Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
comparison imagej2_bunwarpj_compare_elastic_raw.py @ 0:95fb6fa70c2f draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
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date | Tue, 17 Sep 2019 17:06:56 -0400 |
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-1:000000000000 | 0:95fb6fa70c2f |
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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( '--target_elastic_transformation', dest='target_elastic_transformation', help='Target elastic transformation matrix' ) | |
14 parser.add_argument( '--source_raw_transformation', dest='source_raw_transformation', help='Source raw 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 target_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_elastic_transformation, 'txt' ) | |
23 source_raw_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_raw_transformation, 'txt' ) | |
24 # bUnwarpJ produces several lines of output that we need to discard, so | |
25 # we'll use a temporary output file from which we'll read only the last line. | |
26 tmp_output_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.output, 'txt' ) | |
27 | |
28 # Define command response buffers. | |
29 tmp_out = tempfile.NamedTemporaryFile().name | |
30 tmp_stdout = open( tmp_out, 'wb' ) | |
31 tmp_err = tempfile.NamedTemporaryFile().name | |
32 tmp_stderr = open( tmp_err, 'wb' ) | |
33 | |
34 # Build the command line to calculate the warping index. | |
35 cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None ) | |
36 if cmd is None: | |
37 imagej2_base_utils.stop_err( "bUnwarpJ not found!" ) | |
38 cmd += ' -compare_elastic_raw' | |
39 cmd += ' %s' % target_image_path | |
40 cmd += ' %s' % source_image_path | |
41 cmd += ' %s' % target_elastic_transformation_path | |
42 cmd += ' %s' % source_raw_transformation_path | |
43 cmd += ' > %s' % tmp_output_path | |
44 | |
45 # Calculate the warping index of elastic and raw transformations using bUnwarpJ. | |
46 proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True ) | |
47 rc = proc.wait() | |
48 if rc != 0: | |
49 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout ) | |
50 imagej2_base_utils.stop_err( error_message ) | |
51 | |
52 # Example contents of tmp_output_path: | |
53 # ['Target image : ~/tmpHdt9Cs.jpg\n', | |
54 # 'Source image : ~/tmpu6kyfc.gif\n', | |
55 # 'Elastic Transformation file : ~/tmp4vZurG.txt\n', | |
56 # 'Raw Transformation file : ~/tmp2PNQcT.txt\n', | |
57 # ' Warping index = 25.007467512204983\n'] | |
58 results = open( tmp_output_path, 'r' ).readlines() | |
59 warp_index = results[ -1 ].split( ' ' )[ -1 ] | |
60 outf = open( args.output, 'wb' ) | |
61 outf.write( '%s' % warp_index ) | |
62 outf.close() | |
63 | |
64 imagej2_base_utils.cleanup_before_exit( tmp_dir ) |