output result as a single stack

with option to save to disk

GroupedProjections.ijm

 // Creates stack projections for subgroups
 //  and saves them to disk.
 
-basePath=getDirectory("Choose output folder");
-//file=File.openDialog("Choose input file");
-// Import file as virtual Stack (using BioFormats as neccesary)
-myStack = getImageID();
+//TODO file=File.openDialog("Choose input file");
+//TODO Import file as virtual Stack (using BioFormats as neccesary)
+inputID = getImageID();
+if (nSlices==1) {exit("This macro only operates on stacks.")};
 
 //Ask user for settings
 Dialog.create("Projection Method");
 Dialog.addChoice("Method:", newArray("Max Intensity", "Min Intensity","Median","Average Intensity"));
 Dialog.addNumber("Size of substack",300);
+Dialog.addCheckbox("Save result to disk", false)
 Dialog.show();
 
 method=Dialog.getChoice();
 subStackSize = Dialog.getNumber();
+saveToDisk = Dialog.getCheckbox();
 
 //Check if sub stack will fit in memory
 maxMem = parseInt(IJ.maxMemory());
@@ -25,45 +27,65 @@ if (stackMem > maxMem) {
 tStart = getTime();
 setBatchMode(true);
 methodPrefix = replace(method,' ','-');
+resultName = methodPrefix;
+//TODO save inputName and store in image info
 iMax = floor(nSlices()/subStackSize)+1;
-print("Saving result files to "+basePath+" ...");
-for (i=0; i<(iMax-1); i++) {
-    //TODO handle smaller substack at the end of original stack
-    start=i*subStackSize+1;
-    stop=start+subStackSize;
-	calculateProjection(start,stop,i,method);
-    print(methodPrefix+"_"+IJ.pad(start,5)+"-"+IJ.pad(stop,5)+".tif");
-    function saveSlice(basePath,methodPrefix,start,stop);
-    selectWindow("SubStack"+i);
-    close();
-    selectImage(myStack);
-}
-//Handle last substack separately
-start=(iMax-1)*subStackSize+1;
-stop=nSlices();
-calculateProjection(start,stop,i,method);
-print(methodPrefix+"_"+IJ.pad(start,5)+"-"+IJ.pad(stop,5)+".tif");
-function saveSlice(basePath,methodPrefix,start,stop);
-selectWindow("SubStack"+i);
-close();
-selectImage(myStack);
+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;
+        stop=nSlices();
+    }
+    sliceName = methodPrefix+"_"+IJ.pad(start,5)+"-"+IJ.pad(stop,5);
+    calculateProjection(start,stop,i,method);
+    rename(sliceName);
+    if (i>1) {
+        addSlice(resultName,resultName,getTitle());
+        selectImage(resultName);
+        setSlice(nSlices);
+        setMetadata("Label", sliceName);
+    }
+    else if (i==1) {
+        addSlice(resultName,slice1,sliceName);
+        selectImage(resultName);
+        setSlice(1);
+        setMetadata("Label", slice1);
+        setSlice(2);
+        setMetadata("Label", sliceName);
+        setBatchMode("show");
+    }
+    else if (i==0) {
+        slice1=getTitle();
 
+    }
+    selectImage(inputID);
+}
 tStop = getTime();
 walltime = (tStop-tStart)/1000/60;
 
+selectImage(resultName);
+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);
-//TODO open completed Max Proj Stack
 print("Done! (took "+d2s(walltime,1)+" min to complete.");
 
 function calculateProjection(iStart,iStop,nSlice,method) {
 	run("Duplicate...", "title=SubStack"+nSlice+" duplicate range="+iStart+"-"+iStop);
-	run("Z Project...", "start=1 stop="+(iStop-iStart+1)+" projection=["+method+"]");
+    if (nSlices>1) {
+        run("Z Project...", "start=1 stop="+(iStop-iStart+1)+" projection=["+method+"]");
+    }
 }
 
-function saveSlice(path,prefix,iStart,iStop) {
-	//TODO save result as tiff stack
-	run("Save", "save=["+path+prefix+"_"+IJ.pad(start,5)+"-"+IJ.pad(iStop,5)+".tif]");
+function addSlice(resultTitle,in1,in2) {
+    run("Concatenate...", "  title=["+resultTitle+"] image1="+in1+" image2="+in2);
 	showStatus("Grouped Stack Proj. ("+i+"/"+iMax+"):");
 	showProgress(i/iMax);
-    close();
 }