Mercurial > repos > imgteam > imagej2_sharpen

comparison imagej2_bunwarpj_adapt_transform.py @ 0:a84f2cbf091b 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 17:08:08 -0400
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-1:000000000000 0:a84f2cbf091b
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( '--input_elastic_transformation', dest='input_elastic_transformation', help='Input elastic transformation matrix' )
14 parser.add_argument( '--image_size_factor', dest='image_size_factor', type=float, help='Image size factor' )
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 input_elastic_transformation_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input_elastic_transformation, 'txt' )
23
24 # Define command response buffers.
25 tmp_out = tempfile.NamedTemporaryFile().name
26 tmp_stdout = open( tmp_out, 'wb' )
27 tmp_err = tempfile.NamedTemporaryFile().name
28 tmp_stderr = open( tmp_err, 'wb' )
29
30 def is_power2( val ):
31 if val < 0:
32 return False
33 if val < 1:
34 val = 1.0 / val
35 val = int( val )
36 return ( ( val & ( val - 1 ) ) == 0 )
37
38 # Build the command line to adapt the transformation.
39 cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None )
40 if cmd is None:
41 imagej2_base_utils.stop_err( "bUnwarpJ not found!" )
42 cmd += ' -adapt_transform'
43
44 # Make sure the value of image_size_factor is a power of 2 (positive or negative).
45 if is_power2( args.image_size_factor ):
46 image_size_factor = args.image_size_factor
47 else:
48 msg = "Image size factor must be a positive or negative power of 2 (0.25, 0.5, 2, 4, 8, etc)."
49 imagej2_base_utils.stop_err( msg )
50
51 # Target is sent before source.
52 cmd += ' %s' % target_image_path
53 cmd += ' %s' % source_image_path
54 cmd += ' %s' % input_elastic_transformation_path
55 cmd += ' %s' % args.output
56 cmd += ' %2.f' % image_size_factor
57
58 # Adapt the transformation based on the image size factor using bUnwarpJ.
59 proc = subprocess.Popen( args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True )
60 rc = proc.wait()
61 if rc != 0:
62 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
63 imagej2_base_utils.stop_err( error_message )
64
65 imagej2_base_utils.cleanup_before_exit( tmp_dir )