comparison imagej2_analyze_particles_binary_jython_script.py @ 2:bdee06a1bcfa draft default tip

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

1:3272e0439968

import sys

from ij import IJ
from ij.plugin.filter import Analyzer


OPTIONS = ['edm=Overwrite', 'iterations=1', 'count=1']

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[-14]
input_file = sys.argv[-13]

if not image_processor_copy.isBinary():
    # Convert the image to binary grayscale.
    IJ.run(input_image_plus_copy, "Make Binary", "")

# Set the options.
options = ['size=%s' % size]
circularity_str = '%.3f-%.3f' % (circularity_min, circularity_max)
options.append('circularity=%s' % circularity_str)
if show.find('_') >= 0:
    show_str = '[%s]' % show.replace('_', ' ')
else:
    show_str = show
options.append('show=%s' % show_str)
if display_results:
    options.append('display')
    if not all_results:
        options.append('summarize')
if exclude_edges:
    options.append('exclude')
if include_holes:
    options.append('include')
# Always run "in_situ".
options.append('in_situ')

# Run the command.
IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options))

# Save outputs.

2:bdee06a1bcfa

import sys

from ij import IJ
from ij.plugin.filter import Analyzer

OPTIONS = ["edm=Overwrite", "iterations=1", "count=1"]

# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[-14]
input_file = sys.argv[-13]

if not image_processor_copy.isBinary():
    # Convert the image to binary grayscale.
    IJ.run(input_image_plus_copy, "Make Binary", "")

# Set the options.
options = ["size=%s" % size]
circularity_str = "%.3f-%.3f" % (circularity_min, circularity_max)
options.append("circularity=%s" % circularity_str)
if show.find("_") >= 0:
    show_str = "[%s]" % show.replace("_", " ")
else:
    show_str = show
options.append("show=%s" % show_str)
if display_results:
    options.append("display")
    if not all_results:
        options.append("summarize")
if exclude_edges:
    options.append("exclude")
if include_holes:
    options.append("include")
# Always run "in_situ".
options.append("in_situ")

# Run the command.
IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options))

# Save outputs.