updated importExport with new label scheme, exportAll

.gitignore

 *.tif
 *.txt
 *.mat
+*.asv

ctc/importExport/exportAll.m

 % exportAll.m
-ROOT='g:\leverjs\ctc2018_finalResults\';
-outfolder='g:\leverjs\ctc2018_finalResuls\results';
-flist=dir(fullfile(ROOT,'**\*.LEVER'));
+% ROOT='g:\leverjs\ctc2018_finalResults\';
+ROOT='\\bioimage32.coe.drexel.edu\f\leverjs\ctc2020rc';
+gtPath='\\bioimage32.coe.drexel.edu\g\gRaw\ctc2020\';
+outfolder='g:\leverjs\ctc2020_finalResults\results';
+flist=dir(fullfile(ROOT,'*\*challenge*.LEVER'));
 
 for ff=1:length(flist)
-    importExport(fullfile(flist(ff).folder,flist(ff).name),outfolder);
+    
+    strDB=fullfile(flist(ff).folder,flist(ff).name);
+    gtFile=findGT(strDB,gtPath);
+    fprintf(1,'%s (%s) \n',strDB,gtFile)
+    
+    importExport(strDB,outfolder);
 end
     
\ No newline at end of file

ctc/importExport/findGT.m

+function gtFile=findGT(strDB,gtPath)
+[folderPath,fullname,~]=fileparts(strDB);
+dsName=fullname;
+dsID=fullname(end-1:end);
+fullname=fullname(1:end-3);
+dsName=strrep(dsName,'_challenge','');
+dsName=dsName(1:end-3);
+folderTree=split(folderPath,filesep);
+xd=folderTree{end};
+gtFile=fullfile(gtPath,[xd '_' fullname],dsName,[dsID '_GT']);
+if ~exist(gtFile,'file')
+    gtFile=[];
+end

ctc/importExport/goGenerateBats.m

+%  generate processing table
+leverRoot='.\leverData';
+flist=dir(fullfile(leverRoot,'*.LEVER'));
+imageRoot='..\';
+rgProcess=[];
+rgp=[];
+batOutFolder='./';
+if ~exist(batOutFolder,'dir')
+    mkdir(batOutFolder);
+end
+for ff=1:length(flist)
+    leverFile=fullfile(flist(ff).folder,flist(ff).name);
+    expname=flist(ff).name(1:end-length('_01.LEVER'));
+    expnumber=flist(ff).name(end-length('01.LEVER')+1:end-length('.LEVER'));
+    gtPath='';
+    imagePath=fullfile(imageRoot,expname,expnumber);
+    if ~exist(imagePath)
+        imagePath=fullfile(imageRoot,expname,expname,expnumber);
+        if ~exist(imagePath)
+            fprintf(2,'image data not found! imagePath=%s\n',imagePath);
+        end
+    end
+    if exist([imagePath '_GT'],'dir')
+        gtPath=[imagePath '_GT'];
+        gtPath=fullfile(gtPath,'TRA','man_track000.tif');
+        if ~exist(gtPath,'file')
+            fprintf(2,'ERROR - bad gtPath file does not exist\n');
+        end
+    end
+    
+    rp.leverFile=leverFile;
+    rp.imagePath=imagePath;
+    rp.gtPath=gtPath;
+    rgProcess=[rgProcess,rp];
+    
+    rgp=[ rgp; {leverFile,imagePath,gtPath}];
+    
+    outfile=fullfile(batOutFolder,[expname '_' expnumber '.bat']);
+    fid=fopen(outfile,'w');
+    if strcmp(gtPath,'')
+        fprintf(fid,'processBatch.bat "%s", "%s"\n',imagePath,leverFile);
+    else
+        fprintf(fid,'processBatch.bat "%s", "%s", "%s"\n',imagePath,leverFile,gtPath);     
+    end
+    fclose(fid);
+end
+   
\ No newline at end of file

ctc/importExport/importExport.m

@@ -74,6 +74,7 @@ function export(filename,outpath,gtFile)
 exp=strrep(exp,'_training','');
 tokens=regexp(exp,'(.+)_(\d\d)','tokens');
 dsName=tokens{1}{1};
+dsName=strrep(dsName,'_challenge','');
 dsID=tokens{1}{2};
 % strip off the _01 or _02 of the exp
 if strcmp(dsID,'01')
@@ -112,7 +113,7 @@ end
 % lbgep=[label, begin, end, parent]
 lbep=[];
 for i=1:length(tids)
-    label=tids(i);
+    label=i; %tids(i);
     cmd=['select min(time),max(time) from tblCells where trackID=' num2str(tids(i))];
     q=ljsFetch(conn,cmd);
     if isempty(q) || 0==size(q,1)
@@ -176,6 +177,15 @@ if 0==size(lbep,1)
     return;
 end
 
+% reset parent trackID to label
+for i=1:size(lbep,1)
+    if 0==lbep(i,4)
+        continue
+    end
+    idxParentLabel=find([lbep(:,5)]==lbep(i,4));
+    lbep(i,4)=lbep(idxParentLabel,1);
+end
+
 if any(lbep(:,2)>lbep(:,3))
     fprintf(2,'bad begin end timing detected ACK\n');
 end
@@ -210,7 +220,9 @@ for t=1:CONSTANTS.imageData.NumberOfFrames
         else
             idx=sub2ind(szImage,iCell.pts(:,2),iCell.pts(:,1));
         end
-        im(idx)=iCell.trackID;
+        idxLabel=find(tids(:,1)==iCell.trackID);
+        im(idx)=tids(idxLabel,2);
+%         im(idx)=iCell.trackID;
     end
     im=setMissingTrackLabels(conn,im,tids,t);
     
@@ -250,7 +262,7 @@ for i=1:length(idsMissing)
     idx0=find(trackTime==t-1);
     idx1=find(trackTime==t+1);
     if isempty(idx0) && isempty(idx1)
-        fprintf(2,'neither t-1 nor t+1 available for interp! guessing...\n');
+        fprintf(2,'neither t-1 nor t+1 available for interp! long range interp...\n');
         tt=trackTime-t;
         tt(tt<0)=[];
         tt1=min(tt);
@@ -274,15 +286,17 @@ for i=1:length(idsMissing)
     w1=1-(trackTime(idx1)-t)/(trackTime(idx1)-trackTime(idx0));
     cxInterp=cx{idx0}.*w0 + cx{idx1} .* w1 ;
     cxInterp=round(cxInterp);
+    idxLabel=find(tids(:,1)==idsMissing(i));
+        
     if length(size(im))<3
         cxInterp=cxInterp(1:2);        
         cxInterp=min(cxInterp,[size(im,2);size(im,1)]);
         cxInterp=max(cxInterp,ones(length(cxInterp),1));
-        im(cxInterp(2),cxInterp(1))=idsMissing(i);
+        im(cxInterp(2),cxInterp(1))=tids(idxLabel,2);
     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);        
+        im(cxInterp(2),cxInterp(1),cxInterp(3))=tids(idxLabel,2);        
     end
 end