Mercurial > repos > iuc > imagej2_convert_format

annotate imagej2_convert_format.py @ 0:312e8ce708b1 draft

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planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
author iuc
date Tue, 09 Jun 2015 12:21:40 -0400
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children 14d09b0ab9e1
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312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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1 #!/usr/bin/env python
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2 # Galaxy wrapper for use with Imagej2 via bioformats and javabridge by Greg Von Kuster
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3 """
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4 A wrapper script for running ImageJ2 commands via bioformats and javabridge.
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5 """
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6 import argparse
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7 import imagej2_base_utils
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8 import imagej2_utils
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9
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10 if __name__=="__main__":
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11 # Parse Command Line.
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12 parser = argparse.ArgumentParser()
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13 parser.add_argument( '--in_fname', dest='in_fname', help='Path to the input file' )
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14 parser.add_argument( '--input_datatype', dest='input_datatype', help='Input image datatype' )
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15 parser.add_argument( '--max_heap_size_type', dest='max_heap_size_type', help='Type (default or megabytes) of max_heap_size value' )
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16 parser.add_argument( '--max_heap_size', dest='max_heap_size', help='Maximum size of the memory allocation pool used by the JVM.' )
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17 parser.add_argument( '--output_datatype', dest='output_datatype', help='Output image datatype' )
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18 parser.add_argument( '--out_fname', help='Path to the output file' )
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19 args = parser.parse_args()
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20 # Set the size of the memory allocation pool used by the JVM.
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21 max_heap_size = imagej2_base_utils.get_max_heap_size_value( args.max_heap_size_type, args.max_heap_size )
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22 # Start the JVM via the Javabridge.
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23 imagej2_utils.start_vm( args=None, class_path=None, max_heap_size=max_heap_size, run_headless=True )
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24 try:
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25 tmp_dir = imagej2_base_utils.get_temp_dir()
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26 in_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.in_fname, args.input_datatype )
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27 # Load the input image.
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28 image, scale = imagej2_utils.load_image( in_image_path, rescale=False, wants_max_intensity=True )
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29 # Write the output image.
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30 out_image_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
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31 imagej2_utils.write_image( image_path=out_image_path, pixels=image, pixel_type=str( image.dtype ), move_to=args.out_fname )
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32 except Exception, e:
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33 imagej2_base_utils.stop_err( str( e ) )
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34 finally:
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35 imagej2_utils.kill_vm()
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36 imagej2_base_utils.cleanup_before_exit( tmp_dir )