add ability to specify overlap of substacks

also specify save target before loop execution

GroupedProjections.ijm

@@ -10,12 +10,19 @@ if (nSlices==1) {exit("This macro only operates on stacks.")};
 Dialog.create("Projection Method");
 Dialog.addChoice("Method:", newArray("Max Intensity", "Min Intensity","Median","Average Intensity"));
 Dialog.addNumber("Size of substack",300);
+Dialog.addNumber("Overlap (frames)",0);
 Dialog.addCheckbox("Save result to disk", false)
 Dialog.show();
 
 method=Dialog.getChoice();
 subStackSize = Dialog.getNumber();
+overlap = Dialog.getNumber();
 saveToDisk = Dialog.getCheckbox();
+if (overlap >= subStackSize) {error("Overlap must be smaller than size of substack");}
+if (saveToDisk) {
+    //TODO get fully qualified filename in stead of only directory
+    basePath=getDirectory("Choose output folder");
+}
 
 //Check if sub stack will fit in memory
 maxMem = parseInt(IJ.maxMemory());
@@ -29,19 +36,18 @@ setBatchMode(true);
 methodPrefix = replace(method,' ','-');
 resultName = methodPrefix;
 //TODO save inputName and store in image info
+//FIXME calculate iMax correctly for overlaps
 iMax = floor(nSlices()/subStackSize)+1;
+print(method+" projection on "+iMax+" substacks, each with "+overlap+" slices overlap...");
 for (i=0; i<iMax; i++) {
-    selectImage(inputID);
-    if (i<(iMax-1)) {
-        start=i*subStackSize+1;
-        stop=start+subStackSize-1;
-    }
-    else {
-        start=i*subStackSize+1;
+    start=i*subStackSize+1;
+    stop=start+subStackSize+overlap;
+    if (stop > nSlices()) {
         stop=nSlices();
+        i = iMax+1;
     }
     sliceName = methodPrefix+"_"+IJ.pad(start,5)+"-"+IJ.pad(stop,5);
-    calculateProjection(start,stop,i,method);
+    calculateProjection(start,stop,"SubStack",method);
     rename(sliceName);
     if (i>1) {
         addSlice(resultName,resultName,getTitle());
@@ -62,23 +68,24 @@ for (i=0; i<iMax; i++) {
         slice1=getTitle();
 
     }
+    selectImage("SubStack");
+    close();
     selectImage(inputID);
 }
-tStop = getTime();
-walltime = (tStop-tStart)/1000/60;
-
 selectImage(resultName);
+setSlice(1);
 run("Enhance Contrast...", "saturated=0.4 process_all");
 if (saveToDisk) {
-    //TODO ask user for file name istead of folder only
-    basePath=getDirectory("Choose output folder");
     saveAs("Tiff",basePath+resultName+"_grouped");
 }
 setBatchMode(false);
+
+tStop = getTime();
+walltime = (tStop-tStart)/1000/60;
 print("Done! (took "+d2s(walltime,1)+" min to complete.");
 
-function calculateProjection(iStart,iStop,nSlice,method) {
-	run("Duplicate...", "title=SubStack"+nSlice+" duplicate range="+iStart+"-"+iStop);
+function calculateProjection(iStart,iStop,resultTitle,method) {
+	run("Duplicate...", "title="+resultTitle+" duplicate range="+iStart+"-"+iStop);
     if (nSlices>1) {
         run("Z Project...", "start=1 stop="+(iStop-iStart+1)+" projection=["+method+"]");
     }