emodpy_malaria.weather.weather_data module

Weather data module implementing functionality for working with binary weather files (.bin.json).

class emodpy_malaria.weather.weather_data.WeatherData(data: ndarray, metadata: WeatherMetadata = None)

Bases: object

Functionality for working with binary weather files (.bin.json).

validate()

Validate data and metadata relationship.

property metadata: WeatherMetadata

Metadata property, exposing weather metadata object.

property data: ndarray

Raw data, reshaped in one row per node weather time series.

classmethod from_dict(node_series: Dict[int, ndarray[float32] | List[float]], same_nodes: Dict[int, List[int]] = None, attributes: WeatherAttributes = None) → WeatherData

Creates a WeatherData object from a dictionary mapping nodes and node weather time series. The method identifies unique node weather time series and produces a corresponding node-offset dictionary.

Args:

node_series: Dictionary with node ids as keys and weather time series as values (don’t have to be unique). same_nodes: (Optional) Dictionary, mapping nodes from ‘node_series’ dictionary to additional nodes

which series are the same. Keys are node ids, values are lists of node ids.

attributes: (Optional) Attributes used to initiate weather metadata. If not provided, defaults are used.

Returns:

WeatherData object.

to_dict(only_unique_series=False, copy_data: bool = True) → Dict[int, ndarray[float32]]

Create a node-to-series dictionary from the current object. This method can be used to edit weather data.

Args:

only_unique_series: (Optional) A flag controlling whether the output dictionary will contain series for all

nodes (if set to true) or only unique series.

copy_data: (Optional) Flag indicating whether to copy data numpy array to prevent unintentional changes.

Returns:

A dictionary with node ids and keys and node weather time series as values.

classmethod from_csv(file_path: str | Path, info: DataFrameInfo = None, attributes: WeatherAttributes = None) → WeatherData

Creates a WeatherData object from a csv file. Used for creating or editing weather files. The method identifies unique node weather time series and produces a corresponding node-offset dictionary.

Args:

file_path: The csv file path from which weather data is loaded (expected columns: node, step, value). info: (Optional) Dataframe info object describing dataframe columns and content. attributes: (Optional) Attributes used to initiate weather metadata. If not provided, defaults are used.

Returns:

WeatherData object.

to_csv(file_path: str | Path, info: DataFrameInfo = None) → DataFrame

Creates a csv file and stores node ids, time steps and weather node weather time series as separate columns.

Args:

file_path: The csv file path into which weather data will be stored. info: (Optional) Dataframe info object describing dataframe columns and content.

Returns:

Dataframe created as an intermediate object used to save data to a csv file.

classmethod from_dataframe(df: pd.DateFrame, info: DataFrameInfo = None, attributes: WeatherAttributes = None) → WeatherData

Creates WeatherData object from the Pandas dataframe. The dataframe is expected to contain node ids, time steps and weather node weather time series as separate columns.

Args:

df: Dataframe containing nodes and weather time series (expected columns: node, step, value). info: (Optional) Dataframe info object describing dataframe columns and content. attributes: (Optional) Attributes used to initiate weather metadata. If not provided, defaults are used.

Returns:

WeatherData object.

to_dataframe(info: DataFrameInfo = None) → DataFrame

Creates a dataframe containing node ids, time steps and weather time series as separate columns.

Args:

info: (Optional) Dataframe info object describing dataframe columns and content.

Returns:

Dataframe containing node ids and weather time series.

classmethod from_file(file_path: str | Path) → WeatherData

Create WeatherData object by reading weather data from binary (.bin) and metadata (.bin.json) files.

Args:

file_path: The weather binary (.bin) file path. The metadata file path is constructed by appending “.json”.

Returns:

WeatherData object.

to_file(file_path: str | Path) → NoReturn

Create weather binary (.bin) and metadata (.json) files, containing weather data and metadata.

Args:

file_path: The weather binary (.bin) file path. The metadata file path is constructed by adding “.json”.

Returns:

None.

class emodpy_malaria.weather.weather_data.DataFrameInfo(node_column: str = None, step_column: str = None, value_column: str = None, only_unique_series: bool = False)

Bases: object

The object containing info about dataframe columns and content. Used to pass dataframe info between methods working with weather dataframes.

property node_column

property step_column

property value_column

classmethod detect_columns(df, column_candidates: Dict[str, List[str]] = None) → DataFrameInfo

Auto-detect required column names (nodes, time-steps and weather time series) for the DataFrameInfo object.

Args:

df: The dataframe containing nodes, time-steps and weather time series. column_candidates: (Optional) Dictionary of candidate column names to be used instead of defaults.

Returns:

DataFrameInfo object with detected column names.