diff imagej2_math_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_math_jython_script.py	Tue Sep 24 17:12:52 2024 +0000
@@ -0,0 +1,82 @@
+import sys
+
+from ij import IJ
+
+# Fiji Jython interpreter implements Python 2.5 which does not
+# provide support for argparse.\
+input_file = sys.argv[-7]
+operation = sys.argv[-6]
+expression = sys.argv[-5]
+if sys.argv[-4] in [None, "None"]:
+    bin_constant = None
+else:
+    bin_constant = int(sys.argv[-4])
+if sys.argv[-3] in [None, "None"]:
+    float_constant = None
+else:
+    float_constant = float(sys.argv[-3])
+tmp_output_path = sys.argv[-2]
+output_datatype = sys.argv[-1]
+
+print("\ninput_file: %s\n" % str(input_file))
+print("\noperation: %s\n" % str(operation))
+print("\nexpression: %s\n" % str(expression))
+print("\nbin_constant: %s\n" % str(bin_constant))
+print("\nfloat_constant: %s\n" % str(float_constant))
+print("\ntmp_output_path: %s\n" % str(tmp_output_path))
+print("\noutput_datatype: %s\n" % str(output_datatype))
+
+# 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()
+bit_depth = image_processor_copy.getBitDepth()
+
+if operation.find("_") > 0:
+    # Square_Root.
+    new_operation = operation.replace("_", " ")
+elif operation in ["Square", "Log", "Exp", "Abs", "Reciprocal"]:
+    # Unfortunately some ImageJ commands require a "..." ending
+    # while others do not.  There seems to be no pattern.
+    new_operation = "%s" % operation
+else:
+    new_operation = "%s..." % operation
+
+if operation == "Macro":
+    # Apply the macro code to the image via a call to it's
+    # ImageProcessor since this option does not work using
+    # the IJ.run() method.
+    new_expression = expression.lstrip('"').rstrip('"')
+    options = "code=%s" % new_expression
+    image_processor_copy.applyMacro(new_expression)
+elif operation == "Min":
+    # Min does not work without using the ImageProcessor.
+    image_processor_copy.min(float_constant)
+elif operation == "Max":
+    # Max does not work without using the ImageProcessor.
+    image_processor_copy.max(float_constant)
+elif operation == "Abs":
+    if bit_depth not in [16, 32]:
+        # Convert the image to 32-bit.
+        IJ.run(input_image_plus_copy, "32-bit", "")
+        IJ.run(input_image_plus_copy, new_operation, "")
+elif operation == "Reciprocal":
+    if bit_depth != 32:
+        # Convert the image to 32 bit.
+        IJ.run(input_image_plus_copy, "32-bit", "")
+        IJ.run(input_image_plus_copy, new_operation, "")
+else:
+    if operation in ["AND", "OR", "XOR"]:
+        # Value is a binary number.
+        options = "value=%d" % bin_constant
+    elif operation in ["Log", "Exp", "Square", "Square_Root"]:
+        # No constant value.
+        options = ""
+    else:
+        # Value is a floating point number.
+        options = "value=%.3f" % float_constant
+    IJ.run(input_image_plus_copy, "%s" % new_operation, "%s" % options)
+# Save the ImagePlus object as a new image.
+IJ.saveAs(input_image_plus_copy, output_datatype, tmp_output_path)