[ImageJ-bugs] [Bug 1107] New: 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

            Bug ID: 1107
           Summary: Cannot run commands from the ijpb/MorphoLibJ plugin in
                    --headless mode using --jython script option
           Product: Fiji
           Version: unspecified
          Hardware: Macintosh
                OS: Mac OS
            Status: NEW
          Severity: normal
          Priority: P5
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: ghv2 at psu.edu

I'm using Fiji version 21041125 and ijpb/MorphoLibJ release v1.0.7.

I've tried several different commands from the fabulous ijpb/MorphoLibJ plugin
library when running Fiji using --headless and --jython.  I have many Jython
scripts that call other Fiji plugin commands successfully.  My scripts that
attempt to use commands generally follow this pattern:

# Open the input image file.
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, "Fill Holes (Binary/Gray)", "" )

# Save the ImagePlus object as a new image.
IJ.saveAs( input_image_plus_copy, output_datatype, output_path )

The script finishes successfully, but no analysis is performed on the image
(i.e., it remains basically the same as the original input).  Also, when
running from the command line (instead of a Browser), the Fiji log ends with a
"Java Null pointer exception".

I'm wondering if I'm missing something, or if there is something that needs to
be added to the ijpb/MorphoLibJ plugin that enables it to be run in headless
mode via Python script calls.  I'm not a Java expert, so any help will be much
appreciated.

Thanks!

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