Mercurial > repos > bgruening > imagej2_crop

annotate imagej2_skeletonize3d_jython_script.py @ 0:018144807556 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author bgruening
date Tue, 24 Sep 2024 17:12:52 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
1 import sys
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
2
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
3 from ij import IJ
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
4
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
5 # Fiji Jython interpreter implements Python 2.5 which does not
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
6 # provide support for argparse.
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
7 input_file = sys.argv[-4]
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
8 black_background = sys.argv[-3] == "yes"
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
9 tmp_output_path = sys.argv[-2]
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
10 output_datatype = sys.argv[-1]
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
11
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
12 # Open the input image file.
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
13 input_image_plus = IJ.openImage(input_file)
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
14
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
15 # Create a copy of the image.
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
16 input_image_plus_copy = input_image_plus.duplicate()
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
17 image_processor_copy = input_image_plus_copy.getProcessor()
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
18
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
19 # Set binary options.
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
20 options = ["edm=Overwrite", "iterations=1", "count=1"]
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
21 if black_background:
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
22 options.append("black")
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
23 options = " ".join(options)
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
24 IJ.run(input_image_plus_copy, "Options...", options)
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
25
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
26 # Convert image to binary if necessary.
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
27 if not image_processor_copy.isBinary():
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
28 # Convert the image to binary grayscale.
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
29 IJ.run(input_image_plus_copy, "Make Binary", "")
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
30
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
31 # Run the command.
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
32 IJ.run(input_image_plus_copy, "Skeletonize (2D/3D)", "")
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
33
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
34 # Save the ImagePlus object as a new image.
018144807556 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
bgruening
parents:
diff changeset
35 IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)