Mercurial > repos > iuc > imagej2_shadows

annotate jython_script.py @ 0:42e645a20a6e draft

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author iuc
date Wed, 26 Aug 2015 14:36:27 -0400
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1 import jython_utils
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2 import sys
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3 from ij import IJ
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4
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5 # Fiji Jython interpreter implements Python 2.5 which does not
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6 # provide support for argparse.
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7 error_log = sys.argv[ -5 ]
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8 input = sys.argv[ -4 ]
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9 direction = sys.argv[ -3 ]
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10 tmp_output_path = sys.argv[ -2 ]
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11 output_datatype = sys.argv[ -1 ]
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12
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13 # Open the input image file.
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14 input_image_plus = IJ.openImage( input )
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16 # Create a copy of the image.
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17 input_image_plus_copy = input_image_plus.duplicate()
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18 image_processor_copy = input_image_plus_copy.getProcessor()
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19
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20 try:
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21 # Run the command.
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22 IJ.run( input_image_plus_copy, direction, "" )
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23 # Save the ImagePlus object as a new image.
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24 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
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25 except Exception, e:
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26 jython_utils.handle_error( error_log, str( e ) )