Bug in setPixels

Posted by Ilan on Apr 09, 2014; 10:45am
URL: http://imagej.273.s1.nabble.com/Bug-in-setPixels-tp5007255.html

A few days ago I reported some strange results with setPixels with the first page of the stack not being updated. It seems that it is a bug in ImageJ. It isn't necessarily the first page, but rather the image which is currently being displayed.
To make a test case I generated a stack using Convert to Mask which gives an image with pixels either 0 or 255. I can supply such data if someone wants it. The data is the result of Convert to Mask which gives either 0 or 255, after which the stack is converted to 16 bits.
Then I can choose any image I wish from the stack as the currently displayed page. I run the program and the displayed page will remain with 0 and 255, with all other pages being 0 or 300. The only sense I can make out of this is that setPixels is failing for the currently displayed slice.

For simplicity, I take the case where only a single ImagePlus is displayed and the program operates on it. This is only for the case of making a reproducible bug. I pulled out only the essentials of the program so that it all fits in a single page. Here is the code which demonstrates the problem:


import ij.ImagePlus;
import ij.ImageStack;
import ij.WindowManager;
import ij.plugin.PlugIn;
import javax.swing.JOptionPane;

/*
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/**
 *
 * @author ilan
 */
public class Nuclear_Bad implements PlugIn {
        ImagePlus imgMask;

        @Override
        public void run(String arg) {
                doIt();
        }
       
        void doIt() {
                int[] myList = WindowManager.getIDList();
                imgMask = WindowManager.getImage(myList[0]);
                doMasking();
        }
       
        void doMasking() {
                int i, j, stkSz, sliceSz;
                short curVal;
                ImageStack maskStack;
                Object pix2;
                short[] maskIn, maskOut;
                stkSz = imgMask.getImageStackSize();
                maskStack = imgMask.getImageStack();
                for( i=1; i<=stkSz; i++) {
                        pix2 = maskStack.getPixels(i);
                        if(!(pix2 instanceof short [])) {
                                JOptionPane.showMessageDialog(null,"Must have 16 bit data on both series");
                                return;
                        }
                        maskIn = (short[]) pix2;
                        sliceSz = maskIn.length;
                        maskOut = new short[sliceSz];
                        for( j=0; j<sliceSz; j++) {
                                curVal = maskIn[j];
                                if( curVal != 0) curVal = 300;
                                maskOut[j] = curVal;
                        }
                        maskStack.setPixels(maskOut, i);
                }
                imgMask.repaintWindow();
        }
       
}

To demonstrate the problem one only needs to put the cursor on the image. On the image which was displayed when the program was run will remain 0 or 255. Scrolling to any other image will give 0 or 300. Scrolling back will return to 0 or 255.
This is so simple that it is hard to imagine anything else than a bug.

Thanks,
Ilan