R/spectralIndices.R
In bleutner/RStoolbox: Remote Sensing Data Analysis
Defines functions
extract_function_string
spectralIndices
Documented in
spectralIndices
#' Spectral Indices
#'
#' Calculate a suite of multispectral indices such as NDVI, SAVI etc. in an efficient way via C++.
#'
#' @param img SpatRaster. Typically remote sensing imagery, which is to be classified.
#' @param blue Character or integer. Blue band.
#' @param green Character or integer. Green band.
#' @param red Character or integer. Red band.
#' @param nir Character or integer. Near-infrared band (700-1100nm).
#' @param redEdge1 Character or integer. Red-edge band (705nm)
#' @param redEdge2 Character or integer. Red-edge band (740nm)
#' @param redEdge3 Character or integer. Red-edge band (783nm)
#' @param swir1 not used
#' @param swir2 Character or integer. Short-wave-infrared band (1400-1800nm).
#' @param swir3 Character or integer. Short-wave-infrared band (2000-2500nm).
#' @param indices Character. One or more spectral indices to calculate (see Details). By default (NULL) all implemented indices given the spectral bands which are provided will be calculated.
#' @param index Character. Alias for \code{indices}.
#' @param maskLayer RasterLayer or SpatRaster containing a mask, e.g. clouds, for which pixels are set to NA. Alternatively a layername or -number can be provided if the mask is part of \code{img}.
#' @param maskValue Integer. Pixel value in \code{maskLayer} which should be masked in output, i.e. will be set to \code{NA} in all calculated indices.
#' @param scaleFactor Numeric. Scale factor for the conversion of scaled reflectances to [0,1] value range (applied as reflectance/scaleFactor) Neccesary for calculating EVI/EVI2 with scaled reflectance values.
#' @param skipRefCheck Logical. When EVI/EVI2 is to be calculated there is a rough heuristic check, whether the data are inside [0,1]+/-0.5 (after applying a potential \code{scaleFactor}).
#' If there are invalid reflectances, e.g. clouds with reflectance > 1 this check will result in a false positive and skip EVI calculation. Use this argument to skip this check in such cases *iff* you are sure the data and scaleFactor are valid.
#' @param coefs List of coefficients (see Details).
#' @param ... further arguments such as filename etc. passed to \link[terra]{writeRaster}
#' @return SpatRaster
#' @template spectralIndices_table
#' @export
#' @examples
#' library(ggplot2)
#' library(terra)
#'
#' ## Calculate NDVI
#' ndvi <- spectralIndices(lsat, red = "B3_dn", nir = "B4_dn", indices = "NDVI")
#' ndvi
#' ggR(ndvi, geom_raster = TRUE) +
#' scale_fill_gradientn(colours = c("black", "white"))
#'
#' \donttest{
#' ## Calculate all possible indices, given the provided bands
#' ## Convert DNs to reflectance (required to calculate EVI and EVI2)
#' mtlFile <- system.file("external/landsat/LT52240631988227CUB02_MTL.txt", package="RStoolbox")
#' lsat_ref <- radCor(lsat, mtlFile, method = "apref")
#'
#' SI <- spectralIndices(lsat_ref, red = "B3_tre", nir = "B4_tre")
#' plot(SI)
#'
#' ## Custom Spectral Index Calculation (beta) (supports only bands right now...)
#' # Get all indices
#' idxdb <- getOption("RStoolbox.idxdb")
#'
#' # Customize the RStoolbox index-database and overwrite the option
#' cdb <- c(idxdb, CUSTOM = list( list(c("Mueller2024", "Super custom index"),
#' function(blue, red) {blue + red})))
#' rsOpts(idxdb = cdb)
#'
#' # Calculate the custom index, (also together with the provided ones)
#' custom_ind <- spectralIndices(lsat, blue = 1, red = 3, nir = 4, indices = c("NDVI", "CUSTOM"))
#' }
spectralIndices <- function(img,
blue=NULL, green=NULL, red=NULL, nir = NULL,
redEdge1 = NULL, redEdge2 = NULL, redEdge3 = NULL,
swir1 = NULL, swir2 =NULL, swir3 = NULL,
scaleFactor = 1, skipRefCheck = FALSE, indices=NULL, index = NULL, maskLayer = NULL, maskValue = 1,
coefs = list(L = 0.5, G = 2.5, L_evi = 1, C1 = 6, C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL),
... ) {
# TODO: soil line estimator
## We will use the following wavlength range definitions (following Schowengerdt 2007, p 10)
# VIS | Visible | 400 - 700 nm
# BLUE |
# GREEN |
# RED |
# redEdge1
# redEdge2
# redEdge3
# NIR | Near infra-red | 700 - 1100 nm
# swir1 | Short-wave infra-red | 1100 - 1351 nm
# swir2 | shortwave infra-red | 1400 - 1800 nm
# swir3 | Shortwave infra-red | 2000 - 2500 nm
# mir1 | midwave infra-red | 3000 - 4000 nm
# mir2 | midwave infra-red | 4500 - 5000 nm
# TIR1 | thermal infra-red | 8000 - 9500 nm
# TIR2 | thermal infra-red | 10000 - 140000 nm
##
img <- .toTerra(img)
if(!is.null(maskLayer)) maskLayer <- .toTerra(maskLayer)
if(!is.null(index)) indices <- index ## argument translation for convenience
if("LSWI" %in% toupper(indices)) stop("LSWI has been deprecated. Use NDWI2 instead; it is identical.")
if(!is.null(swir1)) stop(paste0("Currently there is no spectral index requiring swir1.",
"\nIn case you were using spectralIndices from a previous version of RStoolbox with the swir1 argument,",
"\nplease note that there has been naming correction. Former swir1 is now swir2 and former swir2 is now swir3.",
"\nsee: news(package='RStoolbox')"), call.=FALSE)
## Coefficients
defaultCoefs <- list(L = 0.5, G = 2.5, L_evi = 1, C1 = 6, C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL)
implem <- names(coefs) %in% names(defaultCoefs)
if(any(!implem)) warning("Non-implemented coefficients are ignored: ", paste0(names(coefs)[!implem], collapse=", "),
"\nimplemented coefficients are: ", paste0(names(defaultCoefs), collapse = ", "))
coefs <- c(coefs, defaultCoefs[setdiff(names(defaultCoefs), names(coefs))])
# Update bandsdb
idxdb <- getOption("RStoolbox.idxdb")
BANDSdb <- lapply(lapply(idxdb,"[[", 2), function(x) names(formals(x)))
## Check indices
ind <- if(is.null(indices)) names(BANDSdb) else indices <- toupper(indices)
if((is.null(coefs$swir2ccc) | is.null(coefs$swir2coc))) {
if(!is.null(indices) & ("NDVIC" %in% ind)) warning("NDVIc can only be calculated if swir2ccc and swir2coc coefficients are provided.", call. = FALSE)
coefs$swir2ccc <- 0 ## dummy, cant pass NULL to spectralIndicesCpp
coefs$swir2coc <- 1 ## dummy, cant pass NULL to spectralIndicesCpp
ind <- setdiff(ind, "NDVIC")
}
if(!any(ind %in% names(BANDSdb))) stop("indices must either be NULL to calculate all indices",
"\nor element of c(", paste0(names(BANDSdb),collapse=","),") for specific indices.", call. = FALSE)
coefs$swir2cdiff <- coefs$swir2coc - coefs$swir2ccc
if(coefs$swir2cdiff <= 0) stop("NDVIc coefficient swir2ccc (completeley closed canopy) must be smaller than swir2coc (completely open canopy)", call. = FALSE)
## Gather function arguments (all provided bands) and create args
potArgs <- c("blue", "green", "red", "redEdge1", "redEdge2", "redEdge3", "nir", "swir1", "swir2", "swir3")
actArgs <- vapply(potArgs, function(x) !is.null(get(x)), logical(1))
bands <- potArgs[actArgs]
## Subset calculated indices to possible based on band inputs and / or user request
requested <- BANDSdb[ind]
canCalc <- names(requested)[!vapply(requested, function(x) any(!x %in% bands), logical(1))]
if(!skipRefCheck && any(c("EVI","EVI2") %in% canCalc)){
img[[red]] <- setMinMax(img[[red]])
mm <- minmax(img[[red]])
if(is.nan(mm[2,1]) || is.nan(mm[1,1]) || mm[2,1]/scaleFactor > 1.5 || mm[1,1]/scaleFactor < -0.5){
## checking for range [0,1] +/- .5 to allow for artifacts in reflectance.
warning("EVI/EVI2 parameters L_evi, G, C1 and C2 are defined for reflectance [0,1] but img values are outside of this range.\n",
" If you are using scaled reflectance values please provide the scaleFactor argument.\n",
" If img is in DN or radiance it must be converted to reflectance.\n",
" Skipping EVI calculation.\n", call. = FALSE)
canCalc <- canCalc[!canCalc %in% c("EVI", "EVI2")]
indices <- indices[!indices %in% c("EVI", "EVI2")]
}
}
ind <- ind[ind %in% canCalc]
if(!length(ind)) stop("No index could be calculated. At least for one index you must specify *all* required bands.",
"\n See ?spectralIndices for information on required bands per index.", call. = FALSE)
if(length(ind) < length(indices)){
not <- setdiff(indices,ind)
notbands <- setdiff(unlist(requested[not]), bands)
warning("The following indices were requested but cannot be calculated: ", paste(not, collapse = ", "),
"\n because the following required bands were not specified: ",
paste(notbands, collapse = ", "),
"\n The remaining fully specified indices will be calculated.", call. = FALSE)
}
## Get required designated bands
retrieve <- lapply(bands, get, envir=environment())
bandsCalc <- vapply(retrieve, function(xi) { if(is.character(xi)) match(xi, names(img)) else xi }, numeric(1))
names(bandsCalc) <- bands
## Add mask layer to img if present
if(!is.null(maskLayer)){
if(inherits(maskLayer, "SpatRaster")) {
if(nlyr(maskLayer) > 1) warning(sprintf("maskLayer has %s layers. Only the first layer will be used for masking.", nlyr(maskLayer)),call.=FALSE)
img <- c(img, maskLayer[[1]])
names(img)[nlyr(img)] <- "mask"
} else if (is.numeric(maskLayer)) {
names(img)[maskLayer] <- "mask"
} else if (is.character(maskLayer)) {
if(!maskLayer %in% names(img)) stop(paste0(maskLayer, "is not a layer in img.\nAvailable layers are: ", paste(names(img))), call. =FALSE)
names(img)[names(img) == maskLayer] <- "mask"
} else {
stop("maskLayer must be NULL, a RasterLayer, a layer name or a layer number", call. =FALSE)
}
bandsCalc[["mask"]] <- which(names(img) == "mask")
}
potArgs <- c(potArgs, "mask")
## Adjust layer argument so that the first layer we use is now layer 1, etc.
## This way we don't have to sample the whole stack if we only need a few layers
fullSet <- vapply(potArgs, function(n) match(n, names(bandsCalc)), integer(1))
wopt <- list(...)
filename <- if("filename" %in% names(wopt)) wopt$filename else ""
overwrite <- if("overwrite" %in% names(wopt)) wopt$overwrite else FALSE
wopt[c("filename","overwrite")] <- NULL
# Perform calculations
indexMagic <- terra::app(img[[bandsCalc]], fun = function(m) {
spectralIndicesCpp(
x = m,
indices = canCalc,
blueBand = fullSet[["blue"]],
greenBand = fullSet[["green"]],
redBand = fullSet[["red"]],
redEdge1Band = fullSet[["redEdge1"]],
redEdge2Band = fullSet[["redEdge2"]],
redEdge3Band = fullSet[["redEdge3"]],
nirBand = fullSet[["nir"]],
swir1Band = fullSet[["swir1"]],
swir2Band = fullSet[["swir2"]],
swir3Band = fullSet[["swir3"]],
maskLayer = fullSet[["mask"]],
maskValue = maskValue,
L = coefs[["L"]], G = coefs[["G"]], Levi = coefs[["L_evi"]],
C1 = coefs[["C1"]], C2 = coefs[["C2"]], s = coefs[["s"]],
swir2ccc = coefs[["swir2ccc"]], swir2cdiff = coefs[["swir2cdiff"]], sf = scaleFactor,
formulas = as.vector(unlist(lapply(idxdb[canCalc], FUN = extract_function_string)))
)},
wopt=wopt, filename = filename, overwrite = overwrite)
names(indexMagic) <- canCalc
return(indexMagic)
}
extract_function_string <- function(fn) {
function_body <- body(fn[[2]])
function_string <- deparse(function_body)
function_string <- paste(function_string, collapse = "")
function_string <- gsub("\\s+", "", function_string)
function_string <- gsub("[{}]", "", function_string)
return(function_string)
}
## NOT USED FOR CALCULATIONS ONLY FOR DOCUMENTATION
## SEE /src/spectraIndices.cpp for calculations
#' Database of spectral indices
#' @keywords internal
#' @noRd
.IDXdb <- getOption("RStoolbox.idxdb")
# BANDSdb <- lapply(lapply(.IDXdb,"[[", 2), function(x) names(formals(x)))
.IDXdbFormulae <- lapply(.IDXdb,"[[",2)
.IDX.REFdb <- lapply(.IDXdb,"[[",1)
bleutner/RStoolbox documentation built on Nov. 30, 2024, 9:47 p.m.
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Defines functions extract_function_string spectralIndices
Documented in spectralIndices
#' Spectral Indices
#'
#' Calculate a suite of multispectral indices such as NDVI, SAVI etc. in an efficient way via C++.
#'
#' @param img SpatRaster. Typically remote sensing imagery, which is to be classified.
#' @param blue Character or integer. Blue band.
#' @param green Character or integer. Green band.
#' @param red Character or integer. Red band.
#' @param nir Character or integer. Near-infrared band (700-1100nm).
#' @param redEdge1 Character or integer. Red-edge band (705nm)
#' @param redEdge2 Character or integer. Red-edge band (740nm)
#' @param redEdge3 Character or integer. Red-edge band (783nm)
#' @param swir1 not used
#' @param swir2 Character or integer. Short-wave-infrared band (1400-1800nm).
#' @param swir3 Character or integer. Short-wave-infrared band (2000-2500nm).
#' @param indices Character. One or more spectral indices to calculate (see Details). By default (NULL) all implemented indices given the spectral bands which are provided will be calculated.
#' @param index Character. Alias for \code{indices}.
#' @param maskLayer RasterLayer or SpatRaster containing a mask, e.g. clouds, for which pixels are set to NA. Alternatively a layername or -number can be provided if the mask is part of \code{img}.
#' @param maskValue Integer. Pixel value in \code{maskLayer} which should be masked in output, i.e. will be set to \code{NA} in all calculated indices.
#' @param scaleFactor Numeric. Scale factor for the conversion of scaled reflectances to [0,1] value range (applied as reflectance/scaleFactor) Neccesary for calculating EVI/EVI2 with scaled reflectance values.
#' @param skipRefCheck Logical. When EVI/EVI2 is to be calculated there is a rough heuristic check, whether the data are inside [0,1]+/-0.5 (after applying a potential \code{scaleFactor}).
#' If there are invalid reflectances, e.g. clouds with reflectance > 1 this check will result in a false positive and skip EVI calculation. Use this argument to skip this check in such cases *iff* you are sure the data and scaleFactor are valid.
#' @param coefs List of coefficients (see Details).
#' @param ... further arguments such as filename etc. passed to \link[terra]{writeRaster}
#' @return SpatRaster
#' @template spectralIndices_table
#' @export
#' @examples
#' library(ggplot2)
#' library(terra)
#'
#' ## Calculate NDVI
#' ndvi <- spectralIndices(lsat, red = "B3_dn", nir = "B4_dn", indices = "NDVI")
#' ndvi
#' ggR(ndvi, geom_raster = TRUE) +
#' scale_fill_gradientn(colours = c("black", "white"))
#'
#' \donttest{
#' ## Calculate all possible indices, given the provided bands
#' ## Convert DNs to reflectance (required to calculate EVI and EVI2)
#' mtlFile <- system.file("external/landsat/LT52240631988227CUB02_MTL.txt", package="RStoolbox")
#' lsat_ref <- radCor(lsat, mtlFile, method = "apref")
#'
#' SI <- spectralIndices(lsat_ref, red = "B3_tre", nir = "B4_tre")
#' plot(SI)
#'
#' ## Custom Spectral Index Calculation (beta) (supports only bands right now...)
#' # Get all indices
#' idxdb <- getOption("RStoolbox.idxdb")
#'
#' # Customize the RStoolbox index-database and overwrite the option
#' cdb <- c(idxdb, CUSTOM = list( list(c("Mueller2024", "Super custom index"),
#' function(blue, red) {blue + red})))
#' rsOpts(idxdb = cdb)
#'
#' # Calculate the custom index, (also together with the provided ones)
#' custom_ind <- spectralIndices(lsat, blue = 1, red = 3, nir = 4, indices = c("NDVI", "CUSTOM"))
#' }
spectralIndices <- function(img,
blue=NULL, green=NULL, red=NULL, nir = NULL,
redEdge1 = NULL, redEdge2 = NULL, redEdge3 = NULL,
swir1 = NULL, swir2 =NULL, swir3 = NULL,
scaleFactor = 1, skipRefCheck = FALSE, indices=NULL, index = NULL, maskLayer = NULL, maskValue = 1,
coefs = list(L = 0.5, G = 2.5, L_evi = 1, C1 = 6, C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL),
... ) {
# TODO: soil line estimator
## We will use the following wavlength range definitions (following Schowengerdt 2007, p 10)
# VIS | Visible | 400 - 700 nm
# BLUE |
# GREEN |
# RED |
# redEdge1
# redEdge2
# redEdge3
# NIR | Near infra-red | 700 - 1100 nm
# swir1 | Short-wave infra-red | 1100 - 1351 nm
# swir2 | shortwave infra-red | 1400 - 1800 nm
# swir3 | Shortwave infra-red | 2000 - 2500 nm
# mir1 | midwave infra-red | 3000 - 4000 nm
# mir2 | midwave infra-red | 4500 - 5000 nm
# TIR1 | thermal infra-red | 8000 - 9500 nm
# TIR2 | thermal infra-red | 10000 - 140000 nm
##
img <- .toTerra(img)
if(!is.null(maskLayer)) maskLayer <- .toTerra(maskLayer)
if(!is.null(index)) indices <- index ## argument translation for convenience
if("LSWI" %in% toupper(indices)) stop("LSWI has been deprecated. Use NDWI2 instead; it is identical.")
if(!is.null(swir1)) stop(paste0("Currently there is no spectral index requiring swir1.",
"\nIn case you were using spectralIndices from a previous version of RStoolbox with the swir1 argument,",
"\nplease note that there has been naming correction. Former swir1 is now swir2 and former swir2 is now swir3.",
"\nsee: news(package='RStoolbox')"), call.=FALSE)
## Coefficients
defaultCoefs <- list(L = 0.5, G = 2.5, L_evi = 1, C1 = 6, C2 = 7.5, s = 1, swir2ccc = NULL, swir2coc = NULL)
implem <- names(coefs) %in% names(defaultCoefs)
if(any(!implem)) warning("Non-implemented coefficients are ignored: ", paste0(names(coefs)[!implem], collapse=", "),
"\nimplemented coefficients are: ", paste0(names(defaultCoefs), collapse = ", "))
coefs <- c(coefs, defaultCoefs[setdiff(names(defaultCoefs), names(coefs))])
# Update bandsdb
idxdb <- getOption("RStoolbox.idxdb")
BANDSdb <- lapply(lapply(idxdb,"[[", 2), function(x) names(formals(x)))
## Check indices
ind <- if(is.null(indices)) names(BANDSdb) else indices <- toupper(indices)
if((is.null(coefs$swir2ccc) | is.null(coefs$swir2coc))) {
if(!is.null(indices) & ("NDVIC" %in% ind)) warning("NDVIc can only be calculated if swir2ccc and swir2coc coefficients are provided.", call. = FALSE)
coefs$swir2ccc <- 0 ## dummy, cant pass NULL to spectralIndicesCpp
coefs$swir2coc <- 1 ## dummy, cant pass NULL to spectralIndicesCpp
ind <- setdiff(ind, "NDVIC")
}
if(!any(ind %in% names(BANDSdb))) stop("indices must either be NULL to calculate all indices",
"\nor element of c(", paste0(names(BANDSdb),collapse=","),") for specific indices.", call. = FALSE)
coefs$swir2cdiff <- coefs$swir2coc - coefs$swir2ccc
if(coefs$swir2cdiff <= 0) stop("NDVIc coefficient swir2ccc (completeley closed canopy) must be smaller than swir2coc (completely open canopy)", call. = FALSE)
## Gather function arguments (all provided bands) and create args
potArgs <- c("blue", "green", "red", "redEdge1", "redEdge2", "redEdge3", "nir", "swir1", "swir2", "swir3")
actArgs <- vapply(potArgs, function(x) !is.null(get(x)), logical(1))
bands <- potArgs[actArgs]
## Subset calculated indices to possible based on band inputs and / or user request
requested <- BANDSdb[ind]
canCalc <- names(requested)[!vapply(requested, function(x) any(!x %in% bands), logical(1))]
if(!skipRefCheck && any(c("EVI","EVI2") %in% canCalc)){
img[[red]] <- setMinMax(img[[red]])
mm <- minmax(img[[red]])
if(is.nan(mm[2,1]) || is.nan(mm[1,1]) || mm[2,1]/scaleFactor > 1.5 || mm[1,1]/scaleFactor < -0.5){
## checking for range [0,1] +/- .5 to allow for artifacts in reflectance.
warning("EVI/EVI2 parameters L_evi, G, C1 and C2 are defined for reflectance [0,1] but img values are outside of this range.\n",
" If you are using scaled reflectance values please provide the scaleFactor argument.\n",
" If img is in DN or radiance it must be converted to reflectance.\n",
" Skipping EVI calculation.\n", call. = FALSE)
canCalc <- canCalc[!canCalc %in% c("EVI", "EVI2")]
indices <- indices[!indices %in% c("EVI", "EVI2")]
}
}
ind <- ind[ind %in% canCalc]
if(!length(ind)) stop("No index could be calculated. At least for one index you must specify *all* required bands.",
"\n See ?spectralIndices for information on required bands per index.", call. = FALSE)
if(length(ind) < length(indices)){
not <- setdiff(indices,ind)
notbands <- setdiff(unlist(requested[not]), bands)
warning("The following indices were requested but cannot be calculated: ", paste(not, collapse = ", "),
"\n because the following required bands were not specified: ",
paste(notbands, collapse = ", "),
"\n The remaining fully specified indices will be calculated.", call. = FALSE)
}
## Get required designated bands
retrieve <- lapply(bands, get, envir=environment())
bandsCalc <- vapply(retrieve, function(xi) { if(is.character(xi)) match(xi, names(img)) else xi }, numeric(1))
names(bandsCalc) <- bands
## Add mask layer to img if present
if(!is.null(maskLayer)){
if(inherits(maskLayer, "SpatRaster")) {
if(nlyr(maskLayer) > 1) warning(sprintf("maskLayer has %s layers. Only the first layer will be used for masking.", nlyr(maskLayer)),call.=FALSE)
img <- c(img, maskLayer[[1]])
names(img)[nlyr(img)] <- "mask"
} else if (is.numeric(maskLayer)) {
names(img)[maskLayer] <- "mask"
} else if (is.character(maskLayer)) {
if(!maskLayer %in% names(img)) stop(paste0(maskLayer, "is not a layer in img.\nAvailable layers are: ", paste(names(img))), call. =FALSE)
names(img)[names(img) == maskLayer] <- "mask"
} else {
stop("maskLayer must be NULL, a RasterLayer, a layer name or a layer number", call. =FALSE)
}
bandsCalc[["mask"]] <- which(names(img) == "mask")
}
potArgs <- c(potArgs, "mask")
## Adjust layer argument so that the first layer we use is now layer 1, etc.
## This way we don't have to sample the whole stack if we only need a few layers
fullSet <- vapply(potArgs, function(n) match(n, names(bandsCalc)), integer(1))
wopt <- list(...)
filename <- if("filename" %in% names(wopt)) wopt$filename else ""
overwrite <- if("overwrite" %in% names(wopt)) wopt$overwrite else FALSE
wopt[c("filename","overwrite")] <- NULL
# Perform calculations
indexMagic <- terra::app(img[[bandsCalc]], fun = function(m) {
spectralIndicesCpp(
x = m,
indices = canCalc,
blueBand = fullSet[["blue"]],
greenBand = fullSet[["green"]],
redBand = fullSet[["red"]],
redEdge1Band = fullSet[["redEdge1"]],
redEdge2Band = fullSet[["redEdge2"]],
redEdge3Band = fullSet[["redEdge3"]],
nirBand = fullSet[["nir"]],
swir1Band = fullSet[["swir1"]],
swir2Band = fullSet[["swir2"]],
swir3Band = fullSet[["swir3"]],
maskLayer = fullSet[["mask"]],
maskValue = maskValue,
L = coefs[["L"]], G = coefs[["G"]], Levi = coefs[["L_evi"]],
C1 = coefs[["C1"]], C2 = coefs[["C2"]], s = coefs[["s"]],
swir2ccc = coefs[["swir2ccc"]], swir2cdiff = coefs[["swir2cdiff"]], sf = scaleFactor,
formulas = as.vector(unlist(lapply(idxdb[canCalc], FUN = extract_function_string)))
)},
wopt=wopt, filename = filename, overwrite = overwrite)
names(indexMagic) <- canCalc
return(indexMagic)
}
extract_function_string <- function(fn) {
function_body <- body(fn[[2]])
function_string <- deparse(function_body)
function_string <- paste(function_string, collapse = "")
function_string <- gsub("\\s+", "", function_string)
function_string <- gsub("[{}]", "", function_string)
return(function_string)
}
## NOT USED FOR CALCULATIONS ONLY FOR DOCUMENTATION
## SEE /src/spectraIndices.cpp for calculations
#' Database of spectral indices
#' @keywords internal
#' @noRd
.IDXdb <- getOption("RStoolbox.idxdb")
# BANDSdb <- lapply(lapply(.IDXdb,"[[", 2), function(x) names(formals(x)))
.IDXdbFormulae <- lapply(.IDXdb,"[[",2)
.IDX.REFdb <- lapply(.IDXdb,"[[",1)
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