sits (version 1.1.0)

sits_get_data: Get time series from data cubes and cloud services

Description

Retrieve a set of time series from a data cube or from a time series service. Data cubes and puts it in a "sits tibble". Sits tibbles are the main structures of sits package. They contain both the satellite image time series and their metadata.

Usage

sits_get_data(
  cube,
  samples,
  ...,
  start_date = as.Date(sits_timeline(cube)[1]),
  end_date = as.Date(sits_timeline(cube)[length(sits_timeline(cube))]),
  label = "NoClass",
  bands = sits_bands(cube),
  crs = 4326,
  impute_fn = sits_impute_linear(),
  label_attr = NULL,
  n_sam_pol = 30,
  pol_avg = FALSE,
  pol_id = NULL,
  multicores = 2,
  output_dir = ".",
  progress = FALSE
)
# S3 method for default
sits_get_data(cube, samples, ...)
# S3 method for csv
sits_get_data(
  cube,
  samples,
  ...,
  bands = sits_bands(cube),
  crs = 4326,
  impute_fn = sits_impute_linear(),
  multicores = 2,
  output_dir = ".",
  progress = FALSE
)
# S3 method for shp
sits_get_data(
  cube,
  samples,
  ...,
  label = "NoClass",
  start_date = as.Date(sits_timeline(cube)[1]),
  end_date = as.Date(sits_timeline(cube)[length(sits_timeline(cube))]),
  bands = sits_bands(cube),
  impute_fn = sits_impute_linear(),
  label_attr = NULL,
  n_sam_pol = 30,
  pol_avg = FALSE,
  pol_id = NULL,
  multicores = 2,
  output_dir = ".",
  progress = FALSE
)
# S3 method for sf
sits_get_data(
  cube,
  samples,
  ...,
  bands = sits_bands(cube),
  start_date = as.Date(sits_timeline(cube)[1]),
  end_date = as.Date(sits_timeline(cube)[length(sits_timeline(cube))]),
  impute_fn = sits_impute_linear(),
  label = "NoClass",
  label_attr = NULL,
  n_sam_pol = 30,
  pol_avg = FALSE,
  pol_id = NULL,
  multicores = 2,
  output_dir = ".",
  progress = FALSE
)
# S3 method for sits
sits_get_data(
  cube,
  samples,
  ...,
  bands = sits_bands(cube),
  impute_fn = sits_impute_linear(),
  multicores = 2,
  output_dir = ".",
  progress = FALSE
)
# S3 method for data.frame
sits_get_data(
  cube,
  samples,
  ...,
  start_date = as.Date(sits_timeline(cube)[1]),
  end_date = as.Date(sits_timeline(cube)[length(sits_timeline(cube))]),
  label = "NoClass",
  bands = sits_bands(cube),
  crs = 4326,
  impute_fn = sits_impute_linear(),
  multicores = 2,
  output_dir = ".",
  progress = FALSE
)

Value

A tibble with the metadata and data for each time series <longitude, latitude, start_date, end_date, label, cube, time_series>.

Arguments

cube

Data cube from where data is to be retrieved.

samples

Samples location (sits, sf, or data.frame).

...

Specific parameters for specific cases.

start_date

Start of the interval for the time series in "YYYY-MM-DD" format (optional).

end_date

End of the interval for the time series in "YYYY-MM-DD" format (optional).

label

Label to be assigned to the time series (optional).

bands

Bands to be retrieved (optional).

crs

A coordinate reference system of samples. The provided crs could be a character (e.g, "EPSG:4326" or "WGS84" or a proj4string), or a a numeric with the EPSG code (e.g. 4326). This parameter only works for 'csv' or data.frame' samples. Default is 4326.

impute_fn

Imputation function for NA values.

label_attr

Attribute in the shapefile or sf object to be used as a polygon label.

n_sam_pol

Number of samples per polygon to be read (for POLYGON or MULTIPOLYGON shapefile).

pol_avg

Summarize samples for each polygon?

pol_id

ID attribute for polygons.

multicores

Number of threads to process the time series.

output_dir

Directory where the time series will be saved as rds. Default is the current path.

progress

A logical value indicating if a progress bar should be shown. Default is FALSE.

Author

Gilberto Camara

Examples

if (sits_run_examples()) {
    # reading a lat/long from a local cube
    # create a cube from local files
    data_dir <- system.file("extdata/raster/mod13q1", package = "sits")
    raster_cube <- sits_cube(
        source = "BDC",
        collection = "MOD13Q1-6",
        data_dir = data_dir,
        delim = "_",
        parse_info = c("X1", "X2", "tile", "band", "date")
    )
    samples <- tibble::tibble(longitude = -55.66738, latitude = -11.76990)
    point_ndvi <- sits_get_data(raster_cube, samples)
    #
    # reading samples from a cube based on a  CSV file
    csv_file <- system.file("extdata/samples/samples_sinop_crop.csv",
        package = "sits"
    )
    points <- sits_get_data(cube = raster_cube, samples = csv_file)

    # reading a shapefile from BDC (Brazil Data Cube)
    # needs a BDC access key that can be obtained
    # for free by registering in the BDC website
    if (nchar(Sys.getenv("BDC_ACCESS_KEY")) > 0) {
        # create a data cube from the BDC
        bdc_cube <- sits_cube(
            source = "BDC",
            collection = "CB4_64_16D_STK-1",
            bands = c("NDVI", "EVI"),
            tiles = c("022024", "022025"),
            start_date = "2018-09-01",
            end_date = "2018-10-28"
        )
        # define a shapefile to be read from the cube
        shp_file <- system.file("extdata/shapefiles/bdc-test/samples.shp",
            package = "sits"
        )
        # get samples from the BDC based on the shapefile
        time_series_bdc <- sits_get_data(
            cube = bdc_cube,
            samples = shp_file)
    }
}