 100644
--- a/src/MATLAB/+Editor/ResegBackAction.m
+++ b/src/MATLAB/+Editor/ResegBackAction.m
@@ -4,6 +4,30 @@
% Back up a single frame, undoing whatever reseg actions were taken in the
% current frame
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = ResegBackAction()
historyAction.action = 'Undo';
historyAction.arg = 'Jump';
diff --git a/src/MATLAB/+Editor/ResegFinishAction.m b/src/MATLAB/+Editor/ResegFinishAction.m
index ed51778daaf5ad910caf134f4f5854e45528c88b..89d53a6c59cb1ffd4437002a9458d5809aa6969f 100644
--- a/src/MATLAB/+Editor/ResegFinishAction.m
+++ b/src/MATLAB/+Editor/ResegFinishAction.m
@@ -3,6 +3,30 @@
%
% Finish resegmentation action, (push history)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [historyAction finishTime finalResegState] = ResegFinishAction()
global ResegState bResegPaused
diff --git a/src/MATLAB/+Editor/ResegForwardAction.m b/src/MATLAB/+Editor/ResegForwardAction.m
index e5484d00f5e5858ce4307a02ce49f956a626c2ca..186381e4e89d8bf2ca9006dec5019a248d05f7be 100644
--- a/src/MATLAB/+Editor/ResegForwardAction.m
+++ b/src/MATLAB/+Editor/ResegForwardAction.m
@@ -3,6 +3,30 @@
%
% Single forward reseg (from pause)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = ResegForwardAction()
global bResegPaused
diff --git a/src/MATLAB/+Editor/ResegFrameAction.m b/src/MATLAB/+Editor/ResegFrameAction.m
index 426bea92ef3334f63a283f1b1f6a72b6729dd339..dcda0de520d2519e46da83dc22ef5aeddee1abec 100644
--- a/src/MATLAB/+Editor/ResegFrameAction.m
+++ b/src/MATLAB/+Editor/ResegFrameAction.m
@@ -3,6 +3,30 @@
%
% Resegment a single frame
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [historyAction bFinished] = ResegFrameAction(t, tMax, viewLims)
global ResegState CellFamilies
diff --git a/src/MATLAB/+Editor/ResegInitializeAction.m b/src/MATLAB/+Editor/ResegInitializeAction.m
index 93bf1ffa38987db23eed3fcfcf94001e3e528571..d916703c902965272592923a7ce1facfff515403 100644
--- a/src/MATLAB/+Editor/ResegInitializeAction.m
+++ b/src/MATLAB/+Editor/ResegInitializeAction.m
@@ -3,6 +3,30 @@
%
% Initialize resegmentation state
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = ResegInitializeAction(preserveFamilies, tStart)
global ResegState bResegPaused
diff --git a/src/MATLAB/+Editor/ResegPauseAction.m b/src/MATLAB/+Editor/ResegPauseAction.m
index 413a85d75b5b98df861ad9843552d95f2b687f84..8b17536ba20b90c080b13d0009e19be86ded86ff 100644
--- a/src/MATLAB/+Editor/ResegPauseAction.m
+++ b/src/MATLAB/+Editor/ResegPauseAction.m
@@ -3,6 +3,30 @@
%
% Pause resegmentation
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = ResegPauseAction()
global ResegState bResegPaused
diff --git a/src/MATLAB/+Editor/ResegPlayAction.m b/src/MATLAB/+Editor/ResegPlayAction.m
index e2d97ce254c7ed9d9d781c4786a7e7453c9a0914..62b5d103dd42821a8306ed37c1a6a915e050c367 100644
--- a/src/MATLAB/+Editor/ResegPlayAction.m
+++ b/src/MATLAB/+Editor/ResegPlayAction.m
@@ -3,6 +3,30 @@
%
% Begin resegmenting (from pause)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = ResegPlayAction(tStart)
global bResegPaused
diff --git a/src/MATLAB/+Editor/SafeExecuteAction.m b/src/MATLAB/+Editor/SafeExecuteAction.m
index ce8a3a826ec8471a2072fe6d4c743ce5b764b4e4..c65edcc915f9467a64c02973549d370e88f99a59 100644
--- a/src/MATLAB/+Editor/SafeExecuteAction.m
+++ b/src/MATLAB/+Editor/SafeExecuteAction.m
@@ -5,6 +5,30 @@
% an exception is caught during execution of the function an error is logged
% and the edit is undone.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [bErr historyAction varargout] = SafeExecuteAction(actPtr, varargin)
varargout = cell(1,max(0,nargout-2));
diff --git a/src/MATLAB/+Editor/SliceAtFrameAction.m b/src/MATLAB/+Editor/SliceAtFrameAction.m
index 3a59d54b444f7246a384c1ea579de740ca279b1b..93c7497e60a1e1370d4ef561aff092cdc6108d79 100644
--- a/src/MATLAB/+Editor/SliceAtFrameAction.m
+++ b/src/MATLAB/+Editor/SliceAtFrameAction.m
@@ -3,6 +3,30 @@
%
% Call RemoveFromTree() on all tracks on family at time.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = SliceAtFrameAction(rootTrackID, time)
global CellFamilies CellTracks
diff --git a/src/MATLAB/+Editor/SplitCell.m b/src/MATLAB/+Editor/SplitCell.m
index c46a1587230e7894304c1c42fba357acf1f0a5f7..a8d49c321fdc475567e4065e3d47bbbde19a8969 100644
--- a/src/MATLAB/+Editor/SplitCell.m
+++ b/src/MATLAB/+Editor/SplitCell.m
@@ -3,6 +3,30 @@
%
% Attempt to split specified hull into k pieces.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [historyAction newTracks] = SplitCell(hullID, k)
oldTrackID = Hulls.GetTrackID(hullID);
diff --git a/src/MATLAB/+Editor/StackedHistory.m b/src/MATLAB/+Editor/StackedHistory.m
deleted file mode 100644
index bfb08e8f775f9950c01f73c16afa7634eccd2a4b..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Editor/StackedHistory.m
+++ /dev/null
@@ -1,6 +0,0 @@
-
-function StackedHistory(action)
- switch action
-
- end
-end
diff --git a/src/MATLAB/+Editor/StartReplayableSubtask.m b/src/MATLAB/+Editor/StartReplayableSubtask.m
index 7f82f0a1b0e362ac65df096ade034c998d6172a3..5e80259615ea069070194efa82f3d9ec9ccc1c7c 100644
--- a/src/MATLAB/+Editor/StartReplayableSubtask.m
+++ b/src/MATLAB/+Editor/StartReplayableSubtask.m
@@ -3,6 +3,30 @@
% Begin a new subtask, this creates a new history stack to be used for the
% task.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = StartReplayableSubtask(taskLabel)
global TaskStack
diff --git a/src/MATLAB/+Editor/StopReplayableSubtask.m b/src/MATLAB/+Editor/StopReplayableSubtask.m
index 4bdfadfc8a3bd5e5021552468afbee45650d4595..54bac71bd1ee18b15ff0c17a86c448653c9d3d10 100644
--- a/src/MATLAB/+Editor/StopReplayableSubtask.m
+++ b/src/MATLAB/+Editor/StopReplayableSubtask.m
@@ -3,6 +3,30 @@
% Stop a subtask, the tasklabel should match the task which was added, the
% labels are only an error checking device.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = StopReplayableSubtask(time, taskLabel)
global TaskStack
diff --git a/src/MATLAB/+Editor/Top.m b/src/MATLAB/+Editor/Top.m
index bc5832dec91404e557ecbd0c6c4488afe8da6732..8a6fd7ca9d97f651e754869517cef370e2bf23fb 100644
--- a/src/MATLAB/+Editor/Top.m
+++ b/src/MATLAB/+Editor/Top.m
@@ -4,6 +4,30 @@
% This is purely a placeholder to tell the replay action code that a top
% was performed.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = Top()
historyAction = 'Top';
end
\ No newline at end of file
diff --git a/src/MATLAB/+Editor/TreeFreezeAction.m b/src/MATLAB/+Editor/TreeFreezeAction.m
index 286d43b145eed577e2b3a3738723af2b8f99f065..0cd84c3822ec65e236b0a2ef6d97a33cc9d2ffa4 100644
--- a/src/MATLAB/+Editor/TreeFreezeAction.m
+++ b/src/MATLAB/+Editor/TreeFreezeAction.m
@@ -3,6 +3,30 @@
%
% Toggles frozen property of familyID
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = TreeFreezeAction(familyID)
global CellFamilies
diff --git a/src/MATLAB/+Editor/TreeInference.m b/src/MATLAB/+Editor/TreeInference.m
index e306c76233301750fda01f1d4391fdf2c2a1f871..c101af0b02c628e5faa1fdd4f3d308a8fb338518 100644
--- a/src/MATLAB/+Editor/TreeInference.m
+++ b/src/MATLAB/+Editor/TreeInference.m
@@ -3,6 +3,30 @@
%
% Applies inference to attempt to improve tree structure.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = TreeInference(families, stopTime)
[iters totalTime] = Families.LinkTrees(families, stopTime);
diff --git a/src/MATLAB/+Editor/TreeLockAction.m b/src/MATLAB/+Editor/TreeLockAction.m
index 19187739d4e707d410adb4c0f4e8c11310508a87..91770f2dcba22171b1fd8065d2559ec4a3921b82 100644
--- a/src/MATLAB/+Editor/TreeLockAction.m
+++ b/src/MATLAB/+Editor/TreeLockAction.m
@@ -3,6 +3,30 @@
%
% Toggles lock on familyID
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = TreeLockAction(familyID)
global CellFamilies
diff --git a/src/MATLAB/+Editor/Undo.m b/src/MATLAB/+Editor/Undo.m
index 068a52a484943f8d6b83ed713806f9d7089be0dc..b5c35b1cd68423ba0d91aec9ca5198de14bf4c98 100644
--- a/src/MATLAB/+Editor/Undo.m
+++ b/src/MATLAB/+Editor/Undo.m
@@ -4,6 +4,30 @@
% This is purely a placeholder to tell the replay action code that an undo
% was performed.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function historyAction = Undo()
historyAction = 'Undo';
end
diff --git a/src/MATLAB/+Error/ErrorHandling.m b/src/MATLAB/+Error/ErrorHandling.m
index 5b12f65ff98a214e28ba263ba6f47b1443c7242b..bc0a996c5971834e9670a1e7baf1c3677fee4352 100644
--- a/src/MATLAB/+Error/ErrorHandling.m
+++ b/src/MATLAB/+Error/ErrorHandling.m
@@ -6,10 +6,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Error/LogAction.m b/src/MATLAB/+Error/LogAction.m
index cfb6aff1cef84ae0f26f6b77b994d74ab3676c1f..83c3a131665e9588cadd903b0c1908f73e8602f7 100644
--- a/src/MATLAB/+Error/LogAction.m
+++ b/src/MATLAB/+Error/LogAction.m
@@ -6,10 +6,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -35,13 +35,13 @@ time = clock;%[year month day hour minute seconds]
settings = Load.ReadSettings();
if ( ~isempty(settings.matFilePath) )
logPath = settings.matFilePath;
- logFile = fullfile(logPath, [CONSTANTS.datasetName '_log.csv']);
+ logFile = fullfile(logPath, [Metadata.GetDatasetName() '_log.csv']);
elseif ( isfield(CONSTANTS,'matFullFile') && ~isempty(CONSTANTS.matFullFile) )
logPath = fileparts(CONSTANTS.matFullFile);
- logFile = fullfile(logPath, [CONSTANTS.datasetName '_log.csv']);
+ logFile = fullfile(logPath, [Metadata.GetDatasetName() '_log.csv']);
else
logPath = '.\';
- logFile = fullfile(logPath, [CONSTANTS.datasetName '_log.csv']);
+ logFile = fullfile(logPath, [Metadata.GetDatasetName() '_log.csv']);
end
[x usr] = system('whoami');
@@ -106,7 +106,7 @@ while(file<2)
answer = questdlg('Please close the log.','Log Opened','Use new log name','Try Again','Try Again');
switch answer
case 'Use new log name'
- file = fopen(fullfile(logPath,[CONSTANTS.datasetName '_log2.csv']),'a');
+ file = fopen(fullfile(logPath,[Metadata.GetDatasetName() '_log2.csv']),'a');
case 'Try Again'
file = fopen(logFile,'a');
end
diff --git a/src/MATLAB/+Error/OutputDebugErrorFile.m b/src/MATLAB/+Error/OutputDebugErrorFile.m
index 622b1094e9ad4b06b7cd28c10ffccdd481640000..a014af2d0cb454ad57fa80a73934ac8ca09a70ea 100644
--- a/src/MATLAB/+Error/OutputDebugErrorFile.m
+++ b/src/MATLAB/+Error/OutputDebugErrorFile.m
@@ -2,10 +2,34 @@
% Outputs ReplayEditActions to a file, this should allow for a complete
% reconstruction of an edit set from the original data.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function OutputDebugErrorFile()
- global CONSTANTS Log ReplayEditActions
+ global Log ReplayEditActions
- errfile = [CONSTANTS.datasetName '_DBGEDITS_' num2str(length(Log)) '.mat'];
+ errfile = [Metadata.GetDatasetName() '_DBGEDITS_' num2str(length(Log)) '.mat'];
save(errfile, 'ReplayEditActions');
end
diff --git a/src/MATLAB/+Error/PrintException.m b/src/MATLAB/+Error/PrintException.m
index a8f54571c09be09edebc5e3c6eaf9b8f1f78d7ae..b7726c637ffb359715d88544ea8b8ff0fbdd8f97 100644
--- a/src/MATLAB/+Error/PrintException.m
+++ b/src/MATLAB/+Error/PrintException.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function excpString = PrintException(excp, prefixstr)
if ( ~exist('prefixstr','var') )
prefixstr = ' ';
diff --git a/src/MATLAB/+Families/AddMitosis.m b/src/MATLAB/+Families/AddMitosis.m
index e2af4ea73affd67f6e76e044ebe5ad302bca396c..02529ba14898b0b96021698b9bcd66e726cfebdf 100644
--- a/src/MATLAB/+Families/AddMitosis.m
+++ b/src/MATLAB/+Families/AddMitosis.m
@@ -1,5 +1,29 @@
% droppedTracks = AddMitosis(addTrack, ontoTrack, time)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
% ChangeLog:
% EW 6/7/12 created
function droppedTracks = AddMitosis(addTrack, ontoTrack, time)
diff --git a/src/MATLAB/+Families/AddToTree.m b/src/MATLAB/+Families/AddToTree.m
index 909d7301b0251017990b09aa98e5513cf9b0ac65..6fdb7c20990b0f371750feee8a4e3ab776e2fa48 100644
--- a/src/MATLAB/+Families/AddToTree.m
+++ b/src/MATLAB/+Families/AddToTree.m
@@ -4,6 +4,30 @@
% addTrack.startTime < ontoTrack.startTime
% addTrack.startTime > ontoTrack.endTime
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
% ChangLog
% EW 6/7/12 Created
function droppedTracks = AddToTree(addTrack, ontoTrack)
diff --git a/src/MATLAB/+Families/ChangeTrackAndChildrensFamily.m b/src/MATLAB/+Families/ChangeTrackAndChildrensFamily.m
index a079811e0462867ed654bc4db5f2f20505f63e00..b16b5de24cd0fda991d96f0148c938fe56a12554 100644
--- a/src/MATLAB/+Families/ChangeTrackAndChildrensFamily.m
+++ b/src/MATLAB/+Families/ChangeTrackAndChildrensFamily.m
@@ -8,10 +8,10 @@
% ECW 6/6/12 rewrite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Families/CheckLockedAddMitosis.m b/src/MATLAB/+Families/CheckLockedAddMitosis.m
index 4d46a3a50e14dc9fe8c520c14fe1050f2c868f54..cd61d9f8c50eb114d0d98903bb7414faacf66017 100644
--- a/src/MATLAB/+Families/CheckLockedAddMitosis.m
+++ b/src/MATLAB/+Families/CheckLockedAddMitosis.m
@@ -3,6 +3,30 @@
% This function will check to verify if a "tree-preserving" add mitosis is
% possible.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [bLockedParent bLockedChildren bCanAdd] = CheckLockedAddMitosis(parentTrack, leftChildTrack, siblingTrack, time)
global CellTracks
diff --git a/src/MATLAB/+Families/ComputeTrackHeights.m b/src/MATLAB/+Families/ComputeTrackHeights.m
index c59d14ed8cc98ce9970c881fdc4df73aabedfade..fcafa59427b7708ed9c13bd3513632619a57e167 100644
--- a/src/MATLAB/+Families/ComputeTrackHeights.m
+++ b/src/MATLAB/+Families/ComputeTrackHeights.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function trackHeights = ComputeTrackHeights(rootTrackID)
trackHeights = containers.Map('KeyType', 'uint32', 'ValueType', 'uint32');
diff --git a/src/MATLAB/+Families/CreateEmptyFamily.m b/src/MATLAB/+Families/CreateEmptyFamily.m
index d31c5b60084f443ddf5abac5a827e058c2e1974d..ffceb2db0bbce81caaa46ca984850dc1e3a9a5e5 100644
--- a/src/MATLAB/+Families/CreateEmptyFamily.m
+++ b/src/MATLAB/+Families/CreateEmptyFamily.m
@@ -2,6 +2,30 @@
% Creates an empty family with each of the fields set to [] and returns the
% new family id.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function familyID = CreateEmptyFamily()
global CellFamilies
familyID = length(CellFamilies) +1;
diff --git a/src/MATLAB/+Families/FindLargestTree.m b/src/MATLAB/+Families/FindLargestTree.m
index 023cfbb0a21fd0268352ccc982ec4a664185d982..3e7389fc34a896581372e6253cd413d54bb550e5 100644
--- a/src/MATLAB/+Families/FindLargestTree.m
+++ b/src/MATLAB/+Families/FindLargestTree.m
@@ -2,10 +2,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Families/GetAllHulls.m b/src/MATLAB/+Families/GetAllHulls.m
index 781ecbd6287fcc4cb7276edaddb72dd08e398beb..a5ebebd1c4fc2b6bd34f687102d8d74729aa655e 100644
--- a/src/MATLAB/+Families/GetAllHulls.m
+++ b/src/MATLAB/+Families/GetAllHulls.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function [hullIDs missingHulls] = GetAllHulls(familyID)
global CellFamilies CellTracks
diff --git a/src/MATLAB/+Families/GetFamilyRoots.m b/src/MATLAB/+Families/GetFamilyRoots.m
index 108344b2854f474d237049abaa98a9a3fecabfd0..f422403a47b89f6a3e78fee954bb1c88a5c92e57 100644
--- a/src/MATLAB/+Families/GetFamilyRoots.m
+++ b/src/MATLAB/+Families/GetFamilyRoots.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function roots = GetFamilyRoots(rootTrackID)
global CellFamilies CellTracks
diff --git a/src/MATLAB/+Families/LinkFirstFrameTrees.m b/src/MATLAB/+Families/LinkFirstFrameTrees.m
deleted file mode 100644
index 30d80941d8f485f6643c97dddc4ba8ae48da5f8f..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Families/LinkFirstFrameTrees.m
+++ /dev/null
@@ -1,22 +0,0 @@
-function [iterations totalTime] = LinkFirstFrameTrees()
- global HashedCells
-
- iterations = 0;
-
- % Try to Push/reseg
- totalTime = 0;
- maxPushCount = 10;
- for i=1:maxPushCount
- [assignExt findTime extTime] = Families.LinkTreesForward([HashedCells{1}.trackID]);
-% LogAction(['Tree inference step ' num2str(i)],[assignExt findTime extTime],[]);
- totalTime = totalTime + findTime + extTime;
-
- iterations = i;
-
- if ( assignExt == 0 )
- break;
- end
- end
-
-% LogAction('Completed Tree Inference', [i totalTime],[]);
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Families/LinkTrees.m b/src/MATLAB/+Families/LinkTrees.m
index 06233112498933d0fd4ed0b101ab24499184dd61..734eb34b378b8dcf901e8b65a90c720bff414f4e 100644
--- a/src/MATLAB/+Families/LinkTrees.m
+++ b/src/MATLAB/+Families/LinkTrees.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function [iterations totalTime] = LinkTrees(families, stopTime)
global CellFamilies CellTracks
diff --git a/src/MATLAB/+Families/LinkTreesForward.m b/src/MATLAB/+Families/LinkTreesForward.m
index 977e9191ecd25e0f800023fc34bb2057e08344ac..65c11b18122d5a4c1206d194316d12541812c939 100644
--- a/src/MATLAB/+Families/LinkTreesForward.m
+++ b/src/MATLAB/+Families/LinkTreesForward.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function [assignedExtensions findTime extTime] = LinkTreesForward(rootTracks, stopTime)
global CellHulls CellTracks HashedCells Costs
diff --git a/src/MATLAB/+Families/MultiTreeAllTracks.m b/src/MATLAB/+Families/MultiTreeAllTracks.m
new file mode 100644
index 0000000000000000000000000000000000000000..7d21535584209941ccbea5eb9dd8da5a363493fd
--- /dev/null
+++ b/src/MATLAB/+Families/MultiTreeAllTracks.m
@@ -0,0 +1,33 @@
+% MultiTreeAllTracks.m - Add all tracks on a frame to the same extended
+% family
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function MultiTreeAllTracks(t)
+ global HashedCells CellTracks CellFamilies
+
+ trackIDs = [HashedCells{t}.trackID];
+ familyIDs = [CellTracks(trackIDs).familyID];
+ [CellFamilies(familyIDs).extFamily] = deal(familyIDs);
+end
diff --git a/src/MATLAB/+Families/NewCellFamily.m b/src/MATLAB/+Families/NewCellFamily.m
index 7418cce2f9c3f0af3a23354cc680b97c61e13025..0014b9b9a242140fb4e61555a4b511799dedd44b 100644
--- a/src/MATLAB/+Families/NewCellFamily.m
+++ b/src/MATLAB/+Families/NewCellFamily.m
@@ -5,10 +5,10 @@
% EW 6/6/12 t is no longer a requirement
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Families/ProcessNewborns.m b/src/MATLAB/+Families/ProcessNewborns.m
index 291ce733fa019e4470100f7e0f7607c04b9e4927..f7fb1d7324ed52e28df1595931bb034b9de15faf 100644
--- a/src/MATLAB/+Families/ProcessNewborns.m
+++ b/src/MATLAB/+Families/ProcessNewborns.m
@@ -4,10 +4,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Families/ReconnectParentWithChildren.m b/src/MATLAB/+Families/ReconnectParentWithChildren.m
index 3b9dd65291fba75b2154a624c3603652ba74c1b8..150f577e3362dbe5ba791508d6b6c4da899fc4c5 100644
--- a/src/MATLAB/+Families/ReconnectParentWithChildren.m
+++ b/src/MATLAB/+Families/ReconnectParentWithChildren.m
@@ -7,6 +7,30 @@
% children have parents
% parent has children
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
% ChangeLog
% EW 6/7/12 created
function ReconnectParentWithChildren(parentTrack,children)
diff --git a/src/MATLAB/+Families/RemoveFromTree.m b/src/MATLAB/+Families/RemoveFromTree.m
index 52ee34746525985cff3ab1dd96dc988891f6a39d..fdac66293bc742dcdbffc6e16e7cf3edcc381d8c 100644
--- a/src/MATLAB/+Families/RemoveFromTree.m
+++ b/src/MATLAB/+Families/RemoveFromTree.m
@@ -3,6 +3,30 @@
% Is similar to RemoveFromTreePrune but keeps the other child. This will
% straighten out the parent track with the sibling of the given track
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
% ChangeLog:
% EW 6/7/12 created
function droppedTracks = RemoveFromTree(removeTrackID,time)
diff --git a/src/MATLAB/+Families/RemoveFromTreePrune.m b/src/MATLAB/+Families/RemoveFromTreePrune.m
index e9e2f7aa5f470990ff527553797a5417789d1d0d..bb24243a2834cbd9087cbd208809d1b38bc09756 100644
--- a/src/MATLAB/+Families/RemoveFromTreePrune.m
+++ b/src/MATLAB/+Families/RemoveFromTreePrune.m
@@ -10,10 +10,10 @@
% EW 6/6/12 rewriten
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Families/RemoveTrackFromFamily.m b/src/MATLAB/+Families/RemoveTrackFromFamily.m
index 349f409a2ce761528692fb2792778fd59d632e65..1b2d64037a4fcaf5942f5e82ce7f2ae3319821d8 100644
--- a/src/MATLAB/+Families/RemoveTrackFromFamily.m
+++ b/src/MATLAB/+Families/RemoveTrackFromFamily.m
@@ -8,10 +8,10 @@
% EW 6/6/12 rewrite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Families/UpdateFamilyTimes.m b/src/MATLAB/+Families/UpdateFamilyTimes.m
index 68663b5d31e5d2328915525bd751ee311afad77d..727ec42cce0f4f49c31bf4c3709443a0a86a5e09 100644
--- a/src/MATLAB/+Families/UpdateFamilyTimes.m
+++ b/src/MATLAB/+Families/UpdateFamilyTimes.m
@@ -1,4 +1,28 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
% UpdateLog:
% EW 6/6/12 Created
function UpdateFamilyTimes( familyID )
diff --git a/src/MATLAB/+Helper/CalcConnectedDistance.m b/src/MATLAB/+Helper/CalcConnectedDistance.m
index 1343924af66328a9c6cd392f3850faa689c5e897..e97b3d55d8e9caca49ff4aebe1e52bed80cfc7e3 100644
--- a/src/MATLAB/+Helper/CalcConnectedDistance.m
+++ b/src/MATLAB/+Helper/CalcConnectedDistance.m
@@ -1,10 +1,10 @@
-% dist = CalcConnectedDistance(startHull,nextHull, imageSize, perimMap, cellHulls)
+% dist = CalcConnectedDistance(startHull,nextHull, rcImageDims, perimMap, cellHulls)
% Calculate the connected-component distance from startHull to nextHull.
%
% startHull,nextHull - must be valid indices into the cellHulls structure.
%
-% imageSize - indicates the dimensions of the image or volume the hulls
-% were segmented from (for use in converting cellHulls.indexPixels.
+% rcImageDims - indicates the dimensions (row,column,height) of the image or volume
+% the hulls were segmented from (for use in converting cellHulls.indexPixels.
%
% perimMap = containers.Map('KeyType', 'uint32', 'ValueType', 'any'), must
% be a map handle passed by the calling routine. This shares perimeter
@@ -14,7 +14,31 @@
%
% See Tracker.BuildConnectedDistance() for calling examples.
-function dist = CalcConnectedDistance(startHull,nextHull, imageSize, perimMap, cellHulls)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+function dist = CalcConnectedDistance(startHull,nextHull, rcImageDims, perimMap, cellHulls)
isect = intersect(cellHulls(startHull).indexPixels, cellHulls(nextHull).indexPixels);
if ( ~isempty(isect) )
isectDist = 1 - (length(isect) / min(length(cellHulls(startHull).indexPixels), length(cellHulls(nextHull).indexPixels)));
@@ -22,20 +46,20 @@ function dist = CalcConnectedDistance(startHull,nextHull, imageSize, perimMap, c
return;
end
- addPerim(startHull, imageSize,perimMap,cellHulls);
- addPerim(nextHull, imageSize,perimMap,cellHulls);
+ addPerim(startHull, rcImageDims,perimMap,cellHulls);
+ addPerim(nextHull, rcImageDims,perimMap,cellHulls);
D = pdist2(perimMap(startHull), perimMap(nextHull));
dist = min(D(:));
end
-function addPerim(hullID, imageSize, perimMap, cellHulls)
+function addPerim(hullID, rcImageDims, perimMap, cellHulls)
if ( isKey(perimMap, hullID) )
return
end;
- pxCell = cell(1,length(imageSize));
- [pxCell{:}] = ind2sub(imageSize, cellHulls(hullID).indexPixels);
+ pxCell = cell(1,length(rcImageDims));
+ [pxCell{:}] = ind2sub(rcImageDims, cellHulls(hullID).indexPixels);
pixelCoords = cell2mat(pxCell);
minCoord = min(pixelCoords,[],1);
@@ -49,10 +73,10 @@ function addPerim(hullID, imageSize, perimMap, cellHulls)
end
bwIm = false(locMax);
- locCell = mat2cell(locCoord, size(locCoord,1), ones(1,length(imageSize)));
+ locCell = mat2cell(locCoord, size(locCoord,1), ones(1,length(rcImageDims)));
locInd = sub2ind(locMax, locCell{:});
- perimCell = cell(1,length(imageSize));
+ perimCell = cell(1,length(rcImageDims));
bwIm(locInd) = true;
perimIm = bwperim(bwIm);
diff --git a/src/MATLAB/+Helper/CheckInTracks.m b/src/MATLAB/+Helper/CheckInTracks.m
index b9c4fe1d4b8c8fe77151b00352de18cab0169576..13f30789d974463b18d8bd3806340dc8c57cda4b 100644
--- a/src/MATLAB/+Helper/CheckInTracks.m
+++ b/src/MATLAB/+Helper/CheckInTracks.m
@@ -2,6 +2,30 @@
%
% Check (for reseg or mitosis editing) if time t is within tracks.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function bInTrack = CheckInTracks(t, tracks, bIncludeStart, bIncludeEnd)
global CellTracks
diff --git a/src/MATLAB/+Helper/CheckTreeFrozen.m b/src/MATLAB/+Helper/CheckTreeFrozen.m
index 691e4f13db2e19a37b9e7296b5c076548a874556..721fa4653feba92026380aee75e08f56da35a918 100644
--- a/src/MATLAB/+Helper/CheckTreeFrozen.m
+++ b/src/MATLAB/+Helper/CheckTreeFrozen.m
@@ -3,6 +3,30 @@
% Check if tracks are on frozen families, return list bFrozen with boolean
% indicator per track.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function bFrozen = CheckTreeFrozen(tracks)
global CellTracks CellFamilies
diff --git a/src/MATLAB/+Helper/CheckTreeLocked.m b/src/MATLAB/+Helper/CheckTreeLocked.m
index 75e2b065a19ce8c1945b8f874ffc4bda964a069a..0d745b2871a5bc2a9c7139d0d1a3d171275c7384 100644
--- a/src/MATLAB/+Helper/CheckTreeLocked.m
+++ b/src/MATLAB/+Helper/CheckTreeLocked.m
@@ -3,6 +3,30 @@
% Check if tracks are on locked families, return list bLocked with boolean
% indicator per track.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function bLocked = CheckTreeLocked(tracks)
global CellTracks CellFamilies
diff --git a/src/MATLAB/+Helper/Clamp.m b/src/MATLAB/+Helper/Clamp.m
deleted file mode 100644
index c57bd813f66afe806584cffab16c4a35c2840fd8..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/Clamp.m
+++ /dev/null
@@ -1,4 +0,0 @@
-function x_clamped = Clamp(x, minval, maxval)
- x_clamped = max(cat(3,x,minval*ones(size(x))),[],3);
- x_clamped = min(cat(3,x_clamped,maxval*ones(size(x))),[],3);
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Helper/ClearAllGlobals.m b/src/MATLAB/+Helper/ClearAllGlobals.m
index 73b5f007180c76b2fd270a7d0f441a96482b3f64..72d27ba54d5b96581806f58a97bc774813f94d13 100644
--- a/src/MATLAB/+Helper/ClearAllGlobals.m
+++ b/src/MATLAB/+Helper/ClearAllGlobals.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function ClearAllGlobals()
global CellFamilies CellTracks HashedCells CONSTANTS CellHulls Costs GraphEdits
global CachedCostMatrix ConnectedDist CellPhenotypes SegmentationEdits ReplayEditActions
diff --git a/src/MATLAB/+Helper/ConvexHull.m b/src/MATLAB/+Helper/ConvexHull.m
index 8ff566c1ba55085d345fb864bdad4950b90a6600..cef576de1c7ca9205836c72a4e9173a3131e76c2 100644
--- a/src/MATLAB/+Helper/ConvexHull.m
+++ b/src/MATLAB/+Helper/ConvexHull.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function chIdx = ConvexHull(x,y)
chIdx = [];
diff --git a/src/MATLAB/+Helper/CoordToIndex.m b/src/MATLAB/+Helper/CoordToIndex.m
deleted file mode 100644
index 1c8960267e8ad45c3bc777cfa4d251dbcd1dabfe..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/CoordToIndex.m
+++ /dev/null
@@ -1,4 +0,0 @@
-function arrayIdx = CoordToIndex(arraySize, coords)
- linSize = [1 cumprod(arraySize(1:end-1))];
- arrayIdx = sum((coords-1) .* repmat(linSize, size(coords,1),1), 2) + 1;
-end
diff --git a/src/MATLAB/+Helper/CountResegEdits.m b/src/MATLAB/+Helper/CountResegEdits.m
deleted file mode 100644
index 471152531fd6aa1845f5af33ea9f0cb4baa5ea0a..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/CountResegEdits.m
+++ /dev/null
@@ -1,160 +0,0 @@
-
-function [userEditCount resegEditCount userEditList resegEditList] = CountResegEdits(trackID)
- global ReplayEditActions CellHulls CellTracks CellFamilies
-
- userEditCount = 0;
- resegEditCount = 0;
-
- userEditList = {};
- resegEditList = {};
-
- %blockTypes = {'extra', 'reseg', 'user'};
-
- % Pretty much simulates the undo stacks, but with just edit counts
- typeStack = 1;
- stackEnds = 0;
- editStack = {{}};
-
- totalReseg = 0;
-
- bInReseg = 0;
- for i=1:length(ReplayEditActions)
-
- if ( strcmpi(ReplayEditActions(i).funcName,'Editor.ResegInitializeAction') )
- bInReseg = 1;
- continue;
- end
-
- % TODO: Get reseg edits out here:
- if ( strcmpi(ReplayEditActions(i).funcName,'Editor.ResegFinishAction') )
- bInReseg = 0;
-
- if ( isempty(ReplayEditActions(i).ret) )
- continue;
- end
-
- numEdits = length(ReplayEditActions(i).ret{2}.SegEdits);
-
- totalReseg = totalReseg + numEdits;
-
- newEdit = struct('count',{numEdits}, 'type',{typeStack(end)}, 'editFunc',{'ResegEdits'});
- editStack{end} = [editStack{end}(1:stackEnds(end)); {newEdit}];
-
- stackEnds(end) = stackEnds(end) + 1;
- continue;
- end
-
- % TODO: This is unfortunate, and I need it to really just not happen
- if ( bInReseg && strcmpi(ReplayEditActions(i).funcName,'Editor.InitHistory') )
- warning('RESEG:NoFinish', 'The current file was closed without finishing resegmentation process, edit counts may be inaccurate');
-% return;
- end
-
-% % Increase stack level and pick an edit type if a new subtask is started
-% if ( strcmpi(ReplayEditActions(i).funcName,'Editor.StartReplayableSubtask') )
-% typeStack = [typeStack 1];
-% stackEnds = [stackEnds 0];
-% editStack = [editStack; {{}}];
-%
-% if ( strcmpi(ReplayEditActions(i).args{1},'PauseResegTask') )
-% typeStack(end) = 3;
-% elseif ( strcmpi(ReplayEditActions(i).args{1},'InteractiveResegTask') )
-% typeStack(end) = 2;
-% end
-% continue;
-% end
-%
-% % Reduce stack level and add new edit block to level below (if not empty)
-% if ( strcmpi(ReplayEditActions(i).funcName,'Editor.StopReplayableSubtask') )
-% topStack = editStack{end};
-% topEnd = stackEnds(end);
-%
-% stackEnds = stackEnds(1:(end-1));
-% typeStack = typeStack(1:(end-1));
-% editStack = editStack(1:(end-1));
-%
-% if ( topEnd > 0 )
-% popEntry = topStack(1:topEnd,:);
-% editStack{end} = [editStack{end}(1:stackEnds(end)); {popEntry}];
-% stackEnds(end) = stackEnds(end) + 1;
-% end
-% continue;
-% end
-%
-% % Just drop stack level by one
-% if ( strcmpi(ReplayEditActions(i).funcName,'Editor.DropReplayableSubtask') )
-%
-% stackEnds = stackEnds(1:(end-1));
-% typeStack = typeStack(1:(end-1));
-% editStack = editStack(1:(end-1));
-%
-% if ( strcmpi(ReplayEditActions(i).args{1},'PauseResegTask') )
-% bInPause = 0;
-% end
-% continue;
-% end
-%
-% % Ignore these actions as they have no direct edit significance
-% if ( strcmpi(ReplayEditActions(i).funcName,'Editor.ResegPlayAction') || strcmpi(ReplayEditActions(i).funcName,'Editor.ResegPauseAction') ...
-% || strcmpi(ReplayEditActions(i).funcName,'Editor.ResegBackAction') || strcmpi(ReplayEditActions(i).funcName,'Editor.ResegPauseAction') ...
-% || strcmpi(ReplayEditActions(i).funcName,'Editor.Top') )
-% continue;
-% end
-%
-% % Undo reduces current edit end by one
-% if ( strcmpi(ReplayEditActions(i).funcName,'Editor.Undo') )
-% if ( stackEnds(end) > 0 )
-% stackEnds(end) = stackEnds(end) - 1;
-% end
-%
-% continue;
-% end
-%
-% % Redo increases current edit end by one
-% if ( strcmpi(ReplayEditActions(i).funcName,'Editor.Redo') )
-% if ( stackEnds(end) < size(editStack{end},1) )
-% stackEnds(end) = stackEnds(end) + 1;
-% end
-%
-% continue;
-% end
-%
-% newEdit = struct('count',{1}, 'type',{typeStack(end)}, 'editFunc',{ReplayEditActions(i).funcName});
-% editStack{end} = [editStack{end}(1:stackEnds(end)); {newEdit}];
-%
-% stackEnds(end) = stackEnds(end) + 1;
- end
-
-% [resegEditCount resegEditList] = countAllEdits(editStack{1}, 2);
-% [userEditCount userEditList] = countAllEdits(editStack{1}, 3);
-
- famID = CellTracks(trackID).familyID;
- trackHulls = [CellTracks(CellFamilies(famID).tracks).hulls];
- nzHulls = trackHulls(trackHulls ~= 0);
-
- bUserEdited = [CellHulls(nzHulls).userEdited];
-
- userEditCount = nnz(bUserEdited);
- resegEditCount = totalReseg;
-end
-
-function [editCount editList] = countAllEdits(editStack, editType)
- editCount = 0;
- editList = {};
-
- if ( isstruct(editStack) )
- if ( editType == editStack.type )
- editCount = editStack.count;
- editList = {editStack.editFunc};
- end
-
- return;
- end
-
- for i=1:length(editStack)
- [curCount curList] = countAllEdits(editStack{i}, editType);
-
- editCount = editCount + curCount;
- editList = [editList; curList];
- end
-end
diff --git a/src/MATLAB/+Helper/DropSubtree.m b/src/MATLAB/+Helper/DropSubtree.m
index cd5d23929f881a2523a4cd88b1fe728a46169570..2fcb74cb87ff8ddc03b73786a8537e0dd1b2e7a9 100644
--- a/src/MATLAB/+Helper/DropSubtree.m
+++ b/src/MATLAB/+Helper/DropSubtree.m
@@ -1,4 +1,28 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function DropSubtree(trackID)
global CellTracks
diff --git a/src/MATLAB/+Helper/GetCellHullTemplate.m b/src/MATLAB/+Helper/GetCellHullTemplate.m
index 4f25b3073c415c667318a7c876ec577486029404..4dc81975cf2e7143d9ad379c903ae54a33969fc4 100644
--- a/src/MATLAB/+Helper/GetCellHullTemplate.m
+++ b/src/MATLAB/+Helper/GetCellHullTemplate.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function cellHullsTemplate = GetCellHullTemplate()
cellHullsTemplate = struct('time',{0},...
'points',{[]},...
diff --git a/src/MATLAB/+Helper/GetFamilySegEditCount.m b/src/MATLAB/+Helper/GetFamilySegEditCount.m
index 6a7a06855c50ad4cd6894dd74c154eb7bff21436..a1b9546774f09bf42b74cc4b92dc2ef82ddfa105 100644
--- a/src/MATLAB/+Helper/GetFamilySegEditCount.m
+++ b/src/MATLAB/+Helper/GetFamilySegEditCount.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function segEditCount = GetFamilySegEditCount(familyID, bIncludeUser, bIncludeAuto)
global EditList
diff --git a/src/MATLAB/+Helper/GetFamilyTrackEditCount.m b/src/MATLAB/+Helper/GetFamilyTrackEditCount.m
index 365a375feca95af1d27d1243557cf7d880fd307e..7d46cca09cc6b4b0badcce53b663f163d774c0c3 100644
--- a/src/MATLAB/+Helper/GetFamilyTrackEditCount.m
+++ b/src/MATLAB/+Helper/GetFamilyTrackEditCount.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function edgeEditCount = GetFamilyTrackEditCount(familyID, bIncludeUser, bIncludeAuto)
global EditList
diff --git a/src/MATLAB/+Helper/GetFullImagePath.m b/src/MATLAB/+Helper/GetFullImagePath.m
deleted file mode 100644
index 6f33d07c06dff597eb8330a1b3b06ea506669b75..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/GetFullImagePath.m
+++ /dev/null
@@ -1,8 +0,0 @@
-function pathString = GetFullImagePath(chan, frame)
-global CONSTANTS
-
-imageName = Helper.GetImageName(chan, frame);
-
-pathString = fullfile(CONSTANTS.rootImageFolder,imageName);
-end
-
diff --git a/src/MATLAB/+Helper/GetImListInfo.m b/src/MATLAB/+Helper/GetImListInfo.m
deleted file mode 100644
index 087d8f9fe72f86b58d219ab16eba47e6c2eac92a..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/GetImListInfo.m
+++ /dev/null
@@ -1,53 +0,0 @@
-% [channelList, frameList] = GetImListInfo(rootFolder, namePattern)
-%
-% Use image namePattern to return a list of all unique image frames and channels
-% based on image files in existing under rootFolder.
-%
-% The lists are returned in sorted order.
-
-function [channelList, frameList] = GetImListInfo(rootFolder, namePattern)
- channelList = [];
- frameList = [];
-
- % Generate a directory list glob from namePattern as well as a
- % tokenized set for creating a regexp to match channel and frame numbers
- [prefixString, paramTokens, postfixString] = Helper.SplitNamePattern(namePattern);
- if ( isempty(prefixString) )
- return;
- end
-
- paramGlobs = cellfun(@(x)(['_' x{1} '*']),paramTokens, 'UniformOutput',0);
- dirPattern = [prefixString paramGlobs{:} postfixString];
-
- flist = dir(fullfile(rootFolder,dirPattern));
- if ( isempty(flist) )
- return;
- end
-
- matchPrefix = regexptranslate('escape', prefixString);
- matchPostfix = regexptranslate('escape', postfixString);
- paramPatterns = cellfun(@(x)(['_' x{1} '(\d{' x{2} '})']),paramTokens, 'UniformOutput',0);
-
- matchPattern = [matchPrefix paramPatterns{:} matchPostfix];
-
- fileNames = {flist.name};
- matchTok = regexpi(fileNames, matchPattern, 'tokens','once');
-
- paramOrder = cellfun(@(x)(x{1}),paramTokens, 'UniformOutput',0);
- assumedParams = {'c' 't' 'z'};
- [bHasParam,paramIdx] = ismember(assumedParams, paramOrder);
-
- channelList = 1;
- frameList = 1;
- zList = 1;
-
- if ( bHasParam(1) )
- chans = cellfun(@(x)(str2double(x{paramIdx(1)})), matchTok);
- channelList = unique(chans);
- end
-
- if ( bHasParam(2) )
- times = cellfun(@(x)(str2double(x{paramIdx(2)})), matchTok);
- frameList = unique(times);
- end
-end
diff --git a/src/MATLAB/+Helper/GetImageName.m b/src/MATLAB/+Helper/GetImageName.m
deleted file mode 100644
index ac429d27037514c599cc5087275269b9b64bbf42..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/GetImageName.m
+++ /dev/null
@@ -1,21 +0,0 @@
-function imageName = GetImageName(chan, frame)
-global CONSTANTS
-
-valueNames = {'c' 't'};
-paramValues = {chan frame};
-
-paramTokens = Helper.GetNamePatternParams(CONSTANTS.imageNamePattern);
-paramOrder = cellfun(@(x)(x{1}),paramTokens, 'UniformOutput',0);
-
-[bHasParam,valueIdx] = ismember(paramOrder, valueNames);
-if ( ~all(bHasParam) )
- imageName = '';
-
- missingValues = cellfun(@(x)([' ' x]), paramOrder(bHasParam));
- fprintf('Unspecified value(s) needed to generate image string:%s\n', missingValues);
- return;
-end
-
-imageName = sprintf(CONSTANTS.imageNamePattern, paramValues{valueIdx});
-end
-
diff --git a/src/MATLAB/+Helper/GetNamePatternParams.m b/src/MATLAB/+Helper/GetNamePatternParams.m
deleted file mode 100644
index 2acbebb74f9340822bc74458ae11fe5b7437fa39..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/GetNamePatternParams.m
+++ /dev/null
@@ -1,3 +0,0 @@
-function paramTokens = GetNamePatternParams(namePattern)
- paramTokens = regexp(namePattern, '_([a-zA-Z]{1,2})%0(\d+)d', 'tokens');
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Helper/GetNearestTrackHull.m b/src/MATLAB/+Helper/GetNearestTrackHull.m
index 9dbc6aa642b9fba27e45af0b4ef279ec1f064318..f27a07a3484f3586e12f78ce1cbd826a0c45f599 100644
--- a/src/MATLAB/+Helper/GetNearestTrackHull.m
+++ b/src/MATLAB/+Helper/GetNearestTrackHull.m
@@ -6,6 +6,30 @@
% (searchDir == 0) -> search exact time only.
% returns hull=0 if search fails.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [hull hullTime] = GetNearestTrackHull(trackID, time, searchDir)
global CellTracks CellHulls
diff --git a/src/MATLAB/+Helper/GetRandomState.m b/src/MATLAB/+Helper/GetRandomState.m
index edfeff50a174c8b946e8f0393047e1213e722b3e..e6a5d80620cbf9cd6606c6547587f067aefded65 100644
--- a/src/MATLAB/+Helper/GetRandomState.m
+++ b/src/MATLAB/+Helper/GetRandomState.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function randState = GetRandomState()
globStream = RandStream.getGlobalStream();
randState = globStream.State;
diff --git a/src/MATLAB/+Helper/GetVersion.m b/src/MATLAB/+Helper/GetVersion.m
deleted file mode 100644
index d0f9153699cfb474578712b804e2838a009d7b85..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/GetVersion.m
+++ /dev/null
@@ -1,61 +0,0 @@
-% version = GetVersion(command)
-% Get a version string or number depending on the command argument. This
-% m-file serves as a single repository for all version-related information.
-%
-% Note: Uses autogenerated version information in +Helper\VersionInfo.m
-
-function version = GetVersion(command)
- version = [];
-
- if ( isdeployed )
- verInfo = Helper.VersionInfo();
- else
- verInfo = Dev.MakeVersion(1);
- end
-
- if ( ~exist('command','var') )
- command = 'string';
- end
-
- cleanBranch = strrep(verInfo.branchName, '/', '_');
- cleanBranch = strrep(cleanBranch, '\', '_');
-
- if ( strcmpi(command, 'string') || strcmpi(command, 'versionString') )
- version = [num2str(verInfo.majorVersion) '.' num2str(verInfo.minorVersion) ' ' cleanBranch];
- return;
- end
-
- if ( strcmpi(command, 'buildString') )
- version = [verInfo.buildNumber '/' verInfo.buildMachine];
- return;
- end
-
- if ( strcmpi(command, 'buildHash') )
- version = verInfo.commitHash;
- return
- end
-
- if ( strcmpi(command, 'fullString') )
- version = ['LEVER v' num2str(verInfo.majorVersion) '.' num2str(verInfo.minorVersion) ' ' verInfo.buildNumber '/' verInfo.buildMachine ' ' cleanBranch ' ' verInfo.commitHash];
- return;
- end
-
- if ( strcmpi(command, 'major') )
- version = verInfo.majorVersion;
- return
- end
-
- if ( strcmpi(command, 'minor') )
- version = verInfo.minorVersion;
- return;
- end
-
- if ( strcmpi(command, 'file') )
- minorStr = num2str(verInfo.minorVersion);
- minorStr = strrep(minorStr, '.', '_');
- version = [num2str(verInfo.majorVersion) minorStr '_' cleanBranch];
- return;
- end
-
-end
-
diff --git a/src/MATLAB/+Helper/ImageFileDialog.m b/src/MATLAB/+Helper/ImageFileDialog.m
index 32494cbbea39ad9156a1d7c0bca417781c68d130..384f6c0b4b0265729d6bed525c6ffa2d9ce53137 100644
--- a/src/MATLAB/+Helper/ImageFileDialog.m
+++ b/src/MATLAB/+Helper/ImageFileDialog.m
@@ -1,48 +1,49 @@
-function bOpened = ImageFileDialog()
-global CONSTANTS
-settings = Load.ReadSettings();
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-if ~isfield(settings,'imagePathFl')
- settings.imagePathFl = settings.imagePath;
-end
-
-%find the first image
-imageFilter = [settings.imagePath '*.TIF'];
+function bOpened = ImageFileDialog()
+settings = Load.ReadSettings();
bOpened = 0;
-while ( ~bOpened )
- dataSetString = '';
- if ( isfield(CONSTANTS,'datasetName') )
- dataSetString = CONSTANTS.datasetName;
- end
-
- [settings.imageFile,settings.imagePath,filterIndexImage] = uigetfile(imageFilter,['Open First Image in Dataset (' dataSetString '): ' ]);
- if (filterIndexImage==0)
- return
- end
-
- [imageDataset namePattern] = Helper.ParseImageName(settings.imageFile);
- if ( isempty(imageDataset) )
- error('File name pattern is not supported: %s', settings.imageFile);
+while ( ~bOpened )
+ metadataPath = Load.ImageLoadDialog(settings.imagePath,['Open Dataset Metadata or Image (' Metadata.GetDatasetName() '): ']);
+ if ( isempty(metadataPath) )
+ return;
end
- Load.AddConstant('imageNamePattern', namePattern, 1);
- if ( ~isfield(CONSTANTS,'datasetName') )
- Load.AddConstant('datasetName', imageDataset, 1);
+ [imageData, settings.imagePath] = MicroscopeData.ReadMetadataFile(metadataPath);
+ if ( isempty(imageData) )
+ return;
end
- if ( strcmp(imageDataset, [CONSTANTS.datasetName '_']) )
- Load.AddConstant('datasetName', [CONSTANTS.datasetName '_'], 1);
- bOpened = 1;
- elseif ( ~strcmp(imageDataset, CONSTANTS.datasetName) )
+ if ( ~isempty(Metadata.GetDatasetName()) && ~strcmp(Metadata.GetDatasetName(),imageData.DatasetName) )
answer = questdlg('Image does not match dataset would you like to choose another?','Image Selection','Yes','No','Close LEVer','Yes');
switch answer
case 'Yes'
continue;
case 'No'
- Load.AddConstant('imageNamePattern', '', 1);
bOpened = 1;
case 'Close LEVer'
return
@@ -51,52 +52,11 @@ while ( ~bOpened )
end
end
+ Metadata.SetMetadata(imageData);
+
Load.AddConstant('rootImageFolder', settings.imagePath, 1);
Load.AddConstant('matFullFile', [settings.matFilePath settings.matFile], 1);
- [channelList, frameList] = Helper.GetImListInfo(settings.imagePath, namePattern);
-
- % Verify that channel and time are 1-based.
- remapChan = 1 - channelList(1);
- remapFrame = 1 - frameList(1);
- if ( remapChan ~= 0 || remapFrame ~= 0 )
- queryStr = sprintf('LEVER requires that image channel and frame numbers begin at 1.\nWould you like to automatically rename the images in the selected folder?');
- respStr = questdlg(queryStr,'Image Name Unsupported','Ok','Cancel','Ok');
- if ( strcmpi(respStr,'Cancel') )
- return;
- end
-
- for c=channelList(1):channelList(end)
- for t=frameList(1):frameList(end)
- oldName = Helper.GetImageName(c,t);
- tempName = ['tmp_' Helper.GetImageName(c+remapChan, t+remapFrame)];
- if ( ~exist(fullfile(settings.imagePath,oldName), 'file') )
- continue;
- end
-
- movefile(fullfile(settings.imagePath,oldName), fullfile(settings.imagePath,tempName));
- end
- end
-
- for c=channelList(1):channelList(end)
- for t=frameList(1):frameList(end)
- tempName = ['tmp_' Helper.GetImageName(c+remapChan, t+remapFrame)];
- newName = Helper.GetImageName(c+remapChan, t+remapFrame);
- if ( ~exist(fullfile(settings.imagePath,tempName), 'file') )
- continue;
- end
-
- movefile(fullfile(settings.imagePath,tempName), fullfile(settings.imagePath,newName));
- end
- end
-
- channelList = channelList + remapChan;
- frameList = frameList + remapFrame;
- end
-
- Load.AddConstant('numFrames', frameList(end), 1);
- Load.AddConstant('numChannels', channelList(end), 1);
-
bOpened = 1;
end
diff --git a/src/MATLAB/+Helper/IndexToCoord.m b/src/MATLAB/+Helper/IndexToCoord.m
deleted file mode 100644
index 30129941d10595f1673a8a8168f7c4f67cfbb23b..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/IndexToCoord.m
+++ /dev/null
@@ -1,13 +0,0 @@
-function coord = IndexToCoord(arraySize, arrayIdx)
- coord = zeros(length(arrayIdx),length(arraySize));
-
- linSize = [1 cumprod(arraySize)];
- partialIdx = arrayIdx;
- for i = length(arraySize):-1:1
- r = rem(partialIdx-1, linSize(i)) + 1;
- q = floor((partialIdx-r) / linSize(i)) + 1;
-
- coord(:,i) = q;
- partialIdx = r;
- end
-end
diff --git a/src/MATLAB/+Helper/IsDebug.m b/src/MATLAB/+Helper/IsDebug.m
index fa0d7dbd7d204eb2e6762944487972f69b2b828c..603d936a8049bbe011da0865d10e231d098b6cdc 100644
--- a/src/MATLAB/+Helper/IsDebug.m
+++ b/src/MATLAB/+Helper/IsDebug.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function bDebug = IsDebug()
global bDebugMode
diff --git a/src/MATLAB/+Helper/LoadChannelIntensityImage.m b/src/MATLAB/+Helper/LoadChannelIntensityImage.m
deleted file mode 100644
index a0d26120f7e4d2f1bdb2e042fdcfc9211ef82ec3..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/LoadChannelIntensityImage.m
+++ /dev/null
@@ -1,15 +0,0 @@
-function im = LoadChannelIntensityImage(frame, chanIdx)
- global CONSTANTS
-
- im = zeros(0,0);
- if (chanIdx > CONSTANTS.numChannels)
- return;
- end
-
- imFilename = Helper.GetFullImagePath(chanIdx, frame);
- if ( ~exist(imFilename,'file') )
- return;
- end
-
- im = Helper.LoadIntensityImage(imFilename);
-end
diff --git a/src/MATLAB/+Helper/LoadIntensityImage.m b/src/MATLAB/+Helper/LoadIntensityImage.m
index bc080cf17c3f5c2187930e7d6824dba36af54d25..0a6578ac09ac5c24ef214c08389f2d2d67fa2a09 100644
--- a/src/MATLAB/+Helper/LoadIntensityImage.m
+++ b/src/MATLAB/+Helper/LoadIntensityImage.m
@@ -1,15 +1,38 @@
-% imgray = LoadIntensityImage(filename)
+% imgray = LoadIntensityImage(frame, chan)
% Loads image and calculates "intensity" if it is an rgb image,
% then uses mat2gray to convert to grayscale values on [0,1].
-function imgray = LoadIntensityImage(filename)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+function imgray = LoadIntensityImage(frame, chan)
global CONSTANTS
bitrates = [8 12 16];
- [im map]=imread(filename);
-
+ im = MicroscopeData.Reader('imageData',Metadata.GetImageInfo(), 'chanList',chan, 'timeRange',[frame frame], 'prompt',false);
if ( ndims(im) > 3 )
- error('LEVER tool only supports grayscale images, please select single channel tiff images.');
+ error('LEVER tool only supports grayscale images!');
end
if ( ~isfield(CONSTANTS,'bitrate') )
@@ -33,9 +56,8 @@ function imgray = LoadIntensityImage(filename)
imgray = mat2gray(im);
end
- % Handle "color" images by averaging the color channels to get
- % intensity (should all be the same for all channels)
+ % Handle "color" or 3D images by max intensity projection of the color channels to get intensity
if ( ndims(imgray) == 3 )
- imgray = mean(imgray,3);
+ imgray = max(imgray,[],3);
end
end
diff --git a/src/MATLAB/+Helper/LoadIntensityImageSet.m b/src/MATLAB/+Helper/LoadIntensityImageSet.m
index 7ad6f66135896a6171c996978d9c0c43bb482fb1..25aed55b30a9e2840e32b8dc984ada60642b5b61 100644
--- a/src/MATLAB/+Helper/LoadIntensityImageSet.m
+++ b/src/MATLAB/+Helper/LoadIntensityImageSet.m
@@ -1,17 +1,39 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function chanImSet = LoadIntensityImageSet(frame)
- global CONSTANTS
-
- chanImSet = cell(1,CONSTANTS.numChannels);
+ chanImSet = cell(1, Metadata.GetNumberOfChannels());
bAllMissing = true;
- for c = 1:CONSTANTS.numChannels
- imFilename = Helper.GetFullImagePath(c, frame);
- if ( ~exist(imFilename,'file') )
+ for c = 1:Metadata.GetNumberOfChannels()
+ im = Helper.LoadIntensityImage(frame, c);
+ if ( isempty(im) )
continue;
end
bAllMissing = false;
- chanImSet{c} = Helper.LoadIntensityImage(imFilename);
+ chanImSet{c} = im;
end
if ( bAllMissing )
diff --git a/src/MATLAB/+Helper/LoadPrimaryIntensityImage.m b/src/MATLAB/+Helper/LoadPrimaryIntensityImage.m
deleted file mode 100644
index c6e0143b2f407fe5240654464c8fa0aec6b844f8..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/LoadPrimaryIntensityImage.m
+++ /dev/null
@@ -1,13 +0,0 @@
-function im = LoadPrimaryIntensityImage(frame)
- global CONSTANTS
- primaryChan = CONSTANTS.primaryChannel;
-
- im = zeros(0,0);
-
- imFilename = Helper.GetFullImagePath(primaryChan, frame);
- if ( ~exist(imFilename,'file') )
- return;
- end
-
- im = Helper.LoadIntensityImage(imFilename);
-end
diff --git a/src/MATLAB/+Helper/MakeEmptyStruct.m b/src/MATLAB/+Helper/MakeEmptyStruct.m
index 23faf17c1f0078bd53a5af85f169c8654d2ea0e8..5f8653ccbf8ae0d442a192a7532d35882fd476ab 100644
--- a/src/MATLAB/+Helper/MakeEmptyStruct.m
+++ b/src/MATLAB/+Helper/MakeEmptyStruct.m
@@ -1,6 +1,30 @@
% newStruct = MakeEmptyStruct(inStruct)
% Returns an empty struct based on the fields of inStruct
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function newStruct = MakeEmptyStruct(inStruct)
outFields = fieldnames(inStruct);
newStruct = struct();
diff --git a/src/MATLAB/+Helper/MakeExpandedCVHull.m b/src/MATLAB/+Helper/MakeExpandedCVHull.m
index 4db01269a9bbdf69f6c6db2268586761e18b26cc..fd755eeafe304ea12e61bd9bd2e57f75e9336b89 100644
--- a/src/MATLAB/+Helper/MakeExpandedCVHull.m
+++ b/src/MATLAB/+Helper/MakeExpandedCVHull.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function expandPoints = MakeExpandedCVHull(hullPoints, expandRadius)
expandPoints = [];
if ( size(hullPoints,1) <= 1 )
diff --git a/src/MATLAB/+Helper/MakeInitStruct.m b/src/MATLAB/+Helper/MakeInitStruct.m
index cf2242a51719b17306c911b05f36bf2503b91edd..ee07bd8d1a93fba7f54be9767d7f8ad83e4aa4ff 100644
--- a/src/MATLAB/+Helper/MakeInitStruct.m
+++ b/src/MATLAB/+Helper/MakeInitStruct.m
@@ -1,5 +1,29 @@
% newStruct = MakeInitStruct(outStruct, inStruct)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
% Output a structure entry with fields same as outStruct and any fields
% with the same name copied from inStruct (all others empty)
@@ -26,7 +50,8 @@ function newStruct = MakeInitStruct(templateStruct, initStruct)
end
else
if ( isfield(initStruct,outFields(i)) )
- [newStruct.(outFields{i})] = deal(forceLogical(initStruct.(outFields{i})));
+ logicalData = arrayfun(@(x)(forceLogical(x.(outFields{i}))), initStruct, 'UniformOutput',false);
+ [newStruct.(outFields{i})] = deal(logicalData{:});
else
[newStruct.(outFields{i})] = deal(false);
end
diff --git a/src/MATLAB/+Helper/NonEmptyField.m b/src/MATLAB/+Helper/NonEmptyField.m
index 4e5d676744defc670f17d887a26979451936713e..b15d81658a29098b731e2910301088c6ebc401fc 100644
--- a/src/MATLAB/+Helper/NonEmptyField.m
+++ b/src/MATLAB/+Helper/NonEmptyField.m
@@ -1,4 +1,28 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function bHasNonempty = NonEmptyField(S, fieldname)
bHasNonempty = (isfield(S,fieldname) && ~isempty(S.(fieldname)));
end
\ No newline at end of file
diff --git a/src/MATLAB/+Helper/ParseImageName.m b/src/MATLAB/+Helper/ParseImageName.m
deleted file mode 100644
index 4b83dbbccb39fc8442e127bb1edd245cf117e1d8..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/ParseImageName.m
+++ /dev/null
@@ -1,32 +0,0 @@
-% [datasetName namePattern] = ParseImageName(imageName)
-
-function [datasetName namePattern] = ParseImageName(imageName)
- datasetName = '';
- namePattern = '';
-
- supportedPatterns = {%'^(.+)_(c\d+)_(t\d+)_(z\d+)(.*)$';
- '^(.+)_(c\d+)_(t\d+)(.*)$';
- '^(.+)_(t\d+)(.*)$'};
-
- [filePath fileName fileExt] = fileparts(imageName);
- for i=1:length(supportedPatterns)
- matchTok = regexpi(fileName, supportedPatterns{i}, 'tokens', 'once');
- if ( isempty(matchTok) )
- continue;
- end
-
- paramPatternSet = '';
- for j=2:length(matchTok)-1
- numDigits = length(matchTok{j})-1;
- paramPattern = ['_' matchTok{j}(1) '%0' num2str(numDigits) 'd'];
-
- paramPatternSet = [paramPatternSet paramPattern];
- end
-
- patternPostfix = [matchTok{end} fileExt];
-
- datasetName = [matchTok{1} '_'];
- namePattern = [matchTok{1} paramPatternSet patternPostfix];
- break;
- end
-end
diff --git a/src/MATLAB/+Helper/PushTrackToFrame.m b/src/MATLAB/+Helper/PushTrackToFrame.m
deleted file mode 100644
index f6ee1214272f576d68e82f82d6e7da85e5b26b70..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/PushTrackToFrame.m
+++ /dev/null
@@ -1,45 +0,0 @@
-
-function PushTrackToFrame(trackID, frameTime)
- global CellFamilies CellTracks CellHulls HashedCells
-
- bLockedHulls = false(1,length(CellHulls));
-
- bLockedFamilies = arrayfun(@(x)(x.bLocked > 0),CellFamilies);
- lockedTracks = [CellFamilies(bLockedFamilies).tracks];
- lockTrackHulls = [CellTracks(lockedTracks).hulls];
- nzHulls = lockTrackHulls(lockTrackHulls > 0);
- bLockedHulls(nzHulls) = 1;
-
- costMatrix = Tracker.GetCostMatrix();
-
- startHull = CellTracks(trackID).hulls(1);
- termHulls = [HashedCells{frameTime}.hullID];
- bLockedTerms = bLockedHulls(termHulls);
-
- d = matlab_bgl.dijkstra_sp(costMatrix, startHull);
-
- dTerms = d(termHulls);
- [sortDist srtIdx] = sort(dTerms);
-
- bValid = ~isinf(sortDist);
- checkIdx = srtIdx(bValid);
- if ( isempty(checkIdx) )
- % Try to add a hull somewhere
- error('No hulls available to add');
- return;
- end
-
- bUnlocked = ~bLockedTerms(checkIdx);
- unlockedHulls = termHulls(checkIdx(bUnlocked));
- if ( isempty(unlockedHulls) )
- % Find locked hull to split?
- error('Should probably split a hull here');
- return;
- end
-
- endHull = unlockedHulls(1);
-
- time = CellHulls(endHull).time;
- oldTrackID = Hulls.GetTrackID(endHull);
- Tracks.ChangeLabel(oldTrackID, trackID, time);
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Helper/SaveLEVerState.m b/src/MATLAB/+Helper/SaveLEVerState.m
index 0c538d578b3c6a8d28395f173c593cb85f06a670..b4eb790251bdb41949c8d25865b27b8782717bd7 100644
--- a/src/MATLAB/+Helper/SaveLEVerState.m
+++ b/src/MATLAB/+Helper/SaveLEVerState.m
@@ -2,10 +2,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Helper/SetDebug.m b/src/MATLAB/+Helper/SetDebug.m
index f2719f66ee69d1eea053482617af9bb35e84e638..bac7fc82200dca3dd066fb55d2b4d25e3224844a 100644
--- a/src/MATLAB/+Helper/SetDebug.m
+++ b/src/MATLAB/+Helper/SetDebug.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function SetDebug(bEnable)
global bDebugMode
diff --git a/src/MATLAB/+Helper/SetRandomState.m b/src/MATLAB/+Helper/SetRandomState.m
index 3beb9faee8e213afb40aa9a698ea0359df8e698b..a5cbb49b6f482bdab1ab246637d9cafe3b8f6d04 100644
--- a/src/MATLAB/+Helper/SetRandomState.m
+++ b/src/MATLAB/+Helper/SetRandomState.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function SetRandomState(randState)
globStream = RandStream.getGlobalStream();
globStream.State = randState;
diff --git a/src/MATLAB/+Helper/SetTreeFrozen.m b/src/MATLAB/+Helper/SetTreeFrozen.m
index 7caf9ced6a2648cface8aef9ff43c3650c6808c5..f5391bf502bafdc4b9c3a8114bf7e8cb4d62f219 100644
--- a/src/MATLAB/+Helper/SetTreeFrozen.m
+++ b/src/MATLAB/+Helper/SetTreeFrozen.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function SetTreeFrozen(treeID, bFrozen)
global CellFamilies
diff --git a/src/MATLAB/+Helper/SetTreeLocked.m b/src/MATLAB/+Helper/SetTreeLocked.m
index 0fcda66e3a6779b53145420fce7e8ada3c797a95..8213c6011a1a7c4a41c669860ae3dd9552e1076b 100644
--- a/src/MATLAB/+Helper/SetTreeLocked.m
+++ b/src/MATLAB/+Helper/SetTreeLocked.m
@@ -1,4 +1,28 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function SetTreeLocked(treeID, bLocked)
global CellFamilies
diff --git a/src/MATLAB/+Helper/SplitNamePattern.m b/src/MATLAB/+Helper/SplitNamePattern.m
deleted file mode 100644
index 3604b9dcd733ae75ddbbb6bbdf52f5e4b0774d7e..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Helper/SplitNamePattern.m
+++ /dev/null
@@ -1,21 +0,0 @@
-function [prefixString paramTokens postfixString] = SplitNamePattern(namePattern)
- prefixString = '';
- postfixString = '';
-
- paramTokens = Helper.GetNamePatternParams(namePattern);
- if ( isempty(paramTokens) )
- return;
- end
-
- paramStrings = cellfun(@(x)(['_' x{1} '%0' x{2} 'd']),paramTokens, 'UniformOutput',0);
-
- matchExpr = ['^(.+)' paramStrings{:} '(.*)$'];
- matchTok = regexp(namePattern, matchExpr, 'tokens','once');
- if ( isempty(matchTok) )
- paramTokens = {};
- return;
- end
-
- prefixString = matchTok{1};
- postfixString = matchTok{2};
-end
diff --git a/src/MATLAB/+Helper/SweepDeleted.m b/src/MATLAB/+Helper/SweepDeleted.m
index ee752ea11cbbb595fc45b90b6cb1b6987ba19883..eed0439e1c347b58a9e21e6690ae2b517a9f6cc7 100644
--- a/src/MATLAB/+Helper/SweepDeleted.m
+++ b/src/MATLAB/+Helper/SweepDeleted.m
@@ -1,5 +1,29 @@
% This is a LEVer garbage collection routine to clean up deleted
% tracks and families while keeping all data consistent.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function SweepDeleted()
global CellHulls HashedCells CellTracks CellFamilies Costs ConnectedDist SegmentationEdits
diff --git a/src/MATLAB/+Helper/UpdateFrozenCosts.m b/src/MATLAB/+Helper/UpdateFrozenCosts.m
index 709dab16c5ca694e1b0b39e11da3b5023446af8f..d135edce7c771f78c5365578ac070510d69418ea 100644
--- a/src/MATLAB/+Helper/UpdateFrozenCosts.m
+++ b/src/MATLAB/+Helper/UpdateFrozenCosts.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function UpdateFrozenCosts(treeID, bFrozen)
global CellFamilies CellTracks CachedCostMatrix
diff --git a/src/MATLAB/+Helper/ValidUIHandle.m b/src/MATLAB/+Helper/ValidUIHandle.m
index 76bf7141d1000c60d300c3849744a8b223a0d35a..abb617389c35e4a0cf89f625cabb697bc63c9259 100644
--- a/src/MATLAB/+Helper/ValidUIHandle.m
+++ b/src/MATLAB/+Helper/ValidUIHandle.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function bValid = ValidUIHandle(hCheck)
if ( isempty(hCheck) )
bValid = false;
diff --git a/src/MATLAB/+Helper/WasDropped.m b/src/MATLAB/+Helper/WasDropped.m
index 4ddbd7fbb5814d2f35ace81e5fa90603e35a3144..6eecbe6f8ee787a95669d0958cc5aa082ec6aac1 100644
--- a/src/MATLAB/+Helper/WasDropped.m
+++ b/src/MATLAB/+Helper/WasDropped.m
@@ -1,6 +1,30 @@
% bool = WasDropped(track, list)
% Returns 1 or 0 depending if the track is in the given list
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
% ChangeLog:
% EW 6/8/12 created
function bool = WasDropped(track, list)
diff --git a/src/MATLAB/+Helper/fitGMM.m b/src/MATLAB/+Helper/fitGMM.m
index 07e690e85ece7c8622058ee0a1e63342ca3d97aa..cbfc4ca11212b463af8c73a1489325333f9f6b87 100644
--- a/src/MATLAB/+Helper/fitGMM.m
+++ b/src/MATLAB/+Helper/fitGMM.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function gmmObj = fitGMM(X,k,varargin)
if ( verLessThan('matlab', '8.4.0') )
gmmObj = gmdistribution.fit(X,k, varargin{:});
diff --git a/src/MATLAB/+Hulls/AddHashedCell.m b/src/MATLAB/+Hulls/AddHashedCell.m
index 6367ecc43e17d0fb6c00c92b89b8b5039d4c1560..801a8998eb588d509570cc4e7cc5a0eed0a994ef 100644
--- a/src/MATLAB/+Hulls/AddHashedCell.m
+++ b/src/MATLAB/+Hulls/AddHashedCell.m
@@ -4,10 +4,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Hulls/CheckHullsContainsPoint.m b/src/MATLAB/+Hulls/CheckHullsContainsPoint.m
index 6771d819c7b5a4b36e866edf835974e5c3c677b8..6436970132bf9330281fc3ecf094fb22c81c7ace 100644
--- a/src/MATLAB/+Hulls/CheckHullsContainsPoint.m
+++ b/src/MATLAB/+Hulls/CheckHullsContainsPoint.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Hulls/ClearHull.m b/src/MATLAB/+Hulls/ClearHull.m
index d708ac0ad7fcaee935e11bed201dc85fd712d449..c0f768b63e62e7b53221a1d1fb4a2d25d6caf6f5 100644
--- a/src/MATLAB/+Hulls/ClearHull.m
+++ b/src/MATLAB/+Hulls/ClearHull.m
@@ -1,6 +1,30 @@
% ClearHull( hullID )
% Clears the hull and marks it deleted
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
% ChangeLog:
% EW 6/8/12 created
function ClearHull( hullID )
diff --git a/src/MATLAB/+Hulls/CreateHull.m b/src/MATLAB/+Hulls/CreateHull.m
index 33a778811f4e6b35188b6ed82066cc547e0f6001..87db8b0fd552bc91a360bab1f349270530f0cd1b 100644
--- a/src/MATLAB/+Hulls/CreateHull.m
+++ b/src/MATLAB/+Hulls/CreateHull.m
@@ -1,4 +1,28 @@
-function newHull = CreateHull(imageSize, indexPixels, time, userEdited, tag)
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function newHull = CreateHull(rcImageDims, indexPixels, time, userEdited, tag)
global CellHulls
if ( ~exist('time','var') )
@@ -18,8 +42,8 @@ function newHull = CreateHull(imageSize, indexPixels, time, userEdited, tag)
newHull = Helper.MakeEmptyStruct(CellHulls);
end
- rcCoords = Helper.IndexToCoord(imageSize, indexPixels);
- xyCoords = Helper.SwapXY_RC(rcCoords);
+ rcCoords = Utils.IndToCoord(rcImageDims, indexPixels);
+ xyCoords = Utils.SwapXY_RC(rcCoords);
newHull.indexPixels = indexPixels;
newHull.centerOfMass = mean(rcCoords,1);
@@ -30,7 +54,7 @@ function newHull = CreateHull(imageSize, indexPixels, time, userEdited, tag)
return;
end
- newHull.points = xyCoords(chIdx,:);
+ newHull.points = xyCoords(chIdx,1:2);
newHull.time = time;
newHull.userEdited = (userEdited > 0);
diff --git a/src/MATLAB/+Hulls/ExpandedHullContains.m b/src/MATLAB/+Hulls/ExpandedHullContains.m
index 839cef2262a8c8b3328dfb954650f29a79bc3a7f..c615e7244c159fa26ba0f1f61a1762776f556245 100644
--- a/src/MATLAB/+Hulls/ExpandedHullContains.m
+++ b/src/MATLAB/+Hulls/ExpandedHullContains.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function bInside = ExpandedHullContains(cvHull, expandRadius, pointList)
numPoints = size(pointList,1);
diff --git a/src/MATLAB/+Hulls/FindHull.m b/src/MATLAB/+Hulls/FindHull.m
index 8546fcae32d4e7ffbd742a496c4ed42574069d49..ef2265f57b3634b9e05ca33e29719ee497058f52 100644
--- a/src/MATLAB/+Hulls/FindHull.m
+++ b/src/MATLAB/+Hulls/FindHull.m
@@ -4,10 +4,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Hulls/GetTrackID.m b/src/MATLAB/+Hulls/GetTrackID.m
index 25c6d6e64a01c5c82b0e93ffbe31336c85ab87d0..86cdd359381f2c5c7669d9421cfd905a2034a9fa 100644
--- a/src/MATLAB/+Hulls/GetTrackID.m
+++ b/src/MATLAB/+Hulls/GetTrackID.m
@@ -2,10 +2,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Hulls/RadiusContains.m b/src/MATLAB/+Hulls/RadiusContains.m
index 42e98f2ae46a305e0e68bb7d1fb53b6a9178aa9a..f9c7304dc5b2ccbc4c28edcab778c745789f17fc 100644
--- a/src/MATLAB/+Hulls/RadiusContains.m
+++ b/src/MATLAB/+Hulls/RadiusContains.m
@@ -1,4 +1,28 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function bMayOverlap = RadiusContains(hullIDs, expandRadius, point)
global CellHulls
diff --git a/src/MATLAB/+Hulls/RemoveHull.m b/src/MATLAB/+Hulls/RemoveHull.m
index a0e68155f7cdbd64b8692cd76e93ea6b6fa8b9c8..73d92a2f308f6e3627207d70b26694519080578e 100644
--- a/src/MATLAB/+Hulls/RemoveHull.m
+++ b/src/MATLAB/+Hulls/RemoveHull.m
@@ -7,10 +7,10 @@
% EW 6/6/12 rewrite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Hulls/SetCellHullEntries.m b/src/MATLAB/+Hulls/SetCellHullEntries.m
index 388617ca36343a5d0c46d7c705320f61df6e00fc..8f012dbddaa5e96a5c84954d79411ba36db4b1f1 100644
--- a/src/MATLAB/+Hulls/SetCellHullEntries.m
+++ b/src/MATLAB/+Hulls/SetCellHullEntries.m
@@ -5,6 +5,30 @@
%
% NOTE: This does not automatically update tracking information for hulls
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [newHulls newFamilies] = SetCellHullEntries(setHullIDs, setObjs)
global CellHulls Costs GraphEdits ResegLinks CachedCostMatrix
diff --git a/src/MATLAB/+ImUtils/ConvertType.m b/src/MATLAB/+ImUtils/ConvertType.m
new file mode 100644
index 0000000000000000000000000000000000000000..01756425f863f3ede570b0939b441431438f33d2
--- /dev/null
+++ b/src/MATLAB/+ImUtils/ConvertType.m
@@ -0,0 +1,117 @@
+% [ imageOut ] = ConvertType(IMAGEIN, OUTCLASS, NORMALIZE)
+% ConvertType converts image from current type into the specified type
+% OUTCLASS
+% If normalize==true then each channel/frame will be set between [0,1] prior
+% to conversion, meaning that normalization happens on a frame by frame as
+% well as a channel by channel bases.
+% Assumes a 5D image of (rows,col,z,channels,time). Non-existent dimensions
+% should be singleton.
+
+function [ imageOut ] = ConvertType(imageIn, typ, normalize)
+
+if (~exist('normalize','var') || isempty(normalize))
+ normalize = 0;
+end
+
+if (~strcmpi(typ,'logical'))
+ imageOut = zeros(size(imageIn),typ);
+else
+ imageOut = false(size(imageIn));
+end
+
+if (normalize)
+ for t=1:size(imageIn,5)
+ for c=1:size(imageIn,4)
+ inType = class(imageIn);
+ if (strcmpi(inType,'double') || strcmpi(inType,'uint64') || strcmpi(inType,'int64'))
+ imTemp = double(imageIn(:,:,:,c,t));
+ else
+ imTemp = single(imageIn(:,:,:,c,t));
+ end
+ imTemp = imTemp-min(imTemp(:));
+ imTemp = imTemp./max(imTemp(:));
+
+ switch typ
+ case 'uint8'
+ imageOut(:,:,:,c,t) = im2uint8(imTemp);
+ case 'uint16'
+ imageOut(:,:,:,c,t) = im2uint16(imTemp);
+ case 'int16'
+ imageOut(:,:,:,c,t) = im2int16(imTemp);
+ case 'uint32'
+ imageOut(:,:,:,c,t) = im2uint32(imTemp);
+ case 'int32'
+ imageOut(:,:,:,c,t) = im2int32(imTemp);
+ case 'single'
+ imageOut(:,:,:,c,t) = im2single(imTemp);
+ case 'double'
+ imageOut(:,:,:,c,t) = imTemp;
+ case 'logical'
+ imageOut(:,:,:,c,t) = imTemp>min(imTemp(:));
+ otherwise
+ error('Unkown type of image to convert to!');
+ end
+ end
+ end
+else
+ w = whos('imageIn');
+ switch w.class
+ case 'single'
+ imageIn = convertToMaxOfOne(imageIn,w.class);
+ case 'double'
+ imageIn = convertToMaxOfOne(imageIn,w.class);
+ end
+ if (strcmpi(w.class,typ))
+ imageOut = imageIn;
+ else
+ switch typ
+ case 'uint8'
+ imageOut = im2uint8(imageIn);
+ case 'uint16'
+ imageOut = im2uint16(imageIn);
+ case 'int16'
+ imageOut = im2int16(imageIn);
+ case 'uint32'
+ imageOut = im2uint32(imageIn);
+ case 'int32'
+ imageOut = im2int32(imageIn);
+ case 'single'
+ imageOut = im2single(imageIn);
+ case 'double'
+ imageOut = im2double(imageIn);
+ case 'logical'
+ imageOut = imageIn>min(imageIn(:));
+ otherwise
+ error('Unkown type of image to convert to!');
+ end
+ end
+end
+end
+
+function im = convertToMaxOfOne(im,outTyp)
+switch outTyp
+ case 'uint8'
+ im = im./2^8;
+ case 'uint16'
+ if (max(im(:))<2^12+1)
+ im = im./2^12;
+ else
+ im = im./2^16;
+ end
+ case 'int16'
+ im = im./2^15-1;
+ case 'uint32'
+ im = im./2^32;
+ case 'int32'
+ im = im./2^32-1;
+ case 'single'
+ im = im./max(im(:));
+ case 'double'
+ im = im./max(im(:));
+ case 'logical'
+ % im = im;
+ otherwise
+ error('Unkown type of image to convert to!');
+end
+end
+
diff --git a/src/MATLAB/+Load/AddConstant.m b/src/MATLAB/+Load/AddConstant.m
index c3688d4c80d0a105d34e7edcc8a283e1105c8ed3..9112c6031a1f5ca5606e31e63cb6ac7379083fe4 100644
--- a/src/MATLAB/+Load/AddConstant.m
+++ b/src/MATLAB/+Load/AddConstant.m
@@ -6,10 +6,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Load/AddFamilyEditFields.m b/src/MATLAB/+Load/AddFamilyEditFields.m
index cfc2d78dcfbb58e1fe733238d4d115870b8e9846..313a9eb1032cfd2dce6c93b97b110686a04c7e40 100644
--- a/src/MATLAB/+Load/AddFamilyEditFields.m
+++ b/src/MATLAB/+Load/AddFamilyEditFields.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function bNeedsUpdate = AddFamilyEditFields()
global CellFamilies
diff --git a/src/MATLAB/+Load/AddUserEditedField.m b/src/MATLAB/+Load/AddUserEditedField.m
index 1aa3d8a148b4442618a788a4c5a8141885b513bc..a7a746bbcfb887826418f75702bc079bb89614d1 100644
--- a/src/MATLAB/+Load/AddUserEditedField.m
+++ b/src/MATLAB/+Load/AddUserEditedField.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Load/BuildRenameStruct.m b/src/MATLAB/+Load/BuildRenameStruct.m
new file mode 100644
index 0000000000000000000000000000000000000000..1e4336e782cf5bb8ec6851d3a0d23a1c8dd7ec48
--- /dev/null
+++ b/src/MATLAB/+Load/BuildRenameStruct.m
@@ -0,0 +1,80 @@
+% [renameStruct,bNeedRename] = BuildRenameStruct(imageName)
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+function renameStruct = BuildRenameStruct(imageName)
+ renameStruct = [];
+
+ paramSet = {'c';'t';'z'};
+ paramSize = {2;4;4};
+ requireParam = [false,true,false];
+
+ paramPattern = cellfun(@(x)(['_(' x ')\d+']), paramSet, 'UniformOutput',false);
+
+ [~,fileName,fileExt] = fileparts(imageName);
+ [startMatch,tokMatch] = regexpi(fileName, paramPattern, 'start','tokens');
+
+ % If there are multiple matches to the parameter type, take only the one that's furthest in the name.
+ bFoundParams = cellfun(@(x)(~isempty(x)),startMatch);
+ validStarts = cellfun(@(x)(x(end)), startMatch(bFoundParams));
+ validParams = cellfun(@(x)(x{end}{1}), tokMatch(bFoundParams), 'UniformOutput',false);
+
+ if ( isempty(validStarts) )
+ return;
+ end
+
+ [~,validParamOrder] = sort(validStarts);
+
+ tokPattern = cellfun(@(x)(['_' x '(\d+)']), validParams(validParamOrder), 'UniformOutput',false);
+ buildPattern = ['^(.+)' tokPattern{:} '(.*?)$'];
+
+ tokMatch = regexp(fileName, buildPattern, 'tokens','once');
+ if ( isempty(tokMatch) )
+ return;
+ end
+
+ paramOrder = zeros(1,length(paramSet));
+ paramOrder(bFoundParams) = validParamOrder;
+ if ( ~all(paramOrder(requireParam)>0) )
+ return;
+ end
+
+ prefixStr = regexptranslate('escape',tokMatch{1});
+ postfixStr = regexptranslate('escape',tokMatch{end});
+
+ % Escape some possible file name issues
+ datasetName = tokMatch{1};
+ prefixName = strrep(tokMatch{1},'"','\"');
+ prefixName = strrep(prefixName,'''','\''');
+ prefixName = strrep(prefixName,'%','%%');
+
+ dirBlob = [datasetName '*' fileExt];
+ loadPattern = [prefixStr tokPattern{:} postfixStr '\' fileExt];
+
+ outParams = cellfun(@(x,y)(['_' x '%0' num2str(y) 'd']), paramSet,paramSize, 'UniformOutput',false);
+ outPattern = [prefixName outParams{:} '.tif'];
+
+ renameStruct = struct('datasetName',{datasetName}, 'dirBlob',{dirBlob}, 'loadPattern',{loadPattern}, 'outPattern',{outPattern}, 'paramOrder',{paramOrder});
+end
diff --git a/src/MATLAB/+Load/CheckExportImages.m b/src/MATLAB/+Load/CheckExportImages.m
new file mode 100644
index 0000000000000000000000000000000000000000..d09a71e76827a126dc91052351e14419a60a2da2
--- /dev/null
+++ b/src/MATLAB/+Load/CheckExportImages.m
@@ -0,0 +1,61 @@
+% [bNeedsExport,bInplaceUpdate] = CheckExportImages(rootDir,fileName)
+%
+% Check if these specified image file needs to be exported for LEVER use or
+% or if only an inplace rename and json generation is required.
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+function [bNeedsExport,bWriteable,renameStruct] = CheckExportImages(rootDir,fileName)
+ bNeedsExport = false;
+ bWriteable = false;
+ renameStruct = [];
+
+ [~,chkName,chkExt] = fileparts(fileName);
+ if ( any(strcmpi(chkExt,{'.tif','.tiff'})) )
+ jsonList = dir(fullfile(rootDir,[chkName '*.json']));
+ if ( ~isempty(jsonList) )
+ return;
+ end
+
+ renameStruct = Load.BuildRenameStruct(fileName);
+ end
+
+ bWriteable = ~isempty(renameStruct) && checkWriteable(rootDir);
+ bNeedsExport = true;
+end
+
+function bCanWrite = checkWriteable(rootDir)
+ bCanWrite = false;
+
+ fid = fopen(fullfile(rootDir,'testWriteFile'),'w');
+ if ( fid < 0 )
+ return;
+ end
+ fclose(fid);
+
+ delete(fullfile(rootDir,'testWriteFile'));
+
+ bCanWrite = true;
+end
\ No newline at end of file
diff --git a/src/MATLAB/+Load/CheckFolderExport.m b/src/MATLAB/+Load/CheckFolderExport.m
new file mode 100644
index 0000000000000000000000000000000000000000..eb1cd280429438599b961ced1383d1165d502929
--- /dev/null
+++ b/src/MATLAB/+Load/CheckFolderExport.m
@@ -0,0 +1,100 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function [subPaths,needsExport,renamable] = CheckFolderExport(rootDir)
+ [subPaths,needsExport,renamable] = recursiveCheckExport(rootDir,'');
+end
+
+function [subPaths,needsExport,renamable] = recursiveCheckExport(rootDir,subDir)
+ subPaths = {};
+ needsExport = false(0);
+ renamable = false(0);
+
+ dirList = dir(fullfile(rootDir,subDir));
+
+ bInvalidName = arrayfun(@(x)(strncmpi(x.name,'.',1) || strncmpi(x.name,'..',2)), dirList);
+ bValidDir = ~bInvalidName & (vertcat(dirList.isdir) > 0);
+ bValidFile = ~bInvalidName & (vertcat(dirList.isdir) == 0);
+
+ fileList = dirList(bValidFile);
+ pathList = dirList(bValidDir);
+
+ filenames = {fileList.name}.';
+
+ %% Get a list of valid JSON files
+ jsonMatch = regexpi(filenames, '(\.json$)','once');
+ bJSON = cellfun(@(x)(~isempty(x)),jsonMatch);
+
+ jsonNames = filenames(bJSON);
+ if ( ~isempty(jsonNames) )
+ bValid = cellfun(@(x)(~isempty(MicroscopeData.ReadMetadataFile(fullfile(rootDir,subDir,x)))),jsonNames);
+
+ % Remove files that have the same prefix (datasetName) as .json from the list
+ datasetNames = cellfun(@(x)(x(1:end-5)),jsonNames(bValid),'UniformOutput',false);
+ matchDatasets = cellfun(@(x)(strncmp(x,filenames.',length(x))),datasetNames,'UniformOutput',false);
+ bMatched = any(vertcat(matchDatasets{:}),1);
+ filenames = filenames(~bMatched);
+
+ subPaths = cellfun(@(x)(fullfile(subDir,x)),jsonNames(bValid),'UniformOutput',false);
+ needsExport = false(nnz(bValid),1);
+ renamable = false(nnz(bValid),1);
+ end
+
+ %% Handle folders of TIFs that don't require export or are renamable stacks
+ tifMatch = regexpi(filenames, '(\.tif$)|(\.tiff$)','once');
+ bTIF = cellfun(@(x)(~isempty(x)),tifMatch);
+
+ tifNames = filenames(bTIF);
+ if ( ~isempty(tifNames) )
+ % If these appear to be renameable tifs don't bother with subdirectories
+ [bNeedsExport,bWriteable,renameStruct] = Load.CheckExportImages(fullfile(rootDir,subDir),tifNames{1});
+ if ( ~isempty(renameStruct) )
+ subPaths = {fullfile(subDir,tifNames{1})};
+ needsExport = bNeedsExport;
+ renamable = bWriteable;
+
+ return;
+ end
+ end
+
+ %% Check any other files to see if they are supported and need export
+ if ( ~isempty(filenames) )
+ bCanExport = MicroscopeData.Original.CanExportFormat(filenames);
+ exportNames = filenames(bCanExport);
+
+ subPaths = [subPaths; cellfun(@(x)(fullfile(subDir,x)),exportNames,'UniformOutput',false)];
+ needsExport = [needsExport; true(length(exportNames),1)];
+ renamable = [renamable; false(length(exportNames),1)];
+ end
+
+ %% Deal with further subdirectories
+ for i=1:length(pathList)
+ nextSubDir = fullfile(subDir,pathList(i).name);
+ [newPaths,chkExport,chkRename] = recursiveCheckExport(rootDir,nextSubDir);
+
+ subPaths = [subPaths; newPaths];
+ needsExport = [needsExport; chkExport];
+ renamable = [renamable; chkRename];
+ end
+end
diff --git a/src/MATLAB/+Load/CreateColors.m b/src/MATLAB/+Load/CreateColors.m
index 9b66c6172504832ed8a2a255d8ecaf803c70ac5a..c951a26057e091a13105a2deba837f0fbd6fb7fa 100644
--- a/src/MATLAB/+Load/CreateColors.m
+++ b/src/MATLAB/+Load/CreateColors.m
@@ -5,10 +5,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Load/ExportImages.m b/src/MATLAB/+Load/ExportImages.m
new file mode 100644
index 0000000000000000000000000000000000000000..f2ac3b773a15a893dbbf518c2d2017a818a28ce5
--- /dev/null
+++ b/src/MATLAB/+Load/ExportImages.m
@@ -0,0 +1,34 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function jsonPath = ExportImages(exportDir, inRoot,inFilename)
+ [~,imD] = MicroscopeData.Original.Convert2Tiffs(inRoot,inFilename, exportDir, true, false);
+ if ( length(imD) > 1 )
+ [~,imName] = fileparts(inFilename);
+ exportDir = fullfile(exportDir,imName);
+ end
+
+ [~,chkIdx] = max(cellfun(@(x)((x.NumberOfFrames)),imD));
+ jsonPath = fullfile(exportDir,imD{chkIdx}.DatasetName,[imD{chkIdx}.DatasetName '.json']);
+end
diff --git a/src/MATLAB/+Load/ExportLocationDialog.m b/src/MATLAB/+Load/ExportLocationDialog.m
new file mode 100644
index 0000000000000000000000000000000000000000..fa1ad480445c1ec7a7e299c6058fac225dd5df64
--- /dev/null
+++ b/src/MATLAB/+Load/ExportLocationDialog.m
@@ -0,0 +1,60 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function exportLocation = ExportLocationDialog(rootDir,bInplace)
+ exportLocation = '';
+
+ % Offer to update the image names/json in place if possible.
+ if ( bInplace )
+ selAns = questdlg({'Selected images must be updated to conform to LEVER naming and metadata guidelines:',...
+ 'Image name format: <DatasetName>_c%02d_t%04d_z%04d.tif',...
+ ' ',...
+ 'The images can be updated in place or exported to a new directory.'},...
+ 'Image Export Required', 'Update','Export','Update');
+
+ if ( isempty(selAns) )
+ return;
+ end
+
+ if ( strcmpi(selAns,'Update') )
+ exportLocation = rootDir;
+ return;
+ end
+ end
+
+ while ( true )
+ chkDir = uigetdir(rootDir, 'Image Export Directory');
+ if ( ~chkDir )
+ return;
+ end
+
+ if ( strcmp(chkDir,rootDir) )
+ h = warndlg('Please select or create a different directory to export into.','Export Required');
+ uiwait(h);
+ else
+ exportLocation = chkDir;
+ return;
+ end
+ end
+end
diff --git a/src/MATLAB/+Load/FileVersionGreaterOrEqual.m b/src/MATLAB/+Load/FileVersionGreaterOrEqual.m
index e1b0818d960cb9a6f8bd07065a890b9faa23c5d3..62deed0eeb6ad5f7aab2e8ba9b9d35dd370affb3 100644
--- a/src/MATLAB/+Load/FileVersionGreaterOrEqual.m
+++ b/src/MATLAB/+Load/FileVersionGreaterOrEqual.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Load/FixDefaultPhenotypes.m b/src/MATLAB/+Load/FixDefaultPhenotypes.m
index ace98fd56a83452c7d666f85d06cb9bfe4f30808..4046c5937ebb669c7b0f75ad5aace1ab1e0668ee 100644
--- a/src/MATLAB/+Load/FixDefaultPhenotypes.m
+++ b/src/MATLAB/+Load/FixDefaultPhenotypes.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function bNeedsUpdate = FixDefaultPhenotypes()
% Merge together any duplicate phenotypes (based on description)
bNeedsUpdate = mergeDuplicateIDs();
diff --git a/src/MATLAB/+Load/FixMetadata.m b/src/MATLAB/+Load/FixMetadata.m
new file mode 100644
index 0000000000000000000000000000000000000000..23314303598fabfc1acd6aa22dec415625721a00
--- /dev/null
+++ b/src/MATLAB/+Load/FixMetadata.m
@@ -0,0 +1,43 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function bNeedsUpdate = FixMetadata()
+ global CONSTANTS
+
+ oldFields = {'datasetName'
+ 'numChannels'
+ 'numFrames'
+ 'imageNamePattern'
+ 'imageSize'
+ 'imageSignificantDigits'};
+
+ bNeedsUpdate = false;
+
+ for i=1:length(oldFields)
+ if ( isfield(CONSTANTS,oldFields{i}) )
+ CONSTANTS = rmfield(CONSTANTS,oldFields{i});
+ bNeedsUpdate = true;
+ end
+ end
+end
\ No newline at end of file
diff --git a/src/MATLAB/+Load/FixOldFileVersions.m b/src/MATLAB/+Load/FixOldFileVersions.m
index 29ed9dcb4b0c8e6c11fff42937b0bb72190939ce..8bd241e0e3ecf4ee51a19160f5274d19502351f6 100644
--- a/src/MATLAB/+Load/FixOldFileVersions.m
+++ b/src/MATLAB/+Load/FixOldFileVersions.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -131,6 +131,11 @@ function bNeedsUpdate = FixOldFileVersions()
bNeedsUpdate = true;
end
+ % Properly include image metadata, remove old superfluous fields
+ if ( Load.FixMetadata() )
+ bNeedsUpdate = true;
+ end
+
% % Adds the special origin action, to indicate that this is initial
% % segmentation data from which edit actions are built.
% if ( isempty(ReplayEditActions) || bNeedsUpdate )
diff --git a/src/MATLAB/+Load/FolderExport.m b/src/MATLAB/+Load/FolderExport.m
new file mode 100644
index 0000000000000000000000000000000000000000..c93c912ab9bf37eee01b545de26f9208237ab7fe
--- /dev/null
+++ b/src/MATLAB/+Load/FolderExport.m
@@ -0,0 +1,82 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function exportRoot = FolderExport(rootDir)
+ exportRoot = rootDir;
+
+ [subPaths,needsExport,renamable] = Load.CheckFolderExport(rootDir);
+ if ( isempty(subPaths) )
+ return;
+ end
+
+ bExport = any(needsExport);
+ if ( ~bExport )
+ return;
+ end
+
+ % Allow an inplace update if all exports are renamable
+ exportRenames = renamable(needsExport);
+ exportPaths = subPaths(needsExport);
+
+ bInplace = all(exportRenames);
+ exportRoot = Load.ExportLocationDialog(rootDir, bInplace);
+ if ( isempty(exportRoot) )
+ return;
+ end
+
+ %% Copy all entries that don't need an export if we aren't doing inplace
+ copyPaths = {};
+ if ( ~strcmp(exportRoot,rootDir) )
+ copyPaths = subPaths(~needsExport);
+ end
+
+ %% Copy all valid lever data to export directory
+ for i=1:length(copyPaths)
+ [subDir,filename] = fileparts(exportPaths{i});
+
+ exportDir = fullfile(exportRoot,subDir);
+ importDir = fullfile(rootDir,subDir);
+ if ( ~exist(exportDir,'dir') )
+ mkdir(exportDir);
+ end
+
+ copyfile(fullfile(importDir,[filename '*']),exportDir);
+ end
+
+ %% Export or rename/copy
+ for i=1:length(exportPaths)
+ [subDir,filename,fext] = fileparts(exportPaths{i});
+
+ inputName = [filename fext];
+ exportDir = fullfile(exportRoot,subDir);
+ importDir = fullfile(rootDir,subDir);
+
+ if ( ~exportRenames(i) )
+ Load.ExportImages(exportDir, importDir,inputName);
+ else
+ renameStruct = Load.BuildRenameStruct(inputName);
+ Load.RenameImages(exportDir, importDir,renameStruct,false);
+ end
+ end
+end
diff --git a/src/MATLAB/+Load/GetCellTypeStructure.m b/src/MATLAB/+Load/GetCellTypeStructure.m
index e1f234a3faa4b5a55565fc9862a97f54bfdb8f31..3698078aee64dbcb7c690f9efe226b298ee1aa72 100644
--- a/src/MATLAB/+Load/GetCellTypeStructure.m
+++ b/src/MATLAB/+Load/GetCellTypeStructure.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function typeParams = GetCellTypeStructure(cellType)
cellTypes = Load.GetSupportedCellTypes();
diff --git a/src/MATLAB/+Load/GetSupportedCellTypes.m b/src/MATLAB/+Load/GetSupportedCellTypes.m
index fbbbcf0f2cebda4029a948a86cd67cffd78b3265..4dd7b8017876b62a89fc05091055f96b951a1197 100644
--- a/src/MATLAB/+Load/GetSupportedCellTypes.m
+++ b/src/MATLAB/+Load/GetSupportedCellTypes.m
@@ -10,10 +10,36 @@
%
% See also Segmentation.FrameSegmentor
%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function SupportedTypes = GetSupportedCellTypes()
SupportedTypes = [];
%% Adult neural progenitor cell segmentation algorithm
+ % the embryonic cell type has default settings for all parameters. override
+ % in custom segmentation as needed only.
SupportedTypes = addCellType(SupportedTypes, 'Adult',...
'segRoutine',setAlgorithm(@Segmentation.FrameSegmentor_Adult, setParamValue('imageAlpha', 1.5)),...
'resegRoutine',setAlgorithm(@Segmentation.FrameSegmentor_Adult, setParamRange('imageAlpha', 1.0,0.5,5)),...
@@ -30,7 +56,11 @@ function SupportedTypes = GetSupportedCellTypes()
'trackParams',struct('dMaxCenterOfMass',{80}, 'dMaxConnectComponentTracker',{40}),...
'leverParams',struct('timeResolution',{5}, 'maxPixelDistance',{80}, 'maxCenterOfMassDistance',{80}, 'dMaxConnectComponent',{40}),...
'channelParams',struct('primaryChannel',{1}, 'channelColor',{[1 1 1]}, 'channelFluor',{[false]}));
-
+ %% Three level segmentation
+ SupportedTypes = addCellType(SupportedTypes, 'MultiThreshDark',...
+ 'segRoutine',setAlgorithm(@Segmentation.FrameSegmentor_MDK, setParamValue('imageAlpha', 1)),...
+ 'resegRoutine',setAlgorithm(@Segmentation.FrameSegmentor_MDK, setParamRange('imageAlpha', 1.0,.95,5)),...
+ 'splitParams',struct('useGMM',true));
% TODO: Move channel params and some lever params into metadata structure and parse directly from microscope data.
end
diff --git a/src/MATLAB/+Load/ImageExportDialog.m b/src/MATLAB/+Load/ImageExportDialog.m
new file mode 100644
index 0000000000000000000000000000000000000000..3c4b5eba2a65dd98aa106915b5bef9b9d7c7d107
--- /dev/null
+++ b/src/MATLAB/+Load/ImageExportDialog.m
@@ -0,0 +1,44 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function jsonPath = ImageExportDialog(rootDir,filename)
+ [bNeedsExport,bWriteable,renameStruct] = Load.CheckExportImages(rootDir,filename);
+ if ( ~bNeedsExport )
+ [~,chkName] = fileparts(filename);
+ jsonList = dir(fullfile(rootDir,[chkName '*.json']));
+ jsonPath = fullfile(rootDir,jsonList(1).name);
+ return;
+ end
+
+ exportDir = Load.ExportLocationDialog(rootDir, bWriteable);
+ if ( isempty(exportDir) )
+ return;
+ end
+
+ if ( isempty(renameStruct) )
+ jsonPath = Load.ExportImages(exportDir, rootDir,filename);
+ else
+ jsonPath = Load.RenameImages(exportDir, rootDir, renameStruct);
+ end
+end
diff --git a/src/MATLAB/+Load/ImageLoadDialog.m b/src/MATLAB/+Load/ImageLoadDialog.m
new file mode 100644
index 0000000000000000000000000000000000000000..c4669ca1a61439fd655f06530464bb2d1c8ce6b0
--- /dev/null
+++ b/src/MATLAB/+Load/ImageLoadDialog.m
@@ -0,0 +1,51 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function jsonPath = ImageLoadDialog(initialPath,promptTitle)
+ filterSpecs = {'*.json','LEVER Metadata (*.json)';
+ '*.lif;*.lei','Leica LAS (*.lif,*.lei)';
+ '*.czi;*.lsm;*.zvi','Zeiss (*.czi,*.lsm,*.zvi)';
+ '*.tif;*.tiff','TIFF Images (*.tif,*.tiff)';
+ '*.*','All Files (*.*)'};
+
+ jsonPath = '';
+
+ [fileName,rootDir,filterIndex] = uigetfile(filterSpecs,promptTitle,initialPath);
+ if (filterIndex==0)
+ return
+ end
+
+ if ( filterIndex == 1 )
+ jsonPath = fullfile(rootDir,fileName);
+ return
+ end
+
+ [~,~,chkExt] = fileparts(fileName);
+ if ( filterIndex == length(filterSpecs) && strcmpi(chkExt,'.json') )
+ jsonPath = fullfile(rootDir,fileName);
+ return;
+ end
+
+ jsonPath = Load.ImageExportDialog(rootDir,fileName);
+end
diff --git a/src/MATLAB/+Load/InitializeCachedCosts.m b/src/MATLAB/+Load/InitializeCachedCosts.m
index 8b524ada1c48257e8befd211c6fb1dc3fa1946f5..1f5f1687be6c084ff89be49b3150f2b786f89a95 100644
--- a/src/MATLAB/+Load/InitializeCachedCosts.m
+++ b/src/MATLAB/+Load/InitializeCachedCosts.m
@@ -1,6 +1,30 @@
% InitializeCachedCosts()
% Initialize CachedCostMatrix from current Costs and GraphEdits
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function InitializeCachedCosts(bForceInitialize)
global Costs GraphEdits CellHulls CachedCostMatrix CellFamilies
diff --git a/src/MATLAB/+Load/InitializeConstants.m b/src/MATLAB/+Load/InitializeConstants.m
index b574ff16991a760a87f7ffde9e908df90134d216..45d7927653ca2297cb5f287203997dd0c9c7b28a 100644
--- a/src/MATLAB/+Load/InitializeConstants.m
+++ b/src/MATLAB/+Load/InitializeConstants.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -28,9 +28,6 @@ function InitializeConstants()
%% Set all constants here
global CONSTANTS
-
-Load.SetImageInfo();
-
if (~isfield(CONSTANTS,'cellType') || isempty(CONSTANTS.cellType))
cellType = Load.QueryCellType();
Load.AddConstant('cellType',cellType,1);
@@ -63,13 +60,13 @@ primaryChannel = typeParams.channelParams.primaryChannel;
channelColor = typeParams.channelParams.channelColor;
channelFluor = typeParams.channelParams.channelFluor;
-numMissingChan = CONSTANTS.numChannels - length(channelFluor);
+numMissingChan = Metadata.GetNumberOfChannels() - length(channelFluor);
if ( numMissingChan > 0 )
channelColor = [channelColor; hsv(numMissingChan+2)];
channelFluor = [channelFluor false(1,numMissingChan)];
elseif ( numMissingChan < 0 )
- channelColor = channelColor(1:CONSTANTS.numChannels,:);
- channelFluor = channelFluor(1:CONSTANTS.numChannels);
+ channelColor = channelColor(1:Metadata.GetNumberOfChannels(),:);
+ channelFluor = channelFluor(1:Metadata.GetNumberOfChannels());
end
Load.AddConstant('primaryChannel', primaryChannel);
diff --git a/src/MATLAB/+Load/OpenData.m b/src/MATLAB/+Load/OpenData.m
index d1a9d1b91c9c1dfb458357ea77239eb1925e3f89..28fb9ac5365435d82c490caaa4f0677e50573363 100644
--- a/src/MATLAB/+Load/OpenData.m
+++ b/src/MATLAB/+Load/OpenData.m
@@ -7,10 +7,10 @@
% EW - Rewrite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -31,9 +31,9 @@
function opened = OpenData()
global Figures Colors CONSTANTS
-softwareVersion = Helper.GetVersion();
+softwareVersion = Dev.GetVersion();
if(isempty(Figures))
- fprintf('LEVer ver %s\n***DO NOT DISTRIBUTE***\n\n', softwareVersion);
+ fprintf('%s\n***DO NOT DISTRIBUTE***\n\n', softwareVersion);
end
if(exist('ColorScheme.mat','file'))
@@ -128,26 +128,43 @@ switch answer
end
Load.SaveSettings(settings);
-
Load.AddConstant('matFullFile', [settings.matFilePath settings.matFile], 1);
- bQueryImageDir = false;
- if ( ~isfield(CONSTANTS,'imageNamePattern') )
- bQueryImageDir = true;
- elseif ( ~isfield(CONSTANTS,'primaryChannel') )
- [channelList, frameList] = Helper.GetImListInfo(CONSTANTS.rootImageFolder,CONSTANTS.imageNamePattern);
- bQueryImageDir = isempty(frameList);
- else
- bQueryImageDir = isempty(Helper.LoadPrimaryIntensityImage(1));
+ % Update imageData.DatasetName early enough to check for
+ % image/data match.
+ if ( isfield(CONSTANTS,'datasetName') )
+ oldName = CONSTANTS.datasetName;
+ if ( oldName(end) == '_' )
+ oldName = oldName(1:end-1);
+ end
+
+ Load.AddConstant('imageData.DatasetName',oldName,true);
end
- if ( bQueryImageDir )
- if (~Helper.ImageFileDialog())
+ imageData = MicroscopeData.ReadMetadataFile(fullfile(CONSTANTS.rootImageFolder, [Metadata.GetDatasetName() '.json']));
+ if ( isempty(imageData) )
+ tifList = dir(fullfile(CONSTANTS.rootImageFolder,'*.tif'));
+ if ( exist(CONSTANTS.rootImageFolder,'dir') && ~isempty(tifList) )
+ % Try to export or rename old lever image data
+ metadataPath = Load.ImageExportDialog(CONSTANTS.rootImageFolder,tifList(1).name);
+ if ( isempty(metadataPath) )
+ CONSTANTS = oldCONSTANTS;
+ return;
+ end
+
+ imageData = MicroscopeData.ReadMetadataFile(metadataPath);
+ Metadata.SetMetadata(imageData);
+
+ imageFolder = fileparts(metadataPath);
+ Load.AddConstant('rootImageFolder', imageFolder, 1);
+ elseif (~Helper.ImageFileDialog())
CONSTANTS = oldCONSTANTS;
return
end
+ else
+ Metadata.SetMetadata(imageData);
end
-
+
if(exist('objHulls','var'))
errordlg('Data too old to run with this version of LEVer');
CONSTANTS = oldCONSTANTS;
@@ -168,17 +185,20 @@ switch answer
ovwAns = questdlg('Old file format detected! Update required. Would you like to save the updated file to a new location?', ...
'Verision Update', ...
'Save As...','Overwrite','Overwrite');
-
+
+ bValidAns = false;
% Handle response
switch ovwAns
case 'Save As...'
- if ( ~UI.SaveDataAs(true) )
- warning(['File format must updated. Overwriting file: ' CONSTANTS.matFullFile]);
- Helper.SaveLEVerState(CONSTANTS.matFullFile);
- end
+ bValidAns = UI.SaveDataAs(true);
case 'Overwrite'
+ bValidAns = true;
Helper.SaveLEVerState(CONSTANTS.matFullFile);
- end
+ end
+
+ if ( ~bValidAns )
+ warning('Proceeding without updating file, be sure to save before exiting LEVer!');
+ end
end
UI.InitializeFigures();
diff --git a/src/MATLAB/+Load/QueryCellType.m b/src/MATLAB/+Load/QueryCellType.m
index 04756feb80ff39ef331d23749e6d95a410085a1d..eef2e870c2234bf2fd615418185042b2a6c4e692 100644
--- a/src/MATLAB/+Load/QueryCellType.m
+++ b/src/MATLAB/+Load/QueryCellType.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function cellType = QueryCellType()
SupportedTypes = Load.GetSupportedCellTypes();
diff --git a/src/MATLAB/+Load/ReadSettings.m b/src/MATLAB/+Load/ReadSettings.m
index 3246096c8340cb78e7231e6c69615c2d8395e928..0dc5e82482b05a0ec2a6b89a492fb9f35e369913 100644
--- a/src/MATLAB/+Load/ReadSettings.m
+++ b/src/MATLAB/+Load/ReadSettings.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function settings = ReadSettings()
settingsPath = 'LEVerSettings.mat';
if ( isdeployed() )
diff --git a/src/MATLAB/+Load/RemoveImagePixelsField.m b/src/MATLAB/+Load/RemoveImagePixelsField.m
index 9fb0fed1d3bc5aa0d3826bb550e14324e2470533..b2019cc45491b3e9372c3508bbff1c6ff3631b2a 100644
--- a/src/MATLAB/+Load/RemoveImagePixelsField.m
+++ b/src/MATLAB/+Load/RemoveImagePixelsField.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function RemoveImagePixelsField()
global CellHulls
diff --git a/src/MATLAB/+Load/RenameImages.m b/src/MATLAB/+Load/RenameImages.m
new file mode 100644
index 0000000000000000000000000000000000000000..37fc2c922ce95d3e9e0be8b28abc30f3a779a6ca
--- /dev/null
+++ b/src/MATLAB/+Load/RenameImages.m
@@ -0,0 +1,78 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function jsonPath = RenameImages(exportDir,inRoot, renameStruct, bCreateDatasetDir)
+ if ( ~exist('bCreateDatasetDir','var') )
+ bCreateDatasetDir = true;
+ end
+
+ fileOp = @(src,dst)(movefile(src,dst,'f'));
+ if ( ~strcmp(exportDir,inRoot) )
+ fileOp = @(src,dst)(copyfile(src,dst,'f'));
+
+ if ( bCreateDatasetDir )
+ exportDir = fullfile(exportDir,renameStruct.datasetName);
+ end
+ end
+ % fileOp = @(src,dst)(fprintf('%s -> %s\n', src,dst));
+
+ if ( ~exist(exportDir,'dir') )
+ mkdir(exportDir);
+ end
+
+ flist = dir(fullfile(inRoot,renameStruct.dirBlob));
+ nameList = {flist.name}.';
+
+ loadTok = regexp(nameList, renameStruct.loadPattern, 'tokens','once');
+
+ bValidParams = (renameStruct.paramOrder > 0);
+ paramIdx = find(bValidParams);
+ validOrder = paramIdx(renameStruct.paramOrder(bValidParams));
+
+ bValidNames = cellfun(@(x)(length(x)==nnz(bValidParams)), loadTok);
+ paramTok = vertcat(loadTok{bValidNames});
+
+ paramVals = ones(size(paramTok,1),length(renameStruct.paramOrder));
+ paramVals(:,validOrder) = cellfun(@(x)(str2double(x)), paramTok);
+
+ paramMin = min(paramVals,[],1);
+ paramOffset = 1 - paramMin;
+
+ validNames = nameList(bValidNames);
+ for i=1:length(validNames)
+ paramCell = num2cell(paramVals(i,:)+paramOffset);
+ outName = sprintf(renameStruct.outPattern,paramCell{:});
+
+ if ( strcmp(outName,validNames{i}) )
+ continue;
+ end
+
+ fileOp(fullfile(inRoot,validNames{i}),fullfile(exportDir,outName));
+ end
+
+ imageData = MicroscopeData.MakeMetadataFromFolder(exportDir,renameStruct.datasetName);
+ MicroscopeData.CreateMetadata(exportDir,imageData,true);
+
+ jsonPath = fullfile(exportDir,[renameStruct.datasetName '.json']);
+end
diff --git a/src/MATLAB/+Load/ReplaceConstant.m b/src/MATLAB/+Load/ReplaceConstant.m
index f4222f30f003a95dab4985ec2944225ac5a37215..ce39111bd91d2ea8418bff4f00536991a70f3e91 100644
--- a/src/MATLAB/+Load/ReplaceConstant.m
+++ b/src/MATLAB/+Load/ReplaceConstant.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function ReplaceConstant(curField, newField,newValue)
global CONSTANTS
@@ -8,6 +32,13 @@ function ReplaceConstant(curField, newField,newValue)
constFields = fieldnames(CONSTANTS);
curFieldIdx = find(strcmp(curField,constFields));
+ newFieldIdx = find(strcmp(newField,constFields));
+ if ( ~isempty(newFieldIdx) )
+ warning(['CONSTANTS.' newField ' already exists, removing ''' curField '']);
+ CONSTANTS = rmfield(CONSTANTS, curField);
+ return;
+ end
+
newFieldIdx = find(strcmp(newField,constFields));
if ( ~isempty(newFieldIdx) )
constFields = constFields(setdiff(1:length(constFields),newFieldIdx));
diff --git a/src/MATLAB/+Load/SaveSettings.m b/src/MATLAB/+Load/SaveSettings.m
index 215696ce5950630d0b8181a52851acad0eddf4bf..f2020a1dcb81f926abeb1085627677c1d61e934b 100644
--- a/src/MATLAB/+Load/SaveSettings.m
+++ b/src/MATLAB/+Load/SaveSettings.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function SaveSettings(settings)
save(settings.settingsPath, 'settings');
end
diff --git a/src/MATLAB/+Load/SetImageInfo.m b/src/MATLAB/+Load/SetImageInfo.m
index 1f78449da571393d998f859b9db36e2e55520235..392136c37c3adf129bc6b4e18d5c75565f2bb1a7 100644
--- a/src/MATLAB/+Load/SetImageInfo.m
+++ b/src/MATLAB/+Load/SetImageInfo.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function SetImageInfo()
global CONSTANTS
[channelList, frameList] = Helper.GetImListInfo(CONSTANTS.rootImageFolder, CONSTANTS.imageNamePattern);
diff --git a/src/MATLAB/+Load/SetWorkingDir.m b/src/MATLAB/+Load/SetWorkingDir.m
index adc766c1145dfa37c48dd1864778b90e2b39997e..706ae5747e194b2f63e7c95808f3ced8beb8b471 100644
--- a/src/MATLAB/+Load/SetWorkingDir.m
+++ b/src/MATLAB/+Load/SetWorkingDir.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function SetWorkingDir()
userDir = getenv('USERPROFILE');
if ( isempty(userDir) )
diff --git a/src/MATLAB/+Load/UpdatePhenotypeInfo.m b/src/MATLAB/+Load/UpdatePhenotypeInfo.m
index 0256ed7f06a1ecae4af49ca7984209aeb34711bd..794528441c0af1008599465e7cc22b62b690ac2e 100644
--- a/src/MATLAB/+Load/UpdatePhenotypeInfo.m
+++ b/src/MATLAB/+Load/UpdatePhenotypeInfo.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Families/FindFamiliesAfter.m b/src/MATLAB/+Metadata/GetDatasetName.m
similarity index 65%
rename from src/MATLAB/+Families/FindFamiliesAfter.m
rename to src/MATLAB/+Metadata/GetDatasetName.m
index 807c8ba9bf08ce0798e99448782415ecd60e146d..5626abdd4835083d0ca5daf5e5b7d4454af8d5de 100644
--- a/src/MATLAB/+Families/FindFamiliesAfter.m
+++ b/src/MATLAB/+Metadata/GetDatasetName.m
@@ -1,12 +1,10 @@
-% families = FindFamiliesAfter(trackID)
-% Find the set of families which start after the beginning of this track
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -24,10 +22,13 @@
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-function families = FindFamiliesAfter(trackID)
- global CellTracks CellFamilies
+function datasetName = GetDatasetName()
+ global CONSTANTS
- nefam = find(arrayfun(@(x)(~isempty(x.startTime)), CellFamilies));
+ datasetName = '';
+ if ( ~isfield(CONSTANTS,'imageData') )
+ return;
+ end
- families = nefam([CellFamilies(nefam).startTime] > CellTracks(trackID).startTime);
-end
\ No newline at end of file
+ datasetName = CONSTANTS.imageData.DatasetName;
+end
diff --git a/src/MATLAB/+Metadata/GetDimensions.m b/src/MATLAB/+Metadata/GetDimensions.m
new file mode 100644
index 0000000000000000000000000000000000000000..19583804d2778422c2d4c03874861612957bd82d
--- /dev/null
+++ b/src/MATLAB/+Metadata/GetDimensions.m
@@ -0,0 +1,48 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function dims = GetDimensions(dimOrder)
+ global CONSTANTS
+
+ if ( ~exist('dimOrder','var') )
+ dimOrder = 'xy';
+ end
+
+ dims = [];
+ if ( ~isfield(CONSTANTS,'imageData') )
+ return;
+ end
+
+ numDims = 3;
+ if ( CONSTANTS.imageData.Dimensions(3) == 1 )
+ numDims = 2;
+ end
+
+ selectedDims = 1:numDims;
+ if ( strcmpi(dimOrder,'rc') )
+ selectedDims = Utils.SwapXY_RC(selectedDims);
+ end
+
+ dims = CONSTANTS.imageData.Dimensions(selectedDims);
+end
diff --git a/src/MATLAB/+Metadata/GetImageInfo.m b/src/MATLAB/+Metadata/GetImageInfo.m
new file mode 100644
index 0000000000000000000000000000000000000000..81275132878fc89a6cfba81905e3b0fa07d54eff
--- /dev/null
+++ b/src/MATLAB/+Metadata/GetImageInfo.m
@@ -0,0 +1,34 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function imageData = GetImageInfo()
+ global CONSTANTS
+
+ imageData = [];
+ if ( ~isfield(CONSTANTS,'imageData') )
+ return;
+ end
+
+ imageData = CONSTANTS.imageData;
+end
diff --git a/src/MATLAB/+Metadata/GetNumberOfChannels.m b/src/MATLAB/+Metadata/GetNumberOfChannels.m
new file mode 100644
index 0000000000000000000000000000000000000000..f331fa0007f4a729537348e3ee34da2387448758
--- /dev/null
+++ b/src/MATLAB/+Metadata/GetNumberOfChannels.m
@@ -0,0 +1,34 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function numChannels = GetNumberOfChannels()
+ global CONSTANTS
+
+ numChannels = 0;
+ if ( ~isfield(CONSTANTS,'imageData') )
+ return;
+ end
+
+ numChannels = CONSTANTS.imageData.NumberOfChannels;
+end
diff --git a/src/MATLAB/+Metadata/GetNumberOfFrames.m b/src/MATLAB/+Metadata/GetNumberOfFrames.m
new file mode 100644
index 0000000000000000000000000000000000000000..f57e11e55868836522fcba9aff946bd00d7c0478
--- /dev/null
+++ b/src/MATLAB/+Metadata/GetNumberOfFrames.m
@@ -0,0 +1,34 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function numFrames = GetNumberOfFrames()
+ global CONSTANTS
+
+ numFrames = 0;
+ if ( ~isfield(CONSTANTS,'imageData') )
+ return;
+ end
+
+ numFrames = CONSTANTS.imageData.NumberOfFrames;
+end
diff --git a/src/MATLAB/+Metadata/GetPixelSize.m b/src/MATLAB/+Metadata/GetPixelSize.m
new file mode 100644
index 0000000000000000000000000000000000000000..b677f9024fe2b2b08b9da2e1381ceac2beb3e101
--- /dev/null
+++ b/src/MATLAB/+Metadata/GetPixelSize.m
@@ -0,0 +1,34 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function pixelSize = GetPixelSize()
+ global CONSTANTS
+
+ pixelSize = 0;
+ if ( ~isfield(CONSTANTS,'imageData') )
+ return;
+ end
+
+ pixelSize = CONSTANTS.imageData.PixelPhysicalSize;
+end
diff --git a/src/MATLAB/+Metadata/SetMetadata.m b/src/MATLAB/+Metadata/SetMetadata.m
new file mode 100644
index 0000000000000000000000000000000000000000..1d2d38c70df5eb5c12da03a3f896f24d2d69cb4f
--- /dev/null
+++ b/src/MATLAB/+Metadata/SetMetadata.m
@@ -0,0 +1,29 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function SetMetadata(imageData)
+ global CONSTANTS
+
+ CONSTANTS.imageData = imageData;
+end
\ No newline at end of file
diff --git a/src/MATLAB/+MicroscopeData/+Helper/CreateUniqueWordedPath.m b/src/MATLAB/+MicroscopeData/+Helper/CreateUniqueWordedPath.m
new file mode 100644
index 0000000000000000000000000000000000000000..80c66aa3ba2f292c38e7c5f95da703710b5387f8
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Helper/CreateUniqueWordedPath.m
@@ -0,0 +1,64 @@
+function newFilePath = CreateUniqueWordedPath(fPath)
+%newFilePath = CreateUniqueWordedPath(fPath)
+% Pass in a path with at least two directories with '\' seperating the
+% direcories, and a new path will be generated that removes the words that
+% are repeated. This forces the unique words closer to the file name or
+% most deep directory.
+
+driveIdx = find(fPath==':',1,'first');
+if (~isempty(driveIdx))
+ tmpPath = strtrim(MicroscopeData.Helper.SanitizeString(fPath(driveIdx+1:end)));
+ fPath = [fPath(1:driveIdx),tmpPath];
+else
+ fPath = strtrim(MicroscopeData.Helper.SanitizeString(fPath));
+end
+
+dirs = strsplit(fPath,'\');
+
+newDirs = {};
+for i=1:length(dirs)
+ if (strcmp(dirs{i},'.'))
+ continue
+ end
+ if (strcmp(dirs{i},'..'))
+ newDirs = newDirs(1:end-1);
+ continue
+ end
+ if (isempty(newDirs))
+ newDirs = dirs(i);
+ else
+ newDirs{end+1} = dirs{i};
+ end
+end
+
+dirs = newDirs;
+
+wordList = strsplit(dirs{end},' ');
+
+newFilePath = dirs{end};
+
+for i=length(dirs)-1:-1:1
+ curDir = dirs{i};
+ curWords = strsplit(curDir,' ');
+ keepWords = true(1,length(curWords));
+ for j=1:length(curWords)
+ if (any(strcmpi(curWords{j},wordList)))
+ keepWords(j) = false;
+ else
+ wordList{end+1} = curWords{j};
+ end
+ end
+
+ newDir = '';
+ for j=1:length(keepWords)
+ if (keepWords(j))
+ if (isempty(newDir))
+ newDir = strtrim(curWords{j});
+ else
+ newDir = sprintf('%s %s',newDir,strtrim(curWords{j}));
+ end
+ end
+ end
+ newFilePath = fullfile(newDir,newFilePath);
+end
+end
diff --git a/src/MATLAB/+MicroscopeData/+Helper/GetPixelTypeTIF.m b/src/MATLAB/+MicroscopeData/+Helper/GetPixelTypeTIF.m
new file mode 100644
index 0000000000000000000000000000000000000000..25247b9e1d4018aa97238dfa3930e8fe61a2fabf
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Helper/GetPixelTypeTIF.m
@@ -0,0 +1,37 @@
+% [pixelType,dataTypeLookup] = GetPixelTypeTIF(tifFile)
+
+function [pixelType,imInfo] = GetPixelTypeTIF(tifFile)
+ pixelType = [];
+
+ dataTypeLookup = {'uint8';'uint16';'uint32';'uint64';
+ 'int8';'int16';'int32';'int64';
+ 'single';'double';
+ 'logical'};
+
+ dataTypeSize = [1;2;4;8;
+ 1;2;4;8;
+ 4;8;
+ 1];
+
+ dataTypeFormat = {'Unsigned integer';'Unsigned integer';'Unsigned integer';'Unsigned integer';
+ 'Integer';'Integer';'Integer';'Integer';
+ 'IEEE floating point';'IEEE floating point';
+ 'Unsigned Integer'};
+
+ imInfo = imfinfo(tifFile,'tif');
+ sampleFormat = 'Unsigned integer';
+ if ( isfield(imInfo,'SampleFormat') )
+ sampleFormat = imInfo.SampleFormat;
+ end
+ bitDepth = imInfo.BitDepth;
+
+ bSizeMatch = (dataTypeSize == floor(bitDepth/8));
+ bSampleMatch = strcmpi(sampleFormat,dataTypeFormat);
+
+ formatIdx = find(bSizeMatch & bSampleMatch);
+ if ( isempty(formatIdx) )
+ return;
+ end
+
+ pixelType = dataTypeLookup{formatIdx};
+end
diff --git a/src/MATLAB/+MicroscopeData/+Helper/ParseReaderInputs.m b/src/MATLAB/+MicroscopeData/+Helper/ParseReaderInputs.m
new file mode 100644
index 0000000000000000000000000000000000000000..3e70080448e0f95ba717fd9cd8148fa7ab9b1eb8
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Helper/ParseReaderInputs.m
@@ -0,0 +1,43 @@
+function argStruct = ParseReaderInputs(varargin)
+ dataTypeLookup = {'uint8';'uint16';'uint32';'uint64';
+ 'int8';'int16';'int32';'int64';
+ 'single';'double';
+ 'logical'};
+
+ dataTypeSize = [1;2;4;8;
+ 1;2;4;8;
+ 4;8;
+ 1];
+
+ p = inputParser();
+ p.StructExpand = false;
+
+ % This is ridiculous, but we assume that the optional path is specified if
+ % length(varargin) is odd
+ if ( mod(length(varargin),2) == 1 )
+ addOptional(p,'path','', @ischar);
+ else
+ addParameter(p,'path','', @ischar);
+ end
+
+ addParameter(p,'imageData',[], @(x)(validOrEmpty(@isstruct,x)));
+
+ addParameter(p,'chanList',[], @(x)(validOrEmpty(@isvector,x)));
+ addParameter(p,'timeRange',[], @(x)(validOrEmpty(@(y)(numel(y)==2),x)));
+ addParameter(p,'roi_xyz',[], @(x)(validOrEmpty(@(y)(all(size(y)==[2,3])),x)));
+
+ addParameter(p,'outType',[], @(x)(validOrEmpty(@(y)(any(strcmp(y,dataTypeLookup))),x)));
+ addParameter(p,'normalize',false,@islogical);
+
+ addParameter(p,'verbose',false, @islogical);
+ addParameter(p,'prompt',[], @(x)(validOrEmpty(@islogical,x)));
+ addParameter(p,'promptTitle','', @ischar);
+
+ parse(p,varargin{:});
+ argStruct = p.Results;
+end
+
+% Inputs are valid if they are empty or if they satisfy their validity function
+function bValid = validOrEmpty(validFunc,x)
+ bValid = (isempty(x) || validFunc(x));
+end
diff --git a/src/MATLAB/+MicroscopeData/+Helper/SanitizeString.m b/src/MATLAB/+MicroscopeData/+Helper/SanitizeString.m
new file mode 100644
index 0000000000000000000000000000000000000000..43140f0e05b44030b01a2b61922b48b60c6ff507
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Helper/SanitizeString.m
@@ -0,0 +1,24 @@
+function [ str ] = SanitizeString( str )
+%SANITIZESTRING Summary of this function goes here
+% Detailed explanation goes here
+str = strrep(str, '!', '');
+str = strrep(str, '*', '');
+str = strrep(str, '''', '');
+str = strrep(str, '(', '');
+str = strrep(str, ')', '');
+str = strrep(str, ';', '');
+str = strrep(str, ':', '');
+str = strrep(str, '@', '');
+str = strrep(str, '&', '');
+str = strrep(str, '=', '');
+str = strrep(str, '+', '');
+str = strrep(str, '$', '');
+str = strrep(str, ',', '');
+str = strrep(str, '/', '');
+str = strrep(str, '?', '');
+str = strrep(str, '#', '');
+str = strrep(str, '[', '');
+str = strrep(str, ']', '');
+
+str = strtrim(str);
+end
diff --git a/src/MATLAB/+MicroscopeData/+Original/+BioFormats/CheckJarPath.m b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/CheckJarPath.m
new file mode 100644
index 0000000000000000000000000000000000000000..42ae0e4ee556b23c135446e4ecbc4693ab8ad5d8
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/CheckJarPath.m
@@ -0,0 +1,24 @@
+function CheckJarPath()
+%CHECKJARPATH Summary of this function goes here
+% Detailed explanation goes here
+
+%% ensure that the bioformats jar file is on the path
+dynamicPaths = javaclasspath('-dynamic');
+bfIsLoaded = false;
+if (~isempty(dynamicPaths))
+ for i=1:length(dynamicPaths)
+ [~,name,~] = fileparts(dynamicPaths{i});
+ if (strcmpi('bioformats_package',name))
+ bfIsLoaded = true;
+ break
+ end
+ end
+end
+
+if (~bfIsLoaded)
+ curPath = mfilename('fullpath');
+ [pathstr,~,~] = fileparts(curPath);
+ javaaddpath(fullfile(pathstr,'bioformats_package.jar'),'-end');
+end
+end
+
diff --git a/src/MATLAB/+MicroscopeData/+Original/+BioFormats/CheckJavaMemory.m b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/CheckJavaMemory.m
new file mode 100644
index 0000000000000000000000000000000000000000..92a2223060a7723abedfcaf22a295809a3ecb124
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/CheckJavaMemory.m
@@ -0,0 +1,54 @@
+function [] = bfCheckJavaMemory(varargin)
+% bfCheckJavaMemory warn if too little memory is allocated to Java
+%
+% SYNOPSIS bfCheckJavaMemory()
+%
+% Input
+%
+% minMemory - (Optional) The minimum suggested memory setting in MB.
+% Default: 512
+%
+% Output
+%
+% A warning message is printed if too little memory is allocated.
+
+% OME Bio-Formats package for reading and converting biological file formats.
+%
+% Copyright (C) 2014 Open Microscopy Environment:
+% - Board of Regents of the University of Wisconsin-Madison
+% - Glencoe Software, Inc.
+% - University of Dundee
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as
+% published by the Free Software Foundation, either version 2 of the
+% License, or (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License along
+% with this program; if not, write to the Free Software Foundation, Inc.,
+% 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+runtime = java.lang.Runtime.getRuntime();
+maxMemory = runtime.maxMemory() / (1024 * 1024);
+
+ip = inputParser;
+ip.addOptional('minMemory', 512, @isscalar);
+ip.parse(varargin{:});
+minMemory = ip.Results.minMemory;
+
+warningID = 'BF:lowJavaMemory';
+
+if maxMemory < minMemory - 64
+ warning_msg = [...
+ '*** Insufficient memory detected. ***\n'...
+ '*** %dm found ***\n'...
+ '*** %dm or greater is recommended ***\n'...
+ '*** See http://www.mathworks.com/matlabcentral/answers/92813 ***\n'...
+ '*** for instructions on increasing memory allocation. ***\n'];
+ warning(warningID, warning_msg, round(maxMemory), minMemory);
+end
diff --git a/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetImages.m b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetImages.m
new file mode 100644
index 0000000000000000000000000000000000000000..4ab4ffa76d764824df513dd1e15d88472cff579d
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetImages.m
@@ -0,0 +1,117 @@
+function [ seriesImages ] = GetImages( bfReader, seriesNum )
+%GETIMAGES Summary of this function goes here
+% Detailed explanation goes here
+
+numSeries = bfReader.getSeriesCount();
+
+omeMetadata = bfReader.getMetadataStore();
+prgs = Utils.CmdlnProgress(1,true);
+
+if (exist('seriesNum','var') && ~isempty(seriesNum) && numSeries>=seriesNum)
+ seriesImages = readSeriesImage(bfReader, seriesNum-1, omeMetadata, true, prgs);
+else
+ if (bfReader.getSeriesCount()>1)
+ prgs.SetMaxIterations(bfReader.getSeriesCount());
+
+ onlyOneSeries = false;
+ else
+ prgs.SetMaxIterations(numSeries);
+ onlyOneSeries = true;
+ end
+
+ for series=0:numSeries-1;
+ im = readSeriesImage(bfReader, series, omeMetadata, onlyOneSeries, prgs);
+
+ seriesImages{series+1} = im;
+
+ prgs.PrintProgress(series+1);
+ end
+end
+
+prgs.ClearProgress();
+end
+
+function im = readSeriesImage(bfReader, series, omeMetadata, onlyOneSeries, prgs)
+ bfReader.setSeries(series);
+
+ imageData = [];
+
+ imageData.Dimensions = [safeGetValue(omeMetadata.getPixelsSizeX(series));...
+ safeGetValue(omeMetadata.getPixelsSizeY(series));...
+ safeGetValue(omeMetadata.getPixelsSizeZ(series))];
+
+ imageData.NumberOfChannels = omeMetadata.getChannelCount(series);
+ imageData.NumberOfFrames = safeGetValue(omeMetadata.getPixelsSizeT(series));
+
+ clss = char(omeMetadata.getPixelsType(series));
+ if (strcmpi(clss,'float'))
+ clss = 'single';
+ end
+ im = zeros([Utils.SwapXY_RC(imageData.Dimensions'),imageData.NumberOfChannels,imageData.NumberOfFrames],clss);
+
+ order = char(omeMetadata.getPixelsDimensionOrder(series));
+
+ if (onlyOneSeries)
+ prgs.SetMaxIterations(imageData.NumberOfFrames*imageData.NumberOfChannels*imageData.Dimensions(3));
+ i = 1;
+ end
+
+ for t=1:imageData.NumberOfFrames
+ for z=1:imageData.Dimensions(3)
+ for c=1:imageData.NumberOfChannels
+ ind = calcPlaneInd(order,z,c,t,imageData);
+ im(:,:,z,c,t) = MicroscopeData.Original.BioFormats.GetPlane(bfReader,ind);
+
+ if (onlyOneSeries)
+ prgs.PrintProgress(i);
+ i = i+1;
+ end
+ end
+ end
+ end
+end
+
+function ind = calcPlaneInd(order,z,c,t,imageData)
+switch order(3)
+ case 'Z'
+ ind = z-1;
+ mul = imageData.Dimensions(3);
+ case 'C'
+ ind = c-1;
+ mul = imageData.NumberOfChannels;
+ case 'T'
+ ind = t-1;
+ mul = imageData.NumberOfFrames;
+end
+
+switch order(4)
+ case 'Z'
+ ind = ind + (z-1)*mul;
+ mul = imageData.Dimensions(3)*mul;
+ case 'C'
+ ind = ind + (c-1)*mul;
+ mul = imageData.NumberOfChannels*mul;
+ case 'T'
+ ind = ind + (t-1)*mul;
+ mul = imageData.NumberOfFrames*mul;
+end
+
+switch order(5)
+ case 'Z'
+ ind = ind + (z-1)*mul;
+ case 'C'
+ ind = ind + (c-1)*mul;
+ case 'T'
+ ind = ind + (t-1)*mul;
+end
+
+ind = ind +1;
+end
+
+function val = safeGetValue(varIn)
+if (isempty(varIn))
+ val = 0;
+ return
+end
+val = varIn.getValue();
+end
diff --git a/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetMetadata.m b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetMetadata.m
new file mode 100644
index 0000000000000000000000000000000000000000..decc62a844aa6268d813654caf1ad3b0808abf02
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetMetadata.m
@@ -0,0 +1,171 @@
+function [seriesMetadata, varargout] = GetMetadata( bfReader, datasetExt )
+%GETMETADATA Summary of this function goes here
+% Detailed explanation goes here
+
+seriesMetadata = {};
+
+if (~exist('datasetExt','var') || isempty(datasetExt))
+ datasetExt = '';
+end
+
+orgMetadata = bfReader.getSeriesMetadata();
+omeMetadata = bfReader.getMetadataStore();
+
+onlyOneSeries = true;
+if (bfReader.getSeriesCount()>1)
+ prgs = Utils.CmdlnProgress(bfReader.getSeriesCount(),true);
+ onlyOneSeries = false;
+end
+
+for series=0:bfReader.getSeriesCount()-1;
+ bfReader.setSeries(series);
+
+ imageData = [];
+
+ [~,imageData.DatasetName,~] = fileparts(char(omeMetadata.getImageName(series)));
+
+ imageData.Dimensions = [safeGetValue(omeMetadata.getPixelsSizeX(series)),...
+ safeGetValue(omeMetadata.getPixelsSizeY(series)),...
+ safeGetValue(omeMetadata.getPixelsSizeZ(series))];
+
+ imageData.NumberOfChannels = omeMetadata.getChannelCount(series);
+ imageData.NumberOfFrames = safeGetValue(omeMetadata.getPixelsSizeT(series));
+
+ xPixelPhysicalSize = safeGetValue(omeMetadata.getPixelsPhysicalSizeX(series));
+ if xPixelPhysicalSize==0
+ xPixelPhysicalSize = 1;
+ end
+
+ yPixelPhysicalSize = safeGetValue(omeMetadata.getPixelsPhysicalSizeY(series));
+ if yPixelPhysicalSize==0
+ yPixelPhysicalSize = 1;
+ end
+
+ zPixelPhysicalSize = safeGetValue(omeMetadata.getPixelsPhysicalSizeZ(series));
+ if zPixelPhysicalSize==0
+ zPixelPhysicalSize = 1;
+ end
+
+ imageData.PixelPhysicalSize = [xPixelPhysicalSize, yPixelPhysicalSize, zPixelPhysicalSize];
+
+ if (strcmp(datasetExt,'.czi'))
+ imageData.Position = [orgMetadata.get('Global Information|Image|S|Scene|Position|X #1'),...
+ orgMetadata.get('Global Information|Image|S|Scene|Position|Y #1'),...
+ orgMetadata.get('Global Information|Image|S|Scene|Position|Z #1')];
+ elseif (omeMetadata.getPlaneCount(series)>0)
+ imageData.Position = [double(omeMetadata.getPlanePositionX(series,0)),...
+ double(omeMetadata.getPlanePositionY(series,0)),...
+ double(omeMetadata.getPlanePositionZ(series,0))];
+ end
+
+ imageData.ChannelNames = cell(imageData.NumberOfChannels,1);
+ for c=1:imageData.NumberOfChannels
+ colr = char(omeMetadata.getChannelName(series,c-1));
+
+ if (isempty(colr))
+ colr = sprintf('Channel:%d',c);
+ end
+
+ imageData.ChannelNames{c} = colr;
+ end
+
+ imageData.StartCaptureDate = safeGetValue(omeMetadata.getImageAcquisitionDate(series));
+ ind = strfind(imageData.StartCaptureDate,'T');
+ if (~isempty(ind))
+ imageData.StartCaptureDate(ind) = ' ';
+ end
+
+ imageData.TimeStampDelta = 0;
+
+ order = char(omeMetadata.getPixelsDimensionOrder(series));
+
+ if (onlyOneSeries)
+ prgs = Utils.CmdlnProgress(imageData.NumberOfFrames*imageData.NumberOfChannels*imageData.Dimensions(3),true);
+ i = 1;
+ end
+
+ for t=1:imageData.NumberOfFrames
+ for z=1:imageData.Dimensions(3)
+ for c=1:imageData.NumberOfChannels
+ ind = calcPlaneInd(order,z,c,t,imageData);
+ try
+ delta = omeMetadata.getPlaneDeltaT(series,ind-1);
+ catch er
+ delta = [];
+ end
+ if (~isempty(delta))
+ imageData.TimeStampDelta(z,c,t) = delta.floatValue;
+ end
+ if (onlyOneSeries)
+ prgs.PrintProgress(i);
+ i = i+1;
+ end
+ end
+ end
+ end
+
+ if (size(imageData.TimeStampDelta,1)~=imageData.Dimensions(3) ||...
+ size(imageData.TimeStampDelta,2)~=imageData.NumberOfChannels || ...
+ size(imageData.TimeStampDelta,3)~=imageData.NumberOfFrames)
+ imageData = rmfield(imageData,'TimeStampDelta');
+ end
+
+ seriesMetadata{series+1} = imageData;
+
+ prgs.PrintProgress(series+1);
+end
+
+prgs.ClearProgress();
+
+if (nargout>1)
+ varargout{1} = omeMetadata;
+end
+if (nargout>2)
+ varargout{2} = orgMetadata;
+end
+end
+
+function ind = calcPlaneInd(order,z,c,t,imageData)
+switch order(3)
+ case 'Z'
+ ind = z-1;
+ mul = imageData.Dimensions(3);
+ case 'C'
+ ind = c-1;
+ mul = imageData.NumberOfChannels;
+ case 'T'
+ ind = t-1;
+ mul = imageData.NumberOfFrames;
+end
+
+switch order(4)
+ case 'Z'
+ ind = ind + (z-1)*mul;
+ mul = imageData.Dimensions(3)*mul;
+ case 'C'
+ ind = ind + (c-1)*mul;
+ mul = imageData.NumberOfChannels*mul;
+ case 'T'
+ ind = ind + (t-1)*mul;
+ mul = imageData.NumberOfFrames*mul;
+end
+
+switch order(5)
+ case 'Z'
+ ind = ind + (z-1)*mul;
+ case 'C'
+ ind = ind + (c-1)*mul;
+ case 'T'
+ ind = ind + (t-1)*mul;
+end
+
+ind = ind +1;
+end
+
+function val = safeGetValue(varIn)
+if (isempty(varIn))
+ val = 0;
+ return
+end
+val = varIn.getValue();
+end
diff --git a/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetPlane.m b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetPlane.m
new file mode 100644
index 0000000000000000000000000000000000000000..8794cc475b4a03b382b45c0a2dbbeb966be96e0e
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetPlane.m
@@ -0,0 +1,110 @@
+function I = GetPlane(r, iPlane, varargin)
+% BFGETPLANE Retrieve the plane data from a reader using Bio-Formats
+%
+% I = bfGetPlane(r, iPlane) returns a specified plane from the input
+% format reader. The index specifying the plane to retrieve should be
+% contained between 1 and the number of planes for the series.
+%
+% I = bfGetPlane(r, iPlane, x, y, width, height) only returns the tile
+% which origin is specified by (x, y) and dimensions are specified by
+% (width, height).
+%
+% Examples
+%
+% I = bfGetPlane(r, 1) % First plane of the series
+% I = bfGetPlane(r, r.getImageCount()) % Last plane of the series
+% I = bfGetPlane(r, 1, 1, 1, 20, 20) % 20x20 tile originated at (0, 0)
+%
+% See also: BFGETREADER
+
+% OME Bio-Formats package for reading and converting biological file formats.
+%
+% Copyright (C) 2012 - 2014 Open Microscopy Environment:
+% - Board of Regents of the University of Wisconsin-Madison
+% - Glencoe Software, Inc.
+% - University of Dundee
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as
+% published by the Free Software Foundation, either version 2 of the
+% License, or (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License along
+% with this program; if not, write to the Free Software Foundation, Inc.,
+% 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+% Input check
+ip = inputParser;
+ip.addRequired('r', @(x) isa(x, 'loci.formats.IFormatReader') && ...
+ ~isempty(x.getCurrentFile()));
+ip.parse(r);
+
+% Plane check
+isValidPlane = @(x) isscalar(x) && ismember(x, 1 : r.getImageCount());
+ip.addRequired('iPlane', isValidPlane);
+
+% Optional tile arguments check
+isValidX = @(x) isscalar(x) && ismember(x, 1 : r.getSizeX());
+isValidY = @(x) isscalar(x) && ismember(x, 1 : r.getSizeY());
+ip.addOptional('x', 1, isValidX);
+ip.addOptional('y', 1, isValidY);
+ip.addOptional('width', r.getSizeX(), isValidX);
+ip.addOptional('height', r.getSizeY(), isValidY);
+ip.parse(r, iPlane, varargin{:});
+
+% Additional check for tile size
+assert(ip.Results.x - 1 + ip.Results.width <= r.getSizeX(),...
+ 'MATLAB:InputParser:ArgumentFailedValidation',...
+ 'Invalid tile size');
+assert(ip.Results.y - 1 + ip.Results.height <= r.getSizeY(),...
+ 'MATLAB:InputParser:ArgumentFailedValidation',...
+ 'Invalid tile size');
+
+% Get pixel type
+pixelType = r.getPixelType();
+bpp = loci.formats.FormatTools.getBytesPerPixel(pixelType);
+fp = loci.formats.FormatTools.isFloatingPoint(pixelType);
+sgn = loci.formats.FormatTools.isSigned(pixelType);
+little = r.isLittleEndian();
+
+plane = r.openBytes(iPlane - 1, ip.Results.x - 1, ip.Results.y - 1, ...
+ ip.Results.width, ip.Results.height);
+
+% convert byte array to MATLAB image
+if sgn
+ % can get the data directly to a matrix
+ I = loci.common.DataTools.makeDataArray2D(plane, ...
+ bpp, fp, little, ip.Results.height);
+else
+ % get the data as a vector, either because makeDataArray2D
+ % is not available, or we need a vector for typecast
+ I = loci.common.DataTools.makeDataArray(plane, ...
+ bpp, fp, little);
+end
+
+% Java does not have explicitly unsigned data types;
+% hence, we must inform MATLAB when the data is unsigned
+if ~sgn
+ % NB: arr will always be a vector here
+ switch class(I)
+ case 'int8'
+ I = typecast(I, 'uint8');
+ case 'int16'
+ I = typecast(I, 'uint16');
+ case 'int32'
+ I = typecast(I, 'uint32');
+ case 'int64'
+ I = typecast(I, 'uint64');
+ end
+end
+
+if isvector(I)
+ % convert results from vector to matrix
+ shape = [ip.Results.width ip.Results.height];
+ I = reshape(I, shape)';
+end
diff --git a/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetReader.m b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetReader.m
new file mode 100644
index 0000000000000000000000000000000000000000..80d105a429965219a77bda69109675aa5b95a359
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Original/+BioFormats/GetReader.m
@@ -0,0 +1,22 @@
+function [ bfReader ] = GetReader( fullPath )
+%GETSERIESDATA Summary of this function goes here
+% Detailed explanation goes here
+
+%% read data using bioformats
+MicroscopeData.Original.BioFormats.CheckJavaMemory();
+loci.common.DebugTools.enableLogging('INFO');
+
+bfReader = loci.formats.ChannelFiller();
+bfReader = loci.formats.ChannelSeparator(bfReader);
+OMEXMLService = loci.formats.services.OMEXMLServiceImpl();
+bfReader.setMetadataStore(OMEXMLService.createOMEXMLMetadata());
+
+try
+ bfReader.setId(fullPath);
+catch err
+ warning(err.message);
+ bfReader = [];
+end
+
+end
+
diff --git a/src/MATLAB/+MicroscopeData/+Original/CanExportFormat.m b/src/MATLAB/+MicroscopeData/+Original/CanExportFormat.m
new file mode 100644
index 0000000000000000000000000000000000000000..6ad68667b7a1b8a6012d8322de3dc7b913dc4fb8
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Original/CanExportFormat.m
@@ -0,0 +1,31 @@
+% [bCanExport,guessType] = CanExportFormat(filenames)
+%
+% bCanExport - True for all filenames that match a bioformats supported extension
+% guessType - Cell arry of strings representing a guess at the associated file type
+
+function [bCanExport,guessType] = CanExportFormat(filenames)
+ exportFormats = MicroscopeData.Original.GetSupportedFormats();
+ formatIdx = arrayfun(@(x,y)(repmat(y,length(x{1}),1)),exportFormats(:,2),(1:size(exportFormats,1)).', 'UniformOutput',false);
+
+ allExt = vertcat(exportFormats{:,2});
+ allIdx = vertcat(formatIdx{:});
+
+ [chkExt,idxExt] = unique(allExt);
+ chkIdx = allIdx(idxExt);
+
+ % Can use strncmpi to quickly check extension matches on reversed filenames
+ revExt = cellfun(@(x)(x(end:-1:1)),chkExt, 'UniformOutput',false);
+ revNames = cellfun(@(x)(x(end:-1:1)),filenames, 'UniformOutput',false);
+
+ bCanExport = false(length(filenames),1);
+ guessType = cell(length(filenames),1);
+
+ matchExt = cellfun(@(x)(find(strncmpi(revNames,x,length(x)))),revExt,'UniformOutput',false);
+ matchFormatIdx = arrayfun(@(x,y)(repmat(y,length(x{1}),1)),matchExt,chkIdx,'UniformOutput',false);
+
+ matchedIdx = vertcat(matchExt{:});
+ matchedFormats = vertcat(matchFormatIdx{:});
+
+ bCanExport(matchedIdx) = true;
+ guessType(matchedIdx) = exportFormats(matchedFormats,1);
+end
diff --git a/src/MATLAB/+MicroscopeData/+Original/Convert2Tiffs.m b/src/MATLAB/+MicroscopeData/+Original/Convert2Tiffs.m
new file mode 100644
index 0000000000000000000000000000000000000000..b3863dfb33c7f16166d2e484f03195b4f515ddd2
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Original/Convert2Tiffs.m
@@ -0,0 +1,75 @@
+function [ im, imD ] = Convert2Tiffs( imDir, imName, outDir, overwrite, quiet, cleanName)
+%[ im, imD ] = Convert2Tiffs( imDir, imName, outDir, overwrite, quiet, cleanName)
+
+im = [];
+imD = [];
+
+if (~exist('overwrite','var') || isempty(overwrite))
+ overwrite = false;
+end
+if (~exist('quiet','var') || isempty(quiet))
+ quiet = false;
+end
+
+if (~exist('imDir','var') || isempty(imDir))
+ imDir = '.';
+end
+
+if (~exist('imName','var') || isempty(imName))
+ [imName,imDir,~] = uigetfile('*.*','Choose a Microscope File to Convert');
+ if (imName==0)
+ warning('Nothing read');
+ return
+ end
+end
+
+if (~exist('outDir','var') || isempty(outDir))
+ outDir = uigetdir('.','Choose a folder to output to');
+ if (outDir==0)
+ warning('No where to write!');
+ return
+ end
+end
+
+if (~exist('cleanName','var') || isempty(cleanName))
+ cleanName = false;
+end
+
+if (cleanName)
+ outDir = MicroscopeData.Helper.CreateUniqueWordedPath(outDir);
+end
+
+[~,name,~] = fileparts(imName);
+
+if (~exist(fullfile(outDir,name),'dir') || overwrite)
+
+ imD = MicroscopeData.Original.ReadMetadata(imDir,imName);
+ if ( isempty(imD) )
+ return;
+ end
+
+ if (length(imD)>1)
+ [~,datasetName,~] = fileparts(imName);
+ if (cleanName)
+ datasetName = MicroscopeData.Helper.SanitizeString(datasetName);
+ end
+ outDir = fullfile(outDir,datasetName);
+ end
+
+ % Don't overwrite images that already exist
+ if (exist(fullfile(outDir,imD{1}.DatasetName),'dir') && ~overwrite)
+ return;
+ end
+
+ im = MicroscopeData.Original.ReadImages(imDir,imName);
+ for i=1:length(imD)
+ if (cleanName)
+ imD{i}.DatasetName = MicroscopeData.Helper.SanitizeString(imD{i}.DatasetName);
+ end
+ if (~exist(fullfile(outDir,imD{i}.DatasetName),'dir') || overwrite)
+ MicroscopeData.Writer(im{i},fullfile(outDir,imD{i}.DatasetName),imD{i},[],[],[],quiet);
+ end
+ end
+end
+end
+
diff --git a/src/MATLAB/+MicroscopeData/+Original/GetSupportedFormats.m b/src/MATLAB/+MicroscopeData/+Original/GetSupportedFormats.m
new file mode 100644
index 0000000000000000000000000000000000000000..aef1a75495a2ff02f6f7858499b0c87a6923fa47
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Original/GetSupportedFormats.m
@@ -0,0 +1,294 @@
+% This is just a big list of names and associated extensions supported by bioformats; based on their website:
+% https://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html.
+
+function formats = GetSupportedFormats()
+ extensions = {{'.gif'};
+ {'.jpg'};
+ {'.jp2'};
+ {'.png'};
+ {'.txt'};
+ {'.tif';'.tiff'};
+ {'.bmp'};
+
+ {'.sld'};
+ {'.tif'};
+ {'.aim'};
+ {'.al3d'};
+ {'.gel'};
+ {'.am';'.amiramesh';'.grey';'.hx';'.labels'};
+ {'.cif'};
+ {'.img';'.hdr'};
+ {'.png'};
+ {'.afi';'.svs'};
+ {'.svs'};
+ {'.htd';'.pnl'};
+ {'.avi'};
+ {'.arf'};
+ {'.exp';'.tif'};
+ {'.sdt'};
+ {'.1sc'};
+ {'.pic';'.raw';'.xml'};
+ {'.scn'};
+ {'.ims'};
+ { };
+ {'.img'};
+ {'.cr2';'.crw'};
+ {'.ch5'};
+ {'.c01';'.dib'};
+ {'.vsi'};
+ {'.xml';'.tif'};
+ {'.dv';'.r3d'};
+ {'.dcm';'.dicom'};
+ {'.v'};
+ {'.eps';'.epsi';'.ps'};
+ {'.flex';'.mea';'.res'};
+ {'.img'};
+ {'.tiff'};
+ {'.fits'};
+ {'.dm3';'.dm4'};
+ {'.dm2'};
+ {'.naf'};
+ {'.his'};
+ {'.ndpi';'.ndpis'};
+ {'.vms'};
+ {'.txt';'.tif';'.bmp';'.jpg'};
+ {'.i2i'};
+ {'.ics';'.ids'};
+ {'.fff'};
+ {'.seq'};
+ {'.ipw'};
+ {'.hed';'.img'};
+ {'.mod'};
+ {'.liff'};
+ {'.raw'};
+ {'.tif'};
+ {'.obf';'.msr'};
+ {'.xdce';'.tif'};
+ {'.frm'};
+ {'.inr'};
+ {'.hdr'};
+ {'.ipl'};
+ {'.ipm'};
+ {'.dat';'.img';'.par'};
+ {'.jpk'};
+ {'.jpx'};
+ {'.xv'};
+ {'.bip'};
+ {'.fli'};
+ {'.msr'};
+ {'.lei';'.tif'};
+ {'.lif'};
+ {'.scn'};
+ {'.sxm'};
+ {'.l2d';'.tif';'.scn'};
+ {'.lim'};
+ {'.tiff'};
+ {'.stk';'.nd'};
+ {'.tif'};
+ {'.tif';'.txt';'.xml'};
+ {'.mnc'};
+ {'.mrw'};
+ {'.mng'};
+ {'.stp'};
+ {'.mrc'};
+ {'.nef';'.tif'};
+ {'.img';'.hdr'};
+ {'.tiff'};
+ {'.tiff'};
+ {'.nd2'};
+ {'.nrrd';'.nhdr';'.raw';'.txt'};
+ {'.apl';'.mtb';'.tnb';'.tif';'.obsep'};
+ {'.oib';'.oif'};
+ {'.tif'};
+ {'.xml';'.dat';'.tif'};
+ {'.tiff'};
+ {'.ome.tiff'};
+ {'.ome';'.ome.xml'};
+ {'.top'};
+ {'.pcoraw';'.rec'};
+ {'.pcx'};
+ {'.pds'};
+ {'.im3'};
+ {'.tiff';'.xml'};
+ {'.tif';'.2';'.3';'.4'};
+ {'.pbm';'.pgm';'.ppm'};
+ {'.psd'};
+ {'.tif';'.tiff'};
+ {'.bin'};
+ {'.pict'};
+ {'.tif';'.xml';'.cfg'};
+ {'.afm'};
+ {'.mov'};
+ {'.sm2';'.sm3'};
+ { };
+ {'.xqd';'.xqf'};
+ {'.cxd'};
+ {'.tiff'};
+ { };
+ {'.spi';'.stk'};
+ {'.tga'};
+ {'.vws'};
+ {'.tfr';'.ffr';'.zfr';'.zfp';'.2fl'};
+ {'.tif';'.sld';'.jpg'};
+ {'.pr3'};
+ {'.dat';'.hdr'};
+ {'.fdf'};
+ {'.hdf'};
+ {'.dti'};
+ {'.xys';'.html'};
+ {'.mvd2'};
+ {'.acff'};
+ {'.wat'};
+ {'.wlz'};
+ {'.lms'};
+ {'.xml';'.tiff'};
+ {'.zvi'};
+ {'.czi'};
+ {'.lsm';'.mdb'}};
+
+ names = {'GIF (Graphics Interchange Format)';
+ 'JPEG';
+ 'JPEG 2000';
+ 'PNG (Portable Network Graphics)';
+ 'Text';
+ 'TIFF (Tagged Image File Format)';
+ 'Windows Bitmap';
+
+ '3i SlideBook';
+ 'Andor Bio-Imaging Division (ABD) TIFF';
+ 'AIM';
+ 'Alicona 3D';
+ 'Amersham Biosciences Gel';
+ 'Amira Mesh';
+ 'Amnis FlowSight';
+ 'Analyze 7.5';
+ 'Animated PNG';
+ 'Aperio AFI';
+ 'Aperio SVS TIFF';
+ 'Applied Precision CellWorX';
+ 'AVI (Audio Video Interleave)';
+ 'Axon Raw Format';
+ 'BD Pathway';
+ 'Becker & Hickl SPCImage';
+ 'Bio-Rad Gel';
+ 'Bio-Rad PIC';
+ 'Bio-Rad SCN';
+ 'Bitplane Imaris';
+ 'Bruker MRI';
+ 'Burleigh';
+ 'Canon DNG';
+ 'CellH5';
+ 'Cellomics';
+ 'cellSens VSI';
+ 'CellVoyager';
+ 'DeltaVision';
+ 'DICOM';
+ 'ECAT7';
+ 'EPS (Encapsulated PostScript)';
+ 'Evotec/PerkinElmer Opera Flex';
+ 'FEI';
+ 'FEI TIFF';
+ 'FITS (Flexible Image Transport System)';
+ 'Gatan Digital Micrograph';
+ 'Gatan Digital Micrograph 2';
+ 'Hamamatsu Aquacosmos NAF';
+ 'Hamamatsu HIS';
+ 'Hamamatsu ndpi';
+ 'Hamamatsu VMS';
+ 'Hitachi S-4800';
+ 'I2I';
+ 'ICS (Image Cytometry Standard)';
+ 'Imacon';
+ 'ImagePro Sequence';
+ 'ImagePro Workspace';
+ 'IMAGIC';
+ 'IMOD';
+ 'Improvision Openlab LIFF';
+ 'Improvision Openlab Raw';
+ 'Improvision TIFF';
+ 'Imspector OBF';
+ 'InCell 1000/2000';
+ 'InCell 3000';
+ 'INR';
+ 'Inveon';
+ 'IPLab';
+ 'IVision';
+ 'JEOL';
+ 'JPK';
+ 'JPX';
+ 'Khoros VIFF (Visualization Image File Format) Bitmap';
+ 'Kodak BIP';
+ 'Lambert Instruments FLIM';
+ 'LaVision Imspector';
+ 'Leica LCS LEI';
+ 'Leica LAS AF LIF (Leica Image File Format)';
+ 'Leica SCN';
+ 'LEO';
+ 'Li-Cor L2D';
+ 'LIM (Laboratory Imaging/Nikon)';
+ 'MetaMorph 7.5 TIFF';
+ 'MetaMorph Stack (STK)';
+ 'MIAS (Maia Scientific)';
+ 'Micro-Manager';
+ 'MINC MRI';
+ 'Minolta MRW';
+ 'MNG (Multiple-image Network Graphics)';
+ 'Molecular Imaging';
+ 'MRC (Medical Research Council)';
+ 'NEF (Nikon Electronic Format)';
+ 'NIfTI';
+ 'Nikon Elements TIFF';
+ 'Nikon EZ-C1 TIFF';
+ 'Nikon NIS-Elements ND2';
+ 'NRRD (Nearly Raw Raster Data)';
+ 'Olympus CellR/APL';
+ 'Olympus FluoView FV1000';
+ 'Olympus FluoView TIFF';
+ 'Olympus ScanR';
+ 'Olympus SIS TIFF';
+ 'OME-TIFF';
+ 'OME-XML';
+ 'Oxford Instruments';
+ 'PCORAW';
+ 'PCX (PC Paintbrush)';
+ 'Perkin Elmer Densitometer';
+ 'PerkinElmer Nuance';
+ 'PerkinElmer Operetta';
+ 'PerkinElmer UltraVIEW';
+ 'Portable Any Map';
+ 'Adobe Photoshop PSD';
+ 'Photoshop TIFF';
+ 'PicoQuant Bin';
+ 'PICT (Macintosh Picture)';
+ 'Prairie Technologies TIFF';
+ 'Quesant';
+ 'QuickTime Movie';
+ 'RHK';
+ 'SBIG';
+ 'Seiko';
+ 'SimplePCI & HCImage';
+ 'SimplePCI & HCImage TIFF';
+ 'SM Camera';
+ 'SPIDER';
+ 'Targa';
+ 'TillPhotonics TillVision';
+ 'Topometrix';
+ 'Trestle';
+ 'UBM';
+ 'Unisoku';
+ 'Varian FDF';
+ 'Veeco AFM';
+ 'VG SAM';
+ 'VisiTech XYS';
+ 'Volocity';
+ 'Volocity Library Clipping';
+ 'WA-TOP';
+ 'Woolz';
+ 'Zeiss Axio CSM';
+ 'Zeiss AxioVision TIFF';
+ 'Zeiss AxioVision ZVI (Zeiss Vision Image)';
+ 'Zeiss CZI';
+ 'Zeiss LSM (Laser Scanning Microscope) 510/710'};
+
+ formats = [names extensions];
+end
diff --git a/src/MATLAB/+MicroscopeData/+Original/ReadImages.m b/src/MATLAB/+MicroscopeData/+Original/ReadImages.m
new file mode 100644
index 0000000000000000000000000000000000000000..70732a9ceafa2e4164e09e56fce0c206bc236db1
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Original/ReadImages.m
@@ -0,0 +1,37 @@
+function [ seriesImages ] = ReadImages( dirIn, fileNameIn, seriesNum )
+%READIMAGES [seriesImages] = ReadImages(dirIn, fileNameIn)
+%This function will read in data generated by a microscope and return the
+%image data along with the metadata associated with each of the images.
+% dirIn and fileNameIn are both optional arguments where if either are
+% empty, a get file dialog will appear.
+%
+% Microscope data may contain more than one set of images thus the output
+% of this function will each be cells. Each cell will contain the image
+% data for each microscope run. There are more than one "series" typically
+% when there are multiple stage positions that are being captured over an
+% experiment.
+
+%% get file and properties
+if (~exist('dirIn','var') || ~exist('fileNameIn','var') || isempty(dirIn) || isempty(fileNameIn))
+ [fileNameIn,dirIn,~] = uigetfile('*.*','Select Microscope Data');
+ if (fileNameIn==0)
+ warning('No images read');
+ return
+ end
+end
+
+if (~exist('seriesNum','var'))
+ seriesNum = [];
+end
+
+[datasetPath,datasetName,datasetExt] = fileparts(fullfile(dirIn,fileNameIn));
+
+MicroscopeData.Original.BioFormats.CheckJarPath();
+
+bfReader = MicroscopeData.Original.BioFormats.GetReader(fullfile(datasetPath,[datasetName,datasetExt]));
+
+seriesImages = MicroscopeData.Original.BioFormats.GetImages(bfReader,seriesNum);
+
+bfReader.close();
+end
+
diff --git a/src/MATLAB/+MicroscopeData/+Original/ReadMetadata.m b/src/MATLAB/+MicroscopeData/+Original/ReadMetadata.m
new file mode 100644
index 0000000000000000000000000000000000000000..bebfdb2e1b8aeb0f05acef01b3975c05b26036ce
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/+Original/ReadMetadata.m
@@ -0,0 +1,46 @@
+function [ seriesMetaData, varargout ] = ReadMetadata( dirIn, fileNameIn )
+%READMETADATA [seriesMetadata] = ReadData(dirIn, fileNameIn)
+%This function will read in data generated by a microscope and return the
+%image data along with the metadata associated with each of the images.
+% dirIn and fileNameIn are both optional arguments where if either are
+% empty, a get file dialog will appear.
+%
+% Microscope data may contain more than one set of images thus the output
+% of this function will each be cells. Each cell will contain the associated
+% metadata for each microscope run. There are more than one "series"
+% typically when there are multiple stage positions that are being captured
+% over an experiment.
+
+%% get file and properties
+if (~exist('dirIn','var') || ~exist('fileNameIn','var') || isempty(dirIn) || isempty(fileNameIn))
+ [fileNameIn,dirIn,~] = uigetfile('*.*','Select Microscope Data');
+ if (fileNameIn==0)
+ warning('No images read');
+ return
+ end
+end
+
+[datasetPath,datasetName,datasetExt] = fileparts(fullfile(dirIn,fileNameIn));
+
+MicroscopeData.Original.BioFormats.CheckJarPath();
+
+bfReader = MicroscopeData.Original.BioFormats.GetReader(fullfile(datasetPath,[datasetName,datasetExt]));
+
+if (~isempty(bfReader))
+ [seriesMetaData, omeMetaData, orgMetaData] = MicroscopeData.Original.BioFormats.GetMetadata(bfReader,datasetExt);
+ bfReader.close();
+else
+ seriesMetaData = [];
+ omeMetaData = [];
+ orgMetaData = [];
+end
+
+if (nargout>1)
+ varargout{1} = omeMetaData;
+end
+if (nargout>2)
+ varargout{2} = orgMetaData;
+end
+
+end
+
diff --git a/src/MATLAB/+MicroscopeData/CreateMetadata.m b/src/MATLAB/+MicroscopeData/CreateMetadata.m
new file mode 100644
index 0000000000000000000000000000000000000000..d163e93a166e0052a4085b7a0b95734930d9c240
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/CreateMetadata.m
@@ -0,0 +1,43 @@
+function CreateMetadata(root,imageData,quiet)
+
+if (isempty(root))
+ if (isfield(imageData,'imageDir'))
+ openDir = imageData.imageDir;
+ else
+ openDir = [];
+ end
+ root = uigetdir(openDir,'Directory to Place Metadata');
+ if (root==0)
+ return
+ end
+end
+
+if (~exist(root,'dir'))
+ mkdir(root);
+end
+
+if (~exist('quiet','var') || isempty(quiet))
+ quiet = 0;
+end
+
+fileName = fullfile(root,[imageData.DatasetName '.json']);
+
+if (~quiet)
+ fprintf('Creating Metadata %s...',fileName);
+end
+
+if (isfield(imageData,'imageDir'))
+ imageData = rmfield(imageData,'imageDir');
+end
+
+jsonMetadata = Utils.CreateJSON(imageData);
+fileHandle = fopen(fileName,'wt');
+
+fwrite(fileHandle, jsonMetadata, 'char');
+
+fclose(fileHandle);
+
+if (~quiet)
+ fprintf('Done\n');
+end
+end
\ No newline at end of file
diff --git a/src/MATLAB/+MicroscopeData/GetEmptyMetadata.m b/src/MATLAB/+MicroscopeData/GetEmptyMetadata.m
new file mode 100644
index 0000000000000000000000000000000000000000..5431d4e2aa83307b2f50041d123431f479bbe18c
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/GetEmptyMetadata.m
@@ -0,0 +1,21 @@
+function imageData = GetEmptyMetadata()
+imageData = struct('DatasetName',{''},...
+ 'Dimensions',{[0,0,0]},...
+ 'NumberOfChannels',{0},...
+ 'NumberOfFrames',{0},...
+ 'PixelPhysicalSize',{[1,1,1]},...
+ 'ChannelNames',{''},...
+ 'StartCaptureDate',{},...
+ 'ChannelColors',{[]},...
+ 'PixelFormat',{''});
+
+imageData(1).DatasetName = '';
+imageData.Dimensions = [0,0,0];
+imageData.NumberOfChannels = 0;
+imageData.NumberOfFrames = 0;
+imageData.PixelPhysicalSize = [0,0,0];
+imageData.ChannelNames = '';
+imageData.StartCaptureDate = '';
+imageData.ChannelColors = [];
+imageData.PixelFormat = 'none';
+end
\ No newline at end of file
diff --git a/src/MATLAB/+MicroscopeData/MakeMetadataFromFolder.m b/src/MATLAB/+MicroscopeData/MakeMetadataFromFolder.m
new file mode 100644
index 0000000000000000000000000000000000000000..5bff00d2817e5fb6e9fd82e664ca101adfa98999
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/MakeMetadataFromFolder.m
@@ -0,0 +1,42 @@
+function imageData = MakeMetadataFromFolder(rootDir,datasetName)
+ imageData = MicroscopeData.GetEmptyMetadata();
+
+ tifList = dir(fullfile(rootDir,[datasetName '*.tif']));
+ nameList = {tifList.name}.';
+
+ prefixStr = regexptranslate('escape',datasetName);
+
+ tokMatch = regexp(nameList, [prefixStr '_c(\d+)_t(\d+)_z(\d+)\.tif'], 'tokens','once');
+
+ bValidTok = cellfun(@(x)(length(x)==3), tokMatch);
+ chkTok = vertcat(tokMatch{bValidTok});
+
+ ctzVals = cellfun(@(x)(str2double(x)), chkTok);
+
+ ctzMax = max(ctzVals,[],1);
+
+ chkFilename = sprintf('%s_c%02d_t%04d_z%04d.tif', datasetName,1,1,1);
+ imInfo = imfinfo(fullfile(rootDir,chkFilename));
+
+ imageData.DatasetName = datasetName;
+ imageData.Dimensions = [imInfo.Width, imInfo.Height, ctzMax(3)];
+ imageData.NumberOfChannels = ctzMax(1);
+ imageData.NumberOfFrames = ctzMax(2);
+ imageData.PixelPhysicalSize = [1,1,1];
+
+ colors = [1,0,0;...
+ 0,1,0;...
+ 0,0,1;...
+ 0,1,1;...
+ 1,0,1;...
+ 1,1,0];
+
+ for c=1:imageData.NumberOfChannels
+ imageData.ChannelNames = [imageData.ChannelNames; {sprintf('Channel %d',c)}];
+ colidx = mod(c,size(colors,1));
+ imageData.ChannelColors = vertcat(imageData.ChannelColors,colors(colidx,:));
+ end
+
+ imageData.StartCaptureDate = datestr(now,'yyyy-mm-dd HH:MM:SS');
+ imageData.PixelFormat = MicroscopeData.Helper.GetPixelTypeTIF(fullfile(rootDir,chkFilename));
+end
diff --git a/src/MATLAB/+MicroscopeData/ReadMetadata.m b/src/MATLAB/+MicroscopeData/ReadMetadata.m
new file mode 100644
index 0000000000000000000000000000000000000000..708499193262c55613445264ce5c89a3e23bfdfa
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/ReadMetadata.m
@@ -0,0 +1,46 @@
+function [imageData,jsonDir,jsonFile] = ReadMetadata(root,forcePrompt,promptTitle)
+
+imageData = [];
+jsonDir = [];
+jsonFile = [];
+
+if ( ~exist('promptTitle','var') )
+ promptTitle = [];
+end
+
+if (~exist('forcePrompt','var'))
+ forcePrompt = [];
+end
+
+if (~exist('root','var') || isempty(root))
+ root = '';
+end
+
+if (~isempty(root) && ~any(strcmp(root(end),{'\','/'})) && exist(root,'dir'))
+ root = fullfile(root, filesep);
+end
+
+% This is to help when the filename might have '.' whithin them
+% TODO rework this logic %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+if (exist([root,'.json'],'file'))
+ root = [root,'.json'];
+end
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+bAlwaysPrompt = (~isempty(forcePrompt) && forcePrompt);
+if ( ~bAlwaysPrompt )
+ [imageData,jsonDir,jsonFile] = MicroscopeData.ReadMetadataFile(root);
+end
+
+bNeedData = (isempty(forcePrompt) && isempty(imageData));
+if ( bAlwaysPrompt || bNeedData )
+ [fileName,rootDir,filterIndex] = uigetfile({'*.json','Metadata files (*.json)';'*.*','All Files (*.*)'},promptTitle,root);
+ if (filterIndex==0)
+ return
+ end
+
+ root = fullfile(rootDir,fileName);
+ [imageData,jsonDir,jsonFile] = MicroscopeData.ReadMetadataFile(root);
+end
+
+end
diff --git a/src/MATLAB/+MicroscopeData/ReadMetadataFile.m b/src/MATLAB/+MicroscopeData/ReadMetadataFile.m
new file mode 100644
index 0000000000000000000000000000000000000000..19c3b5fc2358b368d6b5f668fc683fa3de098479
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/ReadMetadataFile.m
@@ -0,0 +1,64 @@
+function [imageData,jsonDir,jsonFile] = ReadMetadataFile(metadataPath)
+ imageData = [];
+ jsonDir = [];
+ jsonFile = [];
+
+ if ( isempty(metadataPath) )
+ metadataPath = '';
+ end
+
+ chkPath = findValidJSON(metadataPath);
+ if ( isempty(chkPath) )
+ return;
+ end
+
+ fileHandle = fopen(chkPath);
+
+ jsonData = fread(fileHandle,'*char').';
+ imageData = Utils.ParseJSON(jsonData);
+
+ fclose(fileHandle);
+
+ [rootDir,fileName] = fileparts(chkPath);
+
+ jsonDir = rootDir;
+ jsonFile = [fileName '.json'];
+
+ imageData.imageDir = jsonDir;
+end
+
+function jsonPath = findValidJSON(chkPath)
+ jsonPath = [];
+
+ [rootDir,fileName,ext] = fileparts(chkPath);
+ if ( ~isempty(ext) )
+ if ( ~strcmpi(ext,'.json') )
+ return;
+ end
+ chkPath = fullfile(rootDir,[fileName,'.json']);
+ elseif (~isempty(fileName))
+ % case root has a file name
+ if (~exist(fullfile(rootDir,[fileName,'.json']),'file'))
+ return;
+ end
+ chkPath = fullfile(rootDir,[fileName,'.json']);
+ elseif (~isempty(rootDir))
+ % case root is a path (e.g. \ terminated)
+ jsonList = dir(fullfile(rootDir,'*.json'));
+ if (isempty(jsonList))
+ return;
+ end
+ chkPath = fullfile(rootDir,jsonList(1).name);
+ end
+
+ [~,~,ext] = fileparts(chkPath);
+ if ( ~strcmpi(ext,'.json') )
+ return;
+ end
+
+ if (~exist(chkPath,'file'))
+ return
+ end
+
+ jsonPath = chkPath;
+end
diff --git a/src/MATLAB/+MicroscopeData/Reader.m b/src/MATLAB/+MicroscopeData/Reader.m
new file mode 100644
index 0000000000000000000000000000000000000000..abafe06ba52e612c88a0e13efd75e934c17b3476
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/Reader.m
@@ -0,0 +1,62 @@
+% [IM, IMAGEDATA] = MicroscopeData.Reader([path], varargin)
+%
+% Optional Parameters (Key,Value pairs):
+%
+% imageData - Input metadata, if specified, the optional path argument is ignored
+% chanList - List of channels to read
+% timeRange - Range min and max times to read
+% roi_xyz - x,y,z min and max roi to read
+% outType - Desired output type, conversion is applied if different from image
+% normalize - Normalize images on [0,1] per frame before conersion to output type
+% verbose - Display verbose output and timing information
+% prompt - False to completely disable prompts, true to force prompt, leave unspecified or empty for default prompt behavior
+% promptTitle - Open dialog title in the case that prompting is required
+
+function [im, imD] = Reader(varargin)
+im = [];
+imD = [];
+
+dataTypeLookup = {'uint8';'uint16';'uint32';'uint64';
+ 'int8';'int16';'int32';'int64';
+ 'single';'double';
+ 'logical'};
+
+args = MicroscopeData.Helper.ParseReaderInputs(varargin{:});
+
+loadPath = '';
+if ( ~isempty(args.imageData) )
+ loadPath = args.imageData.imageDir;
+elseif ( ~isempty(args.path) )
+ loadPath = args.path;
+end
+
+if ( args.prompt )
+ imD = MicroscopeData.ReadMetadata(loadPath,args.prompt,args.promptTitle);
+elseif ( isempty(args.imageData) )
+ imD = MicroscopeData.ReadMetadata(loadPath,args.prompt,args.promptTitle);
+else
+ imD = args.imageData;
+end
+
+if (isempty(imD))
+ warning('No image read!');
+ return
+end
+
+imPath = imD.imageDir;
+hdf5File = fullfile(imPath,[imD.DatasetName '.h5']);
+if ( exist(hdf5File,'file') )
+ [im,imD] = MicroscopeData.ReaderH5('imageData',imD, 'chanList',args.chanList, 'timeRange',args.timeRange, 'roi_xyz',args.roi_xyz,...
+ 'outType',args.outType, 'normalize',args.normalize, 'verbose',args.verbose, 'prompt',false);
+ return;
+end
+
+tifFile = fullfile(imPath,sprintf('%s_c%02d_t%04d_z%04d.tif',imD.DatasetName,1,1,1));
+if ( exist(tifFile,'file') )
+ [im,imD] = MicroscopeData.ReaderTIF('imageData',imD, 'chanList',args.chanList, 'timeRange',args.timeRange, 'roi_xyz',args.roi_xyz,...
+ 'outType',args.outType, 'normalize',args.normalize, 'verbose',args.verbose, 'prompt',false);
+ return;
+end
+
+warning('No supported image type found!');
+end
diff --git a/src/MATLAB/+MicroscopeData/ReaderH5.m b/src/MATLAB/+MicroscopeData/ReaderH5.m
new file mode 100644
index 0000000000000000000000000000000000000000..54a6227016c043339967af3c17cbae517867db57
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/ReaderH5.m
@@ -0,0 +1,141 @@
+% [IM, IMAGEDATA] = MicroscopeData.Sandbox.ReaderH5([path], varargin)
+%
+% Optional Parameters (Key,Value pairs):
+%
+% imageData - Input metadata, if specified, the optional path argument is ignored
+% chanList - List of channels to read
+% timeRange - Range min and max times to read
+% roi_xyz - x,y,z min and max roi to read
+% outType - Desired output type, conversion is applied if different from image
+% normalize - Normalize images on [0,1] per frame before conersion to output type
+% verbose - Display verbose output and timing information
+% prompt - False to completely disable prompts, true to force prompt, leave unspecified or empty for default prompt behavior
+% promptTitle - Open dialog title in the case that prompting is required
+
+function [im, imD] = ReaderH5(varargin)
+im = [];
+
+dataTypeLookup = {'uint8';'uint16';'uint32';'uint64';
+ 'int8';'int16';'int32';'int64';
+ 'single';'double';
+ 'logical'};
+
+dataTypeSize = [1;2;4;8;
+ 1;2;4;8;
+ 4;8;
+ 1];
+
+args = MicroscopeData.Helper.ParseReaderInputs(varargin{:});
+
+loadPath = '';
+if ( ~isempty(args.imageData) )
+ loadPath = args.imageData.imageDir;
+elseif ( ~isempty(args.path) )
+ loadPath = args.path;
+end
+
+if ( args.prompt )
+ imD = MicroscopeData.ReadMetadata(loadPath,args.prompt,args.promptTitle);
+elseif ( isempty(args.imageData) )
+ imD = MicroscopeData.ReadMetadata(loadPath,args.prompt,args.promptTitle);
+else
+ imD = args.imageData;
+end
+
+imPath = imD.imageDir;
+
+if (isempty(args.chanList))
+ args.chanList = 1:imD.NumberOfChannels;
+end
+
+if (isempty(args.timeRange))
+ args.timeRange = [1 imD.NumberOfFrames];
+end
+
+if (isempty(args.roi_xyz))
+ args.roi_xyz = [1 1 1; imD.Dimensions];
+end
+
+if (~exist(fullfile(imPath,[imD.DatasetName '.h5']),'file'))
+ warning('No image to read!');
+ return
+end
+
+inType = class(h5read(fullfile(imPath,[imD.DatasetName '.h5']),'/Data',[1 1 1 1 1],[1 1 1 1 1]));
+inIdx = find(strcmp(inType,dataTypeLookup));
+if ( ~isempty(inIdx) )
+ inBytes = dataTypeSize(inIdx);
+else
+ error('Unsupported image type!');
+end
+
+if (~isfield(imD,'PixelFormat'))
+ imD.PixelFormat = inType;
+end
+
+if ( isempty(args.outType) )
+ if (strcmp(imD.PixelFormat,'logical'))
+ args.outType = 'logical';
+ else
+ args.outType = inType;
+ end
+elseif ( ~any(strcmp(args.outType,dataTypeLookup)) )
+ error('Unsupported output type!');
+end
+
+outIdx = find(strcmp(args.outType,dataTypeLookup));
+if ( ~isempty(outIdx) )
+ outBytes = dataTypeSize(outIdx);
+end
+
+convert = ~strcmpi(inType,args.outType) || args.normalize;
+imSize = [diff(Utils.SwapXY_RC(args.roi_xyz),1)+1,length(args.chanList),(args.timeRange(2)-args.timeRange(1)+1)];
+if (~strcmpi(args.outType,'logical'))
+ im = zeros(imSize, args.outType);
+else
+ im = false(imSize);
+end
+
+if ( args.verbose )
+ orgSize = [imD.Dimensions(1),imD.Dimensions(2),imD.Dimensions(3),imD.NumberOfChannels,imD.NumberOfFrames];
+ fprintf('Reading (%d,%d,%d,%d,%d) %s %5.2fMB --> Into (%d,%d,%d,%d,%d) %s %5.2fMB,',...
+ orgSize(2),orgSize(1),orgSize(3),orgSize(4),orgSize(5),inType,...
+ (prod(orgSize)*inBytes)/(1024*1024),...
+ imSize(1),imSize(2),imSize(3),imSize(4),imSize(5),args.outType,...
+ (prod(imSize)*outBytes)/(1024*1024));
+end
+
+tic
+if ( convert )
+ for c=1:length(args.chanList)
+ for t=1:imSize(5)
+ tempIm = h5read(fullfile(imPath,[imD.DatasetName '.h5']),'/Data', [Utils.SwapXY_RC(args.roi_xyz(1,:)) args.chanList(c) t+args.timeRange(1)-1], [imSize(1:3) 1 1]);
+ im(:,:,:,c,t) = ImUtils.ConvertType(tempIm,args.outType,args.normalize);
+ end
+ end
+
+ clear tempIm;
+else
+ for c=1:length(args.chanList)
+ im(:,:,:,c,:) = h5read(fullfile(imPath,[imD.DatasetName '.h5']),'/Data', [Utils.SwapXY_RC(args.roi_xyz(1,:)) args.chanList(c) args.timeRange(1)], [imSize(1:3) 1 imSize(5)]);
+ end
+end
+if (args.verbose)
+ fprintf(' took:%s\n',Utils.PrintTime(toc));
+end
+
+imD.Dimensions = Utils.SwapXY_RC(imSize(1:3));
+imD.NumberOfChannels = size(im,4);
+imD.NumberOfFrames = size(im,5);
+
+if (isfield(imD,'ChannelNames') && ~isempty(imD.ChannelNames))
+ imD.ChannelNames = imD.ChannelNames(args.chanList)';
+else
+ imD.ChannelNames = {};
+end
+if (isfield(imD,'ChannelColors') && ~isempty(imD.ChannelColors))
+ imD.ChannelColors = imD.ChannelColors(args.chanList,:);
+else
+ imD.ChannelColors = [];
+end
+end
diff --git a/src/MATLAB/+MicroscopeData/ReaderTIF.m b/src/MATLAB/+MicroscopeData/ReaderTIF.m
new file mode 100644
index 0000000000000000000000000000000000000000..8141f486e07bb4d1ab1f7c40d20f400e3c6aa3fc
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/ReaderTIF.m
@@ -0,0 +1,175 @@
+% [IM, IMAGEDATA] = MicroscopeData.Reader([path], varargin)
+%
+% Optional Parameters (Key,Value pairs):
+%
+% imageData - Input metadata, if specified, the optional path argument is ignored
+% chanList - List of channels to read
+% timeRange - Range min and max times to read
+% roi_xyz - x,y,z min and max roi to read
+% outType - Desired output type, conversion is applied if different from image
+% normalize - Normalize images on [0,1] per frame before conersion to output type
+% verbose - Display verbose output and timing information
+% prompt - False to completely disable prompts, true to force prompt, leave unspecified or empty for default prompt behavior
+% promptTitle - Open dialog title in the case that prompting is required
+
+function [im, imD] = ReaderTIF(varargin)
+im = [];
+
+dataTypeLookup = {'uint8';'uint16';'uint32';'uint64';
+ 'int8';'int16';'int32';'int64';
+ 'single';'double';
+ 'logical'};
+
+dataTypeSize = [1;2;4;8;
+ 1;2;4;8;
+ 4;8;
+ 1];
+
+args = MicroscopeData.Helper.ParseReaderInputs(varargin{:});
+
+loadPath = '';
+if ( ~isempty(args.imageData) )
+ loadPath = args.imageData.imageDir;
+elseif ( ~isempty(args.path) )
+ loadPath = args.path;
+end
+
+if ( args.prompt )
+ imD = MicroscopeData.ReadMetadata(loadPath,args.prompt,args.promptTitle);
+elseif ( isempty(args.imageData) )
+ imD = MicroscopeData.ReadMetadata(loadPath,args.prompt,args.promptTitle);
+else
+ imD = args.imageData;
+end
+
+if (isempty(imD))
+ warning('No image read!');
+ return
+end
+
+imPath = imD.imageDir;
+
+if (isempty(args.chanList))
+ args.chanList = 1:imD.NumberOfChannels;
+end
+
+if (isempty(args.timeRange))
+ args.timeRange = [1 imD.NumberOfFrames];
+end
+
+if (isempty(args.roi_xyz))
+ args.roi_xyz = [1 1 1; imD.Dimensions];
+end
+
+if (isempty(args.normalize))
+ args.normalize = false;
+end
+
+if (~exist(fullfile(imPath,sprintf('%s_c%02d_t%04d_z%04d.tif',imD.DatasetName,1,1,1)),'file'))
+ warning('No image to read!');
+ return
+end
+
+useROI = (nnz(args.roi_xyz(:,1:2) ~= [1 1;imD.Dimensions(1:2)]) > 0);
+
+chkFilename = fullfile(imPath,sprintf('%s_c%02d_t%04d_z%04d.tif',imD.DatasetName,1,1,1));
+inType = MicroscopeData.Helper.GetPixelTypeTIF(chkFilename);
+inIdx = find(strcmp(inType,dataTypeLookup));
+if ( ~isempty(inIdx) )
+ inBytes = dataTypeSize(inIdx);
+else
+ error('Unsupported image type!');
+end
+
+if (~isfield(imD,'PixelFormat'))
+ imD.PixelFormat = inType;
+end
+
+if ( isempty(args.outType) )
+ if (strcmp(imD.PixelFormat,'logical'))
+ args.outType = 'logical';
+ else
+ args.outType = inType;
+ end
+elseif ( ~any(strcmp(args.outType,dataTypeLookup)) )
+ error('Unsupported output type!');
+end
+
+outIdx = find(strcmp(args.outType,dataTypeLookup));
+if ( ~isempty(outIdx) )
+ outBytes = dataTypeSize(outIdx);
+end
+
+convert = ~strcmpi(inType,args.outType) || args.normalize;
+imSize = [diff(Utils.SwapXY_RC(args.roi_xyz),1)+1,length(args.chanList),(args.timeRange(2)-args.timeRange(1)+1)];
+if (~strcmpi(args.outType,'logical'))
+ im = zeros(imSize, args.outType);
+else
+ im = false(imSize);
+end
+
+if ( args.verbose )
+ orgSize = [imD.Dimensions(1),imD.Dimensions(2),imD.Dimensions(3),imD.NumberOfChannels,imD.NumberOfFrames];
+ fprintf('Reading (%d,%d,%d,%d,%d) %s %5.2fMB --> Into (%d,%d,%d,%d,%d) %s %5.2fMB,',...
+ orgSize(1),orgSize(2),orgSize(3),orgSize(4),orgSize(5),inType,...
+ (prod(orgSize)*inBytes)/(1024*1024),...
+ imSize(1),imSize(2),imSize(3),imSize(4),imSize(5),args.outType,...
+ (prod(imSize)*outBytes)/(1024*1024));
+end
+
+if ( args.verbose )
+ iter = imSize(5)*length(args.chanList)*imSize(3);
+ cp = Utils.CmdlnProgress(iter,true,sprintf('Reading %s...',imD.DatasetName));
+ i=1;
+end
+
+tic
+for t=1:imSize(5)
+ timeVal = t+args.timeRange(1)-1;
+ for c=1:length(args.chanList)
+ for z=1:imSize(3)
+ zVal = z+args.roi_xyz(1,3)-1;
+
+ tifName = fullfile(imPath,sprintf('%s_c%02d_t%04d_z%04d.tif',imD.DatasetName,args.chanList(c),timeVal,zVal));
+ if (convert || useROI)
+ tempIm(:,:,z) = imread(tifName,'TIF');
+ else
+ im(:,:,z,c,t) = imread(tifName,'TIF');
+ end
+
+ if ( args.verbose )
+ cp.PrintProgress(i);
+ i = i+1;
+ end
+ end
+
+ if (convert)
+ im(:,:,:,c,t) = ImUtils.ConvertType(...
+ tempIm(args.roi_xyz(1,2):args.roi_xyz(2,2),args.roi_xyz(1,1):args.roi_xyz(2,1),:),...
+ args.outType,args.normalize);
+ elseif (useROI)
+ im(:,:,:,c,t) = tempIm(args.roi_xyz(1,2):args.roi_xyz(2,2),args.roi_xyz(1,1):args.roi_xyz(2,1),:);
+ end
+ end
+end
+
+if ( args.verbose )
+ cp.ClearProgress(true);
+ fprintf(' took:%s\n',Utils.PrintTime(toc));
+end
+
+imD.Dimensions = Utils.SwapXY_RC(imSize(1:3));
+imD.NumberOfChannels = size(im,4);
+imD.NumberOfFrames = size(im,5);
+
+if (isfield(imD,'ChannelNames') && ~isempty(imD.ChannelNames))
+ imD.ChannelNames = imD.ChannelNames(args.chanList)';
+else
+ imD.ChannelNames = {};
+end
+if (isfield(imD,'ChannelColors') && ~isempty(imD.ChannelColors))
+ imD.ChannelColors = imD.ChannelColors(args.chanList,:);
+else
+ imD.ChannelColors = [];
+end
+end
diff --git a/src/MATLAB/+MicroscopeData/Writer.m b/src/MATLAB/+MicroscopeData/Writer.m
new file mode 100644
index 0000000000000000000000000000000000000000..a92373d112b18ce3f5cf365aec09100039c6a08f
--- /dev/null
+++ b/src/MATLAB/+MicroscopeData/Writer.m
@@ -0,0 +1,192 @@
+% TIFFWRITER(IM, PREFIX, IMAGEDATA, TIMELIST, CHANLIST, ZLIST, QUIET)
+% TIMELIST, CHANLIST, and ZLIST are optional; pass in empty [] for the
+% arguments that come prior to the one you would like to populate.
+%
+% IM = the image data to write. Assumes a 5-D image in the format
+% (X,Y,Z,channel,time). If the image already exists and TIMELIST, CHANLIST,
+% and ZLIST are populated with less then the whole image, the existing
+% image is updated. If the file does not exist and the image data doesn't
+% fill the whole image, the rest will be filled in with black (zeros)
+% frames.
+%
+% PREFIX = filepath in the format ('c:\path\FilePrefix') unless there is no
+% imagedata in which case it should be ('c:\path)
+% IMAGEDATA = metadata that will be written to accompany the image. If you
+% want this generated from the image data only, this paramater should be
+% just a string representing the dataset name. See PREFIX above in such
+% case.
+% TIMELIST = a list of frames that the fifth dimention represents
+% CHANLIST = the channels that the input image represents
+% ZLIST = the z slices that the input image represents
+% QUITE = suppress printing out progress
+
+function Writer(im, outDir, imageData, timeList, chanList, zList, quiet)
+if (exist('tifflib') ~= 3)
+ tifflibLocation = which('/private/tifflib');
+ if (isempty(tifflibLocation))
+ error('tifflib does not exits on this machine!');
+ end
+ copyfile(tifflibLocation,'.');
+end
+
+if (~exist('quiet','var') || isempty(quiet))
+ quiet = 0;
+end
+
+if (exist('imageData','var') && ~isempty(imageData) && isfield(imageData,'DatasetName'))
+ idx = strfind(imageData.DatasetName,'"');
+ imageData.DatasetName(idx) = [];
+else
+ if isstruct(imageData)
+ error('ImageData struct is malformed!');
+ end
+ dName = imageData;
+ imageData = [];
+ imageData.DatasetName = dName;
+
+ imageData.Dimensions = Utils.SwapXY_RC(size(im));
+ imageData.NumberOfChannels = size(im,4);
+ imageData.NumberOfFrames = size(im,5);
+
+ imageData.PixelPhysicalSize = [1.0, 1.0, 1.0];
+end
+
+w = whos('im');
+switch w.class
+ case 'uint8'
+ tags.SampleFormat = Tiff.SampleFormat.UInt;
+ tags.BitsPerSample = 8;
+ case 'uint16'
+ tags.SampleFormat = Tiff.SampleFormat.UInt;
+ tags.BitsPerSample = 16;
+ case 'uint32'
+ tags.SampleFormat = Tiff.SampleFormat.UInt;
+ tags.BitsPerSample = 32;
+ case 'int8'
+ tags.SampleFormat = Tiff.SampleFormat.Int;
+ tags.BitsPerSample = 8;
+ case 'int16'
+ tags.SampleFormat = Tiff.SampleFormat.Int;
+ tags.BitsPerSample = 16;
+ case 'int32'
+ tags.SampleFormat = Tiff.SampleFormat.Int;
+ tags.BitsPerSample = 32;
+ case 'single'
+ tags.SampleFormat = Tiff.SampleFormat.IEEEFP;
+ tags.BitsPerSample = 32;
+ case 'double'
+ tags.SampleFormat = Tiff.SampleFormat.IEEEFP;
+ tags.BitsPerSample = 64;
+ case 'logical'
+ imtemp = zeros(size(im),'uint8');
+ imtemp(im) = 255;
+ im = imtemp;
+ clear imtemp
+ tags.SampleFormat = Tiff.SampleFormat.UInt;
+ tags.BitsPerSample = 8;
+ otherwise
+ error('Image type unsupported!');
+end
+
+if (~isfield(imageData,'PixelFormat'))
+ imageData.PixelFormat = w.class;
+end
+
+if (exist('outDir','var') && ~isempty(outDir))
+ idx = strfind(outDir,'"');
+ outDir(idx) = [];
+elseif (isfield(imageData,'imageDir') && ~isempty(imageData.imageDir))
+ outDir = imageData.imageDir;
+else
+ outDir = fullfile('.',imageData.DatasetName);
+end
+
+MicroscopeData.CreateMetadata(outDir,imageData,quiet);
+
+if (~exist('timeList','var') || isempty(timeList))
+ timeList = 1:imageData.NumberOfFrames;
+else
+ if (max(timeList(:))>imageData.NumberOfFrames)
+ error('A value in timeList is greater than the number of frames in the image data!');
+ end
+end
+if (size(im,5)~=length(timeList))
+ error('There are %d frames and %d frames to be written!',size(im,5),length(timeList));
+end
+
+if (~exist('chanList','var') || isempty(chanList))
+ chanList = 1:imageData.NumberOfChannels;
+else
+ if (max(chanList(:))>imageData.NumberOfChannels)
+ error('A value in chanList is greater than the number of channels in the image data!');
+ end
+end
+if (size(im,4)~=length(chanList))
+ error('There are %d channels and %d channels to be written!',size(im,4),length(chanList));
+end
+
+if (~exist('zList','var') || isempty(zList))
+ zList = 1:imageData.Dimensions(3);
+else
+ if (max(zList(:))>imageData.Dimensions(3))
+ error('A value in zList is greater than the z dimension in the image data!');
+ end
+end
+if (size(im,3)~=length(zList))
+ error('There are %d z images and %d z images to be written!',size(im,3),length(zList));
+end
+
+tags.ImageLength = size(im,1);
+tags.ImageWidth = size(im,2);
+tags.RowsPerStrip = size(im,2);
+tags.Photometric = Tiff.Photometric.MinIsBlack;
+tags.ExtraSamples = Tiff.ExtraSamples.Unspecified;
+tags.PlanarConfiguration = Tiff.PlanarConfiguration.Chunky;
+tags.SamplesPerPixel = 1;
+tags.Compression = Tiff.Compression.LZW;
+tags.Software = 'MATLAB';
+
+if (~quiet)
+ iter = length(timeList)*length(chanList)*length(zList);
+ cp = Utils.CmdlnProgress(iter,true,sprintf('Writing %s...',imageData.DatasetName));
+ i=1;
+end
+
+isBig = false;
+if (tags.BitsPerSample/8 * prod(imageData.Dimensions) > 0.95*2^32)
+ isBig = true;
+end
+
+tic
+for t=1:length(timeList)
+ for c=1:length(chanList)
+ for z=1:length(zList)
+ if (isBig)
+ tiffObj = Tiff(fullfile(outDir,[imageData.DatasetName,sprintf('_c%02d_t%04d_z%04d.tif',chanList(c),timeList(t),zList(z))]),'w8');
+ else
+ tiffObj = Tiff(fullfile(outDir,[imageData.DatasetName,sprintf('_c%02d_t%04d_z%04d.tif',chanList(c),timeList(t),zList(z))]),'w');
+ end
+ tiffObj.setTag(tags);
+ tiffObj.write(im(:,:,z,c,t),tags);
+ tiffObj.close();
+
+% fname = fullfile(outDir,[imageData.DatasetName,sprintf('_c%02d_t%04d_z%04d.tif',chanList(c),timeList(t),zList(z))]);
+% imwrite(im(:,:,z,c,t),fname,'Compression','lzw');
+
+ if (~quiet)
+ cp.PrintProgress(i);
+ i = i+1;
+ end
+
+ end
+ end
+end
+
+if (~quiet)
+ cp.ClearProgress();
+ fprintf('Wrote %.0fMB in %s\n',...
+ ((tags.BitsPerSample/8)*prod(imageData.Dimensions)*imageData.NumberOfChannels*imageData.NumberOfFrames)/(1024*1024),...
+ Utils.PrintTime(toc));
+end
+end
+
diff --git a/src/MATLAB/+Segmentation/+MitosisEditor/FindChildrenHulls.m b/src/MATLAB/+Segmentation/+MitosisEditor/FindChildrenHulls.m
index b8f595482f199d774ca3c591aaf7cacbba95a1a2..91201ef0c05191a3e9aa2ccd2e35dd7d946b02b4 100644
--- a/src/MATLAB/+Segmentation/+MitosisEditor/FindChildrenHulls.m
+++ b/src/MATLAB/+Segmentation/+MitosisEditor/FindChildrenHulls.m
@@ -51,7 +51,7 @@ function newHulls = splitMitosisHull(hullID, linePoints, bForcePoints)
mitVec = mitVec / norm(mitVec);
- [r c] = ind2sub(CONSTANTS.imageSize, CellHulls(hullID).indexPixels);
+ [r c] = ind2sub(Metadata.GetDimensions('rc'), CellHulls(hullID).indexPixels);
if ( bForcePoints )
distSq = ((c-linePoints(1,1)).^2 + (r-linePoints(1,2)).^2);
@@ -150,7 +150,7 @@ function hullID = mergeOverlapping(chkHulls, chkPoint, time)
objCOM = zeros(length(validHulls),2);
for i=1:length(validHulls)
- [r c] = ind2sub(CONSTANTS.imageSize, validHulls(i).indexPixels);
+ [r c] = ind2sub(Metadata.GetDimensions('rc'), validHulls(i).indexPixels);
objCOM = mean([r c], 1);
end
@@ -159,7 +159,7 @@ function hullID = mergeOverlapping(chkHulls, chkPoint, time)
newHull = validHulls(minIdx);
- [r c] = ind2sub(CONSTANTS.imageSize, newHull.indexPixels);
+ [r c] = ind2sub(Metadata.GetDimensions('rc'), newHull.indexPixels);
newHullEntry = createNewHullStruct(c, r, time);
bMergeHulls = arrayfun(@(x)(nnz(ismember(newHullEntry.indexPixels,CellHulls(x).indexPixels)) > 5), frameHulls);
@@ -197,14 +197,14 @@ function hullID = mergeOverlapping(chkHulls, chkPoint, time)
end
function outHullID = mergeHullValues(hullID, mergeStruct)
- global CONSTANTS CellHulls
+ global CellHulls
outHullID = hullID;
[dump, idxA, idxB] = union(CellHulls(hullID).indexPixels, mergeStruct.indexPixels);
CellHulls(hullID).indexPixels = [CellHulls(hullID).indexPixels(idxA); mergeStruct.indexPixels(idxB)];
- [r c] = ind2sub(CONSTANTS.imageSize, CellHulls(hullID).indexPixels);
+ [r c] = ind2sub(Metadata.GetDimensions('rc'), CellHulls(hullID).indexPixels);
CellHulls(hullID).centerOfMass = mean([r c]);
cvIdx = Helper.ConvexHull(c,r);
if ( isempty(cvIdx) )
@@ -215,12 +215,12 @@ function outHullID = mergeHullValues(hullID, mergeStruct)
end
function subtractHulls(hullID, subHullID)
- global CONSTANTS CellHulls
+ global CellHulls
[dump, subIdx] = union(CellHulls(hullID).indexPixels, CellHulls(subHullID).indexPixels);
CellHulls(hullID).indexPixels = CellHulls(hullID).indexPixels(subIdx);
- [r c] = ind2sub(CONSTANTS.imageSize, CellHulls(hullID).indexPixels);
+ [r c] = ind2sub(Metadata.GetDimensions('rc'), CellHulls(hullID).indexPixels);
CellHulls(hullID).centerOfMass = mean([r c]);
cvIdx = Helper.ConvexHull(c,r);
if ( isempty(cvIdx) )
@@ -239,20 +239,18 @@ function newHullID = addPointHullEntry(chkPoint, time)
end
function newHullID = addHullEntry(hull, time)
- global CONSTANTS
-
- [r c] = ind2sub(CONSTANTS.imageSize, hull.indexPixels);
+ [r c] = ind2sub(Metadata.GetDimensions('rc'), hull.indexPixels);
newHull = createNewHullStruct(c, r, time);
newHullID = Hulls.SetCellHullEntries(0, newHull);
end
function newHull = createNewHullStruct(x,y, time)
- global CONSTANTS CellHulls
+ global CellHulls
newHull = Helper.MakeEmptyStruct(CellHulls);
- idxPix = sub2ind(CONSTANTS.imageSize, y,x);
+ idxPix = sub2ind(Metadata.GetDimensions('rc'), y,x);
newHull.indexPixels = idxPix;
newHull.centerOfMass = mean([y x], 1);
diff --git a/src/MATLAB/+Segmentation/+MitosisEditor/FindParentHull.m b/src/MATLAB/+Segmentation/+MitosisEditor/FindParentHull.m
index 47a2793cf90a5d53172f08b89b593bd9f62b286a..32d77522727db5c1ad53484267e4df2c215bb51e 100644
--- a/src/MATLAB/+Segmentation/+MitosisEditor/FindParentHull.m
+++ b/src/MATLAB/+Segmentation/+MitosisEditor/FindParentHull.m
@@ -34,8 +34,9 @@ function parentHull = FindParentHull(childHulls, linePoints, time, forceParents)
pointCounts = zeros(1,length(chkHulls));
+ rcImageDims = Metadata.GetDimensions('rc');
for i=1:length(chkHulls)
- [r c] = ind2sub(CONSTANTS.imageSize, CellHulls(chkHulls(i)).indexPixels);
+ [r c] = ind2sub(rcImageDims, CellHulls(chkHulls(i)).indexPixels);
bContainsPoints = inpolygon(c,r, mitosisPoints(:,1), mitosisPoints(:,2));
pointCounts(i) = nnz(bContainsPoints);
end
@@ -66,9 +67,10 @@ function parentHull = addParentHull(midpoint, time, mitosisPoints)
hulls = Segmentation.PartialImageSegment(imSet, midpoint, 200, CONSTANTS.primaryChannel, segFunc, segParams);
+ rcImageDims = Metadata.GetDimensions('rc');
pointCounts = zeros(1,length(hulls));
for i=1:length(hulls)
- [r c] = ind2sub(CONSTANTS.imageSize, hulls(i).indexPixels);
+ [r c] = ind2sub(rcImageDims, hulls(i).indexPixels);
bContainsPoints = inpolygon(c,r, mitosisPoints(:,1), mitosisPoints(:,2));
pointCounts(i) = nnz(bContainsPoints);
end
@@ -88,28 +90,25 @@ function newHullID = addPointHullEntry(chkPoint, time)
x = round(chkPoint(1));
y = round(chkPoint(2));
- filename = Helper.GetFullImagePath(time);
- img = Helper.LoadIntensityImage(filename);
+ img = Helper.LoadIntensityImage(time,CONSTANTS.primaryChannel);
newHull = createNewHullStruct(x, y, time);
newHullID = Hulls.SetCellHullEntries(0, newHull);
end
function newHullID = addHullEntry(hull, time)
- global CONSTANTS
-
- [r c] = ind2sub(CONSTANTS.imageSize, hull.indexPixels);
+ [r c] = ind2sub(Metadata.GetDimensions('rc'), hull.indexPixels);
newHull = createNewHullStruct(c, r, time);
newHullID = Hulls.SetCellHullEntries(0, newHull);
end
function newHull = createNewHullStruct(x,y, time)
- global CONSTANTS CellHulls
+ global CellHulls
newHull = Helper.MakeEmptyStruct(CellHulls);
- idxPix = sub2ind(CONSTANTS.imageSize, y,x);
+ idxPix = sub2ind(Metadata.GetDimensions('rc'), y,x);
newHull.indexPixels = idxPix;
newHull.centerOfMass = mean([y x], 1);
diff --git a/src/MATLAB/+Segmentation/+ResegFromTree/AddSegmentation.m b/src/MATLAB/+Segmentation/+ResegFromTree/AddSegmentation.m
index 5712b88ce9f902507741b866e88d59d768b75714..324a9fc4b8e9b9ef66f94768cd85d15aa69ce465 100644
--- a/src/MATLAB/+Segmentation/+ResegFromTree/AddSegmentation.m
+++ b/src/MATLAB/+Segmentation/+ResegFromTree/AddSegmentation.m
@@ -11,8 +11,7 @@ function [addedHull costMatrix nextHulls] = AddSegmentation(prevHull, costMatrix
chanImSet = Helper.LoadIntensityImageSet(time);
- guessPoint = Helper.SwapXY_RC(CellHulls(prevHull).centerOfMass);
-
+ guessPoint = Utils.SwapXY_RC(CellHulls(prevHull).centerOfMass);
chkHull = Segmentation.FindNewSegmentation(chanImSet, guessPoint, 200, bAggressive, CellHulls(prevHull).indexPixels, time);
if ( isempty(chkHull) )
return;
@@ -27,7 +26,7 @@ function [addedHull costMatrix nextHulls] = AddSegmentation(prevHull, costMatrix
return;
end
- newHull = Hulls.CreateHull(CONSTANTS.imageSize, chkPix, time, false, chkHull.tag);
+ newHull = Hulls.CreateHull(Metadata.GetDimensions('rc'), chkPix, time, false, chkHull.tag);
% Use temporary hull to verify cost (not on a track yet)
chkIdx = find(checkHulls == prevHull);
diff --git a/src/MATLAB/+Segmentation/+ResegFromTree/CanExtendTrack.m b/src/MATLAB/+Segmentation/+ResegFromTree/CanExtendTrack.m
deleted file mode 100644
index 8afef1ed74d86be90c01d16142b40cebddfad804..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Segmentation/+ResegFromTree/CanExtendTrack.m
+++ /dev/null
@@ -1,25 +0,0 @@
-
-function bCanExtend = CanExtendTrack(t, tracks)
- global CellHulls
-
- bCanExtend = true(length(tracks),1);
-
- for i=1:length(tracks)
- [phenotype phenoHullID] = Tracks.GetTrackPhenoypeTimes(tracks(i));
- if ( phenotype == 0 )
- continue;
- end
-
- phenoTime = CellHulls(phenoHullID).time;
- if ( t <= phenoTime )
- continue;
- end
-
- prevHullID = Helper.GetNearestTrackHull(tracks(i), t-1, -1);
- if ( prevHullID ~= phenoHullID )
- continue;
- end
-
- bCanExtend(i) = false;
- end
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Segmentation/+ResegFromTree/CheckIgnoreTracks.m b/src/MATLAB/+Segmentation/+ResegFromTree/CheckIgnoreTracks.m
index 658d41bb3064dded632dfe5a6ff7e7b3eebd8cf1..55e46b1bdebb8e9c45100fe691d46c9cc739184b 100644
--- a/src/MATLAB/+Segmentation/+ResegFromTree/CheckIgnoreTracks.m
+++ b/src/MATLAB/+Segmentation/+ResegFromTree/CheckIgnoreTracks.m
@@ -41,7 +41,7 @@ function [bIgnoreEdges, bLongEdges] = CheckIgnoreTracks(t, trackIDs, viewLims)
end
function bInLims = checkHullCOMLims(hullID, xyViewLims)
- global CONSTANTS CellHulls
+ global CellHulls
if ( isempty(hullID) || hullID == 0 )
bInLims = false;
@@ -51,15 +51,15 @@ function bInLims = checkHullCOMLims(hullID, xyViewLims)
lenDims = xyViewLims(:,2) - xyViewLims(:,1);
padScale = 0.05;
- imSize = Helper.SwapXY_RC(CONSTANTS.imageSize);
+ xyImageDims = Metadata.GetDimensions('xy');
bNotEdgeMin = (xyViewLims(:,1) >= 1+5);
- bNotEdgeMax = (xyViewLims(:,2) <= (imSize-5).');
+ bNotEdgeMax = (xyViewLims(:,2) <= (xyImageDims-5).');
padInMin = bNotEdgeMin.*padScale.*lenDims;
padInMax = bNotEdgeMax.*padScale.*lenDims;
- hullCOM = Helper.SwapXY_RC(CellHulls(hullID).centerOfMass).';
+ hullCOM = Utils.SwapXY_RC(CellHulls(hullID).centerOfMass).';
bInDim = ((hullCOM > xyViewLims(:,1)+padInMin) & (hullCOM < xyViewLims(:,2)-padInMax));
diff --git a/src/MATLAB/+Segmentation/+ResegFromTree/FindFrameReseg.m b/src/MATLAB/+Segmentation/+ResegFromTree/FindFrameReseg.m
index c29d67aacf8aeb21207fa0f950b3482cb3acc4e3..11fe507f72533833afffcf0f4f297e65e48190b3 100644
--- a/src/MATLAB/+Segmentation/+ResegFromTree/FindFrameReseg.m
+++ b/src/MATLAB/+Segmentation/+ResegFromTree/FindFrameReseg.m
@@ -97,11 +97,18 @@ function newEdges = FindFrameReseg(t, curEdges, bIgnoreEdges)
bAddedHull(i) = 1;
end
+ % Bump up the cost of splitting a hull
+ [bestInCost,bestInIdx] = min(costMatrix,[],1);
+ idx = sub2ind(size(costMatrix), bestInIdx,(1:size(costMatrix,2)));
+
+ splitCosts = 2*costMatrix;
+ splitCosts(idx) = bestInCost;
+
% Find hulls we may need to split
desiredCellCount = zeros(length(nextHulls),1);
desirers = cell(length(nextHulls),1);
for i=1:length(checkHulls)
- [desiredCosts desiredIdx] = sort(costMatrix(i,:));
+ [desiredCosts,desiredIdx] = sort(splitCosts(i,:));
if ( isinf(desiredCosts(1)) )
continue;
end
diff --git a/src/MATLAB/+Segmentation/+ResegFromTree/GetSubtreeTracks.m b/src/MATLAB/+Segmentation/+ResegFromTree/GetSubtreeTracks.m
deleted file mode 100644
index 59c0b45b864163288137cfbd2c0938a08d7c6785..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Segmentation/+ResegFromTree/GetSubtreeTracks.m
+++ /dev/null
@@ -1,18 +0,0 @@
-% childTracks = GetSubtreeTracks(rootTracks)
-%
-% Returns a list of all tracks which are children of the tracks listed in
-% rootTracks (Includes the rootTracks).
-
-function childTracks = GetSubtreeTracks(rootTracks)
- global CellTracks
-
- childTracks = rootTracks;
- while ( any(~isempty([CellTracks(childTracks).childrenTracks])) )
- newTracks = setdiff([CellTracks(childTracks).childrenTracks], childTracks);
- if ( isempty(newTracks) )
- return;
- end
-
- childTracks = union(childTracks, newTracks);
- end
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Segmentation/+ResegFromTree/SplitDeterministic.m b/src/MATLAB/+Segmentation/+ResegFromTree/SplitDeterministic.m
index 6032433159996bfe6211af53ac0922a0d760c5da..a94958742108673f2d2c3953a99ab2b5a57f070f 100644
--- a/src/MATLAB/+Segmentation/+ResegFromTree/SplitDeterministic.m
+++ b/src/MATLAB/+Segmentation/+ResegFromTree/SplitDeterministic.m
@@ -9,24 +9,25 @@ function newHulls = SplitDeterministic(hull, k, checkHullIDs)
return;
end
- oldMeans = zeros(k, 2);
+ rcImageDims = Metadata.GetDimensions('rc');
+ xyOldMeans = zeros(k, length(rcImageDims));
for i=1:length(checkHullIDs)
- oldCoord = Helper.IndexToCoord(CONSTANTS.imageSize, CellHulls(checkHullIDs(i)).indexPixels);
- oldMeans(i,:) = Helper.SwapXY_RC(mean(oldCoord,1));
+ rcOldCoord = Utils.IndToCoord(rcImageDims, CellHulls(checkHullIDs(i)).indexPixels);
+ xyOldMeans(i,:) = Utils.SwapXY_RC(mean(rcOldCoord,1));
end
if ( length(hull.indexPixels) < 2 )
return;
end
- rcCoords = Helper.IndexToCoord(CONSTANTS.imageSize, hull.indexPixels);
- xyCoords = Helper.SwapXY_RC(rcCoords);
+ rcCoords = Utils.IndToCoord(rcImageDims, hull.indexPixels);
+ xyCoords = Utils.SwapXY_RC(rcCoords);
typeParams = Load.GetCellTypeStructure(CONSTANTS.cellType);
if ( typeParams.splitParams.useGMM )
- kIdx = gmmCluster(xyCoords, k, oldMeans);
+ kIdx = gmmCluster(xyCoords, k, xyOldMeans);
else
- kIdx = kmeans(xyCoords, k, 'start',oldMeans, 'EmptyAction','drop');
+ kIdx = kmeans(xyCoords, k, 'start',xyOldMeans, 'EmptyAction','drop');
end
if ( any(isnan(kIdx)) )
@@ -36,7 +37,7 @@ function newHulls = SplitDeterministic(hull, k, checkHullIDs)
for i=1:k
newHullPixels = hull.indexPixels( kIdx==i );
- outputHull = Hulls.CreateHull(CONSTANTS.imageSize, newHullPixels, hull.time);
+ outputHull = Hulls.CreateHull(rcImageDims, newHullPixels, hull.time);
newHulls = [newHulls outputHull];
end
diff --git a/src/MATLAB/+Segmentation/AddNewSegmentHull.m b/src/MATLAB/+Segmentation/AddNewSegmentHull.m
index 1a71ea6be6c9030f1c1752b91479e0318274f75a..8e15d4af44edb1f14e67ef58f325c2cb487f2e10 100644
--- a/src/MATLAB/+Segmentation/AddNewSegmentHull.m
+++ b/src/MATLAB/+Segmentation/AddNewSegmentHull.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -24,34 +24,27 @@
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-function newTrackID = AddNewSegmentHull(clickPt, time)
- global CONSTANTS CellHulls
+function newTrackID = AddNewSegmentHull(xyClickPt, time)
+ global CellHulls
chanImSet = Helper.LoadIntensityImageSet(time);
-
- if strcmp(CONSTANTS.cellType, 'Hemato')
- subSize = 100;
- else
- subSize = 200;
- end
-
-
- chkHull = Segmentation.FindNewSegmentation(chanImSet, clickPt, subSize, true, [], time);
+ chkHull = Segmentation.FindNewSegmentation(chanImSet, xyClickPt, 200, true, [], time);
newHull = Helper.MakeEmptyStruct(CellHulls);
newHull.userEdited = true;
if ( ~isempty(chkHull) )
- chkHull = Segmentation.ForceDisjointSeg(chkHull, time, clickPt);
+ chkHull = Segmentation.ForceDisjointSeg(chkHull, time, xyClickPt);
end
% TODO: Update manual click hulls for 3D
+ rcImageDims = Metadata.GetDimensions('rc');
if ( isempty(chkHull) )
% Add a point hull since we couldn't find a segmentation containing the click
- clickIndex = Helper.CoordToIndex(CONSTANTS.imageSize, round(Helper.SwapXY_RC(clickPt)));
- newHull = Hulls.CreateHull(CONSTANTS.imageSize, clickIndex, time, true, 'Manual');
+ clickIndex = Utils.CoordToInd(rcImageDims, round(Utils.SwapXY_RC(xyClickPt)));
+ newHull = Hulls.CreateHull(rcImageDims, clickIndex, time, true, 'Manual');
else
- newHull = Hulls.CreateHull(CONSTANTS.imageSize, chkHull.indexPixels, time, true, chkHull.tag);
+ newHull = Hulls.CreateHull(rcImageDims, chkHull.indexPixels, time, true, chkHull.tag);
end
newHullID = Hulls.SetCellHullEntries(0, newHull);
diff --git a/src/MATLAB/+Segmentation/AddSegmentationEdit.m b/src/MATLAB/+Segmentation/AddSegmentationEdit.m
index 101a7f5b5816148cb9cbd3de015387ea11843581..c39e98f8ec316ec60d3220f8eec85df8e6799e8d 100644
--- a/src/MATLAB/+Segmentation/AddSegmentationEdit.m
+++ b/src/MATLAB/+Segmentation/AddSegmentationEdit.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Segmentation/AssignPolyPix.m b/src/MATLAB/+Segmentation/AssignPolyPix.m
deleted file mode 100644
index 3a462de605a0bc2b0b407be9c4b86a40b3faf686..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Segmentation/AssignPolyPix.m
+++ /dev/null
@@ -1,45 +0,0 @@
-function assignIdx = AssignPolyPix(polyPix, connComps, imSize)
- [r c] = ind2sub(imSize, polyPix);
-
- xlims = Helper.Clamp([min(c) max(c)], 1, imSize(2));
- ylims = Helper.Clamp([min(r) max(r)], 1, imSize(1));
-
- rCC = cell(1,length(connComps));
- cCC = cell(1,length(connComps));
- for i=1:length(connComps)
- [rCC{i} cCC{i}] = ind2sub(imSize, connComps{i});
-
- xlims = Helper.Clamp([min([xlims(1); cCC{i}]) max([xlims(2); cCC{i}])], 1, imSize(2));
- ylims = Helper.Clamp([min([ylims(1); rCC{i}]) max([ylims(2); rCC{i}])], 1, imSize(1));
- end
-
- locsz = [ylims(2)-ylims(1) xlims(2)-xlims(1)]+1;
-
- lblim = zeros(locsz);
- bwim = false(locsz);
- for i=1:length(connComps)
- locr = rCC{i} - ylims(1) + 1;
- locc = cCC{i} - xlims(1) + 1;
-
- locind = sub2ind(locsz, locr,locc);
-
- bwim(locind) = 1;
- lblim(locind) = i;
- end
-
- locr = r - ylims(1) + 1;
- locc = c - xlims(1) + 1;
-
- locind = sub2ind(locsz, locr,locc);
-
- [d,L] = bwdist(bwim);
- assignIdx = lblim(L(locind));
-
-% cmap = hsv(length(connComps));
-% figure;imagesc(bwim);colormap(gray);hold on;
-% for i=1:length(connComps)
-% tr = locr(assignIdx == i);
-% tc = locc(assignIdx == i);
-% plot(tc, tr, '.', 'Color',cmap(i,:));
-% end
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Segmentation/BuildPerimPix.m b/src/MATLAB/+Segmentation/BuildPerimPix.m
deleted file mode 100644
index b5df0b52e164d3f6014c2152b3fdfa2211101ade..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Segmentation/BuildPerimPix.m
+++ /dev/null
@@ -1,25 +0,0 @@
-function [perimPix, perimr, perimc] = BuildPerimPix(polyPix, imSize)
- [r c] = ind2sub(imSize, polyPix);
-
- xlims = Helper.Clamp([min(c) max(c)], 1, imSize(2));
- ylims = Helper.Clamp([min(r) max(r)], 1, imSize(1));
-
- locr = r - ylims(1) + 1;
- locc = c - xlims(1) + 1;
-
- locsz = [ylims(2)-ylims(1) xlims(2)-xlims(1)]+1;
- locind = sub2ind(locsz, locr, locc);
-
- bwim = false(locsz);
- bwim(locind) = 1;
-
- B = bwboundaries(bwim, 4, 'noholes');
- perimr = [];
- perimc = [];
- for i=1:length(B)
- perimr = [perimr; B{i}(:,1) + ylims(1) - 1];
- perimc = [perimc; B{i}(:,2) + xlims(1) - 1];
- end
-
- perimPix = unique(sub2ind(imSize, perimr, perimc));
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Segmentation/FindCropRegion.m b/src/MATLAB/+Segmentation/FindCropRegion.m
deleted file mode 100644
index e5e25bc73de9219e652e6b49f4d552a71aa276f2..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Segmentation/FindCropRegion.m
+++ /dev/null
@@ -1,22 +0,0 @@
-function [ region ] = findCropRegion( fname )
- alpha = 0.5;
- border = 5;
-
- im = imread(fname);
- im = mat2gray(im);
- th = graythresh(im);
- bw = im2bw(im, th * alpha);
- % imagesc(bw), colormap(gray);
-
- CC = bwconncomp(bw);
- numPixels = cellfun(@numel,CC.PixelIdxList);
- [biggest idx] = max(numPixels);
- [r c] = ind2sub(size(bw), CC.PixelIdxList{idx});
- minR = min(r);
- minC = min(c);
- maxR = max(r);
- maxC = max(c);
-
- region = [(minR + border) (minC + border) (maxR - border) (maxC - border)];
-end
-
diff --git a/src/MATLAB/+Segmentation/FindNewSegmentation.m b/src/MATLAB/+Segmentation/FindNewSegmentation.m
index 6ca14253ec2ff5b6c491367cfe62e983b598f7b5..57d8cb28b24ce6c7f2abf3e55f14a08265167111 100644
--- a/src/MATLAB/+Segmentation/FindNewSegmentation.m
+++ b/src/MATLAB/+Segmentation/FindNewSegmentation.m
@@ -1,4 +1,28 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function hull = FindNewSegmentation(chanImg, centerPt, subSize, bSearchParams, overlapPoints, time)
global CONSTANTS
diff --git a/src/MATLAB/+Segmentation/ForceDisjointSeg.m b/src/MATLAB/+Segmentation/ForceDisjointSeg.m
index 28d9b1401f3830f9f6dea2ea733b4b233ee048b7..5e959a25cc1a8557f9989f7b4de4df6e7885e6e0 100644
--- a/src/MATLAB/+Segmentation/ForceDisjointSeg.m
+++ b/src/MATLAB/+Segmentation/ForceDisjointSeg.m
@@ -1,9 +1,33 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
%TODO: Maybe handle convex hull intersection instead of interior points as
%the current method still allows considerable hull overlap in some cases.
function newHull = ForceDisjointSeg(hull, time, centerPt)
- global CONSTANTS CellHulls HashedCells
+ global CellHulls HashedCells
newHull = [];
@@ -17,7 +41,7 @@ function newHull = ForceDisjointSeg(hull, time, centerPt)
return;
end
- bwimg = zeros(CONSTANTS.imageSize);
+ bwimg = zeros(Metadata.GetDimensions('rc'));
bwimg(pix(bPickPix)) = 1;
CC = bwconncomp(bwimg,8);
diff --git a/src/MATLAB/+Segmentation/FrameSegmentor.m b/src/MATLAB/+Segmentation/FrameSegmentor.m
index cf27503772dd86a833edfccb478842f83ec75e80..8a02934e94abda142c74225616c6d2e98359ca82 100644
--- a/src/MATLAB/+Segmentation/FrameSegmentor.m
+++ b/src/MATLAB/+Segmentation/FrameSegmentor.m
@@ -32,6 +32,30 @@
%
% See also Load.GetSupportedCellTypes, Segmentation.FrameSegmentor_Adult, REGIONPROPS.
%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function hulls = FrameSegmentor(chanIm, primaryChan, t, vararagin)
hulls = [];
diff --git a/src/MATLAB/+Segmentation/FrameSegmentor_Adult.m b/src/MATLAB/+Segmentation/FrameSegmentor_Adult.m
index 9aa0a01626586cd73f4899af72af7f7b73931f60..e834eaca84dcf3e345248ef9619406a3c4ed6865 100644
--- a/src/MATLAB/+Segmentation/FrameSegmentor_Adult.m
+++ b/src/MATLAB/+Segmentation/FrameSegmentor_Adult.m
@@ -22,6 +22,30 @@
%
% See also Segmentation.FrameSegmentor.
%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function hulls = FrameSegmentor_Adult(chanIm, primaryChan, t, imageAlpha)
hulls = [];
levels = struct('haloLevel',{[]}, 'igLevel',{[]});
diff --git a/src/MATLAB/+Segmentation/FrameSegmentor_Embryonic.m b/src/MATLAB/+Segmentation/FrameSegmentor_Embryonic.m
index f341ec299b8ccadec24c60e513cc6bbad99a8607..8f2ead2f269a59805e40cbf9eec45607d6f7f51b 100644
--- a/src/MATLAB/+Segmentation/FrameSegmentor_Embryonic.m
+++ b/src/MATLAB/+Segmentation/FrameSegmentor_Embryonic.m
@@ -22,6 +22,30 @@
%
% See also Segmentation.FrameSegmentor.
%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function hulls = FrameSegmentor_Embryonic(chanIm, primaryChan, t, imageAlpha)
hulls = [];
diff --git a/src/MATLAB/+Segmentation/FrameSegmentor_MDK.m b/src/MATLAB/+Segmentation/FrameSegmentor_MDK.m
new file mode 100644
index 0000000000000000000000000000000000000000..fdc3088bc4c264517f402873c526b1bc08f119d0
--- /dev/null
+++ b/src/MATLAB/+Segmentation/FrameSegmentor_MDK.m
@@ -0,0 +1,84 @@
+% FrameSegmentor_test - This is a frame segmentor example for identifying
+% cell texture in brightfield imaging and splitting into components using a
+% number of nuclear fluorescent channel markers.
+%
+% hulls = FrameSegmentor(chanIm, primaryChan, t, seRadius)
+% INPUTS:
+% chanIm - A cell array each chanIm{i} contains the image intensity date
+% for the i-th channel at frame t. Some cells may be empty if they were
+% unavailable or not imaged at frame t.
+%
+% primaryChan - A number between 1 and CONSTANTS.numChannels indicating
+% the primary channel for the segmentation. Specific algorithms may use
+% information from other available channels as well.
+%
+% t - The frame number of the image data being passed into the
+% segmentation algorithm.
+%
+% seRadius - Radius of a neaighborhood element for the brightfield
+% texture filter. Increasing the radius will generally connect
+% segmentations.
+%
+%
+% OUTPUTS:
+% hulls - The hulls output should be a structure array with one entry per
+% segmentation result.
+% At a minimum, each hull must contain an 'indexPixels' field, a list of
+% linear indices representing the interior pixels of segmentation results.
+% For example, the PixelIdxList result from a call to regionprops could
+% be used to fill the hulls indexPixels field.
+%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function hulls = FrameSegmentor_MDK(chanIm, primaryChan, t, imageAlpha)
+ hulls = [];
+
+ otherChan = setdiff(1:length(chanIm),primaryChan);
+ % Brightfield texture segmentation
+ im = chanIm{primaryChan};
+ im=mat2gray(im);
+ thresh=imageAlpha*multithresh(im,3);
+ q=imquantize(im,thresh);
+ bw=0*im;
+ bw(q==1)=1;
+ bw=imclose(bw,strel('disk',4));
+
+ [L num]=bwlabel(bw);
+ for n=1:num
+ [r c]=find(L==n);
+ idx=find(L==n);
+ if length(r)<50
+ continue
+ end
+ if length(r)>5000
+ continue;
+ end
+ chIdx = Helper.ConvexHull(c,r);
+ if ( isempty(chIdx) )
+ continue;
+ end
+ nh = struct('indexPixels',idx, 'points',{[c(chIdx), r(chIdx)]});
+ hulls = [hulls nh];
+ end
\ No newline at end of file
diff --git a/src/MATLAB/+Segmentation/GetCellTypeParams.m b/src/MATLAB/+Segmentation/GetCellTypeParams.m
index 3532a63ed6c3cf4f4b0a175914ad0b8fb79dab3f..43c1161c8114da4b2a2697b1a305cc86f2fedb18 100644
--- a/src/MATLAB/+Segmentation/GetCellTypeParams.m
+++ b/src/MATLAB/+Segmentation/GetCellTypeParams.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function segArgs = GetCellTypeParams()
global CONSTANTS
diff --git a/src/MATLAB/+Segmentation/MergeSplitCells.m b/src/MATLAB/+Segmentation/MergeSplitCells.m
index d7b22b49d41735ad092669e9cfa17f1528461d69..935720168b96b337ee55c21ecb369575ee88a643 100644
--- a/src/MATLAB/+Segmentation/MergeSplitCells.m
+++ b/src/MATLAB/+Segmentation/MergeSplitCells.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -126,7 +126,7 @@ function [mergeHull, deleteHullIDs] = createMergeCell(mergeIDs)
deleteHullIDs = mergeIDs;
newIndexPixels = vertcat(CellHulls(deleteHullIDs).indexPixels);
- mergeHull = Hulls.CreateHull(CONSTANTS.imageSize, newIndexPixels, CellHulls(deleteHullIDs(1)).time, true);
+ mergeHull = Hulls.CreateHull(Metadata.GetDimensions('rc'), newIndexPixels, CellHulls(deleteHullIDs(1)).time, true);
end
function edge = getTrackEdge(t, trackID)
diff --git a/src/MATLAB/+Segmentation/Michel.m b/src/MATLAB/+Segmentation/Michel.m
index dfe252c3c8e6a60846c8f920f812f948e0bbb822..89ef91eb77586a998a2df43ed6cca463e3e4fd5e 100644
--- a/src/MATLAB/+Segmentation/Michel.m
+++ b/src/MATLAB/+Segmentation/Michel.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function [bw] = Michel(im,neighborhood)
% create a gaussian kernel and blur the image a lot
h = fspecial('gaussian', 7, 5);
diff --git a/src/MATLAB/+Segmentation/PartialImageSegment.m b/src/MATLAB/+Segmentation/PartialImageSegment.m
index a120858061119608e0f84fc229d9f2f28f497c44..27e8bf97f098761919dcabb055fc52f24d24f42c 100644
--- a/src/MATLAB/+Segmentation/PartialImageSegment.m
+++ b/src/MATLAB/+Segmentation/PartialImageSegment.m
@@ -4,10 +4,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -36,8 +36,8 @@ function hulls = PartialImageSegment(chanImg, xyCenterPt, subSize, primaryChan,
imSize = max([imSize; size(chanImg{c})],[],1);
end
- rcCoordMin = floor(Helper.SwapXY_RC(xyCenterPt) - subSize/2);
- rcCoordMax = ceil(Helper.SwapXY_RC(xyCenterPt) + subSize/2);
+ rcCoordMin = floor(Utils.SwapXY_RC(xyCenterPt) - subSize/2);
+ rcCoordMax = ceil(Utils.SwapXY_RC(xyCenterPt) + subSize/2);
rcCoordMin(rcCoordMin < 1) = 1;
rcCoordMax(rcCoordMax > imSize) = imSize(rcCoordMax > imSize);
@@ -62,15 +62,16 @@ function hulls = PartialImageSegment(chanImg, xyCenterPt, subSize, primaryChan,
end
function newHulls = fixupFromSubimage(rcCoordMin, origSize, subSize, hulls)
- newHulls = hulls;
+ newHulls = [];
rcOffset = rcCoordMin - 1;
for i=1:length(hulls)
- newHulls(i).indexPixels = makeGlobalPix(hulls(i).indexPixels, origSize, subSize, rcOffset);
+ idxPix = makeGlobalPix(hulls(i).indexPixels, origSize, subSize, rcOffset);
+ newHulls = [newHulls Hulls.CreateHull(origSize, idxPix)];
end
end
function globIdx = makeGlobalPix(locIdx, globSz, locSz, rcOffset)
- globCoords = Helper.IndexToCoord(locSz, locIdx) + repmat(rcOffset, size(locIdx,1),1);
- globIdx = Helper.CoordToIndex(globSz, globCoords);
+ globCoords = Utils.IndToCoord(locSz, locIdx) + repmat(rcOffset, size(locIdx,1),1);
+ globIdx = Utils.CoordToInd(globSz, globCoords);
end
diff --git a/src/MATLAB/+Segmentation/RemoveSegmentationEdit.m b/src/MATLAB/+Segmentation/RemoveSegmentationEdit.m
index 2d5d93730b87fdcdcc211a43bed35a51e4595e32..c6e13bed56d11b07aa36224bbedacedfaa670689 100644
--- a/src/MATLAB/+Segmentation/RemoveSegmentationEdit.m
+++ b/src/MATLAB/+Segmentation/RemoveSegmentationEdit.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Segmentation/ResegFromTree.m b/src/MATLAB/+Segmentation/ResegFromTree.m
deleted file mode 100644
index f0146de5279d806c1101b41cea77db90e0aba4b6..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Segmentation/ResegFromTree.m
+++ /dev/null
@@ -1,68 +0,0 @@
-% segEdits = ResegFromTree(rootTracks)
-%
-% Attempt to correct segmentation (and tracking) errors by exploiting a
-% corrected lineage tree.
-%
-% rootTracks - List of root tree tracks to resegment
-
-function tLast = ResegFromTree(rootTracks, tStart, tEnd)
- global HashedCells CellTracks CellHulls Costs
-
- global Figures CONSTANTS
- outMovieDir = fullfile('B:\Users\mwinter\Documents\Figures\Reseg',CONSTANTS.datasetName);
-
- if ( ~exist('tStart','var') )
- tStart = 2;
- end
-
- if ( ~exist('tEnd','var') )
- tEnd = length(HashedCells);
- end
-
- tStart = max(tStart,2);
- tMax = length(HashedCells);
- tEnd = min(tEnd, tMax);
-
- checkTracks = Segmentation.ResegFromTree.GetSubtreeTracks(rootTracks);
-
- invalidPreserveTracks = [];
-
- % Need to worry about deleted hulls?
- costMatrix = Costs;
- bDeleted = ([CellHulls.deleted] > 0);
- costMatrix(bDeleted,:) = 0;
- costMatrix(:,bDeleted) = 0;
-
- mexDijkstra('initGraph', costMatrix);
-
- for t=tStart:tEnd
- checkTracks = setdiff(checkTracks, invalidPreserveTracks);
-
- newPreserveTracks = Segmentation.ResegFromTree.FixupSingleFrame(t, checkTracks, tMax);
-
- checkTracks = [checkTracks newPreserveTracks];
- [dump sortedIdx] = unique(checkTracks, 'first');
- sortedIdx = sort(sortedIdx);
- checkTracks = checkTracks(sortedIdx);
-
- bInvalidPreserveTracks = cellfun(@(x)(isempty(x)),{CellTracks(checkTracks).startTime});
- invalidPreserveTracks = checkTracks(bInvalidPreserveTracks);
-
- % DEBUG
- Figures.time = t;
- validPreserveTracks = checkTracks(~bInvalidPreserveTracks);
- famID = CellTracks(validPreserveTracks(1)).familyID;
-
- UI.DrawTree(famID);
- UI.TimeChange(t);
- drawnow();
-
- % Make Movie code
-% saveMovieFrame(t, famID, outMovieDir);
-
- tLast = t;
- end
-
-% saveMovieFrame(1, famID, outMovieDir);
-end
-
diff --git a/src/MATLAB/+Segmentation/ResegRetrackLink.m b/src/MATLAB/+Segmentation/ResegRetrackLink.m
deleted file mode 100644
index 15f19d7292d6cbf827298c5e4c5e252a34104159..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Segmentation/ResegRetrackLink.m
+++ /dev/null
@@ -1,36 +0,0 @@
-function ResegRetrackLink()
- global HashedCells CellTracks CellFamilies
-
-% [iters totalTime] = LinkFirstFrameTrees();
-% LogAction('Completed Tree Inference', [iters totalTime],[]);
-
- tic();
- % Resegment and track
- goodTracks = [];
- for i=1:length(HashedCells{1})
- trackID = HashedCells{1}(i).trackID;
- familyID = CellTracks(trackID).familyID;
- endTime = CellFamilies(familyID).endTime;
- if ( endTime < length(HashedCells) )
- continue;
- end
-
- goodTracks = [goodTracks trackID];
- end
-
- if ( isempty(goodTracks) )
- return;
- end
-
- Segmentation.ResegmentFromTree(goodTracks);
- tReseg = toc();
-
- tic();
- Tracker.HematoTracker();
- tRetrack = toc();
- Error.LogAction('Resegmentation/Tracking',[tReseg tRetrack],[]);
-
- % Rerun tree-inference for first-frame cells
- [iters totalTime] = Families.LinkFirstFrameTrees();
- Error.LogAction('Completed Tree Inference', [iters totalTime],[]);
-end
\ No newline at end of file
diff --git a/src/MATLAB/+Segmentation/ResegmentHull.m b/src/MATLAB/+Segmentation/ResegmentHull.m
index 8ab4b54a170c3cb27335252b6edceb3976ff3c14..e45d71badd0f2afb8777972b203f03634e938c9e 100644
--- a/src/MATLAB/+Segmentation/ResegmentHull.m
+++ b/src/MATLAB/+Segmentation/ResegmentHull.m
@@ -3,23 +3,23 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-%
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
-%
+%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
-%
+%
% You should have received a copy of the GNU General Public License
-% along with LEVer in file "gnu gpl v3.txt". If not, see
+% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -34,8 +34,9 @@ if ( ~exist('bUserEdit','var') )
end
% guassian clustering (x,y,...) coordinates of cell interior
-rcCoords = Helper.IndexToCoord(CONSTANTS.imageSize, hull.indexPixels);
-xyCoords = Helper.SwapXY_RC(rcCoords);
+rcImageDims = Metadata.GetDimensions('rc');
+rcCoords = Utils.IndToCoord(rcImageDims, hull.indexPixels);
+xyCoords = Utils.SwapXY_RC(rcCoords);
typeParams = Load.GetCellTypeStructure(CONSTANTS.cellType);
if ( typeParams.splitParams.useGMM )
@@ -54,7 +55,7 @@ end
for i=1:k
newHullPixels = hull.indexPixels( kIdx==i );
- outputHull = Hulls.CreateHull(CONSTANTS.imageSize, newHullPixels, hull.time, bUserEdit);
+ outputHull = Hulls.CreateHull(rcImageDims, newHullPixels, hull.time, bUserEdit);
newHulls = [newHulls outputHull];
end
diff --git a/src/MATLAB/+Segmentation/SegAndTrack.m b/src/MATLAB/+Segmentation/SegAndTrack.m
index 6e170204ade844af51775ebc133de1e0f2438241..995a48ba27a79d03f9a7959c878d3ed85ddace75 100644
--- a/src/MATLAB/+Segmentation/SegAndTrack.m
+++ b/src/MATLAB/+Segmentation/SegAndTrack.m
@@ -5,10 +5,10 @@
% EW - rewrite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -35,7 +35,7 @@ function [errStatus, segInfo] = SegAndTrack()
settings = Load.ReadSettings();
[settings.matFile,settings.matFilePath,FilterIndex] = uiputfile('.mat','Save edits',...
- [CONSTANTS.datasetName '_LEVer.mat']);
+ [Metadata.GetDatasetName() '_LEVer.mat']);
if(~FilterIndex)
return;
@@ -52,10 +52,10 @@ function [errStatus, segInfo] = SegAndTrack()
end
segArgs = Segmentation.GetCellTypeParams();
- [errStatus tSeg tTrack] = Segmentation.SegAndTrackDataset(CONSTANTS.rootImageFolder, CONSTANTS.datasetName, CONSTANTS.imageNamePattern, numProcessors, segArgs);
+ [errStatus,tSeg,tTrack] = Segmentation.SegAndTrackDataset(numProcessors, segArgs);
if ( ~isempty(errStatus) )
- errFilename = [CONSTANTS.datasetName '_segtrack_err.log'];
+ errFilename = [Metadata.GetDatasetName() '_segtrack_err.log'];
msgbox(['An error occured during segmentation and tracking. For further details see log file: ' errFilename],'SegAndTrack Error','warn');
diff --git a/src/MATLAB/+Segmentation/SegAndTrackDataset.m b/src/MATLAB/+Segmentation/SegAndTrackDataset.m
index c3b8138498f24790e4c4ba8a01b4c3db522219c0..c5565d328f3a2b23ae599b8d0c447fbe763b36ec 100644
--- a/src/MATLAB/+Segmentation/SegAndTrackDataset.m
+++ b/src/MATLAB/+Segmentation/SegAndTrackDataset.m
@@ -1,4 +1,28 @@
-function [errStatus tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, namePattern, numProcessors, segArgs)
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function [errStatus,tSeg,tTrack] = SegAndTrackDataset(numProcessors, segArgs)
global CONSTANTS CellHulls HashedCells ConnectedDist
errStatus = sprintf('Unknown Error\n');
@@ -8,24 +32,23 @@ function [errStatus tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, n
%% Segmentation
tic
- % Remove trailing \ or / from rootFolder
- if ( (rootFolder(end) == '\') || (rootFolder(end) == '/') )
- rootFolder = rootFolder(1:end-1);
+ if ( Metadata.GetNumberOfFrames() < 1 )
+ return;
end
- % Set CONSTANTS.imageSize as soon as possible
- [channelList,frameList] = Helper.GetImListInfo(CONSTANTS.rootImageFolder, CONSTANTS.imageNamePattern);
-
- Load.AddConstant('numFrames', frameList(end),1);
- Load.AddConstant('numChannels', channelList(end),1);
-
- numProcessors = min(numProcessors, CONSTANTS.numFrames);
-
- if ( CONSTANTS.numFrames < 1 )
- return;
+ numProcessors = min(numProcessors, Metadata.GetNumberOfFrames());
+
+ numProcessors = min(numProcessors, Metadata.GetNumberOfFrames());
+ bytesPerIm = prod(Metadata.GetDimensions()) * Metadata.GetNumberOfChannels() * 8;
+ m = memory;
+ maxWorkers = min(numProcessors,floor(m.MaxPossibleArrayBytes / bytesPerIm));
+
+ % Remove trailing \ or / from rootFolder
+ if ( (CONSTANTS.rootImageFolder(end) == '\') || (CONSTANTS.rootImageFolder(end) == '/') )
+ CONSTANTS.rootImageFolder = CONSTANTS.rootImageFolder(1:end-1);
end
- fprintf('Segmenting (using %s processors)...\n',num2str(numProcessors));
+ fprintf('Segmenting (using %s processors)...\n',num2str(maxWorkers));
if(~isempty(dir('.\segmentationData')))
removeOldFiles('segmentationData', 'err_*.log');
@@ -33,18 +56,9 @@ function [errStatus tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, n
removeOldFiles('segmentationData', 'done_*.txt');
end
- imSet = Helper.LoadIntensityImageSet(1);
-
- imSizes = zeros(length(imSet),2);
- for i=1:length(imSet)
- imSizes(i,:) = size(imSet{i});
- end
-
- Load.AddConstant('imageSize', max(imSizes,[],1),1);
-
- if ( ndims(CONSTANTS.imageSize) < 2 || ndims(CONSTANTS.imageSize) >= 3 )
+ if ( isempty(Metadata.GetDimensions()) )
cltime = clock();
- errStatus = sprintf('%02d:%02d:%02.1f - Images are empty or have incorrect dimensions [%s]\n',cltime(4),cltime(5),cltime(6), num2str(CONSTANTS.imageSize));
+ errStatus = sprintf('%02d:%02d:%02.1f - Images dimensions are empty\n',cltime(4),cltime(5),cltime(6));
return;
end
@@ -53,30 +67,69 @@ function [errStatus tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, n
mkdir('segmentationData');
end
- for procID=1:numProcessors
- segCmd = makeSegCommand(procID,numProcessors,CONSTANTS.numChannels,CONSTANTS.numFrames,CONSTANTS.cellType,CONSTANTS.primaryChannel,rootFolder,namePattern,segArgs);
- system(['start ' segCmd ' && exit']);
+ metadataFile = fullfile(CONSTANTS.rootImageFolder, [Metadata.GetDatasetName() '.json']);
+ primaryChannel = CONSTANTS.primaryChannel;
+ cellType = CONSTANTS.cellType;
+
+ if ( isdeployed() )
+ %% compliled version
+ % Must use separately compiled segmentor algorithm in compiled LEVer
+ % because parallel processing toolkit is unsupported
+ for procID=1:maxWorkers
+ segCmd = makeSegCommand(procID,maxWorkers,primaryChannel,metadataFile,cellType,segArgs);
+ system(['start ' segCmd ' && exit']);
+ end
+ else
+ %% single threaded version
+% for procID=1:maxWorkers
+% Segmentor(procID,maxWorkers,primaryChannel,metadataFile,cellType,segArgs{:});
+% end
+
+ %% spmd version
+ poolObj = gcp('nocreate');
+ if (~isempty(poolObj))
+ oldWorkers = poolObj.NumWorkers;
+ if (oldWorkers~=maxWorkers)
+ delete(poolObj);
+ parpool(maxWorkers);
+ end
+ else
+ oldWorkers = 0;
+ parpool(maxWorkers);
+ end
+
+ spmd
+ Segmentor(labindex,numlabs,primaryChannel,metadataFile,cellType,segArgs{:});
+ end
+
+ if (oldWorkers~=0 && oldWorkers~=maxWorkers)
+ delete(gcp);
+ if (oldWorkers>0)
+ parpool(oldWorkers);
+ end
+ end
end
-% for procID=1:numProcessors
-% Segmentor(procID,numProcessors,CONSTANTS.numChannels,CONSTANTS.numFrames,CONSTANTS.cellType,CONSTANTS.primaryChannel,rootFolder,namePattern,segArgs{:});
-% end
-
- bSegFileExists = false(1,numProcessors);
- for procID=1:numProcessors
- errFile = ['.\segmentationData\err_' num2str(procID) '.log'];
- fileName = ['.\segmentationData\objs_' num2str(procID) '.mat'];
- semFile = ['.\segmentationData\done_' num2str(procID) '.txt'];
- semDesc = dir(semFile);
- fileDescriptor = dir(fileName);
- efd = dir(errFile);
- while((isempty(fileDescriptor) || isempty(semDesc)) && isempty(efd))
- pause(3)
- fileDescriptor = dir(fileName);
- efd = dir(errFile);
- semDesc = dir(semFile);
+
+ %% collate output
+ bSegFileExists = false(1,maxWorkers);
+ bSemFileExists = false(1,maxWorkers);
+ bErrFileExists = false(1,maxWorkers);
+
+ bProcFinish = false(1,maxWorkers);
+ while ( ~all(bProcFinish) )
+ pause(3);
+
+ for procID=1:maxWorkers
+ errFile = ['.\segmentationData\err_' num2str(procID) '.log'];
+ segFile = ['.\segmentationData\objs_' num2str(procID) '.mat'];
+ semFile = ['.\segmentationData\done_' num2str(procID) '.txt'];
+
+ bErrFileExists(procID) = ~isempty(dir(errFile));
+ bSegFileExists(procID) = ~isempty(dir(segFile));
+ bSemFileExists(procID) = ~isempty(dir(semFile));
end
- bSegFileExists(procID) = ~isempty(fileDescriptor);
+ bProcFinish = bErrFileExists | (bSegFileExists & bSemFileExists);
end
if ( ~all(bSegFileExists) )
@@ -104,16 +157,14 @@ function [errStatus tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, n
try
cellSegments = [];
- frameOrder = [];
- for procID=1:numProcessors
- fileName = ['.\segmentationData\objs_' num2str(procID) '.mat'];
+ for procID=1:maxWorkers
+ segFile = ['.\segmentationData\objs_' num2str(procID) '.mat'];
- tstLoad = whos('-file', fileName);
+ tstLoad = whos('-file', segFile);
- load(fileName);
+ load(segFile);
cellSegments = [cellSegments hulls];
- frameOrder = [frameOrder frameTimes];
end
catch excp
@@ -133,20 +184,12 @@ function [errStatus tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, n
% Sort segmentations and fluorescent data so that they are time ordered
segtimes = [cellSegments.time];
- [srtSegs srtIdx] = sort(segtimes);
+ [~,srtIdx] = sort(segtimes);
CellHulls = Helper.MakeInitStruct(Helper.GetCellHullTemplate(), cellSegments(srtIdx));
- % Make sure center of mass is available
- for i=1:length(CellHulls)
- [r c] = ind2sub(CONSTANTS.imageSize, CellHulls(i).indexPixels);
- CellHulls(i).centerOfMass = mean([r c], 1);
- end
-
- [srtFrames srtIdx] = sort(frameOrder);
-
- fprintf('Building Connected Component Distances... ');
- HashedCells = cell(1,CONSTANTS.numFrames);
- for t=1:CONSTANTS.numFrames
+ %% Build hashed cell list
+ HashedCells = cell(1,Metadata.GetNumberOfFrames());
+ for t=1:Metadata.GetNumberOfFrames()
HashedCells{t} = struct('hullID',{}, 'trackID',{});
end
@@ -154,9 +197,10 @@ function [errStatus tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, n
HashedCells{CellHulls(i).time} = [HashedCells{CellHulls(i).time} struct('hullID',{i}, 'trackID',{0})];
end
+ %% Create connected component distances for tracker
+ fprintf('Building Connected Component Distances... ');
ConnectedDist = [];
Tracker.BuildConnectedDistance(1:length(CellHulls), 0, 1);
- Segmentation.WriteSegData('segmentationData',datasetName);
fprintf(1,'\nDone\n');
tSeg = toc;
@@ -164,19 +208,16 @@ function [errStatus tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, n
%% Tracking
tic
fprintf(1,'Tracking...');
- fnameIn=['.\segmentationData\SegObjs_' datasetName '.txt'];
- fnameOut=['.\segmentationData\Tracked_' datasetName '.txt'];
- system(['MTC.exe ' num2str(CONSTANTS.dMaxCenterOfMass) ' ' num2str(CONSTANTS.dMaxConnectComponentTracker) ' "' fnameIn '" "' fnameOut '" > out.txt']);
+ [hullTracks,gConnect] = trackerMex(CellHulls, ConnectedDist, Metadata.GetNumberOfFrames(), CONSTANTS.dMaxCenterOfMass, CONSTANTS.dMaxConnectComponentTracker);
fprintf('Done\n');
tTrack = toc;
%% Import into LEVer's data sturcture
- [objTracks gConnect] = Tracker.ReadTrackData('segmentationData', CONSTANTS.datasetName);
fprintf('Finalizing Data...');
try
- Tracker.BuildTrackingData(objTracks, gConnect);
+ Tracker.BuildTrackingData(hullTracks, gConnect);
catch excp
cltime = clock();
@@ -190,16 +231,13 @@ function [errStatus tSeg tTrack] = SegAndTrackDataset(rootFolder, datasetName, n
errStatus = '';
end
-function segCmd = makeSegCommand(procID, numProc, numChannels, numFrames, cellType, primaryChannel, rootFolder, imagePattern, segArg)
+function segCmd = makeSegCommand(procID, numProc, primaryChannel, metadataFile, cellType, segArg)
segCmd = 'Segmentor';
segCmd = [segCmd ' "' num2str(procID) '"'];
segCmd = [segCmd ' "' num2str(numProc) '"'];
- segCmd = [segCmd ' "' num2str(numChannels) '"'];
- segCmd = [segCmd ' "' num2str(numFrames) '"'];
- segCmd = [segCmd ' "' cellType '"'];
segCmd = [segCmd ' "' num2str(primaryChannel) '"'];
- segCmd = [segCmd ' "' rootFolder '"'];
- segCmd = [segCmd ' "' imagePattern '"'];
+ segCmd = [segCmd ' "' metadataFile '"'];
+ segCmd = [segCmd ' "' cellType '"'];
for i=1:length(segArg)
segCmd = [segCmd ' "' num2str(segArg{i}) '"'];
diff --git a/src/MATLAB/+Segmentation/SplitHull.m b/src/MATLAB/+Segmentation/SplitHull.m
index b5d2b79c12a06cbaca209ec10340b42300656982..3571e70c77eb447b864597384b32df6c84a51f6e 100644
--- a/src/MATLAB/+Segmentation/SplitHull.m
+++ b/src/MATLAB/+Segmentation/SplitHull.m
@@ -4,10 +4,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Segmentation/WriteSegData.m b/src/MATLAB/+Segmentation/WriteSegData.m
index 0d5066fb1df28d866ed4b056b73e3c5139e7903d..87acbaf6e036d8855d6223a82f33638e82aab81b 100644
--- a/src/MATLAB/+Segmentation/WriteSegData.m
+++ b/src/MATLAB/+Segmentation/WriteSegData.m
@@ -1,5 +1,36 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function WriteSegData(DatasetDir, DatasetName)
-global CONSTANTS CellHulls ConnectedDist
+global CellHulls ConnectedDist
+
+% fname=Helper.GetFullImagePath(1);
+% im = Helper.LoadIntensityImage(fname);
+% if isempty(im)
+% fprintf('error - unable to extract image size - tracking will fail\n');
+% end
+rcImageDims = Metadata.GetDimensions('rc');
th = max([CellHulls.time]);
hashedHulls = cell(th,1);
@@ -15,7 +46,7 @@ fprintf(fid,'%d %d\n',th,length(CellHulls) );
for i=1:length(hashedHulls)
fprintf(fid,'%d\n',length(hashedHulls{i}) );
for j=1:length(hashedHulls{i})
- [r c]=ind2sub(CONSTANTS.imageSize,CellHulls(hashedHulls{i}(j)).indexPixels);
+ [r c]=ind2sub(rcImageDims,CellHulls(hashedHulls{i}(j)).indexPixels);
COM=round(mean([r c],1));
fprintf(fid,'%d %d %d %d:',COM(2),COM(1),length(r),size(ConnectedDist{hashedHulls{i}(j)},1) );
for k=1:size(ConnectedDist{hashedHulls{i}(j)},1)
diff --git a/src/MATLAB/+Tracker/AssignEdge.m b/src/MATLAB/+Tracker/AssignEdge.m
index 2e8876b21a9a2d25e92655ed4dbb3062e22992ef..d2d68935f54b4bec68bd3ec0aeff537a9cdcdaa6 100644
--- a/src/MATLAB/+Tracker/AssignEdge.m
+++ b/src/MATLAB/+Tracker/AssignEdge.m
@@ -4,6 +4,30 @@
% assignment for assignHull such that it will be on the same track as
% trackHull.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function changedHulls = AssignEdge(trackHull, assignHull)
global CellHulls CellTracks CellFamilies
diff --git a/src/MATLAB/+Tracker/BuildConnectedDistance.m b/src/MATLAB/+Tracker/BuildConnectedDistance.m
index 87f8ff76cce177ffe53b3b07da7e7029c6c4512e..a7395ddc7a5df5c3b8e5b85eb2e1f3cd36ca6f25 100644
--- a/src/MATLAB/+Tracker/BuildConnectedDistance.m
+++ b/src/MATLAB/+Tracker/BuildConnectedDistance.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/BuildTrackingData.m b/src/MATLAB/+Tracker/BuildTrackingData.m
index 8a57b9f09c0b58ec87e268d909a1c18d3fd68fc5..e31ebce6644de9773ac231b8bbe998b08beac7f6 100644
--- a/src/MATLAB/+Tracker/BuildTrackingData.m
+++ b/src/MATLAB/+Tracker/BuildTrackingData.m
@@ -1,5 +1,29 @@
-function BuildTrackingData(objTracks, gConnect)
- global CONSTANTS Costs GraphEdits ResegLinks CellHulls CellFamilies CellTracks HashedCells CellPhenotypes
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function BuildTrackingData(hullTracks, gConnect)
+ global Costs GraphEdits ResegLinks CellHulls CellFamilies CellTracks HashedCells CellPhenotypes
%ensure that the globals are empty
Costs = gConnect;
@@ -13,18 +37,15 @@ function BuildTrackingData(objTracks, gConnect)
CellPhenotypes = struct('descriptions', {{'died'}}, 'hullPhenoSet', {zeros(2,0)});
hullList = [];
- for i=length(objTracks):-1:1
- UI.Progressbar((length(objTracks)-i) / (length(objTracks)));
+ for i=length(hullTracks):-1:1
+ UI.Progressbar((length(hullTracks)-i) / (length(hullTracks)));
if ( any(ismember(hullList,i)) )
continue;
end
- if ( objTracks(i).inID ~= 0 )
- continue;
- end
-
- hullList = addToTrack(i,hullList,objTracks);
+ allTrackHulls = find(hullTracks == hullTracks(i));
+ hullList = [hullList addToTrack(allTrackHulls)];
end
if ( length(hullList) ~= length(CellHulls) )
@@ -43,36 +64,19 @@ function BuildTrackingData(objTracks, gConnect)
Dev.PrintIntegrityErrors(errors);
end
-
%create the family trees
Families.ProcessNewborns();
end
-function hullList = addToTrack(hullID, hullList, objTracks)
- global CellHulls
-
- if ( any(ismember(hullList,hullID)) || objTracks(hullID).inID ~= 0 )
+function hullList = addToTrack(allTrackHulls)
+ if ( isempty(allTrackHulls) )
return
end
- Families.NewCellFamily(hullID);
- hullList = [hullList hullID];
-
- nextHull = hullID;
- while ( objTracks(nextHull).outID ~= 0 )
- nextHull = objTracks(nextHull).outID;
-
- if ( any(ismember(hullList,nextHull)) )
- break;
- end
-
- if ( any(ismember(hullList,objTracks(nextHull).inID)) )
- Tracks.AddHullToTrack(nextHull,[],objTracks(nextHull).inID);
- else
- %this runs if there was an error in objTracks data structure
- Families.NewCellFamily(hull);
- end
-
- hullList = [hullList nextHull];
+ Families.NewCellFamily(allTrackHulls(1));
+ for i=2:length(allTrackHulls)
+ Tracks.AddHullToTrack(allTrackHulls(i),[],allTrackHulls(i-1));
end
-end
\ No newline at end of file
+
+ hullList = allTrackHulls;
+end
diff --git a/src/MATLAB/+Tracker/CalcHullConnectedDistances.m b/src/MATLAB/+Tracker/CalcHullConnectedDistances.m
index 77d42e286fc4e104b78e359aaa1b2a828cfabe12..4208bcb0af9b81fa79d9af0f7402c9e7222980cc 100644
--- a/src/MATLAB/+Tracker/CalcHullConnectedDistances.m
+++ b/src/MATLAB/+Tracker/CalcHullConnectedDistances.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function ccDist = CalcHullConnectedDistances(hullID, nextHullIDs, hullPerims, hulls)
global CONSTANTS
@@ -20,8 +44,9 @@ function ccDist = CalcHullConnectedDistances(hullID, nextHullIDs, hullPerims, hu
return;
end
+ rcImageDims = Metadata.GetDimensions('rc');
for i=1:length(checkHullIDs)
- chkDist = Helper.CalcConnectedDistance(hullID,checkHullIDs(i), CONSTANTS.imageSize, hullPerims, hulls);
+ chkDist = Helper.CalcConnectedDistance(hullID,checkHullIDs(i), rcImageDims, hullPerims, hulls);
ccDist(chkHullIdx(i)) = chkDist;
end
end
diff --git a/src/MATLAB/+Tracker/CheckGraphEdits.m b/src/MATLAB/+Tracker/CheckGraphEdits.m
index 02423281fc181c9e78ad06b358af6870676cc106..5e9752749b481b736cf061387f8dcf39daa067eb 100644
--- a/src/MATLAB/+Tracker/CheckGraphEdits.m
+++ b/src/MATLAB/+Tracker/CheckGraphEdits.m
@@ -4,10 +4,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/ClearCostHulls.m b/src/MATLAB/+Tracker/ClearCostHulls.m
deleted file mode 100644
index afe45286d5af4be792e1d9a3e4634784afb64d1d..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Tracker/ClearCostHulls.m
+++ /dev/null
@@ -1,18 +0,0 @@
-% ClearCostEdges(hulls)
-% Zeros all incoming and outgoing edges from hulls in Costs graph, also
-% updates GraphEdits and cached cost matrix.
-
-function ClearCostHulls(hulls)
- global Costs GraphEdits CachedCostMatrix
-
- for i=1:length(hulls)
- Costs(hulls(i),:) = 0;
- CachedCostMatrix(hulls(i),:) = 0;
- GraphEdits(hulls(i),:) = 0;
-
- Costs(:,hulls(i)) = 0;
- CachedCostMatrix(:,hulls(i)) = 0;
- GraphEdits(:,hulls(i)) = 0;
- end
-end
-
diff --git a/src/MATLAB/+Tracker/ConvertTrackingData.m b/src/MATLAB/+Tracker/ConvertTrackingData.m
deleted file mode 100644
index 06ffffa6eacdfa7aa6bf3d182cb26f96d33e2b74..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Tracker/ConvertTrackingData.m
+++ /dev/null
@@ -1,159 +0,0 @@
-% ConvertTrackingData.m - Takes the data structure from the tracking data
-% and creates LEVer's data scheme
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-%
-% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-%
-% LEVer is free software: you can redistribute it and/or modify
-% it under the terms of the GNU General Public License as published by
-% the Free Software Foundation, either version 3 of the License, or
-% (at your option) any later version.
-%
-% LEVer is distributed in the hope that it will be useful,
-% but WITHOUT ANY WARRANTY; without even the implied warranty of
-% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-% GNU General Public License for more details.
-%
-% You should have received a copy of the GNU General Public License
-% along with LEVer in file "gnu gpl v3.txt". If not, see
-% <http://www.gnu.org/licenses/>.
-%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-function ConvertTrackingData(objHulls,gConnect)
-
-global Costs GraphEdits ResegLinks CellHulls CellFamilies CellTracks HashedCells CellPhenotypes ConnectedDist Log CONSTANTS
-
-%ensure that the globals are empty
-Costs = [];
-GraphEdits = [];
-ResegLinks = [];
-CellHulls = [];
-CellFamilies = [];
-CellTracks = [];
-HashedCells = [];
-ConnectedDist = [];
-CellPhenotypes = [];
-Log = [];
-
-Costs = gConnect;
-GraphEdits = sparse([], [], [], size(Costs,1), size(Costs,2), round(0.1*size(Costs,2)));
-ResegLinks = sparse([], [], [], size(Costs,1), size(Costs,2), round(0.1*size(Costs,2)));
-
-connDist = cell(1,length(objHulls));
-
-%Initialize Structures
-cellHulls = struct(...
- 'time', {},...
- 'points', {},...
- 'centerOfMass', {},...
- 'indexPixels', {},...
- 'deleted', {},...
- 'userEdited', {});
-%Initialize Cell types
-CellPhenotypes = struct('descriptions', {{'died' 'ambiguous' 'off screen'}}, 'hullPhenoSet', {zeros(2,0)}, 'colors',{[0 0 0;.549 .28235 .6235;0 1 1]});
-
-%loop through the Hulls
-parfor i=1:length(objHulls)
- cellHulls(i).time = objHulls(i).t;
- cellHulls(i).points = objHulls(i).points;
- cellHulls(i).centerOfMass = objHulls(i).COM;
- cellHulls(i).indexPixels = objHulls(i).indPixels;
- cellHulls(i).deleted = false;
- cellHulls(i).userEdited = false;
-
- connDist{i} = updateConnectedDistance(objHulls(i), objHulls, objHulls(i).DarkConnectedHulls);
-end
-ConnectedDist = connDist;
-CellHulls = cellHulls;
-
-% Initialize HashedCells such that
-tmax = max([CellHulls.time]);
-HashedCells = cell(1,tmax);
-for t=1:tmax
- HashedCells{t} = struct('hullID',{}, 'trackID',{});
-end
-
-%walk through the tracks
-progress = 1;
-iterations = length(objHulls);
-hullList = [];
-for i=length(objHulls):-1:1
- progress = progress+1;
- UI.Progressbar(progress/iterations);
- if(any(ismember(hullList,i))),continue,end
- if(objHulls(i).inID~=0),continue,end
- hullList = addToTrack(i,hullList,objHulls);
-end
-
-%add any hulls that were missed
-if(length(hullList)~=length(CellHulls))
- reprocess = find(ismember(1:length(CellHulls),hullList)==0);
- progress = 1;
- iterations = length(objHulls);
- for i=1:length(reprocess)
- progress = progress+1;
- UI.Progressbar(progress/iterations);
- Families.NewCellFamily(reprocess(i));
- end
-end
-UI.Progressbar(1);%clear it out
-
-errors = mexIntegrityCheck();
-if ( ~isempty(errors) )
- Dev.PrintIntegrityErrors(errors);
-end
-
-% Build initial CachedCostMatrix for new data
-Load.InitializeCachedCosts(1);
-
-% try to patch Wehi data
-if strcmp(CONSTANTS.cellType, 'Wehi')
- Tracker.PatchWehi();
-end
-
-%create the family trees
-Families.ProcessNewborns();
-end
-
-function hullList = addToTrack(hull,hullList,objHulls)
-%error checking
-if(any(ismember(hullList,hull)) || objHulls(hull).inID ~= 0)
- %already part of a track
- return
-end
-
-Families.NewCellFamily(hull);
-hullList = [hullList hull];
-
-while(objHulls(hull).outID~=0)
- hull = objHulls(hull).outID;
- if(any(ismember(hullList,hull))),break,end
- if(any(ismember(hullList,objHulls(hull).inID)))
- Tracks.AddHullToTrack(hull,[],objHulls(hull).inID);
- else
- %this runs if there was an error in objHulls data structure
- Families.NewCellFamily(hull);
- end
- hullList = [hullList hull];
-end
-end
-
-function connDist = updateConnectedDistance(fromObj, objHulls, connectedHulls)
- connDist = connectedHulls;
-
- if ( isempty(connectedHulls) )
- return;
- end
-
- zeroDist = find(connectedHulls(:,2) == 0);
- for i=1:length(zeroDist)
- toObj = objHulls(connectedHulls(zeroDist(i),1));
- isectDist = 1 - (length(intersect(fromObj.indPixels, toObj.indPixels)) / min(length(fromObj.indPixels), length( toObj.indPixels)));
- connDist(zeroDist(i),2) = isectDist;
- end
-end
diff --git a/src/MATLAB/+Tracker/GetConnectedDistance.m b/src/MATLAB/+Tracker/GetConnectedDistance.m
index 87d48d139c4ccb87eeedc9408329e9310bae0680..a8a0329bd34f8b7847ea13d0da01480468085543 100644
--- a/src/MATLAB/+Tracker/GetConnectedDistance.m
+++ b/src/MATLAB/+Tracker/GetConnectedDistance.m
@@ -2,10 +2,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/GetCostClique.m b/src/MATLAB/+Tracker/GetCostClique.m
index 6de8bedff77c310b63b038c906c0d7fda8ee1898..1a320075ee7020e3337ffa64e355c7d6955246f4 100644
--- a/src/MATLAB/+Tracker/GetCostClique.m
+++ b/src/MATLAB/+Tracker/GetCostClique.m
@@ -1,4 +1,28 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [startHulls nextHulls] = GetCostClique(startHulls, nextHulls, tMax)
global CellHulls Costs
diff --git a/src/MATLAB/+Tracker/GetCostMatrix.m b/src/MATLAB/+Tracker/GetCostMatrix.m
index 593ec5233fe8d5ffbdcbbe6a7808709f0c486740..b0952c081e66c703c91f0f84672c4d7c7fe756d6 100644
--- a/src/MATLAB/+Tracker/GetCostMatrix.m
+++ b/src/MATLAB/+Tracker/GetCostMatrix.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/GetCostSubmatrix.m b/src/MATLAB/+Tracker/GetCostSubmatrix.m
index 2dd7650f5953b3c676b02b7ef87530e7565926ac..9addd2b6bca0cf4d348abd32f646d31b86cbdfd7 100644
--- a/src/MATLAB/+Tracker/GetCostSubmatrix.m
+++ b/src/MATLAB/+Tracker/GetCostSubmatrix.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/GetTrackSegScore.m b/src/MATLAB/+Tracker/GetTrackSegScore.m
index e5cd8767ea412d5c1b01e4dea154140cf05560e7..8ef911d4d694cbe699faf72ec143d21aa15459eb 100644
--- a/src/MATLAB/+Tracker/GetTrackSegScore.m
+++ b/src/MATLAB/+Tracker/GetTrackSegScore.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function trackSegScore = GetTrackSegScore(trackID)
trackSegScore = 1.0;
end
\ No newline at end of file
diff --git a/src/MATLAB/+Tracker/GetTrackingCosts.m b/src/MATLAB/+Tracker/GetTrackingCosts.m
index 3c010601392b020d1d3708b328225ef607d4aa4e..c2a38bd215811171ef8cf3e4bd25a8ff953f0d19 100644
--- a/src/MATLAB/+Tracker/GetTrackingCosts.m
+++ b/src/MATLAB/+Tracker/GetTrackingCosts.m
@@ -5,10 +5,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/GraphEditAddMitosis.m b/src/MATLAB/+Tracker/GraphEditAddMitosis.m
index b98bc4772ce0af066ea780388b99dd2701e568e9..409130b09cb873647383dc2facb757d7ca8cae96 100644
--- a/src/MATLAB/+Tracker/GraphEditAddMitosis.m
+++ b/src/MATLAB/+Tracker/GraphEditAddMitosis.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/GraphEditRemoveEdge.m b/src/MATLAB/+Tracker/GraphEditRemoveEdge.m
index bdd58c83f7ebe52a5c91d80405294c6b22a4e398..bf1e997ca9b4921ff4744a29ed4018c8f80a4cb0 100644
--- a/src/MATLAB/+Tracker/GraphEditRemoveEdge.m
+++ b/src/MATLAB/+Tracker/GraphEditRemoveEdge.m
@@ -5,10 +5,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/GraphEditSetEdge.m b/src/MATLAB/+Tracker/GraphEditSetEdge.m
index 3bef13801b291c286e80cf5c4014a3afe9b31f07..03eb9b0b5012f78115f63f62ee8afaf8ac412ad2 100644
--- a/src/MATLAB/+Tracker/GraphEditSetEdge.m
+++ b/src/MATLAB/+Tracker/GraphEditSetEdge.m
@@ -4,10 +4,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/GraphEditsResetHulls.m b/src/MATLAB/+Tracker/GraphEditsResetHulls.m
index a1e3aa512f72682edf93cd49192f7bafc0e07985..3ce5e9a56ce68febe6cc87d7bf5322550c4ae32b 100644
--- a/src/MATLAB/+Tracker/GraphEditsResetHulls.m
+++ b/src/MATLAB/+Tracker/GraphEditsResetHulls.m
@@ -3,6 +3,30 @@
% Clears all user edits into (bResetBack) and/or out of (bResetForward)
% a hull, updates associated cached costs.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function GraphEditsResetHulls(hulls, bResetForward, bResetBack)
global Costs GraphEdits
diff --git a/src/MATLAB/+Tracker/PatchMatchedTracks.m b/src/MATLAB/+Tracker/PatchMatchedTracks.m
index 9a35dde3358cba28e47794d33639faac873a5f11..6b669771361afa262a14bf7a4ad9666fc9198823 100644
--- a/src/MATLAB/+Tracker/PatchMatchedTracks.m
+++ b/src/MATLAB/+Tracker/PatchMatchedTracks.m
@@ -5,10 +5,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/PatchTracks.m b/src/MATLAB/+Tracker/PatchTracks.m
index 535d55245b7f7a1a72e85b0445eaeb8c527122c3..2b6571a6d74221921c721a601797a02823a60eff 100644
--- a/src/MATLAB/+Tracker/PatchTracks.m
+++ b/src/MATLAB/+Tracker/PatchTracks.m
@@ -5,10 +5,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/PatchWehi.m b/src/MATLAB/+Tracker/PatchWehi.m
index 428a6759440056202ea6c122af7bb0dd96ca2b8e..acc5e87a180c9b3b99faff1994117bf15d97e517 100644
--- a/src/MATLAB/+Tracker/PatchWehi.m
+++ b/src/MATLAB/+Tracker/PatchWehi.m
@@ -5,10 +5,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Walt Mankowski, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/ReadTrackData.m b/src/MATLAB/+Tracker/ReadTrackData.m
index ba6853f9f4909d17488a105d0dd461f65a2bbaa6..b3a7f31fcccf783b44e0fd8ffffa2ca3616423fa 100644
--- a/src/MATLAB/+Tracker/ReadTrackData.m
+++ b/src/MATLAB/+Tracker/ReadTrackData.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function [objTracks gConnect] = ReadTrackData(DatasetDir, DatasetName)
global CellHulls
diff --git a/src/MATLAB/+Tracker/ReassignTracks.m b/src/MATLAB/+Tracker/ReassignTracks.m
index 6140c443da6ab6aca0aef0709e5971006a54b065..1568d8dc26ff52f9dd414736358900cd437c27c7 100644
--- a/src/MATLAB/+Tracker/ReassignTracks.m
+++ b/src/MATLAB/+Tracker/ReassignTracks.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/SiblingDistance.m b/src/MATLAB/+Tracker/SiblingDistance.m
index 9b8e3faa64afbe3526dc9ecb8f4827c4f9c9f3bf..0d4cecd531452902186daa6d3b5b9b10f4496206 100644
--- a/src/MATLAB/+Tracker/SiblingDistance.m
+++ b/src/MATLAB/+Tracker/SiblingDistance.m
@@ -6,10 +6,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -43,7 +43,7 @@ end
hullPerims = containers.Map('KeyType','uint32', 'ValueType','any');
-ccDist = Helper.CalcConnectedDistance(cell1HullID,cell2HullID, CONSTANTS.imageSize, hullPerims, CellHulls);
+ccDist = Helper.CalcConnectedDistance(cell1HullID,cell2HullID, Metadata.GetDimensions('rc'), hullPerims, CellHulls);
distanceCenterOfMass = norm(CellHulls(cell1HullID).centerOfMass - CellHulls(cell2HullID).centerOfMass);
if(distanceCenterOfMass > CONSTANTS.maxCenterOfMassDistance || ccDist > CONSTANTS.maxPixelDistance)
diff --git a/src/MATLAB/+Tracker/TrackAddedHulls.m b/src/MATLAB/+Tracker/TrackAddedHulls.m
index a7f41144a4212170571651cdbb88d3862d03e4ea..f64cba9c9c37f0657c5abdfe14698dd9610d712c 100644
--- a/src/MATLAB/+Tracker/TrackAddedHulls.m
+++ b/src/MATLAB/+Tracker/TrackAddedHulls.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/TrackThroughMerge.m b/src/MATLAB/+Tracker/TrackThroughMerge.m
index f5fcc199948af332f9573e52c62497f6d1e7ae79..ded88adec16a32099e5f28ac9fca190a96120d6c 100644
--- a/src/MATLAB/+Tracker/TrackThroughMerge.m
+++ b/src/MATLAB/+Tracker/TrackThroughMerge.m
@@ -4,10 +4,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/TrackThroughSplit.m b/src/MATLAB/+Tracker/TrackThroughSplit.m
index fa3c6221786bb94a8a1adb5aebdba96a85f3297e..6dc40baaf88860076392e41bc2e3917030b3c820 100644
--- a/src/MATLAB/+Tracker/TrackThroughSplit.m
+++ b/src/MATLAB/+Tracker/TrackThroughSplit.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracker/UpdateCachedCosts.m b/src/MATLAB/+Tracker/UpdateCachedCosts.m
index 4e174ea7b8c04957a2d66671d6ab3431038d4711..fc07da22c08ecf4870cd5fa1d151aedc7984e8ad 100644
--- a/src/MATLAB/+Tracker/UpdateCachedCosts.m
+++ b/src/MATLAB/+Tracker/UpdateCachedCosts.m
@@ -2,6 +2,30 @@
% This must be run after a cost matrix or graph-edits change to keep cached
% costs up to date.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function UpdateCachedCosts(fromHulls, toHulls)
global CellFamilies CellTracks CellHulls Costs GraphEdits CachedCostMatrix
diff --git a/src/MATLAB/+Tracker/UpdateConnectedDistances.m b/src/MATLAB/+Tracker/UpdateConnectedDistances.m
index 8dcc27a294dca4c5ae1c2abd263dfcc2ec21426f..6ee7ddab1d08b203dbaa203e2d7febdf88738d13 100644
--- a/src/MATLAB/+Tracker/UpdateConnectedDistances.m
+++ b/src/MATLAB/+Tracker/UpdateConnectedDistances.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function connDist = UpdateConnectedDistances(updateCell, t, tNext, hullPerims, connDist, hulls, hash)
global CONSTANTS
diff --git a/src/MATLAB/+Tracker/UpdateCostEdges.m b/src/MATLAB/+Tracker/UpdateCostEdges.m
index 88089ec6144e37699f003cea9e316957971c1677..7dd7a91b18c64f276d48589c13408d9f53e24892 100644
--- a/src/MATLAB/+Tracker/UpdateCostEdges.m
+++ b/src/MATLAB/+Tracker/UpdateCostEdges.m
@@ -2,6 +2,30 @@
% Updates full Cost graph with edges from the costMatrix subgraph.
% Also handles updating the cached matrix used by GetCostMatrix() calls.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function UpdateCostEdges(costMatrix, fromHulls, toHulls)
global Costs
diff --git a/src/MATLAB/+Tracker/UpdateTrackingCosts.m b/src/MATLAB/+Tracker/UpdateTrackingCosts.m
index 4ccecef162e23e63cf9a472c8db22ed1188ddee0..d8d56225ea6ebbc124af9ee65c3a988abb74bbfc 100644
--- a/src/MATLAB/+Tracker/UpdateTrackingCosts.m
+++ b/src/MATLAB/+Tracker/UpdateTrackingCosts.m
@@ -2,10 +2,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/AddHullToTrack.m b/src/MATLAB/+Tracks/AddHullToTrack.m
index 894514a35afecd94651c4bc574f0f5f6eb2816a1..7c60c335eb8eca897fa58b51c047edc23a708865 100644
--- a/src/MATLAB/+Tracks/AddHullToTrack.m
+++ b/src/MATLAB/+Tracks/AddHullToTrack.m
@@ -13,10 +13,10 @@
% EW 6/8/12 rewrite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/ChangeLabel.m b/src/MATLAB/+Tracks/ChangeLabel.m
index 13b9690632cf455871765e0450fea795bb4358d6..643fd850287c1b816f2ccca51b17a85041b379a1 100644
--- a/src/MATLAB/+Tracks/ChangeLabel.m
+++ b/src/MATLAB/+Tracks/ChangeLabel.m
@@ -4,6 +4,30 @@
% time is an optional parameter. If time is not specified, the whole
% currentTrack is changed to the desiredTrack
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
% ChangeLog:
% EW 6/7/12 created
function [droppedTracks bErr] = ChangeLabel(currentTrack, desiredTrack, time)
diff --git a/src/MATLAB/+Tracks/ChangeTrackID.m b/src/MATLAB/+Tracks/ChangeTrackID.m
index 223b1fa11278a680449019cb140aac0b711c7b8b..415cba744318f9b731fcaf5a3c6319cceb885c75 100644
--- a/src/MATLAB/+Tracks/ChangeTrackID.m
+++ b/src/MATLAB/+Tracks/ChangeTrackID.m
@@ -8,10 +8,10 @@
% EW 6/6/12 rewrite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/CheckLockedChangeLabel.m b/src/MATLAB/+Tracks/CheckLockedChangeLabel.m
index 4ee18099cb3bf093a381ba1cfc57f03781d050f3..c424399437f1381fde055510eb42390e6b557ce8 100644
--- a/src/MATLAB/+Tracks/CheckLockedChangeLabel.m
+++ b/src/MATLAB/+Tracks/CheckLockedChangeLabel.m
@@ -3,6 +3,30 @@
% This function will check to verify if a tree-preserving change-label
% needs to be run for the requested change, and if it will succeed.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function [bLocked bCanChange] = CheckLockedChangeLabel(currentTrack, desiredTrack, time)
global CellTracks
diff --git a/src/MATLAB/+Tracks/ClearTrack.m b/src/MATLAB/+Tracks/ClearTrack.m
index a13f40f1a9966fa172ea32caa98b6d3883f706d4..f4a3e2619cc331fc36bc469a1fbb5c1864f8648e 100644
--- a/src/MATLAB/+Tracks/ClearTrack.m
+++ b/src/MATLAB/+Tracks/ClearTrack.m
@@ -2,10 +2,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/GetAllTrackPhenotypes.m b/src/MATLAB/+Tracks/GetAllTrackPhenotypes.m
index 39f46006d4773c667bc61d8042edb8236b887c59..0c36809c267360ccc837a7ce075b35a2f7e82ce5 100644
--- a/src/MATLAB/+Tracks/GetAllTrackPhenotypes.m
+++ b/src/MATLAB/+Tracks/GetAllTrackPhenotypes.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/GetHullID.m b/src/MATLAB/+Tracks/GetHullID.m
index a9a7971ae17042a7c0c093358a9c0a426d904af2..885b9fade8ac74089bdce095e19a0df7359918cd 100644
--- a/src/MATLAB/+Tracks/GetHullID.m
+++ b/src/MATLAB/+Tracks/GetHullID.m
@@ -1,6 +1,30 @@
% hullID = GetHullID(time, trackID)
% Helper function to get a hull given a trackID and time
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function hullID = GetHullID(time, trackID)
global CellTracks
hullID = 0;
diff --git a/src/MATLAB/+Tracks/GetTimeOfDeath.m b/src/MATLAB/+Tracks/GetTimeOfDeath.m
index e025cc0a5533fe3c977450bdc139af4894d5502e..9880a9dcafb75cdd82696a587dd85329f72f1e82 100644
--- a/src/MATLAB/+Tracks/GetTimeOfDeath.m
+++ b/src/MATLAB/+Tracks/GetTimeOfDeath.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/GetTrackPhenotype.m b/src/MATLAB/+Tracks/GetTrackPhenotype.m
index 52ec8b19958487aa7e056ce3b1c08276db8a1fef..2e8cfb20cb12748c90ac998a91fa8a693f42f2dc 100644
--- a/src/MATLAB/+Tracks/GetTrackPhenotype.m
+++ b/src/MATLAB/+Tracks/GetTrackPhenotype.m
@@ -2,10 +2,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/GetTrackPhenoypeTimes.m b/src/MATLAB/+Tracks/GetTrackPhenoypeTimes.m
index ca8ff9a227cc82d3f462fc1495e1cf6d6a86d2d1..346e913f477d913e6f57666873200a3c1ed0600e 100644
--- a/src/MATLAB/+Tracks/GetTrackPhenoypeTimes.m
+++ b/src/MATLAB/+Tracks/GetTrackPhenoypeTimes.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/LockedChangeLabel.m b/src/MATLAB/+Tracks/LockedChangeLabel.m
index e1a2a53497540ddafccf003df09779dc009e40dd..33cd34552c028fc398ab6ef111185a28ca83d66e 100644
--- a/src/MATLAB/+Tracks/LockedChangeLabel.m
+++ b/src/MATLAB/+Tracks/LockedChangeLabel.m
@@ -6,6 +6,30 @@
% This means that the change will move only one hull from one
% track to the other, rather than changing the entire track.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function LockedChangeLabel(currentTrack, desiredTrack, time)
% Completely cop-out if we can't preserve structure
diff --git a/src/MATLAB/+Tracks/LockedSwapLabels.m b/src/MATLAB/+Tracks/LockedSwapLabels.m
index d432cd46d5a95e5829566dfbc968f66e04e956f7..05a8658894380a2d42dde129df3fa020361477da 100644
--- a/src/MATLAB/+Tracks/LockedSwapLabels.m
+++ b/src/MATLAB/+Tracks/LockedSwapLabels.m
@@ -4,6 +4,30 @@
% By it's nature this preserves structures because nothing but hull
% associations are modified.
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
function LockedSwapLabels(trackA, trackB, time)
%% Error Check
diff --git a/src/MATLAB/+Tracks/NewCellTrack.m b/src/MATLAB/+Tracks/NewCellTrack.m
index 779bfb360338d4b5f29bddf4563da5391cb33638..50f1b2125ebb11a460ee9d75e3be5e1c004b3895 100644
--- a/src/MATLAB/+Tracks/NewCellTrack.m
+++ b/src/MATLAB/+Tracks/NewCellTrack.m
@@ -4,10 +4,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/PropagateChanges.m b/src/MATLAB/+Tracks/PropagateChanges.m
index 99f5dc44475999ab98a01a9a7a7f1348dfbbe68f..5810977e2fc0cffbc643a49c947afed49b3e631e 100644
--- a/src/MATLAB/+Tracks/PropagateChanges.m
+++ b/src/MATLAB/+Tracks/PropagateChanges.m
@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/RehashCellTracks.m b/src/MATLAB/+Tracks/RehashCellTracks.m
index 7af2a1a8fa26243184344dbf361e53c82ff05954..2b642f5cbf1849d19fff8460c5491bc851685914 100644
--- a/src/MATLAB/+Tracks/RehashCellTracks.m
+++ b/src/MATLAB/+Tracks/RehashCellTracks.m
@@ -10,10 +10,10 @@
% EW 6/6/12 rewrite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/RemoveHullFromTrack.m b/src/MATLAB/+Tracks/RemoveHullFromTrack.m
index 3c40610be2becab075fe7332e123692b6d711089..dc4cd43ad10f00ae95ab8d9d539567522d576bb4 100644
--- a/src/MATLAB/+Tracks/RemoveHullFromTrack.m
+++ b/src/MATLAB/+Tracks/RemoveHullFromTrack.m
@@ -10,10 +10,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/SetPhenotype.m b/src/MATLAB/+Tracks/SetPhenotype.m
index f08d4a5e9e65af6038ff4be016e72a2f0517b4c8..d86007eaa0689a10fc794044c2231ea78ec40f31 100644
--- a/src/MATLAB/+Tracks/SetPhenotype.m
+++ b/src/MATLAB/+Tracks/SetPhenotype.m
@@ -4,10 +4,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/StraightenTrack.m b/src/MATLAB/+Tracks/StraightenTrack.m
index 42e6f20f8bea48e66bbf58fdf172dba31e692add..f90e4f30eb183e54a59f42edc6df8c17c4c9cb09 100644
--- a/src/MATLAB/+Tracks/StraightenTrack.m
+++ b/src/MATLAB/+Tracks/StraightenTrack.m
@@ -7,10 +7,10 @@
% EW 6/6/12
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/SwapLabels.m b/src/MATLAB/+Tracks/SwapLabels.m
index 425c197391eee0c44923c9a683564659c81c4b76..95e51be178c536951898bf15ce1cf6e9f8ae756b 100644
--- a/src/MATLAB/+Tracks/SwapLabels.m
+++ b/src/MATLAB/+Tracks/SwapLabels.m
@@ -9,10 +9,10 @@
% EW 6/7/12 rewrite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/+Tracks/TearoffHull.m b/src/MATLAB/+Tracks/TearoffHull.m
index b14dc68d0c532a31aeafa2428593728c2e0225eb..419f40974fddda8679c8576da91b982a2e71c1ef 100644
--- a/src/MATLAB/+Tracks/TearoffHull.m
+++ b/src/MATLAB/+Tracks/TearoffHull.m
@@ -1,3 +1,27 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
function newTrackID = TearoffHull(hullID)
global CellHulls CellTracks
diff --git a/src/MATLAB/+UI/CreateContextMenuCells.m b/src/MATLAB/+UI/CreateContextMenuCells.m
index a1c03c1c1f0edcc713a084b15ba3b2d3b651fc23..7abca911ca44629318766a2fd605b5abe5aaf0dd 100644
--- a/src/MATLAB/+UI/CreateContextMenuCells.m
+++ b/src/MATLAB/+UI/CreateContextMenuCells.m
@@ -85,19 +85,30 @@ uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Remove From Tree',...
'CallBack', @removeFromTree);
-uimenu(Figures.cells.contextMenuHandle,...
- 'Label', 'Add To Extended Family',...
- 'CallBack', @addToExtendedFamily,...
+multiTreeMenu = uimenu(Figures.cells.contextMenuHandle,...
+ 'Label', 'Multi Tree',...
'Separator', 'on');
-uimenu(Figures.cells.contextMenuHandle,...
+uimenu(multiTreeMenu,...
+ 'Label', 'Add To Extended Family',...
+ 'CallBack', @addToExtendedFamily)
+
+uimenu(multiTreeMenu,...
'Label', 'Remove From Extended Family',...
'CallBack', @removeFromExtendedFamily);
-uimenu(Figures.cells.contextMenuHandle,...
+uimenu(multiTreeMenu,...
'Label', 'Show Extended Family',...
'CallBack', @showExtendedFamily);
+uimenu(multiTreeMenu,...
+ 'Label', 'Add All To Extended Family',...
+ 'CallBack', @addAllToExtendedFamily);
+
+uimenu(multiTreeMenu,...
+ 'Label', 'Remove All From Extended Family',...
+ 'CallBack', @removeAllFromExtendedFamily);
+
uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Properties',...
'CallBack', @properties,...
@@ -251,10 +262,13 @@ end
function addToExtendedFamily(src,evnt)
global Figures
- [hullID trackID] = UI.GetClosestCell(0);
- if(isempty(trackID)),return,end
+ hullIDs = Figures.cells.selectedHulls;
+ if isempty(hullIDs)
+ [hullIDs ~] = UI.GetClosestCell(0);
+ end
+ if(isempty(hullIDs)),return,end
- Editor.ContextAddToExtendedFamily(trackID);
+ Editor.ContextAddToExtendedFamily(hullIDs);
end
function removeFromExtendedFamily(src,evnt)
@@ -274,6 +288,18 @@ function showExtendedFamily(src,evnt)
msgbox({'Extended family:', num2str(CellFamilies(familyID).extFamily)})
end
+function addAllToExtendedFamily(src,evnt)
+ global Figures
+
+ Editor.ContextAddAllToExtendedFamily(Figures.time);
+end
+
+function removeAllFromExtendedFamily(src,evnt)
+ global Figures
+
+ Editor.ContextRemoveAllFromExtendedFamily();
+end
+
function properties(src,evnt)
[hullID trackID] = UI.GetClosestCell(0);
if(isempty(trackID)),return,end
diff --git a/src/MATLAB/+UI/CreateMenuBar.m b/src/MATLAB/+UI/CreateMenuBar.m
index 0038941d072d88c9714c4cda061e16eacb62fd9e..2af0f6456323a61611416bda3a8b1d6555e6911c 100644
--- a/src/MATLAB/+UI/CreateMenuBar.m
+++ b/src/MATLAB/+UI/CreateMenuBar.m
@@ -454,7 +454,7 @@ function loadStainData(src,evt)
chkDir = fileparts(CONSTANTS.matFullFile);
end
- [stainFile stainPath filterIdx] = uigetfile(fullfile(chkDir,'*_StainInfo.mat'), 'Open Staining Data',fullfile(chkDir, [CONSTANTS.datasetName '_StainInfo.mat']));
+ [stainFile stainPath filterIdx] = uigetfile(fullfile(chkDir,'*_StainInfo.mat'), 'Open Staining Data',fullfile(chkDir, [Metadata.GetDatasetName() '_StainInfo.mat']));
if ( filterIdx == 0 )
return;
end
@@ -581,7 +581,7 @@ end
function nextChannel(src,evnt)
global Figures CONSTANTS
Figures.chanIdx = Figures.chanIdx + 1;
-if Figures.chanIdx > CONSTANTS.numChannels
+if Figures.chanIdx > Metadata.GetNumberOfChannels()
Figures.chanIdx = 1;
end
UI.DrawCells();
@@ -748,7 +748,7 @@ function urlStr = urlifyString(inStr)
end
function createBugReport(src,evnt)
- verString = Helper.GetVersion('fullstring');
+ verString = Dev.GetVersion('fullstring');
% issueLabels = 'bug';
% issueTitle = '<ISSUE TITLE>';
diff --git a/src/MATLAB/+UI/DrawCells.m b/src/MATLAB/+UI/DrawCells.m
index 5bc79cc26896d5546279b15a6f25f847989a3d98..e0190cd52030faa46ac8fca5e01230325638f666 100644
--- a/src/MATLAB/+UI/DrawCells.m
+++ b/src/MATLAB/+UI/DrawCells.m
@@ -55,9 +55,9 @@ else
end
%read in image
-img = Helper.LoadChannelIntensityImage(Figures.time,Figures.chanIdx);
+img = Helper.LoadIntensityImage(Figures.time,Figures.chanIdx);
if ( isempty(img) )
- img = zeros(CONSTANTS.imageSize);
+ img = zeros(Metadata.GetDimensions('rc'));
end
imMax = max(img(:));
@@ -177,7 +177,7 @@ if(strcmp(get(Figures.cells.menuHandles.labelsMenu, 'Checked'),'on'))
colorStruct = UI.GetCellDrawProps(curTrackID, curHullID, drawString);
if(Figures.cells.showInterior)
- [r c] = ind2sub(CONSTANTS.imageSize, CellHulls(curHullID).indexPixels);
+ [r c] = ind2sub(Metadata.GetDimensions('rc'), CellHulls(curHullID).indexPixels);
plot(curAx, c, r, '.', 'Color',colorStruct.edge);
end
@@ -189,7 +189,7 @@ if(strcmp(get(Figures.cells.menuHandles.labelsMenu, 'Checked'),'on'))
'uicontextmenu', Figures.cells.contextMenuHandle,...
'ButtonDownFcn',( @(src,evt) (UI.FigureCellDown(src,evt,curHullID))),...
'LineStyle', colorStruct.edgeStyle,...
- 'LineWidth', colorStruct.edgeWidth);
+ 'LineWidth', 2);
% Plot light-blue border if frozen track
if ( Helper.CheckTreeFrozen(curTrackID) )
diff --git a/src/MATLAB/+UI/ExportAITPD.m b/src/MATLAB/+UI/ExportAITPD.m
index c90b6574ad873239130e0d5fad7a4a4f6e015389..dcdaceaef4a7a172d095e67d9017543627cf81be 100644
--- a/src/MATLAB/+UI/ExportAITPD.m
+++ b/src/MATLAB/+UI/ExportAITPD.m
@@ -52,7 +52,7 @@ trackData = [];
if(CellFamilies(track.familyID).endTime-CellFamilies(track.familyID).startTime < 0.50*length(HashedCells)),return,end
-trackData.datasetName = CONSTANTS.datasetName;
+trackData.datasetName = Metadata.GetDatasetName();
trackData.cellLabel = label;
trackData.parent = track.parentTrack;
trackData.sibling = track.siblingTrack;
@@ -85,7 +85,7 @@ for i=1:length(track.hulls)
trackData.times(length(trackData.times)+1,1) = track.startTime +i -1;
- [x y] = ind2sub(CONSTANTS.imageSize,CellHulls(track.hulls(i)).indexPixels);
+ [x y] = ind2sub(Metadata.GetDimensions('rc'),CellHulls(track.hulls(i)).indexPixels);
x = x(:) - min(x) +2;
y = y(:) - min(y) +2;
im = zeros(max(x)+2,max(y)+2);
@@ -112,7 +112,7 @@ success = 0;
settings = Load.ReadSettings();
[file,filePath,filterIndex] = uiputfile([settings.matFilePath '*.txt'],'Save data',...
- [CONSTANTS.datasetName '_AITPD.txt']);
+ [Metadata.GetDatasetName() '_AITPD.txt']);
if(filterIndex<1),return,end
fout=fopen([filePath file],'w');
diff --git a/src/MATLAB/+UI/ExportTree.m b/src/MATLAB/+UI/ExportTree.m
index aced74a5848815890e5e721eaf9dcbe3679eb5de..09c79f9a6d43ceafbb4b5cd020a5338c4c66686e 100644
--- a/src/MATLAB/+UI/ExportTree.m
+++ b/src/MATLAB/+UI/ExportTree.m
@@ -28,7 +28,7 @@ function ExportTree(src, evt)
global CellFamilies HashedCells Figures CONSTANTS CellTracks CellPhenotypes
figure
-set(gcf,'name',CONSTANTS.datasetName)
+set(gcf,'name', Metadata.GetDatasetName())
set(gcf,'numbertitle','off')
set(gcf,'color','w')
familyID=Figures.tree.familyID;
diff --git a/src/MATLAB/+UI/ExportTreeMetrics.m b/src/MATLAB/+UI/ExportTreeMetrics.m
index 488db45da3573a8e7f9cf4ca6b38ec2cd6b87400..0d15b7e076ce352259d7e6673f1333a24370cdfe 100644
--- a/src/MATLAB/+UI/ExportTreeMetrics.m
+++ b/src/MATLAB/+UI/ExportTreeMetrics.m
@@ -28,8 +28,6 @@ function ExportTreeMetrics(src,evnt)
global CellTracks CellFamilies CONSTANTS Figures
-trackMetrics = [];
-
familyID=Figures.tree.familyID;
rootTrackID = CellFamilies(familyID).rootTrackID;
@@ -38,15 +36,22 @@ famTracks = CellFamilies(familyID).tracks;
settings = Load.ReadSettings();
-[outFile,outPath,FilterIndex] = uiputfile('*.csv',['Export Metrics for clone #' num2str(rootTrackID)],fullfile(settings.matFilePath,[CONSTANTS.datasetName '_' num2str(rootTrackID) '_metrics.csv']));
+[outFile,outPath,FilterIndex] = uiputfile('*.csv',['Export Metrics for clone #' num2str(rootTrackID)],fullfile(settings.matFilePath,[Metadata.GetDatasetName() '_' num2str(rootTrackID) '_metrics.csv']));
if ( FilterIndex == 0 )
return;
end
-trackSortList = zeros(1,length(famTracks));
+trackSortList = [];
+trackMetrics = [];
for i=1:length(famTracks)
- trackSortList(i) = trackHeights(famTracks(i));
- trackMetrics = [trackMetrics getMetrics(famTracks(i),CellTracks(famTracks(i)))];
+ trackEntry = getMetrics(famTracks(i),CellTracks(famTracks(i)));
+
+ if ( isempty(trackEntry) )
+ continue;
+ end
+
+ trackSortList = [trackSortList trackHeights(famTracks(i))];
+ trackMetrics = [trackMetrics trackEntry];
end
[sortedHeights,srtIdx] = sort(trackSortList,'descend');
diff --git a/src/MATLAB/+UI/GenerateAVI.m b/src/MATLAB/+UI/GenerateAVI.m
index 05e1f055c692902b8ddd15ee5e606625a62e6913..9e3ba40e7ff9c3b43941f32ea03680ea16007d56 100644
--- a/src/MATLAB/+UI/GenerateAVI.m
+++ b/src/MATLAB/+UI/GenerateAVI.m
@@ -28,7 +28,7 @@ function GenerateAVI(src, evt)
global Figures CONSTANTS HashedCells
defaultPath = fileparts(CONSTANTS.matFullFile);
-defaultFile = [CONSTANTS.datasetName '.mp4'];
+defaultFile = [Metadata.GetDatasetName() '.mp4'];
[movieFile, moviePath] = uiputfile('*.mp4', 'Save Movie', fullfile(defaultPath, defaultFile));
if ( movieFile == 0 )
diff --git a/src/MATLAB/+UI/InitializeFigures.m b/src/MATLAB/+UI/InitializeFigures.m
index ed9703fe95b734c2e30d6d2c30321094ba0cab02..23738962843eabde2bc7ab4f7fd161cf083f99a5 100644
--- a/src/MATLAB/+UI/InitializeFigures.m
+++ b/src/MATLAB/+UI/InitializeFigures.m
@@ -71,7 +71,7 @@ set(Figures.cells.handle,...
'Interruptible', 'off',...
'CloseRequestFcn', @UI.CloseFigure,...
'NumberTitle', 'off',...
- 'Name', [CONSTANTS.datasetName ' Image Data'],...
+ 'Name', [Metadata.GetDatasetName() ' Image Data'],...
'Tag', 'cells',...
'ResizeFcn', @UI.UpdateSegmentationEditsMenu);
@@ -117,7 +117,7 @@ set(Figures.tree.handle,...
'BusyAction', 'cancel',...
'Interruptible', 'off',...
'NumberTitle', 'off',...
- 'Name', [CONSTANTS.datasetName ' Lineage'],...
+ 'Name', [Metadata.GetDatasetName() ' Lineage'],...
'Tag', 'tree');
addlistener(Figures.tree.handle, 'WindowKeyRelease', @UI.KeyStateRelease);
diff --git a/src/MATLAB/+UI/SaveData.m b/src/MATLAB/+UI/SaveData.m
index 628206bd7028b9cbe9c3236fda78a58433c772a4..2d21015ba50120ab35103bfa3148a01984c2a558 100644
--- a/src/MATLAB/+UI/SaveData.m
+++ b/src/MATLAB/+UI/SaveData.m
@@ -38,9 +38,9 @@ if isfield(CONSTANTS,'matFullFile') && ~isempty(CONSTANTS.matFullFile)
Helper.SaveLEVerState([CONSTANTS.matFullFile]);
else
if(orginal)
- Helper.SaveLEVerState([settings.matFilePath CONSTANTS.datasetName '_LEVer.mat']);
+ Helper.SaveLEVerState(fullfile(settings.matFilePath, [Metadata.GetDatasetName() '_LEVer.mat']));
else
- Helper.SaveLEVerState([settings.matFilePath CONSTANTS.datasetName '_LEVer_edits.mat']);
+ Helper.SaveLEVerState(fullfile(settings.matFilePath, [Metadata.GetDatasetName() '_LEVer_edits.mat']));
end
end
diff --git a/src/MATLAB/+UI/SaveDataAs.m b/src/MATLAB/+UI/SaveDataAs.m
index 5ede68a5ef27687325a5d83970268fb1554a3867..07a7d472a17a8557ed8058367bf09dcfa781e277 100644
--- a/src/MATLAB/+UI/SaveDataAs.m
+++ b/src/MATLAB/+UI/SaveDataAs.m
@@ -38,11 +38,11 @@ settings = Load.ReadSettings();
time = clock;
fprintf('Choose a folder to save current data...\n');
-newName = [CONSTANTS.datasetName '_LEVer.mat'];
+newName = [Metadata.GetDatasetName() '_LEVer.mat'];
bEditName = (~bOverWrite && ~strcmp(settings.matFilePath,'.\'));
if ( bEditName )
- newName = [CONSTANTS.datasetName ' edits ' num2str(time(1)) '-' num2str(time(2),'%02d') '-' num2str(time(3),'%02d') '_LEVer.mat'];
+ newName = [Metadata.GetDatasetName() ' edits ' num2str(time(1)) '-' num2str(time(2),'%02d') '-' num2str(time(3),'%02d') '_LEVer.mat'];
end
if(strcmp(settings.matFilePath,'.\'))
diff --git a/src/MATLAB/+UI/SegPreview.m b/src/MATLAB/+UI/SegPreview.m
index 2ba7a7b6071065cb2d44f9cbf855ef2139998f82..3b6be46edc17294c889340f8a75a52360af24f85 100644
--- a/src/MATLAB/+UI/SegPreview.m
+++ b/src/MATLAB/+UI/SegPreview.m
@@ -4,93 +4,22 @@
function SegPreview()
hPreviewFig = figure();
- Load.SetImageInfo();
-
hAx = axes('Parent',hPreviewFig, 'Position',[0.01 0.01 0.98 0.98], 'XTick',[],'YTick',[]);
hTimeLabel = uicontrol(hPreviewFig,'Style','text', 'Position',[1 0 60 20],'String', ['Time: ' num2str(1)]);
- set(hPreviewFig, 'CurrentAxes',hAx);
+ set(hPreviewFig, 'CurrentAxes',hAx, 'NumberTitle','off', 'Name',[Metadata.GetDatasetName() ' Preview']);
- set(hPreviewFig, 'UserData',struct('time',{1}, 'chan',{1}, 'showInterior',{false} , 'hLabel',{hTimeLabel}), 'Toolbar','figure');
+ set(hPreviewFig, 'UserData',struct('time',{1}, 'chan',{1}, 'showInterior',{false}, 'cacheHulls',{[]}, 'hLabel',{hTimeLabel}), 'Toolbar','figure');
set(hPreviewFig, 'WindowScrollWheelFcn',@windowScrollWheel, 'KeyPressFcn',@windowKeyPress, 'CloseRequestFcn','');
- hSegPropDlg = initSegPropDialog(hPreviewFig);
+ hSegPropDlg = UI.SegPropDialog(hPreviewFig);
drawPreviewImage(hPreviewFig);
uiwait(hSegPropDlg);
end
-function windowKeyPress(src, event)
- previewInfo = get(src, 'UserData');
-
- if ( strcmpi(event.Key, 'uparrow') )
- previewInfo.time = incrementFrame(previewInfo.time, -1);
- elseif ( strcmpi(event.Key, 'leftarrow') )
- previewInfo.time = incrementFrame(previewInfo.time, -1);
- elseif ( strcmpi(event.Key, 'downarrow') )
- previewInfo.time = incrementFrame(previewInfo.time, +1);
- elseif ( strcmpi(event.Key, 'rightarrow') )
- previewInfo.time = incrementFrame(previewInfo.time, +1);
- elseif ( strcmpi(event.Key, 'F12') )
- previewInfo.showInterior = ~previewInfo.showInterior;
- elseif ( strcmpi(event.Key,'t') && any(strcmpi('control',event.Modifier)) )
- chkTime = inputdlg('Enter frame number:','Go to Time',1,{num2str(previewInfo.time)});
- if (isempty(chkTime))
- return;
- end
-
- newTime = str2double(chkTime{1});
- if ( isnan(newTime) )
- return;
- end
-
- newTime = setTime(newTime);
- previewInfo.time = newTime;
- end
-
- set(src, 'UserData',previewInfo);
-
- drawPreviewImage(src);
-end
-
-function windowScrollWheel(src, event)
- previewInfo = get(src, 'UserData');
- time = incrementFrame(previewInfo.time, event.VerticalScrollCount);
-
- previewInfo.time = time;
- set(src, 'UserData',previewInfo);
-
- drawPreviewImage(src);
-end
-
-function time = setTime(time)
- global CONSTANTS
-
- if ( time < 1 )
- time = 1;
- end
-
- if ( time > CONSTANTS.numFrames )
- time = CONSTANTS.numFrames;
- end
-end
-
-function newTime = incrementFrame(time, delta)
- global CONSTANTS
-
- newTime = time + delta;
-
- if ( newTime < 1 )
- newTime = 1;
- end
-
- if ( newTime > CONSTANTS.numFrames )
- newTime = newTime - CONSTANTS.numFrames;
- end
-end
+%% Load and render a preview image with current hull overlays
function drawPreviewImage(hFig)
- global CONSTANTS
-
hAx = get(hFig, 'CurrentAxes');
frameInfo = get(hFig, 'UserData');
@@ -100,23 +29,27 @@ function drawPreviewImage(hFig)
im = imSet{frameInfo.chan};
if ( isempty(im) )
- im = 0.5*ones(CONSTANTS.imageSize);
+ im = 0.5*ones(Metadata.GetDimensions());
end
imMax = max(im(:));
im = mat2gray(im,[0 imMax]);
+ imDims = Metadata.GetDimensions();
+
xl=xlim(hAx);
yl=ylim(hAx);
if ( all(xl == [0 1]) )
- xl = [1 CONSTANTS.imageSize(2)];
- yl = [1 CONSTANTS.imageSize(1)];
+ xl = [1 imDims(1)];
+ yl = [1 imDims(2)];
end
hold(hAx, 'off');
imagesc(im, 'Parent',hAx, [0 1]);
colormap(hAx, gray(256));
+ zoom(hAx, 'reset');
+
xlim(hAx, xl);
ylim(hAx, yl);
@@ -124,20 +57,26 @@ function drawPreviewImage(hFig)
hold(hAx, 'all');
+ if ( ~isempty(frameInfo.cacheHulls) && (frameInfo.cacheHulls(1).time == frameInfo.time) )
+ drawSegHulls(hFig, frameInfo.cacheHulls, frameInfo.showInterior);
+ end
+
drawnow();
end
+%% Render hull overlays on image
function drawSegHulls(hFig,segHulls, bShowInterior)
- global CONSTANTS
-
hAx = get(hFig, 'CurrentAxes');
hold(hAx, 'on');
- allIndexPixels = vertcat(segHulls.indexPixels);
-
+ cmap = hsv(31);
if ( bShowInterior )
- rcCoords = Helper.IndexToCoord(CONSTANTS.imageSize, allIndexPixels);
- plot(hAx, rcCoords(:,2),rcCoords(:,1), '.r');
+ for i=1:length(segHulls)
+ colorIdx = mod(i-1,31)+1;
+
+ rcCoords = Utils.IndToCoord(Metadata.GetDimensions('rc'), segHulls(i).indexPixels);
+ plot(hAx, rcCoords(:,2),rcCoords(:,1), '.', 'Color',cmap(colorIdx,:));
+ end
end
for i=1:length(segHulls)
@@ -146,285 +85,68 @@ function drawSegHulls(hFig,segHulls, bShowInterior)
hold(hAx, 'off');
end
-function dialogInfo = setNewSegParams(dialogInfo)
- selectSeg = dialogInfo.selectSeg;
- chkSegInfo = dialogInfo.segInfo(selectSeg);
+
+function windowKeyPress(src, event)
+ previewInfo = get(src, 'UserData');
- for i=1:length(chkSegInfo.params)
- paramValStr = get(dialogInfo.hParams(i), 'String');
+ if ( strcmpi(event.Key, 'uparrow') )
+ previewInfo.time = incrementFrame(previewInfo.time, -1);
+ elseif ( strcmpi(event.Key, 'leftarrow') )
+ previewInfo.time = incrementFrame(previewInfo.time, -1);
+ elseif ( strcmpi(event.Key, 'downarrow') )
+ previewInfo.time = incrementFrame(previewInfo.time, +1);
+ elseif ( strcmpi(event.Key, 'rightarrow') )
+ previewInfo.time = incrementFrame(previewInfo.time, +1);
+ elseif ( strcmpi(event.Key, 'F12') )
+ previewInfo.showInterior = ~previewInfo.showInterior;
+ elseif ( strcmpi(event.Key,'t') && any(strcmpi('control',event.Modifier)) )
+ chkTime = inputdlg('Enter frame number:','Go to Time',1,{num2str(previewInfo.time)});
+ if (isempty(chkTime))
+ return;
+ end
- chkType = chkSegInfo.params(i).value;
- if ( isa(chkType, 'char') )
- chkSegInfo.params(i).value = paramValStr;
- elseif ( isa(chkType, 'double') )
- chkSegInfo.params(i).value = str2double(paramValStr);
- else
- error('Unexpected parameter type');
+ newTime = str2double(chkTime{1});
+ if ( isnan(newTime) )
+ return;
end
- end
-
- dialogInfo.segInfo(selectSeg) = chkSegInfo;
-end
-
-function [segFunc,segArgs] = getSegInfo(dialogInfo)
- selectSeg = dialogInfo.selectSeg;
- chkSegInfo = dialogInfo.segInfo(selectSeg);
-
- segFunc = chkSegInfo.func;
- segArgs = arrayfun(@(x)(x.value), chkSegInfo.params, 'UniformOutput',0);
-end
-
-function previewSeg(src,event)
- global CONSTANTS
-
- hPreviewSeg = src;
- hSegPropDlg = get(hPreviewSeg,'Parent');
-
- dialogInfo = get(hSegPropDlg, 'UserData');
- dialogInfo = setNewSegParams(dialogInfo);
- set(hSegPropDlg, 'UserData',dialogInfo);
-
- hPreviewFig = dialogInfo.hPreviewFig;
- frameInfo = get(hPreviewFig, 'UserData');
-
- set(hPreviewFig, 'Pointer','watch');
- set(hSegPropDlg, 'Pointer','watch');
- drawnow();
-
- imSet = Helper.LoadIntensityImageSet(frameInfo.time);
- im = imSet{frameInfo.chan};
-
- if ( ~isempty(im) )
- [segFunc, segArgs] = getSegInfo(dialogInfo);
- segHulls = segFunc(imSet, frameInfo.chan, frameInfo.time, segArgs{:});
- end
-
- validHulls = [];
- for i=1:length(segHulls)
- validHulls = [validHulls Hulls.CreateHull(CONSTANTS.imageSize, segHulls(i).indexPixels, frameInfo.time)];
+ newTime = setTime(newTime);
+ previewInfo.time = newTime;
end
- set(hPreviewFig, 'Pointer','arrow');
- set(hSegPropDlg, 'Pointer','arrow');
-
- bShowInterior = frameInfo.showInterior;
-
- drawPreviewImage(hPreviewFig);
- drawSegHulls(hPreviewFig, validHulls, bShowInterior);
-end
-
-function runSeg(src,event)
- hRunSeg = src;
- hSegPropDlg = get(hRunSeg,'Parent');
-
- dialogInfo = get(hSegPropDlg, 'UserData');
- dialogInfo = setNewSegParams(dialogInfo);
- set(hSegPropDlg, 'UserData',dialogInfo);
-
- selectSeg = dialogInfo.selectSeg;
-
- SupportedTypes = Load.GetSupportedCellTypes();
- cellType = SupportedTypes(selectSeg).name;
- Load.AddConstant('cellType',cellType,1);
- Load.AddConstant('primaryChannel', dialogInfo.selectChan,1);
-
- Load.AddConstant('segInfo', dialogInfo.segInfo(selectSeg),1);
-
- closeFigures(hSegPropDlg,[]);
-end
-
-function defaultParams(src,event)
- hResetDefault = src;
- hSegPropDlg = get(hResetDefault,'Parent');
-
- dialogInfo = get(hSegPropDlg, 'UserData');
- selectSeg = dialogInfo.selectSeg;
-
- SupportedTypes = Load.GetSupportedCellTypes();
- defaultSegInfo = SupportedTypes(selectSeg).segRoutine;
-
- dialogInfo.segInfo(selectSeg) = defaultSegInfo;
- set(hSegPropDlg, 'UserData',dialogInfo);
-
- setParamValues(hSegPropDlg, selectSeg);
-end
-
-function closeFigures(src,event)
- hSegPropDlg = src;
- dialogInfo = get(hSegPropDlg, 'UserData');
-
- hPreviewFig = dialogInfo.hPreviewFig;
- delete(hPreviewFig);
- delete(hSegPropDlg);
-end
-
-function hSegPropDlg = initSegPropDialog(hFig)
- global CONSTANTS
-
- hSegPropDlg = dialog('Name','Select Segmentation Properties', 'Visible','on', 'WindowStyle','normal', 'CloseRequestFcn',@closeFigures);
-% WinOnTop(hSegPropDlg,true);
-
- SupportedTypes = Load.GetSupportedCellTypes();
-
- typeNames = {SupportedTypes.name};
- chanStr = arrayfun(@(x)(num2str(x)), 1:CONSTANTS.numChannels, 'UniformOutput',0);
-
- hCellBox = uicontrol(hSegPropDlg, 'Style','popupmenu', 'String',typeNames, 'Callback',@selectedCellType, 'Position',[20 20 100 20]);
- hChanBox = uicontrol(hSegPropDlg, 'Style','popupmenu', 'String',chanStr, 'Callback',@selectedChannel, 'Position',[20 20 100 20]);
- hPreviewSeg = uicontrol(hSegPropDlg, 'Style','pushbutton', 'String','Preview Segmentation', 'Callback',@previewSeg, 'Position',[20 20 100 20]);
- hRunSeg = uicontrol(hSegPropDlg, 'Style','pushbutton', 'String','Run Full Segmentation', 'Callback',@runSeg, 'Position',[20 20 100 20]);
- hCancel = uicontrol(hSegPropDlg, 'Style','pushbutton', 'String','Default Parameters', 'Callback',@defaultParams, 'Position',[20 20 100 20]);
-
- segInfo = [SupportedTypes.segRoutine];
- dialogInfo = struct('hPreviewFig',{hFig}, 'hKeep',{[hCellBox hChanBox hPreviewSeg hRunSeg hCancel]}, 'hParams',{[]}, 'selectSeg',{1}, 'segInfo',{segInfo});
- set(hSegPropDlg, 'UserData',dialogInfo);
-
- selectedCellType(hCellBox, [])
- selectedChannel(hChanBox,[]);
-end
-
-function selectedChannel(src,event)
- hChanBox = src;
- hSegPropDlg = get(hChanBox,'Parent');
-
- selectedIdx = get(hChanBox, 'Value');
- chanStr = get(hChanBox,'String');
- selectedChan = str2double(chanStr{selectedIdx});
-
- dialogInfo = get(hSegPropDlg, 'UserData');
- dialogInfo.selectChan = selectedChan;
- set(hSegPropDlg, 'UserData',dialogInfo);
-
- hPreviewFig = dialogInfo.hPreviewFig;
-
- previewInfo = get(hPreviewFig, 'UserData');
- previewInfo.chan = selectedChan;
- set(hPreviewFig, 'UserData',previewInfo);
+ set(src, 'UserData',previewInfo);
- drawPreviewImage(hPreviewFig);
+ drawPreviewImage(src);
end
-function selectedCellType(src,event)
- hCellBox = src;
- hSegPropDlg = get(hCellBox,'Parent');
+function windowScrollWheel(src, event)
+ previewInfo = get(src, 'UserData');
+ time = incrementFrame(previewInfo.time, event.VerticalScrollCount);
- selectedIdx = get(hCellBox, 'Value');
- createParamControls(hSegPropDlg, selectedIdx);
- setParamValues(hSegPropDlg, selectedIdx);
+ previewInfo.time = time;
+ set(src, 'UserData',previewInfo);
- dialogInfo = get(hSegPropDlg, 'UserData');
- dialogInfo.selectSeg = selectedIdx;
- set(hSegPropDlg, 'UserData',dialogInfo);
+ drawPreviewImage(src);
end
-function setParamValues(hDlg, selectIdx)
- dialogInfo = get(hDlg, 'UserData');
- hParams = dialogInfo.hParams;
+function time = setTime(time)
+ if ( time < 1 )
+ time = 1;
+ end
- segInfo = dialogInfo.segInfo(selectIdx);
- for i=1:length(hParams);
- paramValue = segInfo.params(i).value;
- set(hParams(i), 'String', num2str(paramValue));
+ if ( time > Metadata.GetNumberOfFrames() )
+ time = Metadata.GetNumberOfFrames();
end
end
-function createParamControls(hDlg, selectIdx)
- labelWidth = 70;
- labelHeight = 16;
- labelPad = 1;
-
- controlHeight = 22;
- controlWidth = 100;
-
- buttonWidth = 130;
-
- controlPad = 5;
- controlLeft = 2*controlPad;
-
- dialogInfo = get(hDlg, 'UserData');
-
- hDlgChildren = get(hDlg, 'Children');
- bRmChildren = ~ismember(hDlgChildren, dialogInfo.hKeep);
-
- hChildren = hDlgChildren(bRmChildren);
- for i=1:length(hChildren)
- delete(hChildren(i));
- end
-
- numParams = length(dialogInfo.segInfo(selectIdx).params);
- segFunc = dialogInfo.segInfo(selectIdx).func;
-
- %% Load function help information
- funcName = char(segFunc);
- funcHelp = help(funcName);
- if ( isempty(funcHelp) )
- funcHelp = funcName;
- end
-
- numControls = max(3, numParams + 2);
- dialogWidth = 2*controlPad + labelWidth + controlPad + controlWidth + 2*controlPad + buttonWidth + 2*controlPad;
- dialogHeight = controlPad + controlHeight*numControls + 2*controlPad*(numControls-1) + controlPad;
-
- dialogPos = get(hDlg, 'Position');
- set(hDlg, 'Position',[dialogPos(1:2) dialogWidth dialogHeight]);
-
- hCellBox = dialogInfo.hKeep(1);
- hChanBox = dialogInfo.hKeep(2);
-
- %% Put a segmentation summary from function help into the combo-box tooltip.
- tokMatch = regexp(funcHelp,'^\s*FrameSegmentor_*\w*\s*-\s*(.+?)^\s*$', 'once','tokens','lineanchors');
- if ( isempty(tokMatch) )
- helpLines = strsplit(funcHelp,'\n');
- funcSummary = strtrim(helpLines{1});
- else
- funcSummary = tokMatch{1};
- end
-
- curControlPos = [controlLeft, dialogHeight-controlPad];
- curControlPos = layoutLabelControls(hCellBox, curControlPos, 'Cell Type: ', funcSummary);
- curControlPos = layoutLabelControls(hChanBox, curControlPos, 'Channel: ', '');
-
- %% Try to find parameter help in function documentation to put in label/textbox tooltips
- hParams = zeros(1,numParams);
- for i=1:numParams
- paramName = dialogInfo.segInfo(selectIdx).params(i).name;
-
- paramHelp = '';
- tokMatch = regexp(funcHelp,['^\s*(' paramName '.+?)^\s*$'], 'once','tokens','lineanchors');
- if ( ~isempty(tokMatch) )
- paramHelp = tokMatch{1};
- end
-
- hParams(i) = uicontrol(hDlg, 'Style','edit');
- curControlPos = layoutLabelControls(hParams(i), curControlPos, [paramName ': '], paramHelp);
- end
+function newTime = incrementFrame(time, delta)
+ newTime = time + delta;
- hButtons = dialogInfo.hKeep(3:end);
- curControlPos = [controlLeft + labelWidth + controlPad + controlWidth + 2*controlPad, dialogHeight-controlPad];
- for i=1:length(hButtons);
- curControlPos = layoutButtonControls(hButtons(i), curControlPos);
+ if ( newTime < 1 )
+ newTime = 1;
end
- dialogInfo.hParams = hParams;
- set(hDlg, 'UserData',dialogInfo);
-
- function newPos = layoutLabelControls(hCtrl, startPos, labelStr, tooltip)
- newPos = startPos - [0, controlHeight];
-
- hLabel = uicontrol(hDlg, 'Style','text', 'HorizontalAlignment','right', 'String',labelStr, 'Position',[newPos(1), newPos(2)+labelPad, labelWidth, labelHeight]);
- set(hCtrl, 'Position',[newPos(1) + labelWidth + controlPad, newPos(2), controlWidth, controlHeight]);
-
- set(hCtrl, 'ToolTipString',tooltip);
- set(hLabel, 'ToolTipString',tooltip);
-
- newPos = newPos - [0, 2*controlPad];
- end
-
- function newPos = layoutButtonControls(hCtrl, startPos)
- newPos = startPos - [0, controlHeight];
- set(hCtrl, 'Position',[newPos(1) + controlPad, newPos(2), buttonWidth, controlHeight]);
-
- newPos = newPos - [0, 2*controlPad];
+ if ( newTime > Metadata.GetNumberOfFrames() )
+ newTime = newTime - Metadata.GetNumberOfFrames();
end
end
diff --git a/src/MATLAB/+UI/SegPropDialog.m b/src/MATLAB/+UI/SegPropDialog.m
new file mode 100644
index 0000000000000000000000000000000000000000..1031622112e4078958c0f6d90df0a29f6dd53086
--- /dev/null
+++ b/src/MATLAB/+UI/SegPropDialog.m
@@ -0,0 +1,328 @@
+function hSegPropDlg = SegPropDialog(hFig)
+ if ( ~exist('hFig','var') )
+ hFig = [];
+ end
+
+ hSegPropDlg = dialog('Name','Select Segmentation Properties', 'Visible','on', 'WindowStyle','normal', 'CloseRequestFcn',@closeFigures);
+
+ SupportedTypes = Load.GetSupportedCellTypes();
+
+ typeNames = {SupportedTypes.name};
+
+ % Handle the case that we don't know number of channels
+ if ( Metadata.GetNumberOfChannels() < 1 )
+ chanStr = {'1'};
+ else
+ chanStr = arrayfun(@(x)(num2str(x)), 1:Metadata.GetNumberOfChannels(), 'UniformOutput',0);
+ end
+
+ enableSegPreview = 'off';
+ if ( ishandle(hFig) )
+ enableSegPreview = 'on';
+ end
+
+
+ hCellBox = uicontrol(hSegPropDlg, 'Style','popupmenu', 'String',typeNames, 'Callback',@selectedCellType, 'Position',[20 20 100 20]);
+
+ % Handle the case that we don't know number of channels, use editbox
+ if ( Metadata.GetNumberOfChannels() < 1 )
+ hChanBox = uicontrol(hSegPropDlg, 'Style','edit', 'String',chanStr, 'Callback',@selectedChannel, 'Position',[20 20 100 20]);
+ else
+ hChanBox = uicontrol(hSegPropDlg, 'Style','popupmenu', 'String',chanStr, 'Callback',@selectedChannel, 'Position',[20 20 100 20]);
+ end
+
+ hPreviewSeg = uicontrol(hSegPropDlg, 'Style','pushbutton', 'String','Preview Segmentation', 'Callback',@previewSeg, 'Position',[20 20 100 20], 'Enable',enableSegPreview);
+ hRunSeg = uicontrol(hSegPropDlg, 'Style','pushbutton', 'String','Run Full Segmentation', 'Callback',@runSeg, 'Position',[20 20 100 20]);
+ hCancel = uicontrol(hSegPropDlg, 'Style','pushbutton', 'String','Default Parameters', 'Callback',@defaultParams, 'Position',[20 20 100 20]);
+
+ segInfo = [SupportedTypes.segRoutine];
+ dialogInfo = struct('hPreviewFig',{hFig}, 'hKeep',{[hCellBox hChanBox hPreviewSeg hRunSeg hCancel]}, 'hParams',{[]}, 'selectSeg',{1}, 'segInfo',{segInfo});
+ set(hSegPropDlg, 'UserData',dialogInfo);
+
+ selectedCellType(hCellBox, [])
+ selectedChannel(hChanBox,[]);
+end
+
+%% Update preview window when new primary channel selected for viewing
+function selectedChannel(src,event)
+ hChanBox = src;
+ hSegPropDlg = get(hChanBox,'Parent');
+
+ selectedIdx = get(hChanBox, 'Value');
+ chanStr = get(hChanBox,'String');
+
+
+ if ( selectedIdx < 1 )
+ selectedChan = str2double(chanStr);
+ else
+ selectedChan = str2double(chanStr{selectedIdx});
+ end
+
+ dialogInfo = get(hSegPropDlg, 'UserData');
+ dialogInfo.selectChan = selectedChan;
+ set(hSegPropDlg, 'UserData',dialogInfo);
+
+ hPreviewFig = dialogInfo.hPreviewFig;
+ if ( isempty(hPreviewFig) )
+ return;
+ end
+
+ previewInfo = get(hPreviewFig, 'UserData');
+ previewInfo.chan = selectedChan;
+ set(hPreviewFig, 'UserData',previewInfo);
+
+ forceRefreshPreview(hPreviewFig);
+end
+
+
+%% Update parameters based on new cell type selection
+function selectedCellType(src,event)
+ hCellBox = src;
+ hSegPropDlg = get(hCellBox,'Parent');
+
+ selectedIdx = get(hCellBox, 'Value');
+ createParamControls(hSegPropDlg, selectedIdx);
+ setParamValues(hSegPropDlg, selectedIdx);
+
+ dialogInfo = get(hSegPropDlg, 'UserData');
+ dialogInfo.selectSeg = selectedIdx;
+ set(hSegPropDlg, 'UserData',dialogInfo);
+
+ %Clear cached hull data on algorithm selection change.
+ hPreviewFig = dialogInfo.hPreviewFig;
+ if ( isempty(hPreviewFig) )
+ return;
+ end
+
+ frameInfo = get(hPreviewFig, 'UserData');
+ frameInfo.cacheHulls = [];
+ set(hPreviewFig, 'UserData',frameInfo);
+
+ forceRefreshPreview(hPreviewFig);
+end
+
+%% Set new segmentation parameters
+function dialogInfo = setNewSegParams(dialogInfo)
+ selectSeg = dialogInfo.selectSeg;
+ chkSegInfo = dialogInfo.segInfo(selectSeg);
+
+ for i=1:length(chkSegInfo.params)
+ paramValStr = get(dialogInfo.hParams(i), 'String');
+
+ chkType = chkSegInfo.params(i).value;
+ if ( isa(chkType, 'char') )
+ chkSegInfo.params(i).value = paramValStr;
+ elseif ( isa(chkType, 'double') )
+ chkSegInfo.params(i).value = str2double(paramValStr);
+ else
+ error('Unexpected parameter type');
+ end
+ end
+
+ dialogInfo.segInfo(selectSeg) = chkSegInfo;
+end
+
+%% Finalize parameter selection and close dialog boxes
+function runSeg(src,event)
+ hRunSeg = src;
+ hSegPropDlg = get(hRunSeg,'Parent');
+
+ dialogInfo = get(hSegPropDlg, 'UserData');
+ dialogInfo = setNewSegParams(dialogInfo);
+ set(hSegPropDlg, 'UserData',dialogInfo);
+
+ selectSeg = dialogInfo.selectSeg;
+
+ SupportedTypes = Load.GetSupportedCellTypes();
+ cellType = SupportedTypes(selectSeg).name;
+ Load.AddConstant('cellType',cellType,1);
+ Load.AddConstant('primaryChannel', dialogInfo.selectChan,1);
+
+ Load.AddConstant('segInfo', dialogInfo.segInfo(selectSeg),1);
+
+ closeFigures(hSegPropDlg,[]);
+end
+
+%% Preview single frame segmentation
+function previewSeg(src,event)
+ hPreviewSeg = src;
+ hSegPropDlg = get(hPreviewSeg,'Parent');
+
+ dialogInfo = get(hSegPropDlg, 'UserData');
+ dialogInfo = setNewSegParams(dialogInfo);
+ set(hSegPropDlg, 'UserData',dialogInfo);
+
+ hPreviewFig = dialogInfo.hPreviewFig;
+ frameInfo = get(hPreviewFig, 'UserData');
+
+ set(hPreviewFig, 'Pointer','watch');
+ set(hSegPropDlg, 'Pointer','watch');
+ drawnow();
+
+ imSet = Helper.LoadIntensityImageSet(frameInfo.time);
+ im = imSet{frameInfo.chan};
+
+ if ( ~isempty(im) )
+ [segFunc, segArgs] = getSegInfo(dialogInfo);
+
+ segHulls = segFunc(imSet, frameInfo.chan, frameInfo.time, segArgs{:});
+ end
+
+ validHulls = [];
+ for i=1:length(segHulls)
+ validHulls = [validHulls Hulls.CreateHull(Metadata.GetDimensions('rc'), segHulls(i).indexPixels, frameInfo.time, false, segHulls(i).tag)];
+ end
+
+ frameInfo.cacheHulls = validHulls;
+
+ set(hPreviewFig, 'Pointer','arrow');
+ set(hSegPropDlg, 'Pointer','arrow');
+
+ set(hPreviewFig, 'UserData',frameInfo);
+
+ forceRefreshPreview(hPreviewFig);
+end
+
+%% Hack to force redraw of preview figure
+function forceRefreshPreview(hFig)
+ scrollFunc = get(hFig, 'WindowScrollWheelFcn');
+ scrollFunc(hFig,struct('VerticalScrollCount',{0}));
+end
+
+%% Reset current cell parameters to defaults
+function defaultParams(src,event)
+ hResetDefault = src;
+ hSegPropDlg = get(hResetDefault,'Parent');
+
+ dialogInfo = get(hSegPropDlg, 'UserData');
+ selectSeg = dialogInfo.selectSeg;
+
+ SupportedTypes = Load.GetSupportedCellTypes();
+ defaultSegInfo = SupportedTypes(selectSeg).segRoutine;
+
+ dialogInfo.segInfo(selectSeg) = defaultSegInfo;
+ set(hSegPropDlg, 'UserData',dialogInfo);
+
+ setParamValues(hSegPropDlg, selectSeg);
+end
+
+%% Set up parameter value display
+function setParamValues(hDlg, selectIdx)
+ dialogInfo = get(hDlg, 'UserData');
+ hParams = dialogInfo.hParams;
+
+ segInfo = dialogInfo.segInfo(selectIdx);
+ for i=1:length(hParams);
+ paramValue = segInfo.params(i).value;
+ set(hParams(i), 'String', num2str(paramValue));
+ end
+end
+
+
+%% Close this figure and possibly associated preview windows.
+function closeFigures(src,event)
+ hSegPropDlg = src;
+ dialogInfo = get(hSegPropDlg, 'UserData');
+
+ hPreviewFig = dialogInfo.hPreviewFig;
+ if ( ~isempty(hPreviewFig) )
+ delete(hPreviewFig);
+ end
+
+ delete(hSegPropDlg);
+end
+
+%%
+function [segFunc,segArgs] = getSegInfo(dialogInfo)
+ selectSeg = dialogInfo.selectSeg;
+ chkSegInfo = dialogInfo.segInfo(selectSeg);
+
+ segFunc = chkSegInfo.func;
+ segArgs = arrayfun(@(x)(x.value), chkSegInfo.params, 'UniformOutput',0);
+end
+
+
+%% Create all controls associated with cell type parameters
+function createParamControls(hDlg, selectIdx)
+ labelWidth = 70;
+ labelHeight = 16;
+ labelPad = 1;
+
+ controlHeight = 22;
+ controlWidth = 100;
+
+ buttonWidth = 130;
+
+ controlPad = 5;
+ controlLeft = 2*controlPad;
+
+ dialogInfo = get(hDlg, 'UserData');
+
+ hDlgChildren = get(hDlg, 'Children');
+ bRmChildren = ~ismember(hDlgChildren, dialogInfo.hKeep);
+
+ hChildren = hDlgChildren(bRmChildren);
+ for i=1:length(hChildren)
+ delete(hChildren(i));
+ end
+
+ numParams = length(dialogInfo.segInfo(selectIdx).params);
+ segFunc = dialogInfo.segInfo(selectIdx).func;
+
+ %% Load function help information
+ funcName = char(segFunc);
+ helpStruct = Dev.FrameSegHelp(funcName);
+
+ numControls = max(3, numParams + 2);
+ dialogWidth = 2*controlPad + labelWidth + controlPad + controlWidth + 2*controlPad + buttonWidth + 2*controlPad;
+ dialogHeight = controlPad + controlHeight*numControls + 2*controlPad*(numControls-1) + controlPad;
+
+ dialogPos = get(hDlg, 'Position');
+ set(hDlg, 'Position',[dialogPos(1:2) dialogWidth dialogHeight]);
+
+ hCellBox = dialogInfo.hKeep(1);
+ hChanBox = dialogInfo.hKeep(2);
+
+ curControlPos = [controlLeft, dialogHeight-controlPad];
+ curControlPos = layoutLabelControls(hCellBox, curControlPos, 'Cell Type: ', sprintf(helpStruct.summary));
+ curControlPos = layoutLabelControls(hChanBox, curControlPos, 'Channel: ', '');
+
+ %% Try to find parameter help in function documentation to put in label/textbox tooltips
+ hParams = zeros(1,numParams);
+ for i=1:numParams
+ paramName = dialogInfo.segInfo(selectIdx).params(i).name;
+
+ hParams(i) = uicontrol(hDlg, 'Style','edit');
+ curControlPos = layoutLabelControls(hParams(i), curControlPos, [paramName ': '], sprintf(helpStruct.paramHelp{i}));
+ end
+
+ hButtons = dialogInfo.hKeep(3:end);
+ curControlPos = [controlLeft + labelWidth + controlPad + controlWidth + 2*controlPad, dialogHeight-controlPad];
+ for i=1:length(hButtons);
+ curControlPos = layoutButtonControls(hButtons(i), curControlPos);
+ end
+
+ dialogInfo.hParams = hParams;
+ set(hDlg, 'UserData',dialogInfo);
+
+ function newPos = layoutLabelControls(hCtrl, startPos, labelStr, tooltip)
+ newPos = startPos - [0, controlHeight];
+
+ hLabel = uicontrol(hDlg, 'Style','text', 'HorizontalAlignment','right', 'String',labelStr, 'Position',[newPos(1), newPos(2)+labelPad, labelWidth, labelHeight]);
+ set(hCtrl, 'Position',[newPos(1) + labelWidth + controlPad, newPos(2), controlWidth, controlHeight]);
+
+ set(hCtrl, 'ToolTipString',tooltip);
+ set(hLabel, 'ToolTipString',tooltip);
+
+ newPos = newPos - [0, 2*controlPad];
+ end
+
+ function newPos = layoutButtonControls(hCtrl, startPos)
+ newPos = startPos - [0, controlHeight];
+ set(hCtrl, 'Position',[newPos(1) + controlPad, newPos(2), buttonWidth, controlHeight]);
+
+ newPos = newPos - [0, 2*controlPad];
+ end
+end
+
+
diff --git a/src/MATLAB/+UI/about.m b/src/MATLAB/+UI/about.m
index bff555b78c3effe1a0272bf317833871ec00960b..89be030ea54c1513b32d7f085e32bacd83fbc1da 100644
--- a/src/MATLAB/+UI/about.m
+++ b/src/MATLAB/+UI/about.m
@@ -64,9 +64,9 @@ else
im=255*ones(339,608);
end
imagesc(im)
-softwareVersion = Helper.GetVersion();
-buildNumber = Helper.GetVersion('buildString');
-buildHash = Helper.GetVersion('buildHash');
+softwareVersion = Dev.GetVersion();
+buildNumber = Dev.GetVersion('buildString');
+buildHash = Dev.GetVersion('primaryHash');
cDate = clock();
if ( ~isempty(softwareVersion) )
set(handles.text1,'string',{['LEVER: ' softwareVersion] ; [' ' buildNumber ' '] ;[' ' buildHash(1:20) ' '] ; ['(c) ' num2str(cDate(1))] });
diff --git a/src/MATLAB/+Utils/CmdlnProgress.m b/src/MATLAB/+Utils/CmdlnProgress.m
new file mode 100644
index 0000000000000000000000000000000000000000..320d8a5f59495a18b1b8d8038ec49b0ee39b4de3
--- /dev/null
+++ b/src/MATLAB/+Utils/CmdlnProgress.m
@@ -0,0 +1,130 @@
+classdef CmdlnProgress<handle
+ %PRINTPROGRESS prints the progress and the estimated time of completion on
+ %the commandline.
+ %ENSURE that the code that is being monitored does not have internal
+ %printing to the commandline.
+ % INIT - if init is true, then the val passed in will be used as the
+ % denominator when figuring out the percent completed.
+ % When init is false, the progress is deleted from the command line and the
+ % internal valuse reset.
+ % VAL - when updating the progress enter the number that will be used as
+ % the numerator for the percent completed and ensure that the second
+ % paramater is not used or empty.
+ %
+ % Usage -- Initalize by using CmdlnProgress(number of iterations, true, optionalTitle);
+ % Update by using PrintProgress(current iteration);
+ % Clean up by using PrintProgress(0,false);
+
+ properties
+ backspaces
+ firstTime
+ total
+ useBs
+ titleText
+ end
+
+ methods
+ function obj = CmdlnProgress(iterations,useBackspace,optionalTitle)
+ if(~exist('useBackspace', 'var') || isempty(useBackspace))
+ obj.useBs = true;
+ else
+ obj.useBs = useBackspace;
+ end
+
+ if (~exist('optionalTitle','var') || isempty(optionalTitle))
+ obj.titleText = '';
+ else
+ obj.titleText = optionalTitle;
+ end
+
+ obj.total = iterations;
+
+ obj.backspaces = [];
+ obj.firstTime = now;
+ end
+
+ function SetMaxIterations(obj,iterations)
+ obj.total = iterations;
+ end
+
+ function PrintProgress(obj,val)
+ cur = now;
+
+ prcntDone = val / obj.total;
+ elpsTime = (cur - obj.firstTime) * 86400;
+ totalSec = elpsTime / prcntDone;
+ finDate = obj.firstTime + (totalSec / 86400);
+ timeLeft = (finDate - cur)*86400;
+
+ if (~isempty(obj.titleText))
+ doneStr = sprintf('%s: %5.2f%%%% est. %s @ %s\n',...
+ obj.titleText,...
+ prcntDone*100,...
+ Utils.PrintTime(timeLeft),...
+ datestr(finDate,'HH:MM:SS dd-mmm-yy'));
+ else
+ doneStr = sprintf('%5.2f%%%% est. %s @ %s\n',...
+ prcntDone*100,...
+ Utils.PrintTime(timeLeft),...
+ datestr(finDate,'HH:MM:SS dd-mmm-yy'));
+ end
+ fprintf([obj.backspaces,doneStr]);
+
+ if(obj.useBs)
+ obj.backspaces = repmat(sprintf('\b'),1,length(doneStr)-1);
+ else
+ fprintf('\n');
+ end
+ end
+
+ function ReprintProgress(obj,val)
+ cur = now;
+
+ prcntDone = val / obj.total;
+ elpsTime = (cur - obj.firstTime) * 86400;
+ totalSec = elpsTime / prcntDone;
+ finDate = obj.firstTime + (totalSec / 86400);
+ timeLeft = (finDate - cur)*86400;
+
+ if (~isempty(obj.titleText))
+ doneStr = sprintf('%s: %5.2f%%%% est. %s @ %s\n',...
+ obj.titleText,...
+ prcntDone*100,...
+ Utils.PrintTime(timeLeft),...
+ datestr(finDate,'HH:MM:SS dd-mmm-yy'));
+ else
+ doneStr = sprintf('%5.2f%%%% est. %s @ %s\n',...
+ prcntDone*100,...
+ Utils.PrintTime(timeLeft),...
+ datestr(finDate,'HH:MM:SS dd-mmm-yy'));
+ end
+
+ fprintf(doneStr);
+
+ if(obj.useBs)
+ obj.backspaces = repmat(sprintf('\b'),1,length(doneStr)-1);
+ else
+ fprintf('\n');
+ end
+ end
+
+ function ClearProgress(obj,printTotal)
+ if (~isempty(obj.backspaces))
+ fprintf(obj.backspaces);
+ end
+ if (exist('printTotal','var') && ~isempty(printTotal) && printTotal)
+ cur = now;
+ elpsTime = (cur - obj.firstTime) * 86400;
+ if (~isempty(obj.titleText))
+ fprintf('%s took: %s\n',obj.titleText,Utils.PrintTime(elpsTime))
+ else
+ fprintf('Took: %s\n',Utils.PrintTime(elpsTime))
+ end
+ end
+ obj.backspaces = [];
+ obj.firstTime = 0;
+ obj.total = 0;
+ obj.useBs = false;
+ end
+ end
+end
diff --git a/src/MATLAB/+Utils/CoordToInd.m b/src/MATLAB/+Utils/CoordToInd.m
new file mode 100644
index 0000000000000000000000000000000000000000..0a5ae3e55574b389e66c73e2ee1a2b5036d6387c
--- /dev/null
+++ b/src/MATLAB/+Utils/CoordToInd.m
@@ -0,0 +1,7 @@
+% CoordToInd - Convert subscript indices to linear array indices.
+%
+% arrayIdx = CoordToInd(arraySize, coords)
+function arrayIdx = CoordToInd(arraySize, coords)
+ linSize = [1 cumprod(arraySize(1:end-1))];
+ arrayIdx = sum((coords-1) .* repmat(linSize, size(coords,1),1), 2) + 1;
+end
diff --git a/src/MATLAB/+Utils/CreateJSON.m b/src/MATLAB/+Utils/CreateJSON.m
new file mode 100644
index 0000000000000000000000000000000000000000..6d9d970d990a85353036fb8f11955bced226e586
--- /dev/null
+++ b/src/MATLAB/+Utils/CreateJSON.m
@@ -0,0 +1,155 @@
+function json = CreateJSON(data,bWhitespace)
+ if ( ~exist('bWhitespace','var') )
+ bWhitespace = true;
+ end
+
+ spaceStruct = struct('line',{''}, 'space',{''}, 'indent',{''});
+ if ( bWhitespace )
+ spaceStruct = struct('line',{'\n'}, 'space',{' '}, 'indent',{' '});
+ end
+
+ if ( isstruct(data) )
+ json = writeObject(data,'', spaceStruct);
+ else
+ json = writeArray(data,'', spaceStruct);
+ end
+end
+
+function json = writeObject(data, spacePrefix, spaceStruct)
+ fields = fieldnames(data);
+
+ fieldSep = ',';
+ objJSON = '';
+
+ fieldPattern = ['%s"%s"' spaceStruct.space ':' spaceStruct.space '%s%s'];
+ patternPad = length(sprintf(fieldPattern,'','','',''));
+
+ fieldPrefix = [spacePrefix spaceStruct.indent];
+ for i=1:length(fields)
+ if ( i == length(fields) )
+ fieldSep = '';
+ end
+
+ elemPad = repmat(spaceStruct.space, 1,patternPad+length(fields{i}));
+ elemPrefix = [fieldPrefix elemPad];
+
+ valJSON = writeValue(data.(fields{i}), elemPrefix, spaceStruct);
+ fieldJSON = sprintf([spaceStruct.line fieldPattern], fieldPrefix, fields{i}, valJSON,fieldSep);
+
+ objJSON = [objJSON fieldJSON];
+ end
+
+ objectPattern = ['{%s' spaceStruct.line '%s}'];
+ json = sprintf(objectPattern, objJSON,spacePrefix);
+end
+
+function [json,bSingleLine] = writeArray(data, spacePrefix, spaceStruct)
+ bSingleLine = false;
+ if ( isnumeric(data) && (size(data,1) == numel(data)) )
+ bSingleLine = true;
+ json = writeSingleLineArray(data, spaceStruct);
+ return;
+ end
+
+ valSep = ',';
+ arrayJSON = '';
+
+ valPattern = '%s%s%s';
+
+ valuePrefix = [spacePrefix spaceStruct.indent];
+ for i=1:size(data,1)
+ if ( i == size(data,1) )
+ valSep = '';
+ end
+
+ arrayEntry = squashSelect(data, i);
+ if ( numel(arrayEntry) == 1 )
+ if ( iscell(arrayEntry) )
+ valJSON = writeValue(arrayEntry{1}, valuePrefix, spaceStruct);
+ else
+ valJSON = writeValue(arrayEntry, valuePrefix, spaceStruct);
+ end
+ else
+ [valJSON,bSingleLine] = writeArray(arrayEntry, valuePrefix, spaceStruct);
+ end
+
+ % Combine brackets on one line if all the root array is a single line
+ if ( bSingleLine && (size(data,1) == 1) )
+ json = sprintf('[%s]',valJSON);
+ return
+ else
+ arrayJSON = [arrayJSON sprintf([spaceStruct.line valPattern], valuePrefix, valJSON, valSep)];
+ end
+ end
+
+ arrayPattern = ['[%s' spaceStruct.line '%s]'];
+ json = sprintf(arrayPattern, arrayJSON,spacePrefix);
+end
+
+function arrayEntry = squashSelect(arrayData, i)
+ if ( ndims(arrayData) == 1 )
+ arrayEntry = arrayData(i);
+ return;
+ end
+
+ dimSizes = size(arrayData);
+ if ( length(dimSizes) < 3 )
+ dimSizes = [dimSizes 1];
+ end
+
+ arrayEntry = reshape(arrayData(i,:), dimSizes(2:end));
+end
+
+function json = writeSingleLineArray(data, spaceStruct)
+ valSep = [',' spaceStruct.space];
+ arrayJSON = '';
+ for i=1:length(data)
+ if ( i == length(data) )
+ valSep = '';
+ end
+
+ valJSON = writeValue(data(i),'', spaceStruct);
+ arrayJSON = [arrayJSON sprintf('%s%s', valJSON,valSep)];
+ end
+ json = sprintf('[%s]', arrayJSON);
+end
+
+function json = writeValue(data, spacePrefix, spaceStruct)
+ if ( ischar(data) )
+ json = sprintf('"%s"',escapeString(data));
+ elseif ( iscell(data) || any(size(data) > 1) )
+ json = writeArray(data, spacePrefix, spaceStruct);
+ elseif ( isstruct(data) )
+ json = writeObject(data, spacePrefix, spaceStruct);
+ elseif ( islogical(data) )
+ if ( data )
+ json = 'true';
+ else
+ json = 'false';
+ end
+ elseif ( isempty(data) )
+ json = 'null';
+ elseif ( isnumeric(data) )
+ json = num2str(data);
+ else
+ ME = MException('json:save','Cannot save unsupported type');
+ ME.throw;
+ end
+end
+
+function quotedStr = escapeString(inStr)
+ escChars = {'\' '"' char(8) char(12) char(10) char(13) char(9)};
+ escStr = {'\\' '\"','\b','\f','\n','\r','\t'};
+
+ escMap = containers.Map(escChars,escStr);
+
+ quotedStr = '';
+ for i=1:length(inStr)
+ nextChar = inStr(i);
+ if ( isKey(escMap,nextChar) )
+ nextChar = escMap(nextChar);
+ end
+
+ quotedStr = [quotedStr nextChar];
+ end
+end
diff --git a/src/MATLAB/+Utils/IndToCoord.m b/src/MATLAB/+Utils/IndToCoord.m
new file mode 100644
index 0000000000000000000000000000000000000000..c9edc7b69d15af289c85832d03b66bc343b169a2
--- /dev/null
+++ b/src/MATLAB/+Utils/IndToCoord.m
@@ -0,0 +1,17 @@
+% IndToCoord - Convert linear array indices into a list of subscript
+% indices.
+%
+% coords = IndToCoord(arraySize, arrayIdx)
+function coords = IndToCoord(arraySize, arrayIdx)
+ coords = zeros(length(arrayIdx),length(arraySize));
+
+ linSize = [1 cumprod(arraySize)];
+ partialIdx = arrayIdx;
+ for i = length(arraySize):-1:1
+ r = rem(partialIdx-1, linSize(i)) + 1;
+ q = floor((partialIdx-r) / linSize(i)) + 1;
+
+ coords(:,i) = q;
+ partialIdx = r;
+ end
+end
diff --git a/src/MATLAB/+Utils/ParseJSON.m b/src/MATLAB/+Utils/ParseJSON.m
new file mode 100644
index 0000000000000000000000000000000000000000..b4e9f740fc105268e78cf9ed992a04e454e3e22e
--- /dev/null
+++ b/src/MATLAB/+Utils/ParseJSON.m
@@ -0,0 +1,308 @@
+function data = ParseJSON(json)
+ quoteIdx = regexp(json,'\"', 'start');
+ escStart = regexp(json,'\\([/\"\\bfnrt]|u[a-fA-F\d]{4})', 'start');
+
+ strQuotes = setdiff(quoteIdx,escStart+1);
+ quoteMap = containers.Map(strQuotes(1:end-1),strQuotes(2:end));
+
+ parsePos = ignoreSpace(json,1);
+ assertChar('parse', {'{','['}, json,parsePos);
+
+ if ( json(parsePos) == '{' )
+ [data parsePos] = parseObjectJSON(json,parsePos+1, quoteMap);
+ elseif ( json(parsePos) == '[' )
+ [data parsePos] = parseArrayJSON(json,parsePos+1, quoteMap);
+ end
+
+ data = postprocessObjects(data);
+end
+
+function [objData parsePos] = parseObjectJSON(json, startPos, quoteMap)
+ parsePos = ignoreSpace(json,startPos);
+
+ objData = [];
+ assertInStr('parseObject', '''STRING'' or ''}''', json, parsePos);
+ if ( json(parsePos) == '}' )
+ parsePos = ignoreSpace(json,parsePos+1);
+ return;
+ end
+
+ while ( parsePos <= length(json) )
+ assertChar('parseObject', '"', json,parsePos);
+ [keyStr parsePos] = parseStringJSON(json,parsePos, quoteMap);
+
+ assertChar('parseObject', ':', json,parsePos);
+ [value parsePos] = parseValueJSON(json,parsePos+1, quoteMap);
+% if ( isempty(value) )
+% throwError('parseObject','Expecting ''STRING'', ''NUMBER'', ''NULL'', ''TRUE'', ''FALSE'', ''{'', ''[''', json, parsePos);
+% end
+
+ objData.(validFieldName(keyStr)) = value;
+
+ assertInStr('parseObject', '''}''', json, parsePos);
+ if ( json(parsePos) == '}' )
+ parsePos = ignoreSpace(json,parsePos+1);
+ return;
+ end
+
+ assertChar('parseObject', {',','}'}, json,parsePos);
+ parsePos = ignoreSpace(json,parsePos+1);
+ end
+
+ throwError('parseObject','Expecting closing ''}''', json, parsePos);
+end
+
+function [arrayData parsePos] = parseArrayJSON(json, startPos, quoteMap)
+ parsePos = ignoreSpace(json,startPos);
+
+ arrayData = cell(0,1);
+ if ( json(parsePos) == ']' )
+ parsePos = ignoreSpace(json,parsePos+1);
+ return;
+ end
+
+ while ( parsePos <= length(json) )
+ [value parsePos] = parseValueJSON(json,parsePos, quoteMap);
+% if ( isempty(value) )
+% throwError('parseArray','Expecting ''STRING'', ''NUMBER'', ''NULL'', ''TRUE'', ''FALSE'', ''{'', ''[''', json, parsePos);
+% end
+
+ arrayData{end+1} = value;
+
+ assertInStr('parseArray', ''']''', json, parsePos);
+ if ( json(parsePos) == ']' )
+ parsePos = ignoreSpace(json,parsePos+1);
+ return;
+ end
+
+ assertChar('parseArray', {',',']'}, json,parsePos);
+
+ parsePos = ignoreSpace(json,parsePos+1);
+ end
+
+ throwError('parseArray','Expecting closing '']''', json, parsePos);
+end
+
+function [valueData parsePos] = parseValueJSON(json, startPos, quoteMap)
+ parsePos = ignoreSpace(json,startPos);
+
+ assertInStr('parseValue', '''STRING'', ''NUMBER'', ''NULL'', ''TRUE'', ''FALSE'', ''{'', ''[''', json, parsePos);
+ chkChar = json(parsePos);
+
+ keywordMap = {'true',true; 'false',false; 'null',[]};
+
+ switch(chkChar)
+ case '['
+ [valueData parsePos] = parseArrayJSON(json,parsePos+1, quoteMap);
+ case '{'
+ [valueData parsePos] = parseObjectJSON(json,parsePos+1, quoteMap);
+ case '"'
+ [valueData parsePos] = parseStringJSON(json,parsePos, quoteMap);
+ case {'-','0','1','2','3','4','5','6','7','8','9'}
+ [valueData parsePos] = parseNumberJSON(json,parsePos);
+ otherwise
+ for i=1:size(keywordMap,1)
+ [bMatched parsePos] = matchKeyword(json,parsePos,keywordMap{i,1});
+ if ( bMatched )
+ valueData = keywordMap{i,2};
+ return;
+ end
+ end
+ throwError('parseValue','Expecting ''STRING'', ''NUMBER'', ''NULL'', ''TRUE'', ''FALSE'', ''{'', ''[''', json, parsePos);
+ end
+end
+
+function [stringData parsePos] = parseStringJSON(json, startPos, quoteMap)
+ if ( ~isKey(quoteMap,startPos) )
+ throwError('parseString','Expecting ''STRING''', json, parsePos);
+ end
+
+ startQuote = startPos;
+ endQuote = quoteMap(startPos);
+ escapedStr = json(startQuote+1:endQuote-1);
+
+ stringData = validExpandString(escapedStr, json, startPos);
+ parsePos = ignoreSpace(json,endQuote + 1);
+end
+
+function [numberData parsePos] = parseNumberJSON(json, startPos)
+ numPad = 20;
+ chkEnd = min(startPos+numPad,length(json));
+
+ matchStr = regexp(json(startPos:chkEnd),'^-?(0|[1-9]\d*)(\.\d+)?([eE][+-]?\d+)?', 'once','match');
+ if ( isempty(matchStr) )
+ throwError('parseNumber','Expecting ''NUMBER''', json, startPos);
+ end
+
+ numberData = str2double(matchStr);
+ parsePos = ignoreSpace(json,startPos+length(matchStr));
+end
+
+function [bMatched parsePos] = matchKeyword(json,parsePos, keywordStr)
+ bMatched = false;
+ if ( length(json) < parsePos+length(keywordStr) )
+ return;
+ end
+
+ keywordEnd = parsePos+length(keywordStr)-1;
+ if ( ~strcmpi(json(parsePos:keywordEnd), keywordStr) )
+ return;
+ end
+
+ parsePos = ignoreSpace(json,keywordEnd+1);
+ bMatched = true;
+end
+
+function fieldStr = validFieldName(inStr)
+ fieldStr = inStr;
+ bAlphaNum = isstrprop(inStr,'alphanum');
+ fieldStr(~bAlphaNum) = '_';
+
+ if ( ~isletter(fieldStr(1)) )
+ fieldStr = ['s_' fieldStr];
+ end
+end
+
+function expandStr = validExpandString(escapedStr, json,strPos)
+
+ expandSeq = {'\"','\b','\f','\n','\r','\t'};
+ unescStart = regexp(escapedStr,['[' [expandSeq{:}] ']'], 'start');
+
+ if ( ~isempty(unescStart) )
+ throwError('parseString', 'Invalid character in string', json, strPos+unescStart(1));
+ end
+
+ expandStr = '';
+ bEscape = false;
+ for i=1:length(escapedStr)
+ expandChar = escapedStr(i);
+
+ if ( bEscape )
+ bEscape = false;
+ if ( expandChar == 'u' )
+ continue;
+ end
+
+ if ( ~any(expandChar == '\"bfnrt/') )
+ throwError('parseString', 'Invalid escape sequence in string', json, strPos+i);
+ end
+
+ expandChar = sprintf(['\' expandChar]);
+ elseif ( expandChar == '\' )
+ bEscape = true;
+ continue;
+ end
+
+ expandStr(end+1) = expandChar;
+ end
+end
+
+function dataOut = postprocessObjects(dataEntry)
+ if ( isstruct(dataEntry) )
+ fields = fieldnames(dataEntry);
+ for i=1:length(fields)
+ dataEntry.(fields{i}) = postprocessObjects(dataEntry.(fields{i}));
+ end
+ elseif ( iscell(dataEntry) )
+ dataEntry = postprocessArrays(dataEntry);
+ end
+
+ dataOut = dataEntry;
+end
+
+function dataEntry = postprocessArrays(dataEntry)
+ finalDims = length(dataEntry);
+
+ [bCanExpand expandDims expandTypes] = canExpandArray(dataEntry);
+ if ( ~bCanExpand )
+ finalDims = [finalDims 1];
+ end
+
+ while ( bCanExpand )
+ dataEntry = reshape(dataEntry, numel(dataEntry),1);
+ dataEntry = vertcat(dataEntry{:});
+
+ finalDims = [finalDims expandDims];
+ [bCanExpand expandDims expandTypes] = canExpandArray(dataEntry);
+ end
+
+ dataEntry = reshape(dataEntry, finalDims);
+ if ( length(expandDims) > 1 )
+ for i=1:numel(dataEntry)
+ dataEntry{i} = postprocessObjects(dataEntry{i});
+ end
+ elseif ( length(expandTypes) == 1 && strcmpi(expandTypes{1},'double') )
+ dataEntry = cell2mat(dataEntry);
+ end
+end
+
+function [bCanExpand expandDims expandTypes] = canExpandArray(cellArray)
+ chkType = unique(cellfun(@(x)(class(x)), cellArray(:), 'UniformOutput',0));
+ chkDims = unique(cellfun(@(x)(length(x)), cellArray(:)));
+
+ bCanExpand = (length(chkDims) == 1) && (length(chkType) == 1) && strcmpi(chkType{1},'cell');
+
+ expandTypes = chkType;
+ expandDims = chkDims;
+end
+
+function parsePos = ignoreSpace(json,startPos)
+ for parsePos=startPos:length(json)
+ if ( ~isspace(json(parsePos)) )
+ return;
+ end
+ end
+end
+
+function assertInStr(type, expect, json, parsePos)
+ if ( parsePos > length(json) )
+ if ( isempty(expect) )
+ throwError(type, 'Unexpected end of file', json, parsePos);
+ else
+ throwError(type, ['Unexpected end of file, expecting ' expect], json, parsePos);
+ end
+ end
+end
+
+function assertChar(type, charValue, json, parsePos)
+ if ( ischar(charValue) )
+ charValue = {charValue};
+ end
+
+ if ( parsePos > length(json) )
+ throwError(type, makeAssertStr(charValue), json, parsePos)
+ end
+
+ for i=1:length(charValue)
+ if ( json(parsePos) == charValue{i} )
+ return;
+ end
+ end
+
+ throwError(type,makeAssertStr(charValue), json, parsePos)
+end
+
+function errStr = makeAssertStr(charValues)
+ errStr = 'Expecting';
+
+ for i=1:length(charValues)-1
+ errStr = [errStr ' ''' charValues{i} ''' or'];
+ end
+
+ errStr = [errStr ' ''' charValues{end} ''''];
+end
+
+function throwError(type,message, json, pos)
+ contextPad = 5;
+ contextStart = max(pos-contextPad,1);
+ contextEnd = min(pos+3*contextPad,length(json));
+
+ arrowPos = pos-contextStart;
+ arrowSpace = repmat(' ',1,arrowPos);
+
+ contextStr = json(contextStart:contextEnd);
+ contextStr = strtok(contextStr,sprintf('\n'));
+
+ ME = MException(['json:' type],'Parse error: %s\n\n%s\n%s^', message,contextStr,arrowSpace);
+ ME.throw;
+end
diff --git a/src/MATLAB/+Utils/PrintTime.m b/src/MATLAB/+Utils/PrintTime.m
new file mode 100644
index 0000000000000000000000000000000000000000..5060ef568877fb436d364ac24ad4675e684eea9e
--- /dev/null
+++ b/src/MATLAB/+Utils/PrintTime.m
@@ -0,0 +1,12 @@
+function [ strOut ] = printTime( timeIn )
+%PRINTTIME takes time in sec and outputs a string in the form HH:MM:SS.ss
+
+hr = floor(timeIn/3600);
+tmNew = timeIn - hr*3600;
+mn = floor(tmNew/60);
+tmNew = tmNew - mn*60;
+sc = tmNew;
+
+strOut = sprintf('%02dh:%02dm:%05.2fs',hr,mn,sc);
+end
+
diff --git a/src/MATLAB/+Helper/SwapXY_RC.m b/src/MATLAB/+Utils/SwapXY_RC.m
similarity index 100%
rename from src/MATLAB/+Helper/SwapXY_RC.m
rename to src/MATLAB/+Utils/SwapXY_RC.m
diff --git a/src/MATLAB/+license/LicenseHeader.c b/src/MATLAB/+license/LicenseHeader.c
new file mode 100644
index 0000000000000000000000000000000000000000..0ce60879fc5e555c1d63e8c363212b004ec3dbc2
--- /dev/null
+++ b/src/MATLAB/+license/LicenseHeader.c
@@ -0,0 +1,21 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
diff --git a/src/MATLAB/+license/LicenseHeader.m b/src/MATLAB/+license/LicenseHeader.m
new file mode 100644
index 0000000000000000000000000000000000000000..24b8cb2bd9ce35e299a5dbb25d363f8841821aea
--- /dev/null
+++ b/src/MATLAB/+license/LicenseHeader.m
@@ -0,0 +1,22 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/src/MATLAB/+license/doAllFolders.m b/src/MATLAB/+license/doAllFolders.m
new file mode 100644
index 0000000000000000000000000000000000000000..b159827792e3a33a864d07f96661d520206caae3
--- /dev/null
+++ b/src/MATLAB/+license/doAllFolders.m
@@ -0,0 +1,45 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+dlist = dir('*');
+for dd=1:length(dlist)
+ if ~dlist(dd).isdir || length(dlist(dd).name)<4
+ continue
+ end
+ if strcmp(dlist(dd).name,'+assign') | strcmp(dlist(dd).name,'+matlab_bgl')
+ continue
+ end
+ license.goHeader(['.\' dlist(dd).name '\']);
+
+end
+license.goHeader('.\');
+
+% c files
+excludeFiles={'sha1.h','sha1.c'};
+dlist=dir('..\c');
+for dd=1:length(dlist)
+ if ~dlist(dd).isdir || length(dlist(dd).name)<4
+ continue
+ end
+ license.goHeader(['..\c\' dlist(dd).name '\'],1,excludeFiles);
+end
diff --git a/src/MATLAB/+license/getFileText.m b/src/MATLAB/+license/getFileText.m
new file mode 100644
index 0000000000000000000000000000000000000000..6bb3e0843963954f3ebc1278b78d4d5465cc1646
--- /dev/null
+++ b/src/MATLAB/+license/getFileText.m
@@ -0,0 +1,38 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function txt=getFileText(filename)
+
+fid = fopen(filename,'rt');
+i=1;
+txt= {};
+
+nextLine = fgets(fid);
+while ischar(nextLine)
+
+ txt{i} = nextLine;
+ nextLine=fgets(fid);
+ i=i+1;
+end
+
+fclose(fid);
+
diff --git a/src/MATLAB/+license/goHeader.m b/src/MATLAB/+license/goHeader.m
new file mode 100644
index 0000000000000000000000000000000000000000..410031d348dbf91ea888f3e5661b95f8fccf9842
--- /dev/null
+++ b/src/MATLAB/+license/goHeader.m
@@ -0,0 +1,70 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+function goHeader(folder,bC,excludeFiles)
+if nargin<2
+ bC=0;
+end
+if nargin<3
+ excludeFiles={};
+end
+if bC
+ flist = dir(fullfile(folder, '*.cpp'));
+ flist = [flist;dir(fullfile(folder, '*.c'))];
+ flist = [flist;dir(fullfile(folder, '*.h'))];
+ % note - this is the old token for the c code. this will need to change
+ % to ******* as per the new licenseheader.c
+ % strToken='//////////';
+ strToken='**********';
+ % get matlab headers out of c files...
+% strToken='%%%%%%%%%%';
+ fnamePreamble='.\+license\LicenseHeader.c';
+else
+ flist = dir(fullfile(folder, '*.m'));
+ strToken='%%%%%%%%%%';
+ fnamePreamble='.\+license\LicenseHeader.m';
+end
+for ff=1:length(flist)
+ if any(strcmp(excludeFiles,flist(ff).name))
+ continue
+ end
+ txt = license.getFileText(fullfile(folder,flist(ff).name));
+ txtPreamble = license.getFileText(fnamePreamble);
+ idxPreamble = find(cellfun(@(x) ~isempty(strfind(x,strToken)),txt),2);
+ if length(idxPreamble)~=2
+ fprintf(1,'found file with no license: %s\n',flist(ff).name);
+ % find the first non-comment line
+ idxPreamble = find(cellfun(@(x) x(1)~='%',txt),1);
+ if isempty(idxPreamble)
+ continue
+ end
+ txtPreamble={ char(10), txtPreamble{:}, char(10)};
+
+ else
+ txt(idxPreamble(1):idxPreamble(2))=[];
+ end
+
+ txtRedone={txt{1:idxPreamble(1)-1} txtPreamble{:} txt{idxPreamble(1):end}};
+ license.writeFileText(fullfile(folder,flist(ff).name),txtRedone);
+end
diff --git a/src/MATLAB/+license/writeFileText.m b/src/MATLAB/+license/writeFileText.m
new file mode 100644
index 0000000000000000000000000000000000000000..12d6f817ec23bc275e4cf58a60d8e318d9a8efe1
--- /dev/null
+++ b/src/MATLAB/+license/writeFileText.m
@@ -0,0 +1,30 @@
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2011-2016 Andrew Cohen
+%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function writeFileText(filename,txt)
+fid = fopen(filename,'wt');
+for i=1:length(txt)
+ fprintf(fid,'%s',txt{i});
+end
+fclose(fid);
diff --git a/src/MATLAB/LEVER_SegAndTrackFolders.exe b/src/MATLAB/LEVER_SegAndTrackFolders.exe
index 1d9f15730b67a1dc6f68cc25a76dd4fc5471f4b4..59b002c7389308f269cd3415c3c5fbb0a80cf299 100644
Binary files a/src/MATLAB/LEVER_SegAndTrackFolders.exe and b/src/MATLAB/LEVER_SegAndTrackFolders.exe differ
diff --git a/src/MATLAB/LEVER_SegAndTrackFolders.m b/src/MATLAB/LEVER_SegAndTrackFolders.m
index 089ecba18d0dbde03d05fde90f53b7cf2678491d..57d8b74335cb604bc9bbf1cf3314caf1e944f52f 100644
--- a/src/MATLAB/LEVER_SegAndTrackFolders.m
+++ b/src/MATLAB/LEVER_SegAndTrackFolders.m
@@ -1,44 +1,91 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% This file is part of LEVer.exe
-% (C) 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% This file is part of LEVer - the tool for stem cell lineaging. See
+% http://n2t.net/ark:/87918/d9rp4t for details
+%
+% LEVer is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% LEVer is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with LEVer in file "gnu gpl v3.txt". If not, see
+% <http://www.gnu.org/licenses/>.
+%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% mcc -m LEVER_SegAndTrackFolders.m
function LEVER_SegAndTrackFolders(outputDir, maxProcessors)
global CONSTANTS CellPhenotypes
CONSTANTS=[];
-softwareVersion = Helper.GetVersion();
+if ( ~exist('outputDir','var') )
+ outputDir = '';
+end
+
+% Trial run command
+bTrialRun = false;
+if ( strncmpi(outputDir,'-T',2) )
+ outputDir = outputDir(3:end);
+ bTrialRun = true;
+end
+
+softwareVersion = Dev.GetVersion();
if (isdeployed())
Load.SetWorkingDir();
end
-cellType = Load.QueryCellType();
-Load.AddConstant('cellType',cellType,1);
-
directory_name = uigetdir('','Select Root Folder for Seg and Track');
if ( ~directory_name ),return,end
-if ( ~exist('outputDir','var') )
- outputDir = directory_name;
+% Get initial cell segmentation parameters
+Load.AddConstant('cellType', [], 1);
+
+hDlg = UI.SegPropDialog();
+uiwait(hDlg);
+
+if ( isempty(CONSTANTS.cellType) )
+ return;
end
-% Trial run command
-bTrialRun = 0;
-if ( strcmpi(outputDir(1:2),'-T') )
- outputDir = outputDir(3:end);
- if ( isempty(outputDir) )
- outputDir = directory_name;
- end
- bTrialRun = 1;
+%% Run export of subdirectories if necessary.
+exportRoot = Load.FolderExport(directory_name);
+if ( isempty(exportRoot) )
+ return;
end
-processedDatasets = {};
+if ( isempty(outputDir) )
+ outputDir = exportRoot;
+end
+
+%% Find valid images in exported folder.
+[chkPaths,invalidFile] = Load.CheckFolderExport(exportRoot);
+validJSON = chkPaths(~invalidFile);
+if ( isempty(validJSON) )
+ warning(['No valid data found at: ' exportRoot]);
+ return;
+end
+
+%% Use previewer on first valid directory to get cell type and segmentation parameters
+Load.AddConstant('version',softwareVersion,1);
+
+[imageData,imagePath] = MicroscopeData.ReadMetadataFile(fullfile(exportRoot,validJSON{1}));
+Metadata.SetMetadata(imageData);
+
+Load.AddConstant('rootImageFolder', imagePath, 1);
+Load.AddConstant('matFullFile', fullfile(outputDir, Metadata.GetDatasetName()),1);
+
+%% Use total number of processors or max from command-line
numProcessors = getenv('Number_of_processors');
numProcessors = str2double(numProcessors);
if(isempty(numProcessors) || isnan(numProcessors) || numProcessors < 4)
@@ -52,58 +99,38 @@ if ( exist('maxProcessors','var') )
numProcessors = min(maxProcessors, numProcessors);
end
-dirList = dir(directory_name);
-
-bInvalidName = arrayfun(@(x)(strncmpi(x.name,'.',1) || strncmpi(x.name,'..',2)), dirList);
-bValidDir = ~bInvalidName & (vertcat(dirList.isdir) > 0);
-dirList = dirList(bValidDir);
-
-for dirIdx=1:length(dirList)
- if ( ~(dirList(dirIdx).isdir) )
- continue
- end
-
- validStartFilename = getValidStartFileName(fullfile(directory_name, dirList(dirIdx).name));
- if ( isempty(validStartFilename) )
- fprintf('\n**** Image list does not begin with frame 1 for %s. Skipping\n\n', directory_name);
- continue;
- end
+%% Run segmentation for all valid directories
+processedDatasets = {};
+for dirIdx=1:length(validJSON)
+ subDir = fileparts(validJSON{dirIdx});
+ dataDir = fileparts(subDir);
- [datasetName namePattern] = Helper.ParseImageName(validStartFilename);
- if ( isempty(datasetName) )
- fprintf('\n**** Image names not formatted correctly for %s. Skipping\n\n', directory_name);
- continue;
- end
-
- CONSTANTS.rootImageFolder = fullfile(directory_name, dirList(dirIdx).name);
- CONSTANTS.datasetName = datasetName;
- CONSTANTS.imageNamePattern = namePattern;
- CONSTANTS.matFullFile = fullfile(outputDir, [CONSTANTS.datasetName '_LEVer.mat']);
+ [imageData,imagePath] = MicroscopeData.ReadMetadataFile(fullfile(exportRoot,validJSON{dirIdx}));
+ Metadata.SetMetadata(imageData);
+
+ Load.AddConstant('rootImageFolder', imagePath, 1);
+ Load.AddConstant('matFullFile', fullfile(outputDir,dataDir, [Metadata.GetDatasetName() '_LEVer.mat']),1);
if ( exist(CONSTANTS.matFullFile,'file') )
- fprintf('%s - LEVer data already exists. Skipping\n', CONSTANTS.datasetName);
- continue
- end
-
- fileList = dir(fullfile(directory_name, dirList(dirIdx).name, '*.tif'));
- if ( isempty(fileList) )
+ fprintf('%s - LEVer data already exists. Skipping\n', Metadata.GetDatasetName());
continue
end
Load.AddConstant('version',softwareVersion,1);
- fprintf('Segment & track file : %s\n', CONSTANTS.datasetName);
-
+ %% Segment and track folder
+ fprintf('Segment & track file : %s\n', Metadata.GetDatasetName());
tic
- Load.InitializeConstants();
if ( ~bTrialRun )
+ Load.InitializeConstants();
+
segArgs = Segmentation.GetCellTypeParams();
- [errStatus tSeg tTrack] = Segmentation.SegAndTrackDataset(CONSTANTS.rootImageFolder, CONSTANTS.datasetName, CONSTANTS.imageNamePattern, numProcessors, segArgs);
+ [errStatus tSeg tTrack] = Segmentation.SegAndTrackDataset(numProcessors, segArgs);
if ( ~isempty(errStatus) )
- fprintf('\n\n*** Segmentation/Tracking failed for %s\n\n', CONSTANTS.datasetName);
+ fprintf('\n\n*** Segmentation/Tracking failed for %s\n\n', Metadata.GetDatasetName());
- errFilename = fullfile(outputDir, [CONSTANTS.datasetName '_segtrack_err.log']);
+ errFilename = fullfile(outputDir, [Metadata.GetDatasetName() '_segtrack_err.log']);
fid = fopen(errFilename, 'wt');
fprintf(fid, '%s', errStatus);
fclose(fid);
@@ -119,35 +146,11 @@ for dirIdx=1:length(dirList)
Editor.ReplayableEditAction(@Editor.OriginAction, 1);
Helper.SaveLEVerState([CONSTANTS.matFullFile]);
-
Error.LogAction('Segmentation time - Tracking time',tSeg,tTrack);
end
- processedDatasets = [processedDatasets; {CONSTANTS.datasetName}];
+ processedDatasets = [processedDatasets; {Metadata.GetDatasetName()}];
end %dd
clear global;
end
-
-% This function tries to quickly find one or more files that qualify as an
-% initial image frame for parsing dataset names, etc. Returns the first
-% file name found
-function filename = getValidStartFileName(chkPath)
- filename = '';
-
- flist = [];
- chkDigits = 7:-1:2;
- for i=1:length(chkDigits)
- digitStr = ['%0' num2str(chkDigits(i)) 'd'];
- flist = dir(fullfile(chkPath,['*_t' num2str(1,digitStr) '*.tif']));
- if ( ~isempty(flist) )
- break;
- end
- end
-
- if ( isempty(flist) )
- return;
- end
-
- filename = flist(1).name;
-end
diff --git a/src/MATLAB/LEVer.exe b/src/MATLAB/LEVer.exe
index fc1b01a469a5d4ec7664a39cabc50e9a44b7fd2d..e8d5b9d9561db81d894b43758ebd9937a07bce62 100644
Binary files a/src/MATLAB/LEVer.exe and b/src/MATLAB/LEVer.exe differ
diff --git a/src/MATLAB/LEVer.m b/src/MATLAB/LEVer.m
index 582d6b4a843fb0a4c520f2594874a7167a5d0c86..1ed0724d6383633f99d457334098c5b879226c22 100644
--- a/src/MATLAB/LEVer.m
+++ b/src/MATLAB/LEVer.m
@@ -2,10 +2,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
diff --git a/src/MATLAB/MTC.exe b/src/MATLAB/MTC.exe
deleted file mode 100644
index 041116cabb278981321a8cd7f5978cd015dc6819..0000000000000000000000000000000000000000
Binary files a/src/MATLAB/MTC.exe and /dev/null differ
diff --git a/src/MATLAB/Segmentor.exe b/src/MATLAB/Segmentor.exe
index 6f743777da97bf502da52284a6acce4d84ea218d..a79c01b79d1a5e6138f0c41f584d167ac68e1170 100644
Binary files a/src/MATLAB/Segmentor.exe and b/src/MATLAB/Segmentor.exe differ
diff --git a/src/MATLAB/Segmentor.m b/src/MATLAB/Segmentor.m
index e1079bd0357f3f7c0d3351027a304ccc56f76c34..94e0e227eec68800eb5344f750b877db7281b82e 100644
--- a/src/MATLAB/Segmentor.m
+++ b/src/MATLAB/Segmentor.m
@@ -7,10 +7,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
-% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
+% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
-% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
+% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
@@ -28,10 +28,9 @@
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-function [hulls frameTimes] = Segmentor(varargin)
+function hulls = Segmentor(varargin)
hulls = [];
-frameTimes = [];
supportedCellTypes = Load.GetSupportedCellTypes();
[procArgs,segArgs] = setSegArgs(supportedCellTypes, varargin);
@@ -51,31 +50,32 @@ funcPath = which(funcName);
if ( ~isempty(funcPath) )
segFunc = supportedCellTypes(typeIdx).segRoutine.func;
else
- fprintf(['WARNING: Could not find ' funcName '() using default Segmentation.FrameSegmentor() routine\n']);
+ deployPrint(['WARNING: Could not find ' funcName '() using default Segmentation.FrameSegmentor() routine\n']);
segFunc = @Segmentation.FrameSegmentor;
end
segParams = struct2cell(segArgs);
try
- fprintf(1,'%s\n',procArgs.imagePath);
- fprintf(1,'%s\n',procArgs.imagePattern);
+ deployPrint(1,'%s\n',procArgs.metadataFile);
+
+ imageData = MicroscopeData.ReadMetadata(procArgs.metadataFile,false);
+ if ( isempty(imageData) )
+ error(['Unable to read image metadata file: ' procArgs.metadataFile]);
+ end
- Load.AddConstant('rootImageFolder', procArgs.imagePath, 1);
- Load.AddConstant('imageNamePattern', procArgs.imagePattern, 1);
- Load.AddConstant('numChannels', procArgs.numChannels, 1);
- Load.AddConstant('numFrames', procArgs.numFrames, 1);
Load.AddConstant('primaryChannel', procArgs.primaryChannel, 1);
+ Metadata.SetMetadata(imageData);
tStart = procArgs.procID;
- tEnd = procArgs.numFrames;
+ tEnd = Metadata.GetNumberOfFrames();
tStep = procArgs.numProcesses;
primaryChan = procArgs.primaryChannel;
numImages = floor(tEnd/tStep);
for t = tStart:tStep:tEnd
- fprintf('%d%%...', round(100 * floor(t/tStep) / numImages));
+ deployPrint('%d%%...', round(100 * floor(t/tStep) / numImages));
chanImSet = Helper.LoadIntensityImageSet(t);
if ( isempty(chanImSet) )
@@ -83,17 +83,24 @@ try
end
frameHulls = segFunc(chanImSet, primaryChan, t, segParams{:});
+ if ( isempty(frameHulls) )
+ continue;
+ end
+
+ rcImageDims = Metadata.GetDimensions('rc');
+ validHulls = [];
for i=1:length(frameHulls)
- frameHulls(i).time = t;
- if ( ~isfield(frameHulls(i),'tag') || isempty(frameHulls(i).tag) )
- frameHulls(i).tag = char(segFunc);
- else
- frameHulls(i).tag = [char(segFunc) ':' frameHulls(i).tag];
+ tag = char(segFunc);
+ if ( isfield(frameHulls(i),'tag') && ~isempty(frameHulls(i).tag) )
+ tag = [char(segFunc) ':' frameHulls(i).tag];
end
+
+ newHull = Hulls.CreateHull(rcImageDims, frameHulls(i).indexPixels, t, false, tag);
+ validHulls = [validHulls newHull];
end
- hulls = [hulls frameHulls];
+ hulls = [hulls validHulls];
end
catch excp
@@ -112,19 +119,28 @@ catch excp
end
fileName = fullfile('segmentationData',['objs_' num2str(tStart) '.mat']);
-save(fileName,'hulls','frameTimes');
+save(fileName,'hulls');
% Write this file to indicate that the segmentaiton data is actually fully saved
fSempahore = fopen(fullfile('segmentationData',['done_' num2str(tStart) '.txt']), 'w');
fclose(fSempahore);
-fprintf('\tDone\n');
+deployPrint('\tDone\n');
+end
+
+function deployPrint(varargin)
+ if ( ~isdeployed() )
+ return;
+ end
+
+ fprintf(varargin{:});
end
-function [procArgs segArgs] = setSegArgs(supportedCellTypes, argCell)
- procArgs = struct('procID',{1}, 'numProcesses',{1}, 'numChannels',{0}, 'numFrames',{0}, 'cellType',{''}, 'primaryChannel',{[]}, 'imagePath',{''}, 'imagePattern',{''});
+function [procArgs, segArgs] = setSegArgs(supportedCellTypes, argCell)
+ procArgs = struct('procID',{1}, 'numProcesses',{1}, 'primaryChannel',{1}, 'metadataFile',{''}, 'cellType',{''});
procArgFields = fieldnames(procArgs);
+ procArgFields = reshape(procArgFields,1,length(procArgFields));
procArgTypes = cellfun(@(x)(class(x)), struct2cell(procArgs), 'UniformOutput',0);
segArgs = [];
diff --git a/src/MATLAB/mexDijkstra.mexw64 b/src/MATLAB/mexDijkstra.mexw64
index 6a9e06765e7083af173d46a9e3ab4758f9cc27e6..ae9b02f715bab15572c23277f3d6bbd09975dccd 100644
Binary files a/src/MATLAB/mexDijkstra.mexw64 and b/src/MATLAB/mexDijkstra.mexw64 differ
diff --git a/src/MATLAB/mexGraph.mexw64 b/src/MATLAB/mexGraph.mexw64
index fad04f2e0ef49aaa6ca258bd23ee2f4a7b0358e6..e325cd9768b1ce5ee908d69fdae77362c777c28c 100644
Binary files a/src/MATLAB/mexGraph.mexw64 and b/src/MATLAB/mexGraph.mexw64 differ
diff --git a/src/MATLAB/mexHashData.mexw64 b/src/MATLAB/mexHashData.mexw64
index 2d5cb421a604d490235b4541b7a4c6b17566413e..fbb4ec6535921290d6bc699c647c0ce3158f35e3 100644
Binary files a/src/MATLAB/mexHashData.mexw64 and b/src/MATLAB/mexHashData.mexw64 differ
diff --git a/src/MATLAB/mexIntegrityCheck.mexw64 b/src/MATLAB/mexIntegrityCheck.mexw64
index 80fdbf84abc29dbef2817062d49a18cadebb1dc2..3eec2172e9115d65e94031bbd8bdb23f5e18b262 100644
Binary files a/src/MATLAB/mexIntegrityCheck.mexw64 and b/src/MATLAB/mexIntegrityCheck.mexw64 differ
diff --git a/src/MATLAB/mexMAT.mexw64 b/src/MATLAB/mexMAT.mexw64
index a9ad704988183e8f91c7fa37973cbdaf263ba820..b95eba51d25f605bac2a427efa3b3526ae4d8765 100644
Binary files a/src/MATLAB/mexMAT.mexw64 and b/src/MATLAB/mexMAT.mexw64 differ
diff --git a/src/MATLAB/trackerMex.mexw64 b/src/MATLAB/trackerMex.mexw64
new file mode 100644
index 0000000000000000000000000000000000000000..b251121253d8a3a59c73b8d3a852476d3380e261
Binary files /dev/null and b/src/MATLAB/trackerMex.mexw64 differ
diff --git a/src/MATLAB/tryAutoReseg.m b/src/MATLAB/tryAutoReseg.m
deleted file mode 100644
index c37fc4a499810abd69caa9f348136e8ccc545acd..0000000000000000000000000000000000000000
--- a/src/MATLAB/tryAutoReseg.m
+++ /dev/null
@@ -1,110 +0,0 @@
-function tryAutoReseg(filename, outFilename)
- rootImageDir = 'B:\Data\NYNSCI\Embryonic\SKG_100312_E12_Ant_vs_Post-0003';
-
- if ( ~exist('outFilename','var') )
- [inPath inName, inExt] = fileparts(filename);
- outFilename = fullfile(inPath,[inName '_autoreseg' inExt]);
- end
-
- load(filename);
- Load.AddConstant('matFullFile', filename);
-
- findImageDir(rootImageDir);
-
- Load.InitializeConstants();
- Load.FixOldFileVersions();
-
- % Check this at the end of load now for new and old data alike
- errors = mexIntegrityCheck();
- if ( ~isempty(errors) )
- Dev.PrintIntegrityErrors(errors);
- end
-
- % Initialized cached costs here if necessary (placed after fix old file versions for compatibility)
- Load.InitializeCachedCosts(0);
-
- Editor.ReplayableEditAction(@Editor.InitHistory);
-
- runTreeInference();
- runAutoReseg();
-end
-
-function runTreeInference()
- global CellFamilies HashedCells
-
- neFam = find(arrayfun(@(x)(~isempty(x.startTime)), CellFamilies));
- runFamilies = neFam(arrayfun(@(x)(x.startTime == 1), CellFamilies(neFam)));
-
- Editor.ReplayableEditAction(@Editor.TreeInference, runFamilies,length(HashedCells));
-end
-
-function runAutoReseg()
- global CONSTANTS CellFamilies CellHulls HashedCells Costs
-
- neFam = find(arrayfun(@(x)(~isempty(x.startTime)), CellFamilies));
- runFamilies = neFam(arrayfun(@(x)(x.startTime == 1), CellFamilies(neFam)));
-
- tStart = 2;
- tEnd = length(HashedCells);
-
- bErr = Editor.ReplayableEditAction(@Editor.ResegInitializeAction, runFamilies, 2);
-
- Editor.ReplayableEditAction(@Editor.StartReplayableSubtask, 'AutoResegTask');
-
-%%%%%%%%%
- bFinished = false;
-
- % Need to worry about deleted hulls?
- costMatrix = Costs;
- bDeleted = ([CellHulls.deleted] > 0);
- costMatrix(bDeleted,:) = 0;
- costMatrix(:,bDeleted) = 0;
-
- mexDijkstra('initGraph', costMatrix);
-
-
-
- for t=2:tEnd
- xl = [1 CONSTANTS.imageSize(2)];
- yl = [1 CONSTANTS.imageSize(1)];
-
- bErr = Editor.ReplayableEditAction(@Editor.ResegFrameAction, t, tEnd, [xl;yl]);
-
- if ( bErr )
- return;
- end
- end
-
-%%%%%%%%%
- [bErr finishTime] = Editor.ReplayableEditAction(@Editor.ResegFinishAction);
- Editor.ReplayableEditAction(@Editor.StopReplayableSubtask, tEnd-1, 'AutoResegTask');
-end
-
-function findImageDir(rootSearchDir)
- global CONSTANTS
-
- fileList = dir(fullfile(rootSearchDir,'*'));
- bInvalidName = arrayfun(@(x)(strncmpi(x.name,'.',1) || strncmpi(x.name,'..',2)), fileList);
- bValidDir = ~bInvalidName & (vertcat(fileList.isdir) > 0);
-
- dirList = fileList(bValidDir);
-
- subDirIdx = find(strcmpi(CONSTANTS.datasetName(1:(end-1)),{dirList.name}));
- if ( isempty(subDirIdx) )
- error('Could not find images in specified directory');
- end
-
- imageDir = fullfile(rootSearchDir,dirList(subDirIdx).name);
- imageList = dir(fullfile(imageDir,'*.tif'));
- if ( isempty(imageList) )
- error('Could not find images in specified directory');
- end
-
- [sigDigits imageDataset] = Helper.ParseImageName(imageList(1).name);
- if ( ~strcmpi(imageDataset,CONSTANTS.datasetName) )
- error('Dataset name mismatch');
- end
-
- Load.AddConstant('rootImageFolder', imageDir, 1);
- Load.AddConstant('imageSignificantDigits', sigDigits, 1);
-end
diff --git a/src/MATLAB/version.json b/src/MATLAB/version.json
new file mode 100644
index 0000000000000000000000000000000000000000..6899acbaad0530a54823e20bf3e448544c641940
--- /dev/null
+++ b/src/MATLAB/version.json
@@ -0,0 +1,12 @@
+{
+ "name" : "LEVER",
+ "majorVersion" : 7,
+ "minorVersion" : 14,
+ "branchName" : "master",
+ "buildNumber" : "2016.07.05.18",
+ "buildMachine" : "bioimage28",
+ "commitHash" : [
+ "lever.git : f3caa208f9dfe30ce840b56fd5274a62f15a43b1",
+ "utilities.git : 6537681200925800e61251113576f525237b0af7"
+ ]
+}
diff --git a/src/MATLAB/version.txt b/src/MATLAB/version.txt
deleted file mode 100644
index 6e5a1f11221494a95d31de53629ab5e393595dab..0000000000000000000000000000000000000000
--- a/src/MATLAB/version.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-v7.13.2
-master
-
diff --git a/src/c/MTC.sln b/src/c/MTC.sln
deleted file mode 100644
index 83b641615c917a2804bf3817b9ee6919a9f41ad2..0000000000000000000000000000000000000000
--- a/src/c/MTC.sln
+++ /dev/null
@@ -1,26 +0,0 @@
-
-Microsoft Visual Studio Solution File, Format Version 11.00
-# Visual Studio 2010
-Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MTC", "MTC.vcxproj", "{7991491A-3C3A-4159-B5AA-D801638BD570}"
-EndProject
-Global
- GlobalSection(SolutionConfigurationPlatforms) = preSolution
- Debug|Win32 = Debug|Win32
- Debug|x64 = Debug|x64
- Release|Win32 = Release|Win32
- Release|x64 = Release|x64
- EndGlobalSection
- GlobalSection(ProjectConfigurationPlatforms) = postSolution
- {7991491A-3C3A-4159-B5AA-D801638BD570}.Debug|Win32.ActiveCfg = Debug|Win32
- {7991491A-3C3A-4159-B5AA-D801638BD570}.Debug|Win32.Build.0 = Debug|Win32
- {7991491A-3C3A-4159-B5AA-D801638BD570}.Debug|x64.ActiveCfg = Debug|x64
- {7991491A-3C3A-4159-B5AA-D801638BD570}.Debug|x64.Build.0 = Debug|x64
- {7991491A-3C3A-4159-B5AA-D801638BD570}.Release|Win32.ActiveCfg = Release|Win32
- {7991491A-3C3A-4159-B5AA-D801638BD570}.Release|Win32.Build.0 = Release|Win32
- {7991491A-3C3A-4159-B5AA-D801638BD570}.Release|x64.ActiveCfg = Release|x64
- {7991491A-3C3A-4159-B5AA-D801638BD570}.Release|x64.Build.0 = Release|x64
- EndGlobalSection
- GlobalSection(SolutionProperties) = preSolution
- HideSolutionNode = FALSE
- EndGlobalSection
-EndGlobal
diff --git a/src/c/MTC.vcxproj b/src/c/MTC.vcxproj
deleted file mode 100644
index afdb25d72247f20aadc4c8150ecca4dda9a454be..0000000000000000000000000000000000000000
--- a/src/c/MTC.vcxproj
+++ /dev/null
@@ -1,190 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
- <ItemGroup Label="ProjectConfigurations">
- <ProjectConfiguration Include="Debug|Win32">
- <Configuration>Debug</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
- <ProjectConfiguration Include="Debug|x64">
- <Configuration>Debug</Configuration>
- <Platform>x64</Platform>
- </ProjectConfiguration>
- <ProjectConfiguration Include="Release|Win32">
- <Configuration>Release</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
- <ProjectConfiguration Include="Release|x64">
- <Configuration>Release</Configuration>
- <Platform>x64</Platform>
- </ProjectConfiguration>
- </ItemGroup>
- <PropertyGroup Label="Globals">
- <ProjectGuid>{7991491A-3C3A-4159-B5AA-D801638BD570}</ProjectGuid>
- <RootNamespace>MTC</RootNamespace>
- </PropertyGroup>
- <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
- <ConfigurationType>Application</ConfigurationType>
- <CharacterSet>MultiByte</CharacterSet>
- <WholeProgramOptimization>true</WholeProgramOptimization>
- </PropertyGroup>
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
- <ConfigurationType>Application</ConfigurationType>
- <CharacterSet>MultiByte</CharacterSet>
- </PropertyGroup>
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
- <ConfigurationType>Application</ConfigurationType>
- <CharacterSet>MultiByte</CharacterSet>
- <WholeProgramOptimization>true</WholeProgramOptimization>
- </PropertyGroup>
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
- <ConfigurationType>Application</ConfigurationType>
- <CharacterSet>MultiByte</CharacterSet>
- </PropertyGroup>
- <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
- <ImportGroup Label="ExtensionSettings">
- </ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
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- <PropertyGroup Label="UserMacros" />
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- <PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</PostBuildEventUseInBuild>
- </PropertyGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
- <ClCompile>
- <Optimization>Disabled</Optimization>
- <MinimalRebuild>true</MinimalRebuild>
- <BasicRuntimeChecks>EnableFastChecks</BasicRuntimeChecks>
- <RuntimeLibrary>MultiThreadedDebug</RuntimeLibrary>
- <WarningLevel>Level3</WarningLevel>
- <DebugInformationFormat>EditAndContinue</DebugInformationFormat>
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-copy /Y "$(OutDir)$(ProjectName).pdb" ..\..\bin
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-copy /Y "$(OutDir)$(ProjectName).pdb" ..\..\bin
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- <ClCompile Include="MTC\cost.cpp" />
- <ClCompile Include="MTC\detection.cpp" />
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- <ClCompile Include="MTC\tracker.cpp" />
- </ItemGroup>
- <ItemGroup>
- <ClInclude Include="MTC\cost.h" />
- <ClInclude Include="MTC\detection.h" />
- <ClInclude Include="MTC\paths.h" />
- <ClInclude Include="MTC\tracker.h" />
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diff --git a/src/c/MTC/cost.cpp b/src/c/MTC/cost.cpp
deleted file mode 100644
index e512a17ed8aa78a1bed67ce992407681818196d7..0000000000000000000000000000000000000000
--- a/src/c/MTC/cost.cpp
+++ /dev/null
@@ -1,227 +0,0 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
-#include "tracker.h"
-
-
-#undef max
-#undef min
-
-// Convenience defines
-#define SQR(x) ((x)*(x))
-#define DOT(x1,y1,x2,y2) ((x1)*(x2) + (y1)*(y2))
-#define LENGTH(x,y) (sqrt((SQR(x))+(SQR(y))))
-#define SIGN(x) (((x) >= 0.0) ? (1.0) : (-1.0) )
-
-const double costEpsilon = 1e-3;
-
-double CCDist(int t0,int i0,int t1,int i1)
-{
- int i;
- int nHull1;
-
- nHull1=GetGlobalIdx(t1, i1);
-
- for (i=0;i<rgDetect[t0][i0].nConnectedHulls;i++)
- {
- if (rgDetect[t0][i0].DarkConnectedHulls[i]==nHull1)
- // connected!
- return rgDetect[t0][i0].DarkConnectedCost[i];
- }
- return gCCMax+1.; //dbltype::infinity();
-
-
-} // CCDist
-
-double HullDist(int t0,int i0,int t1,int i1)
-{
- double dx,dy,d;
-
- d=(SQR(rgDetect[t0][i0].X-rgDetect[t1][i1].X) + SQR(rgDetect[t0][i0].Y-rgDetect[t1][i1].Y));
-
- return sqrt(d);
-} // HullDist
-
-double CCHullDist(int t0,int i0,int t1,int i1,double vmax,double ccmax)
-{
- double hd,sd;
- double nmax,nmin,cd;
- int nHull0,nHull1;
- //
- nHull0=GetGlobalIdx(t0, i0);
- nHull1=GetGlobalIdx(t1, i1);
-
- hd=HullDist(t0,i0,t1,i1);
- if (hd>vmax)
- return dbltype::infinity();
-
- nmax=std::max<double>(rgDetect[t0][i0].nPixels, rgDetect[t1][i1].nPixels);
- nmin=std::min<double>(rgDetect[t0][i0].nPixels, rgDetect[t1][i1].nPixels);
-
- cd=CCDist(t0,i0,t1,i1);
- if (cd>ccmax )
- return dbltype::infinity();
-
- if ((cd>ccmax ) && (hd>vmax/2.))
- return dbltype::infinity();
-
- sd = (nmax-nmin)/nmax;
-
- return (10*hd+100.*sd+1000.*cd);
-
-} // CCHullDist
-
-int GetDestinyNode(int nSourceGIdx,int nOffset,int tOffset)
-{
- // Find the assigned in-edge
- int histIndex2 = -1;
-
- int histIdx = gAssignedConnectIn[nSourceGIdx];
- if ( histIdx >=0 )
- {
- CSourcePath* histpath = gConnectIn[nSourceGIdx][histIdx];
- if ( (histpath->frame.size() > nOffset) && (histpath->frame[nOffset] == tOffset) )
- histIndex2 = histpath->index[nOffset];
- }
-
- return histIndex2;
-} // GetDestinyNode
-
-double GetCost(std::vector<int>& frame, std::vector<int>& index, int srcFrameIdx, int bCheck)
-{
- const double intensityCostWeight = 1.0;
- double velo_max= gVMax,cc_max=gCCMax;
- double LocalCost = 0.0;
- double OcclusionCost=1.;
- double DestinyCost=1.;
- double TotalCost = 0.0;
- double localLinearCost = 0.0;
- double dlcd,dccd;
- double LocationCost = 0.0;
- double dlocnX,dlocnY;
- int k;
- int startIdx;
- int ptLoc[3][2];
- int srcGIdx;
-
- int nHull0,nHull1;
- //
- nHull0=GetGlobalIdx(frame[srcFrameIdx], index[srcFrameIdx]);
- nHull1=GetGlobalIdx(frame[srcFrameIdx+1], index[srcFrameIdx+1]);
-
- if ( frame.size() < 2 )
- {
- return dbltype::infinity();
- }
-
- if (bCheck)
- startIdx=frame.size()-2;
- else
- {
- int tStart;
-
- tStart=frame[srcFrameIdx]-gWindowSize+1;
- tStart=std::max<double>(0., tStart);
- startIdx=srcFrameIdx;
- while ((frame[startIdx]>tStart) && (startIdx>0))
- startIdx--;
-
- }
-
- for ( k=startIdx; k < frame.size()-1; ++k )
- {
- dlcd=HullDist(frame[k],index[k],frame[k+1],index[k+1]);
- if (dlcd > velo_max)
- return dbltype::infinity();
-
- OcclusionCost+=frame[k+1]-frame[k]-1;
- }
-
- if (bCheck)
- return 1.;
-
- LocalCost=3*CCHullDist(frame[srcFrameIdx],index[srcFrameIdx],frame[srcFrameIdx+1],index[srcFrameIdx+1],velo_max,cc_max);
-
- if ( LocalCost == dbltype::infinity() )
- return dbltype::infinity();
-
- if (srcFrameIdx>0)
- LocalCost+=CCHullDist(frame[srcFrameIdx-1],index[srcFrameIdx-1],frame[srcFrameIdx+1],index[srcFrameIdx+1], 2*velo_max, 2*cc_max);
- else
- LocalCost*=2;
-
- if ( LocalCost == dbltype::infinity() )
- return dbltype::infinity();
-
- if ((srcFrameIdx<frame.size()-2))
- LocalCost+=CCHullDist(frame[srcFrameIdx],index[srcFrameIdx],frame[srcFrameIdx+2],index[srcFrameIdx+2], 2*velo_max, 2*cc_max);
- else
- LocalCost*=2;
-
- if ( LocalCost == dbltype::infinity() )
- return dbltype::infinity();
-
- //int nDestiny2,nDestiny3;
- //
- //if (srcFrameIdx>0 && frame.size()>srcFrameIdx+2)
- //{
-
- // srcGIdx = GetGlobalIdx(frame[srcFrameIdx], index[srcFrameIdx]);
- // nDestiny2=GetDestinyNode(srcGIdx,2,frame[srcFrameIdx+1]);
- // if (nDestiny2==index[srcFrameIdx+1])
- // LocalCost*=0.5;
- //}
-
- dlocnX=double(rgDetect[frame[srcFrameIdx]][index[srcFrameIdx]].X);
- dlocnY=double(rgDetect[frame[srcFrameIdx]][index[srcFrameIdx]].Y);
- for ( k=startIdx; k < srcFrameIdx; ++k )
- {
- dlocnX+=double(rgDetect[frame[k]][index[k]].X);
- dlocnY+=double(rgDetect[frame[k]][index[k]].Y);
- }
- dlocnX/=(srcFrameIdx-startIdx+1);
- dlocnY/=(srcFrameIdx-startIdx+1);
- for ( k=srcFrameIdx; k < frame.size(); ++k )
- {
- LocationCost+=SQR(double(rgDetect[frame[k]][index[k]].X)-dlocnX)+SQR(double(rgDetect[frame[k]][index[k]].Y)-dlocnY);
- }
- LocationCost/=(frame.size()-srcFrameIdx);
- LocationCost=sqrt(LocationCost);
-
- TotalCost = LocalCost + LocationCost; // + localLinearCost;
- if (frame.size()<2*gWindowSize+1)
- {
- double LengthPenalty;
- LengthPenalty=(2*gWindowSize+1)-frame.size();
- TotalCost = TotalCost*2*LengthPenalty;
- }
-
- if (OcclusionCost>1)
- OcclusionCost*=2;
- TotalCost*=OcclusionCost;
-
- if ( TotalCost < costEpsilon )
- TotalCost = costEpsilon;
-
- return TotalCost;
-}
diff --git a/src/c/MTC/cost.h b/src/c/MTC/cost.h
deleted file mode 100644
index 2afcbdeb48aec5476d8e1175fcf2edcc06f81fd1..0000000000000000000000000000000000000000
--- a/src/c/MTC/cost.h
+++ /dev/null
@@ -1,29 +0,0 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
-
-
-// Get cost based on a frame and index list. The srcFrameIdx is used if there, it is the index into
-// frame/index vectors of the source point(start of new path). srcFrameIdx is trivially 0 if there is
-// no history being used.
-double GetCost(std::vector<int>& frame, std::vector<int>& index, int srcFrameIdx,int bCheck);
\ No newline at end of file
diff --git a/src/c/MTC/detection.cpp b/src/c/MTC/detection.cpp
deleted file mode 100644
index deadbf116573e010698eaf8959bca5029c859527..0000000000000000000000000000000000000000
--- a/src/c/MTC/detection.cpp
+++ /dev/null
@@ -1,143 +0,0 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
-#include "tracker.h"
-
-
-int gnumPts;
-
-int ReadSegmentationData(char* filename, int* numTotalPts, SDetection*** rgDetect, int** detectLengths, int** detectLengthSum)
-{
- int numFrames;
- int numPts;
-
- int* lengthPtr;
- int* lengthSumPtr;
- SDetection* dataPtr;
- SDetection** arrayIdxPtr;
- int nDCH;
- double dDCH;
- FILE* fp;
-
- fp = fopen(filename, "r");
- if ( !fp )
- return -1;
-
- fscanf(fp, "%d %d\n\n", &numFrames, &numPts);
-
- dataPtr = new SDetection[numPts];
- arrayIdxPtr = new SDetection*[numFrames];
- lengthPtr = new int[numFrames];
- lengthSumPtr = new int[numFrames];
-
- int frameOffset = 0;
- for ( int t=0; t < numFrames; ++t )
- {
- int frameDetections;
- fscanf(fp, "%d\n", &frameDetections);
-
- lengthPtr[t] = frameDetections;
- if ( t > 0 )
- lengthSumPtr[t] = lengthSumPtr[t-1] + lengthPtr[t-1];
- else
- lengthSumPtr[t] = 0;
-
- arrayIdxPtr[t] = dataPtr + frameOffset;
-
- for ( int ptItr = 0; ptItr < frameDetections; ++ptItr )
- {
- SDetection* curPt = &arrayIdxPtr[t][ptItr];
- fscanf(fp, "%d %d %d %d:", &(curPt->X), &(curPt->Y),&(curPt->nPixels),&(curPt->nConnectedHulls));
-
- for ( int pixItr = 0; pixItr < curPt->nConnectedHulls; ++pixItr )
- {
- fscanf(fp, " %d,%lf", &(nDCH),&(dDCH));
- nDCH--; //Make 0 offset
- curPt->DarkConnectedHulls.push_back(nDCH);
- curPt->DarkConnectedCost.push_back(dDCH);
- }
-
- fscanf(fp,"\n");
- }
-
- frameOffset += frameDetections;
- }
-
- fclose(fp);
-
- (*numTotalPts) = numPts;
- (*rgDetect) = arrayIdxPtr;
- (*detectLengths) = lengthPtr;
- (*detectLengthSum) = lengthSumPtr;
-
- return numFrames;
-}
-
-
-void DeleteDetections()
-{
- delete[] rgDetect[0];
- delete[] rgDetect;
-
- delete[] rgDetectLengths;
- delete[] rgDetectLengthSum;
-}
-
-int ReadDetectionData(int argc, char* argv[])
-{
-
- int checkResult;
-
- int nxtArg = 1;
- if ( argc >= 5 )
- {
- nxtArg = 3;
- sscanf(argv[1], "%lf", &gVMax);
- sscanf(argv[2], "%lf", &gCCMax);
- }
-
- checkResult = ReadSegmentationData(argv[nxtArg], &gnumPts, &rgDetect, &rgDetectLengths, &rgDetectLengthSum);
- if ( checkResult < 0 )
- return -1;
-
- gNumFrames = checkResult;
-
- gMaxDetections = 0;
- for ( int t=0; t < gNumFrames; ++t )
- gMaxDetections = std::max<int>(gMaxDetections, rgDetectLengths[t]);
-
-
- gConnectOut = new std::map<int,CSourcePath*>[gnumPts];
- gConnectIn = new std::map<int,CSourcePath*>[gnumPts];
- gAssignedConnectIn = new int[gnumPts];
- gAssignedConnectOut = new int[gnumPts];
- gAssignedTrackID = new int[gnumPts];
- for ( int i=0; i < gnumPts; ++i )
- {
- gAssignedConnectIn[i] = -1;
- gAssignedConnectOut[i] = -1;
- gAssignedTrackID[i] = -1;
- }
-
- return (nxtArg+1);
-}
diff --git a/src/c/MTC/detection.h b/src/c/MTC/detection.h
deleted file mode 100644
index 6b117d180fb2e5c405cbff2cda621dd620b59397..0000000000000000000000000000000000000000
--- a/src/c/MTC/detection.h
+++ /dev/null
@@ -1,47 +0,0 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-
-//
-//***********************************************************************
-
-// Detection related types and variables
-struct SDetection
-{
- int X;
- int Y;
- int nPixels;
- int nConnectedHulls;
- std::vector<int>DarkConnectedHulls;
- std::vector<double>DarkConnectedCost;
-
-
-};
-
-// Read and initialize detection related data. All globals listed below must be filled or initialized by the end of this routine.
-// Globals:
-// rgDetect - filled with detection data
-// gNumFrames - length of rows of rgDetect
-// rgDetectLengths - the length of each column of rgDetect
-// rgDetectLengthSum - the cumulative sum of rgDetectLengths, rgDetectLengthSum[0] = 0, rgDetectLengthSum[1] = rgDetectLengths[0], etc.
-// gMaxDetections - maximum detections in any frame
-// gConnectOut,gConnectIn - initialized to numPts(total detections) empty std::maps each
-// gAssignedConnectIn - same size as gConnectIn, initialized to -1
-// gAssignedConnectOut - same as gAssignedConnectIn, these are for quick lookup of assigned paths
-int ReadDetectionData(int argc, char* argv[]);
\ No newline at end of file
diff --git a/src/c/MTC/paths.cpp b/src/c/MTC/paths.cpp
deleted file mode 100644
index c0ab42ff2193c3f3276359e4980daf0d64da8c9a..0000000000000000000000000000000000000000
--- a/src/c/MTC/paths.cpp
+++ /dev/null
@@ -1,161 +0,0 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
-#include "tracker.h"
-
-int GetGlobalIdx(int t, int idx)
-{
- return rgDetectLengthSum[t] + idx;
-}
-
-int GetLocalIdx(int globalIdx)
-{
- int t;
- for ( t=1; t < gNumFrames; ++t )
- {
- if ( globalIdx < rgDetectLengthSum[t] )
- {
- break;
- }
- }
-
- return (globalIdx - rgDetectLengthSum[t-1]);
-}
-
-int BuildHistoryPath(CSourcePath* historyPath, CSourcePath* path, int occlLookback)
-{
- int pathStartGIdx = GetGlobalIdx(path->frame[0], path->index[0]);
-
- // Find the assigned in-edge
- int histTrackID = -1;
- int histIdx = gAssignedConnectIn[pathStartGIdx];
- if ( histIdx >=0 )
- {
- CSourcePath* histpath = gConnectIn[pathStartGIdx][histIdx];
- // Single segment agreement requirement
- if ( histpath->frame.size() > 2 )
- histTrackID = histpath->trackletID;
- }
-
- if ( histTrackID >= 0 )
- {
- tPathList::iterator histIter = gAssignedTracklets[histTrackID].begin();
- while ( histIter != gAssignedTracklets[histTrackID].end() )
- {
- CSourcePath* curPath = *histIter;
-
- historyPath->PushPoint(curPath->frame[0], curPath->index[0]);
- ++histIter;
- }
- }
-
- for ( int i=0; i < path->frame.size(); ++i )
- historyPath->PushPoint(path->frame[i], path->index[i]);
-
- return histTrackID;
-}
-
-int DepthFirstBestPathSearch(CSourcePath path, int bestGIdx, int t, int tEnd, int occlLookback)
-{
- bool bFinishedSearch = true;
- if ( t < tEnd )
- {
- int nextDetections = rgDetectLengths[t];
- for ( int nextPt=0; nextPt < nextDetections; ++nextPt )
- {
- path.PushPoint(t, nextPt);
- double chkCost = GetCost(path.frame, path.index, 0,1);
- path.PopPoint();
-
- if ( chkCost == dbltype::infinity() )
- continue;
-
- bFinishedSearch = false;
-
- path.PushPoint(t, nextPt);
- bestGIdx = DepthFirstBestPathSearch(path, bestGIdx, t+1, tEnd, occlLookback);
- path.PopPoint();
- }
- }
-
- if ( bFinishedSearch && (path.frame.size() > 1) )
- {
- CSourcePath historyPath;
-
- int startGIdx = GetGlobalIdx(path.frame[0], path.index[0]);
- int nextGIdx = GetGlobalIdx(path.frame[1], path.index[1]);
-
- int historyTrackID = BuildHistoryPath(&historyPath, &path, occlLookback);
- int srcPathIdx = historyPath.frame.size() - path.frame.size();
-
- double newPathCost = GetCost(historyPath.frame, historyPath.index, srcPathIdx,0);
- if ( newPathCost == dbltype::infinity() )
- return bestGIdx;
-
- path.trackletID = historyTrackID;
- path.cost = newPathCost;
-
- if ( gConnectOut[startGIdx].count(nextGIdx) == 0 )
- {
- CSourcePath* newPath = new CSourcePath(path);
- gConnectOut[startGIdx].insert(std::pair<int,CSourcePath*>(nextGIdx, newPath));
- gConnectIn[nextGIdx].insert(std::pair<int,CSourcePath*>(startGIdx, newPath));
- }
- else if ( newPathCost < gConnectOut[startGIdx][nextGIdx]->cost )
- {
- *(gConnectOut[startGIdx][nextGIdx]) = path;
- }
-
- if ( bestGIdx < 0 || newPathCost < gConnectOut[startGIdx][bestGIdx]->cost )
- {
- bestGIdx = nextGIdx;
- }
- }
-
- return bestGIdx;
-}
-
-void BuildBestPaths(std::map<int,int>& bestOutEdges, int t, int occlLookback)
-{
- if ( t-occlLookback < 0 )
- return;
-
- int numDetections = rgDetectLengths[t-occlLookback];
-
- int tEnd = std::min<int>(t+gWindowSize, gNumFrames);
-
- for ( int srcIdx=0; srcIdx < numDetections; ++srcIdx )
- {
- int startGIdx = GetGlobalIdx(t-occlLookback, srcIdx);
- if ( occlLookback > 0 && gAssignedConnectOut[startGIdx] > 0 )
- continue;
-
- CSourcePath srcPath;
- srcPath.PushPoint(t-occlLookback, srcIdx);
- int bestGIdx = DepthFirstBestPathSearch(srcPath, -1, t+1, tEnd, occlLookback);
- if ( bestGIdx >= 0 )
- {
- bestOutEdges[startGIdx] = bestGIdx;
- }
- }
-}
\ No newline at end of file
diff --git a/src/c/MTC/paths.h b/src/c/MTC/paths.h
deleted file mode 100644
index f0f1c74ddebcc70ff9f892e99b9e26b653640598..0000000000000000000000000000000000000000
--- a/src/c/MTC/paths.h
+++ /dev/null
@@ -1,66 +0,0 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
-#include <vector>
-#include <list>
-#include <map>
-
-typedef std::numeric_limits<double> dbltype;
-
-class CSourcePath
-{
-public:
- CSourcePath()
- {
- trackletID = -1;
- cost = dbltype::infinity();
- }
-
- void PushPoint(int t, int idx)
- {
- frame.push_back(t);
- index.push_back(idx);
- }
-
- void PopPoint()
- {
- if ( frame.size() <= 1 )
- return;
-
- frame.pop_back();
- index.pop_back();
- }
-
-public:
-
- int trackletID;
- double cost;
-
- std::vector<int> frame;
- std::vector<int> index;
-
-};
-
-int GetGlobalIdx(int t, int idx);
-int GetLocalIdx(int globalIdx);
-void BuildBestPaths(std::map<int,int>& bestOutEdges, int t, int occlLookcback = 0);
diff --git a/src/c/MTC/tracker.cpp b/src/c/MTC/tracker.cpp
deleted file mode 100644
index 6b724ae39e8b40fb69b0c7c9a1df2155b15e94fc..0000000000000000000000000000000000000000
--- a/src/c/MTC/tracker.cpp
+++ /dev/null
@@ -1,220 +0,0 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
-#include "tracker.h"
-
-//Global variables
-int gNumFrames;
-int gMaxDetections;
-int* rgDetectLengths;
-int* rgDetectLengthSum;
-SDetection** rgDetect;
-std::map<int,CSourcePath*>* gConnectOut;
-std::map<int,CSourcePath*>* gConnectIn;
-int* gAssignedConnectOut;
-int* gAssignedConnectIn;
-int* gAssignedTrackID;
-
-std::vector<tPathList> gAssignedTracklets;
-
-int gWindowSize = 4;
-
-double gVMax;
-double gCCMax;
-
-
-void WriteTracklets(int argc, char* argv[], int argIdx)
-{
-
-std::map<int,CSourcePath*>::iterator cIter;
- CSourcePath* inPath;
- double dinCost;
-
- if ( argIdx >= argc )
- return;
- FILE* fPathFile = fopen(argv[argIdx], "w");
-
- if ( !fPathFile )
- return;
-
- for ( int i=0; i < gAssignedTracklets.size(); ++i )
- {
- tPathList::iterator trackIter;
- tPathList::iterator lastPathIter = (--gAssignedTracklets[i].end());
- for ( trackIter=gAssignedTracklets[i].begin(); trackIter != gAssignedTracklets[i].end(); ++trackIter )
- {
- fprintf(fPathFile, "%d,%d,%d,%d,%d\n", i+1,(*trackIter)->frame[0] + 1,(*trackIter)->frame[1] + 1,(*trackIter)->index[0] + 1,(*trackIter)->index[1] + 1);
- }
- }
-
- fprintf(fPathFile, "-1,-1,-1,-1,-1\n");
- for ( int i=0; i < gnumPts; ++i )
- {
- cIter = gConnectIn[i].begin();
- for ( int j=0; j < gConnectIn[i].size(); ++j )
- {
- inPath=cIter->second;
- dinCost=inPath->cost;
- if (dinCost!=dinCost) // test for -1.#IND!
- continue;
- fprintf(fPathFile, "%d,%d,%lf\n",i+1,cIter->first+1,dinCost);
- cIter++;
-
- }
- }
-
- fclose(fPathFile);
-}
-
-void ClearEdges(std::vector<CSourcePath*>* inEdges, CSourcePath** outEdges)
-{
- for ( int i=0; i < gMaxDetections; ++i )
- {
- outEdges[i] = NULL;
- inEdges[i].clear();
- }
-}
-
-double FindMinCostIn(int ID)
-{
- double cmin=dbltype::infinity();
- CSourcePath* inPath;
- std::map<int,CSourcePath*>::iterator cIter;
-
- cIter = gConnectIn[ID].begin();
- for ( int j=0; j < gConnectIn[ID].size(); ++j )
- {
- inPath=cIter->second;
- if (inPath->cost<cmin)
- cmin=inPath->cost;
-
- cIter++;
-
- }
-
- return cmin;
-}
-
-int FindMinInEdgeIdx(int nextGIdx)
-{
- double cmin = dbltype::infinity();
- int bestIdx = -1;
-
- std::map<int,CSourcePath*>::iterator cIter = gConnectIn[nextGIdx].begin();
- while ( cIter != gConnectIn[nextGIdx].end() )
- {
- CSourcePath* inPath = cIter->second;
- if ( inPath->cost < cmin )
- {
- cmin = inPath->cost;
- bestIdx = cIter->first;
- }
-
- ++cIter;
- }
-
- return bestIdx;
-}
-
-int FindMinCostIdx(std::vector<CSourcePath*>& edges)
-{
- int minidx = -1;
- double mincost = dbltype::infinity();
- for ( int i=0; i < edges.size(); ++i )
- {
- if ( edges[i]->cost < mincost )
- {
- minidx = i;
- mincost = edges[i]->cost;
- }
- }
-
- return minidx;
-}
-
-int main(int argc, char* argv[])
-{
- system("echo %TIME% > ttt.txt");
-
- // Set default gate values.
- gVMax = 40.0;
- gCCMax = 20.0;
-
- int outputargidx = ReadDetectionData(argc, argv);
-
- if ( outputargidx < 0 )
- return 0;
-
- std::map<int,int> bestOutEdges;
- for ( int t=0; t < gNumFrames-1; ++t )
- {
- bestOutEdges.clear();
- BuildBestPaths(bestOutEdges, t);
-
- //Occlusions
- for ( int iLookback=1; iLookback < 2; ++iLookback )
- {
- BuildBestPaths(bestOutEdges, t, iLookback);
- }
-
- printf("t = %d, %d detections\n", t, rgDetectLengths[t]);
-
- for ( int destPtIdx=0; destPtIdx < rgDetectLengths[t+1]; ++destPtIdx)
- {
- int nextGIdx = GetGlobalIdx(t+1, destPtIdx);
- int bestTrackletIdx = FindMinInEdgeIdx(nextGIdx);
- if ( bestTrackletIdx < 0 )
- continue;
-
- if ( (bestOutEdges.count(bestTrackletIdx) == 0) || bestOutEdges[bestTrackletIdx] != nextGIdx )
- continue;
-
- int newTrackletID = gConnectOut[bestTrackletIdx][nextGIdx]->trackletID;
-
- if ( newTrackletID < 0 )
- {
- //Add new tracklet to list etc. and set id
- newTrackletID = gAssignedTracklets.size();
- gConnectOut[bestTrackletIdx][nextGIdx]->trackletID = newTrackletID;
-
- tPathList newList;
- gAssignedTracklets.push_back(newList);
-
- gAssignedTrackID[bestTrackletIdx] = newTrackletID;
- }
-
- //Add path to tracklet list
- gAssignedTracklets[newTrackletID].push_back(gConnectOut[bestTrackletIdx][nextGIdx]);
-
- //Keep track of assignment for fast lookup
- gAssignedConnectIn[nextGIdx] = bestTrackletIdx;
- gAssignedConnectOut[bestTrackletIdx] = nextGIdx;
- gAssignedTrackID[nextGIdx] = newTrackletID;
- }
- }
-
- WriteTracklets(argc, argv, outputargidx);
-
- system("echo %TIME% >> ttt.txt");
-
-}
diff --git a/src/c/MTC/tracker.h b/src/c/MTC/tracker.h
deleted file mode 100644
index 30687b972ee0858463b1ce19ffa2b2dfe65291c1..0000000000000000000000000000000000000000
--- a/src/c/MTC/tracker.h
+++ /dev/null
@@ -1,58 +0,0 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
-#include <stdio.h>
-
-#include <list>
-#include <vector>
-#include <limits>
-
-#include "detection.h"
-#include "cost.h"
-#include "paths.h"
-
-typedef std::list<CSourcePath*> tPathList;
-
-//Detection related global variables
-extern int gNumFrames;
-extern int gnumPts;
-extern int gMaxDetections;
-extern int* rgDetectLengths;
-extern int* rgDetectLengthSum;
-extern SDetection** rgDetect;
-
-//Path global variables
-extern std::map<int,CSourcePath*>* gConnectOut;
-extern std::map<int,CSourcePath*>* gConnectIn;
-
-//For quick edge lookup from point (like inID/outID)
-extern int* gAssignedConnectOut;
-extern int* gAssignedConnectIn;
-extern int* gAssignedTrackID;
-
-//Global variables
-extern int gWindowSize;
-extern double gVMax;
-extern double gCCMax;
-
-extern std::vector<tPathList> gAssignedTracklets;
\ No newline at end of file
diff --git a/src/c/Tracker.sln b/src/c/Tracker.sln
new file mode 100644
index 0000000000000000000000000000000000000000..942d3d655006dfac6c345a69cc70048603f491a9
--- /dev/null
+++ b/src/c/Tracker.sln
@@ -0,0 +1,20 @@
+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio 2012
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "TrackerMex", "Tracker.vcxproj", "{EA17F87B-2278-4F65-928A-5F20AD8633D6}"
+EndProject
+Global
+ GlobalSection(SolutionConfigurationPlatforms) = preSolution
+ Debug|x64 = Debug|x64
+ Release|x64 = Release|x64
+ EndGlobalSection
+ GlobalSection(ProjectConfigurationPlatforms) = postSolution
+ {EA17F87B-2278-4F65-928A-5F20AD8633D6}.Debug|x64.ActiveCfg = Debug|x64
+ {EA17F87B-2278-4F65-928A-5F20AD8633D6}.Debug|x64.Build.0 = Debug|x64
+ {EA17F87B-2278-4F65-928A-5F20AD8633D6}.Release|x64.ActiveCfg = Release|x64
+ {EA17F87B-2278-4F65-928A-5F20AD8633D6}.Release|x64.Build.0 = Release|x64
+ EndGlobalSection
+ GlobalSection(SolutionProperties) = preSolution
+ HideSolutionNode = FALSE
+ EndGlobalSection
+EndGlobal
diff --git a/src/c/Tracker.vcxproj b/src/c/Tracker.vcxproj
new file mode 100644
index 0000000000000000000000000000000000000000..b2af52f64d317a0b45248116da2f089cc6ab6370
--- /dev/null
+++ b/src/c/Tracker.vcxproj
@@ -0,0 +1,197 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project DefaultTargets="Build" ToolsVersion="14.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+ <ItemGroup Label="ProjectConfigurations">
+ <ProjectConfiguration Include="Debug|Win32">
+ <Configuration>Debug</Configuration>
+ <Platform>Win32</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Debug|x64">
+ <Configuration>Debug</Configuration>
+ <Platform>x64</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Release|Win32">
+ <Configuration>Release</Configuration>
+ <Platform>Win32</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Release|x64">
+ <Configuration>Release</Configuration>
+ <Platform>x64</Platform>
+ </ProjectConfiguration>
+ </ItemGroup>
+ <PropertyGroup Label="Globals">
+ <ProjectGuid>{EA17F87B-2278-4F65-928A-5F20AD8633D6}</ProjectGuid>
+ <Keyword>Win32Proj</Keyword>
+ <RootNamespace>Tracker</RootNamespace>
+ <ProjectName>TrackerMex</ProjectName>
+ </PropertyGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
+ <ConfigurationType>DynamicLibrary</ConfigurationType>
+ <UseDebugLibraries>true</UseDebugLibraries>
+ <CharacterSet>Unicode</CharacterSet>
+ <PlatformToolset>v140</PlatformToolset>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
+ <ConfigurationType>DynamicLibrary</ConfigurationType>
+ <UseDebugLibraries>true</UseDebugLibraries>
+ <CharacterSet>MultiByte</CharacterSet>
+ <PlatformToolset>v140</PlatformToolset>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
+ <ConfigurationType>DynamicLibrary</ConfigurationType>
+ <UseDebugLibraries>false</UseDebugLibraries>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <CharacterSet>Unicode</CharacterSet>
+ <PlatformToolset>v140</PlatformToolset>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
+ <ConfigurationType>DynamicLibrary</ConfigurationType>
+ <UseDebugLibraries>false</UseDebugLibraries>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <CharacterSet>MultiByte</CharacterSet>
+ <PlatformToolset>v140</PlatformToolset>
+ </PropertyGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
+ <ImportGroup Label="ExtensionSettings">
+ </ImportGroup>
+ <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="PropertySheets">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="PropertySheets">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <PropertyGroup Label="UserMacros" />
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <LinkIncremental>true</LinkIncremental>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
+ <LinkIncremental>true</LinkIncremental>
+ <OutDir>$(SolutionDir)Output\$(ProjectName)\$(Configuration)_$(PlatformName)\</OutDir>
+ <IntDir>$(SolutionDir)Intermediate\$(ProjectName)\$(Configuration)_$(PlatformName)\</IntDir>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+ <LinkIncremental>false</LinkIncremental>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
+ <LinkIncremental>false</LinkIncremental>
+ <OutDir>$(SolutionDir)Output\$(ProjectName)\$(Configuration)_$(PlatformName)\</OutDir>
+ <IntDir>$(SolutionDir)Intermediate\$(ProjectName)\$(Configuration)_$(PlatformName)\</IntDir>
+ </PropertyGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <ClCompile>
+ <PrecompiledHeader>
+ </PrecompiledHeader>
+ <WarningLevel>Level3</WarningLevel>
+ <Optimization>Disabled</Optimization>
+ <PreprocessorDefinitions>WIN32;_DEBUG;_WINDOWS;_USRDLL;TRACKER_EXPORTS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+ </ClCompile>
+ <Link>
+ <SubSystem>Windows</SubSystem>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ </Link>
+ </ItemDefinitionGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
+ <ClCompile>
+ <PrecompiledHeader>
+ </PrecompiledHeader>
+ <WarningLevel>Level3</WarningLevel>
+ <Optimization>Disabled</Optimization>
+ <PreprocessorDefinitions>WIN32;_DEBUG;_WINDOWS;_USRDLL;TRACKER_EXPORTS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+ <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;.\Tracker</AdditionalIncludeDirectories>
+ <OpenMPSupport>true</OpenMPSupport>
+ </ClCompile>
+ <Link>
+ <SubSystem>Windows</SubSystem>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win64\microsoft</AdditionalLibraryDirectories>
+ <AdditionalDependencies>libmx.lib;libmex.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies)</AdditionalDependencies>
+ <ModuleDefinitionFile>.\Tracker\trackerMex.def</ModuleDefinitionFile>
+ </Link>
+ <PostBuildEvent>
+ <Command>echo copy" $(OutDir)trakerMex.dll" "$(ProjectDir)"
+copy "$(OutDir)trackerMex.dll" "$(ProjectDir)"
+echo copy "$(OutDir)trackerMex.pdb" "$(ProjectDir)"
+copy "$(OutDir)trackerMex.pdb" "$(ProjectDir)"
+echo move "$(ProjectDir)trackerMex.dll" "$(ProjectDir)trackerMex.mexw64"
+move "$(ProjectDir)trackerMex.dll" "$(ProjectDir)trackerMex.mexw64"
+echo copy "$(ProjectDir)trackerMex.mexw64" "$(ProjectDir)..\MATLAB\."
+copy "$(ProjectDir)trackerMex.mexw64" "$(ProjectDir)..\MATLAB\."</Command>
+ </PostBuildEvent>
+ </ItemDefinitionGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+ <ClCompile>
+ <WarningLevel>Level3</WarningLevel>
+ <PrecompiledHeader>
+ </PrecompiledHeader>
+ <Optimization>MaxSpeed</Optimization>
+ <FunctionLevelLinking>true</FunctionLevelLinking>
+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <PreprocessorDefinitions>WIN32;NDEBUG;_WINDOWS;_USRDLL;TRACKER_EXPORTS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+ </ClCompile>
+ <Link>
+ <SubSystem>Windows</SubSystem>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ <EnableCOMDATFolding>true</EnableCOMDATFolding>
+ <OptimizeReferences>true</OptimizeReferences>
+ </Link>
+ </ItemDefinitionGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
+ <ClCompile>
+ <WarningLevel>Level3</WarningLevel>
+ <PrecompiledHeader>
+ </PrecompiledHeader>
+ <Optimization>MaxSpeed</Optimization>
+ <FunctionLevelLinking>true</FunctionLevelLinking>
+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <PreprocessorDefinitions>WIN32;NDEBUG;_WINDOWS;_USRDLL;TRACKER_EXPORTS;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+ <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;.\Tracker</AdditionalIncludeDirectories>
+ <OpenMPSupport>true</OpenMPSupport>
+ </ClCompile>
+ <Link>
+ <SubSystem>Windows</SubSystem>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ <EnableCOMDATFolding>true</EnableCOMDATFolding>
+ <OptimizeReferences>true</OptimizeReferences>
+ <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win64\microsoft</AdditionalLibraryDirectories>
+ <AdditionalDependencies>libmx.lib;libmex.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies)</AdditionalDependencies>
+ <ModuleDefinitionFile>.\Tracker\trackerMex.def</ModuleDefinitionFile>
+ </Link>
+ <PostBuildEvent>
+ <Command>echo copy" $(OutDir)trakerMex.dll" "$(ProjectDir)"
+copy "$(OutDir)trackerMex.dll" "$(ProjectDir)"
+echo copy "$(OutDir)trackerMex.pdb" "$(ProjectDir)"
+copy "$(OutDir)trackerMex.pdb" "$(ProjectDir)"
+echo move "$(ProjectDir)trackerMex.dll" "$(ProjectDir)trackerMex.mexw64"
+move "$(ProjectDir)trackerMex.dll" "$(ProjectDir)trackerMex.mexw64"
+echo copy "$(ProjectDir)trackerMex.mexw64" "$(ProjectDir)..\MATLAB\."
+copy "$(ProjectDir)trackerMex.mexw64" "$(ProjectDir)..\MATLAB\."</Command>
+ </PostBuildEvent>
+ </ItemDefinitionGroup>
+ <ItemGroup>
+ <ClCompile Include="Tracker\cost.cpp" />
+ <ClCompile Include="Tracker\Hull.cpp" />
+ <ClCompile Include="Tracker\paths.cpp" />
+ <ClCompile Include="Tracker\tracker.cpp" />
+ <ClCompile Include="Tracker\trackerMex.cpp" />
+ <ClCompile Include="Tracker\Utility.cpp" />
+ </ItemGroup>
+ <ItemGroup>
+ <None Include="Tracker\trackerMex.def" />
+ </ItemGroup>
+ <ItemGroup>
+ <ClInclude Include="Tracker\cost.h" />
+ <ClInclude Include="Tracker\Hull.h" />
+ <ClInclude Include="Tracker\paths.h" />
+ <ClInclude Include="Tracker\tracker.h" />
+ <ClInclude Include="Tracker\Utility.h" />
+ </ItemGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
+ <ImportGroup Label="ExtensionTargets">
+ </ImportGroup>
+</Project>
\ No newline at end of file
diff --git a/src/c/MTC.vcxproj.filters b/src/c/Tracker.vcxproj.filters
similarity index 60%
rename from src/c/MTC.vcxproj.filters
rename to src/c/Tracker.vcxproj.filters
index fb8d41c4c353bfac46f0736086dbe99a81dc9153..aab2d9ef51721e6d558ff72af1767a95beb11294 100644
--- a/src/c/MTC.vcxproj.filters
+++ b/src/c/Tracker.vcxproj.filters
@@ -11,34 +11,48 @@
</Filter>
<Filter Include="Resource Files">
<UniqueIdentifier>{67DA6AB6-F800-4c08-8B7A-83BB121AAD01}</UniqueIdentifier>
- <Extensions>rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav</Extensions>
+ <Extensions>rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav;mfcribbon-ms</Extensions>
</Filter>
</ItemGroup>
<ItemGroup>
- <ClCompile Include="MTC\cost.cpp">
+ <ClCompile Include="Tracker\cost.cpp">
<Filter>Source Files</Filter>
</ClCompile>
- <ClCompile Include="MTC\detection.cpp">
+ <ClCompile Include="Tracker\paths.cpp">
<Filter>Source Files</Filter>
</ClCompile>
- <ClCompile Include="MTC\paths.cpp">
+ <ClCompile Include="Tracker\trackerMex.cpp">
<Filter>Source Files</Filter>
</ClCompile>
- <ClCompile Include="MTC\tracker.cpp">
+ <ClCompile Include="Tracker\Hull.cpp">
+ <Filter>Source Files</Filter>
+ </ClCompile>
+ <ClCompile Include="Tracker\Utility.cpp">
+ <Filter>Source Files</Filter>
+ </ClCompile>
+ <ClCompile Include="Tracker\tracker.cpp">
<Filter>Source Files</Filter>
</ClCompile>
</ItemGroup>
<ItemGroup>
- <ClInclude Include="MTC\cost.h">
+ <None Include="Tracker\trackerMex.def">
+ <Filter>Resource Files</Filter>
+ </None>
+ </ItemGroup>
+ <ItemGroup>
+ <ClInclude Include="Tracker\tracker.h">
+ <Filter>Header Files</Filter>
+ </ClInclude>
+ <ClInclude Include="Tracker\cost.h">
<Filter>Header Files</Filter>
</ClInclude>
- <ClInclude Include="MTC\detection.h">
+ <ClInclude Include="Tracker\paths.h">
<Filter>Header Files</Filter>
</ClInclude>
- <ClInclude Include="MTC\paths.h">
+ <ClInclude Include="Tracker\Hull.h">
<Filter>Header Files</Filter>
</ClInclude>
- <ClInclude Include="MTC\tracker.h">
+ <ClInclude Include="Tracker\Utility.h">
<Filter>Header Files</Filter>
</ClInclude>
</ItemGroup>
diff --git a/src/c/Tracker/Hull.cpp b/src/c/Tracker/Hull.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..f0dd370e3139c9b6168ae51da0a0a859ec647d6b
--- /dev/null
+++ b/src/c/Tracker/Hull.cpp
@@ -0,0 +1,67 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+#include "Hull.h"
+
+#include <set>
+
+std::vector<Hull> gHulls;
+std::vector<std::set<int>> gHashedHulls;
+
+void Hull::clear()
+{
+ frame = UNSET_VAR;
+ centerOfMass.x = UNSET_VAR;
+ centerOfMass.y = UNSET_VAR;
+ centerOfMass.z = UNSET_VAR;
+ track = UNSET_VAR;
+}
+
+
+Hull::Hull()
+{
+ clear();
+}
+
+Hull::Hull(unsigned int frame)
+{
+ clear();
+ this->frame = frame;
+}
+
+Hull::~Hull()
+{
+ clear();
+}
+
+
+void Hull::setCenterOfMass(double* com)
+{
+ centerOfMass.x = com[0];
+ centerOfMass.y = com[1];
+ centerOfMass.z = com[2];
+}
+
+
+void Hull::setFrame(unsigned int frame)
+{
+ this->frame = frame;
+}
\ No newline at end of file
diff --git a/src/c/Tracker/Hull.h b/src/c/Tracker/Hull.h
new file mode 100644
index 0000000000000000000000000000000000000000..fedb5ac3d090c92dde8b0910e49e6292389973bd
--- /dev/null
+++ b/src/c/Tracker/Hull.h
@@ -0,0 +1,69 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+#ifndef HULL_H
+#define HULL_H
+
+#include "Utility.h"
+#include <vector>
+#include <set>
+
+typedef Vec<double> PointType;
+
+class Hull
+{
+public:
+ Hull();
+ Hull(unsigned int frame);
+ ~Hull();
+
+ //getters
+ unsigned int getFrame(){return frame;}
+ Vec<double> getCenterOfMass(){return centerOfMass;}
+ size_t getNumberofVoxels(){return numPixels;}
+ unsigned int getTrack(){return track;}
+
+ void getColor(double* colorOut);
+
+ //setters
+ void setCenterOfMass(double* com);
+ void setFrame(unsigned int frame);
+ void setTrack(double* label){this->track=*label;}
+ void setTrack(int label){this->track=label;}
+ void setNumPixels(size_t numPixels) { this->numPixels = numPixels; }
+
+ void clearTrack(){track=UNSET_VAR;}
+ void logicallyDelete(unsigned int hull);
+
+private:
+ unsigned int frame;
+ Vec<double> centerOfMass;
+ unsigned int track;
+ size_t numPixels;
+
+ void clear();
+ void clearBoundingBox();
+};
+
+extern std::vector<Hull> gHulls;
+extern std::vector<std::set<int>> gHashedHulls;
+
+#endif
\ No newline at end of file
diff --git a/src/c/Tracker/Utility.cpp b/src/c/Tracker/Utility.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..ba91fdab66e9ae7ae57920eb3a6d24fc9b6885db
--- /dev/null
+++ b/src/c/Tracker/Utility.cpp
@@ -0,0 +1,45 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+#include "Utility.h"
+
+Vec<float> gColors[NCOLORS] = {
+ Vec<float>(1,0,0),
+ Vec<float>(1,0.5,0),
+ Vec<float>(1,1,0),
+ Vec<float>(0,1,1),
+ Vec<float>(0,0.5,1),
+ Vec<float>(0.5,0,1),
+ Vec<float>(1,0,0.5),
+ Vec<float>(0,0.75,0.75),
+ Vec<float>(0.75,0,0.75),
+ Vec<float>(0.75,0.75,0),
+ Vec<float>(0.7969,0,0.3984),
+ Vec<float>(0.5977,0.3984,0),
+ Vec<float>(0,0.7969,1),
+ Vec<float>(1,0.5977,0.3984),
+ Vec<float>(0.7969,0.5977,0)
+};
+
+Vec<float> PickColor()
+{
+ return gColors[rand()%NCOLORS];
+}
\ No newline at end of file
diff --git a/src/c/Tracker/Utility.h b/src/c/Tracker/Utility.h
new file mode 100644
index 0000000000000000000000000000000000000000..c6f20d8b052173f346f4bbff602318174628ab59
--- /dev/null
+++ b/src/c/Tracker/Utility.h
@@ -0,0 +1,131 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+#ifndef UTILITY_H
+#define UTILITY_H
+
+#include <string>
+#include <Windows.h>
+
+#define SQR(x) ((x)*(x))
+
+#define ARRAY_SIZE(x) (sizeof(x)/sizeof((x)[0]))
+
+#ifndef SAFE_DELETE
+#define SAFE_DELETE(p) { if (p) { delete (p); (p)=NULL; } }
+#endif
+#ifndef SAFE_DELETE_ARRAY
+#define SAFE_DELETE_ARRAY(p) { if (p) { delete[] (p); (p)=NULL; } }
+#endif
+#ifndef SAFE_RELEASE
+#define SAFE_RELEASE(p) { if (p) { (p)->Release(); (p)=NULL; } }
+#endif
+
+#define MatToC(x) (x-1)
+#define CToMat(x) (x+1)
+
+#define UNSET_VAR (-1)
+#define NCOLORS (15)
+
+#define MAX(x,y) ((x>y)?(x):(y))
+#define MIN(x,y) ((x<y)?(x):(y))
+
+template<typename T>
+struct Vec
+{
+ T x;
+ T y;
+ T z;
+
+ Vec()
+ {
+ x=0;
+ y=0;
+ z=0;
+ }
+
+ Vec(T x, T y, T z)
+ {
+ this->x = x;
+ this->y = y;
+ this->z = z;
+ }
+
+ Vec<T> operator+ (Vec<T> other) const
+ {
+ Vec<T> outVec;
+ outVec.x = x + other.x;
+ outVec.y = y + other.y;
+ outVec.z = z + other.z;
+
+ return outVec;
+ }
+
+ Vec<T> operator- (Vec<T> other) const
+ {
+ Vec<T> outVec;
+ outVec.x = x - other.x;
+ outVec.y = y - other.y;
+ outVec.z = z - other.z;
+
+ return outVec;
+ }
+
+ Vec<T> operator- () const
+ {
+ Vec<T> outVec;
+ outVec.x = -x;
+ outVec.y = -y;
+ outVec.z = -z;
+
+ return outVec;
+ }
+
+ Vec<T>& operator= (const Vec<T> inVec)
+ {
+ x = inVec.x;
+ y = inVec.y;
+ z = inVec.z;
+
+ return *this;
+ }
+
+ size_t product() const
+ {
+ return x*y*z;
+ }
+
+ double EuclideanDistanceTo(Vec<T> other)
+ {
+ return sqrt(SQR((double)x-other.x)+SQR((double)y-other.y)+SQR((double)z-other.z));
+ }
+
+ double SquareDistanceTo(Vec<T> other)
+ {
+ return SQR((double)x-other.x)+SQR((double)y-other.y)+SQR((double)z-other.z);
+ }
+};
+
+extern Vec<float> gColors[NCOLORS];
+
+Vec<float> PickColor();
+
+#endif
\ No newline at end of file
diff --git a/src/c/Tracker/cost.cpp b/src/c/Tracker/cost.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..7f098c982b2a96b6d75be87a02ac2d050839b8d1
--- /dev/null
+++ b/src/c/Tracker/cost.cpp
@@ -0,0 +1,171 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+#include "tracker.h"
+#include "Utility.h"
+#include "Hull.h"
+
+// Convenience defines
+#define DOT(x1,y1,x2,y2) ((x1)*(x2) + (y1)*(y2))
+#define LENGTH(x,y) (sqrt((SQR(x))+(SQR(y))))
+#define SIGN(x) (((x) >= 0.0) ? (1.0) : (-1.0) )
+
+double calcHullDist(int startCellIdx, int nextCellIdx)
+{
+ return gHulls[startCellIdx].getCenterOfMass().EuclideanDistanceTo(gHulls[nextCellIdx].getCenterOfMass());
+}
+
+double calcCCDist(int startCellIdx, int nextCellIdx)
+{
+ if ( gHulls[startCellIdx].getFrame() > gHulls[nextCellIdx].getFrame() )
+ {
+ int tmp = startCellIdx;
+ startCellIdx = nextCellIdx;
+ nextCellIdx = tmp;
+ }
+ return gTrackerData.getDistance(startCellIdx,nextCellIdx,gCCMax);
+
+ //if ( gCCDistMap[startCellIdx].count(nextCellIdx) == 0 )
+ // return gCCMax + 1.0;
+
+ //return gCCDistMap[startCellIdx][nextCellIdx];
+}
+
+double calcFullCellDist(int startCellIdx, int nextCellIdx, double vmax, double ccmax)
+{
+ double hdist = calcHullDist(startCellIdx, nextCellIdx);
+
+ if ( hdist > vmax )
+ return dbltype::infinity();
+
+ double cdist = calcCCDist(startCellIdx, nextCellIdx);
+
+ if ( (cdist > ccmax) && (hdist > (vmax/2.0)) )
+ return dbltype::infinity();
+
+ int startCellSize = gHulls[startCellIdx].getNumberofVoxels();
+ int nextCellSize = gHulls[nextCellIdx].getNumberofVoxels();
+
+ int nmax = MAX(startCellSize, nextCellSize);
+ int nmin = MIN(startCellSize, nextCellSize);
+
+ double sdist = ((double) (nmax - nmin)) / nmax;
+
+ return (10.0*hdist + 100.0*sdist + 1000.0*cdist);
+}
+
+double getCost(std::vector<int>& indices, int sourceIdx, int bCheck)
+{
+ double vmax = gVMax;
+ double ccmax = gCCMax;
+
+ if ( indices.size() - sourceIdx <= 1 )
+ return dbltype::infinity();
+
+ int sourceHull = indices[sourceIdx];
+ int nextHull = indices[sourceIdx+1];
+
+ int dir = 1;
+
+ int startIdx;
+ if ( bCheck )
+ startIdx = indices.size() - 2;
+ else
+ {
+ dir = (gHulls[nextHull].getFrame() - gHulls[sourceHull].getFrame() >= 0) ? 1 : -1;
+
+ int tStart = MAX(gHulls[indices[sourceIdx]].getFrame() - gWindowSize + 1, 0);
+ int tPathStart = gHulls[indices[0]].getFrame();
+ if ( dir < 0 )
+ {
+ tStart = MAX(gHulls[indices[sourceIdx]].getFrame() + gWindowSize - 1, 0);
+ tPathStart = gHulls[indices[0]].getFrame();
+ startIdx = MAX(tPathStart - tStart, 0);
+ }
+ else
+ startIdx = MAX(tStart - tPathStart, 0);
+ }
+
+ for ( int k=startIdx; k < indices.size()-1; ++k )
+ {
+ double dlcd = calcHullDist(indices[k], indices[k+1]);
+
+ if ( dlcd > vmax )
+ return dbltype::infinity();
+ }
+
+ // Just return non-infinite for a successful check.
+ if ( bCheck )
+ return 1.0;
+
+ double localCost = 3*calcFullCellDist(indices[sourceIdx], indices[sourceIdx+1], vmax, ccmax);
+
+ if ( localCost == dbltype::infinity() )
+ return dbltype::infinity();
+
+ // Calculate local surrounding connected-component distance if possible
+ if ( sourceIdx > 0 )
+ localCost += calcFullCellDist(indices[sourceIdx-1], indices[sourceIdx+1], 2*vmax, 2*ccmax);
+ else
+ localCost *= 2.0;
+
+ if ( localCost == dbltype::infinity() )
+ return dbltype::infinity();
+
+ // Calculate forward cc cost if path is long enough
+ if ( sourceIdx < indices.size()-2 )
+ localCost += calcFullCellDist(indices[sourceIdx], indices[sourceIdx+2], 2*vmax, 2*ccmax);
+ else
+ localCost *= 2.0;
+
+ if ( localCost == dbltype::infinity() )
+ return dbltype::infinity();
+
+ double dCenterLoc[3] = {0.0, 0.0, 0.0};
+
+ // Calculate historical center of mass of cell
+ for ( int k=startIdx; k <= sourceIdx; ++k )
+ {
+ dCenterLoc[0] += gHulls[indices[k]].getCenterOfMass().x;
+ dCenterLoc[1] += gHulls[indices[k]].getCenterOfMass().y;
+ dCenterLoc[2] += gHulls[indices[k]].getCenterOfMass().z;
+ }
+ dCenterLoc[0] /= (sourceIdx - startIdx + 1);
+ dCenterLoc[1] /= (sourceIdx - startIdx + 1);
+ dCenterLoc[2] /= (sourceIdx - startIdx + 1);
+
+ // Calculate mean squared deviation of path from historical center
+ double locationCost = 0.0;
+ for ( int k=sourceIdx; k < indices.size(); ++k )
+ {
+ locationCost += SQR(gHulls[indices[k]].getCenterOfMass().x - dCenterLoc[0]) + SQR(gHulls[indices[k]].getCenterOfMass().y - dCenterLoc[1]) + SQR(gHulls[indices[k]].getCenterOfMass().z - dCenterLoc[2]);
+ }
+ locationCost = sqrt(locationCost/(indices.size() - sourceIdx));
+
+ double totalCost = localCost + locationCost;
+ if ( indices.size() < 2*gWindowSize+1 )
+ {
+ double lengthPenalty = (2*gWindowSize+1) - indices.size();
+ totalCost *= (2*lengthPenalty);
+ }
+
+ return totalCost;
+}
\ No newline at end of file
diff --git a/src/c/Tracker/cost.h b/src/c/Tracker/cost.h
new file mode 100644
index 0000000000000000000000000000000000000000..7c5464594f7ae4351f6c1ff29214d5eb0fd1641f
--- /dev/null
+++ b/src/c/Tracker/cost.h
@@ -0,0 +1,32 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+#ifndef COSTS_H
+#define COSTS_H
+
+#include <vector>
+
+// Get cost based on a frame and index list. The srcFrameIdx is used if there, it is the index into
+// frame/index vectors of the source point(start of new path). srcFrameIdx is trivially 0 if there is
+// no history being used.
+double getCost(std::vector<int>& indices, int sourceIdx, int bCheck = 1);
+
+#endif
\ No newline at end of file
diff --git a/src/c/Tracker/paths.cpp b/src/c/Tracker/paths.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..faf1ea8ee6ad29035ed0be994e91425bc8a2022b
--- /dev/null
+++ b/src/c/Tracker/paths.cpp
@@ -0,0 +1,162 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+#include "tracker.h"
+#include "Hull.h"
+
+#include <set>
+
+int buildHistoryPath(CSourcePath* historyPath, CSourcePath* path)
+{
+ int pathStartGIdx = path->indices[0];
+
+ // Find the assigned in-edge
+ int histTrackID = -1;
+ int histIdx = gAssignedConnectIn[pathStartGIdx];
+ if ( histIdx >=0 )
+ {
+ CSourcePath* histpath = gTrackerData.connectIn[pathStartGIdx][histIdx];
+ histTrackID = histpath->trackletID;
+ }
+
+ if ( histTrackID >= 0 )
+ {
+ tPathList::iterator histIter = gAssignedTracklets[histTrackID].begin();
+ while ( (histIter != gAssignedTracklets[histTrackID].end()) )
+ {
+ CSourcePath* curPath = *histIter;
+
+ int startGIdx = curPath->indices[0];
+ int endGIdx = gAssignedConnectOut[startGIdx];
+
+ unsigned int endT = gHulls[endGIdx].getFrame();
+
+ for (unsigned int i=0; gHulls[curPath->indices[i]].getFrame() < endT; ++i )
+ {
+ historyPath->pushPoint(curPath->indices[i]);
+ }
+
+ ++histIter;
+ }
+ }
+
+ for (unsigned int i=0; i < path->length(); ++i )
+ historyPath->pushPoint(path->indices[i]);
+
+ return histTrackID;
+}
+
+int addBestPath(CSourcePath &path, int bestGIdx)
+{
+ if ( path.length() > 1 )
+ {
+ CSourcePath historyPath;
+
+ int startGIdx = path.indices[0];
+ int nextGIdx = path.indices[1];
+
+ int historyTrackID = buildHistoryPath(&historyPath, &path);
+ int srcPathIdx = historyPath.length() - path.length();
+
+ double newPathCost = getCost(historyPath.indices, srcPathIdx, 0);
+ if ( newPathCost == dbltype::infinity() )
+ return bestGIdx;
+
+ path.trackletID = historyTrackID;
+ path.cost = newPathCost;
+
+ if ( gTrackerData.connectOut[startGIdx].count(nextGIdx) == 0 )
+ {
+ CSourcePath* newPath = new CSourcePath(path);
+ gTrackerData.connectOut[startGIdx].insert(std::pair<int,CSourcePath*>(nextGIdx, newPath));
+ gTrackerData.connectIn[nextGIdx].insert(std::pair<int,CSourcePath*>(startGIdx, newPath));
+ }
+ else if ( newPathCost < gTrackerData.connectOut[startGIdx][nextGIdx]->cost )
+ {
+ *(gTrackerData.connectOut[startGIdx][nextGIdx]) = path;
+ }
+
+ if ( (bestGIdx < 0) || (newPathCost < gTrackerData.connectOut[startGIdx][bestGIdx]->cost) )
+ {
+ bestGIdx = nextGIdx;
+ }
+ }
+
+ return bestGIdx;
+}
+
+int bestDepthFirstPathSearch(CSourcePath partialPath, int bestGIdx, int t, int tEnd, int occlLookback)
+{
+ bool bFinishedSearch = true;
+ if ( t < tEnd )
+ {
+ std::set<int>::iterator hullIter = gHashedHulls[t-occlLookback].begin();
+ for ( ; hullIter != gHashedHulls[t-occlLookback].end(); ++hullIter )
+ {
+ int nextIdx = (*hullIter);
+
+ partialPath.pushPoint(nextIdx);
+ double chkCost = getCost(partialPath.indices, 0);
+ partialPath.popPoint();
+
+ if ( chkCost == dbltype::infinity() )
+ continue;
+
+ bFinishedSearch = false;
+
+ partialPath.pushPoint(nextIdx);
+
+ bestGIdx = bestDepthFirstPathSearch(partialPath, bestGIdx, t+1, tEnd, occlLookback);
+ partialPath.popPoint();
+ }
+ }
+
+ if ( bFinishedSearch )
+ {
+ bestGIdx = addBestPath(partialPath, bestGIdx);
+ }
+
+ return bestGIdx;
+}
+
+void BuildBestPaths(std::map<int,int>& bestOutEdges, int t, int occlLookback)
+{
+ if ( t-occlLookback < 0 )
+ return;
+
+ int tEnd = min((unsigned int)t+gWindowSize, (unsigned int)gHashedHulls.size());
+
+ std::set<int>::iterator hullIter = gHashedHulls[t-occlLookback].begin();
+ for ( ; hullIter != gHashedHulls[t-occlLookback].end(); ++hullIter )
+ {
+ int startGIdx = (*hullIter);
+ if ( occlLookback > 0 && gAssignedConnectOut[startGIdx] >= 0 )
+ continue;
+
+ CSourcePath srcPath;
+ srcPath.pushPoint(startGIdx);
+
+ int bestGIdx = bestDepthFirstPathSearch(srcPath, -1, t+1, tEnd, occlLookback);
+
+ if ( bestGIdx >= 0 )
+ bestOutEdges[startGIdx] = bestGIdx;
+ }
+}
\ No newline at end of file
diff --git a/src/c/Tracker/paths.h b/src/c/Tracker/paths.h
new file mode 100644
index 0000000000000000000000000000000000000000..c8a2e477b93b96476e30c192d6beb3810beeada9
--- /dev/null
+++ b/src/c/Tracker/paths.h
@@ -0,0 +1,78 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+#ifndef PATHS_H
+#define PATHS_H
+
+#include "Utility.h"
+
+#include <climits>
+#include <vector>
+#include <map>
+
+typedef std::numeric_limits<double> dbltype;
+
+class CSourcePath
+{
+public:
+ CSourcePath()
+ {
+ trackletID = UNSET_VAR;
+ cost = dbltype::infinity();
+ }
+
+ unsigned int length()
+ {
+ return (unsigned int)indices.size();
+ }
+
+ void pushPoint(int newIdx)
+ {
+ indices.push_back(newIdx);
+ }
+
+ void popPoint()
+ {
+ if ( indices.size() <= 1 )
+ return;
+
+ indices.pop_back();
+ }
+
+ void clear()
+ {
+ trackletID = UNSET_VAR;
+ cost = dbltype::infinity();
+
+ indices.clear();
+ }
+
+public:
+
+ int trackletID;
+ double cost;
+
+ std::vector<int> indices;
+};
+
+void BuildBestPaths(std::map<int,int>& bestOutEdges, int t, int occlLookcback = 0);
+
+#endif
\ No newline at end of file
diff --git a/src/c/Tracker/tracker.cpp b/src/c/Tracker/tracker.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..9b1f0b8af1423acadb8166c9597a523f9ab18d74
--- /dev/null
+++ b/src/c/Tracker/tracker.cpp
@@ -0,0 +1,383 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+#include "tracker.h"
+#include "Hull.h"
+
+TrackerData gTrackerData;
+
+int* gAssignedConnectOut;
+int* gAssignedConnectIn;
+
+std::vector<tPathList> gAssignedTracklets;
+
+double gVMax = 20.0;//TODO try these values
+double gCCMax = 10.0;
+
+int gWindowSize = 4;
+
+TrackerData::TrackerData()
+{
+ connectIn = NULL;
+ connectOut = NULL;
+ ccDistMap = NULL;
+}
+
+TrackerData::~TrackerData()
+{
+ clear();
+}
+
+void TrackerData::clear()
+{
+ if ( connectOut )
+ {
+ delete[] connectOut;
+ connectOut = NULL;
+ }
+
+ if ( connectIn )
+ {
+ delete[] connectIn;
+ connectIn = NULL;
+ }
+
+ if (ccDistMap)
+ {
+ delete[] ccDistMap;
+ ccDistMap = NULL;
+ }
+}
+
+int FindMinInEdgeIdx(int nextGIdx)
+{
+ double cmin = dbltype::infinity();
+ int bestIdx = -1;
+
+ std::map<int,CSourcePath*>::iterator cIter = gTrackerData.connectIn[nextGIdx].begin();
+ while ( cIter != gTrackerData.connectIn[nextGIdx].end() )
+ {
+ CSourcePath* inPath = cIter->second;
+ if ( inPath->cost < cmin )
+ {
+ cmin = inPath->cost;
+ bestIdx = cIter->first;
+ }
+
+ ++cIter;
+ }
+
+ return bestIdx;
+}
+
+void resetIdxTrackletIds(int nodeIdx, int newTrackletID)
+{
+ std::map<int,CSourcePath*>::iterator pathIter = gTrackerData.connectOut[nodeIdx].begin();
+ while ( pathIter != gTrackerData.connectOut[nodeIdx].end() )
+ {
+ pathIter->second->trackletID = newTrackletID;
+
+ ++pathIter;
+ }
+}
+
+void resetForwardTrackletIds(int startingGIdx, int newTrackletID)
+{
+ int oldTrackletID = -1;
+ int nxtGIdx = gAssignedConnectOut[startingGIdx];
+ if ( nxtGIdx >= 0 )
+ oldTrackletID = gTrackerData.connectOut[startingGIdx][nxtGIdx]->trackletID;
+
+ resetIdxTrackletIds(startingGIdx, newTrackletID);
+ while ( nxtGIdx >= 0 )
+ {
+ CSourcePath* curPath = gTrackerData.connectOut[startingGIdx][nxtGIdx];
+ gAssignedTracklets[newTrackletID].push_back(curPath);
+
+ resetIdxTrackletIds(nxtGIdx, newTrackletID);
+
+ startingGIdx = nxtGIdx;
+ nxtGIdx = gAssignedConnectOut[startingGIdx];
+ }
+
+ if ( oldTrackletID >= 0 )
+ gAssignedTracklets[oldTrackletID].clear();
+}
+
+void patchUpResults()
+{
+ std::multimap<double,std::pair<int,int>> patchupList;
+ // Make sorted list of possible patch assignments (maps automatically sort internally)
+ for ( int i=0; i < gHulls.size(); ++i )
+ {
+ if ( gAssignedConnectIn[i] >= 0 )
+ continue;
+
+ std::map<int,CSourcePath*>::iterator inIter = gTrackerData.connectIn[i].begin();
+ while ( inIter != gTrackerData.connectIn[i].end() )
+ {
+ int inGIdx = inIter->first;
+ if ( gAssignedConnectOut[inGIdx] < 0 )
+ {
+ patchupList.insert(std::pair<double,std::pair<int,int>>(inIter->second->cost, std::pair<int,int>(inGIdx,i)));
+ }
+
+ ++inIter;
+ }
+ }
+
+ int totalPatches = 0;
+ std::multimap<double,std::pair<int,int>>::iterator srtIter = patchupList.begin();
+ while ( srtIter != patchupList.end() )
+ {
+ int startGIdx = srtIter->second.first;
+ int destGIdx = srtIter->second.second;
+
+ CSourcePath* curPath = gTrackerData.connectOut[startGIdx][destGIdx];
+ if ( gAssignedConnectOut[startGIdx] < 0 && gAssignedConnectIn[destGIdx] < 0 )
+ {
+ // Get Tracklet ID first from incoming assignment
+ int newTrackletID = curPath->trackletID;
+ if ( newTrackletID < 0 )
+ {
+ // Or from incoming assignment made during patching
+ int prevIdx = gAssignedConnectIn[startGIdx];
+ if ( prevIdx >= 0 )
+ {
+ newTrackletID = gTrackerData.connectOut[prevIdx][startGIdx]->trackletID;
+ curPath->trackletID = newTrackletID;
+ }
+ }
+ //if ( newTrackletID < 0 )
+ //{
+ // // Or from outgoing assignment if the other two don't exist
+ // int nxtGIdx = gAssignedConnectOut[destGIdx];
+ // if ( nxtGIdx >= 0 )
+ // {
+ // newTrackletID = gTrackerData.connectOut[destGIdx][nxtGIdx]->trackletID;
+ // curPath->trackletID = newTrackletID;
+ // }
+ //}
+ if ( newTrackletID < 0 )
+ {
+ //Otherwise add new tracklet to list etc. and set id
+ newTrackletID = gAssignedTracklets.size();
+ curPath->trackletID = newTrackletID;
+
+ tPathList newList;
+ gAssignedTracklets.push_back(newList);
+ }
+
+ int mergeTrackletId = -1;
+ int nxtGIdx = gAssignedConnectOut[destGIdx];
+ if ( nxtGIdx >= 0 )
+ {
+ mergeTrackletId = gTrackerData.connectOut[destGIdx][nxtGIdx]->trackletID;
+ }
+
+ //Add path to tracklet list
+ gAssignedTracklets[newTrackletID].push_back(curPath);
+
+ if ( mergeTrackletId >= 0 )
+ resetForwardTrackletIds(destGIdx, newTrackletID);
+
+ //Keep track of assignment for fast lookup
+ gAssignedConnectIn[destGIdx] = startGIdx;
+ gAssignedConnectOut[startGIdx] = destGIdx;
+
+ ++totalPatches;
+ }
+
+ ++srtIter;
+ }
+}
+
+void destroyTrackStructures()
+{
+ if ( gTrackerData.connectOut )
+ {
+ delete[] gTrackerData.connectOut;
+ gTrackerData.connectOut = NULL;
+ }
+
+ if ( gTrackerData.connectIn )
+ {
+ delete[] gTrackerData.connectIn;
+ gTrackerData.connectIn = NULL;
+ }
+
+ if ( gAssignedConnectOut )
+ {
+ delete[] gAssignedConnectOut;
+ gAssignedConnectOut = NULL;
+ }
+
+ if ( gAssignedConnectIn )
+ {
+ delete[] gAssignedConnectIn;
+ gAssignedConnectIn = NULL;
+ }
+
+ gAssignedTracklets.clear();
+}
+
+void initTrackStrucutres()
+{
+ destroyTrackStructures();
+
+ gTrackerData.connectOut = new std::map<int,CSourcePath*>[gHulls.size()];
+ gTrackerData.connectIn = new std::map<int,CSourcePath*>[gHulls.size()];
+
+ gAssignedConnectOut = new int[gHulls.size()];
+ gAssignedConnectIn = new int[gHulls.size()];
+
+ for ( int i=0; i < gHulls.size(); ++i )
+ {
+ gAssignedConnectOut[i] = -1;
+ gAssignedConnectIn[i] = -1;
+ }
+}
+
+//void setHullInfo(int hullID, int trackID)
+//{
+// //gHulls[hullID].label = trackID;
+// for ( int i=0; i < gHulls[hullID].getNumberOfVertices(); ++i )
+// {
+// gHulls[hullID].getMesh()->m_vertices[i].texUV = gTracks[trackID]->getColor();
+// }
+//}
+
+void trackHulls(unsigned int numFrames)
+{
+ initTrackStrucutres();
+
+ std::map<int,int> bestOutEdges;
+
+ for (unsigned int frame=0; frame<numFrames; ++frame)
+ {
+
+ if (gHashedHulls.size()>frame+1)
+ //for ( int frame=0; frame < gHashedHulls.size()-1; ++frame )
+ {
+
+#ifdef _DEBUG
+ char buffer[255];
+ sprintf_s(buffer,"Tracking frame: %d",frame);
+ printf(buffer);
+#endif // _DEBUG
+
+
+ bestOutEdges.clear();
+ BuildBestPaths(bestOutEdges, frame);
+
+ //Occlusions
+ for ( int iLookback=1; iLookback <= 1; ++iLookback )
+ {
+ //TODO Fix comparison occlusion handling
+ BuildBestPaths(bestOutEdges, frame, iLookback);
+ }
+
+ std::set<int>::iterator nextIdxIter = gHashedHulls[frame+1].begin();
+ for ( ; nextIdxIter != gHashedHulls[frame+1].end(); ++nextIdxIter)
+ {
+ int nextGIdx = *nextIdxIter;
+ int bestTrackletIdx = FindMinInEdgeIdx(nextGIdx);
+ if ( bestTrackletIdx < 0 )
+ continue;
+
+ if ( (bestOutEdges.count(bestTrackletIdx) == 0) || bestOutEdges[bestTrackletIdx] != nextGIdx )
+ continue;
+
+ int newTrackletID = gTrackerData.connectOut[bestTrackletIdx][nextGIdx]->trackletID;
+
+ if ( newTrackletID < 0 )
+ {
+ //Add new tracklet to list etc. and set id
+ newTrackletID = gAssignedTracklets.size();
+ gTrackerData.connectOut[bestTrackletIdx][nextGIdx]->trackletID = newTrackletID;
+
+ tPathList newList;
+ gAssignedTracklets.push_back(newList);
+ }
+
+ //Add path to tracklet list
+ gAssignedTracklets[newTrackletID].push_back(gTrackerData.connectOut[bestTrackletIdx][nextGIdx]);
+
+ //Keep track of assignment for fast lookup
+ gAssignedConnectIn[nextGIdx] = bestTrackletIdx;
+ gAssignedConnectOut[bestTrackletIdx] = nextGIdx;
+ }
+ }
+ }
+
+ patchUpResults();
+
+ int trackIdx = 0;
+ for(int i = 0; i<gAssignedTracklets.size(); ++i)
+ {
+ if(gAssignedTracklets[i].empty())
+ continue;
+
+ tPathList::iterator pathIter = gAssignedTracklets[i].begin();
+ int startIdx = (*pathIter)->indices[0];
+
+ gHulls[startIdx].setTrack(trackIdx);
+
+ for(; pathIter!=gAssignedTracklets[i].end(); ++pathIter)
+ {
+ int nextIdx = (*pathIter)->indices[1];
+ gHulls[nextIdx].setTrack(trackIdx);
+ }
+
+ ++trackIdx;
+ }
+
+ for (unsigned int i=0; i<gHulls.size(); ++i)
+ {
+ if (UNSET_VAR==gHulls[i].getTrack())
+ {
+ gHulls[i].setTrack(trackIdx);
+ ++trackIdx;
+ }
+ }
+}
+
+void TrackerData::setCCdistMap(std::map<int,double>* cCDistMap)
+{
+ if (NULL!=cCDistMap)
+ {
+ if (NULL!=this->ccDistMap)
+ {
+ delete[] this->ccDistMap;
+ ccDistMap = NULL;
+ }
+
+ this->ccDistMap = cCDistMap;
+ }
+}
+
+double TrackerData::getDistance(int hull1, int hull2, double ccMax)
+{
+ if ( gTrackerData.ccDistMap[hull1].count(hull2) == 0 )
+ return ccMax + 1.0;
+
+ return ccDistMap[hull1][hull2];
+}
diff --git a/src/c/Tracker/tracker.h b/src/c/Tracker/tracker.h
new file mode 100644
index 0000000000000000000000000000000000000000..b43cd5bc62d2bb7a639f7015b57a5f3685366a97
--- /dev/null
+++ b/src/c/Tracker/tracker.h
@@ -0,0 +1,69 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+#ifndef _TRACKER_H_
+#define _TRACKER_H_
+
+#include <list>
+#include <vector>
+
+#include "cost.h"
+#include "paths.h"
+
+//For quick edge lookup from point (like inID/outID)
+extern int* gAssignedConnectOut;
+extern int* gAssignedConnectIn;
+
+//Global variables
+extern int gWindowSize;
+
+extern double gVMax;
+extern double gCCMax;
+
+typedef std::list<CSourcePath*> tPathList;
+extern std::vector<tPathList> gAssignedTracklets;
+
+//main tracker function:
+void trackHulls(unsigned int numFrames);
+
+void destroyTrackStructures();
+
+class TrackerData
+{
+public:
+ TrackerData();
+ ~TrackerData();
+
+ //savers
+ void clear();
+
+ double getDistance(int hull1, int hull2, double ccMax);
+ void setCCdistMap(std::map<int,double>* cCDistMap);
+
+ //member variables
+ std::map<int,CSourcePath*>* connectOut;
+ std::map<int,CSourcePath*>* connectIn;
+ std::map<int,double>* ccDistMap;
+};
+
+extern TrackerData gTrackerData;
+
+#endif //_TRACKER_H_
\ No newline at end of file
diff --git a/src/c/Tracker/trackerMex.cpp b/src/c/Tracker/trackerMex.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..297eca6367519187b047e2f426098ca9c70a6a85
--- /dev/null
+++ b/src/c/Tracker/trackerMex.cpp
@@ -0,0 +1,137 @@
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+#include "mex.h"
+
+#include "tracker.h"
+#include "Hull.h"
+
+void loadHulls( const mxArray * hulls, int numFrames )
+{
+ int numHulls = mxGetNumberOfElements(hulls);
+
+ gHulls.clear();
+ gHulls.resize(numHulls);
+ gHashedHulls.clear();
+ gHashedHulls.resize(numFrames);
+
+ for(int hullIdx=0; hullIdx<numHulls; ++hullIdx)
+ {
+ Hull& hull = gHulls[hullIdx];
+ mxArray* framePtr = mxGetField(hulls,hullIdx,"time");
+ if (framePtr==NULL) mexErrMsgTxt("Missing Time!\n");
+ hull.setFrame(MatToC((unsigned int)mxGetScalar(framePtr)));
+
+ mxArray* comPtr = mxGetField(hulls,hullIdx,"centerOfMass");
+ if (comPtr==NULL) mexErrMsgTxt("Missing Center of Mass!\n");
+ hull.setCenterOfMass((double*)mxGetData(comPtr));
+
+ mxArray* pixelPtr = mxGetField(hulls,hullIdx,"indexPixels");
+ if (pixelPtr==NULL) mexErrMsgTxt("Missing pixels!\n");
+
+ size_t numPixels = mxGetM(pixelPtr);
+ hull.setNumPixels(numPixels);
+
+ gHashedHulls[hull.getFrame()].insert(hullIdx);
+ }
+}
+
+void returnHulls(mxArray* plhs[])
+{
+
+ plhs[0] = mxCreateNumericMatrix(1, gHulls.size(), mxDOUBLE_CLASS, mxREAL);
+ double* trackList = (double*)mxGetData(plhs[0]);
+ int numEdges = 0;
+
+ for(int i=0; i<gHulls.size(); ++i)
+ {
+ trackList[i] = gHulls[i].getTrack();
+ numEdges += gTrackerData.connectOut[i].size();
+ }
+
+ mxArray* sparseArray = mxCreateSparse(gHulls.size(), gHulls.size(),numEdges,mxREAL);
+ mwIndex* mxjc = mxGetJc(sparseArray);
+ mwIndex* mxir = mxGetIr(sparseArray);
+ double* mxpr = mxGetPr(sparseArray);
+
+ mxjc[0] = 0;
+
+ std::map<int,CSourcePath*>* inEdges;
+ for (int i=0; i<gHulls.size(); ++i)
+ {
+ inEdges = &gTrackerData.connectIn[i];
+ mxjc[i+1] = mxjc[i]+inEdges->size();
+ std::map<int,CSourcePath*>::iterator it = inEdges->begin();
+ for (int j=0; j<inEdges->size(); ++j, ++it)
+ {
+ mxir[mxjc[i]+j] = it->first;
+ mxpr[mxjc[i]+j] = it->second->cost;
+ }
+ }
+
+ plhs[1] = sparseArray;
+}
+
+void loadDists(const mxArray* ccDists)
+{
+ std::map<int, double>* ccDistMap = new std::map<int, double>[gHulls.size()];
+
+ size_t numHulls = mxGetN(ccDists);
+ for (int i = 0; i < numHulls ; ++i)
+ {
+ mxArray* nextHulls = mxGetCell(ccDists, i);
+ size_t m = mxGetM(nextHulls);
+
+ double* distPairs = (double*)mxGetData(nextHulls);
+
+ for (int j = 0; j < m ; j++)
+ {
+ int nextHull = (int)(distPairs[j*2]);
+ double dist = distPairs[j*2+1];
+
+ ccDistMap[i].insert(std::pair<int, double>(nextHull,dist));
+ }
+ }
+
+ gTrackerData.ccDistMap = ccDistMap;
+}
+
+void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
+{
+ if (nrhs!=5) mexErrMsgTxt("Usage: hulls, CCdists, numFrames, velocity, ccMaxDist\n");
+ if (nlhs!=2) mexErrMsgTxt("Incorrect number of output arguments!\n");
+
+ int numFrames = mxGetScalar(prhs[2]);
+ const mxArray* hulls = prhs[0];
+ if (hulls==NULL) mexErrMsgTxt("No hulls passed as the second argument!\n");
+
+ gVMax = mxGetScalar(prhs[3]);
+ gCCMax = mxGetScalar(prhs[4]);
+
+ const mxArray* ccDists = prhs[1];
+
+ loadHulls(hulls,numFrames);
+ loadDists(ccDists);
+ trackHulls(numFrames);
+ returnHulls(plhs);
+
+ destroyTrackStructures();
+}
\ No newline at end of file
diff --git a/src/c/Tracker/trackerMex.def b/src/c/Tracker/trackerMex.def
new file mode 100644
index 0000000000000000000000000000000000000000..f3dde54921ba04a9f1f6ee0009507831b322b74c
--- /dev/null
+++ b/src/c/Tracker/trackerMex.def
@@ -0,0 +1,3 @@
+LIBRARY "trackerMex"
+EXPORTS DllMain
+EXPORTS mexFunction
\ No newline at end of file
diff --git a/src/c/mexDijkstra.sln b/src/c/mexDijkstra.sln
index 931ac812797f5b3be3b7206625648db89ad1e958..f2b8e9668e75e90dcfa000f07c39db522b7d29d3 100644
--- a/src/c/mexDijkstra.sln
+++ b/src/c/mexDijkstra.sln
@@ -1,22 +1,18 @@

-Microsoft Visual Studio Solution File, Format Version 11.00
-# Visual Studio 2010
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio 14
+VisualStudioVersion = 14.0.24720.0
+MinimumVisualStudioVersion = 10.0.40219.1
Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "mexDijkstra", "mexDijkstra.vcxproj", "{4E22BB6D-1C4B-441D-9436-81224FA01AC3}"
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
- Debug|Win32 = Debug|Win32
Debug|x64 = Debug|x64
- Release|Win32 = Release|Win32
Release|x64 = Release|x64
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|Win32.ActiveCfg = Debug|Win32
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|Win32.Build.0 = Debug|Win32
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|x64.ActiveCfg = Debug|x64
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|x64.Build.0 = Debug|x64
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|Win32.ActiveCfg = Release|Win32
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|Win32.Build.0 = Release|Win32
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|x64.ActiveCfg = Release|x64
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|x64.Build.0 = Release|x64
EndGlobalSection
diff --git a/src/c/mexDijkstra.vcxproj b/src/c/mexDijkstra.vcxproj
index 12ac3faa0c8b34219b9ae4838f4c819380dcc9f7..4aa0fd1c4e0961b4a83ea6f35ad09c4c874b3b65 100644
--- a/src/c/mexDijkstra.vcxproj
+++ b/src/c/mexDijkstra.vcxproj
@@ -1,18 +1,10 @@
<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+<Project DefaultTargets="Build" ToolsVersion="14.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup Label="ProjectConfigurations">
- <ProjectConfiguration Include="Debug|Win32">
- <Configuration>Debug</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
<ProjectConfiguration Include="Debug|x64">
<Configuration>Debug</Configuration>
<Platform>x64</Platform>
</ProjectConfiguration>
- <ProjectConfiguration Include="Release|Win32">
- <Configuration>Release</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
<ProjectConfiguration Include="Release|x64">
<Configuration>Release</Configuration>
<Platform>x64</Platform>
@@ -35,33 +27,20 @@
<Keyword>Win32Proj</Keyword>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
- <ConfigurationType>DynamicLibrary</ConfigurationType>
- <CharacterSet>Unicode</CharacterSet>
- <WholeProgramOptimization>true</WholeProgramOptimization>
- </PropertyGroup>
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
- <ConfigurationType>DynamicLibrary</ConfigurationType>
- <CharacterSet>Unicode</CharacterSet>
- </PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
<ConfigurationType>DynamicLibrary</ConfigurationType>
<CharacterSet>Unicode</CharacterSet>
<WholeProgramOptimization>true</WholeProgramOptimization>
+ <PlatformToolset>v140</PlatformToolset>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
<ConfigurationType>DynamicLibrary</ConfigurationType>
<CharacterSet>Unicode</CharacterSet>
+ <PlatformToolset>v140</PlatformToolset>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
<ImportGroup Label="ExtensionSettings">
</ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
<ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="PropertySheets">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
@@ -71,56 +50,16 @@
<PropertyGroup Label="UserMacros" />
<PropertyGroup>
<_ProjectFileVersion>10.0.40219.1</_ProjectFileVersion>
- <OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
- <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
- <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</LinkIncremental>
- <PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">false</PostBuildEventUseInBuild>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
<LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</LinkIncremental>
<PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">false</PostBuildEventUseInBuild>
- <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
- <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
- <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</LinkIncremental>
- <PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</PostBuildEventUseInBuild>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
<LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</LinkIncremental>
<PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</PostBuildEventUseInBuild>
- <TargetExt Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">.mexw32</TargetExt>
<TargetExt Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">.mexw64</TargetExt>
</PropertyGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
- <ClCompile>
- <Optimization>Disabled</Optimization>
- <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>WIN32;_DEBUG;_WINDOWS;_USRDLL;MEXMAT_EXPORTS;MATLAB_MEX_FILE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <PreprocessToFile>false</PreprocessToFile>
- <PreprocessSuppressLineNumbers>false</PreprocessSuppressLineNumbers>
- <MinimalRebuild>true</MinimalRebuild>
- <BasicRuntimeChecks>EnableFastChecks</BasicRuntimeChecks>
- <RuntimeLibrary>MultiThreadedDebug</RuntimeLibrary>
- <PrecompiledHeader>
- </PrecompiledHeader>
- <WarningLevel>Level3</WarningLevel>
- <DebugInformationFormat>EditAndContinue</DebugInformationFormat>
- </ClCompile>
- <Link>
- <AdditionalDependencies>libmx.lib;libmex.lib;libmat.lib;%(AdditionalDependencies)</AdditionalDependencies>
- <OutputFile>$(OutDir)..\..\..\MATLAB\$(ProjectName).mexw32</OutputFile>
- <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
- <ModuleDefinitionFile>mexDijkstra/mexDijkstra.def</ModuleDefinitionFile>
- <GenerateDebugInformation>true</GenerateDebugInformation>
- <SubSystem>Windows</SubSystem>
- <TargetMachine>MachineX86</TargetMachine>
- </Link>
- <PostBuildEvent>
- <Message>Copy pdb and mex files to bin and MATLAB directories</Message>
- <Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw32"
-copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
-</Command>
- </PostBuildEvent>
- </ItemDefinitionGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<Midl>
<TargetEnvironment>X64</TargetEnvironment>
@@ -152,37 +91,6 @@ copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
<Message>Copy pdb and mex files to bin and MATLAB directories</Message>
<Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw64"
copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
-</Command>
- </PostBuildEvent>
- </ItemDefinitionGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
- <ClCompile>
- <Optimization>MaxSpeed</Optimization>
- <IntrinsicFunctions>true</IntrinsicFunctions>
- <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>WIN32;NDEBUG;_WINDOWS;_USRDLL;MEXMAT_EXPORTS;MATLAB_MEX_FILE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <RuntimeLibrary>MultiThreaded</RuntimeLibrary>
- <FunctionLevelLinking>true</FunctionLevelLinking>
- <PrecompiledHeader>
- </PrecompiledHeader>
- <WarningLevel>Level3</WarningLevel>
- <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
- </ClCompile>
- <Link>
- <AdditionalDependencies>libmx.lib;libmex.lib;libmat.lib;%(AdditionalDependencies)</AdditionalDependencies>
- <OutputFile>$(OutDir)$(ProjectName).dll</OutputFile>
- <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
- <ModuleDefinitionFile>mexDijkstra/mexDijkstra.def</ModuleDefinitionFile>
- <GenerateDebugInformation>true</GenerateDebugInformation>
- <SubSystem>Windows</SubSystem>
- <OptimizeReferences>true</OptimizeReferences>
- <EnableCOMDATFolding>true</EnableCOMDATFolding>
- <TargetMachine>MachineX86</TargetMachine>
- </Link>
- <PostBuildEvent>
- <Message>Copy pdb and mex files to bin and MATLAB directories</Message>
- <Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw32"
-"copy $(OutDir)$(ProjectName).pdb" ..\MATLAB
</Command>
</PostBuildEvent>
</ItemDefinitionGroup>
@@ -223,4 +131,4 @@ copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
<ImportGroup Label="ExtensionTargets">
</ImportGroup>
-</Project>
+</Project>
\ No newline at end of file
diff --git a/src/c/mexDijkstra/CSparseWrapper.cpp b/src/c/mexDijkstra/CSparseWrapper.cpp
index a270057e4622f4601865ef20e106e26a3f2effee..789ebb8f71f858baa499f711eae8983966301228 100644
--- a/src/c/mexDijkstra/CSparseWrapper.cpp
+++ b/src/c/mexDijkstra/CSparseWrapper.cpp
@@ -1,6 +1,30 @@
+
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mexDijkstra.h"
#include "CSparseWrapper.h"
+#include <algorithm>
+
const double CSparseWrapper::noEdge = std::numeric_limits<double>::infinity();
CSparseWrapper::CSparseWrapper(const mxArray* sparseArray)
diff --git a/src/c/mexDijkstra/CSparseWrapper.h b/src/c/mexDijkstra/CSparseWrapper.h
index ca34b85d15bce366060c4a6a036eaa3e8296a076..00761375fedb70b589849daa3917a91a92808fdb 100644
--- a/src/c/mexDijkstra/CSparseWrapper.h
+++ b/src/c/mexDijkstra/CSparseWrapper.h
@@ -1,3 +1,27 @@
+
+
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+
#ifndef CSPARSEWRAPPER_H
#define CSPARSEWRAPPER_H 1
diff --git a/src/c/mexDijkstra/mexDijkstra.cpp b/src/c/mexDijkstra/mexDijkstra.cpp
index 3fa0435d46bf1cde7795ca23a028d3dce782dc73..a80497a4ab601197d9e45fbb29237c2f3ea52f31 100644
--- a/src/c/mexDijkstra/mexDijkstra.cpp
+++ b/src/c/mexDijkstra/mexDijkstra.cpp
@@ -1,25 +1,25 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
+
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mexDijkstra.h"
#include "CSparseWrapper.h"
diff --git a/src/c/mexDijkstra/mexDijkstra.h b/src/c/mexDijkstra/mexDijkstra.h
index 8a49d79f83da3d78c37d15963dd0ac5f3b920b63..8078f56e9063edb0a87a24a7b6dc3106556a69a0 100644
--- a/src/c/mexDijkstra/mexDijkstra.h
+++ b/src/c/mexDijkstra/mexDijkstra.h
@@ -1,25 +1,27 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
+
+
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+
#include "mex.h"
diff --git a/src/c/mexGraph.sln b/src/c/mexGraph.sln
index 7da86f7f084f18eefff9c8be9264cfbc5f6d5bd2..e2bd3c1adc3a806d54d2ef0bbba1b0450b8fef59 100644
--- a/src/c/mexGraph.sln
+++ b/src/c/mexGraph.sln
@@ -1,22 +1,18 @@

-Microsoft Visual Studio Solution File, Format Version 11.00
-# Visual Studio 2010
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio 14
+VisualStudioVersion = 14.0.24720.0
+MinimumVisualStudioVersion = 10.0.40219.1
Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "mexGraph", "mexGraph.vcxproj", "{4E22BB6D-1C4B-441D-9436-81224FA01AC3}"
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
- Debug|Win32 = Debug|Win32
Debug|x64 = Debug|x64
- Release|Win32 = Release|Win32
Release|x64 = Release|x64
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|Win32.ActiveCfg = Debug|Win32
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|Win32.Build.0 = Debug|Win32
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|x64.ActiveCfg = Debug|x64
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|x64.Build.0 = Debug|x64
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|Win32.ActiveCfg = Release|Win32
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|Win32.Build.0 = Release|Win32
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|x64.ActiveCfg = Release|x64
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|x64.Build.0 = Release|x64
EndGlobalSection
diff --git a/src/c/mexGraph.vcxproj b/src/c/mexGraph.vcxproj
index 4f7c69925a0bc21a4d34f5324efa8cbad41d88ad..d69692c7772be852f6a14be0ad125d81e4bbe578 100644
--- a/src/c/mexGraph.vcxproj
+++ b/src/c/mexGraph.vcxproj
@@ -1,18 +1,10 @@
<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+<Project DefaultTargets="Build" ToolsVersion="14.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup Label="ProjectConfigurations">
- <ProjectConfiguration Include="Debug|Win32">
- <Configuration>Debug</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
<ProjectConfiguration Include="Debug|x64">
<Configuration>Debug</Configuration>
<Platform>x64</Platform>
</ProjectConfiguration>
- <ProjectConfiguration Include="Release|Win32">
- <Configuration>Release</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
<ProjectConfiguration Include="Release|x64">
<Configuration>Release</Configuration>
<Platform>x64</Platform>
@@ -35,33 +27,20 @@
<Keyword>Win32Proj</Keyword>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
- <ConfigurationType>DynamicLibrary</ConfigurationType>
- <CharacterSet>Unicode</CharacterSet>
- <WholeProgramOptimization>true</WholeProgramOptimization>
- </PropertyGroup>
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
- <ConfigurationType>DynamicLibrary</ConfigurationType>
- <CharacterSet>Unicode</CharacterSet>
- </PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
<ConfigurationType>DynamicLibrary</ConfigurationType>
<CharacterSet>Unicode</CharacterSet>
<WholeProgramOptimization>true</WholeProgramOptimization>
+ <PlatformToolset>v140</PlatformToolset>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
<ConfigurationType>DynamicLibrary</ConfigurationType>
<CharacterSet>Unicode</CharacterSet>
+ <PlatformToolset>v140</PlatformToolset>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
<ImportGroup Label="ExtensionSettings">
</ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
<ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="PropertySheets">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
@@ -71,56 +50,16 @@
<PropertyGroup Label="UserMacros" />
<PropertyGroup>
<_ProjectFileVersion>10.0.40219.1</_ProjectFileVersion>
- <OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
- <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
- <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</LinkIncremental>
- <PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">false</PostBuildEventUseInBuild>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
<LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</LinkIncremental>
<PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">false</PostBuildEventUseInBuild>
- <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
- <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
- <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</LinkIncremental>
- <PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</PostBuildEventUseInBuild>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
<LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</LinkIncremental>
<PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</PostBuildEventUseInBuild>
- <TargetExt Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">.mexw32</TargetExt>
<TargetExt Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">.mexw64</TargetExt>
</PropertyGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
- <ClCompile>
- <Optimization>Disabled</Optimization>
- <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>WIN32;_DEBUG;_WINDOWS;_USRDLL;MEXMAT_EXPORTS;MATLAB_MEX_FILE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <PreprocessToFile>false</PreprocessToFile>
- <PreprocessSuppressLineNumbers>false</PreprocessSuppressLineNumbers>
- <MinimalRebuild>true</MinimalRebuild>
- <BasicRuntimeChecks>EnableFastChecks</BasicRuntimeChecks>
- <RuntimeLibrary>MultiThreadedDebug</RuntimeLibrary>
- <PrecompiledHeader>
- </PrecompiledHeader>
- <WarningLevel>Level3</WarningLevel>
- <DebugInformationFormat>EditAndContinue</DebugInformationFormat>
- </ClCompile>
- <Link>
- <AdditionalDependencies>libmx.lib;libmex.lib;libmat.lib;%(AdditionalDependencies)</AdditionalDependencies>
- <OutputFile>$(OutDir)..\..\..\MATLAB\$(ProjectName).mexw32</OutputFile>
- <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
- <ModuleDefinitionFile>mexGraph/mexGraph.def</ModuleDefinitionFile>
- <GenerateDebugInformation>true</GenerateDebugInformation>
- <SubSystem>Windows</SubSystem>
- <TargetMachine>MachineX86</TargetMachine>
- </Link>
- <PostBuildEvent>
- <Message>Copy pdb and mex files to bin and MATLAB directories</Message>
- <Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw32"
-copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
-</Command>
- </PostBuildEvent>
- </ItemDefinitionGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<Midl>
<TargetEnvironment>X64</TargetEnvironment>
@@ -152,37 +91,6 @@ copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
<Message>Copy pdb and mex files to bin and MATLAB directories</Message>
<Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw64"
copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
-</Command>
- </PostBuildEvent>
- </ItemDefinitionGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
- <ClCompile>
- <Optimization>MaxSpeed</Optimization>
- <IntrinsicFunctions>true</IntrinsicFunctions>
- <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>WIN32;NDEBUG;_WINDOWS;_USRDLL;MEXMAT_EXPORTS;MATLAB_MEX_FILE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <RuntimeLibrary>MultiThreaded</RuntimeLibrary>
- <FunctionLevelLinking>true</FunctionLevelLinking>
- <PrecompiledHeader>
- </PrecompiledHeader>
- <WarningLevel>Level3</WarningLevel>
- <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
- </ClCompile>
- <Link>
- <AdditionalDependencies>libmx.lib;libmex.lib;libmat.lib;%(AdditionalDependencies)</AdditionalDependencies>
- <OutputFile>$(OutDir)$(ProjectName).dll</OutputFile>
- <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
- <ModuleDefinitionFile>mexGraph/mexGraph.def</ModuleDefinitionFile>
- <GenerateDebugInformation>true</GenerateDebugInformation>
- <SubSystem>Windows</SubSystem>
- <OptimizeReferences>true</OptimizeReferences>
- <EnableCOMDATFolding>true</EnableCOMDATFolding>
- <TargetMachine>MachineX86</TargetMachine>
- </Link>
- <PostBuildEvent>
- <Message>Copy pdb and mex files to bin and MATLAB directories</Message>
- <Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw32"
-copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
</Command>
</PostBuildEvent>
</ItemDefinitionGroup>
@@ -223,4 +131,4 @@ copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
<ImportGroup Label="ExtensionTargets">
</ImportGroup>
-</Project>
+</Project>
\ No newline at end of file
diff --git a/src/c/mexGraph/CSparseWrapper.cpp b/src/c/mexGraph/CSparseWrapper.cpp
index 2b004c22bab9a28fab4700821b94c24f4a2fd3d7..914d04a0c624987e485e2fe9f90b60fbd965d6c7 100644
--- a/src/c/mexGraph/CSparseWrapper.cpp
+++ b/src/c/mexGraph/CSparseWrapper.cpp
@@ -1,6 +1,30 @@
+
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mexGraph.h"
#include "CSparseWrapper.h"
+#include <algorithm>
+
const double CSparseGraph::noEdge = std::numeric_limits<double>::infinity();
CSparseGraph::CSparseGraph(mwSize numHulls)
diff --git a/src/c/mexGraph/CSparseWrapper.h b/src/c/mexGraph/CSparseWrapper.h
index 1d7155e81cb01556bf87c4e5fd4111237c5297c3..9a7e95e44f931c95d90f1d40179394909217756d 100644
--- a/src/c/mexGraph/CSparseWrapper.h
+++ b/src/c/mexGraph/CSparseWrapper.h
@@ -1,3 +1,27 @@
+
+
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+
#ifndef CSPARSEWRAPPER_H
#define CSPARSEWRAPPER_H 1
diff --git a/src/c/mexGraph/mexGraph.cpp b/src/c/mexGraph/mexGraph.cpp
index 224d811edc99821c3db9fd757a6f558babc7e3aa..f21eb373a57003afb56376c4baa5ac3171fb15d3 100644
--- a/src/c/mexGraph/mexGraph.cpp
+++ b/src/c/mexGraph/mexGraph.cpp
@@ -1,25 +1,25 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
+
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mexGraph.h"
#include "CSparseWrapper.h"
diff --git a/src/c/mexGraph/mexGraph.h b/src/c/mexGraph/mexGraph.h
index 8a49d79f83da3d78c37d15963dd0ac5f3b920b63..8078f56e9063edb0a87a24a7b6dc3106556a69a0 100644
--- a/src/c/mexGraph/mexGraph.h
+++ b/src/c/mexGraph/mexGraph.h
@@ -1,25 +1,27 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
+
+
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
+
#include "mex.h"
diff --git a/src/c/mexHashData.sln b/src/c/mexHashData.sln
index 1dd7e359245f6e3d645f21b7a507fb7c6609972b..2633b50fa44218c5aaeaf22a5ec7eecee0355054 100644
--- a/src/c/mexHashData.sln
+++ b/src/c/mexHashData.sln
@@ -1,22 +1,18 @@

-Microsoft Visual Studio Solution File, Format Version 11.00
-# Visual Studio 2010
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio 14
+VisualStudioVersion = 14.0.24720.0
+MinimumVisualStudioVersion = 10.0.40219.1
Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "mexHashData", "mexHashData.vcxproj", "{4E22BB6D-1C4B-441D-9436-81224FA01AC3}"
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
- Debug|Win32 = Debug|Win32
Debug|x64 = Debug|x64
- Release|Win32 = Release|Win32
Release|x64 = Release|x64
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|Win32.ActiveCfg = Debug|Win32
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|Win32.Build.0 = Debug|Win32
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|x64.ActiveCfg = Debug|x64
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|x64.Build.0 = Debug|x64
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|Win32.ActiveCfg = Release|Win32
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|Win32.Build.0 = Release|Win32
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|x64.ActiveCfg = Release|x64
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|x64.Build.0 = Release|x64
EndGlobalSection
diff --git a/src/c/mexHashData.vcxproj b/src/c/mexHashData.vcxproj
index 4805b70138c8fec7922232bf011dfe37c742224f..fb809dfa22a49b4ab94b8752f51d7b4aae02a5ee 100644
--- a/src/c/mexHashData.vcxproj
+++ b/src/c/mexHashData.vcxproj
@@ -1,18 +1,10 @@
<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+<Project DefaultTargets="Build" ToolsVersion="14.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup Label="ProjectConfigurations">
- <ProjectConfiguration Include="Debug|Win32">
- <Configuration>Debug</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
<ProjectConfiguration Include="Debug|x64">
<Configuration>Debug</Configuration>
<Platform>x64</Platform>
</ProjectConfiguration>
- <ProjectConfiguration Include="Release|Win32">
- <Configuration>Release</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
<ProjectConfiguration Include="Release|x64">
<Configuration>Release</Configuration>
<Platform>x64</Platform>
@@ -35,33 +27,20 @@
<Keyword>Win32Proj</Keyword>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
- <ConfigurationType>DynamicLibrary</ConfigurationType>
- <CharacterSet>Unicode</CharacterSet>
- <WholeProgramOptimization>true</WholeProgramOptimization>
- </PropertyGroup>
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
- <ConfigurationType>DynamicLibrary</ConfigurationType>
- <CharacterSet>Unicode</CharacterSet>
- </PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
<ConfigurationType>DynamicLibrary</ConfigurationType>
<CharacterSet>Unicode</CharacterSet>
<WholeProgramOptimization>true</WholeProgramOptimization>
+ <PlatformToolset>v140</PlatformToolset>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
<ConfigurationType>DynamicLibrary</ConfigurationType>
<CharacterSet>Unicode</CharacterSet>
+ <PlatformToolset>v140</PlatformToolset>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
<ImportGroup Label="ExtensionSettings">
</ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
<ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="PropertySheets">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
@@ -71,56 +50,16 @@
<PropertyGroup Label="UserMacros" />
<PropertyGroup>
<_ProjectFileVersion>10.0.40219.1</_ProjectFileVersion>
- <OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
- <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
- <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</LinkIncremental>
- <PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">false</PostBuildEventUseInBuild>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
<LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</LinkIncremental>
<PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">false</PostBuildEventUseInBuild>
- <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
- <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
- <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</LinkIncremental>
- <PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</PostBuildEventUseInBuild>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
<LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</LinkIncremental>
<PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</PostBuildEventUseInBuild>
- <TargetExt Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">.mexw32</TargetExt>
<TargetExt Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">.mexw64</TargetExt>
</PropertyGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
- <ClCompile>
- <Optimization>Disabled</Optimization>
- <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>WIN32;_DEBUG;_WINDOWS;_USRDLL;MEXMAT_EXPORTS;MATLAB_MEX_FILE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <PreprocessToFile>false</PreprocessToFile>
- <PreprocessSuppressLineNumbers>false</PreprocessSuppressLineNumbers>
- <MinimalRebuild>true</MinimalRebuild>
- <BasicRuntimeChecks>EnableFastChecks</BasicRuntimeChecks>
- <RuntimeLibrary>MultiThreadedDebug</RuntimeLibrary>
- <PrecompiledHeader>
- </PrecompiledHeader>
- <WarningLevel>Level3</WarningLevel>
- <DebugInformationFormat>EditAndContinue</DebugInformationFormat>
- </ClCompile>
- <Link>
- <AdditionalDependencies>libmx.lib;libmex.lib;libmat.lib;%(AdditionalDependencies)</AdditionalDependencies>
- <OutputFile>$(OutDir)..\..\..\MATLAB\$(ProjectName).mexw32</OutputFile>
- <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
- <ModuleDefinitionFile>mexDijkstra/mexDijkstra.def</ModuleDefinitionFile>
- <GenerateDebugInformation>true</GenerateDebugInformation>
- <SubSystem>Windows</SubSystem>
- <TargetMachine>MachineX86</TargetMachine>
- </Link>
- <PostBuildEvent>
- <Message>Copy pdb and mex files to bin and MATLAB directories</Message>
- <Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw32"
-copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
-</Command>
- </PostBuildEvent>
- </ItemDefinitionGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<Midl>
<TargetEnvironment>X64</TargetEnvironment>
@@ -152,37 +91,6 @@ copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
<Message>Copy pdb and mex files to bin and MATLAB directories</Message>
<Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw64"
copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
-</Command>
- </PostBuildEvent>
- </ItemDefinitionGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
- <ClCompile>
- <Optimization>MaxSpeed</Optimization>
- <IntrinsicFunctions>true</IntrinsicFunctions>
- <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>WIN32;NDEBUG;_WINDOWS;_USRDLL;MEXMAT_EXPORTS;MATLAB_MEX_FILE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <RuntimeLibrary>MultiThreaded</RuntimeLibrary>
- <FunctionLevelLinking>true</FunctionLevelLinking>
- <PrecompiledHeader>
- </PrecompiledHeader>
- <WarningLevel>Level3</WarningLevel>
- <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
- </ClCompile>
- <Link>
- <AdditionalDependencies>libmx.lib;libmex.lib;libmat.lib;%(AdditionalDependencies)</AdditionalDependencies>
- <OutputFile>$(OutDir)$(ProjectName).dll</OutputFile>
- <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
- <ModuleDefinitionFile>mexDijkstra/mexDijkstra.def</ModuleDefinitionFile>
- <GenerateDebugInformation>true</GenerateDebugInformation>
- <SubSystem>Windows</SubSystem>
- <OptimizeReferences>true</OptimizeReferences>
- <EnableCOMDATFolding>true</EnableCOMDATFolding>
- <TargetMachine>MachineX86</TargetMachine>
- </Link>
- <PostBuildEvent>
- <Message>Copy pdb and mex files to bin and MATLAB directories</Message>
- <Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw32"
-copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
</Command>
</PostBuildEvent>
</ItemDefinitionGroup>
@@ -223,4 +131,4 @@ copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
<ImportGroup Label="ExtensionTargets">
</ImportGroup>
-</Project>
+</Project>
\ No newline at end of file
diff --git a/src/c/mexHashData/mexHashData.cpp b/src/c/mexHashData/mexHashData.cpp
index 1bd6d9a30a4425f976f1c85251e394ad8b852af5..35d03862bd11a582bd3b22a84d95c010b3036c12 100644
--- a/src/c/mexHashData/mexHashData.cpp
+++ b/src/c/mexHashData/mexHashData.cpp
@@ -1,26 +1,24 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mexHashData.h"
#include <string.h>
diff --git a/src/c/mexHashData/mexHashData.h b/src/c/mexHashData/mexHashData.h
index fe4c84ac73fb581625fc9b175b3f502de1cbb738..2c17449e563b490f5704f49b862b492889fdf9f3 100644
--- a/src/c/mexHashData/mexHashData.h
+++ b/src/c/mexHashData/mexHashData.h
@@ -1,26 +1,24 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mex.h"
extern "C"
diff --git a/src/c/mexIntegrityCheck.sln b/src/c/mexIntegrityCheck.sln
index f6aad26503df382a18f1c9a8e84ce993e7db42c0..e532320714f0db8ae869e38b0a91e2a3270ed6c8 100644
--- a/src/c/mexIntegrityCheck.sln
+++ b/src/c/mexIntegrityCheck.sln
@@ -1,22 +1,18 @@

-Microsoft Visual Studio Solution File, Format Version 11.00
-# Visual Studio 2010
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio 14
+VisualStudioVersion = 14.0.24720.0
+MinimumVisualStudioVersion = 10.0.40219.1
Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "mexIntegrityCheck", "mexIntegrityCheck.vcxproj", "{4E22BB6D-1C4B-441D-9436-81224FA01AC3}"
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
- Debug|Win32 = Debug|Win32
Debug|x64 = Debug|x64
- Release|Win32 = Release|Win32
Release|x64 = Release|x64
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|Win32.ActiveCfg = Debug|Win32
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|Win32.Build.0 = Debug|Win32
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|x64.ActiveCfg = Debug|x64
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|x64.Build.0 = Debug|x64
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|Win32.ActiveCfg = Release|Win32
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|Win32.Build.0 = Release|Win32
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|x64.ActiveCfg = Release|x64
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|x64.Build.0 = Release|x64
EndGlobalSection
diff --git a/src/c/mexIntegrityCheck.vcxproj b/src/c/mexIntegrityCheck.vcxproj
index ea5e3577189e0c97c6dba77951cb3d9ebab627a0..aec2705b63f208cc70abd6c8b0191c963c9f05b0 100644
--- a/src/c/mexIntegrityCheck.vcxproj
+++ b/src/c/mexIntegrityCheck.vcxproj
@@ -1,18 +1,10 @@
<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+<Project DefaultTargets="Build" ToolsVersion="14.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup Label="ProjectConfigurations">
- <ProjectConfiguration Include="Debug|Win32">
- <Configuration>Debug</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
<ProjectConfiguration Include="Debug|x64">
<Configuration>Debug</Configuration>
<Platform>x64</Platform>
</ProjectConfiguration>
- <ProjectConfiguration Include="Release|Win32">
- <Configuration>Release</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
<ProjectConfiguration Include="Release|x64">
<Configuration>Release</Configuration>
<Platform>x64</Platform>
@@ -33,33 +25,20 @@
<Keyword>Win32Proj</Keyword>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
- <ConfigurationType>DynamicLibrary</ConfigurationType>
- <CharacterSet>Unicode</CharacterSet>
- <WholeProgramOptimization>true</WholeProgramOptimization>
- </PropertyGroup>
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
- <ConfigurationType>DynamicLibrary</ConfigurationType>
- <CharacterSet>Unicode</CharacterSet>
- </PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
<ConfigurationType>DynamicLibrary</ConfigurationType>
<CharacterSet>Unicode</CharacterSet>
<WholeProgramOptimization>true</WholeProgramOptimization>
+ <PlatformToolset>v140</PlatformToolset>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
<ConfigurationType>DynamicLibrary</ConfigurationType>
<CharacterSet>Unicode</CharacterSet>
+ <PlatformToolset>v140</PlatformToolset>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
<ImportGroup Label="ExtensionSettings">
</ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
<ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="PropertySheets">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
@@ -69,56 +48,16 @@
<PropertyGroup Label="UserMacros" />
<PropertyGroup>
<_ProjectFileVersion>10.0.40219.1</_ProjectFileVersion>
- <OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
- <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
- <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</LinkIncremental>
- <PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">false</PostBuildEventUseInBuild>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
<LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</LinkIncremental>
<PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">false</PostBuildEventUseInBuild>
- <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
- <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
- <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</LinkIncremental>
- <PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</PostBuildEventUseInBuild>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
<LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</LinkIncremental>
<PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</PostBuildEventUseInBuild>
- <TargetExt Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">.mexw32</TargetExt>
<TargetExt Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">.mexw64</TargetExt>
</PropertyGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
- <ClCompile>
- <Optimization>Disabled</Optimization>
- <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>WIN32;_DEBUG;_WINDOWS;_USRDLL;MEXMAT_EXPORTS;MATLAB_MEX_FILE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <PreprocessToFile>false</PreprocessToFile>
- <PreprocessSuppressLineNumbers>false</PreprocessSuppressLineNumbers>
- <MinimalRebuild>true</MinimalRebuild>
- <BasicRuntimeChecks>EnableFastChecks</BasicRuntimeChecks>
- <RuntimeLibrary>MultiThreadedDebug</RuntimeLibrary>
- <PrecompiledHeader>
- </PrecompiledHeader>
- <WarningLevel>Level3</WarningLevel>
- <DebugInformationFormat>EditAndContinue</DebugInformationFormat>
- </ClCompile>
- <Link>
- <AdditionalDependencies>libmx.lib;libmex.lib;libmat.lib;%(AdditionalDependencies)</AdditionalDependencies>
- <OutputFile>$(OutDir)..\..\..\MATLAB\$(ProjectName).mexw32</OutputFile>
- <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
- <ModuleDefinitionFile>mexDijkstra/mexDijkstra.def</ModuleDefinitionFile>
- <GenerateDebugInformation>true</GenerateDebugInformation>
- <SubSystem>Windows</SubSystem>
- <TargetMachine>MachineX86</TargetMachine>
- </Link>
- <PostBuildEvent>
- <Message>Copy pdb and mex files to bin and MATLAB directories</Message>
- <Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw32"
-copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
-</Command>
- </PostBuildEvent>
- </ItemDefinitionGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<Midl>
<TargetEnvironment>X64</TargetEnvironment>
@@ -150,37 +89,6 @@ copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
<Message>Copy pdb and mex files to bin and MATLAB directories</Message>
<Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw64"
copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
-</Command>
- </PostBuildEvent>
- </ItemDefinitionGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
- <ClCompile>
- <Optimization>MaxSpeed</Optimization>
- <IntrinsicFunctions>true</IntrinsicFunctions>
- <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>WIN32;NDEBUG;_WINDOWS;_USRDLL;MEXMAT_EXPORTS;MATLAB_MEX_FILE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <RuntimeLibrary>MultiThreaded</RuntimeLibrary>
- <FunctionLevelLinking>true</FunctionLevelLinking>
- <PrecompiledHeader>
- </PrecompiledHeader>
- <WarningLevel>Level3</WarningLevel>
- <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
- </ClCompile>
- <Link>
- <AdditionalDependencies>libmx.lib;libmex.lib;libmat.lib;%(AdditionalDependencies)</AdditionalDependencies>
- <OutputFile>$(OutDir)$(ProjectName).dll</OutputFile>
- <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
- <ModuleDefinitionFile>mexDijkstra/mexDijkstra.def</ModuleDefinitionFile>
- <GenerateDebugInformation>true</GenerateDebugInformation>
- <SubSystem>Windows</SubSystem>
- <OptimizeReferences>true</OptimizeReferences>
- <EnableCOMDATFolding>true</EnableCOMDATFolding>
- <TargetMachine>MachineX86</TargetMachine>
- </Link>
- <PostBuildEvent>
- <Message>Copy pdb and mex files to bin and MATLAB directories</Message>
- <Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw32"
-copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
</Command>
</PostBuildEvent>
</ItemDefinitionGroup>
@@ -221,4 +129,4 @@ copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
<ImportGroup Label="ExtensionTargets">
</ImportGroup>
-</Project>
+</Project>
\ No newline at end of file
diff --git a/src/c/mexIntegrityCheck/mexIntegrityCheck.cpp b/src/c/mexIntegrityCheck/mexIntegrityCheck.cpp
index 5e580d14b679120b21982146c5e23b929ce1e1d2..8274011096ed6ffc3f2626e5d2801c7bbb6f9fd7 100644
--- a/src/c/mexIntegrityCheck/mexIntegrityCheck.cpp
+++ b/src/c/mexIntegrityCheck/mexIntegrityCheck.cpp
@@ -1,26 +1,24 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mexIntegrityCheck.h"
#include <vector>
diff --git a/src/c/mexIntegrityCheck/mexIntegrityCheck.h b/src/c/mexIntegrityCheck/mexIntegrityCheck.h
index 8a49d79f83da3d78c37d15963dd0ac5f3b920b63..c4d0801b12d186c028537fa31315f184ee313c13 100644
--- a/src/c/mexIntegrityCheck/mexIntegrityCheck.h
+++ b/src/c/mexIntegrityCheck/mexIntegrityCheck.h
@@ -1,26 +1,24 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mex.h"
#ifdef MEXMAT_EXPORTS
diff --git a/src/c/mexMAT.sln b/src/c/mexMAT.sln
index 19927e4bc14e51d45a4a72832ec0ca387bbdf7fb..7065e7f6002ed6a94ae5d06da23304d802848cbc 100644
--- a/src/c/mexMAT.sln
+++ b/src/c/mexMAT.sln
@@ -1,22 +1,18 @@

-Microsoft Visual Studio Solution File, Format Version 11.00
-# Visual Studio 2010
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio 14
+VisualStudioVersion = 14.0.24720.0
+MinimumVisualStudioVersion = 10.0.40219.1
Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "mexMAT", "mexMAT.vcxproj", "{4E22BB6D-1C4B-441D-9436-81224FA01AC3}"
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
- Debug|Win32 = Debug|Win32
Debug|x64 = Debug|x64
- Release|Win32 = Release|Win32
Release|x64 = Release|x64
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|Win32.ActiveCfg = Debug|Win32
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|Win32.Build.0 = Debug|Win32
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|x64.ActiveCfg = Debug|x64
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Debug|x64.Build.0 = Debug|x64
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|Win32.ActiveCfg = Release|Win32
- {4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|Win32.Build.0 = Release|Win32
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|x64.ActiveCfg = Release|x64
{4E22BB6D-1C4B-441D-9436-81224FA01AC3}.Release|x64.Build.0 = Release|x64
EndGlobalSection
diff --git a/src/c/mexMAT.vcxproj b/src/c/mexMAT.vcxproj
index 4dff8fd476dd972c8cffe6cbe99f68cf67575bef..ef20f881aee85854a877593e23b330c2f8f1c696 100644
--- a/src/c/mexMAT.vcxproj
+++ b/src/c/mexMAT.vcxproj
@@ -1,18 +1,10 @@
<?xml version="1.0" encoding="utf-8"?>
-<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+<Project DefaultTargets="Build" ToolsVersion="14.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
<ItemGroup Label="ProjectConfigurations">
- <ProjectConfiguration Include="Debug|Win32">
- <Configuration>Debug</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
<ProjectConfiguration Include="Debug|x64">
<Configuration>Debug</Configuration>
<Platform>x64</Platform>
</ProjectConfiguration>
- <ProjectConfiguration Include="Release|Win32">
- <Configuration>Release</Configuration>
- <Platform>Win32</Platform>
- </ProjectConfiguration>
<ProjectConfiguration Include="Release|x64">
<Configuration>Release</Configuration>
<Platform>x64</Platform>
@@ -24,33 +16,20 @@
<Keyword>Win32Proj</Keyword>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
- <ConfigurationType>DynamicLibrary</ConfigurationType>
- <CharacterSet>Unicode</CharacterSet>
- <WholeProgramOptimization>true</WholeProgramOptimization>
- </PropertyGroup>
- <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
- <ConfigurationType>DynamicLibrary</ConfigurationType>
- <CharacterSet>Unicode</CharacterSet>
- </PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
<ConfigurationType>DynamicLibrary</ConfigurationType>
<CharacterSet>Unicode</CharacterSet>
<WholeProgramOptimization>true</WholeProgramOptimization>
+ <PlatformToolset>v140</PlatformToolset>
</PropertyGroup>
<PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
<ConfigurationType>DynamicLibrary</ConfigurationType>
<CharacterSet>Unicode</CharacterSet>
+ <PlatformToolset>v140</PlatformToolset>
</PropertyGroup>
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
<ImportGroup Label="ExtensionSettings">
</ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
- <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets">
- <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
- </ImportGroup>
<ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="PropertySheets">
<Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
</ImportGroup>
@@ -60,56 +39,16 @@
<PropertyGroup Label="UserMacros" />
<PropertyGroup>
<_ProjectFileVersion>10.0.40219.1</_ProjectFileVersion>
- <OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
- <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
- <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</LinkIncremental>
- <PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">false</PostBuildEventUseInBuild>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
<LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</LinkIncremental>
<PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">false</PostBuildEventUseInBuild>
- <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
- <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
- <LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</LinkIncremental>
- <PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">false</PostBuildEventUseInBuild>
<OutDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(SolutionDir)$(ProjectName)\$(Configuration)_$(Platform)\</OutDir>
<IntDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(ProjectName)\Intermediate\$(Configuration)_$(Platform)\</IntDir>
<LinkIncremental Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</LinkIncremental>
<PostBuildEventUseInBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">false</PostBuildEventUseInBuild>
- <TargetExt Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">.mexw32</TargetExt>
<TargetExt Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">.mexw64</TargetExt>
</PropertyGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
- <ClCompile>
- <Optimization>Disabled</Optimization>
- <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>WIN32;_DEBUG;_WINDOWS;_USRDLL;MEXMAT_EXPORTS;MATLAB_MEX_FILE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <PreprocessToFile>false</PreprocessToFile>
- <PreprocessSuppressLineNumbers>false</PreprocessSuppressLineNumbers>
- <MinimalRebuild>true</MinimalRebuild>
- <BasicRuntimeChecks>EnableFastChecks</BasicRuntimeChecks>
- <RuntimeLibrary>MultiThreadedDebug</RuntimeLibrary>
- <PrecompiledHeader>
- </PrecompiledHeader>
- <WarningLevel>Level3</WarningLevel>
- <DebugInformationFormat>EditAndContinue</DebugInformationFormat>
- </ClCompile>
- <Link>
- <AdditionalDependencies>libmx.lib;libmex.lib;libmat.lib;%(AdditionalDependencies)</AdditionalDependencies>
- <OutputFile>$(OutDir)..\..\..\MATLAB\$(ProjectName).mexw32</OutputFile>
- <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
- <ModuleDefinitionFile>mexMAT/mexMAT.def</ModuleDefinitionFile>
- <GenerateDebugInformation>true</GenerateDebugInformation>
- <SubSystem>Windows</SubSystem>
- <TargetMachine>MachineX86</TargetMachine>
- </Link>
- <PostBuildEvent>
- <Message>Copy pdb and mex files to bin and MATLAB directories</Message>
- <Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw32"
-copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
-</Command>
- </PostBuildEvent>
- </ItemDefinitionGroup>
<ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
<Midl>
<TargetEnvironment>X64</TargetEnvironment>
@@ -141,37 +80,6 @@ copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
<Message>Copy pdb and mex files to bin and MATLAB directories</Message>
<Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw64"
copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
-</Command>
- </PostBuildEvent>
- </ItemDefinitionGroup>
- <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
- <ClCompile>
- <Optimization>MaxSpeed</Optimization>
- <IntrinsicFunctions>true</IntrinsicFunctions>
- <AdditionalIncludeDirectories>$(MATLAB_DIR)\extern\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
- <PreprocessorDefinitions>WIN32;NDEBUG;_WINDOWS;_USRDLL;MEXMAT_EXPORTS;MATLAB_MEX_FILE;%(PreprocessorDefinitions)</PreprocessorDefinitions>
- <RuntimeLibrary>MultiThreaded</RuntimeLibrary>
- <FunctionLevelLinking>true</FunctionLevelLinking>
- <PrecompiledHeader>
- </PrecompiledHeader>
- <WarningLevel>Level3</WarningLevel>
- <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
- </ClCompile>
- <Link>
- <AdditionalDependencies>libmx.lib;libmex.lib;libmat.lib;%(AdditionalDependencies)</AdditionalDependencies>
- <OutputFile>$(OutDir)$(ProjectName).dll</OutputFile>
- <AdditionalLibraryDirectories>$(MATLAB_DIR)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories>
- <ModuleDefinitionFile>mexMAT/mexMAT.def</ModuleDefinitionFile>
- <GenerateDebugInformation>true</GenerateDebugInformation>
- <SubSystem>Windows</SubSystem>
- <OptimizeReferences>true</OptimizeReferences>
- <EnableCOMDATFolding>true</EnableCOMDATFolding>
- <TargetMachine>MachineX86</TargetMachine>
- </Link>
- <PostBuildEvent>
- <Message>Copy pdb and mex files to bin and MATLAB directories</Message>
- <Command>copy "$(OutDir)$(ProjectName).dll" "..\MATLAB\$(ProjectName).mexw32"
-copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
</Command>
</PostBuildEvent>
</ItemDefinitionGroup>
@@ -226,4 +134,4 @@ copy "$(OutDir)$(ProjectName).pdb" ..\MATLAB
<Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
<ImportGroup Label="ExtensionTargets">
</ImportGroup>
-</Project>
+</Project>
\ No newline at end of file
diff --git a/src/c/mexMAT/CEdgeSubgraph.h b/src/c/mexMAT/CEdgeSubgraph.h
index d94c9fa8f5f8c3be0fec4a089839bd44773f8ad9..90e932fba9d728dd50cc03895570c5c756bf1857 100644
--- a/src/c/mexMAT/CEdgeSubgraph.h
+++ b/src/c/mexMAT/CEdgeSubgraph.h
@@ -1,26 +1,24 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#ifndef _CEDGESUBGRAPH_H_
#define _CEDGESUBGRAPH_H_ 1
diff --git a/src/c/mexMAT/bestPaths.cpp b/src/c/mexMAT/bestPaths.cpp
index 2b4761ba0d9eba8f4b2df6193cf69c38e2fde1ec..c07b999c6cd86a5b3d94c9003f628f3cf795b7db 100644
--- a/src/c/mexMAT/bestPaths.cpp
+++ b/src/c/mexMAT/bestPaths.cpp
@@ -1,28 +1,28 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mexMAT.h"
+#include <algorithm>
+
std::vector<CSourcePath> gTrackHistory;
// Find all trackIDs from source hullIDs
diff --git a/src/c/mexMAT/bestPaths.h b/src/c/mexMAT/bestPaths.h
index a533913a64bc0842b88dfb78ecf801e52471c3ee..66175761fd6bef548c49cd574f610ade6968cbe3 100644
--- a/src/c/mexMAT/bestPaths.h
+++ b/src/c/mexMAT/bestPaths.h
@@ -1,26 +1,24 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
// Double limits convenience definition
typedef std::numeric_limits<double> DoubleLims;
diff --git a/src/c/mexMAT/cost.cpp b/src/c/mexMAT/cost.cpp
index 258e1af551274c4f3e8c419009a60056f5c3a397..f88b65ca9cdb83156ce9dc788ff820623c8e9443 100644
--- a/src/c/mexMAT/cost.cpp
+++ b/src/c/mexMAT/cost.cpp
@@ -1,28 +1,27 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mexMAT.h"
+#include <algorithm>
#include <math.h>
#undef max
diff --git a/src/c/mexMAT/cost.h b/src/c/mexMAT/cost.h
index f4ddf675b920bd359d6daf28045636491497c0be..030cc5ccafbe389f3f95ccbbfa6c7afd39c0da4c 100644
--- a/src/c/mexMAT/cost.h
+++ b/src/c/mexMAT/cost.h
@@ -1,26 +1,24 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
// Get cost based on a frame and index list. The srcFrameIdx is used if there, it is the index into
// path vector of the source point(start of new path). srcFrameIdx is trivially 0 if there is
diff --git a/src/c/mexMAT/mexMAT.cpp b/src/c/mexMAT/mexMAT.cpp
index 66d3cd9903cc6857e0b7fba864f9a303c91da69a..c626847af52944879699c8a35799f7b182bf6b31 100644
--- a/src/c/mexMAT/mexMAT.cpp
+++ b/src/c/mexMAT/mexMAT.cpp
@@ -1,26 +1,24 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mexMAT.h"
#define ARRAY_SIZE(x) (sizeof(x) / sizeof((x)[0]))
diff --git a/src/c/mexMAT/mexMAT.h b/src/c/mexMAT/mexMAT.h
index f9d16074327471ac2bc6cf493a1dc461de982874..b432707ab1b589e7f2557d7d27dd68fc5ed6dde1 100644
--- a/src/c/mexMAT/mexMAT.h
+++ b/src/c/mexMAT/mexMAT.h
@@ -1,26 +1,24 @@
-//***********************************************************************
-//
-// Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
-//
-// This file is part of LEVer - the tool for stem cell lineaging. See
-// https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
-//
-// LEVer is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// LEVer is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with LEVer in file "gnu gpl v3.txt". If not, see
-// <http://www.gnu.org/licenses/>.
-//
-//
-//***********************************************************************
-
+/***********************************************************************
+* Copyright 2011-2016 Andrew Cohen
+*
+* This file is part of LEVer - the tool for stem cell lineaging. See
+* http://n2t.net/ark:/87918/d9rp4t for details
+*
+* LEVer is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* LEVer is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with LEVer in file "gnu gpl v3.txt". If not, see
+* <http://www.gnu.org/licenses/>.
+*
+***********************************************************************/
#include "mex.h"
#include <map>