Merge branch 'master' of https://git-bioimage.coe.drexel.edu/opensource/ljsctc

src/+Smooth/batchMerge.m

+outfolder = '/g/leverjs/layton/ctc_default_v2';
+if ~exist(outfolder,'dir')
+    mkdir(outfolder)
+end
+
+sourceFolder = '/g/leverjs/layton/ctc_noMerge';
+
+results = [];
+
+flist = dir(fullfile(sourceFolder,'*training*.LEVER'));
+
+for ff = 1:length(flist)
+
+   strDB = fullfile(flist(ff).folder,flist(ff).name);
+
+   [~,dsName,~] = fileparts(strDB);
+   [conn,~,segParams] = openDB(strDB);
+   close(conn);
+
+   targetWrangle = Helpers.buildWrangleFile(strDB,outfolder,dsName,segParams);
+
+   [conn,CONSTANTS,segParams] = openDB(targetWrangle);
+   
+   nMerged = Smooth.Merge.goMerge(conn,CONSTANTS,segParams,64);
+
+   Smooth.Classify.goClassifyMitosis(conn,CONSTANTS,64);
+   Smooth.extFamily(conn);
+   close(conn)
+
+   ljsctc = get_ljsctc(dsName);
+   res = ctcEval(targetWrangle,[],ljsctc.outPath,ljsctc.gtEvalPath,ljsctc.gtConstraintPath);
+   results = [results;res];
+end
+4; 
\ No newline at end of file

src/+Smooth/batchSplit.m

+outfolder = '/g/leverjs/layton/ctc_split';
+if ~exist(outfolder,'dir')
+    mkdir(outfolder)
+end
+
+sourceFolder = '/g/leverjs/layton/ctc_noMerge';
+
+results = [];
+
+flist = dir(fullfile(sourceFolder,'*training*.LEVER'));
+
+for ff = 1:length(flist)
+
+   strDB = fullfile(flist(ff).folder,flist(ff).name);
+
+   [~,dsName,~] = fileparts(strDB);
+   [conn,~,segParams] = openDB(strDB);
+   close(conn);
+
+   targetWrangle = Helpers.buildWrangleFile(strDB,outfolder,dsName,segParams);
+
+   [conn,CONSTANTS,segParams] = openDB(targetWrangle);
+   
+   Smooth.Split.goSplit(targetWrangle);
+   Smooth.Classify.goClassifyMitosis(conn,CONSTANTS,8);
+   Smooth.extFamily(conn);
+   close(conn)
+
+   ljsctc = get_ljsctc(dsName);
+   res = ctcEval(targetWrangle,[],ljsctc.outPath,ljsctc.gtEvalPath,ljsctc.gtConstraintPath);
+   results = [results;res];
+end
+4; 
\ No newline at end of file

src/+Smooth/testEval.m

+outfolder = '/g/leverjs/layton/ctc_default';
+if ~exist(outfolder,'dir')
+    mkdir(outfolder)
+end
+
+sourceFolder = '/g/leverjs/ctc2021_manual/2d';
+
+results = [];
+
+flist = dir(fullfile(sourceFolder,'*training*.LEVER'));
+
+for ff = 1:length(flist)
+
+   strDB = fullfile(flist(ff).folder,flist(ff).name);
+
+   [~,dsName,~] = fileparts(strDB);
+   [conn,CONSTANTS,segParams] = openDB(strDB);
+   close(conn);
+
+   targetWrangle = Helpers.buildWrangleFile(strDB,outfolder,dsName,segParams);
+
+   Batch.processMovie(targetWrangle,false,96);
+
+   ljsctc = get_ljsctc(dsName);
+   res = ctcEval(targetWrangle,[],ljsctc.outPath,ljsctc.gtEvalPath,ljsctc.gtConstraintPath);
+   results = [results;res];
+end
+4; 
\ No newline at end of file

src/goWrangleCTC.m

+outfolder = '/f/leverjs/g/ctc2021_wrangle';
+if ~exist(outfolder,'dir')
+    mkdir(outfolder);
+end
+
+% (re)-run strDB to targetWrangle
+strDB='/f/leverjs/g/ctc2021ap/2d/Fluo-N2DL-HeLa_training_01.LEVER';
+
+[~,dsName,~] = fileparts(strDB);
+[conn,CONSTANTS,segParams] = openDB(strDB);
+close(conn);
+
+segParams.minimumRadius_um = [1, 0.2, 3];
+targetWrangle = Helpers.buildWrangleFile(strDB,outfolder,dsName,segParams);
+
+Batch.processMovie(targetWrangle,false,18);
+
+% for eval, need ljsctc
+expName='2d_Fluo-N2DL-HeLa_training_01';
+ljsctc = get_ljsctc(expName);
+ctcEval(targetWrangle,[],ljsctc.outPath,ljsctc.gtEvalPath,ljsctc.gtConstraintPath);