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adv.nortek.R
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## abbreviations:
## SIG = System Integrator Guide
## SIG2014 = system-integrator-manual_Dec2014_jan.pdf
## IMU = http://files.microstrain.com/3DM-GX3-35-Data-Communications-Protocol.pdf
read.adv.nortek <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
header=TRUE,
longitude=NA, latitude=NA,
type=c("vector", "aquadopp"),
haveAnalog1=FALSE,
haveAnalog2=FALSE,
debug=getOption("oceDebug"), monitor=FALSE,
processingLog)
{
## vvd=vector velocity data [p35 SIG], containing the data: pressure, vel, amp, corr (plus sensemble counter etc)
## vsd=velocity system data [p36 SIG], containing times, temperatures, angles, etc
## NOTE: we interpolate from vsd to vvd, to get the final data$time, etc.
type <- match.arg(type)
oceDebug(debug, "read.adv.nortek(file=\"", file, "\", from=", format(from),
", to=", if (!missing(to)) format(to) else "(missing)",
", by=", by, ", tz=\"", tz, "\", header=", header, ", longitude=", longitude, ", latitude=", latitude, ", type=\"", type, "\", debug=", debug, ", monitor=", monitor, ", processingLog=(not shown)) {\n", sep="", unindent=1)
if (is.numeric(by) && by < 1)
stop("cannot handle negative 'by' values")
if (by != 1)
warning("'by' argument only applies to fast-scale items such as velocity; temperature, etc. are not affected")
if (is.numeric(from) && from < 1)
stop("argument \"from\" must be 1 or larger")
if (!missing(to) && is.numeric(to) && to < 1)
stop("argument \"to\" must be 1 or larger")
if (is.character(file)) {
filename <- fullFilename(file)
file <- file(file, "rb")
on.exit(close(file))
}
if (!inherits(file, "connection"))
stop("argument `file' must be a character string or connection")
if (!isOpen(file)) {
filename <- "(connection)"
open(file, "rb")
on.exit(close(file))
}
if (!header)
stop("header must be TRUE")
oceDebug(debug, " read.adv.nortek() about to read header\n")
oceDebug(debug, " read.adv.nortek() finished reading header\n")
# find file length
seek(file, 0, "end")
fileSize <- seek(file, 0, "start")
oceDebug(debug, " fileSize=", fileSize, "\n")
buf <- readBin(file, "raw", fileSize)
header <- decodeHeaderNortek(buf, type="vector", debug=debug-1)
if (debug > 1) { # Note: need high debugging to get this
cat("\nheader is as follows:\n")
str(header)
}
res <- new("adv")
res@metadata$manufacturer <- "nortek"
res@metadata$instrumentType <- "vector"
res@metadata$filename <- filename
res@metadata$longitude <- longitude
res@metadata$latitude <- latitude
res@metadata$numberOfSamples <- NA # filled in later
res@metadata$numberOfBeams <- header$head$numberOfBeams # FIXME: check that this is correct
res@metadata$measurementStart <- NA # FIXME
res@metadata$measurementEnd <- NA # FIXME
res@metadata$samplingRate <- 512/header$user$averagingInterval # FIXME: why 512?
res@metadata$serialNumber <- header$hardware$serialNumber
res@metadata$internalCodeVersion <- header$hardware$picVersion
res@metadata$softwareVersion <- header$user$swVersion
res@metadata$hardwareRevision <- header$hardware$hwRevision
res@metadata$recSize <- header$hardware$recSize
res@metadata$velocityRange <- header$hardware$velocityRange
res@metadata$firmwareVersion <- header$hardware$fwVersion
res@metadata$hardwareConfiguration <- header$hardware$config
res@metadata$configPressureSensor <- header$head$configPressureSensor
res@metadata$configMagnetometerSensor <- header$head$configMagnetometerSensor
res@metadata$configTiltSensor <- header$head$configTiltSensor
res@metadata$beamAngle <- 25 # FIXME: should read from file
res@metadata$tiltSensorOrientation <- header$head$tiltSensorOrientation
res@metadata$frequency <- header$head$frequency
res@metadata$headSerialNumber <- header$head$headSerialNumber
res@metadata$bin1Distance <- header$user$blankingDistance # FIXME: is this right?
res@metadata$blankingDistance <- header$user$blankingDistance
res@metadata$measurementInterval <- header$user$measurementInterval
res@metadata$transformationMatrix <- header$head$transformationMatrix
res@metadata$deploymentName <- header$user$deploymentName
res@metadata$cellSize <- header$user$cellSize
res@metadata$velocityScale <- header$user$velocityScale
res@metadata$originalCoordinate <- header$user$originalCoordinate
res@metadata$oceCoordinate <- header$user$originalCoordinate
res@metadata$oceBeamUnspreaded <- FALSE
res@metadata$comments <- header$user$comments
if (missing(processingLog))
processingLog <- paste(deparse(match.call()), sep="", collapse="")
hitem <- processingLogItem(processingLog)
## Find the focus time by bisection, based on "sd" (system data, containing a time).
vsdStart <- NULL # prevent scope warning from rstudio; defined later anyway
bisectNortekVectorSd <- function(tFind, add=0, debug=0) { # tFind=time add=offset debug=debug
oceDebug(debug, "\n")
oceDebug(debug, "bisectNortekVectorSd(tFind=", format(tFind), ", add=", add, ", debug=", debug, ")\n")
vsdLen <- length(vsdStart)
lower <- 1
upper <- vsdLen
passes <- floor(10 + log(vsdLen, 2)) # won't need this many; only do this to catch coding errors
for (pass in 1:passes) {
middle <- floor((upper + lower) / 2)
t <- ISOdatetime(2000 + bcdToInteger(buf[vsdStart[middle]+8]), # year
bcdToInteger(buf[vsdStart[middle]+9]), # month
bcdToInteger(buf[vsdStart[middle]+6]), # day
bcdToInteger(buf[vsdStart[middle]+7]), # hour
bcdToInteger(buf[vsdStart[middle]+4]), # min
bcdToInteger(buf[vsdStart[middle]+5]), # sec
tz=tz)
if (tFind < t)
upper <- middle
else
lower <- middle
if (upper - lower < 2)
break
oceDebug(debug, "examine: t=", format(t), " middle=", middle, " lower=", lower, " upper=", upper, " pass=", pass, " of max=", passes, "\n")
}
middle <- middle + add
if (middle < 1)
middle <- 1
if (middle > vsdLen)
middle <- vsdLen
t <- ISOdatetime(2000 + bcdToInteger(buf[vsdStart[middle]+8]), # year
bcdToInteger(buf[vsdStart[middle]+9]), # month
bcdToInteger(buf[vsdStart[middle]+6]), # day
bcdToInteger(buf[vsdStart[middle]+7]), # hour
bcdToInteger(buf[vsdStart[middle]+4]), # min
bcdToInteger(buf[vsdStart[middle]+5]), # sec
tz=tz)
oceDebug(debug, "result: t=", format(t), " at vsdStart[", middle, "]=", vsdStart[middle], "\n")
return(list(index=middle, time=t)) # index is within vsd
}
## NOTE: system.time() indicates 0.2s to scan a 100Meg file [macpro desktop, circa 2009]
## "vvd" stands for "Vector Velocity Data" [bottom of p35 of SIG]
vvdStart <- .Call("locate_byte_sequences", buf, c(0xa5, 0x10), 24, c(0xb5, 0x8c), 0)
## "vsd" stands for "Vector System Data" [p36 of SIG]
vsdStart <- .Call("locate_byte_sequences", buf, c(0xa5, 0x11), 28, c(0xb5, 0x8c), 0)
## "vvdh" stands for "Vector Velocity Data Header" [p35 of SIG]
vvdhStart <- .Call("locate_byte_sequences", buf, c(0xa5, 0x12), 42, c(0xb5, 0x8c), 0)
## "imu" stands for 'inertial motion unit' [p30 SIG2014]
imuStart <- .Call("locate_vector_imu_sequences", buf)
haveIMU <- length(imuStart) > 0
if (haveIMU) {
IMUtype <- "unknown"
if (buf[imuStart[1]+5] == 0xc3) IMUtype <- "A"
else if (buf[imuStart[1]+5] == 0xcc) IMUtype <- "B"
else if (buf[imuStart[1]+5] == 0xd2) IMUtype <- "C"
else if (buf[imuStart[1]+5] == 0xd3) IMUtype <- "D"
else warning("unknown IMU type, with 5th byte 0x", buf[imuStart[1]+5], "; only 0xc3, 0xcc, 0xd2 and 0xd3 are recognized")
B4 <- sort(c(imuStart, imuStart+1, imuStart+2, imuStart+3))
if (IMUtype == "B") {
## a "tick" of the internal timestamp clock is 16 microseconds [IMU p 78]
IMUaccelx <- readBin(buf[B4+ 6],"numeric",size=4,n=length(imuStart),endian="little")
IMUaccely <- readBin(buf[B4+10],"numeric",size=4,n=length(imuStart),endian="little")
IMUaccelz <- readBin(buf[B4+14],"numeric",size=4,n=length(imuStart),endian="little")
IMUangrtx <- readBin(buf[B4+18],"numeric",size=4,n=length(imuStart),endian="little")
IMUangrty <- readBin(buf[B4+22],"numeric",size=4,n=length(imuStart),endian="little")
IMUangrtz <- readBin(buf[B4+26],"numeric",size=4,n=length(imuStart),endian="little")
IMUmagrtx <- readBin(buf[B4+30],"numeric",size=4,n=length(imuStart),endian="little")
IMUmagrty <- readBin(buf[B4+34],"numeric",size=4,n=length(imuStart),endian="little")
IMUmagrtz <- readBin(buf[B4+38],"numeric",size=4,n=length(imuStart),endian="little")
IMUM11 <- readBin(buf[B4+42],"numeric",size=4,n=length(imuStart),endian="little")
IMUM12 <- readBin(buf[B4+46],"numeric",size=4,n=length(imuStart),endian="little")
IMUM13 <- readBin(buf[B4+50],"numeric",size=4,n=length(imuStart),endian="little")
IMUM21 <- readBin(buf[B4+54],"numeric",size=4,n=length(imuStart),endian="little")
IMUM22 <- readBin(buf[B4+58],"numeric",size=4,n=length(imuStart),endian="little")
IMUM23 <- readBin(buf[B4+62],"numeric",size=4,n=length(imuStart),endian="little")
IMUM31 <- readBin(buf[B4+66],"numeric",size=4,n=length(imuStart),endian="little")
IMUM32 <- readBin(buf[B4+70],"numeric",size=4,n=length(imuStart),endian="little")
IMUM33 <- readBin(buf[B4+74],"numeric",size=4,n=length(imuStart),endian="little")
IMUtime <- readBin(buf[B4+78],"integer",size=4,n=length(imuStart),endian="little")/62500
} else {
warning("IMU type '", IMUtype, "' detected but can only handle type 'B' at present, so no data are being read")
}
}
vvdhTime <- ISOdatetime(2000 + bcdToInteger(buf[vvdhStart+8]), buf[vvdhStart+9], buf[vvdhStart+6], buf[vvdhStart+7], buf[vvdhStart+4],buf[vvdhStart+5], tz=tz)
vvdhRecords <- readBin(buf[sort(c(vvdhStart, vvdhStart+1))+10], "integer", size=2, n=length(vvdhStart), signed=FALSE, endian="little")
## Velocity scale. Nortek's System Integrator Guide (p36) says
## the velocity scale is in bit 1 of "status" byte (at offset 23)
## in the Vector System Data header. However, they seem to count
## bits in the opposite way as oce does, so their bit 1 (starting
## from 0) corresponds to our bit 7 (ending at 8).
##
## NOTE: the S.I.G. is confusing on the velocity scale, and this
## confusion resulted in a change to the present code on
## 2010-09-13. Page 35 of S.I.G. clearly states that velocities
## are in mm/s, which was used in the code previously. However,
## p44 contradicts this, saying that there are two possible scale
## factors, namely 1mm/s and 0.1mm/s. Starting on 2010-09-13, the
## present function started using this possibility of two scale
## factors, as determined in the next code line, following p36.
res@metadata$velocityScale <- if ("0" == substr(byteToBinary(buf[vsdStart[1] + 23], endian="big"), 7, 7)) 1e-3 else 0.1e-3
oceDebug(debug, "velocityScale=", res@metadata$velocityScale, "m/s (from VSD header byte 24, 0x",
as.raw(buf[vsdStart[1] + 23]), "(bit 7 of",
byteToBinary(buf[vsdStart[1] + 23], endian="big"), ")\n")
## Measurement start and end times.
vsdLen <- length(vsdStart)
res@metadata$measurementStart <- ISOdatetime(2000 + bcdToInteger(buf[vsdStart[1]+8]), # year
bcdToInteger(buf[vsdStart[1]+9]), # month
bcdToInteger(buf[vsdStart[1]+6]), # day
bcdToInteger(buf[vsdStart[1]+7]), # hour
bcdToInteger(buf[vsdStart[1]+4]), # min
bcdToInteger(buf[vsdStart[1]+5]), # sec
tz=tz)
res@metadata$measurementEnd <- ISOdatetime(2000 + bcdToInteger(buf[vsdStart[vsdLen]+8]), # year
bcdToInteger(buf[vsdStart[vsdLen]+9]), # month
bcdToInteger(buf[vsdStart[vsdLen]+6]), # day
bcdToInteger(buf[vsdStart[vsdLen]+7]), # hour
bcdToInteger(buf[vsdStart[vsdLen]+4]), # min
bcdToInteger(buf[vsdStart[vsdLen]+5]), # sec
tz=tz)
vvdLen <- length(vvdStart)
res@metadata$measurementDeltat <- (as.numeric(res@metadata$measurementEnd) - as.numeric(res@metadata$measurementStart)) / (vvdLen - 1)
toGiven <- !missing(to)
if (!toGiven) {
to <- length(vvdStart)
oceDebug(debug, "No 'to' given, so using whole dataset: to=", to, "\n")
}
## Window data buffer, using bisection in case of a variable number of vd between sd pairs.
if (inherits(from, "POSIXt")) {
if (!inherits(to, "POSIXt"))
stop("if 'from' is POSIXt, then 'to' must be, also")
fromPair <- bisectNortekVectorSd(from, -1, debug-1)
from <- fromIndex <- fromPair$index
toPair <- bisectNortekVectorSd(to, 1, debug-1)
to <- toIndex <- toPair$index
byTime <- ctimeToSeconds(by)
oceDebug(debug,
" from=", format(fromPair$t), " yields vsdStart[", fromIndex, "]\n",
" to =", format(toPair$t), " yields vsdStart[", toIndex, "]\n",
" by=", by, "byTime=", byTime, "s\n",
"vsdStart[",fromPair$index, "]=", vsdStart[fromPair$index], "at time", format(fromPair$t), "\n",
"vsdStart[", toPair$index, "]=", vsdStart[ toPair$index], "at time", format( toPair$t), "\n")
twoTimes <- ISOdatetime(2000 + bcdToInteger(buf[vsdStart[1:2]+8]), # year
bcdToInteger(buf[vsdStart[1:2]+9]), # month
bcdToInteger(buf[vsdStart[1:2]+6]), # day
bcdToInteger(buf[vsdStart[1:2]+7]), # hour
bcdToInteger(buf[vsdStart[1:2]+4]), # min
bcdToInteger(buf[vsdStart[1:2]+5]), # sec NOTE: nortek files lack fractional seconds
tz=tz)
vsd.dt <- as.numeric(twoTimes[2]) - as.numeric(twoTimes[1]) # FIXME: need # samplesPerBurst here
## Next two lines suggest that readBin() can be used instead of bcdToInteger ... I imagine it would be faster
##cat("month=", readBin(buf[vsdStart[1]+9], "integer", n=1, size=1, endian="little"), "(as readBin)\n")
##cat("month=", bcdToInteger(buf[vsdStart[1]+9]), "(as bcd)\n")
oceDebug(debug, "nrecords=", readBin(buf[vsdStart[1]+10:11], "integer", n=1, size=2, endian="little"), "\n")
oceDebug(debug, "vsd.dt=",vsd.dt,"(from twoTimes)\n")
vvdStart <- vvdStart[vsdStart[fromIndex] <= vvdStart & vvdStart <= vsdStart[toIndex]]
vvdDt <- vsd.dt * (toIndex - fromIndex) / length(vvdStart)
## find vvd region that lies inside the vsd [from, to] region.
vvdStartFrom <- max(1, vvdStart[vvdStart < fromPair$index])
vvdStartTo <- min(length(vvdStart), vvdStart[vvdStart > toPair$index])
} else {
## Window data buffer, using bisection in case of a variable number of vd between sd pairs.
## 2016-03-09: this code could never be executed ... I need a taller monitor or
## better eyes, so I an see bigger chunks of code! This block will get removed
## after the next gitcommit.
## if (inherits(from, "POSIXt")) {
## if (!inherits(to, "POSIXt"))
## stop("if 'from' is POSIXt, then 'to' must be, also")
## fromPair <- bisectNortekVectorSd(from, -1, debug-1)
## from <- fromIndex <- fromPair$index
## toPair <- bisectNortekVectorSd(to, 1, debug-1)
## to <- toIndex <- toPair$index
## byTime <- ctimeToSeconds(by)
## oceDebug(debug,
## " from=", format(fromPair$t), " yields vsdStart[", fromIndex, "]\n",
## " to =", format(toPair$t), " yields vsdStart[", toIndex, "]\n",
## " by=", by, "byTime=", byTime, "s\n",
## "vsdStart[",fromPair$index, "]=", vsdStart[fromPair$index], "at time", format(fromPair$t), "\n",
## "vsdStart[", toPair$index, "]=", vsdStart[ toPair$index], "at time", format( toPair$t), "\n")
## twoTimes <- ISOdatetime(2000 + bcdToInteger(buf[vsdStart[1:2]+8]), # year
## bcdToInteger(buf[vsdStart[1:2]+9]), # month
## bcdToInteger(buf[vsdStart[1:2]+6]), # day
## bcdToInteger(buf[vsdStart[1:2]+7]), # hour
## bcdToInteger(buf[vsdStart[1:2]+4]), # min
## bcdToInteger(buf[vsdStart[1:2]+5]), # sec NOTE: nortek files lack fractional seconds
## tz=tz)
## vsd.dt <- as.numeric(twoTimes[2]) - as.numeric(twoTimes[1]) # FIXME: need # samplesPerBurst here
## ## Next two lines suggest that readBin() can be used instead of bcdToInteger ... I imagine it would be faster
## ##cat("month=", readBin(buf[vsdStart[1]+9], "integer", n=1, size=1, endian="little"), "(as readBin)\n")
## ##cat("month=", bcdToInteger(buf[vsdStart[1]+9]), "(as bcd)\n")
## oceDebug(debug, "nrecords=", readBin(buf[vsdStart[1]+10:11], "integer", n=1, size=2, endian="little"), "\n")
## oceDebug(debug, "vsd.dt=",vsd.dt,"(from twoTimes)\n")
## vvdStart <- vvdStart[vsdStart[fromIndex] < vvdStart & vvdStart < vsdStart[toIndex]]
## vvdDt <- vsd.dt * (toIndex - fromIndex) / length(vvdStart)
## oceDebug(debug,
## 'vvdDt=',vvdDt,'\n',
## 'by=',by, "1/by=",1/by,"\n",
## "vvdStart after indexing:\n",
## str(vvdStart))
## ## find vvd region that lies inside the vsd [from, to] region.
## vvdStartFrom <- max(1, vvdStart[vvdStart < fromPair$index])
## vvdStartTo <- min(length(vvdStart), vvdStart[vvdStart > toPair$index])
## } else {
oceDebug(debug, 'numeric values for args from=',from,'to=',to,'by=', by, '\n')
fromIndex <- from
toIndex <- to
if (toIndex < 1 + fromIndex)
stop("need more separation between from and to")
oceDebug(debug, "fromIndex=", fromIndex, "toIndex=", toIndex, "\n")
oceDebug(debug, vectorShow(vvdStart, "before subset, vvdStart is"))
oceDebug(debug, vectorShow(vsdStart, "before subset, vsdStart is"))
vvdStart <- vvdStart[fromIndex:toIndex]
oceDebug(debug, vectorShow(vvdStart, "after subset, vvdStart is"))
## ensure that vvdStart pointers are bracketed by vsdStart pointers
## FIXME: but will this invalidate fromIndex and toIndex?
vsdStartFrom <- which(vvdStart[1] >= vsdStart)[1]
vsdStartTo <- which(vsdStart >= vvdStart[length(vvdStart)])[1]
oceDebug(debug, "vsdStartFrom=", vsdStartFrom, "and vsdStartTo=", vsdStartTo, "(before NA check)\n")
if (is.na(vsdStartTo))
vsdStartTo <- length(vsdStart)
oceDebug(debug, "vsdStartFrom=", vsdStartFrom, "and vsdStartTo=", vsdStartTo, "(after NA check)\n")
vsdStart <- vsdStart[seq(vsdStartFrom, vsdStartTo)]
oceDebug(debug, vectorShow(vsdStart, "after subset, vsdStart is"))
##}
}
oceDebug(debug, "about to trim vsdStart, based on vvdStart[1]=", vvdStart[1], " and vvdStart[length(vvdStart)]=", vvdStart[length(vvdStart)], "\n")
oceDebug(debug, vectorShow(vsdStart, "before trimming, vsdStart:"))
oceDebug(debug, "from=", from, "to=", to, "\n")
## Find spanning subset, expanded a little for now
subsetStart <- head(which(vvdStart[1] < vsdStart), 1)
if (subsetStart > 1)
subsetStart <- subsetStart - 1 # extend a bit (for now)
subsetEnd <- tail(which(vsdStart < vvdStart[length(vvdStart)]), 1)
oceDebug(debug, "first guess: subsetEnd=", subsetEnd, "\n")
if (subsetEnd < length(vsdStart))
subsetEnd <- subsetEnd + 1
oceDebug(debug, "try start vsdStart[subsetStart=", subsetStart, "] = ", vsdStart[subsetStart], "\n")
oceDebug(debug, "try end vsdStart[subsetEnd= ", subsetEnd, "] = ", vsdStart[subsetEnd], "\n")
oceDebug(debug, vectorShow(vsdStart, "before trimming, vsdStart:"))
vsdStart <- vsdStart[seq(subsetStart, subsetEnd-1, 1)]
oceDebug(debug, vectorShow(vsdStart, "after trimming, vsdStart:"))
if (2 > length(vsdStart))
stop("need at least 2 velocity-system-data chunks to determine the timing; try increasing the difference between 'from' and 'to'")
if (toIndex <= fromIndex)
stop("no data in specified range from=", format(from), " to=", format(to))
## we make the times *after* trimming, because this is a slow operation
## NOTE: the ISOdatetime() call takes 60% of the entire time for this function.
vsdTime <- ISOdatetime(2000 + bcdToInteger(buf[vsdStart+8]), # year
bcdToInteger(buf[vsdStart+9]), # month
bcdToInteger(buf[vsdStart+6]), # day
bcdToInteger(buf[vsdStart+7]), # hour
bcdToInteger(buf[vsdStart+4]), # min
bcdToInteger(buf[vsdStart+5]), # sec
tz=tz)
oceDebug(debug, "reading Nortek Vector, and using timezone: ", tz, "\n")
## update res@metadata$measurementDeltat
res@metadata$measurementDeltat <- mean(diff(as.numeric(vsdTime)), na.rm=TRUE) * length(vsdStart) / length(vvdStart) # FIXME
vsdLen <- length(vsdStart)
vsdStart2 <- sort(c(vsdStart, 1 + vsdStart))
voltage <- 0.1 * readBin(buf[vsdStart2 + 10], "integer", size=2, n=vsdLen, signed=FALSE, endian="little")
heading <- 0.1 * readBin(buf[vsdStart2 + 14], "integer", size=2, n=vsdLen, signed=TRUE, endian="little")
oceDebug(debug, vectorShow(heading, "heading"))
pitch <- 0.1 * readBin(buf[vsdStart2 + 16], "integer", size=2, n=vsdLen, signed=TRUE, endian="little")
oceDebug(debug, vectorShow(pitch, "pitch"))
roll <- 0.1 * readBin(buf[vsdStart2 + 18], "integer", size=2, n=vsdLen, signed=TRUE, endian="little")
oceDebug(debug, vectorShow(roll, "roll"))
temperature <- 0.01 * readBin(buf[vsdStart2 + 20], "integer", size=2, n=vsdLen, signed=TRUE, endian="little")
oceDebug(debug, vectorShow(temperature, "temperature"))
salinity <- header$user$salinity
oceDebug(debug, "salinity (in res@metadata):", salinity, "\n")
## byte 22 is an error code
## byte 23 is status, with bit 0 being orientation (p36 of Nortek's System Integrator Guide)
status <- buf[vsdStart[floor(0.5*length(vsdStart))] + 23]
res@metadata$orientation <- if ("0" == substr(byteToBinary(status, endian="big"), 1, 1)) "upward" else "downward"
# FIXME: should read roll and pitch "out of range" or "OK" here, in bites 3 and 2
##FIXME was wrong## res@metadata$burstLength <- round(length(vvdStart) / length(vsdStart), 0) # FIXME: surely this is in the header (?!?)
##FIXME was wrong## oceDebug(debug, vectorShow(res@metadata$burstLength, "burstLength"))
vvdStart2 <- sort(c(vvdStart, 1 + vvdStart))
vvdLen <- length(vvdStart) # FIXME: should be subsampled with 'by' ... but how???
if (haveAnalog1) { # FIXME: shouldn't this be auto-detected from 'USER' header?
analog1 <- readBin(buf[vvdStart + 8], "integer", n=vvdLen, size=1)
}
if (haveAnalog2) { # FIXME: shouldn't this be auto-detected from 'USER' header?
start <- sort(c(vvdStart+2, vvdStart+5))
analog2 <- readBin(buf[start], "integer", n=vvdLen, size=2, endian="little", signed=FALSE)
}
p.MSB <- as.numeric(buf[vvdStart + 4])
p.LSW <- readBin(buf[vvdStart2 + 6], "integer", size=2, n=vvdLen, signed=FALSE, endian="little")
pressure <- (65536 * p.MSB + p.LSW) / 1000
oceDebug(debug, vectorShow(pressure, "pressure"))
v <- array(double(), dim=c(vvdLen, 3))
v[,1] <- res@metadata$velocityScale*readBin(buf[vvdStart2 + 10], "integer", size=2, n=vvdLen, signed=TRUE, endian="little")
v[,2] <- res@metadata$velocityScale*readBin(buf[vvdStart2 + 12], "integer", size=2, n=vvdLen, signed=TRUE, endian="little")
v[,3] <- res@metadata$velocityScale*readBin(buf[vvdStart2 + 14], "integer", size=2, n=vvdLen, signed=TRUE, endian="little")
if (debug > 0.9) {
oceDebug(debug, "v[", dim(v), "] begins...\n")
print(matrix(as.numeric(v[1:min(3,vvdLen),]), ncol=3))
}
a <- array(raw(), dim=c(vvdLen, 3))
a[,1] <- buf[vvdStart + 16]
a[,2] <- buf[vvdStart + 17]
a[,3] <- buf[vvdStart + 18]
if (debug > 0.9) {
oceDebug(debug, "a[", dim(a), "] begins...\n")
print(matrix(as.numeric(a[1:min(3,vvdLen),]), ncol=3))
}
q <- array(raw(), dim=c(vvdLen, 3))
q[,1] <- buf[vvdStart + 19]
q[,2] <- buf[vvdStart + 20]
q[,3] <- buf[vvdStart + 21]
if (debug > 0.9) {
cat("q[", dim(q), "] begins...\n")
print(matrix(as.numeric(q[1:min(3,vvdLen),]), ncol=3))
}
##sec <- as.numeric(vsdTime) - as.numeric(vsdTime[1])
##vds <- var(diff(sec))
##BAD: vvdSec <- .Call("stutter_time", sec, 8)
#######vvdSec <- approx(seq(0, 1, length.out=length(vsdTime)), vsdTime, seq(0, 1, length.out=length(vvdStart)))$y
#######oceDebug(debug, vectorShow(vvdSec, "vvdSec"))
oceDebug(debug, vectorShow(vsdStart, "vsdStart"))
oceDebug(debug, vectorShow(vvdStart, "vvdStart"))
rm(buf)
gc()
## subset using 'by'
##by.orig <- by
if (is.character(by)) {
oceDebug(debug, "by='",by,"' given as argument to read.adv.nortek()\n",sep="")
oceDebug(debug, " ... infer to be", ctimeToSeconds(by), "s\n")
by <- ctimeToSeconds(by) / res@metadata$measurementDeltat
oceDebug(debug, " ... so step by" ,by,"through the data\n")
}
len <- length(vvdStart)
look <- seq(1, len, by=by)
oceDebug(debug, "length(vvdStart)=",length(vvdStart),"\n")
##vvdStart.orig <- vvdStart
vvdStart <- vvdStart[look]
oceDebug(debug, "length(vvdStart)=",length(vvdStart),"(after 'look'ing) with by=", by, "\n")
######vvdSec <- vvdSec[look]
pressure <- pressure[look] # only output at burst headers, not with velo (FIXME: huh??)
v <- v[look,]
a <- a[look,]
q <- q[look,]
if (0 < sum(vvdhRecords)) {
res@metadata$samplingMode <- "burst"
## Note: if we knew that all bursts were of the same length, we could use the same method
## as for the continuous case, specifying e.g. vvdhRecords[1] instead of 0. But do we know that?
## Also, what I'm doing here is probably fine, since bursts last an hour and so looping
## also them won't be expensive.
sss <- NULL
for (b in 1:length(vvdhRecords)) {
sss <- c(sss, as.numeric(vvdhTime[b]) + seq(0, by=1/res@metadata$samplingRate, length.out=vvdhRecords[b]))
}
time <- sss[look] + (vsdTime[1] - as.numeric(vsdTime[1]))
delayForWarmup <- 2 + 1 / (res@metadata$samplingRate * 2) # FIXME: this is from a forum posting, not an official doc.
time <- time + delayForWarmup
} else {
res@metadata$samplingMode <- "continuous"
time <- numberAsPOSIXct(.Call("adv_vector_time", vvdStart, vsdStart, vsdTime, vvdhStart, vvdhTime, 0, res@metadata$samplingRate))
}
res@metadata$numberOfSamples <- dim(v)[1]
res@metadata$numberOfBeams <- dim(v)[2]
res@metadata$velocityResolution <- res@metadata$velocityScale / 2^15
res@metadata$salinity <- salinity
## FIXME: guess-based kludge to infer whether continuous or burst-mode sample
res@data <- list(v=v, a=a, q=q,
time=time,
pressure=pressure,
timeBurst=vvdhTime,
recordsBurst=vvdhRecords,
voltageSlow=voltage,
timeSlow=vsdTime,
headingSlow=heading,
pitchSlow=pitch,
rollSlow=roll,
temperatureSlow=temperature)
if (haveIMU) {
if (IMUtype == "B") {
res@data$IMUaccelx <- IMUaccelx
res@metadata$units$IMUaccelx=list(unit=expression(m/s^2), scale="")
res@data$IMUaccely <- IMUaccely
res@metadata$units$IMUaccely=list(unit=expression(m/s^2), scale="")
res@data$IMUaccelz <- IMUaccelz
res@metadata$units$IMUaccelz=list(unit=expression(m/s^2), scale="")
res@data$IMUangrtx <- IMUangrtx
res@metadata$units$IMUangrtx=list(unit=expression(degree/s), scale="")
res@data$IMUangrty <- IMUangrty
res@metadata$units$IMUangrty=list(unit=expression(degree/s), scale="")
res@data$IMUangrtz <- IMUangrtz
res@metadata$units$IMUangrtz=list(unit=expression(degree/s), scale="")
res@data$IMUmagrtx <- IMUmagrtx
res@metadata$units$IMUmagrtx=list(unit=expression(gauss), scale="")
res@data$IMUmagrty <- IMUmagrty
res@metadata$units$IMUmagrty=list(unit=expression(gauss), scale="")
res@data$IMUmagrtz <- IMUmagrtz
res@metadata$units$IMUmagrtz=list(unit=expression(gauss), scale="")
res@data$IMUM11 <- IMUM11
res@data$IMUM12 <- IMUM12
res@data$IMUM13 <- IMUM13
res@data$IMUM21 <- IMUM21
res@data$IMUM22 <- IMUM22
res@data$IMUM23 <- IMUM23
res@data$IMUM31 <- IMUM31
res@data$IMUM32 <- IMUM32
res@data$IMUM33 <- IMUM33
res@data$IMUtime <- IMUtime
res@metadata$units$IMUtime=list(unit=expression(s), scale="")
} else {
warning("IMU type '", IMUtype, "' detected but can only handle type 'B' at present, so no data are being stored")
}
}
if (haveAnalog1)
res@data$analog1 <- analog1
if (haveAnalog2)
res@data$analog2 <- analog2
res@metadata$velocityResolution <- res@metadata$velocityScale
res@metadata$velocityMaximum <- res@metadata$velocityScale * 2^15
res@metadata$units$v <- list(unit=expression(m/s), scale="")
res@processingLog <- unclass(hitem)
res@metadata$units$v=list(unit=expression(m/s), scale="")
res@metadata$units$pressure=list(unit=expression(dbar), scale="")
res@metadata$units$headingSlow=list(unit=expression(degree), scale="")
res@metadata$units$pitchSlow=list(unit=expression(degree), scale="")
res@metadata$units$rollSlow=list(unit=expression(degree), scale="")
res@metadata$units$temperatureSlow=list(unit=expression(degree*C), scale="")
oceDebug(debug, "} # read.adv.nortek(file=\"", filename, "\", ...)\n", sep="", unindent=1)
res
}