diff jython_script.py @ 1:269923244cc8 draft

planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty

--- a/jython_script.py	Tue Aug 04 13:21:32 2015 -0400
+++ b/jython_script.py	Wed Aug 26 14:38:34 2015 -0400
@@ -1,33 +1,35 @@
 import jython_utils
 import sys
 from ij import IJ
-from ij import ImagePlus
-
-VALID_IMAGE_TYPES = [ ImagePlus.GRAY8 ]
 
 # Fiji Jython interpreter implements Python 2.5 which does not
 # provide support for argparse.
-error_log = sys.argv[ -4 ]
-input = sys.argv[ -3 ]
+error_log = sys.argv[ -5 ]
+input = sys.argv[ -4 ]
+black_background = jython_utils.asbool( sys.argv[ -3 ] )
 tmp_output_path = sys.argv[ -2 ]
 output_datatype = sys.argv[ -1 ]
 
 # Open the input image file.
 input_image_plus = IJ.openImage( input )
-bit_depth = input_image_plus.getBitDepth()
-image_type = input_image_plus.getType()
 
 # Create a copy of the image.
-input_image_plus_copy = input_image_plus.createImagePlus()
-image_processor_copy = input_image_plus.getProcessor().duplicate()
-input_image_plus_copy.setProcessor( "iCopy", image_processor_copy )
+input_image_plus_copy = input_image_plus.duplicate()
+image_processor_copy = input_image_plus_copy.getProcessor()
 
 try:
-    if image_type not in VALID_IMAGE_TYPES:
+    # Set binary options.
+    options = jython_utils.get_binary_options( black_background=black_background )
+    IJ.run( input_image_plus_copy, "Options...", options )
+
+    # Convert image to binary if necessary.
+    if not image_processor_copy.isBinary():
         # Convert the image to binary grayscale.
-        IJ.run( input_image_plus_copy, "Make Binary","iterations=1 count=1 edm=Overwrite do=Nothing" )
+        IJ.run( input_image_plus_copy, "Make Binary", "" )
+
     # Run the command.
     IJ.run( input_image_plus_copy, "Skeletonize (2D/3D)", "" )
+
     # Save the ImagePlus object as a new image.
     IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
 except Exception, e: