Mercurial > repos > imgteam > imagej2_bunwarpj_compose_raw

comparison imagej2_analyze_skeleton.py @ 0:93b416f8e9e3 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 17:00:19 -0400
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-1:000000000000 0:93b416f8e9e3
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( '--black_background', dest='black_background', help='Black background' )
13 parser.add_argument( '--prune_cycle_method', dest='prune_cycle_method', default='none', help='Prune cycle method' )
14 parser.add_argument( '--prune_ends', dest='prune_ends', default='no', help='Prune ends' )
15 parser.add_argument( '--calculate_largest_shortest_path', dest='calculate_largest_shortest_path', default='no', help='Calculate largest shortest path' )
16 parser.add_argument( '--show_detailed_info', dest='show_detailed_info', default='no', help='Show detailed info' )
17 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
18 parser.add_argument( '--output', dest='output', help='Path to the output file' )
19 args = parser.parse_args()
20
21 tmp_dir = imagej2_base_utils.get_temp_dir()
22 # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not
23 # work for some features. The following creates a symlink with an appropriate file
24 # extension that points to the Galaxy dataset. This symlink is used by ImageJ.
25 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
26
27 # Define command response buffers.
28 tmp_out = tempfile.NamedTemporaryFile().name
29 tmp_stdout = open( tmp_out, 'wb' )
30 tmp_err = tempfile.NamedTemporaryFile().name
31 tmp_stderr = open( tmp_err, 'wb' )
32 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
33 error_log = tempfile.NamedTemporaryFile( delete=False ).name
34
35 # Build the command line.
36 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
37 if cmd is None:
38 imagej2_base_utils.stop_err( "ImageJ not found!" )
39 cmd += ' %s' % error_log
40 cmd += ' %s' % tmp_input_path
41 cmd += ' %s' % args.black_background
42 cmd += ' %s' % args.prune_cycle_method
43 cmd += ' %s' % args.prune_ends
44 cmd += ' %s' % args.calculate_largest_shortest_path
45 cmd += ' %s' % args.show_detailed_info
46 cmd += ' %s' % args.output
47
48 # Run the command.
49 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
50 rc = proc.wait()
51
52 # Handle execution errors.
53 if rc != 0:
54 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
55 imagej2_base_utils.stop_err( error_message )
56 # Handle processing errors.
57 if os.path.getsize( error_log ) > 0:
58 error_message = open( error_log, 'r' ).read()
59 imagej2_base_utils.stop_err( error_message )
60
61 imagej2_base_utils.cleanup_before_exit( tmp_dir )