Re: bar graphs

Posted by Wayne Rasband on Aug 28, 2008; 6:57pm
URL: http://imagej.273.s1.nabble.com/bar-graphs-tp3695266p3695270.html

> I have a (hopefully) related question, so here goes:
>
> I am trying to learn how to call the Analyze/Distribution commands from
> inside a macro.
> I am going through a stack of images with the measure command, which
> generates a Results window.
>
> I then execute the Analyze/Distribution command which takes the list
> in the
> Results window and displays a histogram of values in a Mean
> Distribution
> window.  Clicking on the List command shows a second window named Mean
> Distribution with bins and counts.  I need the second number in the
> "bin
> start" column to use as a threshold in other calculations.
>
> So far, I have figured out how use run("...) commands to get all the
> way to
> showing the first Mean Distribution window, but I can't get it to show
> the
> List Window, or get any values out of the list.
>
> I tried recording a macro and walking through the steps, but it doesn't
> record the commands either.  So far, the record function is the only
> systematic way I have of finding internal commands.  Otherwise I just
> have
> to trip over them in other example macros.

The ImageJ 1.41k daily build adds a Plot.getValues() macro function
that retrieves the X and Y values from plot and histogram windows. Here
is an example:

    run("Blobs (25K)");
    setAutoThreshold();
    run("Analyze Particles...", "size=0 circularity=0.00 clear");
    run("Distribution...", "parameter=Area automatic");
    Plot.getValues(x, y);
    for (i=0; i<x.length; i++)
        print(x[i], y[i]);

-wayne