diff imagej2_enhance_contrast_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_enhance_contrast_jython_script.py	Tue Sep 24 17:12:52 2024 +0000
@@ -0,0 +1,38 @@
+import sys
+
+from ij import IJ
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.
+input = sys.argv[-6]
+equalize_histogram = sys.argv[-5] == "yes"
+saturated_pixels = sys.argv[-4]
+normalize = 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)
+
+# Create a copy of the image.
+input_image_plus_copy = input_image_plus.duplicate()
+image_processor_copy = input_image_plus_copy.getProcessor()
+bit_depth = image_processor_copy.getBitDepth()
+
+# Set the options
+options = []
+# If equalize_histogram, saturated_pixels and normalize are ignored.
+if equalize_histogram:
+    options.append("equalize")
+else:
+    if saturated_pixels not in [None, "None"]:
+        # Fiji allows only a single decimal place for this value.
+        options.append("saturated=%.3f" % float(saturated_pixels))
+    # Normalization of RGB images is not supported.
+    if bit_depth != 24 and normalize:
+        options.append("normalize")
+# Run the command.
+options = "%s" % " ".join(options)
+IJ.run(input_image_plus_copy, "Enhance Contrast...", options)
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)