diff imagej2_math_jython_script.py @ 2:ae4ae9c5c56c draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

--- a/imagej2_math_jython_script.py	Mon Sep 28 16:59:30 2020 +0000
+++ b/imagej2_math_jython_script.py	Sun Nov 05 14:25:37 2023 +0000
@@ -8,11 +8,11 @@
 input_file = sys.argv[-7]
 operation = sys.argv[-6]
 expression = sys.argv[-5]
-if sys.argv[-4] in [None, 'None']:
+if sys.argv[-4] in [None, "None"]:
     bin_constant = None
 else:
     bin_constant = int(sys.argv[-4])
-if sys.argv[-3] in [None, 'None']:
+if sys.argv[-3] in [None, "None"]:
     float_constant = None
 else:
     float_constant = float(sys.argv[-3])
@@ -36,49 +36,49 @@
 image_processor_copy = input_image_plus_copy.getProcessor()
 bit_depth = image_processor_copy.getBitDepth()
 
-if operation.find('_') > 0:
+if operation.find("_") > 0:
     # Square_Root.
-    new_operation = operation.replace('_', ' ')
-elif operation in ['Square', 'Log', 'Exp', 'Abs', 'Reciprocal']:
+    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
+    new_operation = "%s" % operation
 else:
-    new_operation = '%s...' % operation
+    new_operation = "%s..." % operation
 
-if operation == 'Macro':
+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
+    options = "code=%s" % new_expression
     image_processor_copy.applyMacro(new_expression)
-elif operation == 'Min':
+elif operation == "Min":
     # Min does not work without using the ImageProcessor.
     image_processor_copy.min(float_constant)
-elif operation == 'Max':
+elif operation == "Max":
     # Max does not work without using the ImageProcessor.
     image_processor_copy.max(float_constant)
-elif operation == 'Abs':
+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':
+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']:
+    if operation in ["AND", "OR", "XOR"]:
         # Value is a binary number.
-        options = 'value=%d' % bin_constant
-    elif operation in ['Log', 'Exp', 'Square', 'Square_Root']:
+        options = "value=%d" % bin_constant
+    elif operation in ["Log", "Exp", "Square", "Square_Root"]:
         # No constant value.
-        options = ''
+        options = ""
     else:
         # Value is a floating point number.
-        options = 'value=%.3f' % float_constant
+        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)