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aviris module

This module contains functions to read and process NASA AVIRIS hyperspectral data. More info about the data can be found at https://aviris.jpl.nasa.gov. A portion of the source code is adapted from the jjmcnelis/aviris-ng-notebooks repository available at https://bit.ly/4bRCgqs. It is licensed under the MIT License. Credit goes to the original author Jack McNelis.

SPDX-FileCopyrightText = [ "2024 Jack McNelis jjmcne@gmail.com", ] SPDX-License-Identifier = "MIT"

aviris_to_image(dataset, wavelengths=None, method='nearest', output=None, **kwargs)

Converts an AVIRIS dataset to an image.

Parameters:

Name Type Description Default
dataset Union[xr.Dataset, str]

The dataset containing the AVIRIS data or the file path to the dataset.

 required
wavelengths np.ndarray

The specific wavelengths to select. If None, all wavelengths are selected. Defaults to None.

 None
method str

The method to use for data interpolation. Defaults to "nearest".

 'nearest'
output str

The file path where the image will be saved. If None, the image will be returned as a PIL Image object. Defaults to None.

 None
**kwargs Any

Additional keyword arguments to be passed to leafmap.array_to_image.

 {}

Returns:

Type Description
Optional[rasterio.Dataset]

The image converted from the dataset. If output is provided, the image will be saved to the specified file and the function will return None.
Source code in hypercoast/aviris.py 
def aviris_to_image(
    dataset: Union[xr.Dataset, str],
    wavelengths: Optional[np.ndarray] = None,
    method: str = "nearest",
    output: Optional[str] = None,
    **kwargs: Any,
):
    """
    Converts an AVIRIS dataset to an image.

    Args:
        dataset (Union[xr.Dataset, str]): The dataset containing the AVIRIS data
            or the file path to the dataset.
        wavelengths (np.ndarray, optional): The specific wavelengths to select. If None, all
            wavelengths are selected. Defaults to None.
        method (str, optional): The method to use for data interpolation.
            Defaults to "nearest".
        output (str, optional): The file path where the image will be saved. If
            None, the image will be returned as a PIL Image object. Defaults to None.
        **kwargs (Any): Additional keyword arguments to be passed to
            `leafmap.array_to_image`.

    Returns:
        Optional[rasterio.Dataset]: The image converted from the dataset. If
            `output` is provided, the image will be saved to the specified file
            and the function will return None.
    """
    from leafmap import array_to_image

    if isinstance(dataset, str):
        dataset = read_aviris(dataset, method=method)

    if wavelengths is not None:
        dataset = dataset.sel(wavelength=wavelengths, method=method)

    return array_to_image(
        dataset["reflectance"],
        output=output,
        transpose=False,
        dtype=np.float32,
        **kwargs,
    )

extract_aviris(dataset, lat, lon, offset=2.0)

Extracts AVIRIS data from a given xarray Dataset.

Parameters:

Name Type Description Default
dataset xarray.Dataset

The dataset containing the AVIRIS data.

 required
lat float

The latitude of the point to extract.

 required
lon float

The longitude of the point to extract.

 required
offset float

The offset from the point to extract. Defaults to 2.0.

 2.0

Returns:

Type Description
xarray.DataArray

The extracted data.
Source code in hypercoast/aviris.py 
def extract_aviris(
    dataset: xr.Dataset, lat: float, lon: float, offset: float = 2.0
) -> xr.DataArray:
    """
    Extracts AVIRIS data from a given xarray Dataset.

    Args:
        dataset (xarray.Dataset): The dataset containing the AVIRIS data.
        lat (float): The latitude of the point to extract.
        lon (float): The longitude of the point to extract.
        offset (float, optional): The offset from the point to extract. Defaults to 2.0.

    Returns:
        xarray.DataArray: The extracted data.
    """

    crs = dataset.attrs["crs"]

    x, y = convert_coords([[lat, lon]], "epsg:4326", crs)[0]

    da = dataset["reflectance"]

    x_con = (da["xc"] > x - offset) & (da["xc"] < x + offset)
    y_con = (da["yc"] > y - offset) & (da["yc"] < y + offset)

    try:
        data = da.where(x_con & y_con, drop=True)
        data = data.mean(dim=["x", "y"])
    except ValueError:
        data = np.nan * np.ones(da.sizes["wavelength"])

    da = xr.DataArray(
        data, dims=["wavelength"], coords={"wavelength": dataset.coords["wavelength"]}
    )

    return da

read_aviris(filepath, wavelengths=None, method='nearest', **kwargs)

Reads NASA AVIRIS hyperspectral data and returns an xarray dataset.

Parameters:

Name Type Description Default
filepath str

The path to the AVIRIS data.

 required
wavelengths List[float]

The wavelengths to select. If None, all wavelengths are selected. Defaults to None.

 None
method str

The method to use for selection. Defaults to "nearest".

 'nearest'
**kwargs Any

Additional arguments to pass to the selection method.

 {}

Returns:

Type Description
xr.Dataset

The dataset containing the reflectance data.
Source code in hypercoast/aviris.py 
def read_aviris(
    filepath: str,
    wavelengths: Optional[List[float]] = None,
    method: str = "nearest",
    **kwargs: Any,
) -> xr.Dataset:
    """
    Reads NASA AVIRIS hyperspectral data and returns an xarray dataset.

    Args:
        filepath (str): The path to the AVIRIS data.
        wavelengths (List[float], optional): The wavelengths to select. If None,
            all wavelengths are selected. Defaults to None.
        method (str, optional): The method to use for selection. Defaults to
            "nearest".
        **kwargs (Any): Additional arguments to pass to the selection method.

    Returns:
        xr.Dataset: The dataset containing the reflectance data.
    """

    if filepath.endswith(".hdr"):
        filepath = filepath.replace(".hdr", "")

    ds = xr.open_dataset(filepath, engine="rasterio")

    wavelength = ds["wavelength"].values.tolist()
    wavelength = [round(num, 2) for num in wavelength]

    cols = ds.x.size
    rows = ds.y.size

    rio_transform = ds.rio.transform()
    geo_transform = list(rio_transform)[:6]

    # get the raster geotransform as its component parts
    xres, xrot, xmin, yrot, yres, ymax = geo_transform

    # generate coordinate arrays
    xarr = np.array([xmin + i * xres for i in range(0, cols)])
    yarr = np.array([ymax + i * yres for i in range(0, rows)])

    ds["y"] = xr.DataArray(
        data=yarr,
        dims=("y"),
        name="y",
        attrs=dict(
            units="m",
            standard_name="projection_y_coordinate",
            long_name="y coordinate of projection",
        ),
    )

    ds["x"] = xr.DataArray(
        data=xarr,
        dims=("x"),
        name="x",
        attrs=dict(
            units="m",
            standard_name="projection_x_coordinate",
            long_name="x coordinate of projection",
        ),
    )

    global_atts = ds.attrs
    global_atts["Conventions"] = "CF-1.6"
    ds.attrs = dict(
        units="unitless",
        _FillValue=-9999,
        grid_mapping="crs",
        standard_name="reflectance",
        long_name="atmospherically corrected surface reflectance",
    )
    ds.attrs.update(global_atts)

    ds = ds.transpose("y", "x", "band")
    ds = ds.drop_vars(["wavelength"])
    ds = ds.rename({"band": "wavelength", "band_data": "reflectance"})
    ds.coords["wavelength"] = wavelength
    ds.attrs["crs"] = ds.rio.crs.to_string()
    ds.rio.write_transform(rio_transform)

    if wavelengths is not None:
        ds = ds.sel(wavelength=wavelengths, method=method, **kwargs)
    return ds