Visualizing Hyperspectral Data in 3D¶

This notebook demonstrates how to visualize hyperspectral data in 3D using the PyVista plotting backend.

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# %pip install "hypercoast[extra]"

# %pip install "hypercoast[extra]"

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import hypercoast

import hypercoast

Visualize NEON AOP Hyperspectral Data¶

Download a sample NEON AOP hyperspectral data.

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url = "https://github.com/opengeos/datasets/releases/download/hypercoast/NEON_D02_SERC_DP3_368000_4306000_reflectance.h5"
filepath = "data/neon.h5"
hypercoast.download_file(url, filepath)

url = "https://github.com/opengeos/datasets/releases/download/hypercoast/NEON_D02_SERC_DP3_368000_4306000_reflectance.h5" filepath = "data/neon.h5" hypercoast.download_file(url, filepath)

Load the dataset as a xarray.Dataset object.

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dataset = hypercoast.read_neon(filepath)
dataset

dataset = hypercoast.read_neon(filepath) dataset

Visualize the NEON AOP hyperspectral data in 3D with a selected band overlaid on top of the 3D plot.

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cube = hypercoast.image_cube(
    dataset,
    variable="reflectance",
    cmap="jet",
    clim=(0, 0.5),
    rgb_wavelengths=[700],
    title="Reflectance",
)
cube.show()

cube = hypercoast.image_cube( dataset, variable="reflectance", cmap="jet", clim=(0, 0.5), rgb_wavelengths=[700], title="Reflectance", ) cube.show()

Visualize the NEON AOP hyperspectral data in 3D with an RGB image overlaid on top of the 3D plot.

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cube2 = hypercoast.image_cube(
    dataset,
    variable="reflectance",
    cmap="jet",
    clim=(0, 0.5),
    rgb_wavelengths=[1000, 700, 500],
    rgb_gamma=2,
    title="Reflectance",
)
cube2.show()

cube2 = hypercoast.image_cube( dataset, variable="reflectance", cmap="jet", clim=(0, 0.5), rgb_wavelengths=[1000, 700, 500], rgb_gamma=2, title="Reflectance", ) cube2.show()

Visualize NASA EMIT Hyperspectral Data¶

Download a sample EMIT data file from here.

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url = "https://github.com/opengeos/datasets/releases/download/netcdf/EMIT_L2A_RFL_001_20240404T161230_2409511_009.nc"
filepath = "EMIT_L2A_RFL_001_20240404T161230_2409511_009.nc"
hypercoast.download_file(url)

url = "https://github.com/opengeos/datasets/releases/download/netcdf/EMIT_L2A_RFL_001_20240404T161230_2409511_009.nc" filepath = "EMIT_L2A_RFL_001_20240404T161230_2409511_009.nc" hypercoast.download_file(url)

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dataset = hypercoast.read_emit(filepath)
dataset

dataset = hypercoast.read_emit(filepath) dataset

Select a subset of the data to avoid nodata areas.

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ds = dataset.sel(longitude=slice(-90.1482, -89.7321), latitude=slice(30.0225, 29.7451))
ds

ds = dataset.sel(longitude=slice(-90.1482, -89.7321), latitude=slice(30.0225, 29.7451)) ds

Visualize the EMIT data in 3D with an RGB image overlaid on top of the 3D plot.

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cube = hypercoast.image_cube(
    ds,
    variable="reflectance",
    cmap="jet",
    clim=(0, 0.4),
    rgb_wavelengths=[1000, 700, 500],
    rgb_gamma=2,
    title="EMIT Reflectance",
)
cube.show()

cube = hypercoast.image_cube( ds, variable="reflectance", cmap="jet", clim=(0, 0.4), rgb_wavelengths=[1000, 700, 500], rgb_gamma=2, title="EMIT Reflectance", ) cube.show()