Re: combine data from multiple profile measurements of a time series to single data sheet

Posted by cpanders on Apr 14, 2016; 4:12pm
URL: http://imagej.273.s1.nabble.com/combine-data-from-multiple-profile-measurements-of-a-time-series-to-single-data-sheet-tp5016124p5016139.html

Progress! I found a macro (copied below) that will capture the profile plot for each frame of the stack with one click, generating a plot window in which each frame has a page with its unique plot.  However, the "list" and "save" options are absent.  
I now need to extract  the x-y data for each page into a single  sheet containing all plot data for the entire stack for further analysis in R.


Here is the macro which works very nicely as far as it goes:

// StackProfilePlot
// This macro generates profile plots of all the images
// in a stack and stores then in another stack.

macro "Stack profile Plot" {
    ymin = 0;
    ymax = 255;
    saveSettings();
    if (nSlices==1)
      exit("Stack required");
    run("Profile Plot Options...",
      "width=400 height=200 minimum="+ymin+" maximum="+ymax+" fixed");
    setBatchMode(true);
    stack1 = getImageID;
    stack2 = 0;
    n = nSlices;
    for (i=1; i<n; i++) {
        showProgress(i, n);
        selectImage(stack1);
        setSlice(i);
        run("Plot Profile");
        run("Copy");
        w = getWidth; h = getHeight;
        close();
        if (stack2==0) {
            newImage("Plots", "8-bit", w, h, 1);
            stack2 = getImageID;
        } else {
            selectImage(stack2);
            run("Add Slice");
        }
        run("Paste");
    }
    setSlice(1);
    setBatchMode(false);
    restoreSettings();
}