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reorganizedCreateMiddayNDSI.R
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reorganizedCreateMiddayNDSI.R
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#!/usr/bin/env Rscript
#install.packages("/projectnb/dietzelab/kiwheel/NEFI_pheno/PhenologyBayesModeling",repo=NULL)
library("ncdf4")
library(plyr)
library("PhenologyBayesModeling")
library(doParallel)
#detect cores.
n.cores <- 5
#register the cores.
registerDoParallel(cores=n.cores)
##Can only do for same TZ
createNDSI_sub <- function(siteData,orbitVersion,day.time,year){
#print(orbitVersion)
print(day.time)
##Will need to return a vector of the NDSI values
##Create File Paths
ACM.path <- paste("GOES_Data2017/",dir(path="GOES_Data2017",pattern=paste("OR_ABI-L2-ACMC-M3_G16_s",day.time,sep="")),sep="")
filestrC05 <- paste("OR_ABI-L1b-RadC-M3C05_G16_s",day.time,sep="")
#print(filestrC05)
filestrC02 <- paste("OR_ABI-L1b-RadC-M3C02_G16_s",day.time,sep="")
filePathC02 <- paste("GOES_Data2017/",dir(path="GOES_Data2017",pattern=filestrC02),sep="")
filePathC05 <- paste("GOES_Data2017/",dir(path="GOES_Data2017",pattern=filestrC05),sep="")
NDSIs <- numeric()
#print(ACM.path)
#print(filePathC02)
#print(filePathC05)
##Open Files
#print(paste("filePathC02:",filePathC02))
#print(paste("filePathC05:",filePathC05))
if(nchar(filePathC02)>20 && nchar(filePathC05)>20){
if(file.exists(filePathC02) && file.exists(filePathC05) && !dir.exists(filePathC02) && !dir.exists(filePathC05)){
ACM.file <-nc_open(ACM.path)
R2.file <- nc_open(filePathC02)
R5.file <- nc_open(filePathC05)
##Extract Data
R5 <- ncvar_get(R5.file,"Rad")
R2 <- ncvar_get(R2.file,"Rad") #the full R2 dataset
R5.kappa0 <- ncvar_get(R5.file,"kappa0")
R2.kappa0 <- ncvar_get(R2.file,"kappa0")
R5.DQF <- ncvar_get(R5.file,"DQF") #Data Quality Flags
R2.DQF <- ncvar_get(R2.file,"DQF")
R5 <- R5 * R5.kappa0 #done to covert radiance to reflectance
R2 <- R2 * R2.kappa0
clouds <- ncvar_get(ACM.file,"BCM")
clouds.DQF <- ncvar_get(ACM.file,"DQF")
#print(dim(R5.DQF))
for(i in 1:nrow(siteData)){
##General Site Data
siteName <- as.character(siteData[i,1])
lat <- as.numeric(siteData[i,2])
long <- as.numeric(siteData[i,3])
TZ <- as.numeric(siteData[i,6])
##Determine index values
lat.rd <- lat*2*pi/360
long.rd <- long*2*pi/360
Ind2 <- getDataIndex(getABI_Index(lat.rd,long.rd,orbitVersion=orbitVersion),2,orbitVersion=orbitVersion)
Ind5 <- getDataIndex(getABI_Index(lat.rd,long.rd,orbitVersion=orbitVersion),5,orbitVersion=orbitVersion)
ACM.ind <- getDataIndex(getABI_Index(lat.rd,long.rd,orbitVersion=orbitVersion),"ACM",orbitVersion=orbitVersion)
#print(paste("Ind5:",Ind5))
i2 <- Ind2[1]
j2 <- Ind2[2]
i5 <- Ind5[1]
j5 <- Ind5[2]
if(!is.na(R5.DQF[i5,j5]) && !is.na(R2.DQF[i2,j2]) && !is.na(R2.DQF[i2,j2]) && !is.na(R2.DQF[(i2+1),j2]) && !is.na(R2.DQF[i2,(j2+1)]) && !is.na(R2.DQF[(i2+1),(j2+1)]) && !is.na(clouds[ACM.ind[1],ACM.ind[2]]) && !is.na(clouds.DQF[ACM.ind[1],ACM.ind[2]])){
if(R5.DQF[i5,j5]==0 && R2.DQF[i2,j2]==0 && R2.DQF[i2,j2]==0 && R2.DQF[(i2+1),j2]==0 && R2.DQF[i2,(j2+1)]==0 && R2.DQF[(i2+1),(j2+1)]==0 && clouds[ACM.ind[1],ACM.ind[2]] == 0 && clouds.DQF[ACM.ind[1],ACM.ind[2]] == 0){
R5.val <- R5[i5,j5]
R2.val <- mean(R2[i2,j2],R2[(i2+1),j2],R2[i2,(j2+1)],R2[(i2+1),(j2+1)])
output <- calNDSI(R2.val,R5.val)
}
else{
output <- NA
}
}
else{
output <- NA
}
print(paste("NDSI:",output))
NDSIs <- c(NDSIs,output)
}
}
else{
return(rep(NA,nrow(siteData)))
}
}
else{
return(rep(NA,nrow(siteData)))
}
return(NDSIs)
}
createEmptyFiles <- function(siteData,day,year){
for(i in 1:length(siteData)){
siteName <- as.character(siteData[i,1])
fileName <- paste("GOES_NDSI_Midday",siteName,"_",day,"_",day,"_kappaDQF.csv",sep="")
write.table(NA,file=fileName,sep=",",col.names=FALSE,row.names=FALSE)
}
}
checkFileExists <- function(siteName,day){
##Returns True if the file exists
dat <- read.csv(file=paste(siteName,"_missingMidday_NDSI_Days.csv",sep=""),header=FALSE)
for(i in 1:nrow(dat)){
if(as.numeric(dat[i,1])==as.numeric(day)){
return(FALSE)
}
}
return(TRUE)
}
createMissingFilesList <- function(siteName){
diurnal.files <- dir(pattern=paste("GOES_NDSIMidday",siteName,sep=""))
days <- numeric()
#print(paste("Length of diurnal.files:"),length(diurnal.files))
if(length(diurnal.files)!= 0){
for(i in 1:length(diurnal.files)){
#print(diurnal.files[i])
start <- as.numeric(strsplit(diurnal.files[i],"_")[[1]][4])
end <- as.numeric(strsplit(diurnal.files[i],"_")[[1]][5])
#print(start)
#print(end)
dys <- seq(start,end,1)
days <- c(days,dys)
}
}
#sort(days)
#all.days <- c(seq(321,333,1),seq(348,365,1))
all.days <- c(seq(1,333,1),seq(348,365,1))
#all.days <- seq(1,181,1)
missingDays <- numeric()
for(j in 1:length(all.days)){
if((!all.days[j] %in% days)){
missingDays <- c(missingDays,all.days[j])
}
}
#missingDays
#print(length(missingDays))
if(length(missingDays)==0){
missingDays <- c(missingDays,0)
}
write.table(missingDays,file=paste(siteName,"_missingMidday_NDSI_Days.csv",sep=""),sep=",",col.names=FALSE,row.names=FALSE)
}
createNDSI_GOES_MiddayMAIN <- function(day,siteData,orbitVersion,year,TZ){
#print(orbitVersion)
#print("Inside Main")
##hours for Midday calculations
#print(TZ)
hrs <- as.character(seq(10+as.numeric(TZ),(13+as.numeric(TZ)),1))
#print(hrs)
if(as.numeric(day)<10){
day <- paste("00",as.character(day),sep="")
}
else if(as.numeric(day)<100){
day <- paste("0",as.character(day),sep="")
}
else{
day <- as.character(day)
}
##
filestrACM <- paste("OR_ABI-L2-ACMC-M3_G16_s",year,day,sep="")
#print(filestrACM)
ACM.files <- character()
for(q in 1:length(hrs)){
if(as.numeric(hrs[q])<10){
hrs[q] <- paste("0",hrs[q],sep="")
}
else if(as.numeric(hrs[q])>23){
hrs[q] <- paste("0",as.character((hrs[q]-24)),sep="")
day <- as.numeric(day)+1
if(as.numeric(day)<10){
day <- paste("00",as.character(day),sep="")
}
else if(as.numeric(day)<100){
day <- paste("0",as.character(day),sep="")
}
else{
day <- as.character(day)
}
}
#print(c("hrs[q]",hrs[q]))
newFiles <- intersect(dir(path="GOES_Data2017",pattern=filestrACM),dir(path="GOES_Data2017",pattern=paste("s",year,day,hrs[q],sep="")))
ACM.files <- c(ACM.files,newFiles)
}
#print(ACM.files)
if(!dir.exists((paste("GOES_Data2017/",dir(path="GOES_Data2017",pattern=filestrACM),sep="")))){
if(length(ACM.files>1)){
day.time.vals <- character()
NDSI.vals <- matrix(ncol=nrow(siteData),nrow=0)
#print(dim(NDSI.vals))
for(j in 1:length(ACM.files)){
##Open Files
day.time <- substr(ACM.files[j],24,34)
day.time.vals <- c(day.time.vals,day.time)
#print(NDSI)
NDSI.vals <- rbind(NDSI.vals,createNDSI_sub(siteData=siteData,orbitVersion=orbitVersion,day.time=day.time) )
#print(NDSI.vals)
}
#print(dim(NDSI.vals))
for(i in 1:nrow(siteData)){
siteName <- as.character(siteData[i,1])
fileName <- paste("GOES_NDSI_Midday",siteName,"_",day,"_",day,"_kappaDQF.csv",sep="")
#print("Printing NDSI.vals[,i]:")
#print(NDSI.vals[,i])
#print(dim(NDSI.vals[,i]))
output <- rbind(day.time.vals,NDSI.vals[,i])
write.table(output,file=fileName,sep=",",col.names=FALSE,row.names=FALSE)
}
}
else{
createEmptyFiles(siteData=siteData,day=day)
}
}
else{
createEmptyFiles(siteData=siteData,day=day)
}
}
#########
##For TZ == 5
#siteData <- read.csv("GOES_Paper_Sites.csv",header=TRUE)[c(1,2,3,4,5,8,11,16,17,18,19,20,21,22),] ##TZ 5 sites
#siteData <- read.csv("GOES_Paper_Sites.csv",header=TRUE)[c(8,11,16,17,18,19,20),]#[c(2,3,4),]
#siteData <- read.csv("GOES_Paper_Sites.csv",header=TRUE)[c(1,2,3,4,5),]
#siteData <- read.csv("GOES_Paper_Sites.csv",header=TRUE)[c(6,9,10,15),] ##TZ 6 sites
siteData <- read.csv("GOES_Paper_Sites.csv",header=TRUE)[c(7,13,14),]##TZ 7 sites
#siteData <- read.csv("GOES_Paper_Sites.csv",header=TRUE)[c(12),] ##TZ 8
#siteData <- read.csv("GOES_Paper_Sites.csv",header=TRUE)[c(21,22),]
TZ <- as.numeric(siteData[1,6])
PFT <- as.character(siteData[1,5])
for(s in 1:nrow(siteData)){
siteName <- as.character(siteData[s,1])
#print(siteName)
createMissingFilesList(siteName)
}
print("Done creating missing day files")
#all.days <- c(seq(321,333,1),seq(348,365,1))
all.days <- c(seq(1,151,1),seq(274,333,1),seq(348,365,1))
#all.days <- seq(158,181)
#year <- 2017
output <-
foreach (d = 1:length(all.days)) %dopar% {
#for(d in 1:length(all.days)){
print(paste("Starting Day:",all.days[d],sep=" "))
iseq <- numeric()
if(PFT=="SH"){
if(all.days[d]<110){#######Need to change for DB
year <- 2018
}
else{
year <- 2017
}
if(all.days[d]<334 && all.days[d]>109){##Need to change for DB
orbitVersion <- "OLD"
}
else{
orbitVersion <- "NEW"
}
}
else if(PFT=="DB"){
if(all.days[d]<182){
year <- 2018
}
else{
year <- 2017
}
if(all.days[d]<334 && all.days[d]>181){
orbitVersion <- "OLD"
}
else{
orbitVersion <- "NEW"
}
}
for(s in 1:nrow(siteData)){
siteName <- as.character(siteData[s,1])
#print(siteName)
if(!checkFileExists(siteName = siteName,day=all.days[d])){
iseq <- c(iseq,s)
}
}
#print(iseq)
if(length(iseq)>0){
createNDSI_GOES_MiddayMAIN(day=all.days[d],siteData=siteData[iseq,],orbitVersion = orbitVersion,year = year,TZ = TZ)
}
}