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ctd.sbe.R
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ctd.sbe.R
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#' Infer variable name, units and scale from a Seabird (.cnv) header line
#'
#' This function is used by \code{\link{read.ctd.sbe}} to infer data names
#' and units from the coding used by Teledyne/Seabird (SBE) \code{.cnv}
#' files. Lacking access to documentation on the SBE format,
#' the present function is based on inspection of a suite of CNV files
#' available to the \code{oce} developers.
#'
#' A few sample header lines that have been encountered are:
#'\preformatted{
#' # name 4 = t068: temperature, IPTS-68 [deg C]
#' # name 3 = t090C: Temperature [ITS-90, deg C]
#' # name 4 = t190C: Temperature, 2 [ITS-90, deg C]
#'}
#' Examination of several CNV files suggests that it is best to
#' try to infer the name from the characters between the "\code{=}"
#' and "\code{:}" characters, because the material after the colon
#' seems to vary more between sample files.
#'
#' The table given below indicates the translation patterns used. These are
#' taken from [1]. The \code{.cnv} convention for multiple sensors is to
#' include optional extra digits in the name, and these are indicated
#' with \code{~} in the table; their decoding is done with \code{\link{grep}}.
#'
#' It is important to note that this table is by no means complete, since there
#' are a great many SBE names listed in their document [1], plus names
#' not listed there but present in data files
#' supplied by prominent archiving agencies. If an SBE name is not recognized,
#' then the oce name is set to that SBE name. This can cause problems in
#' some other processing steps (e.g. if \code{\link{swRho}} or a similar
#' function is called with an \code{oce} object as first argument), and so
#' users are well-advised to rename the items as appropriate. The first
#' step in doing this is to pass the object to \code{summary()}, to discover
#' the SBE names in question. Then consult the SBE documentation to find
#' an appropriate name for the data, and either manipulate the names in the object
#' data slot directly or use
#' \code{\link{renameData}} to rename the elements. Finally, please publish
#' an 'issue' on the oce Github site \url{https://github.com/dankelley/oce/issues}
#' so that the developers can add the data type in question. (To save
#' development time, there is no plan to add all possible data types without
#' a reasonable and specific expression user interest. Oxygen alone has over forty
#' variants.)
#'
#' \tabular{llll}{
#' \strong{Key} \tab \strong{Result} \tab \strong{Unit;scale} \tab \strong{Notes} \cr
#' \code{alt} \tab \code{altimeter} \tab m \tab \cr
#' \code{altM} \tab \code{altimeter} \tab m \tab \cr
#' \code{accM} \tab \code{acceleration} \tab m/s^2 \tab \cr
#' \code{bat~} \tab \code{beamAttenuation} \tab 1/m \tab \cr
#' \code{C2-C1S/m} \tab \code{conductivityDifference} \tab S/m \tab \cr
#' \code{C2-C1mS/cm} \tab \code{conductivityDifference} \tab mS/cm \tab \cr
#' \code{C2-C1uS/cm} \tab \code{conductivityDifference} \tab uS/cm \tab \cr
#' \code{c~mS/cm} \tab \code{conductivity} \tab mS/cm \tab \cr
#' \code{c~S/m} \tab \code{conductivity} \tab S/m \tab \cr
#' \code{c~uS/cm} \tab \code{conductivity} \tab uS/cm \tab \cr
#' \code{CStarAt~} \tab \code{beamAttenuation} \tab 1/m \tab \cr
#' \code{CStarTr~} \tab \code{beamTransmission} \tab percent \tab \cr
#' \code{density~~} \tab \code{density} \tab kg/m^3 \tab \cr
#' \code{depS} \tab \code{depth} \tab m \tab \cr
#' \code{depSM} \tab \code{depth} \tab m \tab \cr
#' \code{depF} \tab \code{depth} \tab m \tab \cr
#' \code{depFM} \tab \code{depth} \tab m \tab \cr
#' \code{dz/dtM} \tab \code{descentRate} \tab m/s \tab \cr
#' \code{f~} \tab \code{frequency} \tab Hz \tab \cr
#' \code{f~~} \tab \code{frequency} \tab Hz \tab \cr
#' \code{flC~} \tab \code{fluorescence} \tab ug/l; Chelsea Aqua 3\tab \cr
#' \code{flCM} \tab \code{fluorescence} \tab ug/l; Chelsea Mini Chl Con\tab\cr
#' \code{flCUVA~} \tab \code{fluorescence} \tab ug/l; Chelsea UV Aquatracka\tab\cr
#' \code{flEC-AFL~} \tab \code{fluorescence} \tab mg/m^3; WET Labs ECO-AFL/FLtab\cr
#' \code{flS} \tab \code{fluorescence} \tab -; Seatech \tab \cr
#' \code{flScufa~} \tab \code{fluorescence} \tab -; Turner SCUFA [RFU]\tab\cr
#' \code{flSP} \tab \code{fluorescence} \tab -; Seapoint \tab \cr
#' \code{flSPR} \tab \code{fluorescence} \tab -; Seapoint, Rhodamine\tab \cr
#' \code{flSPuv} \tab \code{fluorescence} \tab -; Seapoint, UV \tab \cr
#' \code{flT} \tab \code{fluorescence} \tab -; Turner 10-005 flT\tab \cr
#' \code{gpa} \tab \code{geopotentialAnomaly} \tab -; J/kg \tab \cr
#' \code{latitude} \tab \code{latitude} \tab degN \tab \cr
#' \code{longitude} \tab \code{longitude} \tab degE \tab \cr
#' \code{n2satML/L} \tab \code{nitrogenSaturation} \tab ml/l \tab \cr
#' \code{n2satMg/L} \tab \code{nitrogenSaturation} \tab mg/l \tab \cr
#' \code{n2satumol/kg}\tab \code{nitrogenSaturation} \tab umol/kg \tab \cr
#' \code{nbin} \tab \code{nbin} \tab \tab \cr
#' \code{obsscufa~} \tab \code{backscatter} \tab NTU; Turner SCUFA \tab \cr
#' \code{opoxMg/L} \tab \code{oxygen} \tab mg/l; Optode, Anderaa\tab \cr
#' \code{opoxML/L} \tab \code{oxygen} \tab ml/l; Optode, Anderaa\tab \cr
#' \code{opoxMm/L} \tab \code{oxygen} \tab umol/l; Optode, Anderaa\tab \cr
#' \code{opoxPS} \tab \code{oxygen} \tab percent; Optode, Anderaa\tab \cr
#' \code{oxsatML/L} \tab \code{oxygen} \tab ml/l; Weiss \tab \cr
#' \code{oxsatMg/L} \tab \code{oxygen} \tab mg/l; Weiss \tab \cr
#' \code{oxsatMm/Kg} \tab \code{oxygen} \tab umol/kg; Weiss \tab \cr
#' \code{oxsolML/L} \tab \code{oxygen} \tab ml/l; Garcia-Gordon \tab \cr
#' \code{oxsolMg/L} \tab \code{oxygen} \tab mg/l; Garcia-Gordon \tab \cr
#' \code{oxsolMm/Kg} \tab \code{oxygen} \tab umol/kg; Garcia-Gordon\tab \cr
#' \code{par~} \tab \code{PAR} \tab -; Biospherical/Licor\tab \cr
#' \code{par/log} \tab \code{PAR} \tab log; Satlantic \tab \cr
#' \code{ph} \tab \code{pH} \tab - \tab \cr
#' \code{potemp~68C} \tab \code{thetaM} \tab degC; IPTS-68 \tab \cr
#' \code{potemp~90C} \tab \code{thetaM} \tab degC; ITS-90 \tab \cr
#' \code{pr} \tab \code{pressure} \tab dbar \tab 1 \cr
#' \code{prM} \tab \code{pressure} \tab dbar \tab \cr
#' \code{pr50M} \tab \code{pressure} \tab dbar; SBE50 \tab \cr
#' \code{prSM} \tab \code{pressure} \tab dbar \tab \cr
#' \code{prDM} \tab \code{pressure} \tab dbar; digiquartz \tab \cr
#' \code{prdE} \tab \code{pressure} \tab psi; strain gauge \tab 2 \cr
#' \code{prDE} \tab \code{pressure} \tab psi; digiquartz \tab 2 \cr
#' \code{prdM} \tab \code{pressure} \tab dbar; strain gauge \tab \cr
#' \code{prSM} \tab \code{pressure} \tab dbar; strain gauge \tab \cr
#' \code{ptempC} \tab \code{pressureTemperature} \tab degC; ITS-90 \tab 3 \cr
#' \code{pumps} \tab \code{pumpStatus} \tab \tab \cr
#' \code{rhodflTC~} \tab \code{Rhodamine} \tab ppb; Turner Cyclops \tab \cr
#' \code{sal~~} \tab \code{salinity} \tab -, PSS-78 \tab 4 \cr
#' \code{sbeox~ML/L} \tab \code{oxygen} \tab ml/l; SBE43 \tab \cr
#' \code{sbeox~Mm/Kg} \tab \code{oxygen} \tab umol/kg; SBE43 \tab \cr
#' \code{sbeox~Mm/L} \tab \code{oxygen} \tab umol/l; SBE43 \tab \cr
#' \code{sbeox~PS} \tab \code{oxygen} \tab percent; SBE43 \tab \cr
#' \code{sbeox~V} \tab \code{oxygenRaw} \tab V; SBE43 \tab \cr
#' \code{scan} \tab \code{scan} \tab - \tab \cr
#' \code{seaTurbMtr~} \tab \code{turbidity} \tab FTU; SeaPoint \tab \cr
#' \code{secS-priS} \tab \code{salinityDifference} \tab -, PSS-78 \tab \cr
#' \code{sigma-t} \tab \code{sigmaT} \tab kg/m^3 \tab \cr
#' \code{sigma-theta} \tab \code{sigmaTheta} \tab kg/m^3 \tab 5 \cr
#' \code{sigma-é} \tab \code{sigmaTheta} \tab kg/m^3 \tab 5 \cr
#' \code{spar} \tab \code{spar} \tab - \tab \cr
#' \code{specc} \tab \code{conductivity} \tab uS/cm \tab \cr
#' \code{sva} \tab \code{specificVolumeAnomaly} \tab 1e-8 m^3/kg; \tab \cr
#' \code{svCM~} \tab \code{soundSpeed} \tab m/s; Chen-Millero \tab \cr
#' \code{T2~68C} \tab \code{temperatureDifference} \tab degC; IPTS-68 \tab \cr
#' \code{T2~90C} \tab \code{temperatureDifference} \tab degC; ITS-90 \tab \cr
#' \code{t~68} \tab \code{temperature} \tab degC; IPTS-68 \tab \cr
#' \code{t~90} \tab \code{temperature} \tab degC; ITS-90 \tab \cr
#' \code{t~68} \tab \code{temperature} \tab degC; IPTS-68 \tab \cr
#' \code{t~68C} \tab \code{temperature} \tab degC; IPTS-68 \tab \cr
#' \code{t~90C} \tab \code{temperature} \tab degC; ITS-90 \tab \cr
#' \code{t090Cm} \tab \code{temperature} \tab degC; ITS-90 \tab \cr
#' \code{t4990C} \tab \code{temperature} \tab degC; ITS-90 \tab \cr
#' \code{tnc90C} \tab \code{temperature} \tab degC; ITS-90 \tab \cr
#' \code{tsa} \tab \code{thermostericAnomaly} \tab 1e-8 m^3/kg \tab \cr
#' \code{tv290C} \tab \code{temperature} \tab degC; ITS-90 \tab \cr
#' \code{t4968C} \tab \code{temperature} \tab degC; IPTS-68 \tab \cr
#' \code{tnc68C} \tab \code{temperature} \tab degC; IPTS-68 \tab \cr
#' \code{tv268C} \tab \code{temperature} \tab degC; IPTS-68 \tab \cr
#' \code{t190C} \tab \code{temperature} \tab degC; ITS-90 \tab \cr
#' \code{tnc290C} \tab \code{temperature} \tab degC; ITS-90 \tab \cr
#' \code{tnc268C} \tab \code{temperature} \tab degC; IPTS-68 \tab \cr
#' \code{t3890C~} \tab \code{temperature} \tab degC; ITS-90 \tab \cr
#' \code{t38~90C} \tab \code{temperature} \tab degC; ITS-90 \tab \cr
#' \code{t3868C~} \tab \code{temperature} \tab degC; IPTS-68 \tab \cr
#' \code{t38~38C} \tab \code{temperature} \tab degC; IPTS-68 \tab \cr
#' \code{timeH} \tab \code{time} \tab hour; elapsed \tab \cr
#' \code{timeJ} \tab \code{time} \tab day; elapsed \tab \cr
#' \code{timeK} \tab \code{time} \tab s; since Jan 1, 2000 \tab\cr
#' \code{timeM} \tab \code{time} \tab minute; elapsed \tab \cr
#' \code{timeN} \tab \code{time} \tab s; NMEA since Jan 1, 1970\tab\cr
#' \code{timeQ} \tab \code{time} \tab s; NMEA since Jan 1, 2000\tab\cr
#' \code{timeS} \tab \code{time} \tab s; elapsed \tab \cr
#' \code{turbflTC~} \tab \code{turbidity} \tab NTU; Turner Cyclops \tab \cr
#' \code{turbflTCdiff}\tab \code{turbidityDifference} \tab NTU; Turner Cyclops \tab \cr
#' \code{turbWETbb~} \tab \code{turbidity} \tab 1/(m*sr); WET Labs ECO\tab \cr
#' \code{turbWETbbdiff}\tab \code{turbidityDifference} \tab 1/(m*sr); WET Labs ECO\tab \cr
#' \code{turbWETntu~} \tab \code{turbidity} \tab NTU; WET Labs ECO \tab \cr
#' \code{turbWETntudiff}\tab \code{turbidityDifference} \tab NTU; WET Labs ECO \tab \cr
#' \code{upoly~} \tab \code{upoly} \tab - \tab \cr
#' \code{user~} \tab \code{user} \tab - \tab \cr
#' \code{v~~} \tab \code{voltage} \tab V \tab \cr
#' \code{wetBAttn} \tab \code{beamAttenuation} \tab 1/m; WET Labs AC3 \tab \cr
#' \code{wetBTrans} \tab \code{beamTransmission} \tab percent; WET Labs AC3\tab \cr
#' \code{wetCDOM~} \tab \code{fluorescence} \tab mg/m^3; WET Labs CDOM\tab \cr
#' \code{wetCDOMdiff} \tab \code{fluorescenceDifference} \tab mg/m^3; WET Labs CDOM\tab \cr
#' \code{wetChAbs} \tab \code{fluorescence} \tab 1/m; WET Labs AC3 absorption\tab \cr
#' \code{wetStar~} \tab \code{fluorescence} \tab mg/m^3; WET Labs WETstar\tab \cr
#' \code{wetStardiff} \tab \code{fluorescenceDifference} \tab mg/m^3; WET Labs WETstar\tab \cr
#' \code{xmiss} \tab \code{beamTransmission} \tab percent; Chelsea/Seatech\tab \cr
#' \code{xmiss~} \tab \code{beamTransmission} \tab percent; Chelsea/Seatech\tab \cr
#' }
#' Notes:
#' \itemize{
#' \item{1: 'pr' is in a Dalhousie-generated data file but seems not to be in [1].}
#' \item{2: this is an odd unit, and so if \code{sw*} functions are called on an object
#' containing this, a conversion will be made before performing the computation. Be
#' on the lookout for errors, since this is a rare situation.}
#' \item{3: assume ITS-90 temperature scale, since sample \code{.cnv} file headers do not specify it.}
#' \item{4: some files have PSU for this. Should we handle that? And are there other S scales to consider?}
#' \item{5: 'theta' may appear in different ways with different encoding configurations, set up
#' within R or in the operating system.}
#' }
#'
#' @param h The header line.
#' @param columns Optional list containing name correspondances, as described for
#' \code{\link{read.ctd.sbe}}.
#' @template debugTemplate
#' @return a list containing \code{name} (the oce name), \code{nameOriginal} (the SBE name) and \code{unit}.
#' @author Dan Kelley
#' @references
#' 1. A SBE data processing manual is at \url{http://www.seabird.com/document/sbe-data-processing-manual}.
#'
#' @family things related to \code{ctd} data
#' @family functions that interpret variable names and units from headers
cnvName2oceName <- function(h, columns=NULL, debug=getOption("oceDebug"))
{
if (length(h) != 1)
stop("oceNameFromSBE() expects just 1 line of header")
## An example, for which the grep is designed, is below.
## '# name 4 = t190C: Temperature, 2 [ITS-90, deg C]'
if (1 != length(grep("^# name [0-9][0-9]* = .*:.*$", h, ignore.case=TRUE)))
stop("header line does not contain a variable name")
## message("h: '", h, "'")
name <- gsub("^# name [0-9][0-9]* = (.*):.*$", "\\1", h, ignore.case=TRUE, useBytes=TRUE)
nameOriginal <- name
## If 'name' is mentioned in columns, then use columns and ignore the lookup table.
if (!is.null(columns)) {
##message("name:", name)
cnames <- names(columns)
for (i in seq_along(cnames)) {
if (name == columns[[i]]$name) {
##message("HIT; name=", cnames[i])
##message("HIT; unit$scale=", columns[[i]]$unit$scale)
return(list(name=cnames[i], nameOriginal=name, unit=columns[[i]]$unit))
}
}
}
## Since 'name' is not mentioned in 'columns', try looking it up. Some of these
## tests are a bit subtle, and could be wrong.
if (1 == length(grep("^alt[M]?$", name, useBytes=TRUE))) {
name <- "altimeter"
unit <- list(unit=expression(m), scale="")
} else if (1 == length(grep("^acc[M]?$", name, useBytes=TRUE))) {
name <- "acceleration"
unit <- list(unit=expression(m/s^2), scale="")
} else if (1 == length(grep("^bat[0-9]?$", name, useBytes=TRUE))) {
name <- "beamAttenuation"
unit <- list(unit=expression(1/m), scale="Chelsea/Seatech")
} else if (1 == length(grep("^C2-C1S/m$", name, useBytes=TRUE))) {
name <- "conductivityDifference"
unit <- list(unit=expression(S/m), scale="")
} else if (1 == length(grep("^C2-C1mS/cm$", name, useBytes=TRUE))) {
name <- "conductivityDifference"
unit <- list(unit=expression(mS/cm), scale="")
} else if (1 == length(grep("^C2-C1uS/cm$", name, useBytes=TRUE))) {
name <- "conductivityDifference"
unit <- list(unit=expression(mu*S/cm), scale="")
} else if (1 == length(grep("^c((_)|([0-2]))mS/cm$", name, useBytes=TRUE))) {
name <- "conductivity"
unit <- list(unit=expression(mS/cm), scale="")
} else if (1 == length(grep("^c((_)|([0-2]))S/m$", name, useBytes=TRUE))) {
name <- "conductivity"
unit <- list(unit=expression(S/m), scale="")
} else if (1 == length(grep("^c((_)|([0-2]))uS/cm$", name, useBytes=TRUE))) {
name <- "conductivity"
unit <- list(unit=expression(mu*S/cm), scale="")
} else if (1 == length(grep("^CStarTr[0-9]$", name, useBytes=TRUE))) {
name <- "beamTransmission"
unit <- list(unit=expression(percent), scale="WET Labs C-Star")
} else if (1 == length(grep("^CStarAt[0-9]$", name, useBytes=TRUE))) {
name <- "beamAttenuation"
unit <- list(unit=expression(1/m), scale="")
} else if (1 == length(grep("^density[0-9]{2}$", name, useBytes=TRUE))) {
name <- "density"
unit <- list(unit=expression(kg/m^3), scale="")
} else if (1 == length(grep("^dep[FS][M]?$", name, useBytes=TRUE))) {
name <- "depth"
unit <- list(unit=expression(m), scale="")
} else if (1 == length(grep("^dz/dt[M]?$", name, useBytes=TRUE))) {
name <- "descentRate"
unit <- list(unit=expression(m/s), scale="")
} else if (1 == length(grep("^f[0-9][0-9]?$", name, useBytes=TRUE))) {
name <- "frequency"
unit <- list(unit=expression(Hz), scale="")
} else if (1 == length(grep("^flag$", name, useBytes=TRUE))) {
name <- "flag"
unit <- list(unit=expression(), scale="")
} else if (1 == length(grep("^flC[1]?$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(mu*g/l), scale="Chelsea")
} else if (1 == length(grep("^flCM[1]?$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(mu*g/l), scale="Chelsea Mini Chl Con")
} else if (1 == length(grep("^flCUVA[12]?$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(mu*g/l), scale="Chelsea UV Aquatracka")
} else if (1 == length(grep("^flECO-AFL[0-9]?$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(mg/m^3), scale="WET Labs")
} else if (1 == length(grep("^flflTC[0-1]{1}$", name, useBytes=TRUE))) {
name <- "fluorescein"
unit <- list(unit=expression(ppb), scale="Turner Cyclops")
} else if (1 == length(grep("^flflTCdiff$", name, useBytes=TRUE))) {
name <- "fluoresceinDifference"
unit <- list(unit=expression(ppb), scale="Turner Cyclops")
} else if (1 == length(grep("^flScufa[0-9]?$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(), scale="Turner SCUFA")
} else if (1 == length(grep("^flSP[0-9]?$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(), scale="Seapoint")
} else if (1 == length(grep("^flSPR$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(), scale="Seapoint, Rhodamine")
} else if (1 == length(grep("^flSPuv[0-9]?$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(), scale="Seapoint, UV")
} else if (1 == length(grep("^flS$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(), scale="Seatech")
} else if (1 == length(grep("^flT$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(), scale="Turner")
} else if (1 == length(grep("^gpa$", name, useBytes=TRUE))) {
name <- "geopotentialAnomaly"
unit <- list(unit=expression(J/kg), scale="")
} else if (1 == length(grep("^latitude$", name, useBytes=TRUE))) {
name <- "latitude"
unit <- list(unit=expression(degree*N), scale="")
} else if (1 == length(grep("^longitude$", name, useBytes=TRUE))) {
name <- "longitude"
unit <- list(unit=expression(degree*E), scale="")
} else if (1 == length(grep("^n2satML/L$", name, useBytes=TRUE))) {
name <- "nitrogenSaturation"
unit <- list(unit=expression(ml/l), scale="")
} else if (1 == length(grep("^n2satMg/L$", name, useBytes=TRUE))) {
name <- "nitrogenSaturation"
unit <- list(unit=expression(mg/l), scale="")
} else if (1 == length(grep("^n2satumol/L$", name, useBytes=TRUE))) {
name <- "nitrogenSaturation"
unit <- list(unit=expression(mu*mol/l), scale="")
} else if (1 == length(grep("^n2satumol/kg$", name, useBytes=TRUE))) {
name <- "nitrogenSaturation"
unit <- list(unit=expression(mu*mol/kg), scale="")
} else if (1 == length(grep("^nbin$", name, useBytes=TRUE))) {
name <- "nbin"
unit <- list(unit=expression(), scale="")
} else if (1 == length(grep("^nbf$", name, useBytes=TRUE))) {
name <- "bottlesFired"
unit <- list(unit=expression(), scale="")
} else if (1 == length(grep("^obsscufa[1-9]{0,1}$", name, useBytes=TRUE))) {
name <- "backscatter"
unit <- list(unit=expression(NTU), scale="Turner SCUFA")
} else if (1 == length(grep("^opoxMg/L$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(mg/l), scale="Optode, Anderaa")
} else if (1 == length(grep("^opoxML/L$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(ml/l), scale="Optode, Anderaa")
} else if (1 == length(grep("^opoxMm/L$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(mu*mol/l), scale="Optode, Anderaa")
} else if (1 == length(grep("^opoxPS$", name, useBytes=TRUE))) {
name <- "oxygenSaturation"
unit <- list(unit=expression(percent), scale="Optode, Anderaa")
} else if (1 == length(grep("^oxsatML/L$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(ml/l), scale="Weiss")
} else if (1 == length(grep("^oxsatMg/L$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(mg/l), scale="Weiss")
} else if (1 == length(grep("^oxsatMm/Kg$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(mu*mol/kg), scale="Weiss")
} else if (1 == length(grep("^oxsolML/L$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(ml/l), scale="Garcia-Gordon")
} else if (1 == length(grep("^oxsolMg/L$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(mg/l), scale="Garcia-Gordon")
} else if (1 == length(grep("^oxsolMm/Kg$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(umol/kg), scale="Garcia-Gordon")
} else if (1 == length(grep("^cpar$", name, useBytes=TRUE))) {
name <- "CPAR/Corrected Irradience"
unit <- list(unit=expression(percent), scale="")
} else if (1 == length(grep("^par[0-9]?$", name, useBytes=TRUE))) {
name <- "par"
unit <- list(unit=expression(), scale="Biospherical/Licor")
} else if (1 == length(grep("^par/log$", name, useBytes=TRUE))) {
name <- "par"
unit <- list(unit=expression(log), scale="Satlantic")
} else if (1 == length(grep("^ph$", name, useBytes=TRUE))) {
name <- "pH"
unit <- list(unit=expression(), scale="")
} else if (1 == length(grep("^pr$", name, useBytes=TRUE))) {
name <- "pressure"
unit <- list(unit=expression(dbar), scale="")
} else if (1 == length(grep("^prdE$", name, useBytes=TRUE))) {
## Caution: English unit
name <- "pressurePSI"
unit <- list(unit=expression(psi), scale="")
} else if (1 == length(grep("^prDE$", name, useBytes=TRUE))) {
## Caution: English unit
name <- "pressurePSI"
unit <- list(unit=expression(psi), scale="")
} else if (1 == length(grep("^prM$", name, useBytes=TRUE))) {
name <- "pressure"
unit <- list(unit=expression(dbar), scale="")
} else if (1 == length(grep("^pr50M[0-9]?$", name, useBytes=TRUE))) {
name <- "pressure"
unit <- list(unit=expression(dbar), scale="SBE50")
} else if (1 == length(grep("^prDM$", name, useBytes=TRUE))) {
name <- "pressure"
unit <- list(unit=expression(dbar), scale="Digiquartz")
} else if (1 == length(grep("^pr[dS]M$", name, useBytes=TRUE))) {
name <- "pressure"
unit <- list(unit=expression(dbar), scale="Strain Gauge")
} else if (1 == length(grep("^ptempC$", name, useBytes=TRUE))) {
name <- "pressureTemperature"
unit <- list(unit=expression(degree*C), scale="ITS-90") # FIXME: guess on scale
} else if (1 == length(grep("^potemp[0-9]*68C$", name, useBytes=TRUE))) {
name <- "theta"
unit <- list(unit=expression(degree*C), scale="ITS-68")
} else if (1 == length(grep("^potemp[0-9]*90C$", name, useBytes=TRUE))) {
name <- "theta"
unit <- list(unit=expression(degree*C), scale="ITS-90")
} else if (1 == length(grep("^pumps$", name, useBytes=TRUE))) {
name <- "pumpStatus"
unit <- list(unit=expression(), scale="")
} else if (1 == length(grep("^rhodflTC[0-1]{1}$", name, useBytes=TRUE))) {
name <- "Rhodamine"
unit <- list(unit=expression(ppb), scale="Turner Cyclops")
} else if (1 == length(grep("^rhodflTCdiff$", name, useBytes=TRUE))) {
name <- "RhodamineDifference"
unit <- list(unit=expression(ppb), scale="Turner Cyclops")
} else if (1 == length(grep("^sal[0-9]{2}$", name, useBytes=TRUE))) {
name <- "salinity"
unit <- list(unit=expression(), scale="PSS-78") # FIXME: guess on scale
} else if (1 == length(grep("^sbeox[0-9]ML/L$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(ml/l), scale="SBE43")
} else if (1 == length(grep("^sbeox[0-9]Mg/L$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(mg/l), scale="SBE43")
} else if (1 == length(grep("^sbeox[0-9]Mm/Kg$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(mu*mol/kg), scale="SBE43")
} else if (1 == length(grep("^sbeox[0-9]Mm/L$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(mu*mol/l), scale="SBE43")
} else if (1 == length(grep("^sbeox[0-9]PS$", name, useBytes=TRUE))) {
name <- "oxygen"
unit <- list(unit=expression(percent), scale="SBE43")
} else if (1 == length(grep("^sbeox[0-9]V$", name, useBytes=TRUE))) {
name <- "oxygenRaw"
unit <- list(unit=expression(V), scale="SBE43")
} else if (1 == length(grep("^scan$", name, useBytes=TRUE))) {
name <- "scan"
unit <- list(unit=expression(), scale="")
} else if (1 == length(grep("^secS-priS$", name, useBytes=TRUE))) {
name <- "salinityDifference"
unit <- list(unit=expression(), scale="PSS-78")
} else if (1 == length(grep("^seaTurbMtr[1]?$", name, useBytes=TRUE))) {
name <- "turbidity"
unit <- list(unit=expression(FTU), scale="SeaPoint")
} else if (1 == length(grep("sigma-t[0-9]{2}", name, useBytes=TRUE))) {
name <- "sigmaT"
unit <- list(unit=expression(kg/m^3), scale="")
##} else if (1 == length(grep("sigma-.*[0-9]*", name, ignore.case=TRUE))) {
} else if (1 == length(grep("^sigma", name, useBytes=TRUE))) {
## there are several cases, and we match the sigma-theta case
## by exclusion, because of limited understanding of how
## to match non-ascii characters on Windows machines.
if (1 == length(grep("^sigma-t[0-9]{2}$", name, useBytes=TRUE))) {
name <- "sigmaT"
} else if (1 == length(grep("^sigma-1[0-9]{2}$", name, useBytes=TRUE))) {
name <- "sigma1"
} else if (1 == length(grep("^sigma-2[0-9]{2}$", name, useBytes=TRUE))) {
name <- "sigma2"
} else if (1 == length(grep("^sigma-3[0-9]{2}$", name, useBytes=TRUE))) {
name <- "sigma3"
} else if (1 == length(grep("^sigma-4[0-9]{2}$", name, useBytes=TRUE))) {
name <- "sigma4"
} else if (1 == length(grep("^sigma-\xe9[0-9]{2}$", name, useBytes=TRUE))) {
name <- "sigmaTheta"
## 2016-12-22 DK
## The above regexp matches for what we see in the supplied file
## system.file("extdata", "d201211_0011.cnv", package="oce")
## at line 54, an acute-accented "e" (which maybe looked like
## a theta to someone at SBE, when the format was invented. Clark
## found the SBE docs and did some tests, which made it clear that
## this accented "e" is always used, i.e. it is not just in some
## sample files. Therefore, the above should not need changes.
## However, it is worth explaining more, since the above regexp
## replaces one that we had before today. That older one failed
## on mswindows. On the assumption that this was an encoding issue,
## the readLines() that reads in the data (line 686 of the present file)
## was provided with an encoding of UTF-8, which is almost certainly
## what osx and linux are using by default, but it's a *bad idea*
## to rely on defaults, so we now set the encoding when we read
## the data. Note that this switch also required to use the
## useBytes=TRUE setting in all the grep() calls in the present
## block.
} else {
name <- "sigma" ## give up; this is a default
}
## In all these cases, the unit is the same
unit <- list(unit=expression(kg/m^3), scale="")
} else if (1 == length(grep("^spar$", name, useBytes=TRUE))) {
name <- "spar"
unit <- list(unit=expression(), scale="")
} else if (1 == length(grep("^specc$", name, useBytes=TRUE))) {
name <- "conductivity"
unit <- list(unit=expression(uS/cm), scale="")
} else if (1 == length(grep("^sva$", name, useBytes=TRUE))) {
name <- "specificVolumeAnomaly"
unit <- list(unit=expression(10^-8*m^3/kg), scale="")
} else if (1 == length(grep("^svCM[0-9]?$", name, useBytes=TRUE))) {
name <- "soundSpeed"
unit <- list(unit=expression(m/s), scale="Chen-Millero")
} else if (1 == length(grep("^T2-T[01]68C$", name, useBytes=TRUE))) {
name <- "temperatureDifference"
unit <- list(unit=expression(degree*C), scale="IPTS-68")
} else if (1 == length(grep("^T2-T[01]90C$", name, useBytes=TRUE))) {
name <- "temperatureDifference"
unit <- list(unit=expression(degree*C), scale="ITS-90")
} else if (1 == length(grep("^t[0-9]68((C)|(Cm))?$", name, useBytes=TRUE))) {
name <- "temperature"
unit <- list(unit=expression(degree*C), scale="IPTS-68")
} else if (1 == length(grep("^t[0-9]90((C)|(Cm))?$", name, useBytes=TRUE))) {
name <- "temperature"
unit <- list(unit=expression(degree*C), scale="ITS-90")
} else if (name %in% c("t4968C", "tnc68C", "tv268C", "tnc268C", "t3868C", "t3836C1", "t38_68C")) {
## [1] p169-170
name <- "temperature"
unit <- list(unit=expression(degree*C), scale="IPTS-68")
} else if (name %in% c("t4990C", "tnc90C", "tv290C", "tnc290C", "t3890C", "t3890C1", "t38_90C")) {
## [1] p169-170
name <- "temperature"
unit <- list(unit=expression(degree*C), scale="ITS-90")
} else if (1 == length(grep("^timeH$", name, useBytes=TRUE))) {
name <- "time"
unit <- list(unit=expression(hour), scale="elapsed")
} else if (1 == length(grep("^timeJ$", name, useBytes=TRUE))) {
name <- "time"
unit <- list(unit=expression(day), scale="elapsed")
} else if (1 == length(grep("^timeK$", name, useBytes=TRUE))) {
name <- "time"
unit <- list(unit=expression(s), scale="since Jan 1, 2000")
} else if (1 == length(grep("^timeM$", name, useBytes=TRUE))) {
name <- "time"
unit <- list(unit=expression(minute), scale="elapsed")
} else if (1 == length(grep("^timeN$", name, useBytes=TRUE))) {
name <- "time"
unit <- list(unit=expression(s), scale="NMEA since Jan 1, 1970")
} else if (1 == length(grep("^timeQ$", name, useBytes=TRUE))) {
name <- "time"
unit <- list(unit=expression(s), scale="NMEA since Jan 1, 2000")
} else if (1 == length(grep("^timeS$", name, useBytes=TRUE))) {
name <- "time"
unit <- list(unit=expression(s), scale="elapsed")
} else if (1 == length(grep("^tsa$", name, useBytes=TRUE))) {
name <- "thermostericAnomaly"
unit <- list(unit=expression(10^-8*m^3/kg), scale="")
} else if (1 == length(grep("^turbflTC[0-1]$", name, useBytes=TRUE))) {
name <- "turbidity"
unit <- list(unit=expression(NTU), scale="Turner Cyclops")
} else if (1 == length(grep("^turbflTCdiff$", name, useBytes=TRUE))) {
name <- "turbidityDifference"
unit <- list(unit=expression(NTU), scale="Turner Cyclops")
} else if (1 == length(grep("^turbWETbb[0-4]$", name, useBytes=TRUE))) {
name <- "turbidity"
unit <- list(unit=expression(1/m*sr), scale="WET Labs ECO")
} else if (1 == length(grep("^turbWETbbdiff$", name, useBytes=TRUE))) {
name <- "turbidityDifference"
unit <- list(unit=expression(1/m*sr), scale="WET Labs ECO")
} else if (1 == length(grep("^turbWETntu[0-5]$", name, useBytes=TRUE))) {
name <- "turbidity"
unit <- list(unit=expression(NTU), scale="WET Labs ECO")
} else if (1 == length(grep("^turbWETntudiff$", name, useBytes=TRUE))) {
name <- "turbidityDifference"
unit <- list(unit=expression(NTU), scale="WET Labs ECO")
} else if (1 == length(grep("^upoly[0-2]$", name, useBytes=TRUE))) {
name <- "upoly"
unit <- list(unit=expression(), scale="")
} else if (1 == length(grep("^user[1-5]$", name, useBytes=TRUE))) {
name <- "user"
unit <- list(unit=expression(), scale="")
} else if (1 == length(grep("^v[0-9][0-9]?$", name, useBytes=TRUE))) {
unit <- list(unit=expression(V), scale="")
} else if (1 == length(grep("^wetBAttn$", name, useBytes=TRUE))) {
name <- "beamAttenuation"
unit <- list(unit=expression(1/m), scale="WET Labs AC3")
} else if (1 == length(grep("^wetBTrans$", name, useBytes=TRUE))) {
name <- "beamTransmission"
unit <- list(unit=expression(percent), scale="WET Labs AC3")
} else if (1 == length(grep("^wetCDOM[0-5]{0,1}$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(mg/m^3), scale="WET Labs CDOM")
} else if (1 == length(grep("^wetCDOMdiff$", name, useBytes=TRUE))) {
name <- "fluorescenceDifference"
unit <- list(unit=expression(mg/m^3), scale="WET Labs CDOM")
} else if (1 == length(grep("^wetChAbs$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(1/m), scale="WET Labs AC3 absorption")
} else if (1 == length(grep("^wetStar[0-9]?$", name, useBytes=TRUE))) {
name <- "fluorescence"
unit <- list(unit=expression(mg/m^3), scale="WET Labs WETstar")
} else if (1 == length(grep("^wetStardiff$", name, useBytes=TRUE))) {
name <- "fluorescenceDifference"
unit <- list(unit=expression(mg/m^3), scale="WET Labs WETstar")
} else if (1 == length(grep("^xmiss[0-9]?$", name, useBytes=TRUE))) {
name <- "beamTransmission"
unit <- list(unit=expression(percent), scale="Chelsea/Seatech")
} else {
warning("unrecognized SBE name '", name, "'; consider using 'columns' to define this name")
unit <- list(unit=expression(), scale="")
}
if (debug > 0)
message("cnvName2oceName(): '", nameOriginal, "' -> '", name, "' (", unit$scale, ")")
list(name=name, nameOriginal=nameOriginal, unit=unit)
}
#' Read a Seabird CTD File
#' @template readCtdTemplate
#'
#' @details
#' This function reads files stored in Seabird \code{.cnv} format.
#' Note that these files can contain multiple sensors for a given field. For example,
#' the file might contain a column named \code{t090C} for one
#' temperature sensor and \code{t190C} for a second. The first will be denoted
#' \code{temperature} in the \code{data} slot of the return value, and the second
#' will be denoted \code{temperature1}. This means that the first sensor
#' will be used in any future processing that accesses \code{temperature}. This
#' is for convenience of processing, and it does not pose a limitation, because the
#' data from the second sensor are also available as e.g. \code{x[["temperature1"]]},
#' where \code{x} is the name of the returned value. For the details of the
#' mapping from \code{.cnv} names to \code{ctd} names, see \code{\link{cnvName2oceName}}.
#'
#' The original data names as stored in \code{file} are stored within the \code{metadata}
#' slot as \code{dataNamesOriginal}, and are displayed with \code{summary} alongside the
#' numerical summary. See the Appendix VI of [2] for the meanings of these
#' names (in the "Short Name" column of the table spanning pages 161 through 172).
#'
#' @section A note on sampling times:
#' SBE files can be somewhat confusing as regards the time of measurement. If
#' the data file contains metadata item called \code{start_time}, then
#' it is converted to a POSIX time object by \code{read.ctd.sbe} and stored
#' within the \code{metadata} slot as \code{"startTime"}. Until 2018-07-05, that
#' value was also stored in a \code{metadata} item named \code{"time"}, but this
#' caused confusion for data files that also have an elapsed-time column, and so
#' an entry named \code{"time"} is no longer stored in the \code{metadata} slot,
#' for those cases in which an elapsed-time column exists in the data file.
#' Importantly, there is a possibility for confusion in the storage
#' of that elapsed-time entry within the \code{data} slot, because \code{read.ctd.sbe}
#' renames all of the ten variants of elapsed time (see [2] for a list)
#' as, simply, \code{"time"} in the \code{data} slot of the returned value.
#' (Numerical suffices will be used if the file contains multiple elapsed-time
#' columns.) This imposes upon the user the burden of using \code{summary()} on
#' the return value, to discover the original name of the elapsed time column,
#' because \code{read.ctd.sbe} does not convert the 10 possible units to
#' a standard, but rather simply records the numerical values that are in
#' the data file. The most common column name is likely \code{timeS}, for
#' elapsed time in seconds; see [2] for the meanings of the other 9
#' schemes.
#'
#' @section A note on scales:
#' The user might encounter data files with a variety of scales for temperature and
#' salinity. Oce keeps track of these scales in the units it sets up for the stored
#' variables. For example, if \code{A} is a CTD object, then
#' \code{A[["temperatureUnit"]]$scale} is a character string that will indicate the scale.
#' Modern-day data will have \code{"ITS-90"} for that scale, and old data may have
#' \code{"IPTS-68"}. The point of saving the scale in this way is so that the various
#' formulas that deal with water properties can account for the scale, e.g. converting
#' from numerical values saved on the \code{"IPTS-68"} scale to the newer scale, using
#' \code{\link{T90fromT68}} before doing calculations that are expressed in
#' terms of the \code{"ITS-90"} scale. This is taken care of by retrieving temperatures
#' with the accessor function, e.g. writing \code{A[["temperature"]]} will either
#' retrieve the stored values (if the scale is ITS-90) or converted values (if
#' the scale is IPTS-68). Even though this procedure should work, users who
#' really care about the details of their data are well-advised to do a couple
#' of tests after examining the first data line of their data file in an editor.
#' Note that reading a file that contains IPTS-68 temperatures produces a warning.
#'
#' @examples
#' f <- system.file("extdata", "ctd.cnv", package="oce")
#' ## Read the file in the normal way
#' d <- read.ctd(f)
#' ## Read an imaginary file, in which salinity is named 'salt'
#' d <- read.ctd(f, columns=list(
#' salinity=list(name="salt", unit=list(expression(), scale="PSS-78"))))
#'
#' @references
#' 1. The Sea-Bird SBE 19plus profiler is described at
#' \code{http://www.seabird.com/products/spec_sheets/19plusdata.htm}. Some more
#' information is given in the Sea-Bird data-processing manual
#' \url{http://www.seabird.com/document/sbe-data-processing-manual}.
#'
#' 2. A SBE data processing manual is at \url{http://www.seabird.com/document/sbe-data-processing-manual};
#' as of 2018-07-05, the latest version was named
#' \code{SBEDataProcessing_7.26.4.pdf} and had release date 12/08/2017.
read.ctd.sbe <- function(file, columns=NULL, station=NULL, missingValue,
monitor=FALSE, debug=getOption("oceDebug"), processingLog, ...)
{
if (length(grep("\\*", file, ignore.case=TRUE))) {
oceDebug(debug, "read.ctd.sbe(file=\"", file, "\") { # will read a series of files\n", unindent=1)
files <- list.files(pattern=file)
nfiles <- length(files)
if (monitor)
pb <- txtProgressBar(1, nfiles, style=3)
res <- vector("list", nfiles)
for (i in 1:nfiles) {
res[[i]] <- read.ctd.sbe(files[i], debug=debug-1)
if (monitor)
setTxtProgressBar(pb, i)
}
oceDebug(debug, "} # read.ctd.sbe() {\n")
return(res)
}
oceDebug(debug, "read.ctd.sbe(file=\"", file, "\") {\n", unindent=1)
## Read Seabird data file. Note on headers: '*' is machine-generated,
## '**' is a user header, and '#' is a post-processing header.
filename <- ""
if (is.character(file)) {
filename <- fullFilename(file)
file <- file(file, "r")
on.exit(close(file))
}
if (!inherits(file, "connection"))
stop("argument `file' must be a character string or connection")
if (!isOpen(file)) {
open(file, "r")
on.exit(close(file))
}
res <- new("ctd")
## Header
scientist <- ship <- institute <- address <- cruise <- hexfilename <- ""
sampleInterval <- NA
sampleIntervalUnits <- ""
systemUploadTime <- NULL
latitude <- longitude <- NA
startTime <- NULL
waterDepth <- NA
date <- recovery <- NA
header <- c()
##conductivity.standard <- 4.2914
foundHeaderLatitude <- foundHeaderLongitude <- FALSE
serialNumber <- serialNumberConductivity <- serialNumberTemperature <- ""
## units$conductivity <- list(unit=expression(), scale="") # guess; other types are "mS/cm" and "S/m"
## units$temperature <- list(unit=expression(degree*C), scale="ITS-90") # guess; other option is IPTS-68
pressureType <- "sea" # guess; other option is "absolute"
## Silence warnings because binary files have 'NUL' characters that spew many warnings
warn <- options("warn")$warn
options(warn=-1)
lines <- readLines(file, encoding="UTF-8")
options(warn=warn)
## Get names and units of columns in the SBE data file
nameLines <- grep("^# name [0-9][0-9]* = .*:.*$", lines, ignore.case=TRUE)
colUnits <- vector("list", length(nameLines))
colNamesInferred <- NULL
dataNamesOriginal <- list()
namesUsed <- NULL
for (iline in seq_along(nameLines)) {
nu <- cnvName2oceName(lines[nameLines[iline]], columns, debug=debug-1)
##newname <- unduplicateName(nu$name, colNamesInferred)
##colNamesInferred <- c(colNamesInferred, newname)
## dataNamesOriginal[[newname]] <- nu$nameOriginal
if (nu$name %in% namesUsed) {
trial <- 2
while (paste(nu$name, trial, sep="") %in% namesUsed) {
trial <- trial + 1
##message("trial=", trial)
if (trial > 10)
break
}
## message("** REUSING NAME '", nu$name)
nu$name <- paste(nu$name, trial, sep="")
##message(" -> '", nu$name, "'")
}
namesUsed <- c(namesUsed, nu$name)
dataNamesOriginal[[nu$name]] <- nu$nameOriginal
colUnits[[iline]] <- nu$unit
colNamesInferred <- c(colNamesInferred, nu$name)
##message("SBE name=", nu$name, "; nameOriginal=", nu$nameOriginal, "; unit='", as.character(nu$unit$unit),"'")
}
colNamesInferred <- unduplicateNames(colNamesInferred)
names(colUnits) <- colNamesInferred
##print(colUnits)
## names(dataNamesOriginal) <- colNamesInferred
res@metadata$dataNamesOriginal <- dataNamesOriginal
##found.scan <- "scan" %in% colNamesInferred
##found.temperature <- "temperature" %in% colNamesInferred
foundPressure <- "pressure" %in% colNamesInferred
foundSalinity <- "salinity" %in% colNamesInferred
##found.time <- "time" %in% colNamesInferred
foundDepth <- "depth" %in% colNamesInferred
foundConductivity <- "conductivity" %in% colNamesInferred
foundConductivityRatio <- "conductivity.ratio" %in% colNamesInferred
## FIXME: should we insist on having salinity, temperature, and pressure?
fileType <- "unknown"
for (iline in seq_along(lines)) {
##message("** scan at iline ", iline)
line <- lines[iline]
##message(line)
#line <- scan(file, what='char', sep="\n", n=1, quiet=TRUE)
oceDebug(debug, paste("Examining header line '", line, "'\n", sep=""))
header <- c(header, line)
##if (length(grep("\*END\*", line))) #BUG# why is this regexp no good (new with R-2.1.0)
aline <- iconv(line, from="UTF-8", to="ASCII", sub="?")
if (length(grep("^\\s*\\*END\\*\\s*$", aline, perl=TRUE, useBytes=TRUE))) {
##message("got *END* at line ", iline)
## Sometimes SBE files have a header line after the *END* line.
iline <- iline + 1
if (length(grep("[a-cf-zA-CF-Z]", lines[iline])))
iline <- iline + 1
break
}
##if (iline>129) browser()
lline <- tolower(aline)
if (0 < regexpr(".*seacat profiler.*", lline))
serialNumber <- gsub("[ ].*$", "", gsub(".*sn[ ]*", "", lline))
if (length(grep("^\\* Temperature SN", lline, ignore.case=TRUE)))
serialNumberTemperature <- gsub("^.*=\\s", "", lline)
if (length(grep("^\\* Conductivity SN", lline, ignore.case=TRUE)))
serialNumberConductivity <- gsub("^.*=\\s", "", lline)
if (0 < (r<-regexpr("date:", lline))) {
d <- sub("(.*)date:([ ])*", "", lline)
date <- decodeTime(d, "%Y%m%d") # e.g. 20130701 Canada Day
}
if (length(grep("^#[ \t]*file_type[ \t]*=[ \t]*", lline))) {
## file_type = ascii
## file_type = binary
fileType <- gsub("[ \t\n]+$", "", gsub(".*=[ \t]*", "", lline))
##> message("fileType='", fileType, "'")
##> message("lline='", lline, "'")
}
##* NMEA UTC (Time) = Jul 28 2011 04:17:53
##* system upload time = jan 26 2010 13:02:57
if (length(grep("^\\* .*time.*=.*$", lline))) {
if (0 == length(grep("real-time sample interval", lline))) {
d <- sub(".*=", "", lline)
d <- sub("^ *", "", d)
d <- sub(" *$", "", d)
date <- decodeTime(d)
}
}
if (length(grep("^\\* Sea-Bird SBE (.*) Data File:$", lline, ignore.case=TRUE))) {
model <- gsub("^\\* sea-bird sbe (.*) data file:$", "\\1", lline)
res@metadata$model <- model
}
if (0 < (r<-regexpr("filename", lline)))
hexfilename <- sub("(.*)FileName =([ ])*", "", ignore.case=TRUE, lline)
if (0 < (r<-regexpr("system upload time", lline))) {
d <- sub("([^=]*)[ ]*=[ ]*", "", ignore.case=TRUE, lline)
systemUploadTime <- decodeTime(d)
oceDebug(debug, " systemUploadTime ", format(systemUploadTime), " inferred from substring '", d, "'\n", sep="")
}
## Styles:
## * NMEA Latitude = 47 54.760 N
## ** Latitude: 47 53.27 N
if (!foundHeaderLatitude && (0 < (r<-regexpr("latitude*[0-8]*", lline, ignore.case=TRUE)))) {
latitude <- parseLatLon(lline, debug=debug-1)
foundHeaderLatitude <- TRUE
}
if (!foundHeaderLongitude && (0 < (r<-regexpr("longitude*[0-8]*", lline, ignore.case=TRUE)))) {
longitude <- parseLatLon(lline, debug=debug-1)
foundHeaderLongitude <- TRUE
}
if (0 < (r<-regexpr("start_time =", lline))) {
d <- sub("#[ ]*start_time[ ]*=[ ]*", "", lline)
startTime <- decodeTime(d)
oceDebug(debug, " startTime ", format(startTime), "' inferred from substring '", d, "'\n", sep="")
}
if (0 < (r<-regexpr("ship:", lline))) {
ship <- sub("(.*)ship:([ \t])*", "", ignore.case=TRUE, line) # note: using full string
ship <- sub("[ \t]*$", "", ship)
}
if (0 < (r<-regexpr("scientist:", lline)))
scientist <- sub("(.*)scientist:([ ])*", "", ignore.case=TRUE, line) # full string
if (0 < (r<-regexpr("chef", lline)))
scientist <- sub("(.*):([ ])*", "", ignore.case=TRUE, line) # full string
if (0 < (r<-regexpr("institute:", lline)))
institute <- sub("(.*)institute:([ ])*", "", ignore.case=TRUE, line) # full string
if (0 < (r<-regexpr("address:", lline)))
address <- sub("(.*)address:([ ])*", "", ignore.case=TRUE, line) # full string
if (0 < (r<-regexpr("cruise:", lline))) {
cruise <- sub("(.*)cruise:([ ])*", "", ignore.case=TRUE, line) # full string
cruise <- sub("[ ]*$", "", ignore.case=TRUE, cruise) # full string
}
if (is.null(station)) {
if (0 < (r<-regexpr("station:", lline)))
station <- sub("[ ]*$", "", sub("(.*)station:([ ])*", "", ignore.case=TRUE, line))
if (0 < (r<-regexpr("station_name:", lline)))
station <- sub("[ ]*$", "", sub("(.*)station_name:([ ])*", "", ignore.case=TRUE, line))
}
if (0 < (r<-regexpr("recovery:", lline)))
recovery <- sub("(.*)recovery:([ ])*", "", lline)
if (length(grep("^#[ \t]+bad_flag[ \t]*=", lline))) {
## bad_flag = -9.990e-29
bad_flag <- sub("#[ \t]*bad_flag[ \t]*=[ \t]*", "", lline)
if (missing(missingValue))
missingValue <- as.numeric(bad_flag)
}
if (0 < (r<-regexpr("depth", lline))) {
## "** Depth (m): 3447 "
look <- sub("[a-z:()]*", "", lline, ignore.case=TRUE)
look <- gsub("^[*a-zA-Z\\(\\) :]*", "", lline, ignore.case=TRUE)
look <- gsub("[ ]*", "", look, ignore.case=TRUE)
oceDebug(debug, " trying to get water depth from '", lline, "', reduced to '", look, "'\n", sep="")
if (!length(grep('[a-zA-Z]', look))) {
waterDepth<- as.numeric(look)
oceDebug(debug, "got waterDepth: ", waterDepth, "\n")
}
}
if (0 < (r<-regexpr("water depth:", lline))
|| 0 < (r<-regexpr(pattern="profondeur", text=lline))) {
## Examples from files in use by author:
##** Profondeur: 76
##** Water Depth: 40 m
look <- sub("[ ]*$", "", sub(".*:[ ]*", "", lline))
linesplit <- strsplit(look, " ")[[1]]
nitems <- length(linesplit)
if (nitems == 1) {
waterDepth <- as.numeric(linesplit[1])
} else if (nitems == 2) {
unit <- linesplit[2]
if (unit == "m") {
waterDepth <- as.numeric(linesplit[1])
} else if (unit == "km") {
waterDepth <- 1000 * as.numeric(linesplit[1])
} else {
warning("ignoring unit on water depth '", look, "'")
}
} else {
warning("cannot interpret water depth from '", lline, "'")
}
}
## [1] "# interval = seconds: 1
## [1] "# interval = decibars: 1
if (length(grep("^# interval = .*$", lline))) {
##print(lline)
value <- gsub("^.*:[ ]*([0-9.]*)[ ]*$", "\\1", lline)
##cat("value='", value, "'\n", sep="")
##cat("value='", as.numeric(value), "'\n", sep="")
units <- gsub("^.*=[ ]*(.*):(.*)$", "\\1", lline)
##cat("units='", units, "'\n", sep="")
sampleInterval <- as.numeric(value)
if (units == "seconds")
units <- "s"
else if (units == "decibars")
units <- "dbar"
##cat("units='", units, "'\n", sep="")
sampleIntervalUnits <- units
} else if (0 < (r<-regexpr("^. sample rate =", lline))) {
## * sample rate = 1 scan every 5.0 seconds
rtmp <- lline
rtmp <- sub("(.*) sample rate = ", "", rtmp)
rtmp <- sub("scan every ", "", rtmp)
rtmp <- strsplit(rtmp, " ")
## if (length(rtmp[[1]]) != 3)
## warning("cannot parse sample-rate string in `",line,"'")
sampleInterval <- as.double(rtmp[[1]][2]) / as.double(rtmp[[1]][1])
sampleIntervalUnits <- "s"
if (rtmp[[1]][3] == "minutes") {
sampleInterval <- sampleInterval / 60
} else {
if (rtmp[[1]][3] == "hours") {
sampleInterval <- sampleInterval / 3600
} else {
warning("cannot understand `", rtmp[[1]][2], "' as a unit of time for sampleInterval")
}
}
}
}
oceDebug(debug, "Finished reading header\n")
if (debug > 0) {
if (is.nan(sampleInterval))
warning("'* sample rate =' not found in header")
if (is.nan(latitude))
warning("'** Latitude:' not found in header")
if (is.nan(longitude))
warning("'** Longitude:' not found in header")
if (is.null(date))
warning("'** Date:' not found in header")
if (is.null(recovery))
warning("'** Recovery' not found in header")
}
## Require p,S,T data at least
if (!("temperature" %in% colNamesInferred))
warning("cannot find temperature in this file; try using columns argument if this is an error")
res@metadata$header <- header
res@metadata$type <- "SBE"
res@metadata$hexfilename <- hexfilename # from instrument
res@metadata$serialNumber <- serialNumber
res@metadata$serialNumberTemperature <- serialNumberTemperature
res@metadata$serialNumberConductivity <- serialNumberConductivity
res@metadata$pressureType <- pressureType
res@metadata$units <- colUnits
names(res@metadata$units) <- colNamesInferred
res@metadata$systemUploadTime <- systemUploadTime
res@metadata$ship <- ship
res@metadata$scientist <- scientist
res@metadata$institute <- institute
res@metadata$address <- address
res@metadata$cruise <- cruise
res@metadata$station <- station
res@metadata$deploymentType <- "unknown"
res@metadata$date <- date