Mercurial > repos > iuc > imagej2_bunwarpj_elastic_transform

annotate jython_script.py @ 0:0219a764e425 draft

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planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
author iuc
date Fri, 19 Jun 2015 17:00:07 -0400
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0219a764e425 planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
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1 import sys
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2 import jython_utils
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3 from ij import IJ
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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
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8 source_tiff_path = sys.argv[ -3 ]
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9 source_datatype = sys.argv[ -2 ]
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10 source_path = sys.argv[ -1 ]
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12 # Save the Registered Source Image.
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13 registered_source_image = IJ.openImage( source_tiff_path )
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14 if source_datatype == 'tiff':
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15 registered_source_image = jython_utils.convert_before_saving_as_tiff( registered_source_image )
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16 IJ.saveAs( registered_source_image, source_datatype, source_path )