Specifying
the processing parameters in the function call
All processing parameters can be set in the call to
MODIStsp(). Mandatory parameters are selprod
(specifying the MODIS product), (one of) bandsel,
quality_bandsel or indexes_bandsel, (that
specify the desired output layers), out_folder and
start_date and end_date. user and
password are also needed if download_server is
not equal to "offline".
The function MODIStsp_get_prodlayers() allows to easily
retrieve the names of products and available layers based on product
code, such as in:
library(MODIStsp)
MODIStsp_get_prodlayers("M*D13Q1")
The other parameters are set automatically to default values (see the
function reference for details on the different available function
arguments).
For example, the following code processes 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():
library(MODIStsp)
# **NOTE** Output files of examples are saved to file.path by setting out_folder to $tempdir.
# --> See name and available layers for product M*D13Q1
# MODIStsp_get_prodlayers("M*D13A2")
# --> Launch the processing
MODIStsp(
gui = FALSE,
out_folder = "$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
)
# Outputs are in this case in subfolder "MODIStsp/VI_16Days_1Km_v6" of
# `base::tempdir()`:
out_fold <- file.path(tempdir(), "MODIStsp/VI_16Days_1Km_v6/")
list.files(out_fold)
list.files(file.path(out_fold ,"EVI"))
list.files(file.path(out_fold ,"QA_usef"))
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.
Launching
MODIStsp using a saved “Options file”
Alternatively, you can run MODIStsp() without opening
the GUI by specifying a previously saved options file:
library(MODIStsp)
# **NOTE** Output files of examples are saved to file.path(tempdir(), "MODIStsp").
# --> Specify the path to a valid options file saved in advance from MODIStsp GUI
# 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")
# --> Launch the processing
MODIStsp(gui = FALSE, opts_file = opts_file, verbose = FALSE, parallel = FALSE)
# Outputs are in this case in subfolder "MODIStsp/VI_16Days_1Km_v6" of
# tempdir():
out_fold <- file.path(tempdir(), "MODIStsp/VI_16Days_1Km_v6")
list.files(out_fold)
list.files(file.path(out_fold ,"EVI"))
Looping over
different Options files
If you need to process different MODIS products, you can prepare
beforehand different MODIStsp options files by using the GUI, and then
loop over them like this:
opts_files <- c(system.file("testdata/test_MOD13A2.json", package = "MODIStsp"),
system.file("testdata/test_MOD10A2.json", package = "MODIStsp"))
for (opts_file in opts_files) {
MODIStsp(gui = FALSE, opts_file = opts_file, verbose = FALSE, parallel = FALSE)
}
# MOD13A2 ouptuts
out_fold <- file.path(tempdir(), "MODIStsp/VI_16Days_1Km_v6")
list.files(out_fold)
list.files(file.path(out_fold ,"NDVI"))
# MOD10A2 ouptuts
out_fold <- file.path(tempdir(), "MODIStsp/Surf_Temp_8Days_1Km_v6")
list.files(out_fold)
list.files(file.path(out_fold ,"LST_Night_1km"))
Specifying
the processing parameters using a previously saved options file and
overwriting some parameters
Finally, it is possible to both specify a previously saved options
file AND setting some parameters in the call to the function. This
allows easily performing similar processings, by only updating
the required arguments, as in the examples below.
Looping over
different spatial extents
Specifying the spafile parameter while setting the
spatmeth parameter to "file" overrides for
example the output extent of the selected Options File. This allows
performing the same preprocessing on different extents using a single
Options File. For example:
# Run 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
library(MODIStsp)
opts_file <- system.file("testdata/test_MOD13A2.json", package = "MODIStsp")
spatial_file <- system.file("testdata/lakeshapes/garda_lake.shp", package = "MODIStsp")
MODIStsp(
gui = FALSE,
opts_file = opts_file,
spatmeth = "file",
spafile = spatial_file,
verbose = FALSE,
parallel = FALSE
)
# --> Create a character array containing a list of shapefiles (or other spatial files)
extent_list <- list.files(system.file("testdata/lakeshapes/", package = "MODIStsp"), full.names = TRUE, "\\.shp$")
extent_list
# --> Loop on the list of spatial files and run MODIStsp using each of them to
# automatically define the output extent (A separate output folder is created for
# each input spatial file).
for (single_shape in extent_list) {
MODIStsp(
gui = FALSE,
opts_file = opts_file,
spatmeth = "file",
spafile = single_shape,
verbose = FALSE,
parallel = FALSE
)
}
# output files are placed in separate folders:
outfiles_garda <- list.files(
file.path(tempdir(), "MODIStsp/garda_lake/VI_16Days_1Km_v6/EVI"),
full.names = TRUE)
outfiles_garda
library(raster)
plot(raster(outfiles_garda[1]))
outfiles_iseo <- list.files(
file.path(tempdir(), "MODIStsp/iseo_lake/VI_16Days_1Km_v6/EVI"),
full.names = TRUE)
outfiles_iseo
plot(raster(outfiles_iseo[1]))
