From b8078501148558abdce7b71540506f877af7b728 Mon Sep 17 00:00:00 2001
From: Eric Wait <eric@waitphoto.com>
Date: Fri, 8 Apr 2011 22:47:18 -0500
Subject: [PATCH] LEVer 4.1
---
.gitignore | 1 +
src/MATLAB/AddConstant.m | 21 +++++++++++++++++++
src/MATLAB/InitializeConstants.m | 35 ++++++++++++++++----------------
src/MATLAB/OpenData.m | 21 +++++++------------
src/MATLAB/SegAndTrack.m | 1 -
src/MATLAB/Segmentor.m | 9 ++++++--
src/MATLAB/TrackSplitHulls.m | 7 ++++++-
7 files changed, 59 insertions(+), 36 deletions(-)
create mode 100644 src/MATLAB/AddConstant.m
diff --git a/.gitignore b/.gitignore
index 85223e81..867e20ea 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
+*~
bin/*.c
bin/*.log
*.mat
diff --git a/src/MATLAB/AddConstant.m b/src/MATLAB/AddConstant.m
new file mode 100644
index 00000000..1f131407
--- /dev/null
+++ b/src/MATLAB/AddConstant.m
@@ -0,0 +1,21 @@
+function AddConstant(field,val,overWrite)
+% AddConstant(field,val,overWrite) will add the given field to the
+% CONSTANTS global variable and assign it the given value.
+% overWrite - is an optional flag {0,1} that will force the new value if
+% the field exists. Zero will keep the old value, One will overwrite the
+% current value
+
+%--Eric Wait
+
+global CONSTANTS
+
+if(~exist('overWrite','var'))
+ overWrite = 0;
+end
+
+if(~isfield(CONSTANTS,field))
+ CONSTANTS.(field) = val;
+elseif(overWrite)
+ CONSTANTS.(field) = val;
+end
+end
\ No newline at end of file
diff --git a/src/MATLAB/InitializeConstants.m b/src/MATLAB/InitializeConstants.m
index e61181fa..b82f31f5 100644
--- a/src/MATLAB/InitializeConstants.m
+++ b/src/MATLAB/InitializeConstants.m
@@ -2,23 +2,22 @@ function InitializeConstants()
%Set all constants here
%--Eric Wait
-global CONSTANTS
-CONSTANTS.imageAlpha = 1;
-CONSTANTS.maxRetrackDistSq = 40^2;
-CONSTANTS.maxPixelDistance = 40;
-CONSTANTS.maxCenterOfMassDistance = 80;
-CONSTANTS.minParentCandidateTimeFrame = 5;
-CONSTANTS.minParentHistoryTimeFrame = 5;
-CONSTANTS.minParentFuture = 5;
-CONSTANTS.minFamilyTimeFrame = 5;
-CONSTANTS.maxFrameDifference = 5;
-CONSTANTS.historySize = 50;
-CONSTANTS.clickMargin = 500;
-CONSTANTS.timeResolution = 10; %in frames per min
-CONSTANTS.dMaxConnectComponet = 40;
-CONSTANTS.dMaxCenterOfMass = 80;
-CONSTANTS.lookAhead = 2;
-CONSTANTS.minPlayer = 9;
-CONSTANTS.minMitosis = 30;
+AddConstant('imageAlpha',1.5);
+AddConstant('maxRetrackDistSq',40^2);
+AddConstant('maxPixelDistance',40);
+AddConstant('maxCenterOfMassDistance',80);
+AddConstant('minParentCandidateTimeFrame',5);
+AddConstant('minParentHistoryTimeFrame',5);
+AddConstant('minParentFuture',5);
+AddConstant('minFamilyTimeFrame',5);
+AddConstant('maxFrameDifference',5);
+AddConstant('historySize',50);
+AddConstant('clickMargin',500);
+AddConstant('timeResolution',10); %in frames per min
+AddConstant('dMaxConnectComponet',40);
+AddConstant('dMaxCenterOfMass',80);
+AddConstant('lookAhead',2);
+AddConstant('minPlayer',9);
+AddConstant('minMitosis',30);
end
\ No newline at end of file
diff --git a/src/MATLAB/OpenData.m b/src/MATLAB/OpenData.m
index a08b6921..7aad96c8 100644
--- a/src/MATLAB/OpenData.m
+++ b/src/MATLAB/OpenData.m
@@ -7,7 +7,7 @@ function opened = OpenData()
global Figures Colors CONSTANTS CellFamilies CellHulls HashedCells Costs CellTracks
if(isempty(Figures))
- fprintf('LEVer ver 4.0\n***DO NOT DISTRIBUTE***\n\n');
+ fprintf('LEVer ver 4.1\n***DO NOT DISTRIBUTE***\n\n');
end
if(exist('ColorScheme.mat','file'))
@@ -30,11 +30,6 @@ if (~exist('settings','var') || isempty(settings))
end
filterIndexImage = 0;
-matFile = [];
-matFilePath = [];
-imageFile = [];
-imagePath = [];
-imageDataset = [];
goodLoad = 0;
opened = 0;
@@ -56,7 +51,6 @@ if(~isempty(Figures))
end
oldCONSTANTS = CONSTANTS;
-InitializeConstants();
%find the first image
imageFilter = [settings.imagePath '*.TIF'];
@@ -70,7 +64,6 @@ while (filterIndexImage==0)
end
index = strfind(settings.imageFile,'_t');
-frameT = '001';
if (~isempty(index) && filterIndexImage~=0)
CONSTANTS.rootImageFolder = settings.imagePath;
imageDataset = settings.imageFile(1:(index(length(index))-1));
@@ -117,11 +110,11 @@ switch answer
end
catch
end
- CellFamilies = [];
- CellTracks = [];
- CellHulls = [];
- HashedCells = [];
- Costs = [];
+% CellFamilies = [];
+% CellTracks = [];
+% CellHulls = [];
+% HashedCells = [];
+% Costs = [];
rootImageFolder = CONSTANTS.rootImageFolder;
imageSignificantDigits = CONSTANTS.imageSignificantDigits;
@@ -160,7 +153,7 @@ switch answer
Figures.time = 1;
- LogAction(['Opened file ' matFile],[],[]);
+ LogAction(['Opened file ' settings.matFile],[],[]);
otherwise
return
end
diff --git a/src/MATLAB/SegAndTrack.m b/src/MATLAB/SegAndTrack.m
index a80271ef..ddb2799e 100644
--- a/src/MATLAB/SegAndTrack.m
+++ b/src/MATLAB/SegAndTrack.m
@@ -51,7 +51,6 @@ WriteSegData(cellSegments,CONSTANTS.datasetName);
fprintf(1,'\nDone\n');
-load ( ['SegObjs_' CONSTANTS.datasetName '.mat']);
fnameIn=['SegObjs_' CONSTANTS.datasetName '.txt'];
fnameOut=['Tracked_' CONSTANTS.datasetName '.txt'];
tSeg=toc;
diff --git a/src/MATLAB/Segmentor.m b/src/MATLAB/Segmentor.m
index 1e01b415..b14d8ca7 100644
--- a/src/MATLAB/Segmentor.m
+++ b/src/MATLAB/Segmentor.m
@@ -8,7 +8,7 @@ function objs = Segmentor(tStart,tLength,rootImageFolder,datasetName,imageAlpha,
%--Andrew Cohen
% global CONSTANTS
-se=strel('square',3);
+
objs=[];
if(ischar(tStart)),tStart = str2double(tStart);end
@@ -30,6 +30,11 @@ for t = tStart:tStart + tLength
fname=[rootImageFolder '\' datasetName '_t' frameT '.TIF'];
if(isempty(dir(fname))),continue,end
+ fprintf('%d, ', t);
+ if ( mod(t,20) == 0 )
+ fprintf('\n');
+ end
+
[im map]=imread(fname);
im=mat2gray(im);
@@ -44,7 +49,7 @@ for t = tStart:tStart + tLength
% bwNorm=GetNormalVectors(bwHalo,bwDark);
bwNorm=0*bwDark;
-
+ se=strel('square',3);
gd=imdilate(im,se);
ge=imerode(im,se);
ig=gd-ge;
diff --git a/src/MATLAB/TrackSplitHulls.m b/src/MATLAB/TrackSplitHulls.m
index d5ba2212..5ca54d55 100644
--- a/src/MATLAB/TrackSplitHulls.m
+++ b/src/MATLAB/TrackSplitHulls.m
@@ -2,7 +2,12 @@ function trackIDs = TrackSplitHulls(newHulls, forceTracks, COM)
global CONSTANTS CellHulls HashedCells
t = CellHulls(newHulls(1)).time;
- trackIDs = [CellHulls(newHulls).trackID];
+
+ trackIDs = [];
+ for i = 1:length(newHulls)
+ trackIDs = [trackIDs GetTrackID(newHulls(i))];
+ end
+
if ( t <= 1 )
return;
end
--
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