# 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.




; -------- READ ME --- How to set parameters to None ? --------
; All the input parameters of this file are considered strings. If you write "parameter  :  None",
; you are not setting your parameter at the None value but you assigned the string 'None' to the parameter.
; In order to set the parameter to the None value, write "parameter" without anything behind (even not a ":").
; See the example below:

[Example]
; RIGHT WAY TO SET YOUR PARAMETER TO None:
parameter

; if you write:
parameter2                  :
; then your parameter has the value empty string: '', and not None
parameter3                  :   None
; then your parameter has the value string: 'None', and not None

[Input]
data_path                   :   D:\MorganeNadal\IBA1-Microglies\standard conditions\020620_ST8_20W_1_2.lif - Position 3.tif
; direct data path to the image
file_path
# D:\\MorganeNadal\\IBA1-Microglies
; path to the repository containing the different condition repository
; Set to None if data_path exists
conditions
# ["CHO_1H_D_1.70_3.3", "CHO_3H_H_1.82_3.2", "CHO_6H_LL_1.70_1.3", "DIO_1H_16_1.58_2.1", "DIO_3H_F_1.82_3.1", "DIO_6H_6_1.70bis_2.2"]
; list of the repository containing the different conditions
; Set to None if data_path exists
channel
; Can take the values R, G or B.
; Can also be set to None (cf. README above).
size_voxel_in_micron       :    [0.071, 0.071, 0.4997]
; size_voxel_in_micron ->  [X,Y,Z]
; Can also be set to None (cf. README above).
save_images
; if None, no saving. Otherwise, path where to save images # TODO add in search_parameters.py

[Somas]
soma_low_c                 :    0.15
; this is a coefficient => not in micron
soma_high_c                :    0.7126
; this is a coefficient => not in micron
soma_selem_micron_c        :    0.481
soma_min_area_c            :    58
soma_max_area_c            :    580

[Extensions]
adapt_hist_equalization    :    True
; for hysteresis
ext_low_c                  :    10
#7.5e-8
#1e-20
ext_high_c                 :    0.6
#1e-5
# 0.5e-5
; for morphological cleaning
ext_selem_micron_c         :    0.2405
ext_min_area_c             :    5.7840
ext_max_length_c           :    60

[Connexions]
max_straight_sq_dist_c     :    216.45
max_weighted_length_c      :    4.81

[Frangi]
scale_range                :    (0.1,6.1)
; Stop at max 3.1 for number of Z stacks < 18
; write min,max scale range
scale_step                 :    2.5
#  1.0 for Z stacks < 18
alpha                      :    0.8
# 0.8
beta                       :    0.5
# 0.5
frangi_c                   :    30
## 12.5 if normalized btw 0 and 1
# 60.12506 # 500.0
bright_on_dark             :    True
method                     :    c

[Features Extraction]
; histograms of extensions lengths
hist_min_length
#:    0
; in micron
; by default, 0
hist_step_length
#:    6
; in micron
number_of_bins_length
#:    5
; by default, 5
; extensions generally do not exceed 30 microns

; if the above parameters are set to None, you can directly use the boundaries of your choice for the histogram:
hist_bins_borders_length   :    (0, 0.5, 1, 5, 10, 50)

; histograms of extensions curvatures
hist_min_curvature
#:    0
hist_step_curvature
#:    6
number_of_bins_curvature
#:    5

; if the above parameters are set to None, you can directly use the boundaries of your choice for the histogram:
hist_bins_borders_curvature :    (0, 0.05, 0.3, 1, 10, 50)


[Program Running]
with_plot                  :    False
in_parallel                :    False