# Create a copy of the image.
input_image_plus_copy = input_image_plus.duplicate()
image_processor_copy = input_image_plus_copy.getProcessor()
try:
# Set binary options.
options = jython_utils.get_binary_options(
black_background=black_background)
IJ.run(input_image_plus_copy, "Options...", options)
# Convert image to binary if necessary.
if not image_processor_copy.isBinary():
IJ.run(input_image_plus_copy, "Make Binary", "")
# Run AnalyzeSkeleton
analyze_skeleton = AnalyzeSkeleton_()
analyze_skeleton.setup("", input_image_plus_copy)
if prune_cycle_method == 'none':
prune_index = analyze_skeleton.NONE
elif prune_cycle_method == 'shortest_branch':
prune_index = analyze_skeleton.SHORTEST_BRANCH
elif prune_cycle_method == 'lowest_intensity_voxel':
prune_index = analyze_skeleton.LOWEST_INTENSITY_VOXEL
elif prune_cycle_method == 'lowest_intensity_branch':
prune_index = analyze_skeleton.LOWEST_INTENSITY_BRANCH
result = analyze_skeleton.run(prune_index, prune_ends,
calculate_largest_shortest_path,
input_image_plus_copy, True, True)
# Save the results.
save(result, output, show_detailed_info, calculate_largest_shortest_path)
except Exception, e:
