Mercurial > repos > imgteam > imagej2_skeletonize3d

comparison imagej2_bunwarpj_compose_raw_elastic.py @ 0:f6df6830d5ec draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 16:57:15 -0400
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-1:000000000000 0:f6df6830d5ec
1 #!/usr/bin/env python
2 import argparse
3 import subprocess
4 import tempfile
5 import imagej2_base_utils
6
7 # Parse Command Line.
8 parser = argparse.ArgumentParser()
9 parser.add_argument( '--source_image', dest='source_image', help='Source image' )
10 parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
11 parser.add_argument( '--target_image', dest='target_image', help='Target image' )
12 parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
13 parser.add_argument( '--source_elastic_transformation', dest='source_elastic_transformation', help='Direct source transformation matrix' )
14 parser.add_argument( '--target_raw_transformation', dest='target_raw_transformation', help='Inverse target transformation matrix' )
15 parser.add_argument( '--output', dest='output', help='Warping index' )
16
17 args = parser.parse_args()
18
19 tmp_dir = imagej2_base_utils.get_temp_dir()
20 source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
21 target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
22 source_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_elastic_transformation, 'txt' )
23 target_raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_raw_transformation, 'txt' )
24
25 # Define command response buffers.
26 tmp_out = tempfile.NamedTemporaryFile().name
27 tmp_stdout = open( tmp_out, 'wb' )
28 tmp_err = tempfile.NamedTemporaryFile().name
29 tmp_stderr = open( tmp_err, 'wb' )
30
31 # Build the command line to compose the raw and elastic transformations.
32 cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
33 if cmd is None:
34 imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
35 cmd += ' -compose_raw_elastic'
36 # Target is sent before source.
37 cmd += ' %s' % target_image_path
38 cmd += ' %s' % source_image_path
39 cmd += ' %s' % target_raw_transformation_path
40 cmd += ' %s' % source_elastic_transformation_path
41 cmd += ' %s' % args.output
42
43 # Compose the raw and elastic transformations into another raw transformation using bUnwarpJ.
44 proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True )
45 rc = proc.wait()
46 if rc != 0:
47 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
48 imagej2_base_utils.stop_err( error_message )
49
50 imagej2_base_utils.cleanup_before_exit( tmp_dir )