Extract something from the metadata or data slot of an
amsr-class object.
The [[ method works for all oce objects, i.e.
objects inheriting from oce-class. The purpose
is to insulate users from the internal details of oce
objects, by looking for items within the various storage
slots of the object. Items that are not actually stored in
the object can also be extracted, including derived data such
as potential temperature, the units of measurement for
the data, data-quality flags, etc.
# S4 method for amsr
[[(x, i, j, ...)An amsr object, i.e. one inheriting from amsr-class.
Character string indicating the name of item to extract.
Optional additional information on the i item.
Optional additional information (ignored).
In all cases, the returned value is a matrix with
with NA values inserted at locations where
the raw data equal as.raw(251:255), as explained
in “Details”.
If the specialized method produces no matches, the following generalized
method is applied. As with the specialized method, the procedure hinges
first on the values of i and, optionally, j. The work
proceeds in steps, by testing a sequence of possible conditions
in sequence.
A check is made as to whether i names one of the standard
oce slots. If so, [[ returns the slot contents of that slot.
Thus, x[["metadata"]] will retrieve the metadata slot,
while x[["data"]] and x[["processingLog"]] return
those slots.
If i is a string ending in the
"Unit", then the characters preceding that string
are taken to be the name of an item in the data object, and a list
containing the unit is returned. This list consists of an item
named unit, which is an expression, and
an item named scale, which is a string describing the
measurement scale. If the string ends in " unit", e.g.
x[["temperature unit"]] (note the space),
then just the expression is returned, and if it ends in
" scale", then just the scale is returned.
If i is a string ending in "Flag", then the corresponding
data-quality flag is returned (or NULL if there is no such flag).
For example, x[["salinityFlag"]] returns a vector of salinity
flags if x is a ctd object.
If i is "sigmaTheta", then the value of
swSigmaTheta(x) is returned. Similarly,
"sigma0" returns swSigma0(x) and
"spice" returns swSpice(x). Note that
these relate to seawater properties and only make sense for
certain object types.
After these possibilities are eliminated,
the action depends on whether j has been provided.
If j is not provided, or is the string "",
then i is sought
in the metadata slot, and then in the data slot,
returning whichever is found first. In other words, if j
is not provided, the metadata slot takes preference over
the data slot. However, if j is provided, then
it must be either the string "metadata" or "data",
and it directs where to look.
If none of the above-listed conditions holds, then NULL is returned,
without the issuance of a warning or error message. (This silent operation
is employed so that [[ will behave like the normal R version.)
Partial matches for i
are permitted for metadata, and j is ignored for
metadata.
Data within the data slot may be found directly, e.g.
j="SSTDay" will yield sea-surface temperature in the daytime
satellite, and j="SSTNight" is used to access the nighttime data. In
addition, j="SST" yields an average of the night and day values
(using just one of these, if the other is missing). This scheme works for
all the data stored in amsr objects, namely:
time, SST, LFwind, MFwind,
vapor, cloud and rain. In each case, the default
is to calculate values in scientific units, unless j="raw", in
which case the raw data are returned.
The "raw" mode can be useful
in decoding the various types of missing value that are used by amsr
data, namely as.raw(255) for land, as.raw(254) for
a missing observation, as.raw(253) for a bad observation,
as.raw(252) for sea ice, or as.raw(251) for missing SST
due to rain or missing water vapour due to heavy rain. Note that
something special has to be done for e.g. d[["SST", "raw"]]
because the idea is that this syntax (as opposed to specifying
"SSTDay") is a request to try to find good
data by looking at both the Day and Night measurements. The scheme
employed is quite detailed. Denote by "A" the raw value of the desired field
in the daytime pass, and by "B" the corresponding value in the
nighttime pass. If either A or B is 255, the code for land, then the
result will be 255. If A is 254 (i.e. there is no observation),
then B is returned, and the reverse holds also. Similarly, if either
A or B equals 253 (bad observation), then the other is returned.
The same is done for code 252 (ice) and code 251 (rain).
A two-step process is used to try to find the requested information. First, a class-specific function tries to find it, but if that fails, then a general function is used (see next section).
Other functions that extract parts of oce objects: [[,adp-method,
[[,adv-method,
[[,argo-method,
[[,bremen-method,
[[,cm-method,
[[,coastline-method,
[[,ctd-method,
[[,echosounder-method,
[[,g1sst-method,
[[,gps-method,
[[,ladp-method,
[[,landsat-method,
[[,lisst-method,
[[,lobo-method,
[[,met-method, [[,oce-method,
[[,odf-method, [[,rsk-method,
[[,sealevel-method,
[[,section-method,
[[,tidem-method,
[[,topo-method,
[[,windrose-method,
[[<-,adv-method
Other things related to amsr data: [[<-,amsr-method,
amsr-class,
composite,amsr-method,
download.amsr,
plot,amsr-method, read.amsr,
subset,amsr-method,
summary,amsr-method
# NOT RUN {
# Show a daytime SST image, along with an indication of whether
# the NA values are from rain.
library(oce)
earth <- read.amsr("f34_20160102v7.2.gz")
fclat <- subset(earth , 35 <= latitude & latitude <= 55)
fc <- subset(fclat , -70 <= longitude & longitude <= -30)
par(mfrow=c(2, 1))
plot(fc, "SSTDay")
rainy <- fc[["SSTDay", "raw"]] == as.raw(0xfb)
lon <- fc[["longitude"]]
lat <- fc[["latitude"]]
asp <- 1 / cos(pi*mean(lat)/180)
imagep(lon, lat, rainy, asp=asp)
mtext("red: too rainy to sense SSTDay")
# }
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