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argonaut: read much of the third header
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@dankelley
dankelley committed Jan 9, 2020
1 parent 01cd61b commit f36061f
Showing 1 changed file with 94 additions and 7 deletions.
101 changes: 94 additions & 7 deletions R/adp.sontek.R
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Original file line number Diff line number Diff line change
@@ -1,5 +1,17 @@
## vim: tw=120 shiftwidth=4 softtabstop=4 expandtab:

sontekDateTime <- function(bytes, tz="UTC")
{
## Note the odd ordering of elements. See e.g. page 87 of [1]
ISOdatetime(readBin(bytes[1:2], "integer", size=2, endian="little"),
as.integer(bytes[4]), # month
as.integer(bytes[3]), # day
as.integer(bytes[6]), # hour
as.integer(bytes[5]), # minute
as.integer(bytes[8]) + as.integer(bytes[7])/100.0, # second + sec100
tz=tz)
}

#' Read a SonTek ADP File
#'
#' Read a SonTek acoustic-Doppler profiler file (see reference 1).
Expand Down Expand Up @@ -173,12 +185,15 @@ read.adp.sontek <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
## 36 = spare
## 37 int[16], so I guess 2-byte ints, signed?
} else if (type == "argonaut_adp") {
bufEXPORT<<-buf;message("exported bufEXPORT")
## See reference [2] print page 87, PDF page 99.
oceDebug(debug, "about to read 'Argonaut sensor configuration structure' (96 bytes)\n", style="red")
bytesInConfiguration <- readBin(buf[3:4], "integer", n=1, size=2, endian="little")
if (bytesInConfiguration != 96)
warning("bytes 3:4 of the header suggest", bytesInConfiguration, "but this should be 96\n")
## skip DateTimeType, which is 8 bytes long, in bytes 5:12
## 5:12 DateTimeType ConfigTime;
ConfigTime <- sontekDateTime(buf[5:12])
oceDebug(debug, vectorShow(ConfigTime))
cpuSoftwareVerNum <- as.integer(buf[13]) / 10 # CPUSoftwareVerNum [p83]
dspSoftwareVerNum <- as.integer(buf[14]) / 10 # DSPSoftwareVerNum [p83]
boardRev <- readBin(buf[15], "character", n=1, size=1, signed=TRUE) # BoardRev [p83]
Expand Down Expand Up @@ -217,16 +232,19 @@ read.adp.sontek <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
press.installed <- switch(as.integer(buf[35]) + 1, FALSE, TRUE) # nolint (variable not used)
oceDebug(debug, "skipping several things in 'Argonaut sensor configuration structure'\n")
## FIXME: there are quite a few more things defined in the table, but we skip for now.
if (buf[97] == 0x41 && buf[98] == 0x02) {
off <- 96
oceDebug(debug, "about to read 'Argonaut operation configuration structure' (64 bytes)\n", style="red")
nbytes <- readBin(buf[99:100], "integer", size=2, endian="little")
if (nbytes != 64)
warning("'Argonaut operation configuration structure' nbytes should be 64 but it is", nbytes, "\n")
off <- 96
oceDebug(debug, "about to see if we have 'Argonaut operation configuration structure' (64 bytes)\n")
if (buf[off+1] == 0x41 && buf[off+2] == 0x02) {
oceDebug(debug, "found 2-byte preface to 'Argonaut operation configuration structure' (64 bytes)\n", style="red")
## 1 char ConfigType;
## 2 char ConfigVer;
## 3:4 int Nbytes;
Nbytes <- readBin(buf[off+3:4], "integer", size=2, endian="little")
if (Nbytes != 64)
stop("'Argonaut operation configuration structure' nbytes should be 64 but it is ", Nbytes, "\n")
## 5:12 DateTimeType ConfigTime;
ConfigTime <- sontekDateTime(buf[off+5:12])
oceDebug(debug, vectorShow(ConfigTime))
## 13:14 int NpingsPerBeam;
NpingsPerBeam <- readBin(buf[off+13:14], "integer", size=2, endian="little")
oceDebug(debug, vectorShow(NpingsPerBeam))
Expand Down Expand Up @@ -267,6 +285,75 @@ read.adp.sontek <- function(file, from=1, to, by=1, tz=getOption("oceTz"),
## 57 char SdiFormat;
## 58:63 char Spare[6];
## 64 char DebugOn;
off <- off + 64
oceDebug(debug, "about to check for a 'User setup parameters structure' (258 bytes)\n")
if (buf[off+1] == 0x42 && buf[off+2] == 0x02) {
oceDebug(debug, "found 'User setup configuration structure' (258 bytes)\n", style="red")
## User setup parameters structure (258 bytes)
## 1 unsigned char ConfigType; 0x42
## 2 unsigned char ConfigVer; 0x02
## 3:4 unsigned int Nbytes; 258
nbytes <- readBin(buf[off+3:4], "integer", size=2, signed=FALSE, endian="little")
if (nbytes != 258)
stop("'Argonaut operation configuration structure' nbytes should be 258 but it is ", nbytes, "\n")
## 5:12 DateTimeType ConfigTime;
ConfigTime <- sontekDateTime(buf[off+5:12])
oceDebug(debug, vectorShow(ConfigTime))
## 13:14 int Temp;
## 15:16 int Sal;
## 17:18 int Cw;
## 19:20 unsigned int BlankDistance;
BlankDistance <- readBin(buf[off+19:20], "integer", size=2, signed=FALSE, endian="little")
oceDebug(debug, vectorShow(BlankDistance, postscript=" cm [expect ?? for issue 1637]"))
## 21:22 unsigned int PulseLength;
## 23:24 unsigned int CellSize;
CellSize <- readBin(buf[off+23:24], "integer", size=2, signed=FALSE, endian="little")
oceDebug(debug, vectorShow(CellSize, postscript=" cm [expect 350 for issue 1637]"))
## 25 char TempMode;
## 26:29 long AvgInterval;
## 30:33 long SampleInterval;
## 34:35 unsigned int PingInterval;
## 36:37 unsigned int BurstMode;
## 38:41 long BurstInterval;
## 42:43 unsigned int SamplesPerBurst;
## 44 char CoordSystem;
## 45 char OutMode;
## 46 char OutFormat;
## 47 char RecorderEnabled;
## 48 char RecorderMode;
## 49 char DeploymentMode;
## 50:58 char DeploymentName[9]
DeploymentName <- readBin(buf[off+50:59], "character", size=9, endian="little")
oceDebug(debug, vectorShow(DeploymentName))
## 59:66 DateTimeType BeginDeploymentDateTime
BeginDepoymentTime <- sontekDateTime(buf[off+59:66])
oceDebug(debug, vectorShow(BeginDepoymentTime))
## 67:126 char CommentLine1[60];
CommentLine1 <- readBin(buf[off+67:126], "character", size=60, endian="little")
oceDebug(debug, vectorShow(CommentLine1))
## 127:186 char CommentLine2[60];
CommentLine2 <- readBin(buf[off+127:186], "character", size=60, endian="little")
oceDebug(debug, vectorShow(CommentLine2))
## 187:246 char CommentLine3[60];
CommentLine3 <- readBin(buf[off+187:246], "character", size=60, endian="little")
oceDebug(debug, vectorShow(CommentLine3))
## 247 char AutoSleep;
## 248 char DynBoundAdj;
## 249:250 int CellBegin;
CellBegin <- readBin(buf[off+249:250], "integer", size=2, endian="little")
oceDebug(debug, vectorShow(CellBegin, postscript=" [expect ??? for issue 1637]"))
## 251:252 int CellEnd;
CellEnd <- readBin(buf[off+251:252], "integer", size=2, endian="little")
oceDebug(debug, vectorShow(CellEnd, postscript=" [expect ??? for issue 1637]"))
## 253:254 int CohLag;
## 255 char DataFormat;
## 256 char WaveSpectra;
## 257:258 int WaterDepth;
WaterDepth <- readBin(buf[off+251:252], "integer", size=2, endian="little")
oceDebug(debug, vectorShow(WaterDepth, postscript=" [expect ??? for issue 1637]"))
off <- off + 258
oceDebug(debug, "done with 'User setup configuration structure' (258 bytes); off=", off, "\n", style="bold")
}
} else {
warning("Argonaut operation configuration structure (64 bytes) not found; expected 0x41 0x02 0x40 but got",
" 0x", buf[97], " 0x", buf[98], " 0x", buf[99], sep="")
Expand Down

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