Mercurial > repos > iuc > imagej2_make_binary

comparison imagej2_make_binary.py @ 1:d26f11339f08 draft

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planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:37:41 -0400
parents 66d9e595dff2
children
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0:66d9e595dff2 1:d26f11339f08
12 parser.add_argument( '--iterations', dest='iterations', type=int, help='Iterations' ) 12 parser.add_argument( '--iterations', dest='iterations', type=int, help='Iterations' )
13 parser.add_argument( '--count', dest='count', type=int, help='Count' ) 13 parser.add_argument( '--count', dest='count', type=int, help='Count' )
14 parser.add_argument( '--black_background', dest='black_background', help='Black background' ) 14 parser.add_argument( '--black_background', dest='black_background', help='Black background' )
15 parser.add_argument( '--pad_edges_when_eroding', dest='pad_edges_when_eroding', help='Pad edges when eroding' ) 15 parser.add_argument( '--pad_edges_when_eroding', dest='pad_edges_when_eroding', help='Pad edges when eroding' )
16 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) 16 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' )
17 parser.add_argument( '--max_heap_size_type', dest='max_heap_size_type', help='Type (default or megabytes) of max_heap_size value' )
18 parser.add_argument( '--max_heap_size', dest='max_heap_size', help='Maximum size of the memory allocation pool used by the JVM.' )
19 parser.add_argument( '--output', dest='output', help='Path to the output file' ) 17 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' ) 18 parser.add_argument( '--output_datatype', dest='output_datatype', help='Datatype of the output image' )
21 args = parser.parse_args() 19 args = parser.parse_args()
22 20
23 tmp_dir = imagej2_base_utils.get_temp_dir() 21 tmp_dir = imagej2_base_utils.get_temp_dir()
24 # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not 22 # 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 23 # 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. 24 # 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 ) 25 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 ) 26 tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
29 # Set the size of the memory allocation pool used by the JVM.
30 memory_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size )
31 # Define command response buffers. 27 # Define command response buffers.
32 tmp_out = tempfile.NamedTemporaryFile().name 28 tmp_out = tempfile.NamedTemporaryFile().name
33 tmp_stdout = open( tmp_out, 'wb' ) 29 tmp_stdout = open( tmp_out, 'wb' )
34 tmp_err = tempfile.NamedTemporaryFile().name 30 tmp_err = tempfile.NamedTemporaryFile().name
35 tmp_stderr = open( tmp_err, 'wb' ) 31 tmp_stderr = open( tmp_err, 'wb' )
36 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors. 32 # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors.
37 error_log = tempfile.NamedTemporaryFile( delete=False ).name 33 error_log = tempfile.NamedTemporaryFile( delete=False ).name
38 # Build the command line. 34 # Build the command line.
39 cmd = imagej2_base_utils.get_base_command_imagej2( memory_size, jython_script=args.jython_script ) 35 cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script )
40 if cmd is None: 36 if cmd is None:
41 imagej2_base_utils.stop_err( "ImageJ not found!" ) 37 imagej2_base_utils.stop_err( "ImageJ not found!" )
42 cmd += ' %s' % error_log 38 cmd += ' %s' % error_log
43 cmd += ' %s' % tmp_input_path 39 cmd += ' %s' % tmp_input_path
44 cmd += ' %d' % args.iterations 40 cmd += ' %d' % args.iterations