Mercurial > repos > bgruening > imagej2_bunwarpj_convert_to_raw

annotate imagej2_bunwarpj_convert_to_raw.py @ 0:191d574ddd8d 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 b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
author bgruening
date Sat, 18 Mar 2017 09:43:20 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
1 #!/usr/bin/env python
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
2 import argparse
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
3 import subprocess
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
4 import tempfile
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
5 import imagej2_base_utils
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
6
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
7 # Parse Command Line.
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
8 parser = argparse.ArgumentParser()
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
9 parser.add_argument( '--source_image', dest='source_image', help='Source image' )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
10 parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
11 parser.add_argument( '--target_image', dest='target_image', help='Target image' )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
12 parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
13 parser.add_argument( '--elastic_transformation', dest='elastic_transformation', help='Elastic transformation as saved by bUnwarpJ in elastic format' )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
14 parser.add_argument( '--raw_transformation', dest='raw_transformation', help='Raw transformation' )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
15
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
16 args = parser.parse_args()
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
17
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
18 tmp_dir = imagej2_base_utils.get_temp_dir()
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
19 source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
20 target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
21 elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.elastic_transformation, 'txt' )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
22
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
23 # Define command response buffers.
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
24 tmp_out = tempfile.NamedTemporaryFile().name
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
25 tmp_stdout = open( tmp_out, 'wb' )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
26 tmp_err = tempfile.NamedTemporaryFile().name
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
27 tmp_stderr = open( tmp_err, 'wb' )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
28
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
29 # Build the command line to convert the B-spline (i.e., elastic) transformation to raw.
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
30 cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
31 if cmd is None:
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
32 imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
33 cmd += ' -convert_to_raw'
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
34 # Target is sent before source.
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
35 cmd += ' %s' % target_image_path
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
36 cmd += ' %s' % source_image_path
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
37 cmd += ' %s' % elastic_transformation_path
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
38 cmd += ' %s' % args.raw_transformation
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
39
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
40 # Convert the elastic transformation to raw using bUnwarpJ.
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
41 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
42 rc = proc.wait()
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
43 if rc != 0:
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
44 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
45 imagej2_base_utils.stop_err( error_message )
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
46
191d574ddd8d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
bgruening
parents:
diff changeset
47 imagej2_base_utils.cleanup_before_exit( tmp_dir )