From a1ca3abb2cb07e4a9c724482e4ffe79ce796f4a3 Mon Sep 17 00:00:00 2001
From: Eric Wait <eric@waitphoto.com>
Date: Fri, 8 Apr 2011 22:41:22 -0500
Subject: [PATCH] LEVer 4.0
---
bin/CompileLEVer.m | 6 ++++-
src/MATLAB/InitializeFigures.m | 17 ++++++++++++
src/MATLAB/OpenData.m | 48 ++++++++++++----------------------
src/MATLAB/ProcessNewborns.m | 2 +-
src/MATLAB/SaveData.m | 2 +-
src/MATLAB/SaveDataAs.m | 14 ++++++----
src/MATLAB/SegAndTrack.m | 2 ++
src/MATLAB/TrackSplitHulls.m | 1 +
8 files changed, 53 insertions(+), 39 deletions(-)
diff --git a/bin/CompileLEVer.m b/bin/CompileLEVer.m
index fec62063..aa9094db 100644
--- a/bin/CompileLEVer.m
+++ b/bin/CompileLEVer.m
@@ -1 +1,5 @@
-mcc -m ../LEVer.m
\ No newline at end of file
+mcc -m ../LEVer.m
+mcc -m ../Segmentor.m
+if(isempty(dir('./MTC.exe')))
+ warndlg('Make sure that MTC.exe is in the same dir as LEVer.exe');
+end
\ No newline at end of file
diff --git a/src/MATLAB/InitializeFigures.m b/src/MATLAB/InitializeFigures.m
index 4cd18456..acdb4788 100644
--- a/src/MATLAB/InitializeFigures.m
+++ b/src/MATLAB/InitializeFigures.m
@@ -10,6 +10,13 @@ global Figures CONSTANTS
Figures.time = 1;
+oldCellsHandle = [];
+oldTreeHandle = [];
+if(isfield(Figures,'cells') && isfield(Figures.cells,'handle') && ~isempty(Figures.cells.handle))
+ oldCellsHandle = Figures.cells.handle;
+ oldTreeHandle = Figures.tree.handle;
+end
+
Figures.cells.handle = figure();
Figures.tree.handle = figure();
@@ -68,6 +75,16 @@ Figures.tree.timeLabel = uicontrol(Figures.tree.handle,...
'String',['Time: ' num2str(Figures.time)]);
FindLargestTree([],[]);
+
+if(~isempty(oldCellsHandle) && ishandle(oldCellsHandle))
+ set(oldCellsHandle,'CloseRequestFcn','remove');
+ close(oldCellsHandle);
+end
+if(~isempty(oldTreeHandle) && ishandle(oldTreeHandle))
+ set(oldTreeHandle,'CloseRequestFcn','remove');
+ close(oldTreeHandle);
+end
+
% DrawTree(1);
% figure(Figures.tree.handle);
%
diff --git a/src/MATLAB/OpenData.m b/src/MATLAB/OpenData.m
index 581d302a..a08b6921 100644
--- a/src/MATLAB/OpenData.m
+++ b/src/MATLAB/OpenData.m
@@ -31,7 +31,7 @@ end
filterIndexImage = 0;
matFile = [];
-matPath = [];
+matFilePath = [];
imageFile = [];
imagePath = [];
imageDataset = [];
@@ -56,39 +56,40 @@ if(~isempty(Figures))
end
oldCONSTANTS = CONSTANTS;
+InitializeConstants();
%find the first image
imageFilter = [settings.imagePath '*.TIF'];
while (filterIndexImage==0)
fprintf('\nSelect first .TIF image...\n\n');
- [imageFile,imagePath,filterIndexImage] = uigetfile(imageFilter,'Open First Image in dataset: ');
+ [settings.imageFile,settings.imagePath,filterIndexImage] = uigetfile(imageFilter,'Open First Image in dataset: ');
if (filterIndexImage==0)
CONSTANTS = oldCONSTANTS;
return
end
end
-index = strfind(imageFile,'_t');
+index = strfind(settings.imageFile,'_t');
frameT = '001';
if (~isempty(index) && filterIndexImage~=0)
- CONSTANTS.rootImageFolder = imagePath;
- imageDataset = imageFile(1:(index(length(index))-1));
+ CONSTANTS.rootImageFolder = settings.imagePath;
+ imageDataset = settings.imageFile(1:(index(length(index))-1));
CONSTANTS.imageDatasetName = imageDataset;
CONSTANTS.datasetName = imageDataset;
- index2 = strfind(imageFile,'.');
+ index2 = strfind(settings.imageFile,'.');
CONSTANTS.imageSignificantDigits = index2 - index - 2;
fileName=[CONSTANTS.rootImageFolder imageDataset '_t' SignificantDigits(1) '.TIF'];
end
while (isempty(index) || ~exist(fileName,'file'))
fprintf(['Image file name not in correct format: ' CONSTANTS.datasetName '_t' frameT '.TIF\nPlease choose another...\n']);
- [imageFile,imagePath,filterIndexImage] = uigetfile(settings.imagePath,'Open First Image');
+ [settings.imageFile,settings.imagePath,filterIndexImage] = uigetfile(settings.imagePath,'Open First Image');
if(filterIndexImage==0)
CONSTANTS = oldCONSTANTS;
return
end
index = strfind(imageFile,'t');
- CONSTANTS.rootImageFolder = [imagePath '\'];
+ CONSTANTS.rootImageFolder = [settings.imagePath '\'];
imageDataset = imageFile(1:(index(length(index))-2));
fileName=[CONSTANTS.rootImageFolder imageDataSet '_t' SignificantDigits(t) '.TIF'];
end
@@ -96,12 +97,13 @@ end
answer = questdlg('Run Segmentation and Tracking or Use Existing Data?','Data Source','Segment & Track','Existing','Existing');
switch answer
case 'Segment & Track'
+ save('LEVerSettings.mat','settings');
InitializeConstants();
SegAndTrack();
case 'Existing'
while(~goodLoad)
fprintf('Select .mat data file...\n');
- [matFile,matPath,filterIndexMatFile] = uigetfile([settings.matFilePath '*.mat'],...
+ [settings.matFile,settings.matFilePath,filterIndexMatFile] = uigetfile([settings.matFilePath '*.mat'],...
'Open Data');
if (filterIndexMatFile==0)
@@ -124,7 +126,7 @@ switch answer
imageSignificantDigits = CONSTANTS.imageSignificantDigits;
try
- load([matPath matFile]);
+ load([settings.matFilePath settings.matFile]);
fprintf('\nFile open.\n\n');
catch exception
%DEBUG -- Uncomment
@@ -132,21 +134,16 @@ switch answer
end
end
- if(~isfield(CONSTANTS,'rootImageFolder'))
- CONSTANTS.rootImageFolder = rootImageFolder;
- end
-
- if(~isfield(CONSTANTS,'imageSignificantDigits'))
- CONSTANTS.imageSignificantDigits = imageSignificantDigits;
- end
+ CONSTANTS.rootImageFolder = rootImageFolder;
+ CONSTANTS.imageSignificantDigits = imageSignificantDigits;
+ InitializeConstants();
if(exist('objHulls','var'))
fprintf('Converting File...');
- InitializeConstants();
ConvertTrackingData(objHulls,gConnect);
fprintf('\nFile Converted.\n');
CONSTANTS.datasetName = strtok(matFile,' ');
- save([matPath CONSTANTS.datasetName '_LEVer'],...
+ save([settings.matFilePath CONSTANTS.datasetName '_LEVer'],...
'CellFamilies','CellHulls','CellTracks','HashedCells','Costs','CONSTANTS');
fprintf(['New file saved as:\n' CONSTANTS.datasetName '_LEVer.mat']);
goodLoad = 1;
@@ -159,9 +156,6 @@ switch answer
end
%save out settings
- settings.matFilePath = matPath;
- settings.imageFile = imageFile;
- settings.imagePath = [imagePath '\'];
save('LEVerSettings.mat','settings');
Figures.time = 1;
@@ -176,7 +170,7 @@ if ( ~isfield(CellHulls, 'imagePixels') )
fprintf('Adding Image Pixel Information...\n');
AddImagePixelsField();
fprintf('Image Information Added\n');
- save([matPath matFile],...
+ save([settings.matFilePath settings.matFile],...
'CellFamilies','CellHulls','CellTracks','HashedCells','Costs','CONSTANTS');
end
@@ -186,12 +180,4 @@ if (~strcmp(imageDataset,CONSTANTS.datasetName))
warndlg({'Image file name does not match .mat dataset name' '' 'LEVer may display cells incorectly!'},'Name mismatch','modal');
end
-% if(~isempty(Figures) && ishandle(Figures.cells.handle))
-% close(Figures.cells.handle);
-% end
-
-% Figures.time = 1;
-
-% LogAction(['Opened file ' matFile],[],[]);
-
end
diff --git a/src/MATLAB/ProcessNewborns.m b/src/MATLAB/ProcessNewborns.m
index 86fecd5b..5d8942d3 100644
--- a/src/MATLAB/ProcessNewborns.m
+++ b/src/MATLAB/ProcessNewborns.m
@@ -15,7 +15,7 @@ for i=1:size
%Get all the possible hulls that could have been connected
childHullID = CellTracks(childTrackID).hulls(1);
- if(childHullID>length(Costs)),continue,end
+ if(childHullID>length(Costs) || childHullID==0),continue,end
parentHullCandidates = find(Costs(:,childHullID));
if(isempty(parentHullCandidates)),continue,end
diff --git a/src/MATLAB/SaveData.m b/src/MATLAB/SaveData.m
index 03269839..f13d696f 100644
--- a/src/MATLAB/SaveData.m
+++ b/src/MATLAB/SaveData.m
@@ -8,7 +8,7 @@ global CellFamilies CellTracks HashedCells CONSTANTS Costs CellHulls Figures
if (exist('LEVerSettings.mat','file')~=0)
load('LEVerSettings.mat');
else
- settings.matPath = ['.\' CONSTANTS.datasetName '_LEVer_edits.mat'];
+ settings.matFilePath = '.\';
end
%let the user know that this might take a while
diff --git a/src/MATLAB/SaveDataAs.m b/src/MATLAB/SaveDataAs.m
index b0af3b07..685b8736 100644
--- a/src/MATLAB/SaveDataAs.m
+++ b/src/MATLAB/SaveDataAs.m
@@ -8,7 +8,7 @@ global CellFamilies CellTracks HashedCells CONSTANTS Costs CellHulls Figures
if (exist('LEVerSettings.mat','file')~=0)
load('LEVerSettings.mat');
else
- settings.matPath = ['.\' CONSTANTS.datasetName '_LEVer.mat'];
+ settings.matFilePath = '.\';
end
goodSave = 1;
@@ -16,21 +16,25 @@ goodSave = 1;
while(goodSave)
time = clock;
fprintf('Choose a folder to save current data...\n');
- [FileName,PathName,FilterIndex] = uiputfile('.mat','Save edits',...
+ if(strcmp(settings.matFilePath,'.\'))
+ [settings.matFile,settings.matFilePath,FilterIndex] = uiputfile('.mat','Save edits',...
+ [CONSTANTS.datasetName '_LEVer.mat']);
+ else
+ [settings.matFile,settings.matFilePath,FilterIndex] = uiputfile('.mat','Save edits',...
[CONSTANTS.datasetName ' edits ' num2str(time(1)) '-' num2str(time(2),'%02d') '-' num2str(time(3),'%02d') '_LEVer.mat']);
+ end
if (FilterIndex~=0)
- save([PathName FileName],...
+ save([settings.matFilePath settings.matFile],...
'CellFamilies','CellTracks','HashedCells','CONSTANTS','Costs','CellHulls');
goodSave = 0;
end
end
-settings.matPath = [FileName PathName];
save('LEVerSettings.mat','settings');
%no longer "dirty"
set(Figures.tree.menuHandles.saveMenu,'Enable','off');
set(Figures.cells.menuHandles.saveMenu,'Enable','off');
-LogAction(['Saved As: ' FileName],[],[]);
+LogAction(['Saved As: ' settings.matFile],[],[]);
end
diff --git a/src/MATLAB/SegAndTrack.m b/src/MATLAB/SegAndTrack.m
index e3f16b94..a80271ef 100644
--- a/src/MATLAB/SegAndTrack.m
+++ b/src/MATLAB/SegAndTrack.m
@@ -43,6 +43,8 @@ for i=1:step:numberOfImages
pause(1)
end
+fprintf('Please wait...');
+
cellSegments = GetDarkConnectedHulls(cellSegments);
save ( ['SegObjs_' CONSTANTS.datasetName '.mat'],'cellSegments');
WriteSegData(cellSegments,CONSTANTS.datasetName);
diff --git a/src/MATLAB/TrackSplitHulls.m b/src/MATLAB/TrackSplitHulls.m
index 8a6471d8..d5ba2212 100644
--- a/src/MATLAB/TrackSplitHulls.m
+++ b/src/MATLAB/TrackSplitHulls.m
@@ -2,6 +2,7 @@ function trackIDs = TrackSplitHulls(newHulls, forceTracks, COM)
global CONSTANTS CellHulls HashedCells
t = CellHulls(newHulls(1)).time;
+ trackIDs = [CellHulls(newHulls).trackID];
if ( t <= 1 )
return;
end
--
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