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OGIIR_2_srTopoBRDF.R
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OGIIR_2_srTopoBRDF.R
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## Version 3.0
## Author: Jasper Van doninck
## Contact: jasper.vandoninck@utu.fi, vandoninck.jasper@gmail.com
##
## Description:
## Process Landsat Collection 1 Level 1 image to surface reflectance
## Includes BRDF+topographic correction
## WARNING: required ESPA software to be installed!
## For instructions:
## * ESPA product formatter: https://github.com/USGS-EROS/espa-product-formatter
## * LEDAPS: https://github.com/USGS-EROS/espa-surface-reflectance/tree/master/ledaps
##
## Usage:
## surfaceReflectance(fid,inDir,outDir,tempDirRoot,
## removeTmpFiles=TRUE, ptstart=proc.time(),
## bs=100,
## brdf=NULL, outSZA=30,
## topo=NULL, demFile=NULL)
##
## Arguments:
## fid: Character. Landsat file ID
## inDir: Character. Directory of Landsat L1 .tar.gz file.
## outDir: Character. Directory of output L2 files.
## tempDirRoot: Character. Path to directory in which temporary directory will be created.
## removeTmpFiles: Logical. Defines whether temporary files are to be removed.
## ptstart: Object of class "proc.time". Used to track progress.
## bs: Numeric. Defines number of image lines read into memory simultaneously
## brdf: NULL or character (one of "Roy"/"Flood"/"UTU"). See details.
## outSZA: Numeric. Solar zenith angle (in degrees) of BRDF-normalized image. Only required if argument "brdf" is not NULL.
## topo: Null or character ("C"). See details.
## demFile: Character. Filename of digital elevation model covering extent of Landsat image. Only required if parameter "topo" is not NULL.
##
## Details:
## Parameter "brdf" defines the parameters of the BRDF correction to be applied.
## Possible values:
## "Roy": set of global parameters obtained from MODIS (Roy, D. P., H. K. Zhang, J. Ju, J. L. Gomez-Dans, P. E. Lewis, C. B. Schaaf, Q. Sun, J. Li, H. Huang, and V. Kovalskyy. 2016. "A General Method to Normalize Landsat Reflectance Data to Nadir BRDF Adjusted Reflectance." Remote Sensing of Environment 176 (April): 255-71. https://doi.org/10.1016/j.rse.2016.01.023.)
## "Flood": set of parameters derived for Australia (Flood, N., T. Danaher, T. Gill, and S. Gillingham. 2013. "An Operational Scheme for Deriving Standardised Surface Reflectance from Landsat TM/ETM+ and SPOT HRG Imagery for Eastern Australia." Remote Sensing 5 (1): 83-109. https://doi.org/10.3390/rs5010083.)
## "UTU": set of parameters derived for Amazonian forests (Van doninck, J., and H. Tuomisto. 2017. "Evaluation of Directional Normalization Methods for Landsat TM/ETM+ over Primary Amazonian Lowland Forests." International Journal of Applied Earth Observation and Geoinformation 58 (June): 249-63. https://doi.org/10.1016/j.jag.2017.01.017.)
##
## Parameter "topo" defines topographic correction. Only C-correction is implemented.
##
## Value:
## Numeric.
## 0: Processing completed correctly.
## 1: Error in unpacking .tar.gz file or while running ESPA software.
## 3: Processing skipped. Insufficient cloud-free pixels in image.
## 5: Processing skipped. Incorrect input argument(s).
##
## Used packages:
## raster
## rgdal
## RStoolbox
#install.packages(c("raster", "rgdal", "RStoolbox"))
surfaceReflectance <- function(fid,inDir,outDir,tempDirRoot,
removeTmpFiles=TRUE,
ptstart=proc.time(),
bs=100,
brdf=NULL,
outSZA=30,
topo=NULL,
demFile=NULL){
## Load libraries and functions
require(raster)
require(rgdal)
#Kvol - RossThick kernel for volume scattering (Roujean et al., 1992)
Kvol <- function(sunza, satza, relaz, degrees=FALSE){
if (degrees){
sunza <- sunza*pi/180
satza <- satza*pi/180
relaz <- relaz*pi/180
}
ph_an <- acos((cos(sunza)*cos(satza))+(sin(sunza)*sin(satza)*cos(relaz)))
result <- (((pi/2-ph_an)*cos(ph_an)+sin(ph_an))/(cos(sunza)+cos(satza)))-(pi/4)
return(result)
}
#Kgeo - LiSparse-R kernel for geometric-optical surface scattering (Wanner et al., 1995)
Kgeo <- function(sunza, satza, relaz, degrees=FALSE){
if (degrees){
sunza <- sunza*pi/180
satza <- satza*pi/180
relaz <- relaz*pi/180
}
#br <- 1
hb <- 2
ph_an <- acos((cos(sunza)*cos(satza))+(sin(sunza)*sin(satza)*cos(relaz)))
D <- sqrt((tan(sunza))^2+(tan(satza))^2-2*tan(sunza)*tan(satza)*cos(relaz))
cost <- (hb*(sqrt(D^2+(tan(sunza)*tan(satza)*sin(relaz))^2)/((1/cos(sunza))+(1/cos(satza)))))
cost[cost > 1] <- 1
cost[cost < -1] <- -1
t <- acos(cost)
O=(1/pi)*(t-sin(t)*cos(t))*((1/cos(sunza))+(1/cos(satza)))
result <- O-(1/cos(sunza))-(1/cos(satza))+0.5*(1+cos(ph_an))*(1/cos(sunza))*(1/cos(satza))
return(result)
}
#Some other helper functions
nearest.vec <- function(x, vec){
smallCandidate <- findInterval(x, vec, all.inside=TRUE)
largeCandidate <- smallCandidate + 1
#nudge is TRUE if large candidate is nearer, FALSE otherwise
nudge <- 2 * x > vec[smallCandidate] + vec[largeCandidate]
return(smallCandidate + nudge)
}
timeStamp <- function(pt.start){
pt <- proc.time()-pt.start
pt <- pt["elapsed"]/(60*60)
hh <- floor(pt)
pt <- (pt-hh)*60
mm <- floor(pt)
ss <- floor((pt-mm)*60)
if (hh<10) hhtxt <- paste0("0",as.character(hh)) else hhtxt <- as.character(hh)
if (mm<10) mmtxt <- paste0("0",as.character(mm)) else mmtxt <- as.character(mm)
if (ss<10) sstxt <- paste0("0",as.character(ss)) else sstxt <- as.character(ss)
return(paste0("[",hhtxt,":",mmtxt,":",sstxt,"]"))
}
## Define constants
# Sensor
sensor <- substr(fid,1,4)
# Landsat bands
sbands <- c(1,2,3,4,5,7)
# Normalized angles
if(!is.null(brdf)){
Kgeo.norm <- Kgeo(outSZA, 0,0, degrees=TRUE)
Kvol.norm <- Kvol(outSZA, 0,0, degrees=TRUE)
}
## Check input parameters
if (!is.null(topo)){
# Check if parameter "topo" is accepted value
if (!isTRUE(topo=="C")){
cat("[ERROR] Parameter \"topo\" must one of (NULL, \"C\").\n", sep="")
return(5)
}
# Check if DEM raster exists (in case topographic correction performed)
if(!is.character(demFile)){
cat("[ERROR] Parameter \"demFile\" is not a character variable.\n", sep="")
return(5)
}
if(isFALSE(file.exists(demFile))){
cat("[ERROR] File \"",demFile ,"\" does not exist.\n", sep="")
return(5)
}
}
# Check BRDF model parameters
fpData <- switch(tolower(brdf),
"roy" = c(0.0372, 0.0580, 0.0574, 0.1535, 0.1154, 0.0639,
0.0079, 0.0178, 0.0227, 0.0330, 0.0453, 0.0387)/
c(0.0774, 0.1306, 0.1690, 0.3093, 0.3430, 0.2658),
"flood" = c(0.93125413991, 0.687401438519, 0.645033011917, 0.704036740665, 0.360201003097, 0.290061903555,
0.260953557124, 0.213872135374, 0.180032152925, 0.093518142066, 0.162796996525, 0.147723009593),
"utu" = c(1.2933, 0.5550, 0.9937, 0.3489, 1.0129, 1.2742,
0.1902, 0.2456, 0.0000, 0.2755, 0.2348, 0.2426),
NA)
if(isTRUE(sum(is.na(fpData)))){
cat("[ERROR] Parameter \"brdf\" must be one of (\"Roy\", \"Flood\", \"UTU\").\n", sep="")
return(5)
} else fp <- matrix(data= fpData, ncol=2, dimnames=list(sbands, c("vol", "geo")))
# Create/set directories
tempDir <- paste0(tempDirRoot,"/",fid)
if (!file.exists(tempDir)) dir.create(tempDir, recursive=TRUE)
if (!file.exists(outDir)) dir.create(outDir, recursive=TRUE)
wdir <- tempDir
cwdir <- getwd()
setwd(wdir)
# Set temporal directory for "raster" package
rasterTmpDir <- file.path(wdir,"rasterTmpDir")
if (!file.exists(rasterTmpDir)) dir.create(rasterTmpDir)
options(rasterTmpDir=rasterTmpDir)
# Check if file is available untar .tar.gz file
cat(timeStamp(ptstart)," ",fid,": Untar/LEDAPS/CFMASK/angles\n", sep="")
if (!file.exists(file.path(inDir,paste0(fid,".tar.gz")))){
cat("[ERROR] ",fid,": File not found\n", sep="")
setwd(cwdir)
unlink(wdir, recursive=TRUE)
return(1)
}
untar(file.path(inDir,paste0(fid,".tar.gz")), exdir=wdir)
#Convert LPGS to ESPA format:
if (system(paste0("convert_lpgs_to_espa --mtl ",fid,"_MTL.txt --xml ",fid,".xml --del_src_files"), intern=FALSE, ignore.stdout=TRUE)){
cat("[ERROR] ",fid,": Error converting LPGS to ESPA\n", sep="")
setwd(cwdir)
unlink(wdir, recursive=TRUE)
return(1)
}
# Apply LEDAPS
if (system(paste0("do_ledaps.py --xml ",fid,".xml"), intern=FALSE, ignore.stdout=TRUE, ignore.stderr=TRUE)){
ledaps.fail <- 1
nTry <- 2
while (ledaps.fail & nTry <5){
cat("[WARNING] ",fid,": Error running LEDAPS, attempt ",nTry,"\n", sep="")
ledaps.fail <- system(paste0("do_ledaps.py --xml ",fid,".xml"), intern=FALSE, ignore.stdout=TRUE, ignore.stderr=TRUE)
nTry <- nTry+1
}
if (ledaps.fail){
cat("[ERROR] ",fid,": Error running LEDAPS\n", sep="")
setwd(cwdir)
unlink(wdir, recursive=TRUE)
return(1)
}
}
# CFMASK
if (system(paste0("cfmask --xml ",fid,".xml"), intern=FALSE, ignore.stdout=TRUE, ignore.stderr=TRUE)){
cat("[ERROR] ",fid,": Error running CFMASK\n", sep="")
setwd(cwdir)
unlink(wdir, recursive=TRUE)
return(1)
}
## Landsat angles --> ONLY IF !is.null(brdf)
if (system(paste0("landsat_angles ",fid,"_ANG.txt"), intern=FALSE, ignore.stdout=TRUE, ignore.stderr=TRUE)){
cat("[ERROR] ",fid,": Error running Landsat angles\n", sep="")
setwd(cwdir)
unlink(wdir, recursive=TRUE)
return(1)
}
# Clean up intermediate files (DN + TOA)
if(removeTmpFiles) dummy <- file.remove(list.files(wdir, pattern=paste0(fid,"_B"), full.names=TRUE))
if(removeTmpFiles) dummy <- file.remove(list.files(wdir, pattern=paste0(fid,"_toa"), full.names=TRUE))
# Create empty raster template
nullR <- raster(file.path(wdir, paste0(fid, "_sr_fill_qa.img")), vals=FALSE)
nullR <- raster(nrows=nrow(nullR), ncols=ncol(nullR), ext=extent(nullR), crs=crs(nullR), resolution=res(nullR))
nullR_ext <- extent(nullR)
nullR_ext_p <- extent(t(project(t(as.matrix(nullR_ext)), projection(nullR), inv=TRUE)))
# Create masks from QA bands and check number of unmasked pixels
cat(timeStamp(ptstart)," ",fid,": Create mask\n",sep="")
maskR<- overlay(raster(file.path(wdir, paste0(fid, "_sr_fill_qa.img"))),
raster(file.path(wdir, paste0(fid, "_sr_cloud_qa.img"))),
raster(file.path(wdir, paste0(fid, "_sr_cloud_shadow_qa.img"))),
raster(file.path(wdir, paste0(fid, "_sr_adjacent_cloud_qa.img"))),
raster(file.path(wdir, paste0(fid, "_sr_band1.img"))),
raster(file.path(wdir, paste0(fid, "_sr_band2.img"))),
raster(file.path(wdir, paste0(fid, "_sr_band3.img"))),
raster(file.path(wdir, paste0(fid, "_sr_band4.img"))),
raster(file.path(wdir, paste0(fid, "_sr_band5.img"))),
raster(file.path(wdir, paste0(fid, "_sr_band7.img"))),
raster(file.path(wdir, paste0(fid, "_cfmask.img"))),
fun=function(fi,cl,cs,ac,a,b,c,d,e,f,g)
{return(fi==0 & cl==0 & cs==0 & ac==0 & a!=2000 & b!=2000 & c!=2000 & d!=2000 & e!=2000 & f!=2000 & (!is.na(g) & g<2) )},
filename=file.path(wdir,paste0(fid,"_mask.grd")), overwrite=TRUE)
if (cellStats(maskR,stat='sum')<10000){ # Exit if too few unmasked pixels
cat(timeStamp(ptstart)," ",fid,": <10000 pixels, abort\n",sep="")
setwd(cwdir)
unlink(wdir, recursive=TRUE)
return(2)
}
## BRDF correction
if(is.null(brdf)){
#No BRDF correction
rho_brdf <- stack(as.list(file.path(tempDir, paste0(fid,"_sr_band",sbands,".img"))))
rho_brdf <- mask(rho_brdf,maskR, maskvalue=0,updatevalue=NA,
file.path(rasterTmpDir,paste0(fid,"_rho_brdf.grd")), overwrite=TRUE, datatype="INT2S")
} else {
#Perform BRDF correction
cat(timeStamp(ptstart)," ",fid,": BRDF normalisation.\n",sep="")
rho_brdf <- brick(nullR, nl=length(sbands))
rho_brdf <- writeStart(rho_brdf, file.path(rasterTmpDir,paste0(fid,"_rho_brdf.grd")), overwrite=TRUE, datatype="INT2S")
for(row_in in seq(1,nrow(nullR),bs)){
#Read row(s) from rasters
sun.zen_row <- getValues(raster(file.path(wdir,"angle_solar_B04.img"),band=1),row_in,bs)*0.01*pi/180
sun.azi_row <- getValues(raster(file.path(wdir,"angle_solar_B04.img"),band=2),row_in,bs)*0.01*pi/180
sat.zen_row <- getValues(raster(file.path(wdir,"angle_sensor_B04.img"),band=1),row_in,bs)*0.01*pi/180
sat.azi_row <- getValues(raster(file.path(wdir,"angle_sensor_B04.img"),band=2),row_in,bs)*0.01*pi/180
Kgeo.init.h_row <-Kgeo(sun.zen_row, sat.zen_row, sun.azi_row-sat.azi_row)
Kvol.init.h_row <-Kvol(sun.zen_row, sat.zen_row, sun.azi_row-sat.azi_row)
mask_row <- getValues(maskR,row_in,bs)
rho_std_row <- matrix(data=NA, ncol=length(sbands), nrow=length(mask_row))
for (b in 1:6){
rho_dir <- getValues(raster(file.path(wdir, paste0(fid,"_sr_band",sbands[b],".img"))),row_in,bs)
gamma <- (1+fp[b,"vol"]*Kvol.norm+fp[b,"geo"]*Kgeo.norm)/(1+fp[b,"vol"]*Kvol.init.h_row+fp[b,"geo"]*Kgeo.init.h_row)
rho_norm <- round(gamma*rho_dir)
rho_norm[mask_row==0] <- NA
rho_norm[rho_norm<0] <- 0
rho_norm[rho_norm>10000] <- 10000
rho_std_row[,b] <- rho_norm
}
rho_brdf <- writeValues(rho_brdf,rho_std_row,row_in)
}
rho_brdf <- writeStop(rho_brdf)
}
## Topographic correction
if(is.null(topo)){
rho_topo <- rho_brdf
} else {
#Combined BRDF/topograpgic correction is not implemented in this version,
#use "topCor" in RStoolbox package for now, only "C" implemented.
cat(timeStamp(ptstart)," ",fid,": Topographic correction\n",sep="")
library(RStoolbox)
## Topographic correction (to be move )
dem.crop <- crop(raster(demFile), nullR_ext_p)
dem.elev <- projectRaster(dem.crop, nullR, method="bilinear",
filename=file.path(rasterTmpDir,paste0(fid,"_dem_elev.grd")), overwrite=TRUE)
rho_topo <- topCor(rho_brdf, dem.elev, file.path(tempDir,paste0(fid,"_MTL.txt")), method=topo)
}
rho_out <- writeRaster(rho_topo, file.path(outDir, paste0(fid,".tif")), overwrite=TRUE, datatype="INT2S")
#Clean up
cat(timeStamp(ptstart)," ",fid,": Clean up \n", sep="")
setwd(cwdir)
options(rasterTmpDir=tempdir())
if(removeTmpFiles) unlink(wdir, recursive=TRUE)
rm(list=ls())
dummy <- gc()
return(0)
}