In macro going through slices, Geodesic Distance Map (2D) stops after the first slice

[linshaova]

Hello MorphoLibJ developers,

I'm trying to generate Geodesic Distance Map (GDM) for a series of of 2D masks stored in a 3D stack, together with a marker stack of the same dimensions. What I noticed is that if I perform anything with the GDM output image before closing it, the for loop would just exit after the first slice. Here is my simple IJ macro script:

mask = "motion_compen_mask.tif";
marker = "Mask3d.tif";
selectWindow(mask);
print(nSlices);

for (i=0; i<nSlices; i++) {
  print(i);
  selectWindow(mask);
  setSlice(i+1);
  selectWindow(marker);
  setSlice(i+1);
  run("Geodesic Distance Map", "marker="+marker+" mask="+mask+" distances=[Chessknight (5,7,11)] output=[32 bits] 
  normalize");
  gdwindow = getTitle();
// If I do anything here before closing the GDM output window, the for loop would just exit after i=0
// For example, a simple duplication of the GDM output would make it exit after i=0:
  run("Duplicate...", "title=dup");
// If you comment out the above line, the for loop would run through
  print("here");
  close(gdwindow);
// If close() is not called here, the for loop would also exit after i=0, no matter if anything was done to gdwindow
}
print("loop exited");

Could this a be a bug or by design? I'm attaching a ZIP file with the two TIFF files used in this script. Thank you very much!

--lin

tiffs.zip

[dlegland]

Hi,

well, this seems to be strange... I do not have clear idea right now.

Just to clarify, what do you want as output? Another 3D stack containing the concatenation of each slice processing?

[linshaova]

Yes, exactly! My plan was to duplicate the GDM result into another window for the 1st slice, and then append the results from subsequent slices to this window to form a 3D stack of 2D-GDM results.

I found a work-around since the first posting: after each slice's processing, I could save the result into a TIFF (i.e., one TIFF per slice) without interrupting the for loop, and then import the 2D TIFFs as a sequence. But of course it'd be nicer to not have to have this intermediate step.

Thank you!

lin

[linshaova]

Forgot to mention that I have an almost identical experience with applying Marker-Controlled Watershed (MCW) on a series of 2D slices from 3D stacks input. And the same saving-result-into-one-TIFF-per-slice workaround works. The only difference is that for MCW to work in 2D mode with 3D stacks as inputs, I had to duplicate the slices of the same slice# from the input stacks and use the those slices as input to MCW; just setSlice(i+1) wouldn't be enough, which is fine.

lin