diff imagej2_skeletonize3d_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_skeletonize3d_jython_script.py	Tue Sep 24 17:12:52 2024 +0000
@@ -0,0 +1,35 @@
+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]
+black_background = sys.argv[-3] == "yes"
+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()
+
+# Set binary options.
+options = ["edm=Overwrite", "iterations=1", "count=1"]
+if black_background:
+    options.append("black")
+options = " ".join(options)
+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", "")
+
+# 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)