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annotate imagej2_find_edges_jython_script.py @ 2:ef4de385bbde draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
author iuc
date Fri, 22 Jul 2016 23:22:12 -0400
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ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
1 import jython_utils
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
2 import sys
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
3 from ij import IJ
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
4
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
5 # Fiji Jython interpreter implements Python 2.5 which does not
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
6 # provide support for argparse.
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
7 error_log = sys.argv[ -4 ]
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
8 input = sys.argv[ -3 ]
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
9 tmp_output_path = sys.argv[ -2 ]
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
10 output_datatype = sys.argv[ -1 ]
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
11
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
12 # Open the input image file.
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
13 input_image_plus = IJ.openImage( input )
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
14
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
15 # Create a copy of the image.
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
16 input_image_plus_copy = input_image_plus.duplicate()
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
17 image_processor_copy = input_image_plus_copy.getProcessor()
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
18
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
19 try:
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
20 # Run the command.
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
21 IJ.run( input_image_plus_copy, "Find Edges", "" )
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
22 # Save the ImagePlus object as a new image.
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
23 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
24 except Exception, e:
ef4de385bbde planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
25 jython_utils.handle_error( error_log, str( e ) )