Copy volume from within stack to new stack

Posted by Michael Doube on Jan 19, 2009; 5:52pm
URL: http://imagej.273.s1.nabble.com/Copy-volume-from-within-stack-to-new-stack-tp3693965.html

Hi all

I think my brain turned to mush over New Years because I can't get this
simple task to work.  I have a stack, coordinates of a start position
and a volume of interest's width, height and depth.  I want to copy the
source stack's pixel values into a new stack which has the same
dimensions of the volume of interest. This code results in a new stack
("Target") containing the last slice of the volume of interest on all of
its slices:

Cheers,

Mike

//copy box of pixels that contains sphere (i.e. is centred on centroid
//and has 2*radius sides)
        int startX = (int)Math.round((centroid[0]-radius)/vW);
        int startY = (int)Math.round((centroid[1]-radius)/vH);
        int startZ = (int)Math.round((centroid[2]-radius)/vD);
        int roiWidth = (int)Math.round(2*radius/vW);
        int roiHeight = (int)Math.round(2*radius/vH);
        int roiDepth = (int)Math.round(2*radius/vD);
        ImageStack targetStack = new ImageStack(roiWidth,roiHeight);
        short[] roiPixels = new short[roiWidth*roiHeight];
        for (int z = startZ; z <= startZ+roiDepth; z++){
                imp.setSlice(z);
                int nRows = 0;
                for (int y = startY; y < startY+roiHeight; y++){
                        int index = nRows*roiWidth;
                        int nCols = 0;
                        for (int x = startX; x < startX+roiWidth; x++){
                                roiPixels[index+nCols] = (short)ip.getPixel(x,y);
                                nCols++;
                        }
                        nRows++;
                }
                targetStack.addSlice("slice "+z, roiPixels);
        }
        ImagePlus target = new ImagePlus("Target", targetStack);
        target.show();