Read an adp File in Teledyne/RDI Format

Read a Teledyne/RDI ADCP file (called 'adp' in oce). This can handle a variety of file/instrument types, by recognizing telltale byte sequences in the data. The scope is limited to types that are documented adequately in Teledyne/RDI manuals. In some instances, the manuals provide some information but not enough to enable inclusion here, for example in the case for wave data (see https://github.com/dankelley/oce/issues/2216).

Usage

read.adp.rdi(
  file,
  from,
  to,
  by,
  tz = getOption("oceTz"),
  longitude = NA,
  latitude = NA,
  type = c("workhorse"),
  which,
  encoding = NA,
  monitor = FALSE,
  despike = FALSE,
  processingLog,
  testing = FALSE,
  debug = getOption("oceDebug"),
  ...
)

Arguments

file: a connection or a character string giving the name of the file to load. (For read.adp.sontek.serial, this is generally a list of files, which will be concatenated.)
from: indication of the first profile to read. This can be an integer, the sequence number of the first profile to read, or a POSIXt time before which profiles should be skipped, or a character string that converts to a POSIXt time (assuming UTC timezone). See “Examples”, and make careful note of the use of the tz argument. If from is not supplied, it defaults to 1.
to: an optional indication of the last profile to read, in a format as described for from. As a special case, to=0 means to read the file to the end. If to is not supplied, then it defaults to 0.
by: an optional indication of the stride length to use while walking through the file. If this is an integer, then by-1 profiles are skipped between each pair of profiles that is read, e.g. the default by=1 means to read all the data. (For RDI files only, there are some extra features to avoid running out of memory; see “Memory considerations”.)
tz: character string indicating time zone to be assumed in the data.
longitude: optional signed number indicating the longitude in degrees East.
latitude: optional signed number indicating the latitude in degrees North.
type: character string indicating the type of instrument.
which: optional character value. If this is "??" then the only other parameters that are examined are file and debug, read.adp.rdi() works by locating the indices in file at which data segments begin, and storing them as index in a list that is returned. The other entry of the list is time, the time of the observation.
encoding: ignored.
monitor: boolean value indicating whether to indicate the progress of reading the file, by using txtProgressBar() or otherwise. The value of monitor is changed to FALSE automatically, for non-interactive sessions.
despike: if TRUE, despike() will be used to clean anomalous spikes in heading, etc.
processingLog: if provided, the action item to be stored in the log. (Typically only provided for internal calls; the default that it provides is better for normal calls by a user.)
testing: logical value (IGNORED).
debug: a flag that turns on debugging. Set to 1 to get a moderate amount of debugging information, or to 2 to get more.
...: optional additional arguments that some (but not all) read.adp.*() functions pass to lower-level functions.

Value

An adp object. The contents of that object make sense for the particular instrument type under study, e.g. if the data file contains NMEA strings, then navigational data will be stored in an item called nmea in the data slot).

Details

If a heading bias had been set with the EB command during the setup for the deployment, then a heading bias will have been stored in the file's header. This value is stored in the object's metadata as metadata$heading.bias. Importantly, this value is subtracted from the headings stored in the file, and the result of this subtraction is stored in the objects heading value (in data$heading). It should be noted that read.adp.rdi() was tested for firmware version 16.30. For other versions, there may be problems. For example, the serial number is not recognized properly for version 16.28.

In Teledyne/RDI ADP data files, velocities are coded to signed 2-byte integers, with a scale factor being used to convert to velocity in metres per second. These two facts control the maximum recordable velocity and the velocity resolution, values that may be retrieved for an ADP object name d with d[["velocityMaximum"]] and d[["velocityResolution"]].

Handling of old file formats

Early PD0 file formats stored the year of sampling with a different base year than that used in modern files. To accommodate this, read.adp.rdi examines the inferred year, and if it is greater than 2050, then 100 years are subtracted from the time. This offset was inferred by tests with sample files, but not from RDI documentation, so it is somewhat risky. If the authors can find RDI documentation that indicates the condition in which this century offset is required, then a change will be made to the code. Even if not, the method should not cause problems for a long time.

Names of items in data slot

The names of items in the data slot are below. Not all items are present for ll file varieties; use e.g. names(d[["data"]]) to determine the names used in an object named d. In this list, items are either a vector (with one sample per time of measurement), a matrix with first index for time and second for bin number, or an array with first index for time, second for bin number, and third for beam number. Items are of vector type, unless otherwise indicated.

Item	Meaning
`a`	signal amplitude array (units?)
`ambientTemp`	ambient temperature (degC)
`attitude`	attitude (deg)
`attitudeTemp`	(FIXME add a description here)
`avgMagnitudeVelocityEast`	(FIXME add a description here)
`avgMagnitudeVelocityNorth`	(FIXME add a description here)
`avgSpeed`	(FIXME add a description here)
`avgTrackMagnetic`	(FIXME add a description here)
`avgTrackTrue`	(FIXME add a description here)
`avgTrueVelocityEast`	(FIXME add a description here)
`avgTrueVelocityNorth`	(FIXME add a description here)
`br`	bottom range matrix (m)
`bv`	bottom velocity matrix (m/s)
`contaminationSensor`	(FIXME add a description here)
`depth`	depth (m)
`directionMadeGood`	(FIXME add a description here)
`distance`	(FIXME add a description here)
`firstLatitude`	latitude at start of profile (deg)
`firstLongitude`	longitude at start of profile (deg)
`firstTime`	(FIXME add a description here)
`g`	data goodness matrix (units?)
`heading`	instrument heading (degrees)
`headingStd`	instrument heading std-dev (deg)
`lastLatitude`	latitude at end of profile (deg)
`lastLongitude`	longitude at end of profile (deg)
`lastTime`	(FIXME add a description here)
`numberOfHeadingSamplesAveraged`	(FIXME add a description here)
`numberOfMagneticTrackSamplesAveraged`	(FIXME add a description here)
`numberOfPitchRollSamplesAveraged`	(FIXME add a description here)
`numberOfSpeedSamplesAveraged`	(FIXME add a description here)
`numberOfTrueTrackSamplesAveraged`	(FIXME add a description here)
`pitch`	instrument pitch (deg)
`pitchStd`	instrument pitch std-dev (deg)
`pressure`	pressure (dbar)
`pressureMinus`	(FIXME add a description here)
`pressurePlus`	(FIXME add a description here)
`pressureStd`	pressure std-dev (dbar)
`primaryFlags`	(FIXME add a description here)
`q`	data quality array
`roll`	instrument roll (deg)
`rollStd`	instrument roll std-dev (deg)
`salinity`	salinity
`shipHeading`	ship heading (deg)
`shipPitch`	ship pitch (deg)
`shipRoll`	ship roll (deg)
`soundSpeed`	sound speed (m/s)
`speedMadeGood`	speed over ground (?) (m/s)
`speedMadeGoodEast`	(FIXME add a description here)
`speedMadeGoodNorth`	(FIXME add a description here)
`temperature`	temperature (degC)
`time`	profile time (POSIXct)
`v`	velocity array (m/s)
`xmitCurrent`	transmit current (unit?)
`xmitVoltage`	transmit voltage

Memory considerations

For RDI files only, and only in the case where by is not specified, an attempt is made to avoid running out of memory by skipping some profiles in large input files. This only applies if from and to are both integers; if they are times, none of the rest of this section applies.

A key issue is that RDI files store velocities in 2-byte values, which is not a format that R supports. These velocities become 8-byte (numeric) values in R. Thus, the R object created by read.adp.rdi will require more memory than that of the data file. A scale factor can be estimated by ignoring vector quantities (e.g. time, which has just one value per profile) and concentrating on matrix properties such as velocity, backscatter, and correlation. These three elements have equal dimensions. Thus, each 4-byte slide in the data file (2 bytes + 1 byte + 1 byte) corresponds to 10 bytes in the object (8 bytes + 1 byte + 1 byte). Rounding up the resultant 10/4 to 3 for safety, we conclude that any limit on the size of the R object corresponds to a 3X smaller limit on file size.

Various things can limit the size of objects in R, but a strong upper limit is set by the space the operating system provides to R. The least-performant machines in typical use appear to be Microsoft-Windows systems, which limit R objects to about 2e6 bytes (see ?Memory-limits). Since R routinely duplicates objects for certain tasks (e.g. for call-by-value in function evaluation), read.adp.rdi uses a safety factor in its calculation of when to auto-decimate a file. This factor is set to 3, based partly on the developers' experience with datasets in their possession. Multiplied by the previously stated safety factor of 3, this suggests that the 2 GB limit on R objects corresponds to approximately a 222 MB limit on file size. In the present version of read.adp.rdi, this value is lowered to 200 MB for simplicity. Larger files are considered to be "big", and are decimated unless the user supplies a value for the by argument.

The decimation procedure has two cases.

If from=1 and to=0 (or if neither from or to is given), then the intention is to process the full span of the data. If the input file is under 200 MB, then by defaults to 1, so that all profiles are read. For larger files, by is set to the ceiling() of the ratio of input file size to 200 MB.
If from exceeds 1, and/or to is nonzero, then the intention is to process only an interior subset of the file. In this case, by is calculated as the ceiling() of the ratio of bbp*(1+to-from) to 200 MB, where bbp is the number of file bytes per profile. Of course, by is set to 1, if this ratio is less than 1.

If the result of these calculations is that by exceeds 1, then messages are printed to alert the user that the file will be decimated, and also monitor is set to TRUE, so that a textual progress bar is shown (if the session is interactive).

Development Notes

An important part of the work of this function is to recognize what will be called "data chunks" by two-byte ID sequences. This function is developed in a practical way, with emphasis being focussed on data files in the possession of the developers. Since Teledyne-RDI tends to introduce new ID codes with new instruments, that means that read.adp.rdi may not work on recently-developed instruments.

The following two-byte ID codes are recognized by read.adp.rdi at this time (with bytes listed in natural order, LSB byte before MSB). Items preceded by an asterisk are recognized, but not handled, and so produce a warning.

Byte 1	Byte 2	Meaning
0x00	0x01	velocity
0x00	0x01	velocity
0x00	0x02	correlation
0x00	0x03	echo intensity
0x00	0x04	percent good
0x00	0x06	bottom track
0x00	0x0a	Sentinel vertical beam velocity
0x00	0x0b	Sentinel vertical beam correlation
0x00	0x0c	Sentinel vertical beam amplitude
0x00	0x0d	Sentinel vertical beam percent good
0x00	0x20	VMDASS
0x00	0x30	Binary Fixed Attitude header
0x00	0x32	Sentinel transformation matrix
0x00	0x0a	Sentinel data
0x00	0x0b	Sentinel correlation
0x00	0x0c	Sentinel amplitude
0x00	0x0d	Sentinel percent good
0x01	0x0f	?? something to do with V series and 4-beam

Lacking a comprehensive Teledyne-RDI listing of ID codes, the authors have cobbled together a listing from documents to which they have access, as follows.

Table 33 of reference 3 lists codes as follows:

Standard ID	Standard plus 1D	DESCRIPTION
MSB LSB	MSB LSB
— —	— —
7F 7F	7F 7F	Header
00 00	00 01	Fixed Leader
00 80	00 81	Variable Leader
01 00	01 01	Velocity Profile Data
02 00	02 01	Correlation Profile Data
03 00	03 01	Echo Intensity Profile Data
04 00	04 01	Percent Good Profile Data
05 00	05 01	Status Profile Data
06 00	06 01	Bottom Track Data
20 00	20 00	Navigation
30 00	30 00	Binary Fixed Attitude
30 40-F0	30 40-F0	Binary Variable Attitude

Table 6 on p90 of reference 4 lists "Fixed Leader Navigation" ID codes (none of which are handled by read.adp.rdi yet) as follows (the format is reproduced literally; note that e.g. 0x2100 is 0x00,0x21 in the oce notation):

ID	Description
0x2100	$xxDBT
0x2101	$xxGGA
0x2102	$xxVTG
0x2103	$xxGSA
0x2104	$xxHDT, $xxHGD or $PRDID

and following pages in that manual reveal the following meanings

Symbol	Meaning
`DBT`	depth below transducer
`GGA`	global positioning system
`VTA`	track made good and ground speed
`GSA`	GPS DOP and active satellites
`HDT`	heading, true
`HDG`	heading, deviation, and variation
`PRDID`	heading, pitch and roll

Error recovery

Files can sometimes be corrupted, and read.adp.rdi has ways to handle two types of error that have been noticed in files supplied by users.

There are two bytes within each ensemble that indicate the number of bytes to check within that ensemble, to get the checksum. Sometimes, those two bytes can be erroneous, so that the wrong number of bytes are checked, leading to a failed checksum. As a preventative measure, read.adp.rdi checks the stated ensemble length, whenever it detects a failed checksum. If that length agrees with the length of the most recent ensemble that had a good checksum, then the ensemble is declared as faulty and is ignored. However, if the length differs from that of the most recent accepted ensemble, then read.adp.rdi goes back to just after the start of the ensemble, and searches forward for the next two-byte pair, namely 0x7f 0x7f, that designates the start of an ensemble. Distinct notifications are given about these two cases, and they give the byte numbers in the original file, as a way to help analysts who want to look at the data stream with other tools.
At the end of an ensemble, the next two characters ought to be 0x7f 0x7f, and if they are not, then the next ensemble is faulty. If this error occurs, read.adp.rdi attempts to recover by searching forward to the next instance of this two-byte pair, discarding any information that is present in the mangled ensemble.

In each of these cases, warnings are printed about ensembles that seem problematic. Advanced users who want to diagnose the problem further might find it helpful to examine the original data file using other tools. To this end, read.adp.rdi inserts an element named ensembleInFile into the metadata slot. This gives the starting byte number of each inferred ensemble within the original data file. For example, if d is an object read with read.adp.rdi, then using

plot(d[["time"]][-1], diff(d[["ensembleInFile"]]))

can be a good way to narrow in on problems.

Changes

The bq (bottom-track quality) field was called bc until 2023-02-09. See https://github.com/dankelley/oce/issues/2039 for discussion.

How the binary file is decoded

This file type, like other acoustic-Doppler types, is read with a hybrid R/C++ system, for efficiency. The processing steps are sketched below, for users who want to inspect the code or build upon it.

In R, readBin() is used to insert the file contents into a vector of type raw.
In C++, this raw vector is scanned byte by byte, to find the starting indices of data "chunks", or subsections of the data that correspond to individual sampling times. Checksum computations are also done at this stage, to detect possible data corruption. Warnings are issued for any bad chunks, and they are skipped in further processing. The valid starting points are then passed back to R as a vector of type integer.
In R, readBin() is used to read the components of each chunk. For speed, this is done in a vectorized fashion. For example, all the velocities in the whole file are read in a single call to readBin(). This process is done for each of the data fields that are to be handled. Importantly, these readBin() calls are tailored to the data, using values of the size, endian and signed parameters that are tailored to the structure of the given component. Scaling factors are then applied as required, to convert the components to physical units.
Finally, in R, the acquired items are inserted into the data or metadata slot of the return value, according to oce convention.

References

Teledyne-RDI, 2007. WorkHorse commands and output data format. P/N 957-6156-00 (November 2007). (Section 5.3 h details the binary format, e.g. the file should start with the byte 0x7f repeated twice, and each profile starts with the bytes 0x80, followed by 0x00, followed by the sequence number of the profile, represented as a little-endian two-byte short integer. read.adp.rdi uses these sequences to interpret data files.)
Teledyne RD Instruments, 2015. V Series monitor, sentinel Output Data Format. P/N 95D-6022-00 (May 2015). SV_ODF_May15.pdf
Teledyne RD Instruments, 2014. Ocean Surveyor / Ocean Observer Technical Manual. P/N 95A-6012-00 (April 2014). OS_TM_Apr14.pdf
Teledyne RD Instruments, 2001. WinRiver User's Guide International Version. P/N 957-6171-00 (June 2001) WinRiver User Guide International Version.pdf.pdf

Author

Dan Kelley and Clark Richards

Examples

adp <- read.adp.rdi(system.file("extdata", "adp_rdi.000", package = "oce"))
summary(adp)
#> ADP Summary
#> -----------
#> 
#> * Filename:          "/private/var/folders/8b/l4h64m1j22v5pb7vj049ff140000gn/T/Rtmp7MlyRz/temp_libpathefc53c50397f/oce/extdata/adp_rdi.000"
#> * Instrument:        adcp
#> * Manufacturer:      teledyne rdi
#> * Serial number:     unknown
#> * Firmware:          16.28
#> * Cell Size:         0.50 m
#> * Beam Angle:        20 deg
#> * Location:          unknown latitude, unknown longitude
#> * Frequency:         600 kHz
#> * Ensemble Numbers:   1, 2, ..., 8, 9
#> * Transformation matrix::
#>      1.462  -1.462   0.000   0.000
#>      0.000   0.000  -1.462   1.462
#>      0.266   0.266   0.266   0.266
#>      1.034   1.034  -1.034  -1.034
#> * Time: 2008-06-25 10:00:00 to 2008-06-25 10:01:20 (9 samples, mean increment 10 s)
#> * Data Overview
#> 
#>                              Min.                Mean                Max.                Dim.     NAs
#>     v [m/s]                  -0.416              0.011534            0.406               "9x84x4" 0  
#>     q                        NA                  NA                  NA                  "9x84x4" 0  
#>     a                        NA                  NA                  NA                  "9x84x4" 0  
#>     g                        NA                  NA                  NA                  "9x84x4" 0  
#>     distance [m]             2.23                22.98               43.73               84       0  
#>     time                     2008-06-25 10:00:00 2008-06-25 10:00:40 2008-06-25 10:01:20 9        0  
#>     pressure [dbar]          -0.274              -0.23489            -0.193              9        0  
#>     temperature [°C, ITS-90] 12.06               12.082              12.11               9        0  
#>     salinity [PSS-78]        35                  35                  35                  9        0  
#>     depth [m]                0                   0                   0                   9        0  
#>     soundSpeed [m/s]         1497                1497                1497                9        0  
#>     heading [°]              276.39              277.14              278.14              9        0  
#>     pitch [°]                1.1209              1.2033              1.4212              9        0  
#>     roll [°]                 -2.49               -2.4033             -2.35               9        0  
#>     headingStd [°]           0                   0.22222             1                   9        0  
#>     pitchStd [°]             0.1                 0.11111             0.2                 9        0  
#>     rollStd [°]              0                   0.088889            0.1                 9        0  
#>     pressureStd              76                  100                 135                 9        0  
#>     xmitCurrent              61                  61                  61                  9        0  
#>     xmitVoltage              155                 155                 155                 9        0  
#>     ambientTemp              103                 103                 103                 9        0  
#>     pressurePlus             77                  77                  77                  9        0  
#>     pressureMinus            76                  76.778              77                  9        0  
#>     attitudeTemp             101                 101                 101                 9        0  
#>     attitude [°]             130                 130                 130                 9        0  
#>     contaminationSensor      159                 159                 159                 9        0  
#> 
#> * Processing Log
#> 
#>     - 2024-12-21 18:03:27 UTC: `read.adp.rdi(file = system.file("extdata", "adp_rdi.000", package = "oce"))`