Mercurial > repos > imgteam > imagej2_bunwarpj_adapt_transform
comparison imagej2_bunwarpj_align.py @ 0:706af1d7028a 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 17:11:26 -0400 |
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-1:000000000000 | 0:706af1d7028a |
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1 #!/usr/bin/env python | |
2 import argparse | |
3 import os | |
4 import shutil | |
5 import subprocess | |
6 import tempfile | |
7 import imagej2_base_utils | |
8 | |
9 # Parse Command Line. | |
10 parser = argparse.ArgumentParser() | |
11 parser.add_argument( '--source_image', dest='source_image', help='Source image' ) | |
12 parser.add_argument( '--source_image_format', dest='source_image_format', help='Source image format' ) | |
13 parser.add_argument( '--source_mask', dest='source_mask', default=None, help='Source mask' ) | |
14 parser.add_argument( '--source_mask_format', dest='source_mask_format', default=None, help='Source mask image format' ) | |
15 parser.add_argument( '--target_image', dest='target_image', help='Target image' ) | |
16 parser.add_argument( '--target_image_format', dest='target_image_format', help='Target image format' ) | |
17 parser.add_argument( '--target_mask', dest='target_mask', default=None, help='Target mask' ) | |
18 parser.add_argument( '--target_mask_format', dest='target_mask_format', default=None, help='Target mask image format' ) | |
19 parser.add_argument( '--min_scale_def', dest='min_scale_def', type=int, help='Initial deformation' ) | |
20 parser.add_argument( '--max_scale_def', dest='max_scale_def', type=int, help='Final deformation' ) | |
21 parser.add_argument( '--max_subsamp_fact', dest='max_subsamp_fact', type=int, help='Image sub-sample factor' ) | |
22 parser.add_argument( '--divergence_weight', dest='divergence_weight', type=float, help='Divergence weight' ) | |
23 parser.add_argument( '--curl_weight', dest='curl_weight', type=float, help='Curl weight' ) | |
24 parser.add_argument( '--image_weight', dest='image_weight', type=float, help='Image weight' ) | |
25 parser.add_argument( '--consistency_weight', dest='consistency_weight', type=float, help='Consistency weight' ) | |
26 parser.add_argument( '--landmarks_weight', dest='landmarks_weight', type=float, help='Landmarks weight' ) | |
27 parser.add_argument( '--landmarks_file', dest='landmarks_file', default=None, help='Landmarks file' ) | |
28 parser.add_argument( '--source_affine_file', dest='source_affine_file', default=None, help='Initial source affine matrix transformation' ) | |
29 parser.add_argument( '--target_affine_file', dest='target_affine_file', default=None, help='Initial target affine matrix transformation' ) | |
30 parser.add_argument( '--mono', dest='mono', default=False, help='Unidirectional registration (source to target)' ) | |
31 parser.add_argument( '--source_trans_out', dest='source_trans_out', default=None, help='Direct source transformation matrix' ) | |
32 parser.add_argument( '--target_trans_out', dest='target_trans_out', default=None, help='Inverse target transformation matrix' ) | |
33 parser.add_argument( '--source_out', help='Output source image' ) | |
34 parser.add_argument( '--source_out_datatype', help='Output registered source image format' ) | |
35 parser.add_argument( '--target_out', default=None, help='Output target image' ) | |
36 parser.add_argument( '--target_out_datatype', default=None, help='Output registered target image format' ) | |
37 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) | |
38 | |
39 args = parser.parse_args() | |
40 | |
41 if args.source_trans_out is not None and args.target_trans_out is not None: | |
42 save_transformation = True | |
43 else: | |
44 save_transformation = False | |
45 | |
46 tmp_dir = imagej2_base_utils.get_temp_dir() | |
47 source_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_image, args.source_image_format ) | |
48 tmp_source_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' ) | |
49 tmp_source_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.source_out_datatype ) | |
50 target_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_image, args.target_image_format ) | |
51 if not args.mono: | |
52 tmp_target_out_tiff_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'tiff' ) | |
53 tmp_target_out_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.target_out_datatype ) | |
54 if args.source_mask is not None and args.target_mask is not None: | |
55 tmp_source_mask_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.source_mask, args.source_mask_format ) | |
56 tmp_target_mask_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.target_mask, args.target_mask_format ) | |
57 if save_transformation: | |
58 # bUnwarpJ automatically names the transformation files based on the names | |
59 # of the source and target image file names. We've defined symlinks to | |
60 # temporary files with valid image extensions since ImageJ does not handle | |
61 # the Galaxy "dataset.dat" file extensions. | |
62 source_file_name = imagej2_base_utils.get_file_name_without_extension( tmp_source_out_tiff_path ) | |
63 tmp_source_out_transf_path = os.path.join( tmp_dir, '%s_transf.txt' % source_file_name ) | |
64 target_file_name = imagej2_base_utils.get_file_name_without_extension( tmp_target_out_tiff_path ) | |
65 tmp_target_out_transf_path = os.path.join( tmp_dir, '%s_transf.txt' % target_file_name ) | |
66 | |
67 # Define command response buffers. | |
68 tmp_out = tempfile.NamedTemporaryFile().name | |
69 tmp_stdout = open( tmp_out, 'wb' ) | |
70 tmp_err = tempfile.NamedTemporaryFile().name | |
71 tmp_stderr = open( tmp_err, 'wb' ) | |
72 | |
73 # Build the command line to align the two images. | |
74 cmd = imagej2_base_utils.get_base_cmd_bunwarpj( None ) | |
75 if cmd is None: | |
76 imagej2_base_utils.stop_err( "bUnwarpJ not found!" ) | |
77 cmd += ' -align' | |
78 # Target is sent before source. | |
79 cmd += ' %s' % target_image_path | |
80 if args.target_mask is None: | |
81 target_mask_str = ' NULL' | |
82 else: | |
83 target_mask_str = ' %s' % tmp_target_mask_path | |
84 cmd += target_mask_str | |
85 cmd += ' %s' % source_image_path | |
86 if args.source_mask is None: | |
87 source_mask_str = ' NULL' | |
88 else: | |
89 source_mask_str = ' %s' % tmp_source_mask_path | |
90 cmd += source_mask_str | |
91 cmd += ' %d' % args.min_scale_def | |
92 cmd += ' %d' % args.max_scale_def | |
93 cmd += ' %d' % args.max_subsamp_fact | |
94 cmd += ' %.1f' % args.divergence_weight | |
95 cmd += ' %.1f' % args.curl_weight | |
96 cmd += ' %.1f' % args.image_weight | |
97 cmd += ' %.1f' % args.consistency_weight | |
98 # Source is produced before target. | |
99 cmd += ' %s' % tmp_source_out_tiff_path | |
100 if not args.mono: | |
101 cmd += ' %s' % tmp_target_out_tiff_path | |
102 if args.landmarks_file is not None: | |
103 # We have to create a temporary file with a .txt extension here so that | |
104 # bUnwarpJ will not ignore the Galaxy "dataset.dat" file. | |
105 tmp_landmarks_file_path = imagej2_base_utils.get_input_image_path( tmp_dir, | |
106 args.landmarks_file, | |
107 'txt' ) | |
108 cmd += ' -landmarks' | |
109 cmd += ' %.1f' % args.landmarks_weight | |
110 cmd += ' %s' % tmp_landmarks_file_path | |
111 if args.source_affine_file is not None and args.target_affine_file is not None: | |
112 # Target is sent before source. | |
113 cmd += ' -affine' | |
114 cmd += ' %s' % args.target_affine_file | |
115 cmd += ' %s' % args.source_affine_file | |
116 if args.mono: | |
117 cmd += ' -mono' | |
118 if save_transformation: | |
119 cmd += ' -save_transformation' | |
120 | |
121 # Align the two images using bUnwarpJ. | |
122 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True ) | |
123 rc = proc.wait() | |
124 if rc != 0: | |
125 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout ) | |
126 imagej2_base_utils.stop_err( error_message ) | |
127 | |
128 # bUnwarpJ produces tiff image stacks consisting of 3 slices which can be viewed in ImageJ. | |
129 # The 3 slices are:: 1) the registered image, 2) the target image and 3) the black/white | |
130 # warp image. Galaxy supports only single-layered images, so we'll convert the images so they | |
131 # can be viewed in Galaxy. | |
132 | |
133 # Define command response buffers. | |
134 tmp_out = tempfile.NamedTemporaryFile().name | |
135 tmp_stdout = open( tmp_out, 'wb' ) | |
136 tmp_err = tempfile.NamedTemporaryFile().name | |
137 tmp_stderr = open( tmp_err, 'wb' ) | |
138 | |
139 # Build the command line to handle the multi-slice tiff images. | |
140 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script ) | |
141 if cmd is None: | |
142 imagej2_base_utils.stop_err( "ImageJ not found!" ) | |
143 if args.mono: | |
144 # bUnwarpJ will produce only a registered source image. | |
145 cmd += ' %s %s %s %s' % ( tmp_source_out_tiff_path, | |
146 args.source_out_datatype, | |
147 tmp_source_out_path, | |
148 args.mono ) | |
149 else: | |
150 # bUnwarpJ will produce registered source and target images. | |
151 cmd += ' %s %s %s %s %s %s %s' % ( tmp_source_out_tiff_path, | |
152 args.source_out_datatype, | |
153 tmp_source_out_path, | |
154 tmp_target_out_tiff_path, | |
155 args.target_out_datatype, | |
156 tmp_target_out_path, | |
157 args.mono ) | |
158 | |
159 # Merge the multi-slice tiff layers into an image that can be viewed in Galaxy. | |
160 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True ) | |
161 rc = proc.wait() | |
162 if rc != 0: | |
163 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout ) | |
164 imagej2_base_utils.stop_err( error_message ) | |
165 | |
166 # Save the Registered Source Image to the output dataset. | |
167 shutil.move( tmp_source_out_path, args.source_out ) | |
168 if not args.mono: | |
169 # Move the Registered Target Image to the output dataset. | |
170 shutil.move( tmp_target_out_path, args.target_out ) | |
171 | |
172 # If requested, save matrix transformations as additional datasets. | |
173 if save_transformation: | |
174 shutil.move( tmp_source_out_transf_path, args.source_trans_out ) | |
175 if not args.mono: | |
176 shutil.move( tmp_target_out_transf_path, args.target_trans_out ) | |
177 | |
178 imagej2_base_utils.cleanup_before_exit( tmp_dir ) |