annotate imagej2_analyze_particles_binary_jython_script.py @ 3:2b007b1e6c1b draft default tip

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

import sys

from ij import IJ, Prefs
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.
roi_coordinate_file = sys.argv[-13]
input_file = sys.argv[-12]
black_background = sys.argv[-11] == "yes"
size = sys.argv[-10]
circularity_min = float(sys.argv[-9])
circularity_max = float(sys.argv[-8])
show = sys.argv[-7]
display_results = sys.argv[-6] == "yes"
exclude_edges = sys.argv[-5] == "yes"
include_holes = sys.argv[-4] == "yes"
output_filename = sys.argv[-3]
output_datatype = sys.argv[-2]
results_path = sys.argv[-1]


if black_background:
    Prefs.blackBackground = True
else:
    Prefs.blackBackground = False

# 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()
analyzer = Analyzer(input_image_plus_copy)

# Set binary options.
options_list = OPTIONS
if black_background:
    options_list.append("black")
options = " ".join(options_list)
IJ.run(input_image_plus_copy, "Options...", options)

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, "stack"]
circularity_str = "%.3f-%.3f" % (circularity_min, circularity_max)
options.append("circularity=%s" % circularity_str)
if exclude_edges:
    options.append("exclude")
if include_holes:
    options.append("include")

# If you need the coordinates of ROIs we compute it twice
if len(roi_coordinate_file) > 0:
    options2 = list(options)
    options2.append("show=Overlay")
    IJ.run(input_image_plus_copy, "Analyze Particles...", " ".join(options2))
    ov = input_image_plus_copy.getOverlay()
    with open(roi_coordinate_file, 'w') as fo:
        fo.write("shape\tpoints\tlabel\tt\tz\n")
        for i, roi in enumerate(ov):
            if roi.getName() is None:
                roi.name = "ROI_%d" % i
            poly = roi.getPolygon()
            x_values = poly.xpoints
            y_values = poly.ypoints
            points_coo = ",".join(["(%d,%d)" % (x, y) for x, y in zip(x_values, y_values)])
            fo.write("Polygon\t%s\t%s\t%d\t%d\n" % (points_coo, roi.getName(), roi.getTPosition(), roi.getZPosition()))
    analyzer.resetCounter()

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")
# Always run "in_situ".
options.append("in_situ")

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

# Save outputs.
if len(output_filename) > 0:
    # Save the ImagePlus object as a new image.
    IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)
if len(results_path) > 0:
    results_table = analyzer.getResultsTable()
    results_table.saveAs(results_path)