ImageStack unexpected behaviour

Posted by Seamus Holden on Jul 29, 2013; 1:41pm
URL: http://imagej.273.s1.nabble.com/ImageStack-unexpected-behaviour-tp5004200.html

Hi there

I am trying to preallocate a stack and then write some data to it
(specifically images from a microscope in micromanager).

Every time I try to write images to the preallocated stack, the first
image is always blank. I have no idea why!
Specifically, the script below gives a blank first frame, all other
frames have a white diagonal as expected.

Can anyone see where I am going wrong?

Thanks in advance for your help.
Regards,
Seamus

[test script]

import ij.*;
import ij.gui.*;

int numImages=10;
int w = 16;
int h = 16;

ImagePlus acqIm = NewImage.createShortImage("test", w, h, numImages,
NewImage.FILL_BLACK);
ImageStack acqStack = acqIm.getStack();

int nn = 1;
for (int i = 0; i < numImages; i++) {
   short[] pixels = new short[w * h]; // zero-filled
   for (int j = 0; j < w && j < h; j++) { // set diagonal to nonzero
     pixels[j + w * j] = (short)15000;
   }

   acqStack.setPixels(pixels, nn);
   nn++;
}
acqIm.show();

[end of test script]



--
Dr Seamus Holden
Post-doctoral Fellow
Bâtiment des Sciences Physiques
École Polytechnique Fédérale de Lausanne
CH-1015 Lausanne, Switzerland

Phone: [phone]

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