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1 import imagej2_base_utils
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2 from ij import IJ
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3
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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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6
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7 def asbool( val ):
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8 return str( val ).lower() in [ 'yes', 'true' ]
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9
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10 def convert_before_saving_as_tiff( image_plus ):
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11 # The bUnwarpJ plug-in produces TIFF image stacks consisting of 3
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12 # slices which can be viewed in ImageJ. The 3 slices are: 1) the
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13 # registered image, 2) the target image and 3) the black/white warp
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14 # image. When running bUnwarpJ from the command line (as these
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15 # Galaxy wrappers do) the initial call to IJ.openImage() (to open the
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16 # registered source and target images produced by bUnwarpJ) in the
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17 # tool's jython_script.py returns an ImagePlus object with a single
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18 # slice which is the "generally undesired" slice 3 discussed above.
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19 # However, a call to IJ.saveAs() will convert the single-slice TIFF
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20 # into a 3-slice TIFF image stack (as described above) if the selected
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21 # format for saving is TIFF. Galaxy supports only single-layered
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22 # images, so to work around this behavior, we have to convert the
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23 # image to something other than TIFF so that slices are eliminated.
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24 # We can then convert back to TIFF for saving. There might be a way
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25 # to do this without converting twice, but I spent a lot of time looking
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26 # and I have yet to discover it.
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27 tmp_dir = imagej2_base_utils.get_temp_dir()
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28 tmp_out_png_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'png' )
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29 IJ.saveAs( image_plus, 'png', tmp_out_png_path )
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30 return IJ.openImage( tmp_out_png_path )
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31
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32 def get_binary_options( black_background, iterations=1, count=1, pad_edges_when_eroding='no' ):
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33 options = [ 'edm=Overwrite', 'iterations=%d' % iterations, 'count=%d' % count ]
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34 if asbool( pad_edges_when_eroding ):
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35 options.append( 'pad' )
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36 if asbool( black_background ):
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37 options.append( "black" )
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38 return " ".join( options )
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39
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40 def get_display_image_type( image_type ):
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41 return IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES.get( str( image_type ), None )
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42
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43 def handle_error( error_log, msg ):
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44 # Java writes a lot of stuff to stderr, so the received error_log
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45 # will log actual errors.
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46 elh = open( error_log, 'wb' )
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47 elh.write( msg )
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48 elh.close()
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