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]¶