# Copyright CNRS/Inria/UNS
# Contributor(s): Eric Debreuve (since 2019), Morgane Nadal (2020)
#
# eric.debreuve@cnrs.fr
#
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# "http://www.cecill.info".
#
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; -------- 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\\DIO_3H_F_1.82_3.1\\DIO_3H_F_1.82_3.1_1.tif
#D:\\MorganeNadal\\IBA1-Microglies\\DIO_1H_16_1.58_2.1\\DIO_1H_16_1.58_2.1_4.tif
#./data/DIO_6H_6_1.70bis_2.2_3.tif
channel                    :    G
; Can take the values R, G or B.
; Can also be set to None (cf. README above).
size_voxel_in_micron
; 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        :    0.24050024 * 2
soma_min_area_c            :    (0.24050024 ** 2) * 1000

[Extensions]
; 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         :    0.24050024 * 1
ext_min_area_c             :    (0.24050024 ** 2) * 100

[Connexions]
max_straight_sq_dist_c     :    0.24050024 * (30 ** 2)
max_weighted_length_c      :    0.24050024 * 20.0

[Frangi]
scale_range                :    (0.024,0.745)
; Stop at max 3.1 (<=> 0.745) for number of Z stacks < 18
; write min,max scale range
scale_step                 :    0.24
#  1.0
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