read raster/array dataset from file or connection
Usage
read_stars(
.x,
sub = TRUE,
...,
options = character(0),
driver = character(0),
quiet = FALSE,
NA_value = NA_real_,
along = NA_integer_,
RasterIO = list(),
proxy = getOption("stars.n_proxy") %||% 1e+08,
curvilinear = character(0),
normalize_path = TRUE,
RAT = character(0),
tolerance = 1e-10,
exclude = "",
shorten = TRUE
)Arguments
- .x
character vector with name(s) of file(s) or data source(s) to be read, or a function that returns such a vector
- sub
character, integer or logical; name, index or indicator of sub-dataset(s) to be read
- ...
passed on to st_as_stars if
curvilinearwas set- options
character; opening options
- driver
character; driver to use for opening file. To override fixing for subdatasets and autodetect them as well, use
NULL.- quiet
logical; print progress output?
- NA_value
numeric value to be used for conversion into NA values; by default this is read from the input file
- along
length-one character or integer, or list; determines how several arrays are combined, see Details.
- RasterIO
list with named parameters for GDAL's RasterIO, to further control the extent, resolution and bands to be read from the data source; see details.
- proxy
logical; if
TRUE, an object of classstars_proxyis read which contains array metadata only; ifFALSEthe full array data is read in memory. AlwaysFALSEfor curvilinear girds. If set to a number, defaults toTRUEwhen the number of cells to be read is larger than that number.- curvilinear
length two character vector with names of subdatasets holding longitude and latitude values for all raster cells, or named length 2 list holding longitude and latitude matrices; the names of this list should correspond to raster dimensions referred to
- normalize_path
logical; if
FALSE, suppress a call to normalizePath on.x- RAT
character; raster attribute table column name to use as factor levels
- tolerance
numeric; passed on to all.equal for comparing dimension parameters.
- exclude
character; vector with category value(s) to exclude
- shorten
logical or character; if
TRUEandlength(.x) > 1, remove common start and end parts of array names; if character a new prefix
Details
In case .x contains multiple files, they will all be read and combined with c.stars. Along which dimension, or how should objects be merged? If along is set to NA it will merge arrays as new attributes if all objects have identical dimensions, or else try to merge along time if a dimension called time indicates different time stamps. A single name (or positive value) for along will merge along that dimension, or create a new one if it does not already exist. If the arrays should be arranged along one of more dimensions with values (e.g. time stamps), a named list can passed to along to specify them; see example.
RasterIO is a list with zero or more of the following named arguments:
nXOff, nYOff (both 1-based: the first row/col has offset value 1),
nXSize, nYSize, nBufXSize, nBufYSize, bands, resample.
See https://gdal.org/en/latest/doxygen/classGDALDataset.html for their meaning;
bands is an integer vector containing the band numbers to be read (1-based: first band is 1).
Note that if nBufXSize or nBufYSize are specified for downsampling an image,
resulting in an adjusted geotransform. resample reflects the resampling method and
has to be one of: "nearest_neighbour" (the default),
"bilinear", "cubic", "cubic_spline", "lanczos", "average", "mode", or "Gauss".
Data that are read into memory (proxy=FALSE) are read into a numeric (double) array, except for categorical variables which are read into an numeric (integer) array of class factor.
Examples
tif = system.file("tif/L7_ETMs.tif", package = "stars")
(x1 = read_stars(tif))
#> stars object with 3 dimensions and 1 attribute
#> attribute(s):
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> L7_ETMs.tif 1 54 69 68.91242 86 255
#> dimension(s):
#> from to offset delta refsys point x/y
#> x 1 349 288776 28.5 SIRGAS 2000 / UTM zone 25S FALSE [x]
#> y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE [y]
#> band 1 6 NA NA NA NA
(x2 = read_stars(c(tif, tif)))
#> stars object with 3 dimensions and 2 attributes
#> attribute(s):
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> L7_ETMs.tif 1 54 69 68.91242 86 255
#> L7_ETMs.tif.1 1 54 69 68.91242 86 255
#> dimension(s):
#> from to offset delta refsys point x/y
#> x 1 349 288776 28.5 SIRGAS 2000 / UTM zone 25S FALSE [x]
#> y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE [y]
#> band 1 6 NA NA NA NA
(x3 = read_stars(c(tif, tif), along = "band"))
#> stars object with 3 dimensions and 1 attribute
#> attribute(s), summary of first 1e+05 cells:
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> L7_ETMs.tif 47 65 76 77.3419 87 255
#> dimension(s):
#> from to offset delta refsys point x/y
#> x 1 349 288776 28.5 SIRGAS 2000 / UTM zone 25S FALSE [x]
#> y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE [y]
#> band 1 12 NA NA NA NA
(x4 = read_stars(c(tif, tif), along = "new_dimensions")) # create 4-dimensional array
#> stars object with 4 dimensions and 1 attribute
#> attribute(s), summary of first 1e+05 cells:
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> L7_ETMs.tif 47 65 76 77.3419 87 255
#> dimension(s):
#> from to offset delta refsys point x/y
#> x 1 349 288776 28.5 SIRGAS 2000 / UTM zone 25S FALSE [x]
#> y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE [y]
#> band 1 6 NA NA NA NA
#> new_dimensions 1 2 NA NA NA NA
x1o = read_stars(tif, options = "OVERVIEW_LEVEL=1")
t1 = as.Date("2018-07-31")
# along is a named list indicating two dimensions:
read_stars(c(tif, tif, tif, tif), along = list(foo = c("bar1", "bar2"), time = c(t1, t1+2)))
#> stars object with 5 dimensions and 1 attribute
#> attribute(s), summary of first 1e+05 cells:
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> L7_ETMs.tif 47 65 76 77.3419 87 255
#> dimension(s):
#> from to offset delta refsys point values x/y
#> x 1 349 288776 28.5 SIRGAS 2000 / UTM zone 25S FALSE NULL [x]
#> y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE NULL [y]
#> band 1 6 NA NA NA NA NULL
#> foo 1 2 NA NA NA NA bar1, bar2
#> time 1 2 2018-07-31 2 days Date NA NULL
m = matrix(1:120, nrow = 12, ncol = 10)
dim(m) = c(x = 10, y = 12) # named dim
st = st_as_stars(m)
attr(st, "dimensions")$y$delta = -1
attr(st, "dimensions")$y$offset = 12
st
#> stars object with 2 dimensions and 1 attribute
#> attribute(s):
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> A1 1 30.75 60.5 60.5 90.25 120
#> dimension(s):
#> from to offset delta point x/y
#> x 1 10 0 1 FALSE [x]
#> y 1 12 12 -1 FALSE [y]
tmp = tempfile(fileext = ".tif")
write_stars(st, tmp)
(red <- read_stars(tmp))
#> stars object with 2 dimensions and 1 attribute
#> attribute(s):
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> file23a6162b944e.tif 1 30.75 60.5 60.5 90.25 120
#> dimension(s):
#> from to offset delta x/y
#> x 1 10 0 1 [x]
#> y 1 12 12 -1 [y]
read_stars(tmp, RasterIO = list(nXOff = 1, nYOff = 1, nXSize = 10, nYSize = 12,
nBufXSize = 2, nBufYSize = 2))[[1]]
#> [,1] [,2]
#> [1,] 33 93
#> [2,] 38 98
(red <- read_stars(tmp, RasterIO = list(nXOff = 1, nYOff = 1, nXSize = 10, nYSize = 12,
nBufXSize = 2, nBufYSize = 2)))
#> stars object with 2 dimensions and 1 attribute
#> attribute(s):
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> file23a6162b944e.tif 33 36.75 65.5 65.5 94.25 98
#> dimension(s):
#> from to offset delta x/y
#> x 1 2 0 5 [x]
#> y 1 2 12 -6 [y]
red[[1]] # cell values of subsample grid:
#> [,1] [,2]
#> [1,] 33 93
#> [2,] 38 98
if (FALSE) { # \dontrun{
plot(st, reset = FALSE, axes = TRUE, ylim = c(-.1,12.1), xlim = c(-.1,10.1),
main = "nBufXSize & nBufYSize demo", text_values = TRUE)
plot(st_as_sfc(red, as_points = TRUE), add = TRUE, col = 'red', pch = 16)
plot(st_as_sfc(st_as_stars(st), as_points = FALSE), add = TRUE, border = 'grey')
plot(st_as_sfc(red, as_points = FALSE), add = TRUE, border = 'green', lwd = 2)
} # }
file.remove(tmp)
#> [1] TRUE