R/run.process.ECO.batch.R
In belasi01/Riops: IOPs data processing
Defines functions
run.process.ECO.batch
Documented in
run.process.ECO.batch
#'
#' Run batch processing to convert ECO meter data in raw format to backscattering coefficients.
#'
#' The processing includes the application of the calibration coefficients to convert the raw numerical counts into VSF.
#' The dark offsets may be taken from the calibration file (device file) or from the dark measurements taken on the field.
#' Next, if absorption coefficients are provided, the VSF is corrected for loss of photons
#' due to attenuation along the pathlength.
#' The VSF is finaly converted in to total backscattering and particles backscattering.
#'
#' @param log.file is the name of the ASCII file in .csv (comma separated value) containing the
#' list of samples to process (see details below).
#' @param data.path is the full path where the ECO data are stored
#'
#' @details The most important thing to do before runing this programm is to prepare
#' the log.file. This file contains fields (comma delimiter) :
#' ECO.filename; dev.file; ECO.type; ECO.bands; Station; Date; UTCTime;
#' Depth; Salinity; dark.file; start; end; process; Anw1;..;AnwX
#' The ASCII files are:
#'\itemize{
#' \item{ECO.filename: }{is the file name of an ECO file without the path. It must be put in a sub-folder named raw/ in the data.path;}
#' \item{dev.file: }{is the full path and name of the device file (i.e. the calibration file) of the actual instrument;}
#' \item{ECO.type: }{is a character string for the type of ECO meter: BB9, BB3, VSF3.}
#' \item{ECO.bands: }{is a character string indicating the bands of the VSF3 meter.
#' It could take one of these character: "B", "G", "R" or "BG", or "BGR".
#' It is ignore when the ECO type is a BB meter}
#' \item{Station: }{is the station ID. It will be store in the RData output;}
#' \item{Date: }{is the date in format YYYYMMDD}
#' \item{UTCTime: }{is the is the time and minute in HH:MM format}
#' \item{Salinity: }{is the salinity of the sample.}
#' \item{dark.file: }{is the name of the file containing raw dark measurements made
#' on the field using black tape places on the LED.
#' It must be put in a sub-folder named dark/ in the data.path and be consistent with the ECO.type}
#' \item{start: }{is the begining of the cast in seconds after the instrument warming period.
#' If 999 then the user is prompt to click on the plot of
#' VSF versus Time to choose the start and the end of the cast interactively.}
#' \item{end: }{is the end of the cast in second. If 999 then it takes
#' the end of the cast.}
#' \item{process: }{is a boolean value indicating if the file has to be process (1) or not (0) }
#' \item{Anw1..AnwX: }{is the non-water absorption for each wavelength of the ECO meter.
#' For a BB9, for example, nine columns are expected}
#' }
#'
#' The code will process each file one by one and will output a RData file for each raw file processed.
#'
#' @author Simon Belanger
#' @export
#'
run.process.ECO.batch <- function(log.file="log.txt", data.path="./"){
if (file.exists(data.path)) {
print("Data path exists")
print(data.path)
} else {
stop("data.path: ",data.path,"/n does not exist!")
}
# Check the output directories and Create them if they are not available.
path.png = file.path(data.path,"png/") #paste(data.path,"/png/", sep="")
path.out = file.path(data.path,"RData/") #paste(data.path,"/RData/", sep="")
path.dark = file.path(data.path,"dark")
path.raw = file.path(data.path,"raw")
if (!file.exists(path.dark)) {
print("No folder named dark found")
print("STOP processing")
print("Create a folder:")
print(path.dark)
print("and put your dark files in it")
stop()
} else print(paste("Dark in :",path.dark))
if (!file.exists(path.raw)) {
print("No folder named raw found")
print("STOP processing")
print("Create a folder:")
print(path.raw)
print("and put your data files in it")
stop()
} else print(paste("Raw data in :",path.raw))
if (!file.exists(path.png)) dir.create(path.png)
if (!file.exists(path.out)) dir.create(path.out)
if (!file.exists(log.file)) {
default.log.file = file.path(Sys.getenv("Riop_DATA_DIR"), "log.ECO.txt")
file.copy(from = default.log.file, to = log.file)
stop("EDIT file", log.file, "and CUSTOMIZE IT\n")
}
print("Read Log with comma delimiter" )
log = read.table(file=log.file, header=T, sep=",")
nfiles = length(log$ECO.filename)
print(paste(nfiles, "files to process."))
for (i in 1:nfiles) {
if (log$process[i] == 1) {
raw.file <- file.path(path.raw,paste0(log$ECO.filename[i],".raw"))
if (file.exists(raw.file)) {
message("Processing ", raw.file)
if (log$ECO.type[i] == "VSF3") raw <- read.ECOVSF(raw.file, ECO.bands=log$ECO.bands[i])
if (log$ECO.type[i] == "BB9") raw <- read.BB9(raw.file, raw=TRUE)
if (log$ECO.type[i] == "BB3") raw <- read.BB3(raw.file, raw=TRUE)
} else {
stop("no raw file: ",raw.file)
}
if (file.exists(as.character(log$dev.file[i]))) {
cal <- read.ECO.dev.file(as.character(log$dev.file[i]), ECO.type = log$ECO.type[i])
} else {
stop("No device file found: ", log$dev.file[i])
}
dark.file <- file.path(path.dark,log$dark.file[i])
if (file.exists(dark.file)) {
eco <- apply.ECO.cal(raw,
dev.file = as.character(log$dev.file[i]),
dark.file = as.character(dark.file),
ECO.type = log$ECO.type[i],
ECO.bands =log$ECO.bands[i])
} else {
warning("no dark data file or dark file not found")
eco <- apply.ECO.cal(raw,
dev.file = as.character(log$dev.file[i]),
dark.file = NA,
ECO.type = log$ECO.type[i],
ECO.bands =log$ECO.bands[i])
}
DateTime = as.POSIXct(paste(as.character(log$Date[i]),
as.character(log$UTCTime[i])),
"%Y%m%d %H:%M",
tz="UTC")
Anw <- as.numeric(log[i,grep("Anw",names(log))])
bb=compute.bb.discrete.from.ECO(eco,
ECO.type = log$ECO.type[i],
ECO.bands = log$ECO.bands[i],
Station = log$Station[i],
DateTime = DateTime,
Depth = log$Depth[i],
Anw = Anw,
Salinity = log$Salinity[i],
start = log$start[i],
end = log$end[i])
# update log
log$start[i] <- bb$start
log$end[i] <- bb$end
# plot data
time <- paste(unlist(str_split(log$UTCTime[i],":"))[1], unlist(str_split(log$UTCTime[i],":"))[2],sep="")
if (as.character(log$ECO.type[i]) == "VSF3") {
print("Plot VSF3 data")
if (log$ECO.bands[i] == "BG") {
minVSF = min(bb$Betau.mean - bb$Betau.sd)
maxVSF = max(bb$Betau.mean + bb$Betau.sd)
png(file=paste(path.png,"/",log$ECO.filename[i], ".png", sep=""),
width=6, height=8, units="in", res=300)
par(mfrow=c(3,1))
par(mar=c(4,5,1,1))
plot(bb$scattering.angle, eco$offset[1,],
xlab="Scattering Angle",
ylab="Offset",
ylim=c(min(c(eco$offset,cal$cal$Offset)),
max(c(eco$offset,cal$cal$Offset))),
xlim=c(90,180), col=4, pch=19)
points(bb$scattering.angle, eco$offset[2,],
col=3, pch=19)
lines(bb$scattering.angle, eco$offset[2,],
col=3)
lines(bb$scattering.angle, eco$offset[1,],
col=4)
lines(bb$scattering.angle, cal$cal$Offset[4:6],
col=3,lwd=3, lty=2)
lines(bb$scattering.angle, cal$cal$Offset[1:3],
col=4,lwd=3, lty=2)
legend("topright", c("Darks", "Calibration"), lwd=c(1,3), lty=c(1,2))
plot(bb$scattering.angle, bb$Betau.mean[,1],
xlim=c(90,180), pch=19, col=4,
ylim=c(minVSF, maxVSF),
xlab="Scattering Angle",
ylab=expression(paste(beta,"(",m^-1 ,sr^-1,")")),
main=paste(log$Station[i], log$DateTime[i]))
if (eco$dark.offset) title(sub="Dark offset applied")
errorbars(bb$scattering.angle, bb$Betau.mean[,1],xe=c(0,0,0),ye=bb$Betau.sd[,1], col=4)
points(bb$scattering.angle, bb$Betau.mean[,2],
pch=19, col=3)
lines(bb$scattering.angle, bb$Betau.mean[,1],
col=4)
lines(bb$scattering.angle, bb$Betau.mean[,2],
col=3)
errorbars(bb$scattering.angle,bb$Betau.mean[,2],xe=c(0,0,0),ye=bb$Betau.sd[,2], col=3)
points(bb$scattering.angle, bb$Beta[,1],
pch=25, col=4)
points(bb$scattering.angle, bb$Beta[,2],
pch=25, col=3)
legend("topright", c("uncor.", "corrected"), pch=c(19,25))
legend("bottomright", c("470", "532"), pch=c(19,19), col=c(4,3))
plot(bb$waves, bb$bb,
xlab="Wavelength", pch=19,
ylab=expression(b[b](m^-1)))
lines(bb$waves, bb$bb)
dev.off()
} else {
minVSF = min(bb$Betau.mean - bb$Betau.sd)
maxVSF = max(bb$Betau.mean + bb$Betau.sd)
png(file=paste(path.png,"/",log$ECO.filename[i], ".png", sep=""),
width=6, height=8, units="in", res=300)
par(mfrow=c(3,1))
par(mar=c(4,5,1,1))
plot(bb$scattering.angle, eco$offset,
xlab="Scattering Angle",
ylab="Offset",
ylim=c(min(c(eco$offset,cal$cal$Offset)),
max(c(eco$offset,cal$cal$Offset))),
xlim=c(90,180), pch=19)
lines(bb$scattering.angle, eco$offset)
if (log$ECO.bands[i] =="B") lines(bb$scattering.angle, cal$cal$Offset[1:3],lwd=3, lty=2)
if (log$ECO.bands[i] =="G") lines(bb$scattering.angle, cal$cal$Offset[4:6],lwd=3, lty=2)
if (log$ECO.bands[i] =="R") lines(bb$scattering.angle, cal$cal$Offset[7:9],lwd=3, lty=2)
legend("topright", c("Darks", "Calibration"), lwd=c(1,3), lty=c(1,2))
plot(bb$scattering.angle, bb$Betau.mean,
xlim=c(90,180), pch=19, col=4,
ylim=c(minVSF, maxVSF),
xlab="Scattering Angle",
ylab=expression(paste(beta,"(",m^-1 ,sr^-1,")")),
main=paste(log$Station[i], log$DateTime[i]))
if (eco$dark.offset) title(sub="Dark offset applied")
errorbars(bb$scattering.angle, bb$Betau.mean,xe=c(0,0,0),ye=bb$Betau.sd)
lines(bb$scattering.angle, bb$Betau.mean)
points(bb$scattering.angle, bb$Beta,pch=25)
legend("topright", c("uncor.", "corrected"), pch=c(19,25))
legend("bottomright", as.character(bb$waves),pch=c(19,25))
plot(bb$waves, bb$bb,
xlab="Wavelength", pch=19,
ylab=expression(b[b](m^-1)))
dev.off()
}
}
if (as.character(log$ECO.type[i]) == "BB9") {
print("Plot BB9 data")
minVSF = min(bb$Betau.mean - bb$Betau.sd)
maxVSF = max(bb$Betau.mean + bb$Betau.sd)
png(file=paste(path.png,"/",log$ECO.filename[i], ".png", sep=""),
width=6, height=8, units="in", res=300)
par(mfrow=c(3,1))
par(mar=c(4,5,1,1))
##### Plot the Offsets
plot(bb$waves, eco$offset,
xlab=expression(lambda),
ylab="Offset",
ylim=c(min(c(eco$offset,cal$cal$Offset)),
max(c(eco$offset,cal$cal$Offset))),
pch=19)
lines(bb$waves, eco$offset)
lines(bb$waves, cal$cal$Offset,lwd=3, lty=2)
legend("topright", c("Darks", "Calibration"), lwd=c(1,3), lty=c(1,2))
##### Plot the VSF
plot(bb$waves, bb$Betau.mean,
pch=19, col=4,
ylim=c(minVSF, maxVSF),
xlab=expression(lambda),
ylab=expression(paste(beta,"(",m^-1 ,sr^-1,")")),
main=paste(log$Station[i], log$DateTime[i]))
if (eco$dark.offset) title(sub="Dark offset applied")
errorbars(bb$waves, bb$Betau.mean,xe=rep(0,9),ye=bb$Betau.sd)
lines(bb$waves, bb$Betau.mean)
points(bb$waves, bb$Beta,pch=25)
legend("topright", c("uncor.", "corrected"), pch=c(19,25))
plot(bb$waves, bb$bbP,
xlab="Wavelength", pch=19,
ylab=expression(b[bp](m^-1)))
lines(bb$waves, bb$bbP)
dev.off()
}
# Save data in RData file format
save(bb, file=file.path(path.out,paste0(log$ECO.filename[i], ".RData")))
# update log file
write.table(log, file=log.file, quote = F, row.names = F, sep=",")
} else print(paste("Skipping file:", log$ECO.filename[i]))
}
}
belasi01/Riops documentation built on Sept. 5, 2022, 6:38 p.m.
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Defines functions run.process.ECO.batch
Documented in run.process.ECO.batch
#'
#' Run batch processing to convert ECO meter data in raw format to backscattering coefficients.
#'
#' The processing includes the application of the calibration coefficients to convert the raw numerical counts into VSF.
#' The dark offsets may be taken from the calibration file (device file) or from the dark measurements taken on the field.
#' Next, if absorption coefficients are provided, the VSF is corrected for loss of photons
#' due to attenuation along the pathlength.
#' The VSF is finaly converted in to total backscattering and particles backscattering.
#'
#' @param log.file is the name of the ASCII file in .csv (comma separated value) containing the
#' list of samples to process (see details below).
#' @param data.path is the full path where the ECO data are stored
#'
#' @details The most important thing to do before runing this programm is to prepare
#' the log.file. This file contains fields (comma delimiter) :
#' ECO.filename; dev.file; ECO.type; ECO.bands; Station; Date; UTCTime;
#' Depth; Salinity; dark.file; start; end; process; Anw1;..;AnwX
#' The ASCII files are:
#'\itemize{
#' \item{ECO.filename: }{is the file name of an ECO file without the path. It must be put in a sub-folder named raw/ in the data.path;}
#' \item{dev.file: }{is the full path and name of the device file (i.e. the calibration file) of the actual instrument;}
#' \item{ECO.type: }{is a character string for the type of ECO meter: BB9, BB3, VSF3.}
#' \item{ECO.bands: }{is a character string indicating the bands of the VSF3 meter.
#' It could take one of these character: "B", "G", "R" or "BG", or "BGR".
#' It is ignore when the ECO type is a BB meter}
#' \item{Station: }{is the station ID. It will be store in the RData output;}
#' \item{Date: }{is the date in format YYYYMMDD}
#' \item{UTCTime: }{is the is the time and minute in HH:MM format}
#' \item{Salinity: }{is the salinity of the sample.}
#' \item{dark.file: }{is the name of the file containing raw dark measurements made
#' on the field using black tape places on the LED.
#' It must be put in a sub-folder named dark/ in the data.path and be consistent with the ECO.type}
#' \item{start: }{is the begining of the cast in seconds after the instrument warming period.
#' If 999 then the user is prompt to click on the plot of
#' VSF versus Time to choose the start and the end of the cast interactively.}
#' \item{end: }{is the end of the cast in second. If 999 then it takes
#' the end of the cast.}
#' \item{process: }{is a boolean value indicating if the file has to be process (1) or not (0) }
#' \item{Anw1..AnwX: }{is the non-water absorption for each wavelength of the ECO meter.
#' For a BB9, for example, nine columns are expected}
#' }
#'
#' The code will process each file one by one and will output a RData file for each raw file processed.
#'
#' @author Simon Belanger
#' @export
#'
run.process.ECO.batch <- function(log.file="log.txt", data.path="./"){
if (file.exists(data.path)) {
print("Data path exists")
print(data.path)
} else {
stop("data.path: ",data.path,"/n does not exist!")
}
# Check the output directories and Create them if they are not available.
path.png = file.path(data.path,"png/") #paste(data.path,"/png/", sep="")
path.out = file.path(data.path,"RData/") #paste(data.path,"/RData/", sep="")
path.dark = file.path(data.path,"dark")
path.raw = file.path(data.path,"raw")
if (!file.exists(path.dark)) {
print("No folder named dark found")
print("STOP processing")
print("Create a folder:")
print(path.dark)
print("and put your dark files in it")
stop()
} else print(paste("Dark in :",path.dark))
if (!file.exists(path.raw)) {
print("No folder named raw found")
print("STOP processing")
print("Create a folder:")
print(path.raw)
print("and put your data files in it")
stop()
} else print(paste("Raw data in :",path.raw))
if (!file.exists(path.png)) dir.create(path.png)
if (!file.exists(path.out)) dir.create(path.out)
if (!file.exists(log.file)) {
default.log.file = file.path(Sys.getenv("Riop_DATA_DIR"), "log.ECO.txt")
file.copy(from = default.log.file, to = log.file)
stop("EDIT file", log.file, "and CUSTOMIZE IT\n")
}
print("Read Log with comma delimiter" )
log = read.table(file=log.file, header=T, sep=",")
nfiles = length(log$ECO.filename)
print(paste(nfiles, "files to process."))
for (i in 1:nfiles) {
if (log$process[i] == 1) {
raw.file <- file.path(path.raw,paste0(log$ECO.filename[i],".raw"))
if (file.exists(raw.file)) {
message("Processing ", raw.file)
if (log$ECO.type[i] == "VSF3") raw <- read.ECOVSF(raw.file, ECO.bands=log$ECO.bands[i])
if (log$ECO.type[i] == "BB9") raw <- read.BB9(raw.file, raw=TRUE)
if (log$ECO.type[i] == "BB3") raw <- read.BB3(raw.file, raw=TRUE)
} else {
stop("no raw file: ",raw.file)
}
if (file.exists(as.character(log$dev.file[i]))) {
cal <- read.ECO.dev.file(as.character(log$dev.file[i]), ECO.type = log$ECO.type[i])
} else {
stop("No device file found: ", log$dev.file[i])
}
dark.file <- file.path(path.dark,log$dark.file[i])
if (file.exists(dark.file)) {
eco <- apply.ECO.cal(raw,
dev.file = as.character(log$dev.file[i]),
dark.file = as.character(dark.file),
ECO.type = log$ECO.type[i],
ECO.bands =log$ECO.bands[i])
} else {
warning("no dark data file or dark file not found")
eco <- apply.ECO.cal(raw,
dev.file = as.character(log$dev.file[i]),
dark.file = NA,
ECO.type = log$ECO.type[i],
ECO.bands =log$ECO.bands[i])
}
DateTime = as.POSIXct(paste(as.character(log$Date[i]),
as.character(log$UTCTime[i])),
"%Y%m%d %H:%M",
tz="UTC")
Anw <- as.numeric(log[i,grep("Anw",names(log))])
bb=compute.bb.discrete.from.ECO(eco,
ECO.type = log$ECO.type[i],
ECO.bands = log$ECO.bands[i],
Station = log$Station[i],
DateTime = DateTime,
Depth = log$Depth[i],
Anw = Anw,
Salinity = log$Salinity[i],
start = log$start[i],
end = log$end[i])
# update log
log$start[i] <- bb$start
log$end[i] <- bb$end
# plot data
time <- paste(unlist(str_split(log$UTCTime[i],":"))[1], unlist(str_split(log$UTCTime[i],":"))[2],sep="")
if (as.character(log$ECO.type[i]) == "VSF3") {
print("Plot VSF3 data")
if (log$ECO.bands[i] == "BG") {
minVSF = min(bb$Betau.mean - bb$Betau.sd)
maxVSF = max(bb$Betau.mean + bb$Betau.sd)
png(file=paste(path.png,"/",log$ECO.filename[i], ".png", sep=""),
width=6, height=8, units="in", res=300)
par(mfrow=c(3,1))
par(mar=c(4,5,1,1))
plot(bb$scattering.angle, eco$offset[1,],
xlab="Scattering Angle",
ylab="Offset",
ylim=c(min(c(eco$offset,cal$cal$Offset)),
max(c(eco$offset,cal$cal$Offset))),
xlim=c(90,180), col=4, pch=19)
points(bb$scattering.angle, eco$offset[2,],
col=3, pch=19)
lines(bb$scattering.angle, eco$offset[2,],
col=3)
lines(bb$scattering.angle, eco$offset[1,],
col=4)
lines(bb$scattering.angle, cal$cal$Offset[4:6],
col=3,lwd=3, lty=2)
lines(bb$scattering.angle, cal$cal$Offset[1:3],
col=4,lwd=3, lty=2)
legend("topright", c("Darks", "Calibration"), lwd=c(1,3), lty=c(1,2))
plot(bb$scattering.angle, bb$Betau.mean[,1],
xlim=c(90,180), pch=19, col=4,
ylim=c(minVSF, maxVSF),
xlab="Scattering Angle",
ylab=expression(paste(beta,"(",m^-1 ,sr^-1,")")),
main=paste(log$Station[i], log$DateTime[i]))
if (eco$dark.offset) title(sub="Dark offset applied")
errorbars(bb$scattering.angle, bb$Betau.mean[,1],xe=c(0,0,0),ye=bb$Betau.sd[,1], col=4)
points(bb$scattering.angle, bb$Betau.mean[,2],
pch=19, col=3)
lines(bb$scattering.angle, bb$Betau.mean[,1],
col=4)
lines(bb$scattering.angle, bb$Betau.mean[,2],
col=3)
errorbars(bb$scattering.angle,bb$Betau.mean[,2],xe=c(0,0,0),ye=bb$Betau.sd[,2], col=3)
points(bb$scattering.angle, bb$Beta[,1],
pch=25, col=4)
points(bb$scattering.angle, bb$Beta[,2],
pch=25, col=3)
legend("topright", c("uncor.", "corrected"), pch=c(19,25))
legend("bottomright", c("470", "532"), pch=c(19,19), col=c(4,3))
plot(bb$waves, bb$bb,
xlab="Wavelength", pch=19,
ylab=expression(b[b](m^-1)))
lines(bb$waves, bb$bb)
dev.off()
} else {
minVSF = min(bb$Betau.mean - bb$Betau.sd)
maxVSF = max(bb$Betau.mean + bb$Betau.sd)
png(file=paste(path.png,"/",log$ECO.filename[i], ".png", sep=""),
width=6, height=8, units="in", res=300)
par(mfrow=c(3,1))
par(mar=c(4,5,1,1))
plot(bb$scattering.angle, eco$offset,
xlab="Scattering Angle",
ylab="Offset",
ylim=c(min(c(eco$offset,cal$cal$Offset)),
max(c(eco$offset,cal$cal$Offset))),
xlim=c(90,180), pch=19)
lines(bb$scattering.angle, eco$offset)
if (log$ECO.bands[i] =="B") lines(bb$scattering.angle, cal$cal$Offset[1:3],lwd=3, lty=2)
if (log$ECO.bands[i] =="G") lines(bb$scattering.angle, cal$cal$Offset[4:6],lwd=3, lty=2)
if (log$ECO.bands[i] =="R") lines(bb$scattering.angle, cal$cal$Offset[7:9],lwd=3, lty=2)
legend("topright", c("Darks", "Calibration"), lwd=c(1,3), lty=c(1,2))
plot(bb$scattering.angle, bb$Betau.mean,
xlim=c(90,180), pch=19, col=4,
ylim=c(minVSF, maxVSF),
xlab="Scattering Angle",
ylab=expression(paste(beta,"(",m^-1 ,sr^-1,")")),
main=paste(log$Station[i], log$DateTime[i]))
if (eco$dark.offset) title(sub="Dark offset applied")
errorbars(bb$scattering.angle, bb$Betau.mean,xe=c(0,0,0),ye=bb$Betau.sd)
lines(bb$scattering.angle, bb$Betau.mean)
points(bb$scattering.angle, bb$Beta,pch=25)
legend("topright", c("uncor.", "corrected"), pch=c(19,25))
legend("bottomright", as.character(bb$waves),pch=c(19,25))
plot(bb$waves, bb$bb,
xlab="Wavelength", pch=19,
ylab=expression(b[b](m^-1)))
dev.off()
}
}
if (as.character(log$ECO.type[i]) == "BB9") {
print("Plot BB9 data")
minVSF = min(bb$Betau.mean - bb$Betau.sd)
maxVSF = max(bb$Betau.mean + bb$Betau.sd)
png(file=paste(path.png,"/",log$ECO.filename[i], ".png", sep=""),
width=6, height=8, units="in", res=300)
par(mfrow=c(3,1))
par(mar=c(4,5,1,1))
##### Plot the Offsets
plot(bb$waves, eco$offset,
xlab=expression(lambda),
ylab="Offset",
ylim=c(min(c(eco$offset,cal$cal$Offset)),
max(c(eco$offset,cal$cal$Offset))),
pch=19)
lines(bb$waves, eco$offset)
lines(bb$waves, cal$cal$Offset,lwd=3, lty=2)
legend("topright", c("Darks", "Calibration"), lwd=c(1,3), lty=c(1,2))
##### Plot the VSF
plot(bb$waves, bb$Betau.mean,
pch=19, col=4,
ylim=c(minVSF, maxVSF),
xlab=expression(lambda),
ylab=expression(paste(beta,"(",m^-1 ,sr^-1,")")),
main=paste(log$Station[i], log$DateTime[i]))
if (eco$dark.offset) title(sub="Dark offset applied")
errorbars(bb$waves, bb$Betau.mean,xe=rep(0,9),ye=bb$Betau.sd)
lines(bb$waves, bb$Betau.mean)
points(bb$waves, bb$Beta,pch=25)
legend("topright", c("uncor.", "corrected"), pch=c(19,25))
plot(bb$waves, bb$bbP,
xlab="Wavelength", pch=19,
ylab=expression(b[bp](m^-1)))
lines(bb$waves, bb$bbP)
dev.off()
}
# Save data in RData file format
save(bb, file=file.path(path.out,paste0(log$ECO.filename[i], ".RData")))
# update log file
write.table(log, file=log.file, quote = F, row.names = F, sep=",")
} else print(paste("Skipping file:", log$ECO.filename[i]))
}
}
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