Mercurial > repos > imgteam > imagej2_noise

comparison imagej2_skeletonize3d.py @ 0:3f6599ec7d30 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 16:58:28 -0400
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-1:000000000000 0:3f6599ec7d30
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( '--jython_script', dest='jython_script', help='Path to the Jython script' )
14 parser.add_argument( '--output', dest='output', help='Path to the output file' )
15 parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' )
16 args = parser.parse_args()
17
18 tmp_dir = imagej2_base_utils.get_temp_dir()
19 # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not
20 # work for some features. The following creates a symlink with an appropriate file
21 # extension that points to the Galaxy dataset. This symlink is used by ImageJ.
22 tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype )
23 tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
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 # Build the command line.
32 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
33 if cmd is None:
34 imagej2_base_utils.stop_err( "ImageJ not found!" )
35 cmd += ' %s' % error_log
36 cmd += ' %s' % tmp_input_path
37 cmd += ' %s' % args.black_background
38 cmd += ' %s' % tmp_output_path
39 cmd += ' %s' % args.output_datatype
40 # Run the command.
41 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True )
42 rc = proc.wait()
43 # Handle execution errors.
44 if rc != 0:
45 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout )
46 imagej2_base_utils.stop_err( error_message )
47 # Handle processing errors.
48 if os.path.getsize( error_log ) > 0:
49 error_message = open( error_log, 'r' ).read()
50 imagej2_base_utils.stop_err( error_message )
51 # Save the output image.
52 shutil.move( tmp_output_path, args.output )
53 imagej2_base_utils.cleanup_before_exit( tmp_dir )