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# R script for calculating row-wise RMSEs and row-wise correlation coefficients.
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#
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# The results (plots) are saved at
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# "/data/project/organisms/DEM?Yuni/documents/rmse_cor"
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#
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#
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# Original author: Jim Regetz
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# [13-JUL-2011]
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# Edits by Yuni to apply ASTER GDEM2, instead of GDEM1, as well as auto-applying
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# for each nine region. [9-Dec-2011]
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#
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# simple helper function to calculate row-wise RMSEs
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rmse <- function(r1, r2, na.rm=TRUE, use) {
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diffs <- abs(as.matrix(r1) - as.matrix(r2))
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if (!missing(use)) diffs[!use] <- NA
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sqrt(rowMeans(diffs^2, na.rm=na.rm))
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}
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# simple helper function to calculate row-wise correlation coefficients
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corByLat <- function(r1, r2, rows) {
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if (missing(rows)) {
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rows <- 1:nrow(r1)
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}
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m1 <- as.matrix(r1)
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m2 <- as.matrix(r2)
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sapply(rows, function(row) cor(m1[row,], m2[row,],
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use="pairwise.complete.obs"))
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}
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library(raster)
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aster.dir <- "/data/project/organisms/DEM/Yuni/Data/aster2"
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srtm.dir <- "/data/project/organisms/DEM/Yuni/Data/srtm"
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aster.straddle <- list.files(aster.dir, pattern="^aster2.*_straddle_s.tif")
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srtm.below <- list.files(srtm.dir, pattern="^srtm_.*_below_s.tif")
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fused.straddle <- list.files(aster.dir, pattern="^fused.*_straddle_s.tif")
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fused.bgau <- list.files(aster.dir, pattern="^fused.*_blendgau_s.tif")
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rmse.corByLat <- function(d.aster2, d.srtm, d.uncor2, d.bg2, file.name, aster.dir, srtm.dir){
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# extract raster latitudes for later
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lats2400 <- yFromRow(d.aster2, 1:nrow(d.aster2))
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lats1200 <- yFromRow(d.srtm, 1:nrow(d.srtm))
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# initialize output pdf device driver
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name <- paste("rmse.cor_", file.name, ".pdf", sep="")
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pdf(file.path("/data/project/organisms/DEM/Yuni/documents/rmse_cor", file=name), height=8, width=11.5)
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par(mfrow=c(2,2), omi=c(1,1,1,1))
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ylim <- c(0,30)
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# plot rmse
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par(mfrow=c(2,3), omi=c(1,1,1,1))
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ylim <- ylim
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# with uncorrected fusion
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plot(lats2400, rmse(d.uncor2, d.aster2), type="l", xlab="Latitude", ylab="RMSE", ylim=ylim)
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lines(lats1200, rmse(crop(d.uncor2, extent(d.srtm)), d.srtm), col="blue")
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legend("topright", legend=c("ASTER2", "SRTM"), col=c("black", "blue"), lty=c(1, 1), bty="n")
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text(min(lats2400), max(ylim)-1, pos=4, font=3, labels="simple fuse")
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abline(v=60, col="red", lty=2)
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mtext(expression(paste("Elevation discrepancies with respect to separate ASTER2/SRTM components", file.name)), adj=0, line=2, font=2)
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# with gaussian fusion
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plot(lats2400, rmse(d.bg2, d.aster2), type="l", xlab="Latitude", ylab="RMSE", ylim=ylim)
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lines(lats1200, rmse(crop(d.bg2, extent(d.srtm)), d.srtm), col="blue")
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legend("topright", legend=c("ASTER2", "SRTM"), col=c("black", "blue"), lty=c(1, 1),
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bty="n")
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text(min(lats2400), max(ylim)-1, pos=4, font=3, labels="gaussian blend")
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abline(v=60, col="red", lty=2)
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# plot latitudinal profiles of correlation coefficients
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par(mfrow=c(2,3), omi=c(1,1,1,1))
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ylim <- c(0.99, 1)
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plot(lats2400, corByLat(d.uncor2, d.aster2), type="l", xlab="Latitude",
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ylab="Correlation", ylim=ylim)
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lines(lats1200, corByLat(crop(d.uncor2, extent(d.srtm)), d.srtm), col="blue")
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legend("bottomright", legend=c("ASTER2", "SRTM"), col=c("black", "blue"),
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lty=c(1, 1), bty="n")
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text(min(lats2400), min(ylim), pos=4, font=3, labels="simple fuse")
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abline(v=60, col="red", lty=2)
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mtext(expression(paste("Elevation correlations with respect to separate ASTER2/SRTM components", file.name)), adj=0, line=2, font=2)
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plot(lats2400, corByLat(d.bg2, d.aster2), type="l", xlab="Latitude",
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ylab="Correlation", ylim=ylim)
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lines(lats1200, corByLat(crop(d.bg2, extent(d.srtm)), d.srtm), col="blue")
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legend("bottomright", legend=c("ASTER2", "SRTM"), col=c("black", "blue"),
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lty=c(1, 1), bty="n")
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text(min(lats2400), min(ylim), pos=4, font=3, labels="gaussian blend")
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abline(v=60, col="red", lty=2)
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dev.off ()
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}
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num.regions <- 9
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plot.rmse.corByLat <-lapply(1:num.regions, function(region, aster.dir, srtm.dir){
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d.aster <- raster(file.path(aster.dir, aster.straddle[region]))
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d.srtm <- raster(file.path(srtm.dir, srtm.below[region]))
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d.uncor <- raster(file.path(aster.dir, fused.straddle[region]))
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d.bg <- raster(file.path(aster.dir, fused.bgau[region]))
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file.name <- substr(srtm.below[region], 6, 13)
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rmse.corByLat(d.aster, d.srtm, d.uncor, d.bg, file.name, aster.dir, srtm.dir)
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}, aster.dir=aster.dir, srtm.dir=srtm.dir)
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