Source code for openghg.util._domain

from typing import Any, Dict, Tuple, List, Optional

import numpy as np
from numpy import ndarray

from openghg.types import optionalPathType, ArrayLikeMatch, ArrayLike, XrDataLike, XrDataLikeMatch

__all__ = ["get_domain_info", "find_domain", "convert_longitude"]

def get_domain_info(domain_filepath: optionalPathType = None) -> Dict[str, Any]:
    """Extract data from domain info JSON file as a dictionary.

    This uses the data stored within openghg_defs/domain_info JSON file by default.

        domain_filepath: Alternative domain info file.
        dict: Data from domain JSON file
    from openghg_defs import domain_info_file
    from openghg.util import load_json

    if domain_filepath is None:
        domain_info_json = load_json(path=domain_info_file)
        domain_info_json = load_json(path=domain_filepath)

    return domain_info_json

[docs] def find_domain(domain: str, domain_filepath: optionalPathType = None) -> Tuple[ndarray, ndarray]: """Finds the latitude and longitude values in degrees associated with a given domain name. Args: domain: Pre-defined domain name domain_filepath: Alternative domain info file. Defaults to openghg_defs input. Returns: array, array : Latitude and longitude values for the domain in degrees. """ domain_info = get_domain_info(domain_filepath) # Look for domain in domain_info file if domain in domain_info: domain_data = domain_info[domain] elif domain.upper() in domain_info: domain = domain.upper() domain_data = domain_info[domain] else: raise ValueError(f"Pre-defined domain '{domain}' not found") # Extract or create latitude and longitude data latitude = _get_coord_data("latitude", domain_data, domain) longitude = _get_coord_data("longitude", domain_data, domain) return latitude, longitude
def _get_coord_data(coord: str, data: Dict[str, Any], domain: str) -> ndarray: """Attempts to extract or derive coordinate (typically latitude/longitude) values for a domain from provided data dictionary (typically this can be derived from 'domain_info.json' file). This looks for: - File containing coordinate values (in degrees) - Looks for "{coord}_file" attribute e.g. "latitude_file" - OR for a file within "domain" subfolder called "{domain}_{coord}.dat" e.g. "EUROPE_latitude.dat" - "{coord}_range" and "{coord}_increment" attributes to use to construct the coordinate values e.g. "latitude_range" to include the start and end (inclusive) range and "latitude_increment" for the step in degrees. Args: coord: Name of coordinate (e.g. latitude, longitude) data: Data dictionary containing details of domain (e.g. derived from 'domain_info.json') domain: Name of domain Returns: array: Extracted or derived coordinate values """ from openghg_defs import data_path # Look for explicit file keyword in data e.g. "latitude_file" # Extract data from file if found and return filename_str = f"{coord}_file" if filename_str in data: full_filename = data_path / data[filename_str] coord_data: ndarray = np.loadtxt(full_filename) return coord_data # If no explicit file name defined, look within known location to see # if data is present by looking for file of form "domain/{domain}_{coord}.csv" # e.g. "domain/EUROPE_latitude.csv" (within "openghg/openghg/data" folder) try: full_filename = data_path / "domain" / f"{domain}_{coord}.dat" coord_data = np.loadtxt(full_filename) except OSError: pass else: return coord_data # If no data files can be found, look for coordinate range and increment values # If present, create the coordinate data. If not raise a ValueError. try: coord_range = data[f"{coord}_range"] increment = data[f"{coord}_increment"] except KeyError: raise ValueError(f"Unable to get {coord} coordinate data for domain: {domain}") coord_min = float(coord_range[0]) coord_max = float(coord_range[-1]) increment = float(increment) coord_data = np.arange(coord_min, coord_max + increment, increment) return coord_data def find_coord_name(data: XrDataLike, options: List[str]) -> Optional[str]: """ Find the name of a coordinate based on input options. Only the first found value will be returned. Args: data: xarray Data structure options: List of options to check. Will be checked in order. Returns: str / None: Name of coordinate if located within data. None otherwise. """ for option in options: if option in data.coords: name = option break else: return None return name
[docs] def convert_longitude(longitude: ArrayLikeMatch) -> ArrayLikeMatch: """ Convert longitude extent from (0 to 360) to (-180 to 180). This does *not* reorder the values. Args: longitude: Valid longitude values in degrees. Returns: ndarray / DataArray : Updated longitude values in the same order. """ # Check range of longitude values and convert to -180 - +180 longitude = ((longitude - 180) % 360) - 180 return longitude
def convert_internal_longitude(data: XrDataLikeMatch, lon_name: Optional[str] = None, reorder: bool = True) -> XrDataLikeMatch: """ Convert longitude coordinate within an xarray data structure (DataArray or Dataset). Args: data: Data with longitude values to convert. lon_name: By default will look a coord called "lon" or "longitude". Otherwise must be specified. reorder: Whether to reorder the data based on the converted longitude values. Returns: DataArray / Dataset: Input data with updated longitude values """ if lon_name is None: lon_options = ["lon", "longitude"] lon_name = find_coord_name(data, lon_options) if lon_name is None: raise ValueError("Please specify 'lon_name'.") longitude = data[lon_name] longitude = convert_longitude(longitude) data = data.assign_coords({lon_name: longitude}) if reorder: data = data.sortby(lon_name) return data def cut_data_extent(data: XrDataLikeMatch, lat_out: ArrayLike, lon_out: ArrayLike, lat_name: Optional[str] = None, lon_name: Optional[str] = None, copy: bool = False) -> XrDataLikeMatch: """ Cut down extent of data within an xarray data structure (DataArray or Dataset) against an output latitude and longitude range. A buffer based on the maximum difference along the lon_out and lat_out dimensions will be added when the data is cut. Args: data: Data to be cut down lat_out: Array containing output latitude values lon_out: Array containing output longitude values lat_name: Name of latitude dimension. Must be specified if not "lat" or "latitude". lon_name: Name of longitude dimension. Must be specified if not "lon" or "longitude". copy: Whether to explicitly copy the data. Returns: xarray.DataArray / xarray.Dataset: data with reduced lat, lon ranges. """ if lat_name is None: lat_options = ["lat", "latitude"] lat_name = find_coord_name(data, lat_options) if lat_name is None: raise ValueError("Please specify 'lat_name'.") if lon_name is None: lon_options = ["lon", "longitude"] lon_name = find_coord_name(data, lon_options) if lon_name is None: raise ValueError("Please specify 'lon_name'.") if isinstance(lat_out, np.ndarray): lat_out.sort() else: lat_out = lat_out.sortby(lat_out[lat_name]) if isinstance(lon_out, np.ndarray): lon_out.sort() else: lon_out = lon_out.sortby(lon_out[lon_name]) lat_diff = (lat_out[1:] - lat_out[:-1]).max() lon_diff = (lon_out[1:] - lon_out[:-1]).max() lat_low = np.min(lat_out) - lat_diff lat_high = np.max(lat_out) + lat_diff lon_low = np.min(lon_out) - lon_diff lon_high = np.max(lon_out) + lon_diff lat_cut_wide_range = slice(lat_low, lat_high) lon_cut_wide_range = slice(lon_low, lon_high) if copy: data_cut = data.copy() else: data_cut = data data_cut = data_cut.sel({lat_name: lat_cut_wide_range, lon_name: lon_cut_wide_range}) return data_cut