axon-projection/example/config_synthesis_example.cfg at main · BlueBrain/axon-projection · GitHub

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debug = True
log_level = debug
seed = 0

[global]
morphology_dir = data/morphologies_for_synthesis

[[atlas]]
path = data
region_filename = brain_regions.nrrd

[[create_graph]]
intermediate_number = 10
min_intermediate_distance = 500
min_random_point_distance = 500
voronoi_steps = 1
use_orientation_penalty = True
orientation_penalty_exponent = 0.1
orientation_penalty_amplitude = 1
use_depth_penalty = True
depth_penalty_sigma = 0.25
depth_penalty_amplitude = 2
use_terminal_penalty = True
favored_regions = ["fiber tracts"]
favored_region_min_random_point_distance = 100

[[post_processing]]
random_coeff = 1
length_coeff = 1
global_target_sigma_coeff = 10
target_sigma_coeff = 2
history_sigma_coeff = 2

[[outputs]]
enable_final_figures = True
enable_graph_creation_figures = False
enable_graph_creation_data = False
enable_main_trunk_figures = False
enable_main_trunk_morphologies = False
enable_morphologies = True
enable_postprocess_trunk_figures = False
enable_postprocess_trunk_morphologies = True
enable_steiner_tree_solution_figures = False
enable_steiner_tree_solutions = False
enable_target_point_figures = False
enable_target_points = False
enable_tuft_figures = False
enable_tuft_morphologies = True

[create-inputs]
output_dir = inputs
clustering_parameters = '''{
	"sphere_parents": {"method": "sphere_parents", "sphere_radius": 300, "max_path_distance": 300}
}
'''

[[wmr]]
path = WMR.yaml

[synthesize]
output_dir = out

[validation]

[[mimic]]
output_dir = mimic_validation
clustering_parameters = '''{
	"sphere_parents": {"method": "sphere_parents", "sphere_radius": 300, "max_path_distance": 300}
}
'''