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# Copyright CNRS/Inria/UNS
# Contributor(s): Eric Debreuve (since 2019), Morgane Nadal (2020)
#
# eric.debreuve@cnrs.fr
#
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info".
#
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
#
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
#
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
import configparser
# --Parameters from .INI file
parameters = configparser.ConfigParser(allow_no_value=True)
parameters.read('parameters.ini')
def IfNotFloat(section: str, key: str) -> float:
try:
value = parameters.getfloat(section, key)
return value
except:
return eval(parameters.get(section, key))
# [Input]
data_path = parameters['Input']['data_path']
channel = parameters['Input']['channel']
try:
size_voxel_in_micron = parameters['Input']['size_voxel_in_micron']
if size_voxel_in_micron is not None:
size_voxel_in_micron = size_voxel_in_micron.split(',')
size_voxel_in_micron = list(float(size_voxel_in_micron[i]) for i in range(len(size_voxel_in_micron)))
except:
raise ValueError('The voxel size parameter is not given correctly. Write X,Y,Z without () or [] or spaces. Do not '
'forget ":" between size_voxel_in_micron and its value')
# [Somas]
soma_low_c = IfNotFloat('Somas', 'soma_low_c')
soma_high_c = IfNotFloat('Somas', 'soma_high_c')
soma_selem_micron_c = IfNotFloat('Somas', 'soma_selem_micron_c')
soma_min_area_c = IfNotFloat('Somas', 'soma_min_area_c')
# [Extensions]
ext_low_c = IfNotFloat('Extensions', 'ext_low_c')
ext_high_c = IfNotFloat('Extensions', 'ext_high_c')
ext_selem_micron_c = IfNotFloat('Extensions', 'ext_selem_micron_c')
ext_min_area_c = IfNotFloat('Extensions', 'ext_min_area_c')
# [Connexions]
max_straight_sq_dist_c = IfNotFloat('Connexions', 'max_straight_sq_dist_c')
max_weighted_length_c = IfNotFloat('Connexions', 'max_weighted_length_c')
try:
scale_range = parameters['Frangi']['scale_range']
scale_range = scale_range.split(',')
scale_range = tuple(float(scale_range[i]) for i in range(len(scale_range)))
except:
raise ValueError('The scale range parameter is not given correctly. Write min,max without () or [] or spaces. '
'Do not forget ":" between scale_range and its value')
scale_step = IfNotFloat('Frangi', 'scale_step')
alpha = IfNotFloat('Frangi', 'alpha')
beta = IfNotFloat('Frangi', 'beta')
frangi_c = IfNotFloat('Frangi', 'frangi_c')
bright_on_dark = parameters.getboolean('Frangi', 'bright_on_dark')
method = parameters['Frangi']['method']
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# [Program running]
with_plot = parameters.getboolean('Program Running', 'with_plot')
in_parallel = parameters.getboolean('Program Running', 'in_parallel')
# data_path = "./data/DIO_6H_6_1.70bis_2.2_3.tif"
# channel = 'G'
# size_voxel_in_micron = None # -> list [X,Y,Z]
# with_plot = False
#
# soma_low_c = 0.15
# soma_high_c = 0.7126
# ext_low_c = 0.2 #3 #1e-7 ##0.2 # 0.02 # 0.2 # ext_low_c = 9.0e-4
# ext_high_c = 0.6 #1e-10 #1.2e-7 ##0.6 # 0.04 # 0.6 # high_ext = 8.0e-3
#
# # soma_selem_c = mp_.disk(2)
# # ext_selem_c = mp_.disk(1)
# soma_selem_micron_c = 0.24050024 * 2
# ext_selem_micron_c = 0.24050024 * 1
#
# max_straight_sq_dist_c = (30 ** 2) * 0.24050024
# max_weighted_length_c = 20.0 * 0.24050024
#
# soma_min_area_c = 1000 * (0.24050024 ** 2)
# ext_min_area_c = 100 * (0.24050024 ** 2)
# # soma_min_area_c = 1000
# # ext_min_area_c = 100
#
# in_parallel = False