// 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+ list[i], outputDir);
	}
}

// Single file projections
function processFile(inputFile,basePath) {
// open input input file
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 for\n"+inputFile+"...");

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);
}
}
}