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577 lines
19 KiB
Python
577 lines
19 KiB
Python
# Author: João Gustavo A. Amorim
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# Author email: joaogustavoamorim@gmail.com
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# Coding date: jan 2019
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# python/black: True
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# Imports
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import numpy as np
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# Class implemented to calculus the index
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class IndexCalculation:
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"""
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# Class Summary
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This algorithm consists in calculating vegetation indices, these
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indices can be used for precision agriculture for example (or remote
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sensing). There are functions to define the data and to calculate the
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implemented indices.
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# Vegetation index
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https://en.wikipedia.org/wiki/Vegetation_Index
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A Vegetation Index (VI) is a spectral transformation of two or more bands
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designed to enhance the contribution of vegetation properties and allow
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reliable spatial and temporal inter-comparisons of terrestrial
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photosynthetic activity and canopy structural variations
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# Information about channels (Wavelength range for each)
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* nir - near-infrared
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https://www.malvernpanalytical.com/br/products/technology/near-infrared-spectroscopy
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Wavelength Range 700 nm to 2500 nm
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* Red Edge
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https://en.wikipedia.org/wiki/Red_edge
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Wavelength Range 680 nm to 730 nm
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* red
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https://en.wikipedia.org/wiki/Color
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Wavelength Range 635 nm to 700 nm
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* blue
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https://en.wikipedia.org/wiki/Color
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Wavelength Range 450 nm to 490 nm
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* green
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https://en.wikipedia.org/wiki/Color
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Wavelength Range 520 nm to 560 nm
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# Implemented index list
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#"abbreviationOfIndexName" -- list of channels used
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#"ARVI2" -- red, nir
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#"CCCI" -- red, redEdge, nir
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#"CVI" -- red, green, nir
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#"GLI" -- red, green, blue
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#"NDVI" -- red, nir
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#"BNDVI" -- blue, nir
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#"redEdgeNDVI" -- red, redEdge
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#"GNDVI" -- green, nir
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#"GBNDVI" -- green, blue, nir
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#"GRNDVI" -- red, green, nir
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#"RBNDVI" -- red, blue, nir
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#"PNDVI" -- red, green, blue, nir
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#"ATSAVI" -- red, nir
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#"BWDRVI" -- blue, nir
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#"CIgreen" -- green, nir
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#"CIrededge" -- redEdge, nir
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#"CI" -- red, blue
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#"CTVI" -- red, nir
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#"GDVI" -- green, nir
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#"EVI" -- red, blue, nir
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#"GEMI" -- red, nir
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#"GOSAVI" -- green, nir
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#"GSAVI" -- green, nir
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#"Hue" -- red, green, blue
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#"IVI" -- red, nir
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#"IPVI" -- red, nir
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#"I" -- red, green, blue
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#"RVI" -- red, nir
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#"MRVI" -- red, nir
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#"MSAVI" -- red, nir
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#"NormG" -- red, green, nir
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#"NormNIR" -- red, green, nir
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#"NormR" -- red, green, nir
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#"NGRDI" -- red, green
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#"RI" -- red, green
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#"S" -- red, green, blue
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#"IF" -- red, green, blue
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#"DVI" -- red, nir
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#"TVI" -- red, nir
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#"NDRE" -- redEdge, nir
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#list of all index implemented
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#allIndex = ["ARVI2", "CCCI", "CVI", "GLI", "NDVI", "BNDVI", "redEdgeNDVI",
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"GNDVI", "GBNDVI", "GRNDVI", "RBNDVI", "PNDVI", "ATSAVI",
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"BWDRVI", "CIgreen", "CIrededge", "CI", "CTVI", "GDVI", "EVI",
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"GEMI", "GOSAVI", "GSAVI", "Hue", "IVI", "IPVI", "I", "RVI",
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"MRVI", "MSAVI", "NormG", "NormNIR", "NormR", "NGRDI", "RI",
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"S", "IF", "DVI", "TVI", "NDRE"]
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#list of index with not blue channel
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#notBlueIndex = ["ARVI2", "CCCI", "CVI", "NDVI", "redEdgeNDVI", "GNDVI",
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"GRNDVI", "ATSAVI", "CIgreen", "CIrededge", "CTVI", "GDVI",
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"GEMI", "GOSAVI", "GSAVI", "IVI", "IPVI", "RVI", "MRVI",
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"MSAVI", "NormG", "NormNIR", "NormR", "NGRDI", "RI", "DVI",
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"TVI", "NDRE"]
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#list of index just with RGB channels
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#RGBIndex = ["GLI", "CI", "Hue", "I", "NGRDI", "RI", "S", "IF"]
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"""
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def __init__(self, red=None, green=None, blue=None, redEdge=None, nir=None):
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# print("Numpy version: " + np.__version__)
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self.setMatrices(red=red, green=green, blue=blue, redEdge=redEdge, nir=nir)
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def setMatrices(self, red=None, green=None, blue=None, redEdge=None, nir=None):
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if red is not None:
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self.red = red
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if green is not None:
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self.green = green
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if blue is not None:
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self.blue = blue
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if redEdge is not None:
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self.redEdge = redEdge
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if nir is not None:
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self.nir = nir
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return True
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def calculation(
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self, index="", red=None, green=None, blue=None, redEdge=None, nir=None
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):
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"""
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performs the calculation of the index with the values instantiated in the class
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:str index: abbreviation of index name to perform
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"""
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self.setMatrices(red=red, green=green, blue=blue, redEdge=redEdge, nir=nir)
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funcs = {
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"ARVI2": self.ARVI2,
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"CCCI": self.CCCI,
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"CVI": self.CVI,
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"GLI": self.GLI,
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"NDVI": self.NDVI,
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"BNDVI": self.BNDVI,
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"redEdgeNDVI": self.redEdgeNDVI,
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"GNDVI": self.GNDVI,
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"GBNDVI": self.GBNDVI,
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"GRNDVI": self.GRNDVI,
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"RBNDVI": self.RBNDVI,
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"PNDVI": self.PNDVI,
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"ATSAVI": self.ATSAVI,
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"BWDRVI": self.BWDRVI,
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"CIgreen": self.CIgreen,
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"CIrededge": self.CIrededge,
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"CI": self.CI,
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"CTVI": self.CTVI,
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"GDVI": self.GDVI,
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"EVI": self.EVI,
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"GEMI": self.GEMI,
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"GOSAVI": self.GOSAVI,
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"GSAVI": self.GSAVI,
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"Hue": self.Hue,
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"IVI": self.IVI,
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"IPVI": self.IPVI,
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"I": self.I,
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"RVI": self.RVI,
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"MRVI": self.MRVI,
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"MSAVI": self.MSAVI,
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"NormG": self.NormG,
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"NormNIR": self.NormNIR,
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"NormR": self.NormR,
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"NGRDI": self.NGRDI,
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"RI": self.RI,
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"S": self.S,
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"IF": self.IF,
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"DVI": self.DVI,
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"TVI": self.TVI,
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"NDRE": self.NDRE,
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}
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try:
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return funcs[index]()
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except KeyError:
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print("Index not in the list!")
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return False
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def ARVI2(self):
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"""
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Atmospherically Resistant Vegetation Index 2
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https://www.indexdatabase.de/db/i-single.php?id=396
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:return: index
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−0.18+1.17*(self.nir−self.red)/(self.nir+self.red)
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"""
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return -0.18 + (1.17 * ((self.nir - self.red) / (self.nir + self.red)))
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def CCCI(self):
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"""
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Canopy Chlorophyll Content Index
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https://www.indexdatabase.de/db/i-single.php?id=224
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:return: index
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"""
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return ((self.nir - self.redEdge) / (self.nir + self.redEdge)) / (
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(self.nir - self.red) / (self.nir + self.red)
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)
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def CVI(self):
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"""
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Chlorophyll vegetation index
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https://www.indexdatabase.de/db/i-single.php?id=391
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:return: index
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"""
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return self.nir * (self.red / (self.green**2))
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def GLI(self):
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"""
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self.green leaf index
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https://www.indexdatabase.de/db/i-single.php?id=375
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:return: index
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"""
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return (2 * self.green - self.red - self.blue) / (
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2 * self.green + self.red + self.blue
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)
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def NDVI(self):
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"""
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Normalized Difference self.nir/self.red Normalized Difference Vegetation
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Index, Calibrated NDVI - CDVI
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https://www.indexdatabase.de/db/i-single.php?id=58
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:return: index
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"""
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return (self.nir - self.red) / (self.nir + self.red)
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def BNDVI(self):
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"""
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Normalized Difference self.nir/self.blue self.blue-normalized difference
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vegetation index
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https://www.indexdatabase.de/db/i-single.php?id=135
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:return: index
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"""
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return (self.nir - self.blue) / (self.nir + self.blue)
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def redEdgeNDVI(self):
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"""
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Normalized Difference self.rededge/self.red
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https://www.indexdatabase.de/db/i-single.php?id=235
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:return: index
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"""
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return (self.redEdge - self.red) / (self.redEdge + self.red)
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def GNDVI(self):
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"""
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Normalized Difference self.nir/self.green self.green NDVI
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https://www.indexdatabase.de/db/i-single.php?id=401
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:return: index
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"""
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return (self.nir - self.green) / (self.nir + self.green)
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def GBNDVI(self):
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"""
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self.green-self.blue NDVI
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https://www.indexdatabase.de/db/i-single.php?id=186
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:return: index
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"""
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return (self.nir - (self.green + self.blue)) / (
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self.nir + (self.green + self.blue)
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)
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def GRNDVI(self):
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"""
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self.green-self.red NDVI
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https://www.indexdatabase.de/db/i-single.php?id=185
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:return: index
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"""
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return (self.nir - (self.green + self.red)) / (
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self.nir + (self.green + self.red)
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)
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def RBNDVI(self):
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"""
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self.red-self.blue NDVI
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https://www.indexdatabase.de/db/i-single.php?id=187
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:return: index
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"""
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return (self.nir - (self.blue + self.red)) / (self.nir + (self.blue + self.red))
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def PNDVI(self):
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"""
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Pan NDVI
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https://www.indexdatabase.de/db/i-single.php?id=188
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:return: index
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"""
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return (self.nir - (self.green + self.red + self.blue)) / (
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self.nir + (self.green + self.red + self.blue)
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)
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def ATSAVI(self, X=0.08, a=1.22, b=0.03):
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"""
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Adjusted transformed soil-adjusted VI
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https://www.indexdatabase.de/db/i-single.php?id=209
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:return: index
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"""
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return a * (
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(self.nir - a * self.red - b)
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/ (a * self.nir + self.red - a * b + X * (1 + a**2))
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)
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def BWDRVI(self):
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"""
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self.blue-wide dynamic range vegetation index
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https://www.indexdatabase.de/db/i-single.php?id=136
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:return: index
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"""
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return (0.1 * self.nir - self.blue) / (0.1 * self.nir + self.blue)
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def CIgreen(self):
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"""
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Chlorophyll Index self.green
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https://www.indexdatabase.de/db/i-single.php?id=128
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:return: index
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"""
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return (self.nir / self.green) - 1
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def CIrededge(self):
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"""
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Chlorophyll Index self.redEdge
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https://www.indexdatabase.de/db/i-single.php?id=131
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:return: index
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"""
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return (self.nir / self.redEdge) - 1
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def CI(self):
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"""
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Coloration Index
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https://www.indexdatabase.de/db/i-single.php?id=11
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:return: index
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"""
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return (self.red - self.blue) / self.red
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def CTVI(self):
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"""
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Corrected Transformed Vegetation Index
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https://www.indexdatabase.de/db/i-single.php?id=244
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:return: index
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"""
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ndvi = self.NDVI()
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return ((ndvi + 0.5) / (abs(ndvi + 0.5))) * (abs(ndvi + 0.5) ** (1 / 2))
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def GDVI(self):
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"""
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Difference self.nir/self.green self.green Difference Vegetation Index
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https://www.indexdatabase.de/db/i-single.php?id=27
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:return: index
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"""
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return self.nir - self.green
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def EVI(self):
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"""
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Enhanced Vegetation Index
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https://www.indexdatabase.de/db/i-single.php?id=16
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:return: index
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"""
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return 2.5 * (
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(self.nir - self.red) / (self.nir + 6 * self.red - 7.5 * self.blue + 1)
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)
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def GEMI(self):
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"""
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Global Environment Monitoring Index
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https://www.indexdatabase.de/db/i-single.php?id=25
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:return: index
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"""
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n = (2 * (self.nir**2 - self.red**2) + 1.5 * self.nir + 0.5 * self.red) / (
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self.nir + self.red + 0.5
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)
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return n * (1 - 0.25 * n) - (self.red - 0.125) / (1 - self.red)
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def GOSAVI(self, Y=0.16):
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"""
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self.green Optimized Soil Adjusted Vegetation Index
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https://www.indexdatabase.de/db/i-single.php?id=29
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mit Y = 0,16
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:return: index
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"""
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return (self.nir - self.green) / (self.nir + self.green + Y)
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def GSAVI(self, L=0.5):
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"""
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self.green Soil Adjusted Vegetation Index
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https://www.indexdatabase.de/db/i-single.php?id=31
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mit L = 0,5
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:return: index
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"""
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return ((self.nir - self.green) / (self.nir + self.green + L)) * (1 + L)
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def Hue(self):
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"""
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Hue
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https://www.indexdatabase.de/db/i-single.php?id=34
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:return: index
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"""
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return np.arctan(
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((2 * self.red - self.green - self.blue) / 30.5) * (self.green - self.blue)
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)
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def IVI(self, a=None, b=None):
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"""
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Ideal vegetation index
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https://www.indexdatabase.de/db/i-single.php?id=276
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b=intercept of vegetation line
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a=soil line slope
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:return: index
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"""
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return (self.nir - b) / (a * self.red)
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def IPVI(self):
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"""
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Infraself.red percentage vegetation index
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https://www.indexdatabase.de/db/i-single.php?id=35
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:return: index
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"""
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return (self.nir / ((self.nir + self.red) / 2)) * (self.NDVI() + 1)
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def I(self): # noqa: E741,E743
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"""
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Intensity
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https://www.indexdatabase.de/db/i-single.php?id=36
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:return: index
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"""
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return (self.red + self.green + self.blue) / 30.5
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def RVI(self):
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"""
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Ratio-Vegetation-Index
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http://www.seos-project.eu/modules/remotesensing/remotesensing-c03-s01-p01.html
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:return: index
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"""
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return self.nir / self.red
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def MRVI(self):
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"""
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Modified Normalized Difference Vegetation Index RVI
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https://www.indexdatabase.de/db/i-single.php?id=275
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:return: index
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"""
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return (self.RVI() - 1) / (self.RVI() + 1)
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def MSAVI(self):
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"""
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Modified Soil Adjusted Vegetation Index
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https://www.indexdatabase.de/db/i-single.php?id=44
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:return: index
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"""
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return (
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(2 * self.nir + 1)
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- ((2 * self.nir + 1) ** 2 - 8 * (self.nir - self.red)) ** (1 / 2)
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) / 2
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def NormG(self):
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"""
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Norm G
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https://www.indexdatabase.de/db/i-single.php?id=50
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:return: index
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"""
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return self.green / (self.nir + self.red + self.green)
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def NormNIR(self):
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"""
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Norm self.nir
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https://www.indexdatabase.de/db/i-single.php?id=51
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:return: index
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"""
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return self.nir / (self.nir + self.red + self.green)
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def NormR(self):
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"""
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Norm R
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https://www.indexdatabase.de/db/i-single.php?id=52
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:return: index
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"""
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return self.red / (self.nir + self.red + self.green)
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def NGRDI(self):
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"""
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Normalized Difference self.green/self.red Normalized self.green self.red
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difference index, Visible Atmospherically Resistant Indices self.green
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(VIself.green)
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https://www.indexdatabase.de/db/i-single.php?id=390
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:return: index
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"""
|
||
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 = np.max([np.max(self.red), np.max(self.green), np.max(self.blue)])
|
||
min = np.min([np.min(self.red), np.min(self.green), np.min(self.blue)])
|
||
return (max - min) / max
|
||
|
||
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)
|
||
"""
|