Mercurial > repos > imgteam > imagej2_bunwarpj_compose_raw
view imagej2_enhance_contrast_jython_script.py @ 0:93b416f8e9e3 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
---|---|
date | Tue, 17 Sep 2019 17:00:19 -0400 |
parents | |
children | 8c0ace7ae77c |
line wrap: on
line source
import jython_utils import sys from ij import IJ # Fiji Jython interpreter implements Python 2.5 which does not # provide support for argparse. error_log = sys.argv[ -7 ] input = sys.argv[ -6 ] equalize_histogram = jython_utils.asbool( sys.argv[ -5 ] ) saturated_pixels = sys.argv[ -4 ] normalize = jython_utils.asbool( sys.argv[ -3 ] ) tmp_output_path = sys.argv[ -2 ] output_datatype = sys.argv[ -1 ] # Open the input image file. input_image_plus = IJ.openImage( input ) # Create a copy of the image. input_image_plus_copy = input_image_plus.duplicate() image_processor_copy = input_image_plus_copy.getProcessor() bit_depth = image_processor_copy.getBitDepth() # 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' ) try: # 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 ) except Exception, e: jython_utils.handle_error( error_log, str( e ) )