diff imagej2_shadows_jython_script.py @ 0:018144807556 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_shadows_jython_script.py	Tue Sep 24 17:12:52 2024 +0000
@@ -0,0 +1,22 @@
+import sys
+
+from ij import IJ
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+input_file = sys.argv[-4]
+direction = 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_file)
+
+# Create a copy of the image.
+input_image_plus_copy = input_image_plus.duplicate()
+image_processor_copy = input_image_plus_copy.getProcessor()
+
+# Run the command.
+IJ.run(input_image_plus_copy, direction, "")
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)