Mercurial > repos > imgteam > imagej2_analyze_particles_binary
comparison imagej2_sharpen.py @ 0:aeb9bb864b8c 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 16:56:37 -0400 |
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-1:000000000000 | 0:aeb9bb864b8c |
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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 parser = argparse.ArgumentParser() | |
10 parser.add_argument( '--input', dest='input', help='Path to the input file' ) | |
11 parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' ) | |
12 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) | |
13 parser.add_argument( '--output', dest='output', help='Path to the output file' ) | |
14 parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' ) | |
15 args = parser.parse_args() | |
16 | |
17 tmp_dir = imagej2_base_utils.get_temp_dir() | |
18 # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not | |
19 # work for some features. The following creates a symlink with an appropriate file | |
20 # extension that points to the Galaxy dataset. This symlink is used by ImageJ. | |
21 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype ) | |
22 tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype ) | |
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 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors. | |
30 error_log = tempfile.NamedTemporaryFile( delete=False ).name | |
31 | |
32 # Build the command line. | |
33 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script ) | |
34 if cmd is None: | |
35 imagej2_base_utils.stop_err( "ImageJ not found!" ) | |
36 cmd += ' %s' % error_log | |
37 cmd += ' %s' % tmp_input_path | |
38 cmd += ' %s' % tmp_output_path | |
39 cmd += ' %s' % args.output_datatype | |
40 | |
41 # Run the command. | |
42 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True ) | |
43 rc = proc.wait() | |
44 | |
45 # Handle execution errors. | |
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 # Handle processing errors. | |
51 if os.path.getsize( error_log ) > 0: | |
52 error_message = open( error_log, 'r' ).read() | |
53 imagej2_base_utils.stop_err( error_message ) | |
54 | |
55 # Save the output image. | |
56 shutil.move( tmp_output_path, args.output ) | |
57 imagej2_base_utils.cleanup_before_exit( tmp_dir ) |