Interactive slicing and thresholding of hyperspectral data with HyperCoast¶

This notebook demonstrates how to perform interactive slicing and thresholding of hyperspectral data with HyperCoast using the PyVista plotting backend.

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# %pip install "hypercoast[extra]"

# %pip install "hypercoast[extra]"

In [ ]:

import hypercoast

import hypercoast

NEON AOP¶

Download a sample NEON AOP hyperspectral dataset.

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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

Extract a small subset of the dataset for demonstration purposes.

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ds = dataset.isel(x=slice(100, 200), y=slice(100, 200))
ds

ds = dataset.isel(x=slice(100, 200), y=slice(100, 200)) ds

Interactive slicing along the z-axis (band)

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p = hypercoast.image_cube(
    ds,
    variable="reflectance",
    cmap="jet",
    clim=(0, 0.5),
    rgb_wavelengths=[1000, 700, 500],
    rgb_gamma=2,
    widget="slice",
)
p.add_text("Band slicing ", position="upper_right", font_size=14)
p.show()

p = hypercoast.image_cube( ds, variable="reflectance", cmap="jet", clim=(0, 0.5), rgb_wavelengths=[1000, 700, 500], rgb_gamma=2, widget="slice", ) p.add_text("Band slicing ", position="upper_right", font_size=14) p.show()

Interactive slicing along the x-axis (longitude).

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p = hypercoast.image_cube(
    ds,
    variable="reflectance",
    cmap="jet",
    clim=(0, 0.5),
    rgb_wavelengths=[1000, 700, 500],
    rgb_gamma=2,
    widget="slice",
    normal="x",
)
p.add_text("X-axis slicing ", position="upper_right", font_size=14)
p.show()

p = hypercoast.image_cube( ds, variable="reflectance", cmap="jet", clim=(0, 0.5), rgb_wavelengths=[1000, 700, 500], rgb_gamma=2, widget="slice", normal="x", ) p.add_text("X-axis slicing ", position="upper_right", font_size=14) p.show()

Orthogonal slicing.

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p = hypercoast.image_cube(
    ds,
    variable="reflectance",
    cmap="jet",
    clim=(0, 0.5),
    rgb_wavelengths=[1000, 700, 500],
    rgb_gamma=2,
    widget="orthogonal",
)
p.add_text("Orthogonal slicing", position="upper_right", font_size=14)
p.show()

p = hypercoast.image_cube( ds, variable="reflectance", cmap="jet", clim=(0, 0.5), rgb_wavelengths=[1000, 700, 500], rgb_gamma=2, widget="orthogonal", ) p.add_text("Orthogonal slicing", position="upper_right", font_size=14) p.show()

Clip the image cube with a plane (band slicing).

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p = hypercoast.image_cube(
    ds,
    variable="reflectance",
    cmap="jet",
    clim=(0, 0.5),
    rgb_wavelengths=[1000, 700, 500],
    rgb_gamma=2,
    widget="plane",
)
p.add_text("Band slicing", position="upper_right", font_size=14)
p.show()

p = hypercoast.image_cube( ds, variable="reflectance", cmap="jet", clim=(0, 0.5), rgb_wavelengths=[1000, 700, 500], rgb_gamma=2, widget="plane", ) p.add_text("Band slicing", position="upper_right", font_size=14) p.show()

Interactive thresholding.

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p = hypercoast.image_cube(
    ds,
    variable="reflectance",
    cmap="jet",
    clim=(0, 0.5),
    rgb_wavelengths=[1000, 700, 500],
    rgb_gamma=2,
    widget="threshold",
)
p.add_text("Thresholding", position="upper_right", font_size=14)
p.show()

p = hypercoast.image_cube( ds, variable="reflectance", cmap="jet", clim=(0, 0.5), rgb_wavelengths=[1000, 700, 500], rgb_gamma=2, widget="threshold", ) p.add_text("Thresholding", position="upper_right", font_size=14) p.show()

NASA EMIT¶

Download a sample NASA EMIT hyperspectral dataset from here.

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

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

Load the dataset as a xarray.Dataset object.

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dataset = hypercoast.read_emit(filepath)
dataset

dataset = hypercoast.read_emit(filepath) dataset

Select a subset of the data for demonstration purposes.

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ds = dataset.sel(longitude=slice(-90.05, -89.99), latitude=slice(30.00, 29.93))
ds

ds = dataset.sel(longitude=slice(-90.05, -89.99), latitude=slice(30.00, 29.93)) ds

Interactive slicing along the z-axis (band).

In [ ]:

p = hypercoast.image_cube(
    ds,
    variable="reflectance",
    cmap="jet",
    clim=(0, 0.5),
    rgb_wavelengths=[1000, 700, 500],
    rgb_gamma=2,
    title="EMIT Reflectance",
    widget="plane",
)
p.add_text("Band slicing", position="upper_right", font_size=14)
p.show()

p = hypercoast.image_cube( ds, variable="reflectance", cmap="jet", clim=(0, 0.5), rgb_wavelengths=[1000, 700, 500], rgb_gamma=2, title="EMIT Reflectance", widget="plane", ) p.add_text("Band slicing", position="upper_right", font_size=14) p.show()

Interactive thresholding.

In [ ]:

p = hypercoast.image_cube(
    ds,
    variable="reflectance",
    cmap="jet",
    clim=(0, 0.5),
    rgb_wavelengths=[1000, 700, 500],
    rgb_gamma=2,
    title="EMIT Reflectance",
    widget="threshold",
)
p.add_text("Thresholding", position="upper_right", font_size=14)
p.show()

p = hypercoast.image_cube( ds, variable="reflectance", cmap="jet", clim=(0, 0.5), rgb_wavelengths=[1000, 700, 500], rgb_gamma=2, title="EMIT Reflectance", widget="threshold", ) p.add_text("Thresholding", position="upper_right", font_size=14) p.show()