Parameters¶

This page describes the format of the expected parameters used by region-grower.

Note

These schemas only contain the entries used in region-grower, not the ones used by its dependencies.

Parameters¶

The parameters are given as a JSON file with one entry per mtype (the key must be equal to the mtype name). Each of these entries must follow the following schema:

TMD parameters¶

The TMD parameters used to synthesize the cells
type	object
patternProperties
.*	The TMD parameters used to synthesize the cells for a region
	patternProperties
	.*	The TMD parameters used to synthesize the cells of the given mtype
		properties
		context_constraints	Context constraints
			The constraints to obey in the given context
			type	object
			properties
			apical_dendrite	Specific constraints for basals
				Hard limit with extent
			basal_dendrite	Specific constraints for basals
				Hard limit with extent
			axon	Specific constraints for axons
				Hard limit
			additionalProperties	False
		diameter_params	type	object
			properties
			method	type	string
			additionalProperties	True
		grow_types	type	array
			items	type	string
				enum	basal_dendrite, apical_dendrite, axon
		orientation	type	array
			items	type	number
		additionalProperties	True

Fraction¶

The relative position in a layer (0 for the bottom and 1 for the top)
type	number

Layer¶

The index of a layer
type	integer
maximum	6
minimum	1

Limit properties¶

Properties of a specific limit
type	object
properties
fraction	Fraction
layer	Layer
additionalProperties	False

Hard limit¶

Min and max of a hard limit
type	object
properties
hard_limit_max	The max of the hard limit
	Limit properties
hard_limit_min	The min of the hard limit
	Limit properties
additionalProperties	False

Hard limit with extent¶

Min and max of a hard limit with extent_to_target
type	object
properties
extent_to_target	The target depth given as a fraction of a layer and the properties of the fit of the Y extent relative to the path length
	type	object
	properties
	fraction	Fraction
	intercept	type	number
	layer	Layer
	slope	type	number
	additionalProperties	False
hard_limit_max	The max of the hard limit
	Limit properties
hard_limit_min	The min of the hard limit
	Limit properties
additionalProperties	False

Distributions¶

The distributions are given as a JSON file which must follow the following schema:

TMD distributions¶

The TMD distributions used to synthesize the cells
type	object
patternProperties
.*	The mtype properties given to TNS
	type	object
additionalProperties	True