From 232053bb87933fbba675991b640a653e5af774d6 Mon Sep 17 00:00:00 2001
From: Eric Wait <eric@waitphoto.com>
Date: Fri, 8 Apr 2011 22:49:01 -0500
Subject: [PATCH] LEVer 4.2
---
bin/CompileLEVer.m | 5 +++--
src/MATLAB/AddFields.m | 12 +++++++++++
src/MATLAB/AddHull.m | 2 +-
src/MATLAB/ContextChangeParent.m | 2 +-
src/MATLAB/CreateContextMenuCells.m | 33 +++++++++++------------------
src/MATLAB/CreateContextMenuTree.m | 4 ++--
src/MATLAB/CreateMenuBar.m | 2 +-
src/MATLAB/GetDarkConnectedHulls.m | 8 +++----
src/MATLAB/GetTrackID.m | 29 ++++++++++++++++---------
src/MATLAB/OpenData.m | 3 ++-
src/MATLAB/SegAndTrack.m | 8 ++++---
src/MATLAB/Segmentor.m | 7 +++---
src/MATLAB/TestDataIntegrity.m | 33 +++++++++++++++--------------
src/MATLAB/WriteSegData.m | 2 +-
14 files changed, 83 insertions(+), 67 deletions(-)
create mode 100644 src/MATLAB/AddFields.m
diff --git a/bin/CompileLEVer.m b/bin/CompileLEVer.m
index aa9094db..0abcfb46 100644
--- a/bin/CompileLEVer.m
+++ b/bin/CompileLEVer.m
@@ -1,5 +1,6 @@
-mcc -m ../LEVer.m
-mcc -m ../Segmentor.m
+mcc -m ..\LEVer.m
+mcc -m ..\Segmentor.m
+system('copy Segmentor.exe ..\.');
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/AddFields.m b/src/MATLAB/AddFields.m
new file mode 100644
index 00000000..d6bd5763
--- /dev/null
+++ b/src/MATLAB/AddFields.m
@@ -0,0 +1,12 @@
+function AddFields()
+
+global HashedCells
+
+if(~isfield([HashedCells{:}],'editedFlag'))
+ for i=1:length(HashedCells)
+ for j = 1:length(HashedCells{i})
+ HashedCells{i}(j).editedFlag = 0;
+ end
+ end
+end
+end
\ No newline at end of file
diff --git a/src/MATLAB/AddHull.m b/src/MATLAB/AddHull.m
index 090b6e82..48f4a5b5 100644
--- a/src/MATLAB/AddHull.m
+++ b/src/MATLAB/AddHull.m
@@ -17,7 +17,7 @@ if(~isempty(trackID))
% Try to split the existing hull
History('Push');
try
- newTracks = SplitHull(hullID,num+1);%adding one to the number so that the original hull is accounted for
+ newTracks = SplitHull(hullID,num);
if(isempty(newTracks))
msgbox(['Unable to split ' num2str(trackID) ' any further in this frame'],'Unable to Split','help','modal');
return
diff --git a/src/MATLAB/ContextChangeParent.m b/src/MATLAB/ContextChangeParent.m
index 83c0db2d..e38608b4 100644
--- a/src/MATLAB/ContextChangeParent.m
+++ b/src/MATLAB/ContextChangeParent.m
@@ -18,7 +18,7 @@ if(CellTracks(newParentID).startTime > time)
msgbox(['Parent ' num2str(newParentID) ' comes after ' num2str(trackID) ' consider a different edit.'],'Parent Change','warn');
return
elseif(CellTracks(trackID).endTime < CellTracks(newParentID).startTime)
- msgbox(['Sibling ' num2str(trackID) ' exists completely before ' num2str(newParentID) ' consider a rename instead.'],'Parent Change','warn');
+ msgbox(['Sister Cell ' num2str(trackID) ' exists completely before ' num2str(newParentID) ' consider a rename instead.'],'Parent Change','warn');
return
end
diff --git a/src/MATLAB/CreateContextMenuCells.m b/src/MATLAB/CreateContextMenuCells.m
index 426a271c..52b6dca5 100644
--- a/src/MATLAB/CreateContextMenuCells.m
+++ b/src/MATLAB/CreateContextMenuCells.m
@@ -32,28 +32,23 @@ uimenu(Figures.cells.contextMenuHandle,...
% 'CallBack', @changeParent);
addHull = uimenu(Figures.cells.contextMenuHandle,...
- 'Label', 'Add Hull',...
+ 'Label', 'Add Segmentation',...
'Separator', 'on');
uimenu(addHull,...
- 'Label', 'Number of Hulls to add');
-
-uimenu(addHull,...
- 'Label', '1',...
- 'Separator', 'on',...
- 'CallBack', @addHull1);
+ 'Label', 'Number of Cells');
uimenu(addHull,...
'Label', '2',...
- 'CallBack', @addHull2);
+ 'CallBack', @addHull1);
uimenu(addHull,...
'Label', '3',...
- 'CallBack', @addHull3);
+ 'CallBack', @addHull1);
uimenu(addHull,...
'Label', '4',...
- 'CallBack', @addHull4);
+ 'CallBack', @addHull3);
uimenu(addHull,...
'Label', 'Other',...
@@ -61,7 +56,7 @@ uimenu(addHull,...
'CallBack', @addHullOther);
uimenu(Figures.cells.contextMenuHandle,...
- 'Label', 'Remove Hull',...
+ 'Label', 'Remove Cell',...
'CallBack', @removeHull);
uimenu(Figures.cells.contextMenuHandle,...
@@ -141,7 +136,7 @@ if(isempty(trackID)),return,end
% answer = inputdlg({['Enter new sibling of ' num2str(trackID)],'Enter Time of Mitosis'},...
% 'Add Mitosis',1,{'',num2str(Figures.time)});
-answer = inputdlg({['Enter new sibling of ' num2str(trackID)]},...
+answer = inputdlg({['Enter new sister of cell' num2str(trackID)]},...
'Add Mitosis',1,{''});
if(isempty(answer)),return,end
@@ -154,11 +149,11 @@ if(siblingTrack>length(CellTracks) || isempty(CellTracks(siblingTrack).hulls))
return
end
if(CellTracks(siblingTrack).endTime<time || siblingTrack==trackID)
- msgbox([answer(1) ' is not a valid sibling'],'Not a valid sibling','error');
+ msgbox([answer(1) ' is not a valid sister cell'],'Not a valid sister cell','error');
return
end
if(CellTracks(trackID).startTime>time)
- msgbox([num2str(trackID) ' exists after ' answer(1)],'Not a valid child','error');
+ msgbox([num2str(trackID) ' exists after ' answer(1)],'Not a valid daughter cell','error');
return
end
if(~isempty(CellTracks(siblingTrack).timeOfDeath) && CellTracks(siblingTrack).timeOfDeath<=time)
@@ -201,7 +196,7 @@ elseif(CellTracks(siblingTrack).startTime==time && CellTracks(trackID).startTime
elseif(CellTracks(siblingTrack).startTime==time && CellTracks(trackID).startTime==time)
valid = 0;
while(~valid)
- answer = inputdlg({'Enter parent of these siblings '},'Parent',1,{''});
+ answer = inputdlg({'Enter parent of these daughter cells '},'Parent',1,{''});
if(isempty(answer)),return,end
parentTrack = str2double(answer(1));
@@ -297,10 +292,6 @@ if(isempty(trackID)),return,end
ContextChangeParent(trackID,Figures.time);
end
-function addHull1(src,evnt)
-AddHull(1);
-end
-
function addHull2(src,evnt)
AddHull(2);
end
@@ -314,7 +305,7 @@ AddHull(4);
end
function addHullOther(src,evnt)
-num = inputdlg('Enter Number of Hulls to Add','Add Hulls',1,{'1'});
+num = inputdlg('Enter Number of Cells Present','Add Hulls',1,{'1'});
if(isempty(num)),return,end;
num = str2double(num(1));
AddHull(num);
@@ -352,7 +343,7 @@ if(isempty(CellFamilies(Figures.tree.familyID).tracks))
end
DrawTree(Figures.tree.familyID);
DrawCells();
- msgbox(['By removing this hull, the complete tree is no more. Displaying tree rooted at ' num2str(CellFamilies(i).rootTrackID) ' instead'],'Displaying Tree','help');
+ msgbox(['By removing this cell, the complete tree is no more. Displaying clone rooted at ' num2str(CellFamilies(i).rootTrackID) ' instead'],'Displaying Tree','help');
return
end
diff --git a/src/MATLAB/CreateContextMenuTree.m b/src/MATLAB/CreateContextMenuTree.m
index 25cb6f83..cad163c6 100644
--- a/src/MATLAB/CreateContextMenuTree.m
+++ b/src/MATLAB/CreateContextMenuTree.m
@@ -140,7 +140,7 @@ trackID = get(gco,'UserData');
time = get(gca,'CurrentPoint');
time = round(time(1,2));
-answer = inputdlg({'Enter Time of Mitosis',['Enter new sibling of ' num2str(trackID)]},...
+answer = inputdlg({'Enter Time of Mitosis',['Enter new sister cell of ' num2str(trackID)]},...
'Add Mitosis',1,{num2str(time),''});
if(isempty(answer)),return,end
@@ -153,7 +153,7 @@ if(siblingTrack>length(CellTracks) || isempty(CellTracks(siblingTrack).hulls))
return
end
if(CellTracks(trackID).startTime>time)
- msgbox([num2str(trackID) ' exists after ' answer(1)],'Not a valid child','error');
+ msgbox([num2str(trackID) ' exists after ' answer(1)],'Not a valid daughter cell','error');
return
end
diff --git a/src/MATLAB/CreateMenuBar.m b/src/MATLAB/CreateMenuBar.m
index f0a735a2..5f33810c 100644
--- a/src/MATLAB/CreateMenuBar.m
+++ b/src/MATLAB/CreateMenuBar.m
@@ -97,7 +97,7 @@ labelsMenu = uimenu(...
siblingsMenu = uimenu(...
'Parent', viewMenu,...
- 'Label', 'Show Sibling Relationships',...
+ 'Label', 'Show Sister Cell Relationships',...
'HandleVisibility', 'callback',...
'Callback', @toggleSiblings,...
'Checked', 'off',...
diff --git a/src/MATLAB/GetDarkConnectedHulls.m b/src/MATLAB/GetDarkConnectedHulls.m
index 6ffd5ffc..2d2e2dd0 100644
--- a/src/MATLAB/GetDarkConnectedHulls.m
+++ b/src/MATLAB/GetDarkConnectedHulls.m
@@ -36,10 +36,10 @@ end
function objsSegment=GetDistances(objsSegment,HashedHulls,t1,t2)
- bwHalo1=GetHalo(t1);
- bwHalo2=GetHalo(t2);
- bwCombo=GetCombo(bwHalo1,bwHalo2,objsSegment,HashedHulls,t1,t2);
- LCombo=bwlabel(bwCombo);
+% bwHalo1=GetHalo(t1);
+% bwHalo2=GetHalo(t2);
+% bwCombo=GetCombo(bwHalo1,bwHalo2,objsSegment,HashedHulls,t1,t2);
+% LCombo=bwlabel(bwCombo);
for i=1:length(HashedHulls{t1})
hi=HashedHulls{t1}(i);
ipix=objsSegment(hi).indPixels;
diff --git a/src/MATLAB/GetTrackID.m b/src/MATLAB/GetTrackID.m
index 8da8ff2a..260906d7 100644
--- a/src/MATLAB/GetTrackID.m
+++ b/src/MATLAB/GetTrackID.m
@@ -1,18 +1,27 @@
-function trackID = GetTrackID(hullID)
+function trackIDs = GetTrackID(hullIDs,time)
%Given a hull ID a track ID will be returned or [] if none found
%--Eric Wait
global CellHulls HashedCells
-trackID = [];
+trackIDs = [];
-if(hullID>length(CellHulls))
- return
+if(~exist('time','var'))
+ for i=1:length(hullIDs)
+ if(hullIDs(i)>length(CellHulls))
+ continue
+ else
+ hullTime = CellHulls(hullIDs(i)).time;
+ hashedCellIndex = [HashedCells{hullTime}.hullID] == hullIDs(i);
+ if(isempty(hashedCellIndex)),continue,end
+ trackIDs = [trackIDs HashedCells{hullTime}(hashedCellIndex).trackID];
+ end
+ end
else
- hullTime = CellHulls(hullID).time;
- hashedCellIndex = [HashedCells{hullTime}.hullID] == hullID;
- if(isempty(hashedCellIndex)),return,end
- trackID = HashedCells{hullTime}(hashedCellIndex).trackID;
-end
-end
+ if(time>length(HashedCells))
+ return
+ else
+ trackIDs = [HashedCells{time}(ismember([HashedCells{time}.hullID],hullIDs)).trackID];
+ end
+end
\ No newline at end of file
diff --git a/src/MATLAB/OpenData.m b/src/MATLAB/OpenData.m
index 7aad96c8..9a164f78 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 4.1\n***DO NOT DISTRIBUTE***\n\n');
+ fprintf('LEVer ver 4.2\n***DO NOT DISTRIBUTE***\n\n');
end
if(exist('ColorScheme.mat','file'))
@@ -141,6 +141,7 @@ switch answer
fprintf(['New file saved as:\n' CONSTANTS.datasetName '_LEVer.mat']);
goodLoad = 1;
elseif(exist('CellHulls','var'))
+ TestDataIntegrity(1);
goodLoad = 1;
else
errordlg('Data either did not load properly or is not the right format for LEVer.');
diff --git a/src/MATLAB/SegAndTrack.m b/src/MATLAB/SegAndTrack.m
index ddb2799e..e597b55c 100644
--- a/src/MATLAB/SegAndTrack.m
+++ b/src/MATLAB/SegAndTrack.m
@@ -24,6 +24,8 @@ for timeStart=1:step:numberOfImages
system(['start Segmentor ' num2str(timeStart) ' ' num2str(step-1) ' "' ...
CONSTANTS.rootImageFolder(1:end-1) '" ' CONSTANTS.datasetName ' ' ...
num2str(CONSTANTS.imageAlpha) ' ' num2str(CONSTANTS.imageSignificantDigits) ' && exit']);
+ %use line below instead of the 3 lines above for non-parallel or to debug
+% Segmentor(timeStart,step-1,CONSTANTS.rootImageFolder(1:end-1),CONSTANTS.datasetName,CONSTANTS.imageAlpha,CONSTANTS.imageSignificantDigits);
end
for i=1:step:numberOfImages
@@ -46,13 +48,13 @@ end
fprintf('Please wait...');
cellSegments = GetDarkConnectedHulls(cellSegments);
-save ( ['SegObjs_' CONSTANTS.datasetName '.mat'],'cellSegments');
+save ( ['.\segmentationData\SegObjs_' CONSTANTS.datasetName '.mat'],'cellSegments');
WriteSegData(cellSegments,CONSTANTS.datasetName);
fprintf(1,'\nDone\n');
-fnameIn=['SegObjs_' CONSTANTS.datasetName '.txt'];
-fnameOut=['Tracked_' CONSTANTS.datasetName '.txt'];
+fnameIn=['.\segmentationData\SegObjs_' CONSTANTS.datasetName '.txt'];
+fnameOut=['.\segmentationData\Tracked_' CONSTANTS.datasetName '.txt'];
tSeg=toc;
%% Tracking
diff --git a/src/MATLAB/Segmentor.m b/src/MATLAB/Segmentor.m
index b14d8ca7..8f130880 100644
--- a/src/MATLAB/Segmentor.m
+++ b/src/MATLAB/Segmentor.m
@@ -30,10 +30,7 @@ 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
+ fprintf('%d%%...',ceil((t-tStart)/tLength*100));
[im map]=imread(fname);
im=mat2gray(im);
@@ -254,4 +251,6 @@ end
fileName = ['.\segmentationData\objs_' num2str(tStart) '.mat'];
if(isempty(dir('.\segmentationData'))),system('mkdir .\segmentationData');end
save(fileName,'objs');
+
+fprintf('\tDone\n');
end
\ No newline at end of file
diff --git a/src/MATLAB/TestDataIntegrity.m b/src/MATLAB/TestDataIntegrity.m
index 1f0aedd4..7d3088eb 100644
--- a/src/MATLAB/TestDataIntegrity.m
+++ b/src/MATLAB/TestDataIntegrity.m
@@ -1,6 +1,6 @@
function TestDataIntegrity(correct)
%TestDataIntegrity(correct) tests to make sure that the database is consistant.
-%Takes the CellTracks as the most accurate. If correct=='yes', this
+%Takes the CellTracks as the most accurate. If correct==1, this
%function will attempt to correct the error using the data from CellTracks
%***USE SPARINGLY, TAKES A LOT OF TIME***
@@ -10,6 +10,7 @@ global CellTracks CellHulls CellFamilies HashedCells
hullsList = [];
fprintf('Checking CellTracks...');
+AddFields();
progress = 0;
iterations = length(CellTracks);
for i=1:length(CellTracks)
@@ -117,21 +118,21 @@ end
%% check CellHulls
% if(length(hullsList)~=length(find([CellHulls.deleted]==0)))
missingHulls = find(ismember(find([CellHulls.deleted]==0),hullsList')==0);
-% if(~isempty(missingHulls))
-% if(correct)
-% progress = 0;
-% iterations = length(missingHulls);
-% for i=1:length(missingHulls)
-% progress = progress+1;
-% Progressbar(progress/iterations);
-% if(isempty(CellHulls(missingHulls(i)).points))
-% CellHulls(missingHulls(i)).deleted = 1;
-% end
-% end
-% else
-% error('HullsList ~= CellHulls');
-% end
-% end
+if(~isempty(missingHulls))
+ if(correct)
+ progress = 0;
+ iterations = length(missingHulls);
+ for i=1:length(missingHulls)
+ progress = progress+1;
+ Progressbar(progress/iterations);
+ if(isempty(CellHulls(missingHulls(i)).points))
+ CellHulls(missingHulls(i)).deleted = 1;
+ end
+ end
+ else
+ error('HullsList ~= CellHulls');
+ end
+end
Progressbar(1);%clear it out
fprintf('\nDone\n');
diff --git a/src/MATLAB/WriteSegData.m b/src/MATLAB/WriteSegData.m
index fd44da27..6c285d4f 100644
--- a/src/MATLAB/WriteSegData.m
+++ b/src/MATLAB/WriteSegData.m
@@ -7,7 +7,7 @@ HashedHulls=cell(th,1);
for n=1:length(objsSegment)
HashedHulls{objsSegment(n).t}=[HashedHulls{objsSegment(n).t};n];
end
-fname=['SegObjs_' DatasetName '.txt'];
+fname=['.\segmentationData\SegObjs_' DatasetName '.txt'];
fid=fopen(fname,'wt');
fprintf(fid,'%d %d\n',th,length(objsSegment) );
for i=1:length(HashedHulls)
--
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