base Package

base Package

class CurrentClamp(cell_location, **kwargs)[source]

Bases: morphforge.simulation.base.stimulation.Stimulation

class Recordables[source]

Bases: object

Current = 'Current'
CurrentClamp.get_summary_description()[source]
class VoltageClamp(cell_location, **kwargs)[source]

Bases: morphforge.simulation.base.stimulation.Stimulation

class Recordables[source]

Bases: object

Current = 'Current'
VoltageClamp.get_summary_description()[source]
class CurrentClampStepChange(amp, dur, delay, **kwargs)[source]

Bases: morphforge.simulation.base.stimulation.CurrentClamp

__init__(amp, dur, delay, **kwargs)[source]
get_summary_description()[source]
class VoltageClampStepChange(dur1, amp1, dur2='0:ms', dur3='0:ms', amp2='0:mV', amp3='0:mV', rs='0.01:MOhm', **kwargs)[source]

Bases: morphforge.simulation.base.stimulation.VoltageClamp

__init__(dur1, amp1, dur2='0:ms', dur3='0:ms', amp2='0:mV', amp3='0:mV', rs='0.01:MOhm', **kwargs)[source]
get_summary_description()[source]
class Simulation(name, environment, **kwargs)[source]

Bases: object

__init__(name, environment, **kwargs)[source]
add_cell(cell)[source]
add_cell_backend_specific(cell)[source]
add_currentclamp(cc)[source]
add_currentclamp_backend_specific(vc)[source]
add_gapjunction(gj)[source]
add_gapjunction_backend_specific(syn)[source]
add_recordable(recordable)[source]
add_recordable_backend_specific(recordable)[source]
add_synapse(syn)[source]
add_synapse_backend_specific(syn)[source]
add_voltageclamp(vc)[source]
add_voltageclamp_backend_specific(vc)[source]
are_all_cells_in_pops
cells
create_cell(**kwargs)[source]
create_currentclamp(**kwargs)[source]
create_gapjunction(**kwargs)[source]
create_synapse(trigger, postsynaptic_mech, **kwargs)[source]
create_voltageclamp(**kwargs)[source]
current_clamps
do_result_post_processing()[source]
gapjunctions
get_all_channels()[source]
get_cell(cellname=None)[source]

Either return a cell by name if there is more than one cell, otherwise the single cell

neuron_populations
objectnames
objects
postsynaptic_templates
record(recordable_src=None, **kwargs)[source]
recordables
recordall(membrane_mech, **kwargs)[source]
run(**kwargs)[source]
synapse_populations
synapses
voltage_clamps
class SimulationResult(traces, evsets, simulation)[source]

Bases: object

traces is a list of trace Objects

__init__(traces, evsets, simulation)[source]
add_evset(evset)[source]
get_evset(obj)[source]
get_trace(obj)[source]
get_trace_by_tagselection(ts)[source]
get_traces()[source]
hocfilename
classmethod load_from_file(filename)[source]
save_to_file(filename)[source]
set_simulation_time(t_start, t_stop)[source]
class Cell(morphology=None, area=None, segmenter=None, initial_voltage=None, cell_tags=None, cell_type=None, **kwargs)[source]

Bases: morphforge.simulation.base.base_classes.NamedSimulationObject

class Recordables[source]

Bases: object

MembraneVoltage = 'Voltage'
Cell.__init__(morphology=None, area=None, segmenter=None, initial_voltage=None, cell_tags=None, cell_type=None, **kwargs)[source]
Cell.apply_channel(*args, **kwargs)[source]
Cell.cell_type
Cell.cell_type_str
Cell.electrical_connections
Cell.get_biophysics()[source]
Cell.get_location(idtag, sectionpos=0.5)[source]
Cell.get_region(region_name)[source]
Cell.get_regions()[source]
Cell.get_segmenter()[source]
Cell.index_in_pop
Cell.is_single_compartment
Cell.postsynaptic_connections
Cell.presynaptic_connections
Cell.segmenter
Cell.set_passive(*args, **kwargs)[source]
Cell.soma
class CellLocation(cell, morphlocation=None, section=None, sectionpos=None)[source]

Bases: object

__init__(cell, morphlocation=None, section=None, sectionpos=None)[source]
cell
get_3d_position()[source]
get_cell()[source]
get_location_description_str()[source]
section
sectionpos
class SimulationEnvironment[source]

Bases: object

Cell(**kwargs)[source]
Channel(**kwargs)[source]
CurrentClamp(**kwargs)[source]
GapJunction(**kwargs)[source]
Simulation(**kwargs)[source]
SimulationSettings(**kwargs)[source]
Synapse(**kwargs)[source]
VoltageClamp(**kwargs)[source]
__init__()[source]
class AbstCellSegmenter(cell=None, **kwargs)[source]

Bases: object

__init__(cell=None, **kwargs)[source]
get_num_segment_region(region)[source]
get_num_segment_total(cell)[source]
get_num_segments(section)[source]
class CellSegmenter_MaxCompartmentLength(max_segment_length=5, **kwargs)[source]

Bases: morphforge.simulation.base.segmentation.cellsegmenter.CellSegmenterStd

__init__(max_segment_length=5, **kwargs)[source]
_get_n_segments(section)[source]
class CellBiophysics(cell)[source]

Bases: object

__init__(cell)[source]
add_channel(channel, targetter, applicator)[source]
add_passive(passiveproperty, targetter, value)[source]
apply_channel(channel, where=None, parameter_overrides=None, parameter_multipliers=None)[source]

A simplified interface to applying channels.

get_all_channels_applied_to_cell()[source]
get_applied_mtas()[source]
get_applied_passives()[source]
get_channel(name)[source]
get_passive_property_for_section(section, passive)[source]
get_passives_for_section(section)[source]
get_resolved_mtas_for_section(section)[source]
set_passive(passiveproperty, value, where=None)[source]
class Channel(**kwargs)[source]

Bases: morphforge.simulation.base.base_classes.NamedSimulationObject

__init__(**kwargs)[source]
get_default(key)[source]
get_defaults()[source]
get_variables()[source]
record_all(sim, cell_location)[source]
class ChannelApplicator[source]

Bases: object

__init__()[source]
get_description()[source]
get_variable_value_for_section(variablename, section)[source]
get_variables_overriden()[source]
set_target_channel(target_channel)[source]
class ChannelApplicatorUniform(parameter_multipliers=None, parameter_overrides=None)[source]

Bases: morphforge.simulation.base.biophysics.channelapplicators.ChannelApplicator

__init__(parameter_multipliers=None, parameter_overrides=None)[source]
get_description()[source]
get_variable_value_for_section(variable_name, section)[source]
get_variables_overriden()[source]
class Targeter(priority, **kwargs)[source]

Bases: object

__init__(priority, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
get_priority()[source]
class ChannelTargeterEverywhere(priority=10, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(priority=10, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class ChannelTargeterRegion(region, priority=20, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(region, priority=20, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class ChannelTargeterSection(section, priority=40, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(section, priority=40, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class ChannelTargeterSectionPath(priority, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

does_target_section(section)[source]
get_description()[source]
class PassiveTargetterEverywhere(priority=5, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(priority=5, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class PassiveTargetterEverywhereDefault(priority=0, **kwargs)[source]

Bases: morphforge.simulation.base.biophysics.channeltargetters.Targeter

__init__(priority=0, **kwargs)[source]
does_target_section(section)[source]
get_description()[source]
class PassiveProperty[source]

Bases: object

AxialResistance = 'AxialResistance'
SpecificCapacitance = 'SpecificCapacitance'
all = ['SpecificCapacitance', 'AxialResistance']
defaults = {'SpecificCapacitance': <Mock object at 0x7f0ab2145a50>, 'AxialResistance': <Mock object at 0x7f0ab21459d0>}
class Synapse(trigger, postsynaptic_mech)[source]

Bases: object

class Recordables[source]

Bases: object

SynapticConductance = 'SynapticConductance'
SynapticCurrent = 'SynapticCurrent'
Synapse.__init__(trigger, postsynaptic_mech)[source]
Synapse.get_postsynaptic_cell()[source]
Synapse.get_postsynaptic_mechanism()[source]
Synapse.get_presynaptic_cell()[source]
Synapse.get_trigger()[source]
class GapJunction(celllocation1, celllocation2, resistance, **kwargs)[source]

Bases: object

__init__(celllocation1, celllocation2, resistance, **kwargs)[source]
connected_cells
class PostSynapticMech(cell_location, **kwargs)[source]

Bases: object

__init__(cell_location, **kwargs)[source]
get_postsynaptic_cell()[source]
classmethod get_variables()[source]
synapse
class SynapticTrigger[source]

Bases: object

__init__()[source]
get_presynaptic_cell()[source]
get_type()[source]
synapse
class NamedSimulationObject(simulation=None, name=None, does_require_simulation=True, **kwargs)[source]

Bases: object

A base class for any object in a simulation that needs a name.

This class ensures that no two objects in a simulation have the same name.

  • _obj_names: A dictionary -> set mapping, recording what object names are in

    use at all simulations

__init__(simulation=None, name=None, does_require_simulation=True, **kwargs)[source]
_obj_names = {}
get_name()[source]
name
simulation
class PostSynapticMechTemplate(template_name=None, **kwargs)[source]

Bases: object

__init__(template_name=None, **kwargs)[source]
get_variables()[source]
instantiate(**kwargs)[source]
class PostSynapticMechInstantiation(cell_location, **kwargs)[source]

Bases: morphforge.simulation.base.networks.PostSynapticMech

base_classes Module

class NamedSimulationObject(simulation=None, name=None, does_require_simulation=True, **kwargs)[source]

Bases: object

A base class for any object in a simulation that needs a name.

This class ensures that no two objects in a simulation have the same name.

  • _obj_names: A dictionary -> set mapping, recording what object names are in

    use at all simulations

__init__(simulation=None, name=None, does_require_simulation=True, **kwargs)[source]
_obj_names = {}
get_name()[source]
name
simulation