Configuration files

Each workflow needs a different configuration, depending on the tasks that are included in it. These configurations are stored in luigi.cfg files. This page shows examples of such files.

Example for the tasks.workflows.ValidateVacuumSynthesis workflow

# luigi parameters
[core]
logging_conf_file = logging.conf

[RunnerConfig]
nb_jobs = 1

# global parameters
[PathConfig]
result_path = out_vacuum
morphology_path = morphology_path

###################################
# ########## Synthesis ########## #
###################################
# prepare step
[GetSynthesisInputs]
url = ssh://bbpcode.epfl.ch/project/proj82
git_synthesis_input_path = entities/bionames/rat/vacuum/synthesis_input

[BuildMorphsDF]
neurondb_path = <path_to_neuronDB.xml>
morphology_dirs = {"morphology_path": "<path_to_input_cells>"}

# synthesis setup
[ApplySubstitutionRules]
substitution_rules_path = substitution_rules.yaml

# synthesize in vacuum
[VacuumSynthesize]
n_cells = 10

####################################
# ########## Validation ########## #
####################################
# validation plots
[ValidateVacuumSynthesis]
with_morphometrics = True
with_density_profiles = True
with_vacuum_morphologies= True

Example for the tasks.workflows.ValidateSynthesis workflow

[core]
logging_conf_file = logging.conf

[RunnerConfig]
nb_jobs = 1

[CircuitConfig]
circuit_somata_path = circuit_somata.mvd3
region = O0
atlas_path = <path_to_atlas_directory>

[PathConfig]
result_path = out
morphology_path = morphology_path

#################################
# ########## Circuit ########## #
#################################
[BuildCircuit]
density_factor = 1
seed = 0

[SliceCircuit]
sliced_circuit_path = sliced_circuit_somata.mvd3

[CreateAtlasPlanes]
plane_type = aligned
plane_count = 1
centerline_axis = 0
slice_thickness = 800

###################################
# ########## Synthesis ########## #
###################################
[GetSynthesisInputs]
url = ssh://bbpcode.epfl.ch/project/proj82
git_synthesis_input_path = entities/bionames/rat/synthesis_input

[BuildMorphsDF]
neurondb_path = <path_to_neuronDB.xml>
morphology_dirs = {"morphology_path": "<path_to_input_cells>"}

[Synthesize]
debug_region_grower_scales = true
out_circuit_path = circuit.mvd3

[BuildAxonMorphologies]
axon_cells_path = <path_to_clones>

[PlotCollage]
realistic_diameters = False
linewidth = 0.04
diameter_scale =

####################################
# ########## Validation ########## #
####################################
[ValidateSynthesis]
with_morphometrics = False
with_collage = True
with_path_distance_fits = True
with_density_profiles = False
with_scale_statistics = True