modified importExport and optimize for evalRC

ctc/importExport/importExport.m

@@ -71,7 +71,8 @@ MicroscopeData.WriterH5(im,'imageData',imd,'path',outfolder);
 function export(filename,outpath,gtFile)
 
 [~,exp,~]=fileparts(filename);
-tokens=regexp(exp,'(\D+)_(\d+)','tokens');
+exp=strrep(exp,'_training','');
+tokens=regexp(exp,'(.+)_(\d\d)','tokens');
 dsName=tokens{1}{1};
 dsID=tokens{1}{2};
 % strip off the _01 or _02 of the exp
@@ -81,11 +82,11 @@ else
     subdir='02_RES';
 end
 % exp=exp(1:end-3);
-outpath=fullfile(outpath,exp,subdir);
-if ~exist(outpath,'dir')
-    mkdir(outpath);
+outpath=fullfile(outpath,dsName,subdir);
+if exist(outpath,'dir')
+    rmdir(outpath,'s');
 end
-
+mkdir(outpath);
 fprintf(1,'exporting to folder %s\n',outpath);
 
 conn = database(filename, '','', 'org.sqlite.JDBC', 'jdbc:sqlite:');
@@ -189,6 +190,9 @@ if size(tids,1)>1
 else
     tidString=['(' jsonencode(tids(1)) ')'];
 end
+tDigits=ceil(log10(CONSTANTS.imageData.NumberOfFrames));
+tDigits=max(tDigits,3);
+digitFormat=['%0' num2str(tDigits) 'd'];
 for t=1:CONSTANTS.imageData.NumberOfFrames
     tImageLabels=[0]; % make sure no one gets over written 
     % NOTE -- add segCC asc as there is an issue with segCC's of -1 (from
@@ -210,7 +214,7 @@ for t=1:CONSTANTS.imageData.NumberOfFrames
     end
     im=setMissingTrackLabels(conn,im,tids,t);
     
-    fname=['mask' num2str(t-1,'%03d') '.tif'];
+    fname=['mask' num2str(t-1,digitFormat) '.tif'];
     im=uint16(im);
     if size(im,3)>1
         imwrite(im(:,:,1),fullfile(outpath,fname));
@@ -272,10 +276,14 @@ for i=1:length(idsMissing)
     cxInterp=round(cxInterp);
     if length(size(im))<3
         cxInterp=cxInterp(1:2);        
-    end
         cxInterp=min(cxInterp,[size(im,2);size(im,1)]);
         cxInterp=max(cxInterp,ones(length(cxInterp),1));
         im(cxInterp(2),cxInterp(1))=idsMissing(i);
+    else        
+        cxInterp=min(cxInterp,[size(im,2);size(im,1);size(im,3)]);
+        cxInterp=max(cxInterp,ones(length(cxInterp),1));
+        im(cxInterp(2),cxInterp(1),cxInterp(3))=idsMissing(i);        
+    end
 end
     
 

ctcOptimize/ctcEval1.m

@@ -9,43 +9,32 @@ path(path,fullfile(thisFolder,'..','ctc/importExport'));
 
 outfolder=fullfile(evalFolder,'eval');
 
-% results file
-if ~exist('./evalScore','dir')
-    mkdir('./evalScore');
-end
-
-idxParam=strfind(targetName,'_param');
-if ~isempty(idxParam)
-    strResults=targetName(1:idxParam-1);
-else
-    strResults=targetName;
-end
-strResults=fullfile('./evalScore',[strResults '_res.txt']);
-
-if exist(strResults,'file')
-    res=readtable(strResults,'delimiter',',');
-else
-    res=[];
-end
-
 fname=strDB;
 fname=strrep(fname,'_training','');
 
 tokens=regexp(targetName,'(.*)_training_(\d\d)','tokens');
+if isempty(tokens)
+    fprintf(2,'file %s training info not found - skipping \n',strDB);
+    return
+end
 dsName=tokens{1}{1};
 dsID=tokens{1}{2};
 
 importExport(strDB,outfolder, [])
 
 % copy over the ground truth
+gtTarget=fullfile(outfolder,dsName,[dsID '_GT']);
+if ~exist(gtTarget,'dir')    
     gtSource=fullfile(gtPath,['2d_' dsName '_training'],dsName,[dsID '_GT']);
     if ~exist(gtSource,'dir')
         gtSource=fullfile(gtPath,['3d_' dsName '_training'],dsName,[dsID '_GT']);
     end
     if ~exist(gtSource,'dir')
         fprintf(2,'ground truth not found, skipping : %s\n',gtSource);
+        return
+    end
+    copyfile(gtSource,gtTarget);
 end   
-copyfile(gtSource,fullfile(outfolder,targetName,[dsID '_GT']),'f');
 
 if ispc
     TRA='TRAMeasure.exe';
@@ -60,13 +49,13 @@ else
 end
 
 system([fullfile(exePath,TRA) ' ' ...
-    fullfile(outfolder,targetName) ' ' dsID ' > score.txt']);
+    fullfile(outfolder,dsName) ' ' dsID ' > score.txt']);
 
 system([fullfile(exePath,SEG) ' ' ...
-    fullfile(outfolder,targetName) ' ' dsID ' >> score.txt']);
+    fullfile(outfolder,dsName) ' ' dsID ' >> score.txt']);
 
 system([fullfile(exePath,DET) ' ' ...
-    fullfile(outfolder,targetName) ' ' dsID ' >>  score.txt']);
+    fullfile(outfolder,dsName) ' ' dsID ' >>  score.txt']);
 
 fid=fopen('score.txt');
 scoreTxt=fscanf(fid,'%s');
@@ -80,14 +69,9 @@ fprintf(1,'TRAmeasure:%f, SEGmeasure:%f, DETmeasure:%f\n',sx(1),sx(2),sx(3));
 [conn,CONSTANTS]=openDB(strDB);
 segParams=Read.getSegmentationParams(conn);
 
-if isempty(res)
 res=table(sx(1),sx(2),sx(3),{jsonencode(segParams)},'VariableNames',{'TRA','SEG','DET','segParams'});
-else
-    res=[res;sx(1),sx(2),sx(3),{jsonencode(segParams)}];
-end
 
 close(conn);
 
 
-writetable(res,strResults);
 

ctcOptimize/evalRC.m

+
+% eval all the datasets in the release folder
+ROOT='/f/leverjs/ctc2020rc'
+flist=dir(fullfile(ROOT,'**/*training*.LEVER'));
+results=[];
+for ff=1:length(flist)
+    
+    if strcmp(flist(ff).name(1:2),'BF')
+        continue
+    end
+    strDB=fullfile(flist(ff).folder,flist(ff).name);
+    
+    res=ctcEval1(strDB);
+    % drop the segparams
+    res=res(1,1:3);
+    res=[{datetime},{strDB},res];
+    res.Properties.VariableNames{1}='date-time';
+    res.Properties.VariableNames{2}='strDB';
+    results=[results;res]
+end
+writetable(results,'/f/leverjs/ctc2020rc/results.txt')
\ No newline at end of file