Mercurial > repos > iuc > imagej2_create_image
comparison imagej2_create_image.py @ 0:dfe318d97378 draft
planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
| author | iuc |
|---|---|
| date | Tue, 09 Jun 2015 12:22:03 -0400 |
| parents | |
| children | 26703988cdb3 |
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| -1:000000000000 | 0:dfe318d97378 |
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| 1 #!/usr/bin/env python | |
| 2 # Galaxy wrapper for use with Imagej2 by Greg Von Kuster | |
| 3 """ | |
| 4 A wrapper script for running ImageJ2 Jython scripts. | |
| 5 """ | |
| 6 import argparse | |
| 7 import shutil | |
| 8 import subprocess | |
| 9 import tempfile | |
| 10 import imagej2_base_utils | |
| 11 | |
| 12 if __name__=="__main__": | |
| 13 # Parse Command Line. | |
| 14 parser = argparse.ArgumentParser() | |
| 15 parser.add_argument( '--width', dest='width', type=int, help='Image width in pixels' ) | |
| 16 parser.add_argument( '--height', dest='height', type=int, help='Image height in pixels' ) | |
| 17 parser.add_argument( '--depth', dest='depth', type=int, help='Image depth (specifies the number of stack slices)' ) | |
| 18 parser.add_argument( '--image_type', dest='image_type', help='Image type' ) | |
| 19 parser.add_argument( '--image_title', dest='image_title', default='', help='Image title' ) | |
| 20 parser.add_argument( '--max_heap_size_type', dest='max_heap_size_type', help='Type (default or megabytes) of max_heap_size value' ) | |
| 21 parser.add_argument( '--max_heap_size', dest='max_heap_size', help='Maximum size of the memory allocation pool used by the JVM.' ) | |
| 22 parser.add_argument( '--output_datatype', dest='output_datatype', help='Output image format' ) | |
| 23 parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) | |
| 24 parser.add_argument( '--out_fname', help='Path to the output file' ) | |
| 25 args = parser.parse_args() | |
| 26 | |
| 27 tmp_dir = imagej2_base_utils.get_temp_dir() | |
| 28 tmp_image_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 | |
| 32 # Define command response buffers. | |
| 33 tmp_out = tempfile.NamedTemporaryFile().name | |
| 34 tmp_stdout = open( tmp_out, 'wb' ) | |
| 35 tmp_err = tempfile.NamedTemporaryFile().name | |
| 36 tmp_stderr = open( tmp_err, 'wb' ) | |
| 37 # Build the command line. | |
| 38 cmd = imagej2_base_utils.get_base_command_imagej2( memory_size, jython_script=args.jython_script ) | |
| 39 if cmd is None: | |
| 40 imagej2_base_utils.stop_err( "ImageJ not found!" ) | |
| 41 cmd += ' %s %d %d %d %s %s' % ( args.image_title, args.width, args.height, args.depth, args.image_type, tmp_image_path ) | |
| 42 proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True ) | |
| 43 rc = proc.wait() | |
| 44 if rc != 0: | |
| 45 error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_stdout ) | |
| 46 imagej2_base_utils.stop_err( error_message ) | |
| 47 shutil.move( tmp_image_path, args.out_fname ) | |
| 48 imagej2_base_utils.cleanup_before_exit( tmp_dir ) |