Can't save rois with RoiManager in plugin

Posted by Adam Waite on Feb 25, 2010; 7:48am
URL: http://imagej.273.s1.nabble.com/Can-t-save-rois-with-RoiManager-in-plugin-tp3689085.html

Hi List,

I'm trying to write a plugin that
1) Uses MaximumFinder to produce a watershed image
2) Uses ParticleAnalyzer to make rois from these segments
3) Saves these rois with RoiManager

I can successfully make the watershed image and analyze the particles.  However, if I try to save the resulting rois using the code below, RoiManager gives me an error "the selection list is empty".  However, while this code is running, I can see the RoiManager, and there are selections in the window.  Furthermore, if I run the "Show All" command on the image containing the particles, they show up as expected.

I've made this same sequence work without problems using the macro language.  I'm including the code I run to accomplish this below, as well.  Can anyone tell me what I'm doing wrong/differently than the macro case?


Thanks,
Adam


----------- This plugin code does not work -----------------------
            ResultsTable rt = new ResultsTable();
            boolean excludeOnEdges = false;
            boolean isEDM = false;
            ImagePlus max =
              new ImagePlus("segmented",
                  mf.findMaxima(pmanip,1,1,MaximumFinder.SEGMENTED,
                                excludeOnEdges,isEDM));          
           
           RoiManager rm = new RoiManager(false);
           
            int options =
              ParticleAnalyzer.ADD_TO_MANAGER+ParticleAnalyzer.INCLUDE_HOLES+ParticleAnalyzer.SHOW_NONE;
            int measurements = 0;
            double minSize = 0;
            double maxSize = 1000;
            double minCirc = 0;
            double maxCirc = 1;
            ParticleAnalyzer pa =
               new ParticleAnalyzer(
                                               options,measurements,rt,
                                               minSize,maxSize,minCirc,maxCirc);
            pa.analyze(max);
            max.show();
            rm.runCommand("Show All"); // This shows the rois, so I know they're in the RoiManager
            rm.runCommand("Save","1.zip"); // Won't save... "selection list is empty"
-------------- End plugin code -----------------------

----------------- This macro code works fine ------------------
    run("Find Maxima...", "noise=1 output=[Segmented Particles]");

    cell_mask = getImageID();

    roiManager("Reset");
    run("Analyze Particles...", "size=0-Infinity circularity=0-1 show=Nothing clear add");
    roiManager("Save", path_to_selections);
    selectImage(cell_mask);
    close();
--------------- end macro code -----------------

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