bluepyopt.ephys.locations¶
Location classes
- class bluepyopt.ephys.locations.ArbBranchLocation(name, branch, comment='')[source]¶
Branch in an Arbor morphology.
Arbor’s counterpart of NrnSeclistSecLocation.
- class bluepyopt.ephys.locations.ArbBranchRelLocation(name, branch, pos, comment='')[source]¶
Relative position on a branch in an Arbor morphology.
Arbor’s counterpart of NrnSeclistCompLocation.
- class bluepyopt.ephys.locations.ArbLocsetLocation(name, locset, comment='')[source]¶
Arbor location set defined by a user-supplied string (S-expression).
- class bluepyopt.ephys.locations.ArbRegionLocation(name, region, comment='')[source]¶
Arbor region defined by a user-supplied string (S-expression).
- class bluepyopt.ephys.locations.ArbSegmentLocation(name, segment, comment='')[source]¶
Segment in an Arbor morphology.
- class bluepyopt.ephys.locations.ArbSegmentRelLocation(name, segment, pos, comment='')[source]¶
Relative position on a segment in an Arbor morphology.
- exception bluepyopt.ephys.locations.EPhysLocAccException(message)[source]¶
All exceptions generated by ACC label creation
Constructor
- exception bluepyopt.ephys.locations.EPhysLocInstantiateException(message)[source]¶
All exceptions generated by location instantiation
Constructor
- 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
- class bluepyopt.ephys.locations.NrnSecSomaDistanceCompLocation(name, soma_distance=None, sec_index=None, seclist_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
seclist_name (str) – name of Neuron sections (ex: ‘apic’)
- 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
- 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’)
- 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
- 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
- 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’)
- class bluepyopt.ephys.locations.NrnTrunkSomaDistanceCompLocation(name, soma_distance=None, sec_index=None, seclist_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]