neuronunit.models package¶
Subpackages¶
- neuronunit.models.backends package
- Submodules
- neuronunit.models.backends.base module
- neuronunit.models.backends.brian_multi_comp_ca2_HH module
- neuronunit.models.backends.fhn module
- neuronunit.models.backends.general_pyNN module
- neuronunit.models.backends.geppetto module
- neuronunit.models.backends.glif module
- neuronunit.models.backends.hhrawf module
- neuronunit.models.backends.jNeuroML module
- neuronunit.models.backends.neuron module
- neuronunit.models.backends.parse_glif module
- neuronunit.models.backends.rawpy module
- Module contents
Submodules¶
neuronunit.models.channel module¶
NeuronUnit model class for ion channels models
-
class
neuronunit.models.channel.
ChannelModel
(channel_file_path_or_url, channel_index=0, name=None, backend='jNeuroML')[source]¶ Bases:
neuronunit.models.lems.LEMSModel
,neuronunit.capabilities.channel.NML2ChannelAnalysis
A model for ion channels
neuronunit.models.lems module¶
Model classes for NeuronUnit.
-
class
neuronunit.models.lems.
LEMSModel
(LEMS_file_path_or_url, name=None, backend=None, attrs=None)[source]¶ Bases:
sciunit.models.runnable.RunnableModel
A generic LEMS model.
-
create_lems_file_copy
(name=None, use=True)[source]¶ Create a temporary, writable copy of the original LEMS file.
Used so that e.g. edits can be made to it programatically before simulation.
-
extra_capability_checks
= {<class 'neuronunit.capabilities.ReceivesSquareCurrent'>: 'has_pulse_generator'}¶
-
from_url
= None¶
-
get_nml_paths
(lems_tree=None, absolute=True, original=False)[source]¶ Get all NeuroML file paths associated with the model.
-
has_pulse_generator
(tree=None)[source]¶ Return True if this model instance contains a pulse generator.
It must be a NeuroML implementation of a pulse generator attached to an explicit input.
-
set_lems_run_params
(verbose=False)[source]¶ Set run_param equivalents in the LEMS file and write it to disk.
-
temp_dir
¶
-
neuronunit.models.morphology module¶
NeuronUnit model class for NEURON HOC defined cell models
-
class
neuronunit.models.morphology.
SwcCellModel
(swc_path, name=None)[source]¶ Bases:
sciunit.models.base.Model
,neuronunit.capabilities.morphology.ProducesSWC
A model for cells defined using SWC files. Requires a path to the SWC file.
neuronunit.models.reduced module¶
NeuronUnit model class for reduced neuron models.
-
class
neuronunit.models.reduced.
ReducedModel
(LEMS_file_path, name=None, backend=None, attrs=None)[source]¶ Bases:
neuronunit.models.lems.LEMSModel
,neuronunit.capabilities.ReceivesSquareCurrent
,neuronunit.capabilities.ProducesActionPotentials
Base class for reduced models, using LEMS
-
get_APs
(**run_params)[source]¶ Get action potential waveform chunks from the model.
Must return a neo.core.AnalogSignal. Each column of the AnalogSignal should be a spike waveform.
-
-
class
neuronunit.models.reduced.
VeryReducedModel
(name=None, backend=None, attrs=None)[source]¶ Bases:
neuronunit.models.static.ExternalModel
,neuronunit.capabilities.ReceivesCurrent
,neuronunit.capabilities.ProducesActionPotentials
Base class for reduced models, using LEMS
-
get_APs
(**run_params)[source]¶ Get action potential waveform chunks from the model.
Must return a neo.core.AnalogSignal. Each column of the AnalogSignal should be a spike waveform.
-
get_spike_train
(**run_params)[source]¶ Get computed spike times from the model.
Arguments: None. Returns: a neo.core.SpikeTrain object.
-
neuronunit.models.section_extension module¶
These classes are for compatibility w/ the old neuronunit.neuron module.
neuronunit.models.static module¶
-
class
neuronunit.models.static.
ExternalModel
[source]¶ Bases:
sciunit.models.base.Model
,neuronunit.capabilities.ProducesMembranePotential
,sciunit.capabilities.Runnable
A model which produces a frozen membrane potential waveform.
-
class
neuronunit.models.static.
StaticModel
(vm)[source]¶ Bases:
sciunit.models.base.Model
,neuronunit.capabilities.ReceivesSquareCurrent
,neuronunit.capabilities.ProducesActionPotentials
,neuronunit.capabilities.ProducesMembranePotential
A model which produces a frozen membrane potential waveform.
neuronunit.models.very_reduced module¶
NeuronUnit model class for reduced neuron models.
-
class
neuronunit.models.very_reduced.
VeryReducedModel
(name=None, backend=None, attrs=None)[source]¶ Bases:
neuronunit.models.static.ExternalModel
,neuronunit.capabilities.ReceivesCurrent
,neuronunit.capabilities.ProducesActionPotentials
Base class for reduced models, not using LEMS, and not requiring file paths this is to wrap pyNN models, Brian models, and other self contained models+model descriptions
-
get_APs
(**run_params)[source]¶ Get action potential waveform chunks from the model.
Must return a neo.core.AnalogSignal. Each column of the AnalogSignal should be a spike waveform.
-
Module contents¶
Model classes for NeuronUnit