Module pycascadia.grid

Grid contains a grid of data in xarray format

"""Grid contains a grid of data in xarray format"""

import os
import pandas
from pygmt import grdcut

from pycascadia.loaders import load_source, extract_region
from pycascadia.utility import region_to_str, xr_to_xyz, filter_nodata


class Grid:
    """Grid contains a grid of data in xarray format and optionally as xyz points in pandas dataframe format.

    Grids are intended to be initially loaded from file and can be further manipulated in the following ways:

    - resampling to a different grid spacing
    - cropping to a given region
    - conversion to a list of xyz datapoints.
    - saved to file

    Coordinates will be labelled `x` and `y`, and (depth/elevation) values will be labelled `z`.

    The internal grid may also be manipulated and is exposed through Grid.grid or Grid.xyz (if the grid has already been converted).
    """

    def __init__(self, fname: str, convert_to_xyz: bool = False) -> None:
        """
        Constructor

        Args:
            fname: Input grid filename.
            convert_to_xyz: Whether the grid should be converted to xyz points.
        """
        self.load(fname)

        if convert_to_xyz:
            self.xyz = self.as_xyz()

    def load(self, fname: str) -> None:
        """
        Loads data from file. See loaders for supported file formats.

        Args:
            fname: Input grid filename.
        """
        self.grid, self.region, self.spacing = load_source(fname)

    def crop(self, region: list) -> None:
        """
        Crops grid using grdcut.

        Args:
            region: Bounding box of region to crop to (in format [xmin, xmax, ymin, ymax]).
        """
        if region == self.region:
            return

        self.grid = grdcut(self.grid, region=region)
        self.region = extract_region(self.grid)

    def resample(self, spacing: float) -> None:
        """
        Resamples the loaded grid using gdal's grdsample.

        Args:
            spacing: Grid spacing of resampled grid.
        """
        if spacing == self.spacing:
            return

        print(f"Resampling from {self.spacing} to {spacing}")
        in_fname = "original.nc"
        self.save_grid(in_fname)
        out_fname = "resampled.nc"
        os.system(
            f"gmt grdsample {in_fname} -G{out_fname} -R{region_to_str(self.region)} -I{spacing} -V"
        )
        self.load(out_fname)
        os.remove(in_fname)
        os.remove(out_fname)

    def as_xyz(self) -> pandas.DataFrame:
        """
        Returns pandas dataframe representation.
        """
        xyz_data = xr_to_xyz(self.grid)
        if hasattr(self.grid, "nodatavals"):
            filter_nodata(xyz_data, self.grid.nodatavals)
        return xyz_data

    def plot(self, ax=None) -> None:
        """
        Plots data (useful for testing).

        Args:
            ax: Axis used for plotting (will be created if not supplied).
        """
        self.grid.plot(ax=ax)

    def save_grid(self, fname: str) -> None:
        """
        Saves grid to netcdf file.

        Args:
            fname: Output filename.
        """
        self.grid.to_netcdf(fname)

Classes

class Grid (fname: str, convert_to_xyz: bool = False)

Grid contains a grid of data in xarray format and optionally as xyz points in pandas dataframe format.

Grids are intended to be initially loaded from file and can be further manipulated in the following ways:

• resampling to a different grid spacing
• cropping to a given region
• conversion to a list of xyz datapoints.
• saved to file

Coordinates will be labelled x and y, and (depth/elevation) values will be labelled z.

The internal grid may also be manipulated and is exposed through Grid.grid or Grid.xyz (if the grid has already been converted).

Constructor

Args

fname

Input grid filename.

convert_to_xyz

Whether the grid should be converted to xyz points.

Expand source code

class Grid:
    """Grid contains a grid of data in xarray format and optionally as xyz points in pandas dataframe format.

    Grids are intended to be initially loaded from file and can be further manipulated in the following ways:

    - resampling to a different grid spacing
    - cropping to a given region
    - conversion to a list of xyz datapoints.
    - saved to file

    Coordinates will be labelled `x` and `y`, and (depth/elevation) values will be labelled `z`.

    The internal grid may also be manipulated and is exposed through Grid.grid or Grid.xyz (if the grid has already been converted).
    """

    def __init__(self, fname: str, convert_to_xyz: bool = False) -> None:
        """
        Constructor

        Args:
            fname: Input grid filename.
            convert_to_xyz: Whether the grid should be converted to xyz points.
        """
        self.load(fname)

        if convert_to_xyz:
            self.xyz = self.as_xyz()

    def load(self, fname: str) -> None:
        """
        Loads data from file. See loaders for supported file formats.

        Args:
            fname: Input grid filename.
        """
        self.grid, self.region, self.spacing = load_source(fname)

    def crop(self, region: list) -> None:
        """
        Crops grid using grdcut.

        Args:
            region: Bounding box of region to crop to (in format [xmin, xmax, ymin, ymax]).
        """
        if region == self.region:
            return

        self.grid = grdcut(self.grid, region=region)
        self.region = extract_region(self.grid)

    def resample(self, spacing: float) -> None:
        """
        Resamples the loaded grid using gdal's grdsample.

        Args:
            spacing: Grid spacing of resampled grid.
        """
        if spacing == self.spacing:
            return

        print(f"Resampling from {self.spacing} to {spacing}")
        in_fname = "original.nc"
        self.save_grid(in_fname)
        out_fname = "resampled.nc"
        os.system(
            f"gmt grdsample {in_fname} -G{out_fname} -R{region_to_str(self.region)} -I{spacing} -V"
        )
        self.load(out_fname)
        os.remove(in_fname)
        os.remove(out_fname)

    def as_xyz(self) -> pandas.DataFrame:
        """
        Returns pandas dataframe representation.
        """
        xyz_data = xr_to_xyz(self.grid)
        if hasattr(self.grid, "nodatavals"):
            filter_nodata(xyz_data, self.grid.nodatavals)
        return xyz_data

    def plot(self, ax=None) -> None:
        """
        Plots data (useful for testing).

        Args:
            ax: Axis used for plotting (will be created if not supplied).
        """
        self.grid.plot(ax=ax)

    def save_grid(self, fname: str) -> None:
        """
        Saves grid to netcdf file.

        Args:
            fname: Output filename.
        """
        self.grid.to_netcdf(fname)

Methods

def as_xyz(self) -> pandas.core.frame.DataFrame

Returns pandas dataframe representation.

Expand source code

def as_xyz(self) -> pandas.DataFrame:
    """
    Returns pandas dataframe representation.
    """
    xyz_data = xr_to_xyz(self.grid)
    if hasattr(self.grid, "nodatavals"):
        filter_nodata(xyz_data, self.grid.nodatavals)
    return xyz_data

def crop(self, region: list) -> NoneType

Crops grid using grdcut.

Args

region

Bounding box of region to crop to (in format [xmin, xmax, ymin, ymax]).

Expand source code

def crop(self, region: list) -> None:
    """
    Crops grid using grdcut.

    Args:
        region: Bounding box of region to crop to (in format [xmin, xmax, ymin, ymax]).
    """
    if region == self.region:
        return

    self.grid = grdcut(self.grid, region=region)
    self.region = extract_region(self.grid)

def load(self, fname: str) -> NoneType

Loads data from file. See loaders for supported file formats.

Args

fname

Input grid filename.

Expand source code

def load(self, fname: str) -> None:
    """
    Loads data from file. See loaders for supported file formats.

    Args:
        fname: Input grid filename.
    """
    self.grid, self.region, self.spacing = load_source(fname)

def plot(self, ax=None) -> NoneType

Plots data (useful for testing).

Args

ax

Axis used for plotting (will be created if not supplied).

Expand source code

def plot(self, ax=None) -> None:
    """
    Plots data (useful for testing).

    Args:
        ax: Axis used for plotting (will be created if not supplied).
    """
    self.grid.plot(ax=ax)

def resample(self, spacing: float) -> NoneType

Resamples the loaded grid using gdal's grdsample.

Args

spacing

Grid spacing of resampled grid.

Expand source code

def resample(self, spacing: float) -> None:
    """
    Resamples the loaded grid using gdal's grdsample.

    Args:
        spacing: Grid spacing of resampled grid.
    """
    if spacing == self.spacing:
        return

    print(f"Resampling from {self.spacing} to {spacing}")
    in_fname = "original.nc"
    self.save_grid(in_fname)
    out_fname = "resampled.nc"
    os.system(
        f"gmt grdsample {in_fname} -G{out_fname} -R{region_to_str(self.region)} -I{spacing} -V"
    )
    self.load(out_fname)
    os.remove(in_fname)
    os.remove(out_fname)

def save_grid(self, fname: str) -> NoneType

Saves grid to netcdf file.

Args

fname

Output filename.

Expand source code

def save_grid(self, fname: str) -> None:
    """
    Saves grid to netcdf file.

    Args:
        fname: Output filename.
    """
    self.grid.to_netcdf(fname)