Mercurial > repos > iuc > imagej2_convert_format

annotate imagej2_convert_format.py @ 5:a3806b0a32ed draft default tip

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planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
author iuc
date Sun, 11 Oct 2015 13:30:31 -0400
parents 7a8b05b111f9
children
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1 #!/usr/bin/env python
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2 import argparse
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3 import imagej2_base_utils
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4 import imagej2_utils
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6 if __name__=="__main__":
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7 # Parse Command Line.
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8 parser = argparse.ArgumentParser()
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9 parser.add_argument( '--in_fname', dest='in_fname', help='Path to the input file' )
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10 parser.add_argument( '--input_datatype', dest='input_datatype', help='Input image datatype' )
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11 parser.add_argument( '--output_datatype', dest='output_datatype', help='Output image datatype' )
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12 parser.add_argument( '--out_fname', help='Path to the output file' )
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13 args = parser.parse_args()
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15 # Start the JVM via the Javabridge.
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16 imagej2_utils.start_vm( args=None, class_path=None, max_heap_size=None, run_headless=True )
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17 try:
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18 tmp_dir = imagej2_base_utils.get_temp_dir()
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19 in_image_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.in_fname, args.input_datatype )
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20 # Load the input image.
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21 image, scale = imagej2_utils.load_image( in_image_path, rescale=False, wants_max_intensity=True )
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22 # Write the output image.
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23 out_image_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.output_datatype )
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24 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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25 except Exception, e:
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26 imagej2_base_utils.stop_err( str( e ) )
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27 finally:
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28 imagej2_utils.kill_vm()
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29 imagej2_base_utils.cleanup_before_exit( tmp_dir )