--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_crop_jython_script.py	Wed Sep 25 15:58:30 2024 +0000
@@ -0,0 +1,55 @@
+import sys
+
+from ij import IJ
+from ij.plugin import Duplicator
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+input_file = sys.argv[-13]
+xleft = int(sys.argv[-12])
+width = int(sys.argv[-11])
+ytop = int(sys.argv[-10])
+height = int(sys.argv[-9])
+first_channel = int(sys.argv[-8])
+last_channel = int(sys.argv[-7])
+first_slice = int(sys.argv[-6])
+last_slice = int(sys.argv[-5])
+first_frame = int(sys.argv[-4])
+last_frame = int(sys.argv[-3])
+output_filename = sys.argv[-2]
+output_datatype = sys.argv[-1]
+
+# Open the input image file.
+input_image_plus = IJ.openImage(input_file)
+
+# Get image dimensions (width, height, nChannels, nSlices, nFrames)
+image_dims = input_image_plus.getDimensions()
+
+# Create a copy of the image.
+input_image_plus_copy = input_image_plus.duplicate()
+
+# Determine if crop in XY is needed:
+if xleft != 0 or width != 0 or ytop != 0 or height != 0:
+    # Need to define a ROI
+    if width == 0:
+        width = image_dims[0] - xleft
+    if height == 0:
+        height = image_dims[1] - ytop
+    input_image_plus_copy.setRoi(xleft, ytop, width, height)
+
+# Replace 0's with default:
+if last_channel == 0:
+    last_channel = image_dims[2]
+if last_slice == 0:
+    last_slice = image_dims[3]
+if last_frame == 0:
+    last_frame = image_dims[4]
+print("Original dimensions:")
+print(image_dims)
+# This will also crop in XY is a ROI has been set
+input_image_plus_copy = Duplicator().run(input_image_plus_copy, first_channel, last_channel, first_slice, last_slice, first_frame, last_frame)
+print("Final dimensions:")
+print(input_image_plus_copy.getDimensions())
+
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)