Mercurial > repos > imgteam > imagej2_bunwarpj_elastic_transform

comparison imagej2_bunwarpj_elastic_transform.py @ 0:301f24849032 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 17:10:48 -0400
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-1:000000000000 0:301f24849032
1 #!/usr/bin/env python
2 import argparse
3 import shutil
4 import subprocess
5 import tempfile
6 import imagej2_base_utils
7
8 # Parse Command Line.
9 parser = argparse.ArgumentParser()
10 parser.add_argument( '--source_image', dest='source_image', help='Source image' )
11 parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' )
12 parser.add_argument( '--target_image', dest='target_image', help='Target image' )
13 parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' )
14 parser.add_argument( '--elastic_transformation', dest='elastic_transformation', help='Elastic transformation as saved by bUnwarpJ in elastic format' )
15 parser.add_argument( '--source_out', help='Output source image' )
16 parser.add_argument( '--source_out_datatype', help='Output registered source image format' )
17 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
18
19 args = parser.parse_args()
20
21 tmp_dir = imagej2_base_utils.get_temp_dir()
22 source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format )
23 tmp_source_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' )
24 tmp_source_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.source_out_datatype )
25 target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format )
26 elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.elastic_transformation, '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 apply the transformation.
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 += ' -elastic_transform'
39 # Target is sent before source.
40 cmd += ' %s' % target_image_path
41 cmd += ' %s' % source_image_path
42 cmd += ' %s' % elastic_transformation_path
43 cmd += ' %s' % tmp_source_out_tiff_path
44
45 # Apply the elastic transformation using bUnwarpJ.
46 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, 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 # Convert the registered image to the specified output format.
53 tmp_out = tempfile.NamedTemporaryFile().name
54 tmp_stdout = open( tmp_out, 'wb' )
55 tmp_err = tempfile.NamedTemporaryFile().name
56 tmp_stderr = open( tmp_err, 'wb' )
57
58 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
59 if cmd is None:
60 imagej2_base_utils.stop_err( "ImageJ not found!" )
61 cmd += ' %s %s %s' % ( tmp_source_out_tiff_path,
62 args.source_out_datatype,
63 tmp_source_out_path )
64
65 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
66 rc = proc.wait()
67 if rc != 0:
68 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
69 imagej2_base_utils.stop_err( error_message )
70
71 # Save the Registered Source Image to the defined output.
72 shutil.move( tmp_source_out_path, args.source_out )
73 imagej2_base_utils.cleanup_before_exit( tmp_dir )