MODIStsp | R Documentation |
Main function for the MODIS Time Series Processing Tool (MODIStsp)
MODIStsp(
...,
gui = TRUE,
out_folder = NULL,
out_folder_mod = NULL,
opts_file = NULL,
selprod = NULL,
prod_version = NULL,
bandsel = NULL,
quality_bandsel = NULL,
indexes_bandsel = NULL,
sensor = NULL,
download_server = NULL,
downloader = NULL,
user = NULL,
password = NULL,
download_range = NULL,
start_date = NULL,
end_date = NULL,
spatmeth = NULL,
start_x = NULL,
end_x = NULL,
start_y = NULL,
end_y = NULL,
bbox = NULL,
spafile = NULL,
out_projsel = NULL,
output_proj = NULL,
out_res_sel = NULL,
out_res = NULL,
resampling = NULL,
reprocess = NULL,
delete_hdf = NULL,
nodata_change = NULL,
scale_val = NULL,
ts_format = NULL,
out_format = NULL,
compress = NULL,
test = NULL,
n_retries = 5,
verbose = TRUE,
parallel = TRUE
)
... |
not used for values, forces later arguments to bind by name |
gui |
|
out_folder |
|
out_folder_mod |
|
opts_file |
|
selprod |
|
prod_version |
Version of the selected MODIS product.
Currently versions |
bandsel |
|
quality_bandsel |
|
indexes_bandsel |
|
sensor |
|
download_server |
|
downloader |
download_server |
user |
|
password |
|
download_range |
|
start_date |
|
end_date |
|
spatmeth |
|
start_x |
|
end_x |
|
start_y |
|
end_y |
|
bbox |
|
spafile |
|
out_projsel |
|
output_proj |
|
out_res_sel |
|
out_res |
|
resampling |
|
reprocess |
|
delete_hdf |
|
nodata_change |
|
scale_val |
|
ts_format |
|
out_format |
|
compress |
|
test |
|
n_retries |
|
verbose |
|
parallel |
|
The function is used to:
initialize the processing (folder names, packages, etc.);
launch the GUI (MODIStsp_GUI()
) on interactive
execution, or load an options file to set processing arguments and/or
retrieve CLI inputs and run processing on non-interactive execution;
launch the routines for downloading and processing the requested datasets.
(MODIStsp_process()
)
launching the function with GUI = FALSE and without specifying a opts_file initializes arguments with default values. This allows making a test run.
License: GPL 3.0
Lorenzo Busetto, phD (2014-2017)
Luigi Ranghetti, phD (2015-2017)
MODIStsp_GUI()
, MODIStsp_process()
#' # - Running the tool using the GUI
# Running the tool without any option will start the GUI with the default or
# last used settings, in interactive mode (i.e., with gui = TRUE).
if (interactive()) {
MODIStsp()
}
#' # - Running the tool specifying processing arguments in the call
# **NOTE** Output files of examples are saved to file.path(tempdir(), "MODIStsp").
# Here we process layers __NDVI__ and __EVI__ and quality indicator __usefulness__
# of product __M*D13Q1__, considering both Terra and Aqua platforms, for dates
# comprised between 2020-06-01 and 2020-06-15 and saves output to R tempdir
# --> See name and available layers for product M*D13Q1.
# Note that this example (as well as the following ones) is run in single
# core to follow CRAN policies, by setting parallel = FALSE.
# Users can exploit multicore functionalities skipping to set this argument.
# The following check is performed in order not to provide errors
# running the examples if HDF4 is not supported.
is_hdf4_supported <- "HDF4" %in% sf::st_drivers("raster")$name
MODIStsp_get_prodlayers("M*D13A2")
if (is_hdf4_supported) {
MODIStsp(
gui = FALSE,
out_folder = "$tempdir",
selprod = "Vegetation_Indexes_16Days_1Km (M*D13A2)",
bandsel = c("EVI", "NDVI"),
quality_bandsel = "QA_usef",
indexes_bandsel = "SR",
user = "mstp_test" ,
password = "MSTP_test_01",
start_date = "2020.06.01",
end_date = "2020.06.15",
verbose = FALSE,
parallel = FALSE
)
}
#' # - Running the tool using the settings previously saved in a specific options file
# **NOTE** Output files of examples are saved to file.path(tempdir(), "MODIStsp").
# You can run the examples with `gui = TRUE` to set a different output folder!
# Here we use a test json file saved in MODIStsp installation folder which
# downloads and processed 3 MOD13A2 images over the Como Lake (Lombardy, Italy)
# and retrieves NDVI and EVI data, plus the Usefulness Index Quality Indicator.
opts_file <- system.file("testdata/test_MOD13A2.json", package = "MODIStsp")
if (is_hdf4_supported) {
MODIStsp(gui = FALSE, opts_file = opts_file, verbose = TRUE, parallel = FALSE)
}
# Running the tool using the settings previously saved in a specific option file
# and specifying the extent from a spatial file allows to re-use the same
# processing settings to perform download and reprocessing on a different area
opts_file <- system.file("testdata/test_MOD13A2.json", package = "MODIStsp")
spatial_file <- system.file("testdata/lakeshapes/garda_lake.shp", package = "MODIStsp")
if (is_hdf4_supported) {
MODIStsp(
gui = FALSE,
opts_file = opts_file,
spatmeth = "file",
spafile = spatial_file,
verbose = TRUE,
parallel = FALSE
)
}
# Running the tool using the settings previously saved in a
# specific options file and specifying each time the extent from a different
# spatial file (e.g., to perform the same processing on several extents)
# Note that you can also put all your extent files in a specific folder and
# create the extent list using for example.
extent_list = list.files(
system.file("testdata/lakeshapes/", package = "MODIStsp"),
"\\.shp$",
full.names = TRUE
)
extent_list
opts_file <- system.file("testdata/test_MOD13A2.json", package = "MODIStsp")
if (is_hdf4_supported) {
for (single_shape in extent_list) {
MODIStsp(
gui = FALSE,
opts_file = opts_file,
spatmeth = "file",
spafile = single_shape,
verbose = TRUE,
parallel = FALSE
)
}
}
# output files are placed in separate folders:
outfiles_garda <- list.files(
file.path(tempdir(), "MODIStsp/garda_lake/VI_16Days_1Km_v61/NDVI"),
full.names = TRUE
)
outfiles_garda
require(raster)
if (length(outfiles_garda) > 0) {
plot(raster(outfiles_garda[1] ))
}
outfiles_iseo <- list.files(
file.path(tempdir(), "MODIStsp/iseo_lake/VI_16Days_1Km_v61/NDVI"),
full.names = TRUE
)
outfiles_iseo
if (length(outfiles_garda) > 0) {
plot(raster(outfiles_iseo[1]))
}
# See also https://docs.ropensci.org/MODIStsp/articles/noninteractive_execution.html
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