Mercurial > repos > iuc > imagej2_make_binary

diff imagej2_bunwarpj_raw_transform_jython_script.py @ 3:bb7bfa5bc1b0 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 23:21:29 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_bunwarpj_raw_transform_jython_script.py	Fri Jul 22 23:21:29 2016 -0400
@@ -0,0 +1,16 @@
+import sys
+import jython_utils
+from ij import IJ
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+
+source_tiff_path = sys.argv[ -3 ]
+source_datatype = sys.argv[ -2 ]
+source_path = sys.argv[ -1 ]
+
+# Save the Registered Source Image.
+registered_source_image = IJ.openImage( source_tiff_path )
+if source_datatype == 'tiff':
+    registered_source_image = jython_utils.convert_before_saving_as_tiff( registered_source_image )
+IJ.saveAs( registered_source_image, source_datatype, source_path )