Mercurial > repos > imgteam > imagej2_bunwarpj_compare_elastic
view imagej2_filter_jython_script.py @ 3:f9f2d9746a01 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author | imgteam |
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date | Wed, 25 Sep 2024 16:12:07 +0000 |
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import sys from ij import IJ # Fiji Jython interpreter implements Python 2.5 which does not # provide support for argparse. input_file = sys.argv[-8] image_datatype = sys.argv[-7] filter = sys.argv[-6] radius = sys.argv[-5] mask = sys.argv[-4] light_background = sys.argv[-3] dont_substract = sys.argv[-2] tmp_output_path = sys.argv[-1] # Open the input image file. image_plus = IJ.openImage(input_file) # Create an ImagePlus object for the image. image_plus_copy = image_plus.duplicate() # Perform the analysis on the ImagePlus object. try: if filter == "gaussian_blur": IJ.run(image_plus_copy, "Gaussian Blur...", "sigma=%s stack" % radius) elif filter in ["median", "mean", "minimum", "maximum", "variance"]: IJ.run(image_plus_copy, "%s..." % filter.title(), "radius=%s stack" % radius) elif filter == "unsharp_mask": IJ.run(image_plus_copy, "Unsharp Mask...", "radius=%s mask=%s stack" % (radius, mask)) elif filter == "top_hat": print("radius=%s %s %s" % (radius, light_background, dont_substract.replace('dont', "don't"))) IJ.run(image_plus_copy, "Top Hat...", "radius=%s %s %s stack" % (radius, light_background, dont_substract.replace('dont', "don't"))) except Exception as e: # This is due to some operations like gaussian_blur which block the script print(e) exit(1) # Save the ImagePlus object as a new image. IJ.saveAs(image_plus_copy, image_datatype, tmp_output_path) # This is due to some operations like gaussian_blur which block the script exit(0)