read.aquadoppHR: Read Nortek Aquadopp-HR File

Description

The R code is based on information in the Nortek System Integrator Guide (2008) and on postings on the Nortek ``knowledge center'' discussion board. One might assume that the latter is less authoritative than the former. For example, the inference of cell size follows advice found at https://www.nortekusa.com/en/knowledge-center/forum/hr-profilers/736804717, which contains a typo in an early posting that is corrected later on.

Usage

read.aquadoppHR(
  file,
  from = 1,
  to,
  by = 1,
  tz = getOption("oceTz"),
  longitude = NA,
  latitude = NA,
  orientation = orientation,
  distance,
  monitor = FALSE,
  despike = FALSE,
  encoding = NA,
  processingLog,
  debug = getOption("oceDebug"),
  ...
)

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).

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.
orientation: Optional character string specifying the orientation of the sensor, provided for those cases in which it cannot be inferred from the data file. The valid choices are "upward", "downward", and "sideward".
distance: Optional vector holding the distances of bin centres from the sensor. This argument is ignored except for Nortek profilers, and need not be given if the function determines the distances correctly from the data. The problem is that the distance is poorly documented in the Nortek System Integrator Guide (2008 edition, page 31), so the function must rely on word-of-mouth formulae that do not work in all cases.
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.
encoding: ignored.
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.)
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.

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.

Author

Dan Kelley

References

Information on Nortek profilers (including the System Integrator Guide, which explains the data format byte-by-byte) is available at https://www.nortekusa.com/. (One must join the site to see the manuals.)
The Nortek Knowledge Center https://www.nortekusa.com/en/knowledge-center may be of help if problems arise in dealing with data from Nortek instruments.