Posted by
Fred Damen on
Mar 15, 2018; 11:47pm
URL: http://imagej.273.s1.nabble.com/Using-SubHyperstackMaker-makeSubhyperstack-to-extract-a-single-frame-tp5020295.html
Greetings,
I am trying to use SubHyperstackMaker.makeSubhyperstack to process the
hyperstack through the frame dimension. When the number of frames to be
extracted is more than a single frame (frames = "1-2" or "1,2") everything
seems to work fine. When a single frame (frames = "1") is requested the
resultant hyperstack (A1) is all zeros, see Java code below.
A second problem that is perplexing and I can not reproduce in a snippet of
code is that when attempting to extract a single frame from the aforementioned
frame with all zeros, the original contents of the frame is returned, thus the
reason for the A2 ImagePlus in the code below. As this is magically working
in my original code, I am only interested in why.
Just in case your wondering why I would want to do this:
The original dataset has many frames of volumes in which some frames/volumes
are tagged and some are not. I need to separate the frames/volumes into the
two groups and calculate the mean of each group voxel-wise across their
volumes. If anyone knows an easier way, I'm all ears.
Thanks in advance,
Fred
import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import ij.plugin.*;
import ij.plugin.frame.*;
import ij.plugin.SubHyperstackMaker.*;
public class tmp_Plugin implements PlugIn {
public void run(String arg) {
String frames = "1";
ImagePlus A = IJ.createHyperStack("A", 128, 128, 1, 1, 2, 32);
IJ.run(A,"Set...","value=1 stack");
A.show();
ImagePlus A1 = SubHyperstackMaker.makeSubhyperstack(A,"1","1-1",frames);
A1.setTitle("A1");
A1.show();
ImagePlus A2 = SubHyperstackMaker.makeSubhyperstack(A1,"1","1-1",frames);
A2.setTitle("A2");
A2.show();
}
}
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