comparison imagej2_enhance_contrast_jython_script.py @ 2:55bf135d6b0c draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

1:39b2bc251b2f

# Set the options
options = []
# If equalize_histogram, saturated_pixels and normalize are ignored.
if equalize_histogram:
    options.append('equalize')
else:
    if saturated_pixels not in [None, 'None']:
        # Fiji allows only a single decimal place for this value.
        options.append('saturated=%.3f' % float(saturated_pixels))
    # Normalization of RGB images is not supported.
    if bit_depth != 24 and normalize:
        options.append('normalize')
# Run the command.
options = "%s" % ' '.join(options)
IJ.run(input_image_plus_copy, "Enhance Contrast...", options)
# Save the ImagePlus object as a new image.
IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)

2:55bf135d6b0c

# Set the options
options = []
# If equalize_histogram, saturated_pixels and normalize are ignored.
if equalize_histogram:
    options.append("equalize")
else:
    if saturated_pixels not in [None, "None"]:
        # Fiji allows only a single decimal place for this value.
        options.append("saturated=%.3f" % float(saturated_pixels))
    # Normalization of RGB images is not supported.
    if bit_depth != 24 and normalize:
        options.append("normalize")
# Run the command.
options = "%s" % " ".join(options)
IJ.run(input_image_plus_copy, "Enhance Contrast...", options)
# Save the ImagePlus object as a new image.
IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)