[ImageJ-bugs] [Bug 1107] Cannot run commands from the ijpb/MorphoLibJ plugin in --headless mode using --jython script option

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1107

--- Comment #1 from Greg Von Kuster <ghv2 at psu.edu> ---
After working with additional plugins from the command line (e.g.,
http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:edge_detection:start,
http://imagejdocu.tudor.lu/doku.php?id=plugin:morphology:skeletonize3d:start ),
it seems that plugins may be producing output images in various ways, and that
may be causing the behavior I'm seeing.

For example, the skeletonize3d plugin allows me to save the analyzed image
using the following commands from a Python script:

input_image_plus = IJ.openImage( input )
# Create a copy of the image.
input_image_plus_copy = input_image_plus.createImagePlus()
image_processor_copy = input_image_plus.getProcessor().duplicate()
input_image_plus_copy.setProcessor( "iCopy", image_processor_copy )
# Run the command.
IJ.run( input_image_plus_copy, "Skeletonize (2D/3D)", "" )
# Save the ImagePlus object as a new image.
IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )

In some way, the plugin "overlays" the original input_image_plus_copy object
with the new analyzed image, so when I save it, I have what I expect.

However, using similar commands with the edge_detection plugin does not behave
the same way.  It must be producing a separate image (to which I do not know
how to get a handle from the command line), so the original
input_image_plus_copy object is saved rather than the analyzed image.  The
behavior of this plugin is similar to the behavior of the ijpb/MorphoLibJ
plugin.

So is it possible to get a handle on output images for those plugins that do
not "overlay" the original image when run from the command line?

I've looked everywhere in (the Fiji tutorials and docs, OpenStack, etc), but
have not found any information about this.

Thanks very much for any insight on this.

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