bluepyopt.ephys.locations#

Location classes

class bluepyopt.ephys.locations.ArbBranchLocation(name, branch, comment='')[source]#

Bases: ArbLocation

Branch in an Arbor morphology.

Arbor’s counterpart of NrnSeclistSecLocation.

acc_label()[source]#

Arbor label

class bluepyopt.ephys.locations.ArbBranchRelLocation(name, branch, pos, comment='')[source]#

Bases: ArbLocation

Relative position on a branch in an Arbor morphology.

Arbor’s counterpart of NrnSeclistCompLocation.

acc_label()[source]#

Arbor label

class bluepyopt.ephys.locations.ArbLocation(name='', comment='')[source]#

Bases: Location

Arbor Location

instantiate(sim=None, icell=None)[source]#

Find the instantiate compartment (default implementation)

class bluepyopt.ephys.locations.ArbLocsetLocation(name, locset, comment='')[source]#

Bases: ArbLocation

Arbor location set defined by a user-supplied string (S-expression).

acc_label()[source]#

Arbor label

class bluepyopt.ephys.locations.ArbRegionLocation(name, region, comment='')[source]#

Bases: ArbLocation

Arbor region defined by a user-supplied string (S-expression).

acc_label()[source]#

Arbor label

class bluepyopt.ephys.locations.ArbSegmentLocation(name, segment, comment='')[source]#

Bases: ArbLocation

Segment in an Arbor morphology.

acc_label()[source]#

Arbor label

class bluepyopt.ephys.locations.ArbSegmentRelLocation(name, segment, pos, comment='')[source]#

Bases: ArbLocation

Relative position on a segment in an Arbor morphology.

acc_label()[source]#

Arbor label

exception bluepyopt.ephys.locations.EPhysLocAccException(message)[source]#

Bases: Exception

All exceptions generated by ACC label creation

Constructor

exception bluepyopt.ephys.locations.EPhysLocInstantiateException(message)[source]#

Bases: Exception

All exceptions generated by location instantiation

Constructor

class bluepyopt.ephys.locations.Location[source]#

Bases: BaseEPhys

class bluepyopt.ephys.locations.NrnPointProcessLocation(name, pprocess_mech, comment='')[source]#

Bases: Location

Point process location

Constructor

Parameters:

  • name (str) – name of the object

  • pprocess_mech (str) – point process mechanism

acc_label()[source]#

Arbor label

instantiate(sim=None, icell=None)[source]#

Find the instantiated point processes

class bluepyopt.ephys.locations.NrnSecSomaDistanceCompLocation(name, soma_distance=None, sec_index=None, seclist_name=None, comment='')[source]#

Bases: NrnSomaDistanceCompLocation

Compartment on a section defined both by a section index and distance from the soma

Constructor

Parameters:

  • name (str) – name of this object

  • soma_distance (float) – distance from soma to this compartment

  • sec_index (int) – index of the section to consider

  • seclist_name (str) – name of Neuron sections (ex: ‘apic’)

acc_label()[source]#

Arbor label

instantiate(sim=None, icell=None)[source]#

Find the instantiate compartment

class bluepyopt.ephys.locations.NrnSeclistCompLocation(name, seclist_name=None, sec_index=None, comp_x=None, comment='')[source]#

Bases: Location, DictMixin

Compartment in a sectionlist

Constructor

Parameters:

  • name (str) – name of the object

  • seclist_name (str) – name of Neuron section list (ex: ‘somatic’)

  • sec_index (int) – index of the section in the section list

  • comp_x (float) – segx (0..1) of segment inside section

acc_label()[source]#

Arbor label

instantiate(sim=None, icell=None)[source]#

Find the instantiate compartment

class bluepyopt.ephys.locations.NrnSeclistLocation(name, seclist_name=None, comment='')[source]#

Bases: Location, DictMixin

Section in a sectionlist

Constructor

Parameters:

  • name (str) – name of the object

  • seclist_name (str) – name of NEURON section list (ex: ‘somatic’)

acc_label()[source]#

Arbor label

instantiate(sim=None, icell=None)[source]#

Find the instantiate compartment

class bluepyopt.ephys.locations.NrnSeclistSecLocation(name, seclist_name=None, sec_index=None, comment='')[source]#

Bases: Location, DictMixin

Section in a sectionlist

Constructor

Parameters:

  • name (str) – name of this object

  • seclist_name (str) – name of Neuron section list (ex: ‘somatic’)

  • sec_index (int) – index of the section

acc_label()[source]#

Arbor label

instantiate(sim=None, icell=None)[source]#

Find the instantiate compartment

class bluepyopt.ephys.locations.NrnSectionCompLocation(name, sec_name=None, comp_x=None, comment='')[source]#

Bases: Location, DictMixin

Compartment in a section

Constructor

Parameters:

  • name (str) – name of the object

  • sec_name (str) – name of Neuron section (ex: ‘soma[0]’)

  • comp_x (float) – segx (0..1) of segment inside section

acc_label()[source]#

Arbor label

instantiate(sim=None, icell=None)[source]#

Find the instantiate compartment

class bluepyopt.ephys.locations.NrnSomaDistanceCompLocation(name, soma_distance=None, seclist_name=None, comment='')[source]#

Bases: Location, DictMixin

Compartment at distance from soma

Constructor

Parameters:

  • name (str) – name of this object

  • soma_distance (float) – distance from soma to this compartment

  • seclist_name (str) – name of Neuron section list (ex: ‘apical’)

acc_label()[source]#

Arbor label

find_icomp(sim, iseclist)[source]#

Find the index of the compartment based on a list of isec and a distance

instantiate(sim=None, icell=None)[source]#

Find the instantiate compartment

class bluepyopt.ephys.locations.NrnTrunkSomaDistanceCompLocation(name, soma_distance=None, sec_index=None, seclist_name=None, direction=None, comment='')[source]#

Bases: NrnSecSomaDistanceCompLocation

Location at a distance from soma along a main direction.

We search for the section that is the furthest away from some along a direction, and pick a location at a given distance from soma along the path to that section.

If direction == ‘radial’, the largest radial direction is used.

This is most useful to follow the trunk of an apical dendrite without knowing the apical point, but only that apical trunk goes along y.

Constructor

Parameters:

  • name (str) – name of this object

  • soma_distance (float) – distance from soma to this compartment

  • sec_index (int) – index of the section to consider

  • sec_name (str) – name of Neuron sections (ex: ‘apic’)

  • direction (list of 3 elements) – 3d vector representing direction, if None, default is [0, 1, 0]

acc_label()[source]#

Arbor label

set_sec_index(icell=None)[source]#

Search for the point furthest away along given direction.