Mercurial > repos > imgteam > imagej2_enhance_contrast

comparison imagej2_math.py @ 0:2560c3f1445a draft default tip

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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 16:57:26 -0400
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-1:000000000000 0:2560c3f1445a
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( '--operation', dest='operation', help='Operation' )
13 parser.add_argument( '--expression', dest='expression', default=None, help='Expression' )
14 parser.add_argument( '--bin_constant', dest='bin_constant', type=int, default=None, help='Constant of type binary integer' )
15 parser.add_argument( '--float_constant', dest='float_constant', type=float, default=None, help='Constant of type float' )
16 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
17 parser.add_argument( '--output', dest='output', help='Path to the output file' )
18 parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' )
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 tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
27
28 # Define command response buffers.
29 tmp_out = tempfile.NamedTemporaryFile().name
30 tmp_stdout = open( tmp_out, 'wb' )
31 tmp_err = tempfile.NamedTemporaryFile().name
32 tmp_stderr = open( tmp_err, 'wb' )
33 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
34 error_log = tempfile.NamedTemporaryFile( delete=False ).name
35
36 # Build the command line.
37 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
38 if cmd is None:
39 imagej2_base_utils.stop_err( "ImageJ not found!" )
40 cmd += ' %s' % error_log
41 cmd += ' %s' % tmp_input_path
42 cmd += ' %s' % args.operation
43 # Handle the expression, which must be enclosed in " if not None.
44 if args.expression in [ None, 'None' ]:
45 cmd += ' None'
46 else:
47 cmd += ' "%s"' % args.expression
48 cmd += imagej2_base_utils.handle_none_type( args.bin_constant, val_type='int' )
49 cmd += imagej2_base_utils.handle_none_type( args.float_constant )
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 )