Mercurial > repos > iuc > imagej2_convert_format

comparison imagej2_convert_format.py @ 4:7a8b05b111f9 draft

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planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:37:12 -0400
parents 14d09b0ab9e1
children
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3:9a24b7e68010 4:7a8b05b111f9
6 if __name__=="__main__": 6 if __name__=="__main__":
7 # Parse Command Line. 7 # Parse Command Line.
8 parser = argparse.ArgumentParser() 8 parser = argparse.ArgumentParser()
9 parser.add_argument( '--in_fname', dest='in_fname', help='Path to the input file' ) 9 parser.add_argument( '--in_fname', dest='in_fname', help='Path to the input file' )
10 parser.add_argument( '--input_datatype', dest='input_datatype', help='Input image datatype' ) 10 parser.add_argument( '--input_datatype', dest='input_datatype', help='Input image datatype' )
11 parser.add_argument( '--max_heap_size_type', dest='max_heap_size_type', help='Type (default or megabytes) of max_heap_size value' )
12 parser.add_argument( '--max_heap_size', dest='max_heap_size', help='Maximum size of the memory allocation pool used by the JVM.' )
13 parser.add_argument( '--output_datatype', dest='output_datatype', help='Output image datatype' ) 11 parser.add_argument( '--output_datatype', dest='output_datatype', help='Output image datatype' )
14 parser.add_argument( '--out_fname', help='Path to the output file' ) 12 parser.add_argument( '--out_fname', help='Path to the output file' )
15 args = parser.parse_args() 13 args = parser.parse_args()
16 # Set the size of the memory allocation pool used by the JVM. 14
17 max_heap_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size )
18 # Start the JVM via the Javabridge. 15 # Start the JVM via the Javabridge.
19 imagej2_utils.start_vm( args=None, class_path=None, max_heap_size=max_heap_size, run_headless=True ) 16 imagej2_utils.start_vm( args=None, class_path=None, max_heap_size=None, run_headless=True )
20 try: 17 try:
21 tmp_dir = imagej2_base_utils.get_temp_dir() 18 tmp_dir = imagej2_base_utils.get_temp_dir()
22 in_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.in_fname, args.input_datatype ) 19 in_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.in_fname, args.input_datatype )
23 # Load the input image. 20 # Load the input image.
24 image, scale = imagej2_utils.load_image( in_image_path, rescale=False, wants_max_intensity=True ) 21 image, scale = imagej2_utils.load_image( in_image_path, rescale=False, wants_max_intensity=True )