annotate 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

import sys

from ij import IJ

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[-8]
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("\nerror_log: %s\n" % str(error_log))
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)