Re: Using ImageJ in another java pp in the existing jre, and batch mode on linux

Posted by Adam Waite on Feb 13, 2010; 5:27am
URL: http://imagej.273.s1.nabble.com/Using-ImageJ-in-another-java-pp-in-the-existing-jre-and-batch-mode-on-linux-tp3689390p3689392.html

Hi Jared,

I'm glad you wrote to the list.  I have a similar problem that I asked about on February 7th, and also received no response.  My issue also involves trying to use ImageJ as a library for a Java-based image analysis program.  Specifically, my problem is the requirement of the RoiManager class to show a window in order to add a selection.  This forces me to show an image, which prevents this program from running completely in the background, and slows down analysis.

Have you tried to use RoiManager in your programs?  If so, have you found a way to circumvent this requirement?  I'm including the relevant part of my first email below:



Here's what I need to do:
1) Threshold a 16-bit grayscale image. (Using setAutoThreshold).
2) Make a mask out of this threshold. (Using IJ.run(img, "Convert to Mask","");)
3) Make a selection out of this mask.
4) Apply this selection to the original image.

To accomplish the transition between steps 3 and 4, I am using the following code:

<code>

RoiManager rm = new RoiManager(false);

    IJ.run(bgmask, "Create Selection","");
    bgmask.show();
    rm.runCommand("Add");
    bgmask.close();

    Roi[] roi = rm.getRoisAsArray();
    bs.setRoi(roi[0]);
    ImageStatistics fg_stats = bs.getStatistics(ImageStatistics.MEDIAN);
</code>

The problem is that if I don't run "bgmask.show()" the roi manager complains that "there are no images open" and aborts the run.

Thanks for any insights you may have,
Adam

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Science is more of an art than a science.