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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
from typing import Any, Union
def NutrimorphArguments(parameter_file):
""""""
parameters = configparser.ConfigParser(allow_no_value=True)
parameters.read(parameter_file)
# [Input]
data_path = parameters["Input"]["data_path"]
channel = parameters["Input"]["channel"]
size_voxel_in_micron = IfNotFloat(parameters, "Input", "size_voxel_in_micron")
dilatation_erosion = parameters.getboolean("Input", "dilatation_erosion")
save_images = parameters["Input"]["save_images"]
save_csv = parameters["Input"]["save_csv"]
save_features_analysis = parameters["Input"]["save_features_analysis"]
statistical_analysis = parameters.getboolean("Input", "statistical_analysis")
# [Somas]
soma_low_c = IfNotFloat(parameters, "Somas", "soma_low_c")
soma_high_c = IfNotFloat(parameters, "Somas", "soma_high_c")
soma_selem_micron_c = IfNotFloat(parameters, "Somas", "soma_selem_micron_c")
soma_min_area_c = IfNotFloat(parameters, "Somas", "soma_min_area_c")
soma_max_area_c = IfNotFloat(parameters, "Somas", "soma_max_area_c")
# [Extensions]
adapt_hist_equalization = parameters.getboolean(
"Extensions", "adapt_hist_equalization"
)
ext_low_c = IfNotFloat(parameters, "Extensions", "ext_low_c")
ext_high_c = IfNotFloat(parameters, "Extensions", "ext_high_c")
ext_selem_micron_c = IfNotFloat(parameters, "Extensions", "ext_selem_micron_c")
ext_min_area_c = IfNotFloat(parameters, "Extensions", "ext_min_area_c")
# [Connexions]
max_straight_sq_dist_c = IfNotFloat(
parameters, "Connexions", "max_straight_sq_dist_c"
)
max_weighted_length_c = IfNotFloat(
parameters, "Connexions", "max_weighted_length_c"
)
# [Frangi]
scale_range = IfNotFloat(parameters, "Frangi", "scale_range")
scale_step = IfNotFloat(parameters, "Frangi", "scale_step")
alpha = IfNotFloat(parameters, "Frangi", "alpha")
beta = IfNotFloat(parameters, "Frangi", "beta")
frangi_c = IfNotFloat(parameters, "Frangi", "frangi_c")
diff_mode = parameters["Frangi"]["diff_mode"]
bright_on_dark = parameters.getboolean("Frangi", "bright_on_dark")
method = parameters["Frangi"]["method"]
# [Features Extraction]
hist_min_length = IfNotFloat(parameters, "Features Extraction", "hist_min_length")
hist_step_length = IfNotFloat(parameters, "Features Extraction", "hist_step_length")
number_of_bins_length = IfNotFloat(
parameters, "Features Extraction", "number_of_bins_length"
)
hist_bins_borders_length = IfNotFloat(
parameters, "Features Extraction", "hist_bins_borders_length"
)
hist_min_curvature = IfNotFloat(
parameters, "Features Extraction", "hist_min_curvature"
)
hist_step_curvature = IfNotFloat(
parameters, "Features Extraction", "hist_step_curvature"
)
number_of_bins_curvature = IfNotFloat(
parameters, "Features Extraction", "number_of_bins_curvature"
)
hist_bins_borders_curvature = IfNotFloat(
parameters, "Features Extraction", "hist_bins_borders_curvature"
)
# [Program running]
with_plot = parameters.getboolean("Program Running", "with_plot")
interactive = parameters.getboolean("Program Running", "interactive")
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
arguments = {
"channel": channel,
"dilatation_erosion": dilatation_erosion,
"size_voxel_in_micron": size_voxel_in_micron,
"soma_low_c": soma_low_c,
"soma_high_c": soma_high_c,
"soma_selem_micron_c": soma_selem_micron_c,
"soma_min_area_c": soma_min_area_c,
"soma_max_area_c": soma_max_area_c,
"adapt_hist_equalization": adapt_hist_equalization,
"ext_low_c": ext_low_c,
"ext_high_c": ext_high_c,
"ext_selem_micron_c": ext_selem_micron_c,
"ext_min_area_c": ext_min_area_c,
"max_straight_sq_dist_c": max_straight_sq_dist_c,
"max_weighted_length_c": max_weighted_length_c,
"scale_range": scale_range,
"scale_step": scale_step,
"alpha": alpha,
"beta": beta,
"frangi_c": frangi_c,
"diff_mode": diff_mode,
"bright_on_dark": bright_on_dark,
"method": method,
"hist_min_length": hist_min_length,
"hist_step_length": hist_step_length,
"number_of_bins_length": number_of_bins_length,
"hist_bins_borders_length": hist_bins_borders_length,
"hist_min_curvature": hist_min_curvature,
"hist_step_curvature": hist_step_curvature,
"number_of_bins_curvature": number_of_bins_curvature,
"hist_bins_borders_curvature": hist_bins_borders_curvature,
"with_plot": with_plot,
"interactive": interactive,
"in_parallel": in_parallel,
}
return (
data_path,
save_images,
save_csv,
save_features_analysis,
statistical_analysis,
arguments,
)
def IfNotFloat(parameters, section: str, key: str) -> Union[Union[float, str], Any]:
""""""
if parameters.get(section, key) is not None:
try:
value = parameters.getfloat(section, key)
return value
except:
return eval(parameters.get(section, key))
else:
return parameters.get(section, key)