methods for evaluating smoothing operations

src/validate/smoothEval.m

+function results=smoothEval(strDB,nProcessors,gtPath)
+
+[root,~,~] = fileparts(strDB);
+results = [];
+
+if ~(exist('nProcessors','var') && ~isempty(nProcessors))
+    [conn,CONSTANTS]=openDB(strDB);
+    close(conn);
+    nProcessors=ljsNProcs(CONSTANTS);
+end
+
+[conn,CONSTANTS,segParams]=openDB(strDB);
+
+Batch.batchSegment(strDB,nProcessors,false);
+Batch.batchTrack(strDB);
+Smooth.Patch.patch11(conn);
+
+% score after initial segmentation and tracking
+results = smoothScore(conn,strDB,root,gtPath,results);
+
+Smooth.Patch.patch12(conn);
+Smooth.Patch.patch21(conn);
+
+% score after segementation operation: Patch
+results = smoothScore(conn,strDB,root,gtPath,results);
+
+Smooth.Merge.goMerge(conn,CONSTANTS,segParams)
+
+% score after segmentation operation: Merge
+results = smoothScore(conn,strDB,root,gtPath,results);
+
+Smooth.Classify.goClassifyMitosis(conn,CONSTANTS,nProcessors);
+Smooth.extFamily(conn);
+
+% score after mitotic detection is complete for final score
+res = ctcEval1(strDB,[],root,gtPath);
+results = [results;res];
+
+Batch.batchFeatures(conn,CONSTANTS,nProcessors);
+
+close(conn)
+
+function results = smoothScore(conn,strDB,root,gtPath,results)
+
+Smooth.extFamily(conn);
+res = ctcEval1(strDB,[],root,gtPath);
+results = [results;res];

src/validate/smoothEvalAll.m

+gtPath = '\\BIOIMAGE20\g\gRaw\ctc2020';
+sourceFolder='F:\leverjs\temp';
+
+results = [];
+
+flist = dir(fullfile(sourceFolder,'*training*.LEVER'));
+
+% 2d targets list
+% TO DO target list creation method
+targets = {'BF-C2DL-HSC','BF-C2DL-MuSC','DIC-C2DH-HeLa','Fluo-C2DL-Huh7', ...
+    'Fluo-C2DL-MSC','Fluo-N2DH-GOWT1','Fluo-N2DH-SIM+','Fluo-N2DL-HeLa', ...
+    'PhC-C2DL-PSC','PhC-C2DH-U373'};
+
+% 3d targets list
+% TO DO specify 2d and 3d target lists
+% targets = {'Fluo-C3DH-A549-SIM','Fluo-C3DH-A549','Fluo-C3DH-H157','Fluo-C3DL-MDA231', ...
+%     'Fluo-N3DH-CE','Fluo-N3DH-CHO','Fluo-N3DH-SIM+','Fluo-N3DL-DRO', ...
+%     'Fluo-N3DL-TRIC','Fluo-N3DL-TRIF'};
+
+for ff = 1:length(flist)
+    
+    strDB = fullfile(flist(ff).folder,flist(ff).name);
+    % compare to target list
+    match = cellfun(@(x) strfind(strDB,x),targets,'UniformOutput',false);
+    if all(isempty([match{:}]))
+        continue
+    end
+    
+    Helpers.goEraseAll(strDB)
+    res = smoothEval(strDB,[],gtPath);
+    results = [results;res];
+   
+end
+
+writetable(results,fullfile(sourceFolder,'results.txt'));
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