Re: Bug in setPixels

Posted by Rasband, Wayne (NIH/NIMH) [E] on Apr 09, 2014; 3:02pm
URL: http://imagej.273.s1.nabble.com/Bug-in-setPixels-tp5007255p5007262.html

On Apr 9, 2014, at 6:45 AM, Ilan wrote:

> 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.

The test plugin should work as expected if you change

   imgMask.repaintWindow();

to

   imgMask.setStack(maskStack);

In general, you should use ImagePlus#setStack() to redisplay a stack acquired with ImagePlus#getStack() and modified.

-wayne

> 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;
>
> /*
> * To change this license header, choose License Headers in Project
> Properties.
> * To change this template file, choose Tools | Templates
> * and open the template in the editor.
> */
>
> /**
> *
> * @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
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Bug-in-setPixels-tp5007255.html
> Sent from the ImageJ mailing list archive at Nabble.com.\

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