added exportSegmentation to batch processing

.gitignore

@@ -2,3 +2,4 @@
 *.txt
 *.mat
 *.asv
+ctc/importExport/generatedBats/*.bat

ctc/importExport/exportAll.m

 % exportAll.m
 % ROOT='g:\leverjs\ctc2018_finalResults\';
-ROOT='g:\leverjs\ctc2020_final';
+ROOT='f:\leverjs\ctc2020_final';
 gtPath='\\bioimage32.coe.drexel.edu\g\gRaw\ctc2020\';
-outfolder='g:\leverjs\ctc2020_sw';
+outfolder='f:\leverjs\ctc2020_sw';
 flist=dir(fullfile(ROOT,'*\*challenge*.LEVER'));
 
 for ff=1:length(flist)
@@ -11,6 +11,7 @@ for ff=1:length(flist)
     gtFile=findGT(strDB,gtPath);
     fprintf(1,'%s (%s) \n',strDB,gtFile)
     
-    importExport(strDB,outfolder);
+    importExport(strDB,outfolder,gtFile);
+    exportSegmentation(strDB,outfolder);
 end
     
\ No newline at end of file

ctc/importExport/exportSegmentation.m

@@ -19,18 +19,24 @@ fprintf(1,'importExport elapsed time=%3.1f :: %s,%s\n',y,filename,outpath);
 function export(filename,outpath)
 
 [~,exp,~]=fileparts(filename);
+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 exp(end)=='1'
+if strcmp(dsID,'01')
     subdir='01_RES';
 else
     subdir='02_RES';
 end
+
 exp=exp(1:end-3);
-outpath=fullfile(outpath,exp,'CSB',subdir);
-if ~exist(outpath,'dir')
-    mkdir(outpath);
+outpath=fullfile(outpath,dsName,'CSB',subdir);
+if exist(outpath,'dir')
+    rmdir(outpath,'s');
 end
-
+mkdir(outpath);
 fprintf(1,'exporting CSB data to folder %s\n',outpath);
 
 conn = database(filename, '','', 'org.sqlite.JDBC', 'jdbc:sqlite:');

ctc/importExport/generatedBats/processCSB.bat

-@echo off
-REM processCSB
-REM generates all segmentation results (not just ground truth subset) from
-REM leverjs .LEVER files
-REM usage : processBatch leverFile
-REM     assumes tif images are ../
-REM     generates lever .h5 images in ./temporaryImages
-REM     
-
-if not exist %1 (
-    echo %1 -- lever file does not exist. IMPORTANT -- you must run the tracking benchmark before running the CSB output
-    exit /b
-)
-echo.
-echo *** exporting CSB results
-.\exportSegmentation %1 ..\ 
-echo.
-
-

ctc/importExport/goGenerateBats.m

 %  generate processing table
-leverRoot='.\leverData';
-flist=dir(fullfile(leverRoot,'*.LEVER'));
+leverRoot1='g:\leverjs\ctc2020\';
+leverRoot2='f:\leverjs\ctc2020\';
+% flist=[dir(fullfile(leverRoot1,'**\*challenge*.LEVER'));dir(fullfile(leverRoot2,'**\*challenge*.LEVER'))];
 imageRoot='..\';
+gtPath='\\bioimage32.coe.drexel.edu\g\gRaw\ctc2020\';
+
 rgProcess=[];
 rgp=[];
-batOutFolder='./';
+batOutFolder='./generatedBats';
 if ~exist(batOutFolder,'dir')
     mkdir(batOutFolder);
 end
 for ff=1:length(flist)
-    leverFile=fullfile(flist(ff).folder,flist(ff).name);
+    leverFile=fullfile('./leverData',flist(ff).name);
     expname=flist(ff).name(1:end-length('_01.LEVER'));
+    expname=strrep(expname,'_challenge','');
     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');
+    gtFile=findGT(fullfile(flist(ff).folder,flist(ff).name),gtPath);    
+    rp.leverFile=['"' leverFile '"'];        
+    rp.imagePath=['"' fullfile('..',expname,expnumber) '"'];
+    if ~isempty(gtFile)
+        rp.gtPath=['"' fullfile('..',expname,[expnumber '_GT']) '"'];
+    else
+        rp.gtPath='';
     end
+    if ~isempty(strfind(expname,'TRIF'))
+        rp.nProcs='2';
+        rp.gtPath=['"' fullfile('..',expname,[expnumber '_GT']) '"'];
+    else
+        rp.nProcs='';
     end
-    
-    rp.leverFile=leverFile;
-    rp.imagePath=imagePath;
-    rp.gtPath=gtPath;
     rgProcess=[rgProcess,rp];
     
-    rgp=[ rgp; {leverFile,imagePath,gtPath}];
+    rgp=[ rgp; {rp.leverFile,rp.imagePath,rp.gtPath,rp.nProcs}];
     
     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
+    
+    fprintf(fid,'processBatch.bat %s %s %s %s\n',rp.imagePath,rp.leverFile,rp.gtPath,rp.nProcs);
     fclose(fid);
 end
    
\ No newline at end of file

ctc/importExport/importExport.m

@@ -82,7 +82,7 @@ if strcmp(dsID,'01')
 else
     subdir='02_RES';
 end
-% exp=exp(1:end-3);
+
 outpath=fullfile(outpath,dsName,subdir);
 if exist(outpath,'dir')
     rmdir(outpath,'s');

ctc/importExport/processBatch.bat

@@ -7,6 +7,7 @@ REM     assumes tif images are ../
 REM     generates lever .h5 images in ./temporaryImages
 REM     
 echo.
+
 echo *** IMPORT processing %1 (tiffs), lever file=%2, groundTruth=%3 nProcessors=%4
 .\ctcImportExport\importExport.exe %1 .\temporaryImages
 echo *** batch segmentation starting
@@ -15,6 +16,9 @@ echo *** resegAndTrack starting
 .\node.exe .\leverjs\leverjs\resegAndTrackDataset.js %2  resegAll 1 "{}" 
 echo *** exporting results
 .\ctcImportExport\importExport.exe %2 .\ %3
+echo *** exporting CSB results
+.\ctcImportExport\exportSegmentation %2 .\
+
 echo.