exportAvi.ijm

//Batch macro to export avi files from supplied tiff stacks.
// Also prints scale bar and time stamp onto the video.
// Arguments string should be a list of absolute file paths to process.

//This macro can be called in Fiji's headless mode e.g.
// imagej --headless -macro /path-to-macro.ijm /path-to-file.tif
// or by runMacro(macro, arg)

outExtension = ".avi";
frameRate = 20;
barWidth = 2; //µm
barHeight = 4; //px
tUnit = "";
tInterval = 1;

fileList = split(getArgument());

setBatchMode(true);
for (i = 0; i < fileList.length; i++) {
    //parse file name
    dotIndex = lastIndexOf(fileList[i], ".");
    if (dotIndex >= 0) {
        baseName = substring(fileList[i], 0, dotIndex);
    }
    outFile = baseName+outExtension;

    // escape spaces in path with \ and "" // does not work!
    //outFile = "\"" + outFile + "\"";
    //outFile = replace(outFile, " ", "\\\\\\\\ ");
    if ( indexOf(outFile," ") >= 0 ) {
        exit("Input path must no contain whitespace!");
    }
    //print("will export to "+outFile);

    open(fileList[i]);

    //processing steps
    //frameRate = Stack.getFrameRate();
    Stack.getUnits(xUnit, yUnit, zUnit, tUnit, vUnit);
    tInterval = Stack.getFrameInterval();
    print("frame= "+tInterval+" "+tUnit);
    getVoxelSize(x, y, z, u); print("vx size= "+x+"x"+y+"x"+z+" "+u);
    run("8-bit");
    run("Scale Bar...", "width="+barWidth+" height="+barHeight+" font=12 color=White background=None location=[Lower Right] bold label");
    if (tInterval > 0) {
        run("Time Stamper", "starting=0 interval="+tInterval+" x=2 y=15 font=12 decimal=0 anti-aliased or="+tUnit);
        print("muh");
    }
    run("AVI... ", "compression=JPEG frame="+frameRate+" save="+outFile);

    close();
}
setBatchMode(false);