Mercurial > repos > iuc > imagej2_make_binary

annotate jython_utils.py @ 0:66d9e595dff2 draft

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planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
author iuc
date Tue, 04 Aug 2015 13:20:29 -0400
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children d26f11339f08
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66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
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1 import imagej2_base_utils
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2 from ij import IJ
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4 IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES = { '0':'GRAY8', '1':'GRAY16', '2':'GRAY32',
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5 '3':'COLOR_256', '4':'COLOR_RGB' }
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7 def convert_before_saving_as_tiff( image_plus ):
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8 # The bUnwarpJ plug-in produces TIFF image stacks consisting of 3
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
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9 # slices which can be viewed in ImageJ. The 3 slices are: 1) the
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10 # registered image, 2) the target image and 3) the black/white warp
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11 # image. When running bUnwarpJ from the command line (as these
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
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12 # Galaxy wrappers do) the initial call to IJ.openImage() (to open the
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
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13 # registered source and target images produced by bUnwarpJ) in the
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14 # tool's jython_script.py returns an ImagePlus object with a single
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15 # slice which is the "generally undesired" slice 3 discussed above.
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16 # However, a call to IJ.saveAs() will convert the single-slice TIFF
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17 # into a 3-slice TIFF image stack (as described above) if the selected
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18 # format for saving is TIFF. Galaxy supports only single-layered
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19 # images, so to work around this behavior, we have to convert the
66d9e595dff2 planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
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20 # image to something other than TIFF so that slices are eliminated.
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21 # We can then convert back to TIFF for saving. There might be a way
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22 # to do this without converting twice, but I spent a lot of time looking
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23 # and I have yet to discover it.
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24 tmp_dir = imagej2_base_utils.get_temp_dir()
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25 tmp_out_png_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'png' )
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26 IJ.saveAs( image_plus, 'png', tmp_out_png_path )
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27 return IJ.openImage( tmp_out_png_path )
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29 def get_display_image_type( image_type ):
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30 return IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES.get( str( image_type ), None )
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31
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32 def handle_error( error_log, msg ):
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33 # Java writes a lot of stuff to stderr, so the received error_log
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34 # will log actual errors.
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35 elh = open( error_log, 'wb' )
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36 elh.write( msg )
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37 elh.close()