binning without scaling #18

+batch/binMovieFromFile.m

@@ -1,4 +1,4 @@
-function binConfig = binMovieFromFile(inDir,inFileList,outDir,shrinkFactors,depth,trialOption)
+function binConfig = binMovieFromFile(inDir,inFileList,outDir,shrinkFactors,depth,method,trialOption)
 % BINMOVIEFROMFILE bin movies from files in a directory
 %     Args:
 %         inDir (char): input directory
@@ -32,9 +32,9 @@
     disp(fileName)
     filePath = fullfile(inDir,fileName);
     trialOptionCell = helper.structToNameValPair(trialOption);
-    trial = TrialModel(filePath,trialOptionCell{:});
+    trial = TrialModel('filePath', filePath,trialOptionCell{:});
     binned = movieFunc.binMovie(trial.rawMovie,shrinkFactors, ...
-                                'mean');
+                                method);
 
     outFileName = iopath.modifyFileName(fileName,outFilePrefix,'','tif');
     outFilePath = fullfile(outDir,outFileName);

+movieFunc/convertToUint.m

@@ -13,14 +13,18 @@
     depth = 8;
 end
 
-if ~exist('zlim','var')
-    zlim = [min(A(:)), max(A(:))];
+if exist('zlim','var')
+    A = mat2gray(double(A),double(zlim));
+    if depth == 16
+        scaler = (2^16 -1);
+    else
+        scaler = 255;
+    end
+    A = scaler*A;
 end
 
-A = mat2gray(double(A),double(zlim));
-
 if depth == 16
-    A = uint16((2^16 -1)* A);
+    A = uint16(A);
 else
-    A = uint8(255*A);
+    A = uint8(A);
 end

NrModel.m

@@ -565,6 +565,7 @@ function binMovieBatch(self,param,outDir,planeNum,fileIdx)
                                                outSubDir,...
                                                param.shrinkFactors,...
                                                param.depth,...
+                                               param.method,...
                                                trialOption);
             binConfig.outDir = outDir;
             binConfig.trialOption = param.trialOption;