BatchConvertLSMsToNrrds_Jonny.txt

requires("1.33s"); 
dir = getDirectory("Choose a stacks directory");
outputDir = getDirectory("Choose output directory");
setBatchMode(true);
count = 0;
countFiles(dir); //output dir should not be subfolder of input dir!
print("Total files: "+count);
n = 0;
processFiles(dir, outputDir);

function countFiles(dir) {
		list = getFileList(dir);
	for (i=0; i<list.length; i++) {
		if (endsWith(list[i], "/"))
            countFiles(""+dir+list[i]);
	else
		count++;
	}
}

function processFiles(dir,outputDir) {
	list = getFileList(dir);
    for (i=0; i<list.length; i++) {
        if (endsWith(list[i], "/"))
            processFiles(""+dir+list[i], outputDir);
        else {
		showProgress(n++, count);
              processFile(dir,outputDir,list[i]);
        }
    }
}

function processFile(dir,outputDir,file) {

	if (endsWith(file, ".lsm") || endsWith(file,".LSM")) {
		if(File.exists(outputDir+substring(file,0,indexOf(file,".lsm"))+"_01.Nrrd")==1 ) {
			print("image lsm exist" + file);
			return 0;
		}
		path = dir+list[i];
		run("Bio-Formats Importer", "open=" + path + " color_mode=Default split_channels view=[Standard ImageJ] stack_order=Default");
		title=getTitle();
		noImages=parseInt(substring(title,(lengthOf(title)-1),lengthOf(title)));
		workingImage=getImageID();
		noImages++;
		for(i=noImages;i>0;i--){
			if(i==1) channel="_03";
			if(i==2) channel="_01";
			if(i==3) channel="_02";
			selectImage(workingImage);
	//		processImage();
//			run("Biorad ...", "biorad=/Users/jefferis/Desktop/delete.PIC")
run("Nrrd ... ", "nrrd=["+outputDir+substring(file,0,indexOf(file,".lsm"))+channel+".Nrrd]");//		"SAIV"+substring(file,indexOf(file,"_")+2,lastIndexOf(file,"_"))+"-1v_0"+channel+".pic]");
//			saveAs("Jpeg", outputDir+substring(file,0,lengthOf(file)-4)+"_C"+i);
//			close();
			selectImage(workingImage);
			close();
			workingImage++;
		} 
	}
}