Visualizing NEON AOP hyperspectral data interactively with HyperCoast¶

This notebook demonstrates how to visualize NEON AOP hyperspectral data interactively with HyperCoast.

In [1]:

# %pip install "hypercoast[extra]"

# %pip install "hypercoast[extra]"

In [2]:

import hypercoast

import hypercoast

In [3]:

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)

Out[3]:

'/home/runner/work/HyperCoast/HyperCoast/docs/examples/data/neon.h5'

Load the dataset as a xarray.Dataset object.

In [4]:

dataset = hypercoast.read_neon(filepath)
dataset

dataset = hypercoast.read_neon(filepath) dataset

Out[4]:

<xarray.Dataset> Size: 3GB
Dimensions:      (y: 1000, x: 1000, wavelength: 426)
Coordinates:
  * y            (y) float64 8kB 4.307e+06 4.307e+06 ... 4.306e+06 4.306e+06
  * x            (x) float64 8kB 3.68e+05 3.68e+05 ... 3.69e+05 3.69e+05
  * wavelength   (wavelength) float64 3kB 383.9 388.9 ... 2.507e+03 2.512e+03
Data variables:
    reflectance  (y, x, wavelength) float64 3GB 0.1569 0.1206 0.1034 ... nan nan
Attributes:
    scale_factor:   10000.0
    no_data_value:  -9999.0
    crs:            EPSG:32618
    transform:      (1.0, 0.0, 368000.0, 0.0, -1.0, 4307000.0)

xarray.Dataset

• Dimensions:
  • y: 1000
  • x: 1000
  • wavelength: 426
• Coordinates: (3)
  • y
    (y)
    float64
    4.307e+06 4.307e+06 ... 4.306e+06

    array([4307000.      , 4306998.998999, 4306997.997998, ..., 4306002.002002,
           4306001.001001, 4306000.      ])

  • x
    (x)
    float64
    3.68e+05 3.68e+05 ... 3.69e+05

    array([368000.      , 368001.001001, 368002.002002, ..., 368997.997998,
           368998.998999, 369000.      ])

  • wavelength
    (wavelength)
    float64
    383.9 388.9 ... 2.507e+03 2.512e+03

    array([ 383.88,  388.89,  393.9 , ..., 2502.17, 2507.17, 2512.18])

• Data variables: (1)
  • reflectance
    (y, x, wavelength)
    float64
    0.1569 0.1206 0.1034 ... nan nan

    scale_factor :

    10000.0

    no_data_value :

    -9999.0

    crs :

    EPSG:32618

    transform :

    (1.0, 0.0, 368000.0, 0.0, -1.0, 4307000.0)

    array([[[0.1569, 0.1206, 0.1034, ..., 0.1512,    nan,    nan],
            [0.1593, 0.118 , 0.105 , ...,    nan,    nan,    nan],
            [0.1415, 0.1147, 0.1061, ..., 0.    , 0.    ,    nan],
            ...,
            [0.056 , 0.0319, 0.0292, ...,    nan,    nan,    nan],
            [0.0604, 0.0412, 0.0257, ...,    nan,    nan,    nan],
            [0.0723, 0.0444, 0.0366, ..., 0.7853,    nan,    nan]],
    
           [[0.13  , 0.0988, 0.0842, ...,    nan,    nan,    nan],
            [0.1515, 0.0961, 0.0826, ...,    nan,    nan,    nan],
            [0.1431, 0.1253, 0.1069, ...,    nan,    nan,    nan],
            ...,
            [0.0586, 0.0411, 0.0224, ...,    nan,    nan,    nan],
            [0.0467, 0.0424, 0.0289, ..., 0.4019,    nan,    nan],
            [0.074 , 0.0453, 0.0301, ..., 0.7002,    nan,    nan]],
    
           [[0.1026, 0.0716, 0.0623, ...,    nan,    nan,    nan],
            [0.127 , 0.1103, 0.0986, ..., 0.7747,    nan,    nan],
            [0.168 , 0.1335, 0.1359, ...,    nan,    nan,    nan],
            ...,
    ...
            ...,
            [0.0578, 0.0493, 0.0418, ...,    nan,    nan,    nan],
            [0.1047, 0.0788, 0.057 , ...,    nan,    nan,    nan],
            [0.0958, 0.0785, 0.0693, ...,    nan,    nan,    nan]],
    
           [[0.0747, 0.0397, 0.0314, ...,    nan,    nan,    nan],
            [0.065 , 0.041 , 0.0322, ..., 0.9747,    nan,    nan],
            [0.0667, 0.0424, 0.0274, ...,    nan,    nan,    nan],
            ...,
            [0.1335, 0.1008, 0.0878, ..., 0.    ,    nan,    nan],
            [0.1369, 0.0864, 0.0771, ...,    nan,    nan,    nan],
            [0.1144, 0.0958, 0.0857, ...,    nan,    nan,    nan]],
    
           [[0.0738, 0.0392, 0.031 , ...,    nan,    nan,    nan],
            [0.0541, 0.0421, 0.0272, ...,    nan,    nan,    nan],
            [0.0513, 0.0406, 0.0276, ...,    nan,    nan,    nan],
            ...,
            [0.082 , 0.0593, 0.0511, ...,    nan,    nan,    nan],
            [0.0883, 0.0693, 0.0518, ...,    nan,    nan,    nan],
            [0.1128, 0.1   , 0.0844, ..., 0.5833,    nan,    nan]]])

• Indexes: (3)
  • y
    PandasIndex

    PandasIndex(Index([        4307000.0, 4306998.998998999, 4306997.997997998,
           4306996.996996997, 4306995.995995996, 4306994.994994995,
           4306993.993993994, 4306992.992992993, 4306991.991991992,
           4306990.990990991,
           ...
           4306009.009009009, 4306008.008008008, 4306007.007007007,
           4306006.006006006, 4306005.005005005, 4306004.004004004,
           4306003.003003003, 4306002.002002002, 4306001.001001001,
                   4306000.0],
          dtype='float64', name='y', length=1000))

  • x
    PandasIndex

    PandasIndex(Index([          368000.0,   368001.001001001, 368002.00200200203,
             368003.003003003,   368004.004004004,   368005.005005005,
           368006.00600600604,   368007.007007007,   368008.008008008,
             368009.009009009,
           ...
             368990.990990991,   368991.991991992,   368992.992992993,
           368993.99399399396,   368994.994994995,   368995.995995996,
             368996.996996997,   368997.997997998,   368998.998998999,
                     369000.0],
          dtype='float64', name='x', length=1000))

  • wavelength
    PandasIndex

    PandasIndex(Index([ 383.88,  388.89,   393.9,  398.91,  403.92,  408.92,  413.93,  418.94,
            423.95,  428.95,
           ...
           2467.11, 2472.12, 2477.13, 2482.13, 2487.14, 2492.15, 2497.16, 2502.17,
           2507.17, 2512.18],
          dtype='float64', name='wavelength', length=426))

• Attributes: (4)

  scale_factor :

  10000.0

  no_data_value :

  -9999.0

  crs :

  EPSG:32618

  transform :

  (1.0, 0.0, 368000.0, 0.0, -1.0, 4307000.0)

Visualize the data interactively with HyperCoast.

In [5]:

m = hypercoast.Map()
m.add_neon(filepath, wavelengths=[1000, 700, 500], vmin=0, vmax=0.5)
m

m = hypercoast.Map() m.add_neon(filepath, wavelengths=[1000, 700, 500], vmin=0, vmax=0.5) m

Out[5]:

In [6]:

m.set_center(-76.5134, 38.8973, 16)

m.set_center(-76.5134, 38.8973, 16)

In [7]:

m.add("spectral")

m.add("spectral")