R: Read an ADV data file

read.adv.nortek {oce} | R Documentation

## Read an ADV data file

### Description

Read an ADV data file, producing an object of type `adv`. This function works by transferring control to a more specialized function, e.g. `read.adp.nortek()` and `read.adp.sontek()`, and in many cases users will find it preferable to either use these or the several even more specialized functions, if the file type is known.

### Usage

    read.adv.nortek(
      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 = NULL
    )

### Arguments

`file` | a connection or a character string giving the name of the file to load. It is also possible to give `file` as a vector of filenames, to handle the case of data split into files by a data logger. In the multi-file case, `header` must be `FALSE`, `start` must be a vector of times, and `deltat` must be provided.
`from` | index number of the first profile to be read, or the time of that profile, as created with `as.POSIXct()` (hint: use `tz="UTC"`). This argument is ignored if `header==FALSE`. See “Examples”.
`to` | indication of the last profile to read, in a format matching that of `from`. This is ignored if `header==FALSE`.
`by` | an indication of the stride length to use while walking through the file. This is ignored if `header==FALSE`. Otherwise, if this is an integer, then `by-1` profiles are skipped between each pair of profiles that is read. This may not make much sense, if the data are not equi-spaced in time. If `by` is a string representing a time interval, in colon-separated format, then this interval is divided by the sampling interval, to get the stride length. BUG: `by` only partially works; see “Bugs”.
`tz` | character string indicating time zone to be assumed in the data.
`header` | A logical value indicating whether the file starts with a header. (This will not be the case for files that are created by data loggers that chop the raw data up into a series of sub-files, e.g. once per hour.)
`longitude` | optional signed number indicating the longitude in degrees East.
`latitude` | optional signed number indicating the latitude in degrees North.
`type` | A string indicating which type of Nortek device produced the data file, `vector` or `aquadopp`.
`haveAnalog1` | A logical value indicating whether the data file has 'analog1' data.
`haveAnalog2` | A logical value indicating whether the data file has 'analog2' data.
`debug` | a flag that turns on debugging. The value indicates the depth within the call stack to which debugging applies. For example, `read.adv.nortek()` calls `read.header.nortek()`, so that `read.adv.nortek(...,debug=2)` provides information about not just the main body of the data file, but also the details of the header.
`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.
`processingLog` | if provided, the action item to be stored in the log. This parameter is typically only provided for internal calls; the default that it provides is better for normal calls by a user.

### Details

Files without headers may be created in experiments in which a data logger was set up to monitor the serial data stream from an instrument. The lack of header information places a burden on the user, who must supply such basic information as the times of observations, the instrument orientation, the instrument coordinate system, etc. Example 3 below shows how to deal with such files. Three things should be noted.

1. The user must choose the appropriate `read.adv` variant corresponding to the instrument in question. (This is necessary because `oceMagic()`, which is used by the generic `read.oce()` routine, cannot determine the type of instrument by examining a file that lacks a header.)

2. The call to the `read` function must include a start time (`start`) and the number of seconds between data (`deltat`), again, because the instrument data stream may lack those things when the device is set to a serial mode. Also, of course, it is necessary to set `header=FALSE` in the function call.

3. Once the file has been read in, the user will be obliged to specify other information, for the object to be well-formed. For example, the `read` function will have no way of knowing the instrument orientation, the coordinate system being used, the transformation matrix to go from `"beam"` to `"xyz"` coordinates, or the instrument heading, pitch, and roll, to go from `"xyz"` coordinates to `"enu"` coordinates. Such things are illustrated in example 3 below.

In ADV 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 ADV object name `d` with `d[["velocityMaximum"]]` and `d[["velocityResolution"]]`.

### Value

An adv object that contains measurements made with an ADV device.

The `metadata` contains information as given in the following table. The `Nortek name'' is the name used in the Nortek System Integrator Guide (reference 1) and the` Sontek name” is the name used in the relevant Sontek documentation. References are given in square brackets.

`metadata` name | Nortek name | Sontek name | Meaning
`manufacturer` | - | - | Either `"nortek"` or `"sontek"`
`instrumentType` | - | - | Either `"vector"` or `"adv"`
`filename` | - | - | Name of data file(s)
`latitude` | - | - | Latitude of mooring (if applicable)
`longitude` | - | - | Longitude of mooring (if applicable)
`numberOfSamples` | - | - | Number of data samples in file
`numberOfBeams` | NBeams (reference 1, p18) | - | Number of beams (always 3)
`numberOfBeamSequencesPerBurst` | NPings | - | number of beam sequences per burst
`measurementInterval` | MeasInterval (reference 1 p31) | - |
`samplingRate` | 512/(AvgInterval) (reference 1 p30; reference 4) | - #' |

The `data` list contains items with names corresponding to `adp` objects, with an exception for Nortek data. Nortek instruments report some things at a time interval that is longer than the velocity sampling, and these are stored in `data` as `timeSlow`, `headingSlow`, `pitchSlow`, `rollSlow`, and `temperatureSlow`; if burst sampling was used, there will also be items `recordsBurst` and `timeBurst`.

The `processingLog` is in the standard format.

### Nortek files

Sampling-rate and similar issues

The data format is inferred from the System Integrator Guide (reference 1A) and System Integrator Manual (reference 1B). These document lacks clarity in spots, and so `read.adv.nortek` contains some assumptions that are noted here, so that users will be aware of possible problems.

A prominent example is the specification of the sampling rate, stored in `metadata$sampingRate` in the return value. Repeated examination of the System Integrator Guide (reference 1) failed to indicate where this value is stored in the various headers contained in Vector datasets. After some experimentation with a few data files, `read.adv.nortek` was set up to calculate `metadata$samplingRate` as `512/AvgInterval` where `AvgInterval` is a part of the `User Configuration'' header (reference 1 p30), where the explanation is` average interval in seconds”). This formula was developed through trial and error, but it was confirmed later on the Nortek discussion group, and it should appear in upcoming versions of (reference 1).

Another basic issue is the determination of whether an instrument had recorded in continuous mode or burst mode. One might infer that `TimCtrlReg` in the `User Configuration'' header (reference 1 p30) determines this, in bits 1 and 2. However, this was the case in test files available to the author. For this reason, `read.adv.nortek` infers the mode by reverse engineering of data files of known configuration. The present version of `read.adv.nortek` determines the sampling mode from the ```NRecords`'' item of the` Vector Velocity Data” header, which seems to be 0 for data collected continuously, and non-zero for data collected in bursts.

Taking these things together, we come upon the issue of how to infer sampling times for Nortek instruments. There do not seem to be definitive documents on this, and so `read.adv.nortek` is based partly on information (of unknown quality) found on Nortek discussion boards. The present version of `read.adv.nortek` infers the times of velocity observations differently, depending on whether the instrument was set to record in burst mode or continuous mode. For burst mode, times stated in the burst headers are used, but for continuous mode, times stated in the “vector system data” are used. On the advice found on a Nortek discussion board, the burst-mode times are offset by 2 seconds to allow for the instrument warm-up period.

Handling IMU (inertial measurement unit) data

Starting in March 2016, `read.adv.nortek` has offered some support for handling IMU (inertial measurement unit) data incorporated into Nortek binary files. This is not described in the Nortek document named `System Integrator Guide'' (reference 1A) but it appeared in` System Integrator Manual” (reference 1B; reference 1C). Confusingly, 1B described 3 varieties of data, whereas 1C does not describe any of these, but describes instead a fourth variety. As of March 2016, `read.adv.nortek` handles all 4 varieties, because files in the various schemes appear to exist. In `oce`, the varieties are named after the byte code that flags them. (Variety `c3` is the one described in (reference 1C); the others were described in (reference 1B).) The variety is stored in the `metadata` slot of the returned object as a string named `IMUtype`.

For each variety, the reader is cautioned that strong tests have not been performed on the code. One way to test the code is to compare with textual data files produced by the Nortek software. In March 2016, an `oce` user shared a dataset of the `c3` variety, and this permitted detailed comparison between the text file and the values inferred by `read.adv.nortek`. The test suggested agreement (to within the resolution printed in the text file) for velocity (`v` in the `data` slot), signal amplitude (`a`), correlation (`q`), pressure (`p`), the three components of IMU delta angle (`IMUdeltaAngleX` etc), and all components of the rotation matrix (`IMUrotation`). However, the delta velocity signals did not match, with `IMUdeltaVelocityX` disagreeing in the second decimal place, `IMUdeltaVelocityY` component disagreeing in the first, and `IMUdeltaVelocityZ` being out by a factor of about 10. This is github issue 893 (https://github.com/dankelley/oce/issues/893).

- Variety `c3` (signalled by byte 5 of a sequence being `0xc3`) provides information on what Nortek calls DeltaAngle, DeltaVelocity and Orientation Matrix. (Apart from the orientation matrix, Nortek provides no documentation on what these quantities mean.) In the object returned by `read.adv.nortek`, these are stored in the `data` slot as `IMUdeltaAngleX`, `IMUdeltaAngleY`, `IMUdeltaAngleZ`, `IMUdeltaVelocityX`, `IMUdeltaVelocityY`, `IMUdeltaVelocityZ`, and `IMUrotation`, all vectors except the last, which is a 3D array. In addition to these, `IMUtimestamp` is a time-stamp, which is not defined in the Nortek documents but seems, from IMU documents (reference 5), to be defined based on a clock that ticks once per 16 microseconds. Caution may be required in dealing with this timestamp, since it seemed sensible in one test case (variety `d3`) but kept reseting to zero in another (variety `c3`). The lack of Nortek documentation on most of these quantities is a roadblock to implementing `oce` functions dealing with IMU-enabled datasets

- Variety `cc` (signalled by byte 5 of a sequence being `0xcc`) provides information on acceleration, angular rotation rate, magnetic vector and orientation matrix. Each is a timeseries. Acceleration is stored in the `data` slot as `IMUaccelX`, `IMUaccelY`, `IMUaccelz`. The angular rotation components are `IMUngrtX`, `IMUngrtY` and `IMUngrtz`. The magnetic data are in `IMUmagrtx`, `IMUmagrty` and `IMUmagrtz`. Finally, `IMUmatrix` is a rotation matrix made up from elements named `M11`, `M12`, etc in the Nortek documentation. In addition to all of these, `IMUtime` stores time in seconds, with an origin whose definition is not stated in reference 1B.

- Variety `d2` (signalled by byte 5 being `0xd2`) provides information on gyro-stabilized acceleration, angular rate and magnetometer vectors. The data stored `MUaccelX`, `IMUangrtX`, `IMUmagrtX`, with similar for `Y` and `Z`. Again, time is in `IMUtime`. This data type has not been tested as of mid-March 2016, because the developers do not have a test file with which to test.

- Variety `d3` (signalled by byte 5 being `0xd3`) provides information on DeltaAngle, DeltaVelocity and magnetometer vectors, stored in `IMUdeltaAngleX`, `IMUdeltaVelocityX`, and `IMUdeltaMagVectorX`, with similar for `Y` and `Z`. Again, time is in `IMUtime`. This data type has not been tested as of mid-March 2016, because the developers do not have a test file with which to test.

### Author(s)

Dan Kelley

### References

1A. Nortek AS. System Integrator Guide (paradopp family of products). June 2008. (Doc No: PSI00-0101-0608). (Users may find it helpful to also examine newer versions of the guide.)

1B. Nortek AS. System Integrator Manual. Dec 2014. (`system-integrator-manual_Dec2014_jan.pdf`)

1C. Nortek AS. System Integrator Manual. March 2016. (`system-integrator-manual_Mar2016.pdf`)

1. SonTek/YSI ADVField/Hydra Acoustic Doppler Velocimeter (Field) Technical Documentation (Sept 1, 2001).

2. Appendix 2.2.3 of the Sontek ADV operation Manual, Firmware Version 4.0 (Oct 1997).

3. Nortek Knowledge Center (http://www.nortekusa.com/en/knowledge-center)

4. A document describing an IMU unit that seems to be close to the one named in (references 1B and C) as being an adjunct to Nortek Vector systems is at `http://files.microstrain.com/3DM-GX3-35-Data-Communications-Protocol.pdf`

### See Also

Other things related to adv data: `[[,adv-method`, `[[<-,adv-method`, `adv-class`, `adv`, `beamName()`, `beamToXyz()`, `enuToOtherAdv()`, `enuToOther()`, `plot,adv-method`, `read.adv.sontek.adr()`, `read.adv.sontek.serial()`, `read.adv.sontek.text()`, `read.adv()`, `rotateAboutZ()`, `subset,adv-method`, `summary,adv-method`, `toEnuAdv()`, `toEnu()`, `velocityStatistics()`, `xyzToEnuAdv()`, `xyzToEnu()`

### Examples

    ## Not run:
    library(oce)
    # A nortek Vector file
    d <- read.oce("/data/archive/sleiwex/2008/moorings/m05/adv/nortek_1943/raw/adv_nortek_1943.vec",
                  from=as.POSIXct("2008-06-26 00:00:00", tz="UTC"),
                  to=as.POSIXct("2008-06-26 00:00:10", tz="UTC"))
    plot(d, which=c(1:3,15))

    ## End(Not run)

[Package oce version 1.7-2 Index]