emodelrunner.morphology.morphology

Custom Morphology classes.

Classes

SSCXNrnFileMorphology(morphology_path[, ...])

Custom Morphology.

ThalamusNrnFileMorphology(morphology_path[, ...])

Custom Morphology.

class emodelrunner.morphology.morphology.SSCXNrnFileMorphology(morphology_path, do_replace_axon=False, do_set_nseg=True, comment='', replace_axon_hoc=None, nseg_frequency=40, morph_modifiers=None, morph_modifiers_hoc=None, morph_modifiers_kwargs=None)[source]

Bases: NrnFileMorphology

Custom Morphology.

name

name of this object

Type

str

comment

comment

Type

str

morphology_path

location of the file describing the morphology

Type

str

do_replace_axon

Does the axon need to be replaced by an AIS stub with default function ?

Type

bool

replace_axon_hoc

Translation in HOC language for the ‘replace_axon’ method. This code will ‘only’ be used when calling create_hoc on a cell model. While the model is run in python, replace_axon is used instead. Must include ‘proc replace_axon(){ … } If None,the default replace_axon is used

Type

str

do_set_nseg

if True, it will use nseg_frequency

Type

bool

nseg_frequency

frequency of nseg

Type

float

morph_modifiers

list of functions to modify the icell with (sim, icell) as arguments

Type

list

morph_modifiers_hoc

list of hoc strings corresponding to morph_modifiers

Type

list

static replace_axon(sim=None, icell=None)[source]

Replace axon.

Parameters
  • sim (bluepyopt.ephys.NrnSimulator) – neuron simulator

  • icell (neuron cell) – cell instantiation in simulator

class emodelrunner.morphology.morphology.ThalamusNrnFileMorphology(morphology_path, do_replace_axon=False, do_set_nseg=True, comment='', replace_axon_hoc=None, nseg_frequency=40, morph_modifiers=None, morph_modifiers_hoc=None, morph_modifiers_kwargs=None)[source]

Bases: NrnFileMorphology

Custom Morphology.

name

name of this object

Type

str

comment

comment

Type

str

morphology_path

location of the file describing the morphology

Type

str

do_replace_axon

Does the axon need to be replaced by an AIS stub with default function ?

Type

bool

replace_axon_hoc

Translation in HOC language for the ‘replace_axon’ method. This code will ‘only’ be used when calling create_hoc on a cell model. While the model is run in python, replace_axon is used instead. Must include ‘proc replace_axon(){ … } If None,the default replace_axon is used

Type

str

do_set_nseg

if True, it will use nseg_frequency

Type

bool

nseg_frequency

frequency of nseg

Type

float

morph_modifiers

list of functions to modify the icell with (sim, icell) as arguments

Type

list

morph_modifiers_hoc

list of hoc strings corresponding to morph_modifiers

Type

list

static replace_axon(sim=None, icell=None)[source]

Replace axon.

Parameters
  • sim (bluepyopt.ephys.NrnSimulator) – neuron simulator

  • icell (neuron cell) – cell instantiation in simulator