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NADAL Morgane
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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.
; -------- 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:
; then your parameter has the value empty string: '', and not None
parameter3 : None
; then your parameter has the value string: 'None', and not None
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[Input]
data_path : ./data/DIO_6H_6_1.70bis_2.2_3.tif
#/home/eric/Pictures/carole-rovere/clara-test/TO5_2_12W_pos1.tif
#/home/eric/Pictures/carole-rovere/clara-test/ST8_1.tif
#/home/eric/Pictures/carole-rovere/CHO_1H_D_1.70_3.3_8.tif
#.\\data\\DIO_6H_6_1.70bis_2.2_3.tif
; Can take the values R, G or B.
; Can also be set to None (cf. README above).
; Can also be set to None (cf. README above).
save_images : /home/eric/Code/project/mno/nutrimorph/2-morgane/result/image
; if None, no saving. Otherwise, path where to save images (MIP & graphs)
save_csv : /home/eric/Code/project/mno/nutrimorph/2-morgane/result/features
; where to save the csv. if None, by default it is in the .tif directory
save_features_analysis : /home/eric/Code/project/mno/nutrimorph/2-morgane/result/analysis
dilatation_erosion : True
; Choose whether to perform erosion/dilation on the extensions during the connexion process.
; Better results are achieved with it, and doing dilatation_erosion is theoretically more rigorous
statistical_analysis : False
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[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
; below, area correspond to a volume
soma_min_area_c : 116
# 58 if ToPixel (0,1)
soma_max_area_c : 1160
# 580 if ToPixel (0,1)
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[Extensions]
;below, area correspond to a volume
ext_min_area_c : 11.568
# 5.7840 if ToPixel (0,1)
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[Connexions]
max_straight_sq_dist_c : 217
max_weighted_length_c : 5
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; Values can be adapted to the image with the interface of frangi3gui.py
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; Stop at max x.1 with x <= sqrt(Z/2)
; ex: 3.1 for Z stacks < 18 and 5.1 for Z stacks < 50
diff_mode : indirect
[Features Extraction]
; histograms of extensions lengths
hist_min_length
#: 0
; in micron
; by default, 0
hist_step_length
#: 6
number_of_bins_length
#: 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)
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)
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[Program Running]
with_plot : False
in_parallel : False