R: Read a Teledyne/RDI ADP File

read.adp.rdi {oce} | R Documentation

## Read a Teledyne/RDI ADP File

### Description

Read a Teledyne/RDI ADCP file (called 'adp' in oce).

### Usage

    read.adp.rdi(
      file,
      from,
      to,
      by,
      tz = getOption("oceTz"),
      longitude = NA,
      latitude = NA,
      type = c("workhorse"),
      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.
`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.

### Details

As of 2016-09-25, this function has provisional functionality to read data from the new "SentinelV" series ADCP – essentially a combination of a 4 beam workhorse with an additional vertical centre beam.

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"]]`.

### 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).

### Handling of old file formats

1. 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.

1. 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.

2. 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.

1. 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.

2. 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.

### Author(s)

Dan Kelley and Clark Richards

### References

1. 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.)

2. Teledyne RD Instruments, 2015. V Series monitor, sentinel Output Data Format. P/N 95D-6022-00 (May 2015). `SV_ODF_May15.pdf`

3. Teledyne RD Instruments, 2014. Ocean Surveyor / Ocean Observer Technical Manual. P/N 95A-6012-00 (April 2014). `OS_TM_Apr14.pdf`

4. Teledyne RD Instruments, 2001. WinRiver User's Guide International Version. P/N 957-6171-00 (June 2001) `WinRiver User Guide International Version.pdf.pdf`

### See Also

Other things related to adp data: `[[,adp-method`, `[[<-,adp-method`, `ad2cpHeaderValue()`, `adp-class`, `adpConvertRawToNumeric()`, `adpEnsembleAverage()`, `adpFlagPastBoundary()`, `adp_rdi.000`, `adp`, `as.adp()`, `beamName()`, `beamToXyzAdpAD2CP()`, `beamToXyzAdp()`, `beamToXyzAdv()`, `beamToXyz()`, `beamUnspreadAdp()`, `binmapAdp()`, `enuToOtherAdp()`, `enuToOther()`, `handleFlags,adp-method`, `is.ad2cp()`, `plot,adp-method`, `read.adp.ad2cp()`, `read.adp.nortek()`, `read.adp.sontek.serial()`, `read.adp.sontek()`, `read.adp()`, `read.aquadoppHR()`, `read.aquadoppProfiler()`, `read.aquadopp()`, `rotateAboutZ()`, `setFlags,adp-method`, `subset,adp-method`, `subtractBottomVelocity()`, `summary,adp-method`, `toEnuAdp()`, `toEnu()`, `velocityStatistics()`, `xyzToEnuAdpAD2CP()`, `xyzToEnuAdp()`, `xyzToEnu()`

### Examples

    adp <- read.adp.rdi(system.file("extdata", "adp_rdi.000", package="oce"))
    summary(adp)

[Package oce version 1.7-2 Index]