Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
if new_setting_values[UNCLUMP_METHOD_VAR] == cps.DO_NOT_USE:
new_setting_values[UNCLUMP_METHOD_VAR] = UN_NONE
if new_setting_values[WATERSHED_VAR] == cps.DO_NOT_USE:
new_setting_values[WATERSHED_VAR] = WA_NONE
variable_revision_number = 1
from_matlab = False
if (not from_matlab) and variable_revision_number == 1:
# Added LOG method
setting_values = list(setting_values)
setting_values += [ cps.YES, ".5" ]
variable_revision_number = 2
if (not from_matlab) and variable_revision_number == 2:
# Added Otsu options
setting_values = list(setting_values)
setting_values += [cpmi.O_TWO_CLASS, cpmi.O_WEIGHTED_VARIANCE,
cpmi.O_FOREGROUND]
variable_revision_number = 3
if (not from_matlab) and variable_revision_number == 3:
# Added more LOG options
setting_values = setting_values + [cps.YES, "5"]
variable_revision_number = 4
if (not from_matlab) and variable_revision_number == 4:
# Added # of object limits
setting_values = setting_values + [LIMIT_NONE, "500"]
variable_revision_number = 5
if (not from_matlab) and variable_revision_number == 5:
# Changed object number limit option from "No action" to "Continue"
if setting_values[-2] == "No action":
if setting_values[10] == cps.DO_NOT_USE:
new_setting_values.append(cps.NO)
else:
new_setting_values.append(cps.YES)
setting_values = new_setting_values
from_matlab = False
variable_revision_number = 1
if from_matlab:
NotImplementedError("Don't know how to convert Matlab IdentifySecondary revision # %d"%(variable_revision_number))
if variable_revision_number != self.variable_revision_number:
NotImplementedError("Don't know how to handle IdentifySecondary revision # %d"%(variable_revision_number))
if (not from_matlab) and variable_revision_number == 1:
# Removed test mode
# added Otsu parameters.
setting_values = setting_values[:11]+setting_values[12:]
setting_values += [cpmi.O_TWO_CLASS, cpmi.O_WEIGHTED_VARIANCE,
cpmi.O_FOREGROUND]
variable_revision_number = 2
if (not from_matlab) and variable_revision_number == 2:
# Added discarding touching
setting_values = setting_values + [cps.NO, cps.NO, "FilteredNuclei"]
variable_revision_number = 3
if (not from_matlab) and variable_revision_number == 3:
# Added new primary outlines
setting_values = setting_values + [cps.NO, "FilteredNucleiOutlines"]
variable_revision_number = 4
return setting_values, variable_revision_number, from_matlab
def threshold_scale(self):
'''The "scale" for the threshold = minor parameterizations'''
#
# Distinguish Otsu choices from each other
#
threshold_algorithm = self.threshold_algorithm
if threshold_algorithm == cpthresh.TM_OTSU:
if self.two_class_otsu == O_TWO_CLASS:
scale = "2"
else:
scale = "3"
if self.assign_middle_to_foreground == O_FOREGROUND:
scale += "F"
else:
scale += "B"
if self.use_weighted_variance == O_WEIGHTED_VARIANCE:
scale += "W"
else:
scale += "S"
return scale
elif threshold_algorithm == cpthresh.TM_MOG:
return str(int(self.object_fraction.value * 100))