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## ---- eval=FALSE, message=FALSE, warning=FALSE, include=TRUE------------------
# install.packages("remotes")
# library(remotes)
# install_github("ropensci/MODIStsp")
## ---- eval=FALSE, message=FALSE, warning=FALSE, include=TRUE------------------
# install.packages("MODIStsp")
## ---- eval=FALSE, message=FALSE, warning=FALSE, include=TRUE------------------
# library(devtools)
# install_github("ropensci/MODIStsp")
## ---- eval=FALSE, message=FALSE, warning=FALSE, include=TRUE------------------
# install.packages("MODIStsp")
## ---- eval=FALSE, message=FALSE, warning=FALSE, include=TRUE------------------
# library(devtools)
# install_github("ropensci/MODIStsp")
## ---- eval=FALSE, message=FALSE, warning=FALSE, include=TRUE, caption=FALSE----
# library(MODIStsp)
# MODIStsp()
## ----GUIfig, echo=FALSE, fig.align="center", fig.width=10, message=FALSE, warning=FALSE----
library(png)
library(grid)
library(knitr)
img <- readPNG("GUI_1.PNG")
grid.raster(img)
## ----eval=FALSE, echo=TRUE, message=FALSE, warning=FALSE----------------------
# library(MODIStsp)
# MODIStsp_get_prodlayers("M*D13Q1")
## ----eval=FALSE, echo=TRUE, message=FALSE, warning=FALSE----------------------
# 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_v61" of
# # `base::tempdir()`:
#
# out_fold <- file.path(tempdir(), "MODIStsp/VI_16Days_1Km_v61/")
# list.files(out_fold)
# list.files(file.path(out_fold ,"EVI"))
# list.files(file.path(out_fold ,"QA_usef"))
## ----eval=FALSE, echo=TRUE, message=FALSE, warning=FALSE----------------------
# 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_v61" of
# # tempdir():
#
# out_fold <- file.path(tempdir(), "MODIStsp/VI_16Days_1Km_v61")
# list.files(out_fold)
# list.files(file.path(out_fold ,"EVI"))
## ----eval=FALSE, echo=TRUE, message=FALSE, warning=FALSE----------------------
#
# 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_v61")
# list.files(out_fold)
# list.files(file.path(out_fold ,"NDVI"))
#
# # MOD10A2 ouptuts
# out_fold <- file.path(tempdir(), "MODIStsp/Surf_Temp_8Days_1Km_v61")
# list.files(out_fold)
# list.files(file.path(out_fold ,"LST_Night_1km"))
## ----eval=FALSE, echo=TRUE, message=FALSE, warning=FALSE----------------------
# # 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_v61/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_v61/EVI"),
# full.names = TRUE)
# outfiles_iseo
#
# plot(raster(outfiles_iseo[1]))
#
## ----eval=FALSE, tidy=TRUE, highlight=TRUE------------------------------------
# library(raster)
# modistsp_file <- "/my_outfolder/EVI/MOD13Q1_2005_137_EVI.tif"
# my_raster <- raster(modistsp_file)
## ----eval=FALSE---------------------------------------------------------------
# in_virtual_file <- "/my_outfolder/Time_Series/RData/Terra/EVI/MOD13Q1_MYD13Q1_NDVI_49_2000_353_2015_RData.RData"
# indata <- get(load(in_virtual_file))
## ---- eval=FALSE--------------------------------------------------------------
# #Set the input paths to raster and shape file
# infile <- 'myoutfolder/Time_Series/RData/Mixed/MOD13Q1_MYD13Q1_NDVI_49_2000_353_2015_RData.RData'
# shpname <- 'path_to_file/rois.shp'
# #Set the start/end dates for extraction
# startdate <- as.Date("2010-01-01")
# enddate <- as.Date("2014-12-31")
# #Load the RasterStack
# inrts <- get(load(infile))
# # Compute average and St.dev
# dataavg <- MODIStsp_extract(inrts, shpname, startdate, enddate, FUN = 'mean', na.rm = T)
# datasd <- MODIStsp_extract (inrts, shpname, startdate, enddate, FUN = 'sd', na.rm = T)
# # Plot average time series for the polygons
# plot.xts(dataavg)
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