Mercurial > repos > imgteam > imagej2_shadows

comparison imagej2_find_maxima.py @ 0:7baf811ed973 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 16:59:39 -0400
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-1:000000000000 0:7baf811ed973
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( '--scale_when_converting', dest='scale_when_converting', help='Scale when converting RGB image' )
13 parser.add_argument( '--weighted_rgb_conversions', dest='weighted_rgb_conversions', help='Weighted RGB conversions for RGB image' )
14 parser.add_argument( '--noise_tolerance', dest='noise_tolerance', type=int, help='Noise tolerance' )
15 parser.add_argument( '--output_type', dest='output_type', help='Output type' )
16 parser.add_argument( '--exclude_edge_maxima', dest='exclude_edge_maxima', help='Exclude edge maxima' )
17 parser.add_argument( '--light_background', dest='light_background', help='Light background' )
18 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
19 parser.add_argument( '--output', dest='output', help='Path to the output file' )
20 parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' )
21 args = parser.parse_args()
22
23 tmp_dir = imagej2_base_utils.get_temp_dir()
24 # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not
25 # work for some features. The following creates a symlink with an appropriate file
26 # extension that points to the Galaxy dataset. This symlink is used by ImageJ.
27 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
28 tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
29
30 # Define command response buffers.
31 tmp_out = tempfile.NamedTemporaryFile().name
32 tmp_stdout = open( tmp_out, 'wb' )
33 tmp_err = tempfile.NamedTemporaryFile().name
34 tmp_stderr = open( tmp_err, 'wb' )
35 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
36 error_log = tempfile.NamedTemporaryFile( delete=False ).name
37
38 # Build the command line.
39 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
40 if cmd is None:
41 imagej2_base_utils.stop_err( "ImageJ not found!" )
42 cmd += ' %s' % error_log
43 cmd += ' %s' % tmp_input_path
44 cmd += ' %s' % args.scale_when_converting
45 cmd += ' %s' % args.weighted_rgb_conversions
46 cmd += ' %d' % args.noise_tolerance
47 cmd += ' %s' % args.output_type
48 cmd += ' %s' % args.exclude_edge_maxima
49 cmd += ' %s' % args.light_background
50 cmd += ' %s' % tmp_output_path
51 cmd += ' %s' % args.output_datatype
52
53 # Run the command.
54 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
55 rc = proc.wait()
56
57 # Handle execution errors.
58 if rc != 0:
59 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
60 imagej2_base_utils.stop_err( error_message )
61
62 # Handle processing errors.
63 if os.path.getsize( error_log ) > 0:
64 error_message = open( error_log, 'r' ).read()
65 imagej2_base_utils.stop_err( error_message )
66
67 # Save the output image.
68 shutil.move( tmp_output_path, args.output )
69 imagej2_base_utils.cleanup_before_exit( tmp_dir )