comparison imagej2_find_maxima_jython_script.py @ 3:862af85a50ec draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56

2:ae4ae9c5c56c

from ij.plugin.filter import Analyzer, MaximumFinder
from ij.process import ImageProcessor

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[-10]
input_file = sys.argv[-9]
scale_when_converting = sys.argv[-8] == "yes"
weighted_rgb_conversions = sys.argv[-7] == "yes"
noise_tolerance = int(sys.argv[-6])
output_type = sys.argv[-5]

    if scale_when_converting:
        options.append("scale")
    if weighted_rgb_conversions:
        options.append("weighted")
# Perform conversion - must happen even if no options are set.
IJ.run(input_image_plus_copy, "Conversions...", "%s" % " ".join(options))
if output_type in ["List", "Count"]:
    # W're  generating a tabular file for the output.
    # Set the Find Maxima options.
    options = ["noise=%d" % noise_tolerance]
    if output_type.find("_") > 0:

3:862af85a50ec

from ij.plugin.filter import Analyzer, MaximumFinder
from ij.process import ImageProcessor

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
input_file = sys.argv[-9]
scale_when_converting = sys.argv[-8] == "yes"
weighted_rgb_conversions = sys.argv[-7] == "yes"
noise_tolerance = int(sys.argv[-6])
output_type = sys.argv[-5]

    if scale_when_converting:
        options.append("scale")
    if weighted_rgb_conversions:
        options.append("weighted")
# Perform conversion - must happen even if no options are set.
IJ.run(input_image_plus_copy, "Conversions...", " %s" % " ".join(options))
if output_type in ["List", "Count"]:
    # W're  generating a tabular file for the output.
    # Set the Find Maxima options.
    options = ["noise=%d" % noise_tolerance]
    if output_type.find("_") > 0: