Mercurial > repos > iuc > imagej2_binary_to_edm

annotate imagej2_bunwarpj_align_jython_script.py @ 2:c58b939c862a 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 23:15:40 -0400
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2
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
1 import sys
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
2 import jython_utils
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
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3 from ij import IJ
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
4
c58b939c862a 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
c58b939c862a 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.
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
7
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
8 if sys.argv[ -1 ].lower() in [ 'true' ]:
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
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9 mono = True
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
10 else:
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
11 mono = False
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
12
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
13 if mono:
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
14 # bUnwarpJ has been called with the -mono param.
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
15 source_tiff_path = sys.argv[ -4 ]
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
16 source_datatype = sys.argv[ -3 ]
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
17 source_path = sys.argv[ -2 ]
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
18 else:
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
19 source_tiff_path = sys.argv[ -7 ]
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
20 source_datatype = sys.argv[ -6 ]
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
21 source_path = sys.argv[ -5 ]
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
22 target_tiff_path = sys.argv[ -4 ]
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
23 target_datatype = sys.argv[ -3 ]
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
24 target_path = sys.argv[ -2 ]
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
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25
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
26 # Save the Registered Source Image.
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
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27 registered_source_image = IJ.openImage( source_tiff_path )
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
28 if source_datatype == 'tiff':
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
29 registered_source_image = jython_utils.convert_before_saving_as_tiff( registered_source_image )
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
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30 IJ.saveAs( registered_source_image, source_datatype, source_path )
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
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31
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
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32 if not mono:
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
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33 # Save the Registered Target Image.
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
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34 registered_target_image = IJ.openImage( target_tiff_path )
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
35 if target_datatype == 'tiff':
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
36 registered_target_image = jython_utils.convert_before_saving_as_tiff( registered_target_image )
c58b939c862a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents:
diff changeset
37 IJ.saveAs( registered_target_image, target_datatype, target_path )