Python API¶

Python reader for SONATA circuit files

class libsonata.CircuitConfig¶

Circuit Configuration

property config_status¶: ibid

edge_population(*args, **kwargs)¶

Overloaded function.

edge_population(arg0: str) → bbp::sonata::EdgePopulation
edge_population(arg0: str, arg1: libsonata.Hdf5Reader) → bbp::sonata::EdgePopulation

edge_population_properties(name: str) → libsonata.EdgePopulationProperties¶

static from_file(arg0: object) → libsonata.CircuitConfig¶

node_population(arg0: str) → libsonata.NodePopulation¶

node_population_properties(name: str) → libsonata.NodePopulationProperties¶

class libsonata.CircuitConfigStatus¶

Members:

invalid

complete

partial

property name¶

class libsonata.EdgePopulation¶

Collection of edges with attributes and connectivity index

afferent_edges(*args, **kwargs)¶

Overloaded function.

afferent_edges(target: List[int]) → libsonata.Selection

Return inbound edges for given node IDs.
afferent_edges(target: int) → libsonata.Selection

Return inbound edges for given node IDs.

property attribute_names¶: All attribute names (CSV columns + required attributes + union of attributes in groups)

connecting_edges(*args, **kwargs)¶

Overloaded function.

connecting_edges(source: List[int], target: List[int]) → libsonata.Selection

Return edges connecting two given nodes.
connecting_edges(source: int, target: int) → libsonata.Selection

Return edges connecting two given nodes.

property dynamics_attribute_names¶: All dynamics attribute names (JSON keys + union of attributes in groups)

efferent_edges(*args, **kwargs)¶

Overloaded function.

efferent_edges(source: List[int]) → libsonata.Selection

Return outbound edges for given node IDs.
efferent_edges(source: int) → libsonata.Selection

Return outbound edges for given node IDs.

property enumeration_names¶

All attribute names that are explicit enumerations

See also: https://github.com/AllenInstitute/sonata/blob/master/docs/SO NATA_DEVELOPER_GUIDE.md#nodes—enum-datatypes

enumeration_values(name: str) → List[str]¶

Get all allowed attribute enumeration values

Parameter name:: is a string to allow attributes not defined in spec
Raises:: if there is no such attribute for the population

get_attribute(*args, **kwargs)¶

Overloaded function.

get_attribute(name: str, edge_id: int) → object

Get attribute value for a given edge. See below for details.
get_attribute(name: str, selection: libsonata.Selection) → object

Get attribute values for given edge Selection

If string values are requested and the attribute is a explicit enumeration, values will be resolved to strings.

See also: https://github.com/AllenInstitute/sonata/blob/master/docs/SO NATA_DEVELOPER_GUIDE.md#nodes—enum-datatypes

Parameter name:
is a string to allow attributes not defined in spec

Parameter selection:
is a selection to retrieve the attribute values from

Raises:
if there is no such attribute for the population

Raises:
if the attribute is not defined for _any_ element from the selection
get_attribute(name: str, selection: libsonata.Selection, default_value: object) → object

Get attribute values for given edge Selection

If string values are requested and the attribute is a explicit enumeration, values will be resolved to strings.

See also: https://github.com/AllenInstitute/sonata/blob/master/docs/SO NATA_DEVELOPER_GUIDE.md#nodes—enum-datatypes

Parameter name:
is a string to allow attributes not defined in spec

Parameter selection:
is a selection to retrieve the attribute values from

Raises:
if there is no such attribute for the population

Raises:
if the attribute is not defined for _any_ element from the selection

get_dynamics_attribute(*args, **kwargs)¶

Overloaded function.

get_dynamics_attribute(name: str, edge_id: int) → object

Get dynamics attribute value for a given edge. See below for details.
get_dynamics_attribute(name: str, selection: libsonata.Selection) → object

Get dynamics attribute values for given edge Selection

Parameter name:
is a string to allow attributes not defined in spec

Parameter selection:
is a selection to retrieve the dynamics attribute values from

Raises:
if there is no such attribute for the population

Raises:
if the attribute is not defined for _any_ edge from the edge selection
get_dynamics_attribute(name: str, selection: libsonata.Selection, default_value: object) → object

Get dynamics attribute values for given edge Selection

Parameter name:
is a string to allow attributes not defined in spec

Parameter selection:
is a selection to retrieve the dynamics attribute values from

Raises:
if there is no such attribute for the population

Raises:
if the attribute is not defined for _any_ edge from the edge selection

get_enumeration(*args, **kwargs)¶

Overloaded function.

get_enumeration(name: str, edge_id: int) → object

Get enumeration values for a given edge. See below for details.
get_enumeration(name: str, selection: libsonata.Selection) → object

Get all allowed attribute enumeration values

Parameter name:
is a string to allow attributes not defined in spec

Raises:
if there is no such attribute for the population

property name¶: Name of the population used for identifying it in circuit composition

select_all() → libsonata.Selection¶: Selection covering all elements

property size¶: Total number of elements

property source¶: Name of source population extracted from ‘source_node_id’ dataset

source_node(edge_id: int) → int¶: Source node ID for a given edge

source_nodes(selection: libsonata.Selection) → numpy.ndarray¶: Return source node IDs for a given edge selection

property target¶: Name of target population extracted from ‘target_node_id’ dataset

target_node(edge_id: int) → int¶: Target node ID for given edge

target_nodes(selection: libsonata.Selection) → numpy.ndarray¶: Return target node IDs for a given edge selection

static write_indices(h5_filepath: str, population: str, source_node_count: int, target_node_count: int, overwrite: bool = False) → None¶: Write bidirectional node->edge indices to EdgePopulation HDF5.

class libsonata.EdgeStorage¶

Collection of EdgePopulations stored in a H5 file and optional CSV.

open_population(name: str) → libsonata.EdgePopulation¶

Open a specific EdgePopulation by name

Parameter name:: the name of the population to open
Raises:: if no population with such a name exists

property population_names¶: Set of all EdgePopulation names

class libsonata.ElementDataFrame¶: A container of raw reporting data, compatible with Pandas

class libsonata.ElementReportPopulation¶

A population inside a ReportReader

property data_units¶: Return the unit of data.

get(node_ids: libsonata.Selection | None = None, tstart: float | None = None, tstop: float | None = None, tstride: int | None = None, block_gap_limit: int | None = None) → libsonata.ElementDataFrame¶: Return reports with all those node_ids between ‘tstart’ and ‘tstop’ with a stride tstride

get_node_id_element_id_mapping(selection: libsonata.Selection | None = None, block_gap_limit: int | None = None) → numpy.ndarray¶

Return the ElementIds for the passed Node. The return type will depend on the report reader: - For Soma report reader, the return value will be the Node ID to which the report value belongs to. - For Element/full compartment readers, the return value will be an array with 2 elements, the first element is the Node ID and the second element is the compartment ID of the given Node.

Parameter node_ids:: limit the report to the given selection. If nullptr, all nodes in the report are used
Parameter block_gap_limit:: gap limit between each IO block while fetching data from storage

get_node_ids() → List[int]¶: Return the list of nodes ids for this population

property sorted¶: Return true if the data is sorted.

property time_units¶: Return the unit of time

property times¶: Return (tstart, tstop, tstep) of the population

class libsonata.ElementReportReader¶

Used to read somas files

get_population_names() → List[str]¶: Get list of all populations

class libsonata.NodePopulation¶

Collection of nodes with attributes

property attribute_names¶: All attribute names (CSV columns + required attributes + union of attributes in groups)

property dynamics_attribute_names¶: All dynamics attribute names (JSON keys + union of attributes in groups)

property enumeration_names¶

All attribute names that are explicit enumerations

See also: https://github.com/AllenInstitute/sonata/blob/master/docs/SO NATA_DEVELOPER_GUIDE.md#nodes—enum-datatypes

enumeration_values(name: str) → List[str]¶

Get all allowed attribute enumeration values

Parameter name:: is a string to allow attributes not defined in spec
Raises:: if there is no such attribute for the population

get_attribute(*args, **kwargs)¶

Overloaded function.

get_attribute(name: str, node_id: int) → object

Get attribute value for a given node. See below for details.
get_attribute(name: str, selection: libsonata.Selection) → object

Get attribute values for given node Selection

If string values are requested and the attribute is a explicit enumeration, values will be resolved to strings.

See also: https://github.com/AllenInstitute/sonata/blob/master/docs/SO NATA_DEVELOPER_GUIDE.md#nodes—enum-datatypes

Parameter name:
is a string to allow attributes not defined in spec

Parameter selection:
is a selection to retrieve the attribute values from

Raises:
if there is no such attribute for the population

Raises:
if the attribute is not defined for _any_ element from the selection
get_attribute(name: str, selection: libsonata.Selection, default_value: object) → object

Get attribute values for given node Selection

If string values are requested and the attribute is a explicit enumeration, values will be resolved to strings.

See also: https://github.com/AllenInstitute/sonata/blob/master/docs/SO NATA_DEVELOPER_GUIDE.md#nodes—enum-datatypes

Parameter name:
is a string to allow attributes not defined in spec

Parameter selection:
is a selection to retrieve the attribute values from

Raises:
if there is no such attribute for the population

Raises:
if the attribute is not defined for _any_ element from the selection

get_dynamics_attribute(*args, **kwargs)¶

Overloaded function.

get_dynamics_attribute(name: str, node_id: int) → object

Get dynamics attribute value for a given node. See below for details.
get_dynamics_attribute(name: str, selection: libsonata.Selection) → object

Get dynamics attribute values for given node Selection

Parameter name:
is a string to allow attributes not defined in spec

Parameter selection:
is a selection to retrieve the dynamics attribute values from

Raises:
if there is no such attribute for the population

Raises:
if the attribute is not defined for _any_ edge from the edge selection
get_dynamics_attribute(name: str, selection: libsonata.Selection, default_value: object) → object

Get dynamics attribute values for given node Selection

Parameter name:
is a string to allow attributes not defined in spec

Parameter selection:
is a selection to retrieve the dynamics attribute values from

Raises:
if there is no such attribute for the population

Raises:
if the attribute is not defined for _any_ edge from the edge selection

get_enumeration(*args, **kwargs)¶

Overloaded function.

get_enumeration(name: str, node_id: int) → object

Get enumeration values for a given node. See below for details.
get_enumeration(name: str, selection: libsonata.Selection) → object

Get all allowed attribute enumeration values

Parameter name:
is a string to allow attributes not defined in spec

Raises:
if there is no such attribute for the population

match_values(*args, **kwargs)¶

Overloaded function.

match_values(name: str, value: List[int]) → libsonata.Selection

Return selection of where attribute values match value

As per node_set predicates, value must be one of type:
- number H5T_IEEE_*LE, H5T_STD_*LE
- string H5T_C_S1
- bool H5T_STD_I8LE
- null invalid
Raises:
if the attribute dtype is not comparable

Note: This does not match dynamics_params datasets
match_values(name: str, value: List[str]) → libsonata.Selection

Return selection of where attribute values match value

As per node_set predicates, value must be one of type:
- number H5T_IEEE_*LE, H5T_STD_*LE
- string H5T_C_S1
- bool H5T_STD_I8LE
- null invalid
Raises:
if the attribute dtype is not comparable

Note: This does not match dynamics_params datasets
match_values(name: str, value: int) → libsonata.Selection

Return selection of where attribute values match value

As per node_set predicates, value must be one of type:
- number H5T_IEEE_*LE, H5T_STD_*LE
- string H5T_C_S1
- bool H5T_STD_I8LE
- null invalid
Raises:
if the attribute dtype is not comparable

Note: This does not match dynamics_params datasets
match_values(name: str, value: str) → libsonata.Selection

Return selection of where attribute values match value

As per node_set predicates, value must be one of type:
- number H5T_IEEE_*LE, H5T_STD_*LE
- string H5T_C_S1
- bool H5T_STD_I8LE
- null invalid
Raises:
if the attribute dtype is not comparable

Note: This does not match dynamics_params datasets

property name¶: Name of the population used for identifying it in circuit composition

select_all() → libsonata.Selection¶: Selection covering all elements

property size¶: Total number of elements

class libsonata.NodeSets¶

static from_file(arg0: object) → libsonata.NodeSets¶

materialize(arg0: str, arg1: libsonata.NodePopulation) → libsonata.Selection¶

Return a selection corresponding to the node_set name

Parameter name:: is the name of the node_set rule to be evaluated
Parameter population:: is the population for which the returned selection will be valid

property names¶: Names of the node sets available

toJSON() → str¶: Return the nodesets as a JSON string.

update(other: libsonata.NodeSets) → Set[str]¶

Update this to include all nodesets from this and other.

Duplicate names are overridden with the values from other.

The duplicate names are returned.

class libsonata.NodeStorage¶

Collection of NodePopulations stored in a H5 file and optional CSV.

open_population(name: str) → libsonata.NodePopulation¶

Open a specific NodePopulation by name

Parameter name:: the name of the population to open
Raises:: if no population with such a name exists

property population_names¶: Set of all NodePopulation names

class libsonata.Selection¶

ID sequence in the form convenient for querying attributes

property flat_size¶: Total number of elements constituting Selection

flatten() → numpy.ndarray¶: Array of IDs constituting Selection

property ranges¶: Get a list of ranges constituting Selection

class libsonata.SimulationConfig¶

Simulation Configuration

class Conditions¶

Parameters defining global experimental conditions

class SpikeLocation¶

Members:

soma

AIS

property name¶

property celsius¶: Temperature of experiment. Default is 34.0

property extracellular_calcium¶: Extracellular calcium concentration, being applied to the synapse uHill parameter in order to scale the U parameter of synapses. Default is None.

property list_modification_names¶: Returns the names of the modifications

property mechanisms¶: Properties to assign values to variables in synapse MOD files. The format is a dictionary with keys being the SUFFIX names and values being dictionaries of variables’ names and values.

modification(name: str) → Union[bbp::sonata::SimulationConfig::ModificationTTX, bbp::sonata::SimulationConfig::ModificationConfigureAllSections, nonstd::variants::detail::TX<nonstd::variants::detail::S2>, nonstd::variants::detail::TX<nonstd::variants::detail::S3>, nonstd::variants::detail::TX<nonstd::variants::detail::S4>, nonstd::variants::detail::TX<nonstd::variants::detail::S5>, nonstd::variants::detail::TX<nonstd::variants::detail::S6>, nonstd::variants::detail::TX<nonstd::variants::detail::S7>, nonstd::variants::detail::TX<nonstd::variants::detail::S8>, nonstd::variants::detail::TX<nonstd::variants::detail::S9>, nonstd::variants::detail::TX<nonstd::variants::detail::S10>, nonstd::variants::detail::TX<nonstd::variants::detail::S11>, nonstd::variants::detail::TX<nonstd::variants::detail::S12>, nonstd::variants::detail::TX<nonstd::variants::detail::S13>, nonstd::variants::detail::TX<nonstd::variants::detail::S14>, nonstd::variants::detail::TX<nonstd::variants::detail::S15>]¶

Returns the given modification parameters

Raises:: SonataError if the given modification name does not exist

property randomize_gaba_rise_time¶: Enable legacy behavior to randomize the GABA_A rise time in the helper functions. Default is false

property spike_location¶: The spike detection location. Can be either ‘soma’ or ‘AIS’. Default is ‘soma’

property v_init¶: Initial membrane voltage in mV. Default is -80

class ConnectionOverride¶

List of parameters of a connection

property delay¶: Adjustments from weight of this connection_override are applied after the specified delay has elapsed in ms, default = 0.

property modoverride¶: Synapse helper files to instantiate the synapses in this connection_override, default = None

property name¶: the name of the connection override

property neuromodulation_dtc¶: To override the neuromod_dtc values between the selected source and target neurons for the neuromodulatory projection. Given in ms.

property neuromodulation_strength¶: To override the neuromod_strength values between the selected source and target neurons for the neuromodulatory projection. Given in muM.

property source¶: node_set specifying presynaptic nodes

property spont_minis¶: Rate to spontaneously trigger the synapses in this connection_override, default = None

property synapse_configure¶: Snippet of hoc code to be executed on the synapses in this connection_override, default = None

property synapse_delay_override¶: Value to override the synaptic delay time originally set in the edge file (ms), default = None.

property target¶: node_set specifying postsynaptic nodes

property weight¶: Scalar to adjust synaptic strength, default = 1.

class Output¶

Parameters of simulation output

class SpikesSortOrder¶

Members:

none

by_id

by_time

property name¶

property log_file¶: Filename where console output is written. Default is STDOUT.

property output_dir¶: Spike report file output directory. Default is “output”

property spikes_file¶: Spike report file name. Default is “out.h5”

property spikes_sort_order¶: The sorting order of the spike report. Default is “by_time”

class Report¶

Parameters of a report

class Compartments¶

Members:

center

all

property name¶

class Scaling¶

Members:

none

area

property name¶

class Sections¶

Members:

soma :

axon :

dend :

apic :

all :

property name¶

class Type¶

Members:

compartment

lfp

summation

synapse

property name¶

property cells¶: Node sets on which to report

property compartments¶: For compartment type, select compartments to report. Default value: “center”(for sections: soma), “all”(for other sections)

property dt¶: Interval between reporting steps in milliseconds

property enabled¶: Allows for suppressing a report so that is not created. Default is true

property end_time¶: Time to stop reporting in milliseconds

property file_name¶: Report filename. Default is “<report name>.h5”

property scaling¶: For summation type, specify the handling of density values. Default value: “area”

property sections¶

“soma”

Type:: Sections on which to report. Default value

property start_time¶: Time to step reporting in milliseconds

property type¶: Report type.

property unit¶: Descriptive text of the unit recorded. Not validated for correctness

property variable_name¶: The simulation variable to access. The variables available are model dependent. For summation type, it supports multiple variables by comma separated strings. E.g. “ina”, “AdEx.V_M, v”, “i_membrane, IClamp”.

class Run¶

Stores parameters defining global simulation settings

class IntegrationMethod¶

Members:

euler

nicholson

nicholson_ion

property name¶

property dt¶: Integration step duration in milliseconds

property electrodes_file¶: Filename that contains the weights for the LFP calculation.

property integration_method¶: Selects the NEURON/CoreNEURON integration method. This parameter sets the NEURON global variable h.secondorder. Default 0 (‘euler’)

property ionchannel_seed¶: A non-negative integer used for seeding stochastic ion channels, default is 0.

property minis_seed¶: A non-negative integer used for seeding the Poisson processes that drives the minis, default is 0.

property random_seed¶: Random seed

property spike_threshold¶: The spike detection threshold. Default is -30mV

property stimulus_seed¶: A non-negative integer used for seeding noise stimuli and any other future stochastic stimuli, default is 0.

property synapse_seed¶: A non-negative integer used for seeding stochastic synapses, default is 0.

property tstop¶: Biological simulation end time in milliseconds

class SimulatorType¶

SimulatorType Enum

Members:

NEURON

CORENEURON

property name¶

property base_path¶: Returns the base path of the simulation config file

property beta_features¶: Returns the beta_features section

property conditions¶: Returns the Conditions section of the simulation configuration.

connection_overrides() → List[libsonata.SimulationConfig.ConnectionOverride]¶: Returns the full list of connection overrides

property expanded_json¶: Returns the configuration file JSON whose variables have been expanded by the manifest entries.

static from_file(arg0: object) → libsonata.SimulationConfig¶

Loads a SONATA JSON simulation config file from disk and returns a SimulationConfig object which parses it.

Raises:: SonataError on: - Non accesible file (does not exists / does not have read access) - Ill-formed JSON - Missing mandatory entries (in any depth)

input(name: str) → Union[libsonata.SimulationConfig.Linear, libsonata.SimulationConfig.RelativeLinear, libsonata.SimulationConfig.Pulse, libsonata.SimulationConfig.Subthreshold, libsonata.SimulationConfig.Hyperpolarizing, libsonata.SimulationConfig.SynapseReplay, libsonata.SimulationConfig.Seclamp, libsonata.SimulationConfig.Noise, libsonata.SimulationConfig.ShotNoise, libsonata.SimulationConfig.RelativeShotNoise, libsonata.SimulationConfig.AbsoluteShotNoise, libsonata.SimulationConfig.OrnsteinUhlenbeck, libsonata.SimulationConfig.RelativeOrnsteinUhlenbeck, nonstd::variants::detail::TX<nonstd::variants::detail::S13>, nonstd::variants::detail::TX<nonstd::variants::detail::S14>, nonstd::variants::detail::TX<nonstd::variants::detail::S15>]¶

Returns the given input parameters.

Raises:: SonataError if the given input name does not exist

property list_input_names¶: Returns the names of the inputs

property list_report_names¶: Returns the names of the reports

property metadata¶: Returns the metadata section

property network¶: Returns circuit config file associated with this simulation config

property node_set¶: Returns the name of node set to be instantiated for the simulation, default = None

property node_sets_file¶: Returns the path of node sets file overriding node_sets_file provided in _network, default is empty in case of no setting in _network

property output¶: Returns the Output section of the simulation configuration.

report(name: str) → libsonata.SimulationConfig.Report¶

Returns the given report parameters.

Raises:: SonataError if the given report name does not correspond with any existing report.

property run¶: Returns the Run section of the simulation configuration.

property target_simulator¶

Returns the name of simulator, default = NEURON

Raises:: SonataError if the given value is neither NEURON nor CORENEURON

class libsonata.SomaDataFrame¶: A container of raw reporting data, compatible with Pandas

class libsonata.SomaReportPopulation¶

A population inside a ReportReader

property data_units¶: Return the unit of data.

get(node_ids: libsonata.Selection | None = None, tstart: float | None = None, tstop: float | None = None, tstride: int | None = None, block_gap_limit: int | None = None) → libsonata.SomaDataFrame¶: Return reports with all those node_ids between ‘tstart’ and ‘tstop’ with a stride tstride

get_node_id_element_id_mapping(selection: libsonata.Selection | None = None, block_gap_limit: int | None = None) → numpy.ndarray¶

Return the ElementIds for the passed Node. The return type will depend on the report reader: - For Soma report reader, the return value will be the Node ID to which the report value belongs to. - For Element/full compartment readers, the return value will be an array with 2 elements, the first element is the Node ID and the second element is the compartment ID of the given Node.

Parameter node_ids:: limit the report to the given selection. If nullptr, all nodes in the report are used
Parameter block_gap_limit:: gap limit between each IO block while fetching data from storage

get_node_ids() → List[int]¶: Return the list of nodes ids for this population

property sorted¶: Return true if the data is sorted.

property time_units¶: Return the unit of time

property times¶: Return (tstart, tstop, tstep) of the population

class libsonata.SomaReportReader¶

Used to read somas files

get_population_names() → List[str]¶: Get list of all populations

exception libsonata.SonataError¶

class libsonata.SpikePopulation¶

A population inside a SpikeReader

get(node_ids: libsonata.Selection | None = None, tstart: float | None = None, tstop: float | None = None) → List[Tuple[int, float]]¶: Return spikes with all those node_ids between ‘tstart’ and ‘tstop’

get_dict(node_ids: object = None, tstart: object = None, tstop: object = None) → dict¶

property sorting¶: Return the way data are sorted (‘none’, ‘by_id’, ‘by_time’)

property times¶: Return (tstart, tstop) of the population

class libsonata.SpikeReader¶

Used to read spike files

get_population_names() → List[str]¶: Return a list of all population names.