diff jython_utils.py @ 0:aeb9bb864b8c draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jython_utils.py	Tue Sep 17 16:56:37 2019 -0400
@@ -0,0 +1,48 @@
+import imagej2_base_utils
+from ij import IJ
+
+IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES = { '0':'GRAY8', '1':'GRAY16', '2':'GRAY32',
+                                       '3':'COLOR_256', '4':'COLOR_RGB' }
+
+def asbool( val ):
+    return str( val ).lower() in [ 'yes', 'true' ]
+
+def convert_before_saving_as_tiff( image_plus ):
+    # The bUnwarpJ plug-in produces TIFF image stacks consisting of 3
+    # slices which can be viewed in ImageJ.  The 3 slices are: 1) the
+    # registered image, 2) the target image and 3) the black/white warp
+    # image.  When running bUnwarpJ from the command line (as these
+    # Galaxy wrappers do) the initial call to IJ.openImage() (to open the
+    # registered source and target images produced by bUnwarpJ) in the
+    # tool's jython_script.py returns an ImagePlus object with a single
+    # slice which is the "generally undesired" slice 3 discussed above.
+    # However, a call to IJ.saveAs() will convert the single-slice TIFF
+    # into a 3-slice TIFF image stack (as described above) if the selected
+    # format for saving is TIFF.  Galaxy supports only single-layered
+    # images, so to work around this behavior, we have to convert the
+    # image to something other than TIFF so that slices are eliminated.
+    # We can then convert back to TIFF for saving.  There might be a way
+    # to do this without converting twice, but I spent a lot of time looking
+    # and I have yet to discover it.
+    tmp_dir = imagej2_base_utils.get_temp_dir()
+    tmp_out_png_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'png' )
+    IJ.saveAs( image_plus, 'png', tmp_out_png_path )
+    return IJ.openImage( tmp_out_png_path )
+
+def get_binary_options( black_background, iterations=1, count=1, pad_edges_when_eroding='no' ):
+    options = [ 'edm=Overwrite', 'iterations=%d' % iterations, 'count=%d' % count ]
+    if asbool( pad_edges_when_eroding ):
+        options.append( 'pad' )
+    if asbool( black_background ):
+        options.append( "black" )
+    return " ".join( options )
+
+def get_display_image_type( image_type ):
+    return IMAGE_PLUS_IMAGE_TYPE_FIELD_VALUES.get( str( image_type ), None )
+
+def handle_error( error_log, msg ):
+    # Java writes a lot of stuff to stderr, so the received error_log 
+    # will log actual errors.
+    elh = open( error_log, 'wb' )
+    elh.write( msg )
+    elh.close()