diff --git a/contrib/visveg/vegind.py b/contrib/visveg/vegind.py new file mode 100644 index 00000000..9abb58dc --- /dev/null +++ b/contrib/visveg/vegind.py @@ -0,0 +1,93 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- +import rasterio, os, sys +import numpy as np + +class bcolors: + OKBLUE = '\033[94m' + OKGREEN = '\033[92m' + WARNING = '\033[93m' + FAIL = '\033[91m' + ENDC = '\033[0m' + BOLD = '\033[1m' + UNDERLINE = '\033[4m' + +try: + file = sys.argv[1] + typ = sys.argv[2] + (fileRoot, fileExt) = os.path.splitext(file) + outFileName = fileRoot + "_" + typ + fileExt +except (TypeError, IndexError, NameError): + print bcolors.FAIL + 'Arguments messed up. Check arguments order and index name' + bcolors.ENDC + print 'Usage: ./vegind.py orto index' + print ' orto - filepath to RGB orthophoto' + print ' index - Vegetation Index' + print bcolors.OKGREEN + 'Available indexes: vari, ngrdi, tgi' + bcolors.ENDC + sys.exit() + + +def calcNgrdi(red, green): + """ + Normalized green red difference index + Tucker,C.J.,1979. + Red and photographic infrared linear combinations for monitoring vegetation. + Remote Sensing of Environment 8, 127–150 + :param red: red visible channel + :param green: green visible channel + :return: ngrdi index array + """ + mask = np.not_equal(np.add(red,green), 0.0) + return np.choose(mask, (-9999.0, np.true_divide( + np.subtract(green,red), + np.add(red,green)))) + +def calcVari(red,green,blue): + """ + Calculates Visible Atmospheric Resistant Index + Gitelson, A.A., Kaufman, Y.J., Stark, R., Rundquist, D., 2002. + Novel algorithms for remote estimation of vegetation fraction. + Remote Sensing of Environment 80, 76–87. + :param red: red visible channel + :param green: green visible channel + :param blue: blue visible channel + :return: vari index array, that will be saved to tiff + """ + mask = np.not_equal(np.subtract(np.add(green,red),blue), 0.0) + return np.choose(mask, (-9999.0, np.true_divide(np.subtract(green,red),np.subtract(np.add(green,red),blue)))) + +def calcTgi(red,green,blue): + """ + Calculates Triangular Greenness Index + Hunt, E. Raymond Jr.; Doraiswamy, Paul C.; McMurtrey, James E.; Daughtry, Craig S.T.; Perry, Eileen M.; and Akhmedov, Bakhyt, + A visible band index for remote sensing leaf chlorophyll content at the canopy scale (2013). + Publications from USDA-ARS / UNL Faculty. Paper 1156. + http://digitalcommons.unl.edu/usdaarsfacpub/1156 + :param red: red channel + :param green: green channel + :param blue: blue channel + :return: tgi index array, that will be saved to tiff + """ + mask = np.not_equal(green-red+blue-255.0, 0.0) + return np.choose(mask, (-9999.0, np.subtract(green, np.multiply(0.39,red), np.multiply(0.61, blue)))) + +try: + with rasterio.Env(): + ds = rasterio.open(file) + profile = ds.profile + profile.update(dtype=rasterio.float32, count=1, nodata=-9999) + red = np.float32(ds.read(1)) + green = np.float32(ds.read(2)) + blue = np.float32(ds.read(3)) + np.seterr(divide='ignore', invalid='ignore') + if typ == 'ngrdi': + indeks = calcNgrdi(red,green) + elif typ == 'vari': + indeks = calcVari(red, green, blue) + elif typ == 'tgi': + indeks = calcTgi(red, green, blue) + + with rasterio.open(outFileName, 'w', **profile) as dst: + dst.write(indeks.astype(rasterio.float32), 1) +except rasterio.errors.RasterioIOError: + print bcolors.FAIL + 'Orthophoto file not found or access denied' + bcolors.ENDC + sys.exit()