Mercurial > repos > imgteam > imagej2_binary_to_edm
comparison imagej2_filter_jython_script.py @ 3:91b8f4730a93 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 16:07:20 +0000 |
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2:182994b12622 | 3:91b8f4730a93 |
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1 import sys | |
2 | |
3 from ij import IJ | |
4 | |
5 # Fiji Jython interpreter implements Python 2.5 which does not | |
6 # provide support for argparse. | |
7 input_file = sys.argv[-8] | |
8 image_datatype = sys.argv[-7] | |
9 filter = sys.argv[-6] | |
10 radius = sys.argv[-5] | |
11 mask = sys.argv[-4] | |
12 light_background = sys.argv[-3] | |
13 dont_substract = sys.argv[-2] | |
14 tmp_output_path = sys.argv[-1] | |
15 | |
16 # Open the input image file. | |
17 image_plus = IJ.openImage(input_file) | |
18 # Create an ImagePlus object for the image. | |
19 image_plus_copy = image_plus.duplicate() | |
20 | |
21 # Perform the analysis on the ImagePlus object. | |
22 try: | |
23 if filter == "gaussian_blur": | |
24 IJ.run(image_plus_copy, "Gaussian Blur...", "sigma=%s stack" % radius) | |
25 elif filter in ["median", "mean", "minimum", "maximum", "variance"]: | |
26 IJ.run(image_plus_copy, "%s..." % filter.title(), "radius=%s stack" % radius) | |
27 elif filter == "unsharp_mask": | |
28 IJ.run(image_plus_copy, "Unsharp Mask...", "radius=%s mask=%s stack" % (radius, mask)) | |
29 elif filter == "top_hat": | |
30 print("radius=%s %s %s" % (radius, light_background, dont_substract.replace('dont', "don't"))) | |
31 IJ.run(image_plus_copy, "Top Hat...", "radius=%s %s %s stack" % (radius, light_background, dont_substract.replace('dont', "don't"))) | |
32 except Exception as e: | |
33 # This is due to some operations like gaussian_blur which block the script | |
34 print(e) | |
35 exit(1) | |
36 # Save the ImagePlus object as a new image. | |
37 IJ.saveAs(image_plus_copy, image_datatype, tmp_output_path) | |
38 # This is due to some operations like gaussian_blur which block the script | |
39 exit(0) |