diff jython_utils.py @ 1:d26f11339f08 draft

planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:37:41 -0400
parents 66d9e595dff2
children
line wrap: on
line diff
--- a/jython_utils.py	Tue Aug 04 13:20:29 2015 -0400
+++ b/jython_utils.py	Wed Aug 26 14:37:41 2015 -0400
@@ -4,6 +4,9 @@
 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
@@ -26,6 +29,14 @@
     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 )