Mercurial > repos > imgteam > imagej2_bunwarpj_compare_raw
view imagej2_enhance_contrast_jython_script.py @ 1:9349961e09ce draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author | imgteam |
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date | Mon, 28 Sep 2020 16:50:39 +0000 |
parents | d17be9aef142 |
children | 77411a986a70 |
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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 = 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) # 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') # 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)