Mercurial > repos > imgteam > imagej2_find_maxima
diff imagej2_enhance_contrast_jython_script.py @ 1:e2622ebb5ce4 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
---|---|
date | Mon, 28 Sep 2020 16:49:43 +0000 |
parents | 29b39f5b0e69 |
children | 6a07f71806bb |
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--- a/imagej2_enhance_contrast_jython_script.py Tue Sep 17 17:01:44 2019 -0400 +++ b/imagej2_enhance_contrast_jython_script.py Mon Sep 28 16:49:43 2020 +0000 @@ -1,19 +1,19 @@ -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 ] +error_log = sys.argv[-7] +input = sys.argv[-6] +equalize_histogram = sys.argv[-5] == "yes" +saturated_pixels = sys.argv[-4] +normalize = sys.argv[-3] == "yes" +tmp_output_path = sys.argv[-2] +output_datatype = sys.argv[-1] # Open the input image file. -input_image_plus = IJ.openImage( input ) +input_image_plus = IJ.openImage(input) # Create a copy of the image. input_image_plus_copy = input_image_plus.duplicate() @@ -24,19 +24,16 @@ options = [] # If equalize_histogram, saturated_pixels and normalize are ignored. if equalize_histogram: - options.append( 'equalize' ) + options.append('equalize') else: - if saturated_pixels not in [ None, 'None' ]: + if saturated_pixels not in [None, 'None']: # Fiji allows only a single decimal place for this value. - options.append( 'saturated=%.3f' % float( saturated_pixels ) ) + 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 ) ) + 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)