Read a Teledyne/RDI ADCP file (called 'adp' in oce).
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"), ...)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.)
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.
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.
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”.)
character string indicating time zone to be assumed in the data.
optional signed number indicating the longitude in degrees East.
optional signed number indicating the latitude in degrees North.
character string indicating the type of instrument.
boolean, set to TRUE to provide an indication of progress
in reading the file, either by printing a dot for each profile or by writing
a textual progress bar with txtProgressBar.
if TRUE, despike will be used to clean
anomalous spikes in heading, etc.
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.)
logical value (IGNORED).
a flag that turns on debugging. Set to 1 to get a moderate amount of debugging information, or to 2 to get more.
additional arguments, passed to called routines.
An adp object, i.e. one inheriting from adp-class.
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 [3]. 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.
Case 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.
Case 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.
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"]].
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-RDI, 2015. V Series output data format. P/N 95D-6022-00 (May 2015).
3. See Memory-limits for more on the 2 GB limit for R on windows
machines (but note that this documentation erroneously states the unit as Gb, which is
typically used for gigabits).
Other things related to adp data: [[,adp-method,
[[<-,adp-method, adp-class,
adpEnsembleAverage, adp,
as.adp, beamName,
beamToXyzAdp, beamToXyzAdv,
beamToXyz, beamUnspreadAdp,
binmapAdp, enuToOtherAdp,
enuToOther, plot,adp-method,
read.ad2cp, read.adp.nortek,
read.adp.sontek.serial,
read.adp.sontek, read.adp,
read.aquadoppHR,
read.aquadoppProfiler,
read.aquadopp,
subset,adp-method,
summary,adp-method, toEnuAdp,
toEnu, velocityStatistics,
xyzToEnuAdp, xyzToEnu