changed importExport to use ljsFetch (2019b), added eval1

ctc/importExport/importExport.m

@@ -113,14 +113,14 @@ lbep=[];
 for i=1:length(tids)
     label=tids(i);
     cmd=['select min(time),max(time) from tblCells where trackID=' num2str(tids(i))];
-    q=fetch(conn,cmd);
-    if isempty(q)
+    q=ljsFetch(conn,cmd);
+    if isempty(q) || 0==size(q,1)
         continue
     end
     
     tBegin=q{1};
     tEnd=q{2};
-    if strcmp(tBegin,'null') || strcmp(tEnd,'null')
+    if isempty(tBegin) || isempty(tEnd) || strcmp(tBegin,'null') || strcmp(tEnd,'null')
         continue
     end  
     % find our parent
@@ -128,14 +128,14 @@ for i=1:length(tids)
     cmd=['select cellID,trackID,time from tblCells inner join tblFamilies on '...
         ' cellID=cellID_parent where (cellID_child1=' num2str(tids(i)) ...
         ' or cellID_child2=' num2str(tids(i)) ') and cellID_child2 is not null'];
-    q=fetch(conn,cmd);
-    if isempty(q)
+    q=ljsFetch(conn,cmd);
+    if isempty(q) || size(q,1)==0
         parent=0;
     else
         parent=q{2};
         cmd=['select max(time) from tblCells where trackID=' num2str(parent)];
-        q=fetch(conn,cmd);
-        if ~isempty(q)
+        q=ljsFetch(conn,cmd);
+        if ~isempty(q) || 0==size(q,1)
             if q{1}>tBegin
                 fprintf(2,'found bad mitosis -- skipping\n');
                 parent=0;
@@ -147,8 +147,8 @@ for i=1:length(tids)
     cmd=['select cellID,trackID,time from tblCells inner join tblFamilies on '...
         ' (cellID=cellID_child2 or cellID=cellID_child1) AND cellID_child2 is not null where cellID_parent IN '...
         ' (select cellID from tblCells where trackID=' num2str(tids(i)) ')'];
-    q=fetch(conn,cmd);
-    if isempty(q)
+    q=ljsFetch(conn,cmd);
+    if isempty(q) || 0==size(q,1)
         childIDs=[0,0];
     elseif 2==size(q,1)
         childIDs=[q{1,1},q{2,1}];
@@ -195,7 +195,7 @@ for t=1:CONSTANTS.imageData.NumberOfFrames
     % splits via the tblEnsemble) covering up other segmentations
     cmd=['select cellID,trackID from tblCells where time=' num2str(t)...
         ' and trackID IN ' tidString 'order by segCC asc'];
-    Q=fetch(conn,cmd);
+    Q=ljsFetch(conn,cmd);
     ctID=cell2mat(Q);
     
     im=zeros(szImage);
@@ -240,7 +240,7 @@ end
 for i=1:length(idsMissing)
     % get the centroids
     cmd=['select time,centroid from tblCells where trackID=' num2str(idsMissing(i))];
-    q=fetch(conn,cmd);
+    q=ljsFetch(conn,cmd);
     trackTime=cell2mat(q(:,1));
     cx=cellfun(@jsondecode,q(:,2),'uniformoutput',false);
     idx0=find(trackTime==t-1);

ctcOptimize/ctcEval1.m

+function res=ctcEval1(strDB)
+
+gtPath='/g/gRaw/ctc2020/';
+evalFolder='/f/ctcEval';
+[~,targetName,~]=fileparts(strDB);
+thisFile=mfilename('fullpath');
+[thisFolder,~,~]=fileparts(thisFile);
+path(path,fullfile(thisFolder,'..','ctc/importExport'));
+
+outfolder=fullfile(evalFolder,'eval');
+
+% results file
+strResults=fullfile(evalFolder,[targetName '_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');
+dsName=tokens{1}{1};
+dsID=tokens{1}{2};
+
+importExport(strDB,outfolder, [])
+
+% copy over the ground truth
+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);
+end
+copyfile(gtSource,fullfile(outfolder,targetName,[dsID '_GT']),'f');
+
+if ispc
+    TRA='TRAMeaseure.exe';
+    SEG='SEGMeasure.exe';
+    DET='DETMeasure.exe';
+    exePath=fullfile('./','EvaluationSoftware/Win');
+else 
+    TRA='TRAMeasure';
+    SEG='SEGMeasure';
+    DET='DETMeasure';
+    exePath=fullfile('./','EvaluationSoftware/Linux');
+end
+
+system([fullfile(exePath,TRA) ' ' ...
+    fullfile(outfolder,targetName) ' ' dsID ' > score.txt']);
+
+system([fullfile(exePath,SEG) ' ' ...
+    fullfile(outfolder,targetName) ' ' dsID ' >> score.txt']);
+
+system([fullfile(exePath,DET) ' ' ...
+    fullfile(outfolder,targetName) ' ' dsID ' >>  score.txt']);
+
+fid=fopen('score.txt');
+scoreTxt=fscanf(fid,'%s');
+fclose(fid);
+sx=regexp(scoreTxt,'...measure:(\d\.\d+)','tokens');
+sx=cellfun(@str2double,sx);
+if length(sx)<3 , sx(3)=0; end
+fprintf(1,'TRAmeasure:%f, SEGmeasure:%f, DETmeasure:%f\n',sx(1),sx(2),sx(3));
+
+% get the algorithm settings
+[conn,CONSTANTS]=openDB(strDB);
+segParams=Read.getSegmentationParams(conn);
+
+if isempty(res)
+    res=table(sx,{jsonencode(segParams)},'VariableNames',{'TRA_SEG_DET','segParams'});
+else
+    res=[res;sx,{jsonencode(segParams)}];
+end
+
+close(conn);
+
+
+writetable(res,strResults);
+