added generic param getter

src/get_ljsctc.m

@@ -80,6 +80,8 @@ ljsctc.gtConfig='GT';
 gtRoot=[ljsctc.rawImagePath(1:strfind(ljsctc.rawImagePath,baseName)+length(baseName))];
 gtTraining=[gtRoot 'training/**/man_seg*.tif'];
 ljsctc.gtTrainingPath=gtTraining;
+% verify training path with next line...
+% fprintf(1,'ljsctc found %d training images\n',length(dir(ljsctc.gtTrainingPath)));
 if strcmp(trainOrChallenge,'training')
     % this is passed to CTC scoring code
     ljsctc.gtEvalPath = [gtRoot 'training/' datasetSpecifier '/' movieID '_GT'];

src/get_ljsctc_generic.m

+% % see comments in get_ljsctc
+% % here we provide a generic version, based on the following file structure:
+% % -----------------------------------------------------------------------------------------
+% % - ROOT/Fluo-C3DL-MDA231
+% %   > 01
+%         · images...
+%     > 01_GT
+%         - SEG
+%             · images...
+%                 - TRA
+%             · images...
+%     > 01_ST
+%             - SEG
+%                 · images...
+%             - SEG_org
+%                 · images...
+%     > 02
+%         · images...
+%     > 02_GT
+%         - SEG
+%             · images...
+%         - TRA
+%             · images...
+%     > 02_ST
+%         - SEG
+%             · images...
+%         - SEG_org
+%             · images...
+% % -----------------------------------------------------------------------------------------
+% 
+% % 
+function ljsctc=get_ljsctc_generic(ROOT,dsName,movieID)
+
+ljsctc = [];
+ljsctc.outPath = './output';
+ljsctc.expName=[dsName '_' movieID]; % you could add 'training' or 'challenge' here if you want
+% to omit a field, set it to []. rawImagePath,outPath,segParams expName, are minimum
+% required param set
+ljsctc.rawImagePath = fullfile(ROOT,dsName,movieID);
+% THIS IS IMPORTANT! leverjs uses physical-based measurements. you must set
+% the correct pixel (voxel) physical size...(always a 3 vector). NOTE that
+% some of the pixel physical sizes are encoded in the supplied tiff
+% metadata incorrectly! so, the ones we use are set manually from the ctc
+% website
+% the preferred way to get segparams. if you set segParams, we use that
+% baseName should be short enough to specify a single movie, e.g. Fluo-C3DL-MDA231
+baseName=dsName; 
+[sp,pixelSize]=getSegParams(baseName); % from the manual tuned cache
+if ~isempty(sp)
+    ljsctc.segParams = sp;
+    ljsctc.pixelPhysicalSize=pixelSize;
+else
+    % we didn't find the segparams and pixelsize. we will learn segparams
+    % automatically (likely not as well as the manual param set). pixelSize
+    % is important though. you should get that value from the microscope. it's
+    % given for each dataset on the ctc website. please be sure to get that
+    % correctly. our default is to read it from the raw image tiffs, but
+    % for some of the ctc movies that value is set incorrectly!
+    %
+end
+% which ground truth to use, and where to write exported output
+ljsctc.gtConfig='GT';
+% if no ljsctc.segparams, and no match in the cached settings list, train a new
+% classifier to predict segParams. we'll use all the tiffs returned by this
+% next path string. try e.g. dir(ljsctc.gtTrainingPath) to verify it's the
+% man_seg tiffs
+% e.g. for ST ground truth:
+ljsctc.gtTrainingPath=fullfile(ROOT,dsName,'**/*_ST/man_seg*.tif');
+% if you don't want to run the training:
+% ljsctc.gtTrainingPath=[];
+% if you want to check the training path:
+fprintf(1,'ljsctc found %d training images\n',length(dir(ljsctc.gtTrainingPath)));
+bEvalTrainingMovie=false;
+if bEvalTrainingMovie
+    % this is passed to CTC scoring code
+    % only set this if you want to have the CTC SEG,TRA and DET scores
+    % generated (i.e. if you have a training movie
+    ljsctc.gtEvalPath = fullfile(ROOT,dsName, [movieID '_GT']);
+else
+    % this is passed to CTC scoring code
+    ljsctc.gtEvalPath = [];
+end
+
+% used for e.g. TRIF,TRIC,DRO datasets where we don't export full movie
+% (we still process whole thing though)
+% for this file tree above,  that would be 
+% e.g. ljsctc.gtConstraintPath = fullfile(ROOT,dsName, [movieID '_GT']);
+% 
+ljsctc.gtConstraintPath = [];
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