bluepyopt.ephys.locations

Location classes

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

All exception generated by location instantiation

Constructor

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

Point process location

Constructor

Parameters
  • name (str) – name of the object

  • pprocess_mech (str) – point process mechanism

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

Find the instantiated point processes

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

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

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

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]

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

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

Find the instantiate compartment

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

Section in a sectionlist

Constructor

Parameters
  • name (str) – name of the object

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

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

Find the instantiate compartment

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

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

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

Find the instantiate compartment

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

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

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

Find the instantiate compartment

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

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’)

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, sec_name=None, direction=None, comment='')[source]

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]

set_sec_index(icell=None)[source]

Search for the point furthest away along given direction.