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annotate jython_script.py @ 0:f3ec070f1781 draft

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planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
author iuc
date Sun, 11 Oct 2015 13:31:38 -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[ -4 ]
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8 input = sys.argv[ -3 ]
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9 tmp_output_path = sys.argv[ -2 ]
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10 output_datatype = sys.argv[ -1 ]
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12 # Open the input image file.
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13 input_image_plus = IJ.openImage( input )
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15 # Create a copy of the image.
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16 input_image_plus_copy = input_image_plus.duplicate()
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17 image_processor_copy = input_image_plus_copy.getProcessor()
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18
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19 try:
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20 # Run the command.
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21 IJ.run( input_image_plus_copy, "Smooth", "" )
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22 # Save the ImagePlus object as a new image.
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23 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
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24 except Exception, e:
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25 jython_utils.handle_error( error_log, str( e ) )