Mercurial > repos > iuc > imagej2_skeletonize3d

diff imagej2_smooth_jython_script.py @ 3:39e144c3952b draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
author: iuc
date: Fri, 22 Jul 2016 23:10:42 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_smooth_jython_script.py	Fri Jul 22 23:10:42 2016 -0400
@@ -0,0 +1,25 @@
+import jython_utils
+import sys
+from ij import IJ
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+error_log = sys.argv[ -4 ]
+input = 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 )
+
+# Create a copy of the image.
+input_image_plus_copy = input_image_plus.duplicate()
+image_processor_copy = input_image_plus_copy.getProcessor()
+
+try:
+    # Run the command.
+    IJ.run( input_image_plus_copy, "Smooth", "" )
+    # Save the ImagePlus object as a new image.
+    IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
+except Exception, e:
+    jython_utils.handle_error( error_log, str( e ) )