add batch capability

GroupedProjectionsBatch.ijm

+// Creates stack projections for subgroups
+//  and saves them to disk.
+macro "Grouped Projections Batch" {
+// Parameters
+extension = ".BTF";
+method="Max Intensity"; //one of Max Intensity", "Min Intensity","Median","Average Intensity","Standard Deviation"
+subStackSize = 300;
+overlap = 10;
+
+// Get user input if requiered
+inargs = getArgument();
+if (inargs=="") {
+	//Display dialog and ask for paths
+	inputDir = getDirectory("Input directory");
+	outputDir = getDirectory("Output directory");
+} else {
+	//Parse input and output paths from argumet string
+	paths = split(files," ");
+	inputDir = paths[1]:
+	outputDir = paths[2];
+}
+
+processFolder(inputDir);
+
+// Process all files and recurse into subdirs
+function processFolder(input) {
+	list = getFileList(input);
+	for (i = 0; i < list.length; i++) {
+		if(File.isDirectory(input + list[i]))
+			processFolder("" + input + list[i]);
+		if(endsWith(list[i], extension))
+			processFile(input, outputDir, list[i]);
+	}
+}
+
+// Single file projections
+function processFile(inputFile,basePath) {
+// open input input file
+open(inputFile);
+run("Bio-Formats Importer", "open="+inputFile+" color_mode=Default rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT use_virtual_stack");
+inputID = getImageID();
+
+// Input checking
+if (nSlices() == 1) {exit("This macro only operates on stacks.")};
+if (overlap >= subStackSize) {error("Overlap must be smaller than size of substack");}
+
+//Check if sub stack will fit in memory
+maxMem = parseInt(IJ.maxMemory());
+stackMem = getWidth()*getHeight()*bitDepth()/8*subStackSize;
+if (stackMem > maxMem) {
+    exit("Substack is too large for available memory");
+}
+//FIXME calculate iMax correctly for non zero overlaps
+iMax = floor(nSlices()/subStackSize)+1;
+methodPrefix = replace(method,' ','-');
+resultName = methodPrefix;
+inputInfo = getImageInfo;
+inputName = getInfo("image.filename");
+dotIndex = lastIndexOf(inputName, ".");
+if (dotIndex >= 0) {
+    inputName = substring(inputName, 0, dotIndex);
+}
+
+progressTitle = "[Progress]";
+run("Text Window...", "name="+ progressTitle +" width=30 height=3 monospaced");
+print(progressTitle,"\\Update:0/"+iMax+" substacks (0%)\n"+getBar(0, 100));
+print("Calculating the grouped "+method+" projection...");
+
+setBatchMode(true);
+tStart = getTime();
+for (i=0; i<iMax; i++) {
+    print(progressTitle,"\\Update:"+i+"/"+iMax+" substacks ("+round(i/iMax*100)+"%)\n"+getBar(i, 100));
+    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,"SubStack",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);
+        setMetadata("Info", inputInfo);
+    }
+    else if (i==0) {
+        slice1=getTitle();
+
+    }
+    selectImage("SubStack");
+    close();
+    selectImage(inputID);
+}
+selectImage(resultName);
+setSlice(1);
+run("Enhance Contrast...", "saturated=0.4 process_all");
+if (saveToDisk) {
+    saveAs("Tiff",basePath+inputName+"_"+resultName+"-grouped");
+}
+close();
+close(inputID);
+setBatchMode(false);
+
+tStop = getTime();
+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) {
+        run("Z Project...", "start=1 stop="+(iStop-iStart+1)+" projection=["+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 = "--------------------";
+    bar2 = "********************";
+    index = round(n*(p1/p2));
+    if (index<1) index = 1;
+    if (index>n-1) index = n-1;
+    return substring(bar2, 0, index) + substring(bar1, index+1, n);
+}
+}
+}
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