Mercurial > repos > iuc > imagej2_make_binary
comparison jython_utils.py @ 0:66d9e595dff2 draft
planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
| author | iuc |
|---|---|
| date | Tue, 04 Aug 2015 13:20:29 -0400 |
| parents | |
| children | d26f11339f08 |
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| -1:000000000000 | 0:66d9e595dff2 |
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| 1 import imagej2_base_utils | |
| 2 from ij import IJ | |
| 3 | |
| 4 IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES = { '0':'GRAY8', '1':'GRAY16', '2':'GRAY32', | |
| 5 '3':'COLOR_256', '4':'COLOR_RGB' } | |
| 6 | |
| 7 def convert_before_saving_as_tiff( image_plus ): | |
| 8 # The bUnwarpJ plug-in produces TIFF image stacks consisting of 3 | |
| 9 # slices which can be viewed in ImageJ. The 3 slices are: 1) the | |
| 10 # registered image, 2) the target image and 3) the black/white warp | |
| 11 # image. When running bUnwarpJ from the command line (as these | |
| 12 # Galaxy wrappers do) the initial call to IJ.openImage() (to open the | |
| 13 # registered source and target images produced by bUnwarpJ) in the | |
| 14 # tool's jython_script.py returns an ImagePlus object with a single | |
| 15 # slice which is the "generally undesired" slice 3 discussed above. | |
| 16 # However, a call to IJ.saveAs() will convert the single-slice TIFF | |
| 17 # into a 3-slice TIFF image stack (as described above) if the selected | |
| 18 # format for saving is TIFF. Galaxy supports only single-layered | |
| 19 # images, so to work around this behavior, we have to convert the | |
| 20 # image to something other than TIFF so that slices are eliminated. | |
| 21 # We can then convert back to TIFF for saving. There might be a way | |
| 22 # to do this without converting twice, but I spent a lot of time looking | |
| 23 # and I have yet to discover it. | |
| 24 tmp_dir = imagej2_base_utils.get_temp_dir() | |
| 25 tmp_out_png_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'png' ) | |
| 26 IJ.saveAs( image_plus, 'png', tmp_out_png_path ) | |
| 27 return IJ.openImage( tmp_out_png_path ) | |
| 28 | |
| 29 def get_display_image_type( image_type ): | |
| 30 return IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES.get( str( image_type ), None ) | |
| 31 | |
| 32 def handle_error( error_log, msg ): | |
| 33 # Java writes a lot of stuff to stderr, so the received error_log | |
| 34 # will log actual errors. | |
| 35 elh = open( error_log, 'wb' ) | |
| 36 elh.write( msg ) | |
| 37 elh.close() |