import jython_utils
import sys
from ij import IJ
# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[-7]
input = sys.argv[-6]
equalize_histogram = jython_utils.asbool(sys.argv[-5])
saturated_pixels = sys.argv[-4]
normalize = jython_utils.asbool(sys.argv[-3])
tmp_output_path = sys.argv[-2]
output_datatype = sys.argv[-1]
# Open the input image file.
input_image_plus = IJ.openImage(input)
# 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()
# Set the options
options = []
# If equalize_histogram, saturated_pixels and normalize are ignored.
if equalize_histogram:
options.append('equalize')
else:
if saturated_pixels not in [None, 'None']:
# Fiji allows only a single decimal place for this value.
options.append('saturated=%.3f' % float(saturated_pixels))
import jython_utils
import sys
from ij import IJ
# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[-5]
input = sys.argv[-4]
black_background = jython_utils.asbool(sys.argv[-3])
tmp_output_path = sys.argv[-2]
output_datatype = sys.argv[-1]
# Open the input image file.
input_image_plus = IJ.openImage(input)
# Create a copy of the image.
input_image_plus_copy = input_image_plus.duplicate()
image_processor_copy = input_image_plus_copy.getProcessor()
try:
# Set binary options.
options = jython_utils.get_binary_options(
black_background=black_background)
IJ.run(input_image_plus_copy, "Options...", options)
# Convert image to binary if necessary.
if not image_processor_copy.isBinary():
# Convert the image to binary grayscale.
IJ.run(input_image_plus_copy, "Make Binary", "")
# Run the command.
output_datatype = sys.argv[ -1 ]
# Open the input image file.
input_image_plus = IJ.openImage( input )
# Create a copy of the image.
input_image_plus_copy = input_image_plus.duplicate()
image_processor_copy = input_image_plus_copy.getProcessor()
try:
# Convert image to binary if necessary.
if not image_processor_copy.isBinary():
# Convert the image to binary grayscale.
IJ.run( input_image_plus_copy, "Make Binary","iterations=1 count=1 edm=Overwrite do=Nothing" )
# Set the options.
if jython_utils.asbool( dark_background ):
method_str = "%s dark" % method
else:
method_str = method
IJ.setAutoThreshold( input_image_plus_copy, method_str )
if display == "red":
display_mode = "Red"
elif display == "bw":
display_mode = "Black & White"
elif display == "over_under":
display_mode = "Over/Under"
IJ.setThreshold( input_image_plus_copy, threshold_min, threshold_max, display_mode )
# Run the command.
IJ.run( input_image_plus_copy, "threshold", "" )
# Save the ImagePlus object as a new image.
IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
import jython_utils
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 = sys.argv[ -7 ]
iterations = int( sys.argv[ -6 ] )
count = int( sys.argv[ -5 ] )
black_background = jython_utils.asbool( sys.argv[ -4 ] )
pad_edges_when_eroding = jython_utils.asbool( sys.argv[ -3 ] )
tmp_output_path = sys.argv[ -2 ]
output_datatype = sys.argv[ -1 ]
# Open the input image file.
input_image_plus = IJ.openImage( input )
# Create a copy of the image.
input_image_plus_copy = input_image_plus.duplicate()
image_processor_copy = input_image_plus_copy.getProcessor()
try:
# Set binary options.
options = jython_utils.get_binary_options( black_background=black_background,
iterations=iterations,
count=count,
pad_edges_when_eroding=pad_edges_when_eroding )
IJ.run( input_image_plus_copy, "Options...", options )
# Run the command.
import jython_utils
import sys
from ij import IJ
# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[ -5 ]
input = sys.argv[ -4 ]
black_background = jython_utils.asbool( sys.argv[ -3 ] )
tmp_output_path = sys.argv[ -2 ]
output_datatype = sys.argv[ -1 ]
# Open the input image file.
input_image_plus = IJ.openImage( input )
# Create a copy of the image.
input_image_plus_copy = input_image_plus.duplicate()
image_processor_copy = input_image_plus_copy.getProcessor()
try:
# Set binary options.
options = jython_utils.get_binary_options( black_background=black_background )
IJ.run( input_image_plus_copy, "Options...", options )
# Convert image to binary if necessary.
if not image_processor_copy.isBinary():
# Convert the image to binary grayscale.
IJ.run( input_image_plus_copy, "Make Binary", "" )
# Run the command.
IJ.run( input_image_plus_copy, "Watershed", "" )
import sys
import jython_utils
from ij import ImagePlus, IJ
from ij.plugin.filter import Analyzer, MaximumFinder
from ij.process import ImageProcessor
from jarray import array
# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[ -10 ]
input = sys.argv[ -9 ]
scale_when_converting = jython_utils.asbool( sys.argv[ -8 ] )
weighted_rgb_conversions = jython_utils.asbool( sys.argv[ -7 ] )
noise_tolerance = int( sys.argv[ -6 ] )
output_type = sys.argv[ -5 ]
exclude_edge_maxima = jython_utils.asbool( sys.argv[ -4 ] )
light_background = jython_utils.asbool( sys.argv[ -3 ] )
tmp_output_path = sys.argv[ -2 ]
output_datatype = sys.argv[ -1 ]
# Open the input image file.
input_image_plus = IJ.openImage( input )
# 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()
analyzer = Analyzer( input_image_plus_copy )
try:
# Set the conversion options.
import jython_utils import sys from ij import IJ from ij.plugin.filter import Analyzer # Fiji Jython interpreter implements Python 2.5 which does not # provide support for argparse. error_log = sys.argv[ -14 ] input = sys.argv[ -13 ] black_background = jython_utils.asbool( sys.argv[ -12 ] ) size = sys.argv[ -11 ] circularity_min = float( sys.argv[ -10 ] ) circularity_max = float( sys.argv[ -9 ] ) show = sys.argv[ -8 ] display_results = jython_utils.asbool( sys.argv[ -7 ] ) all_results = jython_utils.asbool( sys.argv[ -6 ] ) exclude_edges = jython_utils.asbool( sys.argv[ -5 ] ) include_holes = jython_utils.asbool( sys.argv[ -4 ] ) tmp_output_path = sys.argv[ -3 ] output_datatype = sys.argv[ -2 ] results_path = sys.argv[ -1 ] # Open the input image file. input_image_plus = IJ.openImage( input ) # 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 ) try:
outf.write( '%.3f' % get_euclidean_distance( vertex1, vertex2 ) )
if calculate_largest_shortest_path:
# Keep number of separated items the same for each line.
outf.write( '%s %s' % ( sep, sep ) )
outf.write( ' %s' % sep )
outf.write( ' %s' % sep )
outf.write( ' \n' )
else:
outf.write( '\n' )
outf.close()
# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[ -8 ]
input = sys.argv[ -7 ]
black_background = jython_utils.asbool( sys.argv[ -6 ] )
prune_cycle_method = sys.argv[ -5 ]
prune_ends = jython_utils.asbool( sys.argv[ -4 ] )
calculate_largest_shortest_path = jython_utils.asbool( sys.argv[ -3 ] )
if calculate_largest_shortest_path:
BASIC_NAMES.extend( [ 'Longest Shortest Path', 'spx', 'spy', 'spz' ] )
DETAIL_NAMES.extend( [ ' ', ' ', ' ', ' ' ] )
show_detailed_info = jython_utils.asbool( sys.argv[ -2 ] )
output = sys.argv[ -1 ]
# Open the input image file.
input_image_plus = IJ.openImage( input )
# Create a copy of the image.
input_image_plus_copy = input_image_plus.duplicate()
image_processor_copy = input_image_plus_copy.getProcessor()
if calculate_largest_shortest_path:
# Keep number of separated items the same for each line.
outf.write('%s %s' % (sep, sep))
outf.write(' %s' % sep)
outf.write(' %s' % sep)
outf.write(' \n')
else:
outf.write('\n')
outf.close()
# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[-8]
input = sys.argv[-7]
black_background = jython_utils.asbool(sys.argv[-6])
prune_cycle_method = sys.argv[-5]
prune_ends = jython_utils.asbool(sys.argv[-4])
calculate_largest_shortest_path = jython_utils.asbool(sys.argv[-3])
if calculate_largest_shortest_path:
BASIC_NAMES.extend(['Longest Shortest Path', 'spx', 'spy', 'spz'])
DETAIL_NAMES.extend([' ', ' ', ' ', ' '])
show_detailed_info = jython_utils.asbool(sys.argv[-2])
output = sys.argv[-1]
# Open the input image file.
input_image_plus = IJ.openImage(input)
# Create a copy of the image.
input_image_plus_copy = input_image_plus.duplicate()
image_processor_copy = input_image_plus_copy.getProcessor()
import sys
import jython_utils
from ij import ImagePlus, IJ
from ij.plugin.filter import Analyzer, MaximumFinder
from ij.process import ImageProcessor
from jarray import array
# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[-10]
input = sys.argv[-9]
scale_when_converting = jython_utils.asbool(sys.argv[-8])
weighted_rgb_conversions = jython_utils.asbool(sys.argv[-7])
noise_tolerance = int(sys.argv[-6])
output_type = sys.argv[-5]
exclude_edge_maxima = jython_utils.asbool(sys.argv[-4])
light_background = jython_utils.asbool(sys.argv[-3])
tmp_output_path = sys.argv[-2]
output_datatype = sys.argv[-1]
# Open the input image file.
input_image_plus = IJ.openImage(input)
# 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()
analyzer = Analyzer(input_image_plus_copy)
try:
# Set the conversion options.
import jython_utils
import sys
from ij import IJ
# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[ -7 ]
input = sys.argv[ -6 ]
equalize_histogram = jython_utils.asbool( sys.argv[ -5 ] )
saturated_pixels = sys.argv[ -4 ]
normalize = jython_utils.asbool( sys.argv[ -3 ] )
tmp_output_path = sys.argv[ -2 ]
output_datatype = sys.argv[ -1 ]
# Open the input image file.
input_image_plus = IJ.openImage( input )
# 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()
# Set the options
options = []
# If equalize_histogram, saturated_pixels and normalize are ignored.
if equalize_histogram:
options.append( 'equalize' )
else:
if saturated_pixels not in [ None, 'None' ]:
# Fiji allows only a single decimal place for this value.
options.append( 'saturated=%.3f' % float( saturated_pixels ) )
import jython_utils
import sys
from ij import IJ
# Fiji Jython interpreter implements Python 2.5 which does not
# provide support for argparse.
error_log = sys.argv[-10]
input = sys.argv[-9]
threshold_min = float(sys.argv[-8])
threshold_max = float(sys.argv[-7])
method = sys.argv[-6]
display = sys.argv[-5]
black_background = jython_utils.asbool(sys.argv[-4])
# TODO: this is not being used.
stack_histogram = jython_utils.asbool(sys.argv[-3])
tmp_output_path = sys.argv[-2]
output_datatype = sys.argv[-1]
# Open the input image file.
input_image_plus = IJ.openImage(input)
# Create a copy of the image.
input_image_plus_copy = input_image_plus.duplicate()
image_processor_copy = input_image_plus_copy.getProcessor()
try:
# Convert image to binary if necessary.
if not image_processor_copy.isBinary():
# Convert the image to binary grayscale.
IJ.run(input_image_plus_copy, "Make Binary",
"iterations=1 count=1 edm=Overwrite do=Nothing")