Mercurial > repos > imgteam > imagej2_create_image
comparison jython_utils.py @ 0:dc3935a0165a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
---|---|
date | Tue, 17 Sep 2019 16:57:52 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:dc3935a0165a |
---|---|
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 asbool( val ): | |
8 return str( val ).lower() in [ 'yes', 'true' ] | |
9 | |
10 def convert_before_saving_as_tiff( image_plus ): | |
11 # The bUnwarpJ plug-in produces TIFF image stacks consisting of 3 | |
12 # slices which can be viewed in ImageJ. The 3 slices are: 1) the | |
13 # registered image, 2) the target image and 3) the black/white warp | |
14 # image. When running bUnwarpJ from the command line (as these | |
15 # Galaxy wrappers do) the initial call to IJ.openImage() (to open the | |
16 # registered source and target images produced by bUnwarpJ) in the | |
17 # tool's jython_script.py returns an ImagePlus object with a single | |
18 # slice which is the "generally undesired" slice 3 discussed above. | |
19 # However, a call to IJ.saveAs() will convert the single-slice TIFF | |
20 # into a 3-slice TIFF image stack (as described above) if the selected | |
21 # format for saving is TIFF. Galaxy supports only single-layered | |
22 # images, so to work around this behavior, we have to convert the | |
23 # image to something other than TIFF so that slices are eliminated. | |
24 # We can then convert back to TIFF for saving. There might be a way | |
25 # to do this without converting twice, but I spent a lot of time looking | |
26 # and I have yet to discover it. | |
27 tmp_dir = imagej2_base_utils.get_temp_dir() | |
28 tmp_out_png_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'png' ) | |
29 IJ.saveAs( image_plus, 'png', tmp_out_png_path ) | |
30 return IJ.openImage( tmp_out_png_path ) | |
31 | |
32 def get_binary_options( black_background, iterations=1, count=1, pad_edges_when_eroding='no' ): | |
33 options = [ 'edm=Overwrite', 'iterations=%d' % iterations, 'count=%d' % count ] | |
34 if asbool( pad_edges_when_eroding ): | |
35 options.append( 'pad' ) | |
36 if asbool( black_background ): | |
37 options.append( "black" ) | |
38 return " ".join( options ) | |
39 | |
40 def get_display_image_type( image_type ): | |
41 return IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES.get( str( image_type ), None ) | |
42 | |
43 def handle_error( error_log, msg ): | |
44 # Java writes a lot of stuff to stderr, so the received error_log | |
45 # will log actual errors. | |
46 elh = open( error_log, 'wb' ) | |
47 elh.write( msg ) | |
48 elh.close() |