'''
Calculating band indices from remote sensing data (NDVI, NDWI etc).
License: The code in this notebook is licensed under the Apache License,
Version 2.0 (https://www.apache.org/licenses/LICENSE-2.0). Digital Earth
Australia data is licensed under the Creative Commons by Attribution 4.0
license (https://creativecommons.org/licenses/by/4.0/).
Contact: If you need assistance, please post a question on the Open Data
Cube Discord chat (https://discord.com/invite/4hhBQVas5U) or on the GIS Stack
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on GitHub (https://github.com/GeoscienceAustralia/dea-notebooks/issues/new).
Last modified: June 2023
'''
# Import required packages
import warnings
import numpy as np
# Define custom functions
[docs]
def calculate_indices(ds,
index=None,
collection=None,
custom_varname=None,
normalise=True,
drop=False,
inplace=False):
"""
Takes an xarray dataset containing spectral bands, calculates one of
a set of remote sensing indices, and adds the resulting array as a
new variable in the original dataset.
Note: by default, this function will create a new copy of the data
in memory. This can be a memory-expensive operation, so to avoid
this, set `inplace=True`.
Last modified: June 2023
Parameters
----------
ds : xarray Dataset
A two-dimensional or multi-dimensional array with containing the
spectral bands required to calculate the index. These bands are
used as inputs to calculate the selected water index.
index : str or list of strs
A string giving the name of the index to calculate or a list of
strings giving the names of the indices to calculate:
* ``'AWEI_ns'`` (Automated Water Extraction Index,
no shadows, Feyisa 2014)
* ``'AWEI_sh'`` (Automated Water Extraction Index,
shadows, Feyisa 2014)
* ``'BAEI'`` (Built-Up Area Extraction Index, Bouzekri et al. 2015)
* ``'BAI'`` (Burn Area Index, Martin 1998)
* ``'BSI'`` (Bare Soil Index, Rikimaru et al. 2002)
* ``'BUI'`` (Built-Up Index, He et al. 2010)
* ``'CMR'`` (Clay Minerals Ratio, Drury 1987)
* ``'EVI'`` (Enhanced Vegetation Index, Huete 2002)
* ``'FMR'`` (Ferrous Minerals Ratio, Segal 1982)
* ``'IOR'`` (Iron Oxide Ratio, Segal 1982)
* ``'LAI'`` (Leaf Area Index, Boegh 2002)
* ``'MNDWI'`` (Modified Normalised Difference Water Index, Xu 1996)
* ``'MSAVI'`` (Modified Soil Adjusted Vegetation Index,
Qi et al. 1994)
* ``'NBI'`` (New Built-Up Index, Jieli et al. 2010)
* ``'NBR'`` (Normalised Burn Ratio, Lopez Garcia 1991)
* ``'NDBI'`` (Normalised Difference Built-Up Index, Zha 2003)
* ``'NDCI'`` (Normalised Difference Chlorophyll Index,
Mishra & Mishra, 2012)
* ``'NDMI'`` (Normalised Difference Moisture Index, Gao 1996)
* ``'NDSI'`` (Normalised Difference Snow Index, Hall 1995)
* ``'NDTI'`` (Normalise Difference Tillage Index,
Van Deventeret et al. 1997)
* ``'NDTI2'`` (Normalised Difference Turbidity Index, Lacaux et al., 2007)
* ``'NDVI'`` (Normalised Difference Vegetation Index, Rouse 1973)
* ``'NDWI'`` (Normalised Difference Water Index, McFeeters 1996)
* ``'SAVI'`` (Soil Adjusted Vegetation Index, Huete 1988)
* ``'TCB'`` (Tasseled Cap Brightness, Crist 1985)
* ``'TCG'`` (Tasseled Cap Greeness, Crist 1985)
* ``'TCW'`` (Tasseled Cap Wetness, Crist 1985)
* ``'TCB_GSO'`` (Tasseled Cap Brightness, Nedkov 2017)
* ``'TCG_GSO'`` (Tasseled Cap Greeness, Nedkov 2017)
* ``'TCW_GSO'`` (Tasseled Cap Wetness, Nedkov 2017)
* ``'WI'`` (Water Index, Fisher 2016)
* ``'kNDVI'`` (Non-linear Normalised Difference Vegation Index,
Camps-Valls et al. 2021)
collection : str
An string that tells the function what data collection is
being used to calculate the index. This is necessary because
different collections use different names for bands covering
a similar spectra.
Valid options are:
* ``'ga_ls_3'`` (for GA Landsat Collection 3)
* ``'ga_s2_3'`` (for GA Sentinel 2 Collection 3)
* ``'ga_gm_3'`` (for GA Geomedian Collection 3)
custom_varname : str, optional
By default, the original dataset will be returned with
a new index variable named after `index` (e.g. 'NDVI'). To
specify a custom name instead, you can supply e.g.
`custom_varname='custom_name'`. Defaults to None, which uses
`index` to name the variable.
normalise : bool, optional
Some coefficient-based indices (e.g. ``'WI'``, ``'BAEI'``,
``'AWEI_ns'``, ``'AWEI_sh'``, ``'TCW'``, ``'TCG'``, ``'TCB'``,
``'TCW_GSO'``, ``'TCG_GSO'``, ``'TCB_GSO'``, ``'EVI'``,
``'LAI'``, ``'SAVI'``, ``'MSAVI'``) produce different results if
surface reflectance values are not scaled between 0.0 and 1.0
prior to calculating the index. Setting `normalise=True` first
scales values to a 0.0-1.0 range by dividing by 10000.0.
Defaults to True.
drop : bool, optional
Provides the option to drop the original input data, thus saving
space. if drop = True, returns only the index and its values.
inplace: bool, optional
If `inplace=True`, calculate_indices will modify the original
array in-place, adding bands to the input dataset. The default
is `inplace=False`, which will instead make a new copy of the
original data (and use twice the memory).
Returns
-------
ds : xarray Dataset
The original xarray Dataset inputted into the function, with a
new varible containing the remote sensing index as a DataArray.
If drop = True, the new variable/s as DataArrays in the
original Dataset.
"""
# Set ds equal to a copy of itself in order to prevent the function
# from editing the input dataset. This can prevent unexpected
# behaviour though it uses twice as much memory.
if not inplace:
ds = ds.copy(deep=True)
# Capture input band names in order to drop these if drop=True
if drop:
bands_to_drop=list(ds.data_vars)
print(f'Dropping bands {bands_to_drop}')
# Dictionary containing remote sensing index band recipes
index_dict = {
# Normalised Difference Vegation Index, Rouse 1973
'NDVI': lambda ds: (ds.nir - ds.red) /
(ds.nir + ds.red),
# Non-linear Normalised Difference Vegation Index,
# Camps-Valls et al. 2021
'kNDVI': lambda ds: np.tanh(((ds.nir - ds.red) /
(ds.nir + ds.red)) ** 2),
# Enhanced Vegetation Index, Huete 2002
'EVI': lambda ds: ((2.5 * (ds.nir - ds.red)) /
(ds.nir + 6 * ds.red -
7.5 * ds.blue + 1)),
# Leaf Area Index, Boegh 2002
'LAI': lambda ds: (3.618 * ((2.5 * (ds.nir - ds.red)) /
(ds.nir + 6 * ds.red -
7.5 * ds.blue + 1)) - 0.118),
# Soil Adjusted Vegetation Index, Huete 1988
'SAVI': lambda ds: ((1.5 * (ds.nir - ds.red)) /
(ds.nir + ds.red + 0.5)),
# Mod. Soil Adjusted Vegetation Index, Qi et al. 1994
'MSAVI': lambda ds: ((2 * ds.nir + 1 -
((2 * ds.nir + 1)**2 -
8 * (ds.nir - ds.red))**0.5) / 2),
# Normalised Difference Moisture Index, Gao 1996
'NDMI': lambda ds: (ds.nir - ds.swir1) /
(ds.nir + ds.swir1),
# Normalised Burn Ratio, Lopez Garcia 1991
'NBR': lambda ds: (ds.nir - ds.swir2) /
(ds.nir + ds.swir2),
# Burn Area Index, Martin 1998
'BAI': lambda ds: (1.0 / ((0.10 - ds.red) ** 2 +
(0.06 - ds.nir) ** 2)),
# Normalised Difference Chlorophyll Index,
# (Mishra & Mishra, 2012)
'NDCI': lambda ds: (ds.red_edge_1 - ds.red) /
(ds.red_edge_1 + ds.red),
# Normalised Difference Snow Index, Hall 1995
'NDSI': lambda ds: (ds.green - ds.swir1) /
(ds.green + ds.swir1),
# Normalised Difference Tillage Index,
# Van Deventer et al. 1997
'NDTI': lambda ds: (ds.swir1 - ds.swir2) /
(ds.swir1 + ds.swir2),
# Normalised Difference Turbidity Index,
# Lacaux et al., 2007
'NDTI2': lambda ds: (ds.red - ds.green) /
(ds.red + ds.green),
# Normalised Difference Water Index, McFeeters 1996
'NDWI': lambda ds: (ds.green - ds.nir) /
(ds.green + ds.nir),
# Modified Normalised Difference Water Index, Xu 2006
'MNDWI': lambda ds: (ds.green - ds.swir1) /
(ds.green + ds.swir1),
# Normalised Difference Built-Up Index, Zha 2003
'NDBI': lambda ds: (ds.swir1 - ds.nir) /
(ds.swir1 + ds.nir),
# Built-Up Index, He et al. 2010
'BUI': lambda ds: ((ds.swir1 - ds.nir) /
(ds.swir1 + ds.nir)) -
((ds.nir - ds.red) /
(ds.nir + ds.red)),
# Built-up Area Extraction Index, Bouzekri et al. 2015
'BAEI': lambda ds: (ds.red + 0.3) /
(ds.green + ds.swir1),
# New Built-up Index, Jieli et al. 2010
'NBI': lambda ds: (ds.swir1 + ds.red) / ds.nir,
# Bare Soil Index, Rikimaru et al. 2002
'BSI': lambda ds: ((ds.swir1 + ds.red) -
(ds.nir + ds.blue)) /
((ds.swir1 + ds.red) +
(ds.nir + ds.blue)),
# Automated Water Extraction Index (no shadows), Feyisa 2014
'AWEI_ns': lambda ds: (4 * (ds.green - ds.swir1) -
(0.25 * ds.nir * + 2.75 * ds.swir2)),
# Automated Water Extraction Index (shadows), Feyisa 2014
'AWEI_sh': lambda ds: (ds.blue + 2.5 * ds.green -
1.5 * (ds.nir + ds.swir1) -
0.25 * ds.swir2),
# Water Index, Fisher 2016
'WI': lambda ds: (1.7204 + 171 * ds.green + 3 * ds.red -
70 * ds.nir - 45 * ds.swir1 -
71 * ds.swir2),
# Tasseled Cap Wetness, Crist 1985
'TCW': lambda ds: (0.0315 * ds.blue + 0.2021 * ds.green +
0.3102 * ds.red + 0.1594 * ds.nir +
-0.6806 * ds.swir1 + -0.6109 * ds.swir2),
# Tasseled Cap Greeness, Crist 1985
'TCG': lambda ds: (-0.1603 * ds.blue + -0.2819 * ds.green +
-0.4934 * ds.red + 0.7940 * ds.nir +
-0.0002 * ds.swir1 + -0.1446 * ds.swir2),
# Tasseled Cap Brightness, Crist 1985
'TCB': lambda ds: (0.2043 * ds.blue + 0.4158 * ds.green +
0.5524 * ds.red + 0.5741 * ds.nir +
0.3124 * ds.swir1 + -0.2303 * ds.swir2),
# Tasseled Cap Transformations with Sentinel-2 coefficients
# after Nedkov 2017 using Gram-Schmidt orthogonalization (GSO)
# Tasseled Cap Wetness, Nedkov 2017
'TCW_GSO': lambda ds: (0.0649 * ds.blue + 0.2802 * ds.green +
0.3072 * ds.red + -0.0807 * ds.nir +
-0.4064 * ds.swir1 + -0.5602 * ds.swir2),
# Tasseled Cap Greeness, Nedkov 2017
'TCG_GSO': lambda ds: (-0.0635 * ds.blue + -0.168 * ds.green +
-0.348 * ds.red + 0.3895 * ds.nir +
-0.4587 * ds.swir1 + -0.4064 * ds.swir2),
# Tasseled Cap Brightness, Nedkov 2017
'TCB_GSO': lambda ds: (0.0822 * ds.blue + 0.136 * ds.green +
0.2611 * ds.red + 0.5741 * ds.nir +
0.3882 * ds.swir1 + 0.1366 * ds.swir2),
# Clay Minerals Ratio, Drury 1987
'CMR': lambda ds: (ds.swir1 / ds.swir2),
# Ferrous Minerals Ratio, Segal 1982
'FMR': lambda ds: (ds.swir1 / ds.nir),
# Iron Oxide Ratio, Segal 1982
'IOR': lambda ds: (ds.red / ds.blue),
}
# If index supplied is not a list, convert to list. This allows us to
# iterate through either multiple or single indices in the loop below
indices = index if isinstance(index, list) else [index]
# Calculate for each index in the list of indices supplied (indexes)
for index in indices:
# Select an index function from the dictionary
index_func = index_dict.get(str(index))
# If no index is provided or if no function is returned due to an
# invalid option being provided, raise an exception informing user to
# choose from the list of valid options
if index is None:
raise ValueError(f"No remote sensing `index` was provided. Please "
"refer to the function \ndocumentation for a full "
"list of valid options for `index` (e.g. 'NDVI')")
elif (index in ['WI', 'BAEI', 'AWEI_ns', 'AWEI_sh',
'EVI', 'LAI', 'SAVI', 'MSAVI']
and not normalise):
warnings.warn(f"\nA coefficient-based index ('{index}') normally "
"applied to surface reflectance values in the \n"
"0.0-1.0 range was applied to values in the 0-10000 "
"range. This can produce unexpected results; \nif "
"required, resolve this by setting `normalise=True`")
elif index_func is None:
raise ValueError(f"The selected index '{index}' is not one of the "
"valid remote sensing index options. \nPlease "
"refer to the function documentation for a full "
"list of valid options for `index`")
# Rename bands to a consistent format if depending on what collection
# is specified in `collection`. This allows the same index calculations
# to be applied to all collections. If no collection was provided,
# raise an exception.
if collection is None:
raise ValueError("'No `collection` was provided. Please specify "
"either 'ga_ls_3', 'ga_s2_3' or 'ga_gm_3' "
"to ensure the function calculates indices "
"using the correct spectral bands")
elif collection == 'ga_ls_3':
# Dictionary mapping full data names to simpler 'red' alias names
bandnames_dict = {
'nbart_nir': 'nir',
'nbart_red': 'red',
'nbart_green': 'green',
'nbart_blue': 'blue',
'nbart_swir_1': 'swir1',
'nbart_swir_2': 'swir2',
'nbar_red': 'red',
'nbar_green': 'green',
'nbar_blue': 'blue',
'nbar_nir': 'nir',
'nbar_swir_1': 'swir1',
'nbar_swir_2': 'swir2'
}
# Rename bands in dataset to use simple names (e.g. 'red')
bands_to_rename = {
a: b for a, b in bandnames_dict.items() if a in ds.variables
}
elif collection == 'ga_s2_3':
# Dictionary mapping full data names to simpler 'red' alias names
bandnames_dict = {
'nbart_red': 'red',
'nbart_green': 'green',
'nbart_blue': 'blue',
'nbart_nir_1': 'nir',
'nbart_red_edge_1': 'red_edge_1',
'nbart_red_edge_2': 'red_edge_2',
'nbart_swir_2': 'swir1',
'nbart_swir_3': 'swir2',
'nbar_red': 'red',
'nbar_green': 'green',
'nbar_blue': 'blue',
'nbar_nir_1': 'nir',
'nbar_red_edge_1': 'red_edge_1',
'nbar_red_edge_2': 'red_edge_2',
'nbar_swir_2': 'swir1',
'nbar_swir_3': 'swir2'
}
# Rename bands in dataset to use simple names (e.g. 'red')
bands_to_rename = {
a: b for a, b in bandnames_dict.items() if a in ds.variables
}
elif collection == 'ga_gm_3':
# Pass an empty dict as no bands need renaming
bands_to_rename = {}
# Raise error if no valid collection name is provided:
else:
raise ValueError(f"'{collection}' is not a valid option for "
"`collection`. Please specify either \n"
"'ga_ls_3', 'ga_s2_3' or 'ga_gm_3'")
# Apply index function
try:
# If normalised=True, divide data by 10,000 before applying func
mult = 10000.0 if normalise else 1.0
index_array = index_func(ds.rename(bands_to_rename) / mult)
except AttributeError:
raise ValueError(f'Please verify that all bands required to '
f'compute {index} are present in `ds`. \n'
f'These bands may vary depending on the `collection` '
f'(e.g. the Landsat `nbart_nir` band \n'
f'is equivelent to `nbart_nir_1` for Sentinel 2)')
# Add as a new variable in dataset
output_band_name = custom_varname if custom_varname else index
ds[output_band_name] = index_array
# Once all indexes are calculated, drop input bands if inplace=False
if drop and not inplace:
ds = ds.drop(bands_to_drop)
# If inplace == True, delete bands in-place instead of using drop
if drop and inplace:
for band_to_drop in bands_to_drop:
del ds[band_to_drop]
# Return input dataset with added water index variable
return ds
