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working on several ODF issues
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@dankelley
dankelley committed Jun 14, 2019
1 parent c901c0d commit 9201141
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50 changes: 43 additions & 7 deletions R/odf.R
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Original file line number Diff line number Diff line change
Expand Up @@ -302,6 +302,7 @@ findInHeader <- function(key, lines, returnOnlyFirst=TRUE, numeric=FALSE, prefix
#' \tabular{lll}{
#' \strong{Regexp} \tab \strong{Result} \tab \strong{Notes} \cr
#' \code{ALTB_*.*} \tab \code{altimeter} \tab \cr
#' \code{ATTU_*.*} \tab \code{attenuation} \tab \cr
#' \code{BATH_*.*} \tab \code{barometricDepth} \tab Barometric depth (of sensor? of water column?) \cr
#' \code{BEAM_*.*} \tab \code{a} \tab Used in \code{adp} objects \cr
#' \code{CNTR_*.*} \tab \code{scan} \tab Used in \code{ctd} objects \cr
Expand All @@ -316,12 +317,14 @@ findInHeader <- function(key, lines, returnOnlyFirst=TRUE, numeric=FALSE, prefix
#' \code{FFFF_*.*} \tab \code{flagArchaic} \tab Old flag name, replaced by \code{QCFF} \cr
#' \code{FLOR_*.*} \tab \code{fluorometer} \tab Used mainly in \code{ctd} objects \cr
#' \code{FWETLABS} \tab \code{fwetlabs} \tab Used in ?? \cr
#' \code{GEOP} \tab \code{geopotential} \tab
#' \code{HCDM} \tab \code{directionMagnetic} \tab \cr
#' \code{HCDT} \tab \code{directionTrue} \tab \cr
#' \code{HCSP} \tab \code{speedHorizontal} \tab \cr
#' \code{LATD_*.*} \tab \code{latitude} \tab \cr
#' \code{LOND_*.*} \tab \code{longitude} \tab \cr
#' \code{NSCT_*.*} \tab \code{v} \tab Used in \code{adp} objects \cr
#' \code{NONE_*.*} \tab \code{noWMOcode} \tab \cr
#' \code{OCUR_*.*} \tab \code{oxygenCurrent} \tab Used mainly in \code{ctd} objects \cr
#' \code{OSAT_*.*} \tab \code{oxygenSaturation} \tab Used mainly in \code{ctd} objects \cr
#' \code{OTMP_*.*} \tab \code{oxygenTemperature} \tab Used mainly in \code{ctd} objects \cr
Expand All @@ -332,14 +335,18 @@ findInHeader <- function(key, lines, returnOnlyFirst=TRUE, numeric=FALSE, prefix
#' \code{PSAL_*.*} \tab \code{salinity} \tab Used mainly in \code{ctd} objects \cr
#' \code{PSAR_*.*} \tab \code{par} \tab Used mainly in \code{ctd} objects \cr
#' \code{QCFF_*.*} \tab \code{flag} \tab Overall flag \cr
#' \code{SIGP_*.*} \tab \code{sigmaTheta} \tab Used mainly in \code{ctd} objects \cr
#' \code{REFR_*.*} \tab \code{reference} \tab \cr
#' \code{SIGP_*.*} \tab \code{sigmaTheta} \tab Used mainly in \code{ctd} objects \cr
#' \code{SIGT_*.*} \tab \code{sigmat} \tab Used mainly in \code{ctd} objects \cr
#' \code{SNCN_*.*} \tab \code{scanCounter} \tab Used mainly in \code{ctd} objects \cr
#' \code{SPAR_*.*} \tab \code{SPAR} \tab \cr
#' \code{SPVA_*.*} \tab \code{specificVolumeAnomaly} \tab \cr
#' \code{SYTM_*.*} \tab \code{time} \tab Used in many objects \cr
#' \code{TE90_*.*} \tab \code{temperature} \tab Used mainly in \code{ctd} objects \cr
#' \code{TEMP_*.*} \tab \code{temperature} \tab Used mainly in \code{ctd} objects \cr
#' \code{TOTP_*.*} \tab \code{pressureAbsolute} \tab Used mainly in \code{ctd} objects \cr
#' \code{UNKN_*.*} \tab \code{-} \tab The result is context-dependent \cr
#' \code{VAIS_*.*} \tab \code{BVFrequency} \tab \cr
#' \code{VCSP_*.*} \tab \code{w} \tab Used in \code{adp} objects \cr
#' }
#' Any code not shown in the list is transferred to the oce object without renaming, apart from
Expand Down Expand Up @@ -381,8 +388,8 @@ ODFNames2oceNames <- function(ODFnames, ODFunits=NULL,
oceDebug(debug, "ODFNames2oceNames() {\n", unindent=1, sep="")
n <- length(ODFnames)
if (n != length(ODFunits)) {
if (debug>0) message("ODFnames: ", paste(ODFnames, collapse=" "))
if (debug>0) message("ODFunits: ", paste(ODFunits, collapse=" "))
if (debug>0) cat("ODFnames: '", paste(ODFnames, collapse="' '"), "'\n", sep="")
if (debug>0) cat("ODFunits: '", paste(ODFunits, collapse="' '"), "'\n", sep="")
if (0 == length(ODFunits)) {
## Handle the case of missing UNITS
ODFunits <- rep("", n)
Expand Down Expand Up @@ -426,6 +433,7 @@ ODFNames2oceNames <- function(ODFnames, ODFunits=NULL,
## or whatever), this is a place to look.
oceDebug(debug, "STAGE 1 names: ", paste(names, collapse=" "), "\n")
names <- gsub("ALTB", "altimeter", names)
names <- gsub("ATTU", "attenuation", names)
names <- gsub("BATH", "waterDepth", names) # FIXME: is this water column depth or sensor depth?
names <- gsub("BEAM", "a", names) # FIXME: is this sensible?
names <- gsub("CNTR", "scan", names)
Expand All @@ -440,11 +448,13 @@ ODFNames2oceNames <- function(ODFnames, ODFunits=NULL,
names <- gsub("FFFF", "overallFlag", names)
names <- gsub("FLOR", "fluorometer", names)
names <- gsub("FWETLABS", "fwetlabs", names) # FIXME: what is this?
names <- gsub("GEOP", "geopotential", names)
names <- gsub("HCSP", "speedHorizontal", names)
names <- gsub("HCDM", "directionMagnetic", names)
names <- gsub("HCDT", "directionTrue", names)
names <- gsub("LATD", "latitude", names)
names <- gsub("LOND", "longitude", names)
names <- gsub("NONE", "noWMOcode", names)
names <- gsub("NSCT", "v", names)
names <- gsub("OCUR", "oxygenCurrent", names)
names <- gsub("OSAT", "oxygenSaturation", names)
Expand All @@ -456,14 +466,18 @@ ODFNames2oceNames <- function(ODFnames, ODFunits=NULL,
names <- gsub("PSAL", "salinity", names)
names <- gsub("PSAR", "par", names)
names <- gsub("QCFF", "QCFlag", names)
names <- gsub("REFR", "reference", names)
names <- gsub("SIGP", "sigmaTheta", names)
names <- gsub("SIGT", "sigmat", names) # in a moored ctd file examined 2014-05-15
names <- gsub("SNCN", "scanCounter", names)
names <- gsub("SPAR", "SPAR", names)
names <- gsub("SPVA", "specificVolumeAnomaly", names)
names <- gsub("SYTM", "time", names) # in a moored ctd file examined 2014-05-15
names <- gsub("TE90", "temperature", names)
names <- gsub("TEMP", "temperature", names)
names <- gsub("TOTP", "pressureAbsolute", names)
names <- gsub("UNKN", "unknown", names)
names <- gsub("VAIS", "BVFrequency", names)
names <- gsub("VCSP", "w", names)
## Step 3: recognize something from moving-vessel CTDs
## Step 4: some meanings inferred (guessed, really) from file CTD_HUD2014030_163_1_DN.ODF
Expand All @@ -485,13 +499,16 @@ ODFNames2oceNames <- function(ODFnames, ODFunits=NULL,
oceDebug(debug, "STAGE 4 names: ", paste(names, collapse=" "), "\n")
## Now deal with units
units <- list()
oceDebug(debug, "STAGE 5 units: ", paste(units, collapse=" "), "\n")
ODFunits <- gsub("^/", "1/",ODFunits)
oceDebug(debug, "STAGE 6 units: ", paste(units, collapse=" "), " (after changing e.g. '/m' to '1/m'\n")
for (i in seq_along(names)) {
## NOTE: this was originally coded with ==, but as errors in ODF
## formatting have been found, I've moved to grep() instead; for
## example, the sigma-theta case is done that way, because the
## original code expected kg/m^3 but then (issue 1051) I ran
## across an ODF file that wrote density as Kg/m^3.
oceDebug(1+debug, paste("ODFnames[",i,"]='",ODFnames[i],"', names[",i,"]='", names[i], "', ODFunits[", i, "]='", ODFunits[i], "'\n", sep=""))
oceDebug(debug, paste("ODFnames[",i,"]='",ODFnames[i],"', names[",i,"]='", names[i], "', ODFunits[", i, "]='", ODFunits[i], "'\n", sep=""))
units[[names[i]]] <- if (ODFunits[i] == "code") {
list(unit=expression(), scale="")
} else if (ODFunits[i] == "counts") {
Expand All @@ -510,12 +527,16 @@ ODFNames2oceNames <- function(ODFnames, ODFunits=NULL,
list(unit=expression(degree*C), scale="ITS-90")
} else if (ODFunits[i] == "ITS-90, deg C") {
list(unit=expression(degree*C), scale="ITS-90")
} else if (1 == length(grep("^hertz", ODFunits[i], ignore.case=TRUE))) {
list(unit=expression(Hz), scale="")
} else if (1 == length(grep("^m$", ODFunits[i], ignore.case=TRUE))) {
list(unit=expression(m), scale="")
} else if (1 == length(grep("^m\\*\\*3/s$", ODFunits[i], ignore.case=TRUE))) {
list(unit=expression(m^3/s), scale="")
} else if (1 == length(grep("^metres$", ODFunits[i], ignore.case=TRUE))) {
list(unit=expression(m), scale="")
} else if (ODFunits[i] == "m**3/kg") {
list(unit=expression(m^3/kg), scale="")
} else if (ODFunits[i] == "mg/m^3") {
list(unit=expression(mg/m^3), scale="")
} else if (ODFunits[i] == "mg/m**3") {
Expand Down Expand Up @@ -567,6 +588,8 @@ ODFNames2oceNames <- function(ODFnames, ODFunits=NULL,
list(unit=expression(mu*einstein/s/m^2), scale="")
} else if (1 == length(grep("^ug/l$", ODFunits[i], ignore.case=TRUE))) {
list(unit=expression(mu*g/l), scale="")
} else if (1 == length(grep("^umol/m\\*\\*2/s$", ODFunits[i], ignore.case=TRUE))) {
list(unit=expression(mu*mol/m^2/s), scale="")
} else if (1 == length(grep("^umol[ ]*photons/m2/s$", ODFunits[i], ignore.case=TRUE))) {
list(unit=expression(mu*mol/m^2/s), scale="")
} else if (1 == length(grep("^UTC$", ODFunits[i], ignore.case=TRUE))) {
Expand All @@ -575,13 +598,22 @@ ODFNames2oceNames <- function(ODFnames, ODFunits=NULL,
list(unit=expression(), scale="")
} else if (ODFunits[i] == "V") {
list(unit=expression(V), scale="")
} else if (ODFunits[i] == "1/cm") {
list(unit=expression(1/cm), scale="")
} else if (ODFunits[i] == "1/m") {
list(unit=expression(1/m), scale="")
} else if (1 == length(grep("^%$", ODFunits[i], ignore.case=TRUE))) {
list(unit=expression("%"), scale="")
} else if (1 == length(grep("^volts", ODFunits[i], ignore.case=TRUE))) {
list(unit=expression(V), scale="")
} else if (nchar(ODFunits[i]) == 0) {
list(unit=expression(), scale="")
} else {
warning("unable to interpret ODFunits[", i, "]='", ODFunits[i], "', for item named '", names[i], "'", sep="")
list(unit=parse(text=ODFunits[i]), scale=ODFunits[i])
warning("unable to interpret ODFunits[", i, "]='", ODFunits[i], "', for item named '", names[i], "', so making an educated guess using parse() or, as a last-ditch effort, simply copying the string", sep="")
uu <- try(parse(text=ODFunits[i]), silent=TRUE)
if (class(uu) == "try-error")
uu <- ODFunits[i]
list(unit=uu, scale="")
}
}
## Catch some problems I've seen in data
Expand Down Expand Up @@ -1142,6 +1174,9 @@ read.odf <- function(file, columns=NULL, header="list", debug=getOption("oceDebu
options(warn=options$warn)
##> oceDebug(debug, "nullValue=", nullValue, "; it's class is ", class(nullValue), "\n")

message("DEBUG: l1177")
browser()

ODFunits <- lines[grep("^\\s*UNITS\\s*=", lines)]
ODFunits <- gsub("^[^']*'(.*)'.*$", "\\1", ODFunits) # e.g. " UNITS= 'none',"
ODFunits <- trimws(ODFunits)
Expand All @@ -1166,6 +1201,7 @@ read.odf <- function(file, columns=NULL, header="list", debug=getOption("oceDebu
##> ODFnames <- gsub("_1$", "", ODFnames)
##> oceDebug(debug, "ODFnames: ", paste(ODFnames, collapse=" "), "\n")

message("DEBUG: about to call ODFNames2oceNames")
namesUnits <- ODFNames2oceNames(ODFnames, ODFunits, PARAMETER_HEADER=NULL, columns=columns, debug=debug-1)
## check for missing units, and warn if pressure and/or temperature lack units
w <- which(namesUnits[[1]]=="pressure")
Expand Down Expand Up @@ -1286,7 +1322,7 @@ read.odf <- function(file, columns=NULL, header="list", debug=getOption("oceDebu
for (w in which) {
ustring <- as.character(namesUnits$units[[w]]$unit)
if (length(ustring) && ustring != "" && ustring != "ratio")
warning("\"", ODFnames[w], "\" should be unitless, i.e. \"\", but the file has \"", ustring, "\" so that is retained in the object metadata; see ?read.odf for an example of rectifying this unit error.")
warning("\"", ODFnames[w], "\" should be unitless, but the file states the unit as \"", ustring, "\" so that is retained in the object metadata. This will likely cause problems. See ?read.odf for an example of rectifying this unit error.")
}
}

Expand Down
9 changes: 8 additions & 1 deletion man/ODFNames2oceNames.Rd
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