remove contrast stretching of projections

GroupedProjections.ijm

@@ -31,10 +31,8 @@ stackMem = getWidth()*getHeight()*bitDepth()/8*subStackSize;
 if (stackMem > maxMem) {
     exit("Substack is too large for available memory");
 }
-//FIXME calculate iMax correctly for overlaps
+//FIXME calculate iMax correctly for non zero overlaps
 iMax = floor(nSlices()/subStackSize)+1;
-//TODO allocate stack memory before running the loop. The programm will then
-// fail right in the beginning if not enough memory is available.
 methodPrefix = replace(method,' ','-');
 resultName = methodPrefix;
 inputInfo = getImageInfo;
@@ -87,7 +85,7 @@ for (i=0; i<iMax; i++) {
 }
 selectImage(resultName);
 setSlice(1);
-run("Enhance Contrast...", "saturated=0.4 process_all");
+//run("Enhance Contrast...", "saturated=0.4 process_all");
 if (saveToDisk) {
     saveAs("Tiff",basePath+inputName+"_"+resultName+"-grouped");
 }
@@ -98,6 +96,7 @@ walltime = (tStop-tStart)/1000/60;
 print("Done! (took "+d2s(walltime,1)+" min to process "+i+" substacks.");
 print(progressTitle, "\\Close");
 
+//Subfunctions
 function calculateProjection(iStart,iStop,resultTitle,method) {
 	run("Duplicate...", "title="+resultTitle+" duplicate range="+iStart+"-"+iStop);
     if (nSlices>1) {
@@ -105,12 +104,14 @@ function calculateProjection(iStart,iStop,resultTitle,method) {
     }
 }
 
+//add projection in2 to existing result stack in2
 function addSlice(resultTitle,in1,in2) {
     run("Concatenate...", "  title=["+resultTitle+"] image1="+in1+" image2="+in2);
 	showStatus("Grouped Stack Proj. ("+i+"/"+iMax+"):");
 	showProgress(i/iMax);
 }
 
+//get string representation of progress bar with p1 out of p2 done
 function getBar(p1, p2) {
     n = 20;
     bar1 = "--------------------";
@@ -120,4 +121,4 @@ function getBar(p1, p2) {
     if (index>n-1) index = n-1;
     return substring(bar2, 0, index) + substring(bar1, index+1, n);
 }
-}
+}
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