diff imagej2_adjust_threshold_binary_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_adjust_threshold_binary_jython_script.py	Tue Sep 24 17:12:52 2024 +0000
@@ -0,0 +1,57 @@
+import sys
+
+from ij import IJ, Prefs
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+input_file = sys.argv[-8]
+threshold_min = float(sys.argv[-7])
+threshold_max = float(sys.argv[-6])
+method = sys.argv[-5]
+display = sys.argv[-4]
+black_background = sys.argv[-3] == "yes"
+output_filename = 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()
+
+bit_depth = input_image_plus_copy.getBitDepth()
+
+if black_background:
+    Prefs.blackBackground = True
+else:
+    Prefs.blackBackground = False
+
+if method != "Manual":
+    # Set the options.
+    if black_background:
+        method_str = "%s dark" % method
+        suffix = "black"
+    else:
+        method_str = method
+        suffix = ""
+    threshold_min = 1
+    # Set threshold_max based on image bit-depth
+    # For 8-bit images, use 255; for 16-bit images, use 65535
+    if bit_depth == 8:
+        threshold_max = 255  # Default for 8-bit images
+    elif bit_depth == 16:
+        threshold_max = 65535  # Default for 16-bit images
+    else:
+        threshold_max = float('inf')  # General fallback if bit depth is unknown
+
+    IJ.setAutoThreshold(input_image_plus_copy, method_str)
+    IJ.run(input_image_plus_copy, "Convert to Mask", "calculate %s" % suffix)
+if display == "red":
+    display_mode = "Red"
+elif display == "bw":
+    display_mode = "Black & White"
+elif display == "over_under":
+    display_mode = "Over/Under"
+IJ.setThreshold(input_image_plus_copy, threshold_min, threshold_max, display_mode)
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)