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digital_image_processing/index_calculation.py
575 строк
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Maxim Smolskiy
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22 апр 2024, 22:51
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22 апр 2024, 22:51
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# 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): 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): """ 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) """