index_calculation.py

# Author: João Gustavo A. Amorim
# Author email: joaogustavoamorim@gmail.com
# Coding date:  jan 2019
# python/black: True

# Imports
import numpy as np


# Class implemented to calculus the index
class IndexCalculation:
    """
    # Class Summary
            This algorithm consists in calculating vegetation indices, these
        indices can be used for precision agriculture for example (or remote
        sensing). There are functions to define the data and to calculate the
        implemented indices.

    # Vegetation index
        https://en.wikipedia.org/wiki/Vegetation_Index
        A Vegetation Index (VI) is a spectral transformation of two or more bands
        designed to enhance the contribution of vegetation properties and allow
        reliable spatial and temporal inter-comparisons of terrestrial
        photosynthetic activity and canopy structural variations

    # Information about channels (Wavelength range for each)
        * nir - near-infrared
            https://www.malvernpanalytical.com/br/products/technology/near-infrared-spectroscopy
            Wavelength Range 700 nm to 2500 nm
        * Red Edge
            https://en.wikipedia.org/wiki/Red_edge
            Wavelength Range 680 nm to 730 nm
        * red
            https://en.wikipedia.org/wiki/Color
            Wavelength Range 635 nm to 700 nm
        * blue
            https://en.wikipedia.org/wiki/Color
            Wavelength Range 450 nm to 490 nm
        * green
            https://en.wikipedia.org/wiki/Color
            Wavelength Range 520 nm to 560 nm


    # Implemented index list
            #"abbreviationOfIndexName" -- list of channels used

            #"ARVI2"            --  red, nir
            #"CCCI"             --  red, redEdge, nir
            #"CVI"              --  red, green, nir
            #"GLI"              --  red, green, blue
            #"NDVI"             --  red, nir
            #"BNDVI"            --  blue, nir
            #"redEdgeNDVI"      --  red, redEdge
            #"GNDVI"            --  green, nir
            #"GBNDVI"           --  green, blue, nir
            #"GRNDVI"           --  red, green, nir
            #"RBNDVI"           --  red, blue, nir
            #"PNDVI"            --  red, green, blue, nir
            #"ATSAVI"           --  red, nir
            #"BWDRVI"           --  blue, nir
            #"CIgreen"          --  green, nir
            #"CIrededge"        --  redEdge, nir
            #"CI"               --  red, blue
            #"CTVI"             --  red, nir
            #"GDVI"             --  green, nir
            #"EVI"              --  red, blue, nir
            #"GEMI"             --  red, nir
            #"GOSAVI"           --  green, nir
            #"GSAVI"            --  green, nir
            #"Hue"              --  red, green, blue
            #"IVI"              --  red, nir
            #"IPVI"             --  red, nir
            #"I"                --  red, green, blue
            #"RVI"              --  red, nir
            #"MRVI"             --  red, nir
            #"MSAVI"            --  red, nir
            #"NormG"            --  red, green, nir
            #"NormNIR"          --  red, green, nir
            #"NormR"            --  red, green, nir
            #"NGRDI"            --  red, green
            #"RI"               --  red, green
            #"S"                --  red, green, blue
            #"IF"               --  red, green, blue
            #"DVI"              --  red, nir
            #"TVI"              --  red, nir
            #"NDRE"               --  redEdge, nir

    #list of all index implemented
        #allIndex = ["ARVI2", "CCCI", "CVI", "GLI", "NDVI", "BNDVI", "redEdgeNDVI",
                    "GNDVI", "GBNDVI", "GRNDVI", "RBNDVI", "PNDVI", "ATSAVI",
                    "BWDRVI", "CIgreen", "CIrededge", "CI", "CTVI", "GDVI", "EVI",
                    "GEMI", "GOSAVI", "GSAVI", "Hue", "IVI", "IPVI", "I", "RVI",
                    "MRVI", "MSAVI", "NormG", "NormNIR", "NormR", "NGRDI", "RI",
                    "S", "IF", "DVI", "TVI", "NDRE"]

    #list of index with not blue channel
        #notBlueIndex = ["ARVI2", "CCCI", "CVI", "NDVI", "redEdgeNDVI", "GNDVI",
                         "GRNDVI", "ATSAVI", "CIgreen", "CIrededge", "CTVI", "GDVI",
                         "GEMI", "GOSAVI", "GSAVI", "IVI", "IPVI", "RVI", "MRVI",
                         "MSAVI", "NormG", "NormNIR", "NormR", "NGRDI", "RI", "DVI",
                         "TVI", "NDRE"]

    #list of index just with RGB channels
        #RGBIndex = ["GLI", "CI", "Hue", "I", "NGRDI", "RI", "S", "IF"]
    """

    def __init__(self, red=None, green=None, blue=None, red_edge=None, nir=None):
        # print("Numpy version: " + np.__version__)
        self.set_matricies(red=red, green=green, blue=blue, red_edge=red_edge, nir=nir)

    def set_matricies(self, red=None, green=None, blue=None, red_edge=None, nir=None):
        if red is not None:
            self.red = red
        if green is not None:
            self.green = green
        if blue is not None:
            self.blue = blue
        if red_edge is not None:
            self.redEdge = red_edge
        if nir is not None:
            self.nir = nir
        return True

    def calculation(
        self, index="", red=None, green=None, blue=None, red_edge=None, nir=None
    ):
        """
        performs the calculation of the index with the values instantiated in the class
        :str index: abbreviation of index name to perform
        """
        self.set_matricies(red=red, green=green, blue=blue, red_edge=red_edge, nir=nir)
        funcs = {
            "ARVI2": self.arv12,
            "CCCI": self.ccci,
            "CVI": self.cvi,
            "GLI": self.gli,
            "NDVI": self.ndvi,
            "BNDVI": self.bndvi,
            "redEdgeNDVI": self.red_edge_ndvi,
            "GNDVI": self.gndvi,
            "GBNDVI": self.gbndvi,
            "GRNDVI": self.grndvi,
            "RBNDVI": self.rbndvi,
            "PNDVI": self.pndvi,
            "ATSAVI": self.atsavi,
            "BWDRVI": self.bwdrvi,
            "CIgreen": self.ci_green,
            "CIrededge": self.ci_rededge,
            "CI": self.ci,
            "CTVI": self.ctvi,
            "GDVI": self.gdvi,
            "EVI": self.evi,
            "GEMI": self.gemi,
            "GOSAVI": self.gosavi,
            "GSAVI": self.gsavi,
            "Hue": self.hue,
            "IVI": self.ivi,
            "IPVI": self.ipvi,
            "I": self.i,
            "RVI": self.rvi,
            "MRVI": self.mrvi,
            "MSAVI": self.m_savi,
            "NormG": self.norm_g,
            "NormNIR": self.norm_nir,
            "NormR": self.norm_r,
            "NGRDI": self.ngrdi,
            "RI": self.ri,
            "S": self.s,
            "IF": self._if,
            "DVI": self.dvi,
            "TVI": self.tvi,
            "NDRE": self.ndre,
        }

        try:
            return funcs[index]()
        except KeyError:
            print("Index not in the list!")
            return False

    def arv12(self):
        """
        Atmospherically Resistant Vegetation Index 2
        https://www.indexdatabase.de/db/i-single.php?id=396
        :return: index
            −0.18+1.17*(self.nir−self.red)/(self.nir+self.red)
        """
        return -0.18 + (1.17 * ((self.nir - self.red) / (self.nir + self.red)))

    def ccci(self):
        """
        Canopy Chlorophyll Content Index
        https://www.indexdatabase.de/db/i-single.php?id=224
        :return: index
        """
        return ((self.nir - self.redEdge) / (self.nir + self.redEdge)) / (
            (self.nir - self.red) / (self.nir + self.red)
        )

    def cvi(self):
        """
        Chlorophyll vegetation index
        https://www.indexdatabase.de/db/i-single.php?id=391
        :return: index
        """
        return self.nir * (self.red / (self.green**2))

    def gli(self):
        """
        self.green leaf index
        https://www.indexdatabase.de/db/i-single.php?id=375
        :return: index
        """
        return (2 * self.green - self.red - self.blue) / (
            2 * self.green + self.red + self.blue
        )

    def ndvi(self):
        """
        Normalized Difference self.nir/self.red Normalized Difference Vegetation
        Index, Calibrated NDVI - CDVI
        https://www.indexdatabase.de/db/i-single.php?id=58
        :return: index
        """
        return (self.nir - self.red) / (self.nir + self.red)

    def bndvi(self):
        """
            Normalized Difference self.nir/self.blue self.blue-normalized difference
        vegetation index
        https://www.indexdatabase.de/db/i-single.php?id=135
        :return: index
        """
        return (self.nir - self.blue) / (self.nir + self.blue)

    def red_edge_ndvi(self):
        """
        Normalized Difference self.rededge/self.red
        https://www.indexdatabase.de/db/i-single.php?id=235
        :return: index
        """
        return (self.redEdge - self.red) / (self.redEdge + self.red)

    def gndvi(self):
        """
        Normalized Difference self.nir/self.green self.green NDVI
        https://www.indexdatabase.de/db/i-single.php?id=401
        :return: index
        """
        return (self.nir - self.green) / (self.nir + self.green)

    def gbndvi(self):
        """
        self.green-self.blue NDVI
        https://www.indexdatabase.de/db/i-single.php?id=186
        :return: index
        """
        return (self.nir - (self.green + self.blue)) / (
            self.nir + (self.green + self.blue)
        )

    def grndvi(self):
        """
        self.green-self.red NDVI
        https://www.indexdatabase.de/db/i-single.php?id=185
        :return: index
        """
        return (self.nir - (self.green + self.red)) / (
            self.nir + (self.green + self.red)
        )

    def rbndvi(self):
        """
        self.red-self.blue NDVI
        https://www.indexdatabase.de/db/i-single.php?id=187
        :return: index
        """
        return (self.nir - (self.blue + self.red)) / (self.nir + (self.blue + self.red))

    def pndvi(self):
        """
        Pan NDVI
        https://www.indexdatabase.de/db/i-single.php?id=188
        :return: index
        """
        return (self.nir - (self.green + self.red + self.blue)) / (
            self.nir + (self.green + self.red + self.blue)
        )

    def atsavi(self, x=0.08, a=1.22, b=0.03):
        """
        Adjusted transformed soil-adjusted VI
        https://www.indexdatabase.de/db/i-single.php?id=209
        :return: index
        """
        return a * (
            (self.nir - a * self.red - b)
            / (a * self.nir + self.red - a * b + x * (1 + a**2))
        )

    def bwdrvi(self):
        """
        self.blue-wide dynamic range vegetation index
        https://www.indexdatabase.de/db/i-single.php?id=136
        :return: index
        """
        return (0.1 * self.nir - self.blue) / (0.1 * self.nir + self.blue)

    def ci_green(self):
        """
        Chlorophyll Index self.green
        https://www.indexdatabase.de/db/i-single.php?id=128
        :return: index
        """
        return (self.nir / self.green) - 1

    def ci_rededge(self):
        """
        Chlorophyll Index self.redEdge
        https://www.indexdatabase.de/db/i-single.php?id=131
        :return: index
        """
        return (self.nir / self.redEdge) - 1

    def ci(self):
        """
        Coloration Index
        https://www.indexdatabase.de/db/i-single.php?id=11
        :return: index
        """
        return (self.red - self.blue) / self.red

    def ctvi(self):
        """
        Corrected Transformed Vegetation Index
        https://www.indexdatabase.de/db/i-single.php?id=244
        :return: index
        """
        ndvi = self.ndvi()
        return ((ndvi + 0.5) / (abs(ndvi + 0.5))) * (abs(ndvi + 0.5) ** (1 / 2))

    def gdvi(self):
        """
        Difference self.nir/self.green self.green Difference Vegetation Index
        https://www.indexdatabase.de/db/i-single.php?id=27
        :return: index
        """
        return self.nir - self.green

    def evi(self):
        """
        Enhanced Vegetation Index
        https://www.indexdatabase.de/db/i-single.php?id=16
        :return: index
        """
        return 2.5 * (
            (self.nir - self.red) / (self.nir + 6 * self.red - 7.5 * self.blue + 1)
        )

    def gemi(self):
        """
        Global Environment Monitoring Index
        https://www.indexdatabase.de/db/i-single.php?id=25
        :return: index
        """
        n = (2 * (self.nir**2 - self.red**2) + 1.5 * self.nir + 0.5 * self.red) / (
            self.nir + self.red + 0.5
        )
        return n * (1 - 0.25 * n) - (self.red - 0.125) / (1 - self.red)

    def gosavi(self, y=0.16):
        """
        self.green Optimized Soil Adjusted Vegetation Index
        https://www.indexdatabase.de/db/i-single.php?id=29
        mit Y = 0,16
        :return: index
        """
        return (self.nir - self.green) / (self.nir + self.green + y)

    def gsavi(self, n=0.5):
        """
        self.green Soil Adjusted Vegetation Index
        https://www.indexdatabase.de/db/i-single.php?id=31
        mit N = 0,5
        :return: index
        """
        return ((self.nir - self.green) / (self.nir + self.green + n)) * (1 + n)

    def hue(self):
        """
        Hue
        https://www.indexdatabase.de/db/i-single.php?id=34
        :return: index
        """
        return np.arctan(
            ((2 * self.red - self.green - self.blue) / 30.5) * (self.green - self.blue)
        )

    def ivi(self, a=None, b=None):
        """
        Ideal vegetation index
        https://www.indexdatabase.de/db/i-single.php?id=276
        b=intercept of vegetation line
        a=soil line slope
        :return: index
        """
        return (self.nir - b) / (a * self.red)

    def ipvi(self):
        """
        Infraself.red percentage vegetation index
        https://www.indexdatabase.de/db/i-single.php?id=35
        :return: index
        """
        return (self.nir / ((self.nir + self.red) / 2)) * (self.ndvi() + 1)

    def i(self):  # noqa: E741,E743
        """
        Intensity
        https://www.indexdatabase.de/db/i-single.php?id=36
        :return: index
        """
        return (self.red + self.green + self.blue) / 30.5

    def rvi(self):
        """
        Ratio-Vegetation-Index
        http://www.seos-project.eu/modules/remotesensing/remotesensing-c03-s01-p01.html
        :return: index
        """
        return self.nir / self.red

    def mrvi(self):
        """
        Modified Normalized Difference Vegetation Index RVI
        https://www.indexdatabase.de/db/i-single.php?id=275
        :return: index
        """
        return (self.rvi() - 1) / (self.rvi() + 1)

    def m_savi(self):
        """
        Modified Soil Adjusted Vegetation Index
        https://www.indexdatabase.de/db/i-single.php?id=44
        :return: index
        """
        return (
            (2 * self.nir + 1)
            - ((2 * self.nir + 1) ** 2 - 8 * (self.nir - self.red)) ** (1 / 2)
        ) / 2

    def norm_g(self):
        """
        Norm G
        https://www.indexdatabase.de/db/i-single.php?id=50
        :return: index
        """
        return self.green / (self.nir + self.red + self.green)

    def norm_nir(self):
        """
        Norm self.nir
        https://www.indexdatabase.de/db/i-single.php?id=51
        :return: index
        """
        return self.nir / (self.nir + self.red + self.green)

    def norm_r(self):
        """
        Norm R
        https://www.indexdatabase.de/db/i-single.php?id=52
        :return: index
        """
        return self.red / (self.nir + self.red + self.green)

    def ngrdi(self):
        """
            Normalized Difference self.green/self.red Normalized self.green self.red
        difference index, Visible Atmospherically Resistant Indices self.green
        (VIself.green)
        https://www.indexdatabase.de/db/i-single.php?id=390
        :return: index
        """
        return (self.green - self.red) / (self.green + self.red)

    def ri(self):
        """
        Normalized Difference self.red/self.green self.redness Index
        https://www.indexdatabase.de/db/i-single.php?id=74
        :return: index
        """
        return (self.red - self.green) / (self.red + self.green)

    def s(self):
        """
        Saturation
        https://www.indexdatabase.de/db/i-single.php?id=77
        :return: index
        """
        max_value = np.max([np.max(self.red), np.max(self.green), np.max(self.blue)])
        min_value = np.min([np.min(self.red), np.min(self.green), np.min(self.blue)])
        return (max_value - min_value) / max_value

    def _if(self):
        """
        Shape Index
        https://www.indexdatabase.de/db/i-single.php?id=79
        :return: index
        """
        return (2 * self.red - self.green - self.blue) / (self.green - self.blue)

    def dvi(self):
        """
        Simple Ratio self.nir/self.red Difference Vegetation Index, Vegetation Index
        Number (VIN)
        https://www.indexdatabase.de/db/i-single.php?id=12
        :return: index
        """
        return self.nir / self.red

    def tvi(self):
        """
        Transformed Vegetation Index
        https://www.indexdatabase.de/db/i-single.php?id=98
        :return: index
        """
        return (self.ndvi() + 0.5) ** (1 / 2)

    def ndre(self):
        return (self.nir - self.redEdge) / (self.nir + self.redEdge)


"""
# genering a random matrices to test this class
red     = np.ones((1000,1000, 1),dtype="float64") * 46787
green   = np.ones((1000,1000, 1),dtype="float64") * 23487
blue    = np.ones((1000,1000, 1),dtype="float64") * 14578
redEdge = np.ones((1000,1000, 1),dtype="float64") * 51045
nir     = np.ones((1000,1000, 1),dtype="float64") * 52200

# Examples of how to use the class

# instantiating the class
cl = IndexCalculation()

# instantiating the class with the values
#cl = indexCalculation(red=red, green=green, blue=blue, redEdge=redEdge, nir=nir)

# how set the values after instantiate the class cl, (for update the data or when don't
# instantiating the class with the values)
cl.setMatrices(red=red, green=green, blue=blue, redEdge=redEdge, nir=nir)

# calculating the indices for the instantiated values in the class
    # Note: the CCCI index can be changed to any index implemented in the class.
indexValue_form1    = cl.calculation("CCCI", red=red, green=green, blue=blue,
                                     redEdge=redEdge, nir=nir).astype(np.float64)
indexValue_form2    = cl.CCCI()

# calculating the index with the values directly -- you can set just the values
# preferred  note: the *calculation* function performs the function *setMatrices*
indexValue_form3    = cl.calculation("CCCI", red=red, green=green, blue=blue,
                                     redEdge=redEdge, nir=nir).astype(np.float64)

print("Form 1: "+np.array2string(indexValue_form1, precision=20, separator=', ',
      floatmode='maxprec_equal'))
print("Form 2: "+np.array2string(indexValue_form2, precision=20, separator=', ',
      floatmode='maxprec_equal'))
print("Form 3: "+np.array2string(indexValue_form3, precision=20, separator=', ',
      floatmode='maxprec_equal'))

# A list of examples results for different type of data at NDVI
# float16 ->    0.31567383              #NDVI (red = 50, nir = 100)
# float32 ->    0.31578946              #NDVI (red = 50, nir = 100)
# float64 ->    0.3157894736842105      #NDVI (red = 50, nir = 100)
# longdouble -> 0.3157894736842105      #NDVI (red = 50, nir = 100)
"""