libsonata

https://libsonata.readthedocs.io/en/latest/
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### Install libsonata from GitHub

Source: https://libsonata.readthedocs.io/en/latest/index.html

Install libsonata directly from its GitHub repository, useful for development or to get the latest unreleased features.

```bash
pip install git+https://github.com/openbraininstitute/libsonata

```

--------------------------------

### Install libsonata from PyPI

Source: https://libsonata.readthedocs.io/en/latest/index.html

Use this command to install the latest stable version of libsonata from the Python Package Index.

```bash
pip install libsonata

```

--------------------------------

### Get Node Sets Path

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Returns the path to the node sets file.

```cpp
const std::string & | getNodeSetsPath () const
```

--------------------------------

### Get Compartment Sets Path

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Returns the path to the compartment sets file.

```cpp
const std::string & | getCompartmentSetsPath () const
```

--------------------------------

### get()

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_report_reader_1_1_population.html

Retrieves data for a population, with options to filter by node IDs, time range, time stride, and block gap limit.

```APIDOC
## get()

### Description
Retrieves data for a population, with options to filter by node IDs, time range, time stride, and block gap limit.

### Method
GET (or equivalent for SDK)

### Endpoint
`/population/get` (Illustrative - actual SDK method call)

### Parameters
#### Path Parameters
None

#### Query Parameters
- **node_ids** (Selection) - Optional - Limits the report to the given selection.
- **tstart** (double) - Optional - Returns voltages occurring on or after tstart. `nonstd::nullopt` indicates no limit.
- **tstop** (double) - Optional - Returns voltages occurring on or before tstop. `nonstd::nullopt` indicates no limit.
- **tstride** (size_t) - Optional - Indicates every how many timesteps data is read. `nonstd::nullopt` indicates that all timesteps are read.
- **block_gap_limit** (size_t) - Optional - Gap limit between each IO block while fetching data from storage.

### Request Example
```json
{
  "node_ids": null, 
  "tstart": null,
  "tstop": null,
  "tstride": null,
  "block_gap_limit": null
}
```

### Response
#### Success Response (200)
- **DataFrame<KeyType>** - The retrieved data.

#### Response Example
```json
{
  "example": "DataFrame content"
}
```
```

--------------------------------

### get()

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_ReportReader%3A%3APopulation.html

Retrieves data from the population, with options to filter by node IDs, time range, and time stride. It also accepts a block gap limit for efficient data fetching.

```APIDOC
## get()

### Description
Retrieves data from the population, with options to filter by node IDs, time range, and time stride. It also accepts a block gap limit for efficient data fetching.

### Method
`get`

### Parameters
#### Path Parameters
None

#### Query Parameters
- **_node_ids_** (nonstd::optional<Selection>) - Optional - Limits the report to the given selection.
- **_tstart_** (nonstd::optional<double>) - Optional - Returns voltages occurring on or after tstart. `nonstd::nullopt` indicates no limit.
- **_tstop_** (nonstd::optional<double>) - Optional - Returns voltages occurring on or before tstop. `nonstd::nullopt` indicates no limit.
- **_tstride_** (nonstd::optional<size_t>) - Optional - Indicates every how many timesteps data is read. `nonstd::nullopt` indicates that all timesteps are read.
- **_block_gap_limit_** (nonstd::optional<size_t>) - Optional - Gap limit between each IO block while fetching data from storage.

### Request Example
```json
{
  "_node_ids_": null,
  "_tstart_": null,
  "_tstop_": null,
  "_tstride_": null,
  "_block_gap_limit_": null
}
```

### Response
#### Success Response (200)
- **DataFrame<KeyType>** - The retrieved data.

#### Response Example
```json
{
  "example": "DataFrame content"
}
```
```

--------------------------------

### EdgeStorage Initialization and Population Listing

Source: https://libsonata.readthedocs.io/en/latest/index.html

Demonstrates how to initialize EdgeStorage and list available population names.

```APIDOC
## EdgeStorage

### Description
Handles population of edges.

### Initialization
```python
import libsonata
edges = libsonata.EdgeStorage('path/to/H5/file')
```

### Methods
#### population_names
Get the names of all populations.
```python
# list populations
print(edges.population_names)
```
```

--------------------------------

### get_population_names (SomaReportReader)

Source: https://libsonata.readthedocs.io/en/latest/api.html

Get a list of all population names from a SomaReportReader.

```APIDOC
## get_population_names (SomaReportReader)

### Description
Get list of all populations.

### Returns
* list[str] - A list of population names.
```

--------------------------------

### Build libsonata C++ Library

Source: https://libsonata.readthedocs.io/en/latest/index.html

Instructions for cloning the repository, configuring the build with CMake, and compiling the C++ library. Ensure you use the same C++ standard as your project.

```bash
git clone git@github.com:openbraininstitute/libsonata.git --recursive
cd libsonata
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release -DEXTLIB_FROM_SUBMODULES=ON ..
make -j

```

--------------------------------

### get (by type)

Source: https://libsonata.readthedocs.io/en/latest/cpp/classnonstd_1_1variants_1_1variant.html

Retrieves the value of the specified type T from the variant.

```APIDOC
## get (by type)

### Description
Retrieves the value of the specified type T from the variant.

### Method
`get<T>()`

### Parameters
- **T** - The type of the value to retrieve.

### Return Value
- `T &` - A reference to the value if the variant holds type T.
- `T const &` - A const reference to the value if the variant holds type T (const version).
```

--------------------------------

### CircuitConfig::getCompartmentSetsPath

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_circuit_config.html

Gets the path to the compartment sets file.

```APIDOC
## CircuitConfig::getCompartmentSetsPath

### Description
Gets the path to the compartment sets file.

### Signature
const std::string & getCompartmentSetsPath() const
```

--------------------------------

### Load and Query Node Sets in Python

Source: https://libsonata.readthedocs.io/en/latest/index.html

Demonstrates loading node sets from a JSON file or string and materializing them into selections for a given population.

```python
# load a node set JSON file
>>> node_sets = libsonata.NodeSets.from_file('node_sets.json')

# list node sets
>>> node_sets.names
{'L6_UPC', 'Layer1', 'Layer2', 'Layer3', ....}

# get the selection of nodes that match in population
>>> selection = node_sets.materialize('Layer1', population)

# node sets can also be loaded from a JSON string
>>> node_sets_manual = libsonata.NodeSets(json.dumps({"SLM_PPA_and_SP_PC": {"mtype": ["SLM_PPA", "SP_PC"]}}))
>>> node_sets_manual.names
{'SLM_PPA_and_SP_PC'}

```

--------------------------------

### Create CircuitConfig from File

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Creates a CircuitConfig object by reading from a specified file path.

```cpp
static CircuitConfig | fromFile (const std::string &path)
```

--------------------------------

### CircuitConfig::getNodeSetsPath

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_circuit_config.html

Gets the path to the node sets file.

```APIDOC
## CircuitConfig::getNodeSetsPath

### Description
Gets the path to the node sets file.

### Signature
const std::string & getNodeSetsPath() const
```

--------------------------------

### ElementReportReader.get_population_names

Source: https://libsonata.readthedocs.io/en/latest/api.html

Gets a list of all population names available in the report reader.

```APIDOC
## ElementReportReader.get_population_names

### Description
Get list of all populations.

### Method
`get_population_names() → list[str]`

### Returns
- list[str] - A list of population names.
```

--------------------------------

### SimulationConfig._from_file

Source: https://libsonata.readthedocs.io/en/latest/api.html

Loads a SONATA JSON simulation configuration file from disk and returns a SimulationConfig object.

```APIDOC
## _from_file(_arg0 : object_) -> libsonata.SimulationConfig

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

### Parameters
#### Path Parameters
- **_arg0** (object) - Description of the file path or object to load from.

### Response
#### Success Response (SimulationConfig)
- Returns a SimulationConfig object.

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

--------------------------------

### CircuitConfig::fromFile

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Creates a CircuitConfig object from a file path.

```APIDOC
## CircuitConfig::fromFile

### Description
Creates a CircuitConfig object from a file path.

### Signature
static CircuitConfig fromFile(const std::string &path)
```

--------------------------------

### _dynamicsAttributeDataType()

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_EdgePopulation.html

Internal function to get the data type of a dynamics attribute.

```APIDOC
## _dynamicsAttributeDataType(const std::string &name) const

### Description
Internal function to get the data type of a dynamics attribute.

### Method
`std::string _dynamicsAttributeDataType(const std::string &name) const`

### Parameters
* **name** (const std::string &) - The name of the dynamics attribute.
```

--------------------------------

### SimulationConfig::fromFile

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_simulation_config.html

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

```APIDOC
## static SimulationConfig bbp::sonata::SimulationConfig::fromFile(const std::string &path)

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

### Parameters
#### Path Parameters
- **path** (const std::string &) - The path to the SONATA JSON simulation configuration file.

### Exceptions
- **SonataError**: Thrown if the file is not accessible (does not exist or no read access), if the JSON is ill-formed, or if mandatory entries are missing.
```

--------------------------------

### Get Edge Population

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Retrieves a specific edge population by its name.

```cpp
EdgePopulation | **getEdgePopulation** (const std::string &name) const
```

--------------------------------

### Get Node Population

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Retrieves a specific node population by its name.

```cpp
NodePopulation | **getNodePopulation** (const std::string &name) const
```

--------------------------------

### Include Configuration Header

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Include the necessary header file for circuit configuration functionalities.

```cpp
#include <config.h>
```

--------------------------------

### Work with Selection Ranges in Python

Source: https://libsonata.readthedocs.io/en/latest/index.html

Illustrates how to create and interpret libsonata.Selection objects, which represent ranges of element IDs for efficient data access.

```python
>>> selection = libsonata.Selection([1, 2, 3, 5])
>>> selection.ranges
[(1, 4), (5, 6)]

```

```python
>>> selection = libsonata.Selection([(1, 4), (5, 6)])
>>> selection.flatten()
[1, 2, 3, 5]
>>> selection.flat_size
4
>>> bool(selection)
True

```

--------------------------------

### _dynamicsAttributeDataType

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_node_population.html

Internal method to get the data type of a dynamics attribute.

```APIDOC
## _dynamicsAttributeDataType

### Description
Internal method to get the data type of a dynamics attribute.

### Method
`_dynamicsAttributeDataType`

### Endpoint
N/A (Method Call)

### Parameters
#### Path Parameters
- **name** (const std::string &) - The name of the dynamics attribute.

### Response
- **std::string** - The data type of the dynamics attribute.
```

--------------------------------

### get (by index)

Source: https://libsonata.readthedocs.io/en/latest/cpp/classnonstd_1_1variants_1_1variant.html

Retrieves the value at the specified index K from the variant.

```APIDOC
## get (by index)

### Description
Retrieves the value at the specified index K from the variant.

### Method
`get<std::size_t K>()`

### Parameters
- **K** - The zero-based index of the type to retrieve.

### Return Value
- `variant_alternative< K, variant >::type &` - A reference to the value at index K.
- `variant_alternative< K, variant >::type const &` - A const reference to the value at index K (const version).
```

--------------------------------

### CircuitConfig::fromFile

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_circuit_config.html

Creates a CircuitConfig object by reading from the specified file path.

```APIDOC
## CircuitConfig::fromFile

### Description
Creates a CircuitConfig object by reading from the specified file path.

### Signature
static CircuitConfig fromFile(const std::string &path)
```

--------------------------------

### NodePopulation.enumeration_values

Source: https://libsonata.readthedocs.io/en/latest/api.html

Gets all allowed attribute enumeration values for a given attribute name.

```APIDOC
## NodePopulation.enumeration_values

### Description
Get all allowed attribute enumeration values.

### Method
`enumeration_values(_name : str_) → list[str]`

### Parameters
- **name** (str) - Required - The name of the attribute to get enumeration values for.

### Returns
- list[str] - A list of allowed enumeration values.

### Raises
- If there is no such attribute for the population.
```

--------------------------------

### Initialize and List Edge Populations

Source: https://libsonata.readthedocs.io/en/latest/index.html

Instantiate EdgeStorage to access edge data and list available population names.

```python
>>> edges = libsonata.EdgeStorage('path/to/H5/file')

# list populations
>>> edges.population_names
```

--------------------------------

### getNetwork

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_SimulationConfig.html

Retrieves the circuit configuration file associated with the simulation.

```APIDOC
## getNetwork()

### Description
Returns the circuit config file associated with this simulation config.

### Method
const std::string& bbp::sonata::SimulationConfig::getNetwork() const noexcept

### Returns
- const std::string&: A const reference to the network configuration file path.
```

--------------------------------

### Population::_dynamicsAttributeDataType

Source: https://libsonata.readthedocs.io/en/latest/cpp/population_8h_source.html

Internal method to get the data type of a dynamics attribute.

```APIDOC
## Population::_dynamicsAttributeDataType

### Description
Internal method to get the data type of a dynamics attribute.

### Signature
```cpp
std::string _dynamicsAttributeDataType(const std::string& name) const;
```
```

--------------------------------

### Get Expanded JSON

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Returns the expanded JSON representation of the circuit configuration.

```cpp
const std::string & | getExpandedJSON () const
```

--------------------------------

### Load and Inspect NodeStorage in Python

Source: https://libsonata.readthedocs.io/en/latest/index.html

Demonstrates how to open a SONATA HDF5 file and access its population names using libsonata's NodeStorage.

```python
>>> import libsonata

>>> nodes = libsonata.NodeStorage('path/to/H5/file')

# list populations
>>> nodes.population_names

# open population
>>> population = nodes.open_population(<name>)

```

--------------------------------

### NodeSets::fromFile

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_NodeSets.html

Opens and reads a SONATA 'node sets' file from the specified file path. This static method is the primary way to load node set configurations from disk.

```APIDOC
## static NodeSets fromFile(const std::string &path)

### Description
Open a SONATA `node sets` file from a path.

### Parameters
* **path** (string) - The file path to the SONATA node sets file.
```

--------------------------------

### CircuitConfig Constructors and Factory Method

Source: https://libsonata.readthedocs.io/en/latest/cpp/config_8h_source.html

Constructs a CircuitConfig object from string contents or loads it from a file.

```APIDOC
## CircuitConfig(const std::string& contents, const std::string& basePath)

### Description
Constructs a CircuitConfig object by parsing the provided JSON string contents and resolving paths relative to basePath.

### Parameters
#### Path Parameters
- **contents** (std::string) - Required - The JSON string representing the circuit configuration.
- **basePath** (std::string) - Required - The base path to resolve relative file paths within the configuration.

## CircuitConfig::fromFile(const std::string& path)

### Description
Loads and parses a CircuitConfig object from a JSON file located at the specified path.

### Method
static

### Parameters
#### Path Parameters
- **path** (std::string) - Required - The file path to the circuit configuration JSON.

### Returns
- CircuitConfig - The loaded circuit configuration object.
```

--------------------------------

### output

Source: https://libsonata.readthedocs.io/en/latest/api.html

Returns the Output section of the simulation configuration.

```APIDOC
## output

### Description
Returns the Output section of the simulation configuration.

### Property
_output
```

--------------------------------

### Get Circuit Configuration Status

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Retrieves the current status of the circuit configuration.

```cpp
ConfigStatus | getCircuitConfigStatus () const
```

--------------------------------

### SimulationConfig Constructors

Source: https://libsonata.readthedocs.io/en/latest/cpp/config_8h_source.html

Constructs a SimulationConfig object from a given content string and base path, or loads it from a file.

```APIDOC
## SimulationConfig(const std::string& content, const std::string& basePath)

### Description
Constructs a SimulationConfig object by parsing the provided content string and setting the base path for relative file paths.

### Parameters
* **content** (std::string) - The configuration content in string format.
* **basePath** (std::string) - The base directory path for resolving relative file paths.

## SimulationConfig::fromFile(const std::string& path)

### Description
Loads and constructs a SimulationConfig object from a configuration file located at the specified path.

### Method
static

### Parameters
* **path** (std::string) - The file path to the simulation configuration file.
```

--------------------------------

### Get Enumeration Values

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_population.html

Retrieves all allowed values for a specified enumeration attribute.

```APIDOC
## enumerationValues()

std::vector<std::string> bbp::sonata::Population::enumerationValues(const std::string& _name_) const

### Description
Get all allowed attribute enumeration values.

### Parameters
* **name** (string): is a string to allow attributes not defined in spec.

### Exceptions
if there is no such attribute for the population.
```

--------------------------------

### Get All Enumeration Names

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_population.html

Returns a set of all attribute names that are explicit enumerations.

```APIDOC
## enumerationNames()

const std::set<std::string>& bbp::sonata::Population::enumerationNames() const

### Description
All attribute names that are explicit enumerations.

### See Also
https://github.com/AllenInstitute/sonata/blob/master/docs/SONATA_DEVELOPER_GUIDE.md#nodes&mdash;enum-datatypes
```

--------------------------------

### run

Source: https://libsonata.readthedocs.io/en/latest/api.html

Returns the Run section of the simulation configuration.

```APIDOC
## run

### Description
Returns the Run section of the simulation configuration.

### Property
_run
```

--------------------------------

### CircuitConfig::fromFile()

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_circuit_config.html

A static method to load and parse a SONATA JSON config file from a given path. It returns a CircuitConfig object and can throw SonataError for file access or parsing problems.

```APIDOC
## fromFile()

static CircuitConfig bbp::sonata::CircuitConfig::fromFile(const std::string& _path_)

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

Exceptions:
     SonataError on:
  * Non accesible file (does not exists / does not have read access)
  * Ill-formed JSON
  * Missing mandatory entries (in any depth)
  * Missing entries which become mandatory when another entry is present
  * Multiple populations with the same name in different edge/node networks
```

--------------------------------

### Get All Attribute Names

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_population.html

Returns a set of all attribute names associated with the population.

```APIDOC
## attributeNames()

const std::set<std::string>& bbp::sonata::Population::attributeNames() const

### Description
All attribute names (CSV columns + required attributes + union of attributes in groups).
```

--------------------------------

### getNetwork()

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_simulation_config.html

Retrieves the circuit configuration file associated with the simulation.

```APIDOC
## ◆ getNetwork()

### Description
Returns circuit config file associated with this simulation config.

### Signature
`const std::string& bbp::sonata::SimulationConfig::getNetwork() const noexcept`
```

--------------------------------

### get (SomaDataFrame)

Source: https://libsonata.readthedocs.io/en/latest/api.html

Return reports with specified node IDs, time range, and stride.

```APIDOC
## get (SomaDataFrame)

### Description
Return reports with all those node_ids between ‘tstart’ and ‘tstop’ with a stride tstride.

### Parameters
* **_node_ids** (libsonata.Selection | None) - Limit the report to the given selection. If nullptr, all nodes in the report are used.
* **_tstart** (float | None) - The start time for the report.
* **_tstop** (float | None) - The stop time for the report.
* **_tstride** (int | None) - The time stride for the report.
* **_block_gap_limit** (int | None) - Gap limit between each IO block while fetching data from storage.

### Returns
* libsonata.SomaDataFrame - The requested report data.
```

--------------------------------

### openFile

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_Hdf5PluginInterface301std%3A%3Atuple301Ts8880140001std%3A%3Atup2aad3a074a6d97aa53b11cdc09840a8e.html

Opens an HDF5 file at the specified path. This is a pure virtual function, meaning it must be implemented by derived classes.

```APIDOC
## openFile

### Description
Opens an HDF5 file at the specified path. This is a pure virtual function that must be implemented by derived classes.

### Method
(Not specified, but typically involves file I/O)

### Endpoint
(Not applicable, this is an interface method)

### Parameters
#### Path Parameters
- **path** (const std::string &) - Required - The path to the HDF5 file to open.

### Response
(Not specified, as this is an interface method. Implementations would define the return type, likely a file handle or object.)
```

--------------------------------

### _attributeDataType()

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_EdgePopulation.html

Internal function to get the data type of an attribute, with an option to translate enumerations.

```APIDOC
## _attributeDataType(const std::string &name, bool translate_enumeration = false) const

### Description
Internal function to get the data type of an attribute.

### Method
`std::string _attributeDataType(const std::string &name, bool translate_enumeration = false) const`

### Parameters
* **name** (const std::string &) - The name of the attribute.
* **translate_enumeration** (bool) - Whether to translate enumerations (default is false).
```

--------------------------------

### network

Source: https://libsonata.readthedocs.io/en/latest/api.html

Returns the circuit configuration file associated with this simulation configuration.

```APIDOC
## network

### Description
Returns circuit config file associated with this simulation config.

### Property
_network
```

--------------------------------

### Get Edge Population Properties

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Retrieves the properties for a given edge population name.

```cpp
EdgePopulationProperties | getEdgePopulationProperties (const std::string &name) const
```

--------------------------------

### CircuitConfig::fromFile

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Loads and parses a SONATA JSON config file from a specified path, returning a CircuitConfig object. This static method handles file access and parsing, throwing SonataError on issues.

```APIDOC
## fromFile(const std::string & _path_)

Loads a SONATA JSON config file from disk and returns a CircuitConfig object.

### Parameters
- `_path_` (const std::string &) - The path to the JSON configuration file.

### Returns
- `CircuitConfig` - An object representing the parsed configuration.

### Exceptions
- `SonataError` - Thrown on:
  * File not accessible (does not exist or no read access).
  * Ill-formed JSON.
  * Missing mandatory entries.
  * Missing entries that become mandatory based on other entries.
  * Duplicate population names in different networks.
```

--------------------------------

### Get Node Population Properties

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Retrieves the properties for a given node population name.

```cpp
NodePopulationProperties | getNodePopulationProperties (const std::string &name) const
```

--------------------------------

### Population::getTimes

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_SpikeReader%3A%3APopulation.html

Returns the start and stop times of the population's spike data.

```APIDOC
## Population::getTimes

### Description
Return (tstart, tstop) of the population.

### Signature
`std::tuple<double, double> getTimes() const`

### Returns
`std::tuple<double, double>`: A tuple containing the start and stop times.
```

--------------------------------

### getOutput()

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_simulation_config.html

Retrieves the Output section of the simulation configuration.

```APIDOC
## getOutput()

### Description
Returns the Output section of the simulation configuration.

### Method
const Output& (const)

### Returns
const Output&
```

--------------------------------

### getOutput()

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_SimulationConfig.html

Retrieves the Output section of the simulation configuration.

```APIDOC
## getOutput()

### Description
Returns the Output section of the simulation configuration.

### Method
const Output& getOutput() const noexcept

### Returns
The Output section of the simulation configuration.
```

--------------------------------

### getTimes()

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_ReportReader%3A%3APopulation.html

Retrieves the start time, stop time, and time step of the population data.

```APIDOC
## getTimes()

### Description
Retrieves the start time, stop time, and time step of the population data.

### Method
`getTimes`

### Parameters
None

### Response
#### Success Response (200)
- **std::tuple<double, double, double>** - A tuple containing (tstart, tstop, tstep).

#### Response Example
```json
{
  "example": [0.0, 100.0, 0.1]
}
```
```

--------------------------------

### getTimes() - Retrieve Time Range

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_spike_reader_1_1_population.html

Returns the start and stop times of the population data.

```APIDOC
## getTimes()

### Description
Return (tstart, tstop) of the population.

### Method
const

### Response
#### Success Response (std::tuple<double, double>)
- Returns a tuple containing the start time and stop time.
```

--------------------------------

### CircuitConfig Constructor

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Initializes a CircuitConfig object with the provided contents and base path.

```APIDOC
## CircuitConfig Constructor

### Description
Initializes a CircuitConfig object with the provided contents and base path.

### Signature
CircuitConfig(const std::string &contents, const std::string &basePath)
```

--------------------------------

### Getting Edge Attributes

Source: https://libsonata.readthedocs.io/en/latest/index.html

Illustrates how to retrieve attribute values for single edges or selections of edges.

```APIDOC
### Methods
#### get_attribute
Retrieves attribute values for edges.

##### Single Edge
```python
# get attribute value for single edge, say 123
delay = population.get_attribute('delay', 123)
```

##### Selection of Edges
```python
# Selection of edges => returns NumPy array with corresponding values
selection = libsonata.Selection([1, 5, 9])
delays = population.get_attribute('delay', selection) # returns delays for edges 1, 5, 9
```
```

--------------------------------

### SimulationConfig::fromFile

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_SimulationConfig.html

Loads a SONATA JSON simulation config file from disk and returns a SimulationConfig object which parses it. This method handles file access, JSON parsing, and validation of mandatory entries.

```APIDOC
## SimulationConfig::fromFile

### Description
Loads a SONATA JSON simulation config file from disk and returns a SimulationConfig object which parses it. This method handles file access, JSON parsing, and validation of mandatory entries.

### Method
static

### Endpoint
N/A (C++ method)

### Parameters
#### Path Parameters
- **path** (const std::string&) - Required - The path to the SONATA JSON simulation config file.

### Exceptions
- SonataError: Thrown if the file is not accessible (does not exist or no read access), if the JSON is ill-formed, or if mandatory entries are missing at any depth.
```

--------------------------------

### bbp::sonata::Population::_dynamicsAttributeDataType

Source: https://libsonata.readthedocs.io/en/latest/cpp/population_8h_source.html

Internal method to get the data type of a dynamics attribute.

```APIDOC
## bbp::sonata::Population::_dynamicsAttributeDataType

### Description
Retrieves the data type of a specified dynamics attribute.

### Signature
std::string _dynamicsAttributeDataType(const std::string &name) const
```

--------------------------------

### getRun()

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_SimulationConfig.html

Retrieves the Run section of the simulation configuration.

```APIDOC
## getRun()

### Description
Returns the Run section of the simulation configuration.

### Method
const Run& getRun() const noexcept

### Returns
The Run section of the simulation configuration.
```

--------------------------------

### _attributeDataType

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_node_population.html

Internal method to get the data type of an attribute. Can optionally translate enumeration types.

```APIDOC
## _attributeDataType

### Description
Internal method to get the data type of an attribute. Can optionally translate enumeration types.

### Method
`_attributeDataType`

### Endpoint
N/A (Method Call)

### Parameters
#### Path Parameters
- **name** (const std::string &) - The name of the attribute.
- **translate_enumeration** (bool) - Whether to translate enumeration types (default is false).

### Response
- **std::string** - The data type of the attribute.
```

--------------------------------

### getRun()

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_simulation_config.html

Retrieves the Run section of the simulation configuration.

```APIDOC
## getRun()

### Description
Returns the Run section of the simulation configuration.

### Method
const Run& (const)

### Returns
const Run&
```

--------------------------------

### NodePopulation Constructors

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_node_population.html

Constructs a NodePopulation object. Two constructors are available, one taking file paths and names, and another that also accepts an Hdf5Reader object for more control over data reading.

```APIDOC
## NodePopulation Constructors

### Description
Constructs a NodePopulation object.

### Method
Constructor

### Parameters
#### Path Parameters
- **h5FilePath** (const std::string &) - Description of the HDF5 file path.
- **csvFilePath** (const std::string &) - Description of the CSV file path.
- **name** (const std::string &) - The name of the node population.
- **hdf5_reader** (const Hdf5Reader &) - An optional Hdf5Reader object for custom data reading.

### Code Example
```cpp
// Example usage of constructors
NodePopulation pop1("path/to/file.h5", "path/to/file.csv", "population_name");
// Hdf5Reader reader;
// NodePopulation pop2("path/to/file.h5", "path/to/file.csv", "population_name", reader);
```
```

--------------------------------

### Get All Dynamics Attribute Names

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_population.html

Returns a set of all dynamics attribute names associated with the population.

```APIDOC
## dynamicsAttributeNames()

const std::set<std::string>& bbp::sonata::Population::dynamicsAttributeNames() const

### Description
All dynamics attribute names (JSON keys + union of attributes in groups).
```

--------------------------------

### bbp::sonata::Hdf5Reader::Hdf5Reader()

Source: https://libsonata.readthedocs.io/en/latest/cpp/hdf5__reader_8h_source.html

Constructs an Hdf5Reader with the default plugin implementation.

```APIDOC
## Hdf5Reader()

### Description
Creates a valid Hdf5Reader with the default plugin.

### Method
Hdf5Reader()
```

--------------------------------

### Get Dynamics Attribute Data Type

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_population.html

Retrieves the data type of a specified dynamics attribute.

```APIDOC
## _dynamicsAttributeDataType()

std::string bbp::sonata::Population::_dynamicsAttributeDataType(const std::string& _name_) const

### Description
Get dynamics attribute data type.

### Parameters
* **_name_** (const std::string&): The name of the dynamics attribute.
```

--------------------------------

### getTimes()

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_report_reader_1_1_population.html

Retrieves the time information (start time, stop time, and time step) for the population.

```APIDOC
## getTimes()

### Description
Retrieves the time information (start time, stop time, and time step) for the population.

### Method
GET (or equivalent for SDK)

### Endpoint
`/population/times` (Illustrative - actual SDK method call)

### Parameters
None

### Response
#### Success Response (200)
- **std::tuple<double, double, double>** - A tuple containing tstart, tstop, and tstep.

#### Response Example
```json
{
  "example": [0.0, 1000.0, 0.1]
}
```
```

--------------------------------

### getConnectionOverrides()

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_simulation_config.html

Retrieves the full list of connection overrides for the simulation.

```APIDOC
## ◆ getConnectionOverrides()

### Description
Returns the full list of connection overrides.

### Signature
`const std::vector<ConnectionOverride>& bbp::sonata::SimulationConfig::getConnectionOverrides() const noexcept`
```

--------------------------------

### Population::_attributeDataType

Source: https://libsonata.readthedocs.io/en/latest/cpp/population_8h_source.html

Internal method to get the data type of an attribute. Can optionally translate enumeration types.

```APIDOC
## Population::_attributeDataType

### Description
Internal method to get the data type of an attribute. Can optionally translate enumeration types.

### Signature
```cpp
std::string _attributeDataType(const std::string& name, bool translate_enumeration = false) const;
```
```

--------------------------------

### Constructors

Source: https://libsonata.readthedocs.io/en/latest/cpp/classnonstd_1_1variants_1_1variant.html

Constructs a variant object, initializing it with one of the possible types.

```APIDOC
## Constructors

### Description
Constructs a variant object, initializing it with one of the possible types.

### Method
Constructor

### Parameters
- **t0** (T0 const &) - Description of parameter t0
- **t1** (T1 const &) - Description of parameter t1
- **t2** (T2 const &) - Description of parameter t2
- **t3** (T3 const &) - Description of parameter t3
- **t4** (T4 const &) - Description of parameter t4
- **t5** (T5 const &) - Description of parameter t5
- **t6** (T6 const &) - Description of parameter t6
- **t7** (T7 const &) - Description of parameter t7
- **t8** (T8 const &) - Description of parameter t8
- **t9** (T9 const &) - Description of parameter t9
- **t10** (T10 const &) - Description of parameter t10
- **t11** (T11 const &) - Description of parameter t11
- **t12** (T12 const &) - Description of parameter t12
- **t13** (T13 const &) - Description of parameter t13
- **t14** (T14 const &) - Description of parameter t14
- **t15** (T15 const &) - Description of parameter t15
- **other** (variant const &) - Copy constructor parameter
```

--------------------------------

### Get Edge Population with Hdf5Reader

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Retrieves a specific edge population using its name and an HDF5 reader.

```cpp
EdgePopulation | getEdgePopulation (const std::string &name, const Hdf5Reader &hdf5_reader) const
```

--------------------------------

### Constructors

Source: https://libsonata.readthedocs.io/en/latest/cpp/optional_8hpp_source.html

Various constructors for initializing an optional object, including in-place construction and construction from values.

```APIDOC
## Constructors

### In-place construction (C++11)

- `optional( nonstd_lite_in_place_t(T), Args&&... args )`: Constructs an optional in-place with the given arguments.
- `optional( nonstd_lite_in_place_t(T), std::initializer_list<U> il, Args&&... args )`: Constructs an optional in-place with an initializer list and additional arguments.

### Value construction (C++11)

- `explicit optional( U && value )`: Explicitly constructs an optional by moving a value, if conversion is not implicitly allowed.
- `optional( U && value )`: Constructs an optional by moving a value, if conversion is implicitly allowed.

### Value construction (C++98)

- `optional( value_type const & value )`: Constructs an optional by copying a value.
```

--------------------------------

### Get Node Population with Hdf5Reader

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_CircuitConfig.html

Retrieves a specific node population using its name and an HDF5 reader.

```cpp
NodePopulation | getNodePopulation (const std::string &name, const Hdf5Reader &hdf5_reader) const
```

--------------------------------

### get() - Retrieve Spikes

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_spike_reader_1_1_population.html

Retrieves spikes for specified node IDs within a given time range.

```APIDOC
## get()

### Description
Return spikes with all those node_ids between 'tstart' and 'tstop'.

### Method
const

### Parameters
#### Path Parameters
- **_node_ids_** (nonstd::optional< Selection >) - Optional - Defaults to `nonstd::nullopt`.
- **_tstart_** (nonstd::optional< double >) - Optional - Defaults to `nonstd::nullopt`.
- **_tstop_** (nonstd::optional< double >) - Optional - Defaults to `nonstd::nullopt`.

### Response
#### Success Response (Spikes)
- Returns a `Spikes` object containing the requested spike data.
```

--------------------------------

### SimulationConfig Constructor

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_simulation_config.html

Constructs a SimulationConfig object from a JSON content string and a base path.

```APIDOC
## SimulationConfig Constructor

### Description
Initializes a SimulationConfig object using a JSON string representing the configuration and a base path for file resolution.

### Signature
`SimulationConfig(const std::string &content, const std::string &basePath)`

### Parameters
- **content** (const std::string &) - The JSON string containing the simulation configuration.
- **basePath** (const std::string &) - The base directory path for resolving relative file paths within the configuration.
```

--------------------------------

### SimulationConfig Constructor

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_SimulationConfig.html

Constructs a SimulationConfig object from a JSON content string and a base path.

```APIDOC
## SimulationConfig Constructor

### Description
Initializes a SimulationConfig object using provided JSON content and a base file path.

### Signature
`SimulationConfig(const std::string &content, const std::string &basePath)`
```

--------------------------------

### ElementReportReader.get

Source: https://libsonata.readthedocs.io/en/latest/api.html

Retrieves reports with specified node IDs between start and stop times, with a given time stride.

```APIDOC
## ElementReportReader.get

### Description
Return reports with all those node_ids between ‘tstart’ and ‘tstop’ with a stride tstride.

### Method
`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`

### Parameters
- **node_ids** (libsonata.Selection | None) - Optional - Limit the report to the given selection. If nullptr, all nodes in the report are used.
- **tstart** (float | None) - Optional - The start time for the report.
- **tstop** (float | None) - Optional - The stop time for the report.
- **tstride** (int | None) - Optional - The time stride.
- **block_gap_limit** (int | None) - Optional - Gap limit between each IO block while fetching data from storage.

### Returns
- libsonata.ElementDataFrame - A container of raw reporting data.
```

--------------------------------

### SpikeReader Constructor

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_SpikeReader.html

Initializes a SpikeReader object with the specified filename.

```APIDOC
## SpikeReader(std::string filename)

### Description
Constructs a SpikeReader object to read spike data from the given file.

### Parameters
#### Path Parameters
- **filename** (std::string) - Required - The path to the spike file to be read.
```

--------------------------------

### CircuitConfig Status and Path Retrieval

Source: https://libsonata.readthedocs.io/en/latest/cpp/config_8h_source.html

Methods to get the status of the circuit configuration and retrieve paths to node sets.

```APIDOC
## CircuitConfig::getCircuitConfigStatus() const

### Description
Retrieves the current status of the circuit configuration, indicating if it's complete, partial, or invalid.

### Returns
- ConfigStatus - The status of the circuit configuration.

## CircuitConfig::getNodeSetsPath() const

### Description
Returns the file path to the node sets configuration.

### Returns
- const std::string& - The path to the node sets file.

## CircuitConfig::getCompartmentSetsPath() const

### Description
Returns the file path to the compartment sets configuration.

### Returns
- const std::string& - The path to the compartment sets file.
```

--------------------------------

### bbp::sonata::CompartmentSets::fromFile

Source: https://libsonata.readthedocs.io/en/latest/cpp/compartment__sets_8h_source.html

Creates a CompartmentSets object by loading data from a specified file path.

```APIDOC
## bbp::sonata::CompartmentSets::fromFile

### Description
Load compartment sets from a file.

### Signature
static CompartmentsSets fromFile(const std::string &path)

### Parameters
#### Path Parameters
- **path** (std::string) - Required - The path to the file containing compartment set data.
```

--------------------------------

### Get Attribute Data Type

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_population.html

Retrieves the data type of a specified attribute. It can optionally translate enumeration types.

```APIDOC
## _attributeDataType()

std::string bbp::sonata::Population::_attributeDataType(const std::string& _name_, bool _translate_enumeration_ = false) const

### Description
Get attribute data type, optionally translating enumeration types.

### Parameters
* **_name_** (const std::string&): The name of the attribute.
* **_translate_enumeration_** (bool): If true, translate enumeration types. Defaults to false.
```

--------------------------------

### Get Edge Attribute for Single Edge or Selection

Source: https://libsonata.readthedocs.io/en/latest/index.html

Retrieve attribute values for a single edge by its ID or for a selection of edges.

```python
# get attribute value for single edge, say 123
>>> population.get_attribute('delay', 123)

# ...or Selection of edges => returns NumPy array with corresponding values
>>> selection = libsonata.Selection([1, 5, 9])
>>> population.get_attribute('delay', selection) # returns delays for edges 1, 5, 9
```

--------------------------------

### get_enumeration

Source: https://libsonata.readthedocs.io/en/latest/api.html

Retrieves enumeration values for a given node or selection of nodes. This function is used to get all allowed attribute enumeration values.

```APIDOC
## get_enumeration

### Description
Overloaded function to get enumeration values for a given node or selection of nodes.

### Signatures
1. `get_enumeration(name: str, node_id: int) -> object`
2. `get_enumeration(name: str, selection: libsonata.Selection) -> object`

### Parameters
- **name** (str) - Required - The name of the attribute for which to retrieve enumeration values. Allows attributes not defined in the spec.
- **node_id** (int) - Required - The ID of the node.
- **selection** (libsonata.Selection) - Required - A selection object to retrieve enumeration values from.

### Raises
- If there is no such attribute for the population.
```

--------------------------------

### getConnectionOverrides

Source: https://libsonata.readthedocs.io/en/latest/cpp/doxygen_SimulationConfig.html

Retrieves the full list of connection overrides for the simulation.

```APIDOC
## getConnectionOverrides()

### Description
Returns the full list of connection overrides for the simulation.

### Method
const std::vector<ConnectionOverride>& bbp::sonata::SimulationConfig::getConnectionOverrides() const noexcept

### Returns
- const std::vector<ConnectionOverride>&: A const reference to a vector of ConnectionOverride objects.
```

--------------------------------

### optional class constructors

Source: https://libsonata.readthedocs.io/en/latest/cpp/optional_8hpp_source.html

Constructors for the optional class, including default construction, construction with nullopt, and copy construction.

```APIDOC
template< typename T>
class optional
{
public:
  typedef T value_type;

  optional_constexpr optional() optional_noexcept
  optional_constexpr optional( nullopt_t /*unused*/ ) optional_noexcept

#if optional_CPP11_OR_GREATER
  template< typename U = T
  optional_REQUIRES_T(
  std::is_copy_constructible<U>::value
  || std11::is_trivially_copy_constructible<U>::value

```

--------------------------------

### InputBase Structure

Source: https://libsonata.readthedocs.io/en/latest/cpp/structbbp_1_1sonata_1_1_simulation_config_1_1_input_base.html

Defines the structure of an input configuration for Sonata simulations.

```APIDOC
## bbp::sonata::SimulationConfig::InputBase

### Description
Represents the base configuration for simulation inputs.

### Public Types

#### enum class Module
Enumerates the types of stimulus modules.
- **invalid**: Invalid module type.
- **linear**: Linear stimulus.
- **relative_linear**: Relative linear stimulus.
- **pulse**: Pulse stimulus.
- **sinusoidal**: Sinusoidal stimulus.
- **subthreshold**: Subthreshold stimulus.
- **hyperpolarizing**: Hyperpolarizing stimulus.
- **synapse_replay**: Synapse replay stimulus.
- **seclamp**: Seclamp stimulus.
- **noise**: Noise stimulus.
- **shot_noise**: Shot noise stimulus.
- **relative_shot_noise**: Relative shot noise stimulus.
- **absolute_shot_noise**: Absolute shot noise stimulus.
- **ornstein_uhlenbeck**: Ornstein-Uhlenbeck process stimulus.
- **relative_ornstein_uhlenbeck**: Relative Ornstein-Uhlenbeck process stimulus.

#### enum class InputType
Enumerates the types of input.
- **invalid**: Invalid input type.
- **spikes**: Spike input.
- **extracellular_stimulation**: Extracellular stimulation.
- **current_clamp**: Current clamp input.
- **voltage_clamp**: Voltage clamp input.
- **conductance**: Conductance input.

### Public Attributes

- **module** (Module): Type of stimulus.
- **inputType** (InputType): Type of input.
- **delay** (double): Time when input is activated (ms).
- **duration** (double): Time duration for how long input is activated (ms).
- **nodeSet** (std::string): Node set which is affected by input.
```

--------------------------------

### Conditional Includes

Source: https://libsonata.readthedocs.io/en/latest/cpp/optional_8hpp_source.html

Includes standard library headers conditionally based on C++ standard version and feature availability. For example, `<stdexcept>` is included unless exceptions are disabled.

```cpp
#if optional_CONFIG_NO_EXCEPTIONS
// already included: <cassert>
#else
# include <stdexcept>
#endif

#if optional_CPP11_OR_GREATER
# include <functional>
#endif

#if optional_HAVE( INITIALIZER_LIST )
# include <initializer_list>
#endif

#if optional_HAVE( TYPE_TRAITS )
# include <type_traits>
#elif optional_HAVE( TR1_TYPE_TRAITS )
# include <tr1/type_traits>
#endif
```

--------------------------------

### bbp::sonata::Hdf5Reader::openFile

Source: https://libsonata.readthedocs.io/en/latest/cpp/hdf5__reader_8h_source.html

Opens an HDF5 file at the specified path.

```APIDOC
## openFile(const std::string& filename) const

### Description
Opens an HDF5 file specified by the filename.

### Method
HighFive::File openFile(const std::string& filename) const

### Parameters
#### Path Parameters
- **filename** (std::string) - Description of the filename parameter
```

--------------------------------

### NodeSets::fromFile

Source: https://libsonata.readthedocs.io/en/latest/cpp/classbbp_1_1sonata_1_1_node_sets.html

Opens and creates a NodeSets object from a SONATA 'node sets' file specified by its path.

```APIDOC
## NodeSets::fromFile(const std::string &path)

### Description
Opens a SONATA `node sets` file from a path.

### Parameters
* **path** (string) - The path to the SONATA node sets file.
```
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