R/fit-filter.R

In cropmodels/phenorice: phenorice

### Fit index

# Fill NAs by fiting with a smoothing spline
pheno_fill_VI <- function(x) {
    # To omit pixel if it has a lot of NA values
    if (length(which(is.na(x))) > length(x)*0.75) return(x)
	
	z <- which(is.na(x))
	nz <- length(z)
	nx <- length(x)
	if (nz == 0 | nz == nx) {
		return(x)
	}
	x[z] <- stats::spline(x = 1:nx, y = x, xout = z, method = "natural")$y
	return(x)
}

# Smooth of time-series data using Savitzky-Golay filter
pheno_filter_VI <- function(x){

	x <- pheno_fill_VI(x)
	if (any(is.na(x))) return(x)
	# Smooth x
	evisgfit <- signal::sgolayfilt(x, p = 4, n = 13, m = 0) 
	resu <- x - evisgfit
	dif <- abs(resu)
	mm <- max(dif)
	weights <- c(1:(length(x)))
	index <- which(resu <= 0)
	if (length(index) > 0){
		weights[index] <- 1 - (dif[index]/mm)
	} 
	gdis <- sum(abs(dif * weights))
	ormax <- gdis
	it <- 1
	imax <- 10
	while ((gdis <= ormax) && (it < imax)){
		ra4 <- x
		index <- which(x < evisgfit)
		if (length(index) > 0){
			ra4[index] <- evisgfit[index]
		} 
		evisgfit <- signal::sgolayfilt(ra4, p = 4, n = 7, m = 0) 
		resu <- x - evisgfit
		ormax <- gdis
		gdis <- sum(abs(resu*weights))
	}
	return(evisgfit)
}