inst/examples/util/rolf_stac.R
In albhasan/sits.prodes: What the Package Does (One Line, Title Case)
#### import libraries ####
library(dplyr)
library(magrittr)
#### fetch S3 ####
url <- aws.s3::get_bucket_df("mod13q1-test", max = Inf)$Key
url <- paste0("http://", "mod13q1-test", ".s3.amazonaws.com/", url)
files_name <- gsub("^.*/(.+)$", "\\1", url)
products <- gsub("^(.{7}).*$", "\\1", files_name)
tiles <- gsub("^.{8}(.{6}).*(_[0-9]+_[0-9]+)_[0-9]+\\.tif$", "\\1", files_name)
collection <- gsub("^.{15}(.{3}).*$", "\\1", files_name)
bands <- gsub("^.*(250m.*)(_[0-9]+){3}\\.tif$", replacement = "\\1", x = files_name)
dates <- as.integer(gsub("^.*_([0-9]+)\\.tif$", replacement = "\\1", x = files_name))
dates <- sits::timeline_2000_2017[dates]
#### fetch localhost ####
url <- list.files(path = "~/Downloads/MODIS/geotif", pattern = "*\\.tif", full.names = TRUE)
files_name <- gsub("^.*/(.+)$", "\\1", url)
products <- gsub("^(.{7}).*$", "\\1", files_name)
tiles <- gsub("^.{8}(.{6}).*(_[0-9]+_[0-9]+)_.*\\.tif$", "\\1\\2", files_name)
collection <- gsub("^.{15}(.{3}).*$", "\\1", files_name)
bands <- gsub("^.*(250m.*).tif$", replacement = "\\1", x = files_name)
dates <- as.character(as.Date(gsub("^.*A([0-9]{7}).*$", replacement = "\\1", x = files_name), format = "%Y%j"))
rm(files_name)
#### metadata functions ####
.file.open <- function(file) {
if (grepl("^https?://.+", file)) {
file = paste0("/vsicurl/", file)
}
brick <- tryCatch(raster::brick(file, values = FALSE), error = function(e) NULL)
if (is.null(brick)) {
stop(sprintf("Error while opening brick '%s'.\nFile is unreachable.", file))
}
return(brick)
}
.file.metadata <- function(file) {
brick <- .file.open(file = file)
extent <- raster::extent(brick)
result <-
tibble::tibble(
nrow = raster::nrow(brick),
ncol = raster::ncol(brick),
time_len = raster::nlayers(brick),
crs = as.character(raster::crs(brick)),
xmin = extent@xmin,
xmax = extent@xmax,
ymin = extent@ymin,
ymax = extent@ymax,
xres = raster::xres(brick),
yres = raster::yres(brick),
data_type = as.character(raster::dataType(brick)))
return(result)
}
.files.metadata <- function(files) {
progress_bar <- length(files) >= 10
if (progress_bar) {
pb <- utils::txtProgressBar(min = 0, max = length(files), style = 3)
}
metadata <- lapply(
files, function(file) {
result <- .file.metadata(file = file)
if (progress_bar) {
utils::setTxtProgressBar(pb = pb, value = utils::getTxtProgressBar(pb) + 1)
}
return(result)
})
if (progress_bar) {
close(pb)
}
metadata <- do.call(rbind, metadata)
metadata <- tibble::as_tibble(metadata)
return(metadata)
}
#### fetch metadata ####
rasters <-
dplyr::tibble(product = products,
tile = tiles, collection = collection,
href = url, bands = bands, date = dates,
type = "image/tiff")
system.time(meta_data <- .files.metadata(rasters$href))
rasters <- dplyr::bind_cols(list(rasters, meta_data))
rasters <-
EOCubes::MOD13Q1_bands %>%
dplyr::mutate(band_long_name = paste0("250m_16_days_", band_long_name)) %>%
dplyr::right_join(rasters, by = c("band_long_name" = "bands"))
rasters$keywords <- list(c("MOD13Q1", "Test Sites"))
#### cubes functions ####
cub_list <- function(. = NULL, .by = NULL, .index = FALSE, ...) {
if (missing(.))
return(list(...))
dots <- substitute(list(...))[-1:0]
.by <- substitute(.by)
if (!is.data.frame(.))
stop("You must inform a data frame as data input.")
.by_values <- eval(.by, envir = ., enclos = environment())
if (length(.by_values) == 0)
.by_values <- rep(1, len = nrow(.))
partitions <- by(., tapply(seq_len(length(.by_values)), .by_values), list)
res <- lapply(partitions, function(.) {
lapply(dots, function(expr) {
eval(expr, envir = ., enclos = environment())
})
})
names(res) <- NULL
if (.index) {
names(res) <- sapply(partitions, function(.) {
eval(.by, envir = .[1,], enclos = environment())
}, USE.NAMES = FALSE)
}
return(res)
}
get_spatial_crs <- function(crs) {
list(type = "name",
properties = list(name = crs))
}
get_spatial_extent <- function(.,
.xmin = "xmin",
.ymin = "ymin",
.xmax = "xmax",
.ymax = "ymax") {
list(type = "Feature",
bbox = c(min(.[[.xmin]]),
min(.[[.ymin]]),
max(.[[.xmax]]),
max(.[[.ymax]])),
geometry = list(type = "Polygon",
coordinates = list(list(c(min(.[[.xmin]]),
min(.[[.ymin]])),
c(min(.[[.xmin]]),
min(.[[.ymax]])),
c(min(.[[.xmax]]),
min(.[[.ymax]])),
c(min(.[[.xmax]]),
min(.[[.ymin]])),
c(min(.[[.xmin]]),
min(.[[.ymin]]))))))
}
get_temporal_extent <- function(., .date = "date") {
.date <- substitute(.date)
if (is.name(.date))
.date <- deparse(.date)
c(min(.[[.date]]), max(.[[.date]]))
}
cub_unique <- function(x) {
res <- unique(x)
if (length(res) > 1)
stop(sprintf(paste("Field '%s's values have not unique values.",
"Values: %s\n", sep = "\n"),
deparse(substitute(x)), paste(res, collapse = ", ")), call. = FALSE)
return(res)
}
cub_node <- function(., .name = NULL, ...) {
dots <- substitute(list(...))[-1:0]
.name <- substitute(.name)
partitions <- .
res <- lapply(partitions, function(.) {
lapply(dots, function(expr) {
eval(expr, envir = ., enclos = environment())
})
})
if (!is.null(.name)) {
names(res) <- sapply(partitions, function(.) {
eval(.name, envir = ., enclos = environment())
}, USE.NAMES = FALSE)
}
return(res)
}
cub_write_json <- function(x, project_path) {
id <- x$id
if (is.null(id))
id <- "/"
project_path <- path.expand(project_path)
path <- paste(dirname(project_path), basename(project_path), id, sep = "/")
if (!dir.exists(path))
dir.create(path, showWarnings = FALSE, recursive = TRUE)
file_path <- paste(path, "catalog.json", sep = "/")
jsonlite::write_json(x, path = file_path, pretty = TRUE, auto_unbox = TRUE)
return(file_path)
}
cub_remote <- function(remotes = NULL, name, base, curators, keywords) {
res <- dplyr::tibble(name = name, base = base, curators = curators, keywords = list(unlist(keywords)))
if (!is.null(remotes))
res <- dplyr::bind_rows(list(remotes, res))
return(res)
}
cub_curator <- function(curators = NULL, name, email) {
res <- list(list(list(name = name, email = email)))
if (!is.null(curators))
res <- list(append(curators[[1]], res[[1]]))
return(res)
}
#### make cubes ####
#### >localhost ####
project_folder <- "~/Documents/EOCubes/localhost"
published_location <- "~/Documents/EOCubes/localhost" # "http://eocubes-test.s3.amazonaws.com"
# complete definition
cube_def <-
rasters %>%
cub_list(.by = paste(product, collection, sep = "/"), .index = TRUE,
id = cub_unique(paste(product, collection, sep = "/")),
meta = list(crs = get_spatial_crs(cub_unique(crs)),
bands = cub_list(., .by = band_short_name, .index = TRUE,
min = cub_unique(min),
max = cub_unique(max),
fill = cub_unique(fill),
scale = cub_unique(scale),
name = cub_unique(band_long_name))),
tiles = cub_list(., .by = tile, .index = TRUE,
id = cub_unique(paste(product, collection, tile, sep = "/")),
extent = get_spatial_extent(.),
meta = list(cube = cub_unique(paste(published_location, product, collection, "catalog.json", sep = "/"))),
bands = cub_list(., .by = band_short_name, .index = TRUE,
layers = cub_list(., .by = date, .index = FALSE,
href = cub_unique(href),
date = cub_unique(date)))))
# cube
cube_lst <-
cube_def %>%
cub_node(.,
id = id,
version = "0.6",
description = "",
keywords = c("USGS/NASA", "MOD13Q1", "Brazil"),
meta = meta,
tiles = cub_node(.$tiles,
href = paste(published_location, id, "catalog.json", sep = "/"),
extent = extent))
cube_lst %>%
lapply(cub_write_json, project_folder)
# tiles
tiles_lst <- unname(cub_node(cube_def[[1]]$tiles,
id = id,
extent = extent,
meta = meta,
bands = cub_node(.$bands,
layers = layers)))
tiles_lst %>%
lapply(cub_write_json, project_folder)
#### make remotes ####
#### >eocubes ####
eocubes_lst <-
cub_remote(name = "eocubes",
base = "http://eocubes-test.s3.amazonaws.com",
curators = cub_curator(name = "Rolf Simoes", email = "<rolf.simoes@inpe.br>") %>%
cub_curator(name = "Ricardo Cartaxo", email = "<ricardo.cartaxo@inpe.br>") %>%
cub_curator(name = "Alber Sanchez", email = "<alber.sanchez@inpe.br>"),
keywords = c("INPE", "EOCubes", "R Package")) %>%
cub_list(curators = unlist(curators, recursive = FALSE),
keywords = unlist(keywords, recursive = FALSE),
cubes = cub_node(list(), .name = id,
description = description,
href = paste(published_location, id, "catalog.json", sep = "/")))
eocubes_lst %>%
lapply(cub_write_json, project_folder)
#### >localhost ####
localhost_lst <-
cub_remote(name = "localhost",
base = project_folder,
curators = cub_curator(name = Sys.info()[["user"]], email = ""),
keywords = c("EOCubes", "Local")) %>%
cub_list(version = "0.6",
description = "Local maintained cubes",
keywords = unlist(keywords, recursive = FALSE),
curators = unlist(curators, recursive = FALSE),
cubes = cub_node(cube_lst, .name = id,
description = description,
keywords = keywords,
href = paste(published_location, id, "catalog.json", sep = "/")))
localhost_lst %>%
lapply(cub_write_json, project_folder)
localhost_lst %>%
jsonlite::toJSON(pretty = T)
##### >root #####
root_lst <-
cub_list(version = "0.6",
default = "localhost",
remotes = cub_node(localhost_lst,
.name = "localhost",
description = description,
keywords = unlist(keywords),
href = cub_unique(paste(project_folder, "catalog.json", sep = "/"))))
root_lst %>%
jsonlite::toJSON(pretty = T, auto_unbox = T)
root_lst %>% jsonlite::write_json(path = "~/.EOCubes/remotes.json", pretty = T)
# publish on AWS S3
input_folder <- path.expand(paste(project_folder, cube_name, sep = "/"))
files <- list.files(path = input_folder, recursive = T, full.names = T)
files_output <- gsub(sprintf("^%s/(.*)$", input_folder), paste0(cube_name, "/\\1"), files)
files <- c(path.expand(paste(project_folder, "catalog.json", sep = "/")), files)
files_output <- c("catalog.json", files_output)
sapply(seq_along(files), function(i) aws.s3::put_object(files[i], files_output[i], "eocubes-test", acl = "public-read"))
#### EOCubes use ####
mod13q1_006 <- cube("MOD13Q1/006")
cube_crs(mod13q1_006)
cube_bands(mod13q1_006)
cube_tiles(mod13q1_006)
city_shp <- sf::read_sf("~/Downloads/test.shp")
cube_tiles(mod13q1_006, which = tiles_intersects(mod13q1_006, city_shp))
h12v10_cube <- filter_tiles(mod13q1_006, which = tiles_intersects(mod13q1_006, city_shp))
test <- make_stacks(h12v10_cube,
bands = c("ndvi", "evi"),
start_dates = seq(as.Date("2000-01-01"), as.Date("2018-01-01"), by = "years"),
end_dates = seq(as.Date("2001-01-01"), as.Date("2019-01-01"), by = "years"),
count = 23)
albhasan/sits.prodes documentation built on Sept. 3, 2020, 2:03 p.m.
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#### import libraries ####
library(dplyr)
library(magrittr)
#### fetch S3 ####
url <- aws.s3::get_bucket_df("mod13q1-test", max = Inf)$Key
url <- paste0("http://", "mod13q1-test", ".s3.amazonaws.com/", url)
files_name <- gsub("^.*/(.+)$", "\\1", url)
products <- gsub("^(.{7}).*$", "\\1", files_name)
tiles <- gsub("^.{8}(.{6}).*(_[0-9]+_[0-9]+)_[0-9]+\\.tif$", "\\1", files_name)
collection <- gsub("^.{15}(.{3}).*$", "\\1", files_name)
bands <- gsub("^.*(250m.*)(_[0-9]+){3}\\.tif$", replacement = "\\1", x = files_name)
dates <- as.integer(gsub("^.*_([0-9]+)\\.tif$", replacement = "\\1", x = files_name))
dates <- sits::timeline_2000_2017[dates]
#### fetch localhost ####
url <- list.files(path = "~/Downloads/MODIS/geotif", pattern = "*\\.tif", full.names = TRUE)
files_name <- gsub("^.*/(.+)$", "\\1", url)
products <- gsub("^(.{7}).*$", "\\1", files_name)
tiles <- gsub("^.{8}(.{6}).*(_[0-9]+_[0-9]+)_.*\\.tif$", "\\1\\2", files_name)
collection <- gsub("^.{15}(.{3}).*$", "\\1", files_name)
bands <- gsub("^.*(250m.*).tif$", replacement = "\\1", x = files_name)
dates <- as.character(as.Date(gsub("^.*A([0-9]{7}).*$", replacement = "\\1", x = files_name), format = "%Y%j"))
rm(files_name)
#### metadata functions ####
.file.open <- function(file) {
if (grepl("^https?://.+", file)) {
file = paste0("/vsicurl/", file)
}
brick <- tryCatch(raster::brick(file, values = FALSE), error = function(e) NULL)
if (is.null(brick)) {
stop(sprintf("Error while opening brick '%s'.\nFile is unreachable.", file))
}
return(brick)
}
.file.metadata <- function(file) {
brick <- .file.open(file = file)
extent <- raster::extent(brick)
result <-
tibble::tibble(
nrow = raster::nrow(brick),
ncol = raster::ncol(brick),
time_len = raster::nlayers(brick),
crs = as.character(raster::crs(brick)),
xmin = extent@xmin,
xmax = extent@xmax,
ymin = extent@ymin,
ymax = extent@ymax,
xres = raster::xres(brick),
yres = raster::yres(brick),
data_type = as.character(raster::dataType(brick)))
return(result)
}
.files.metadata <- function(files) {
progress_bar <- length(files) >= 10
if (progress_bar) {
pb <- utils::txtProgressBar(min = 0, max = length(files), style = 3)
}
metadata <- lapply(
files, function(file) {
result <- .file.metadata(file = file)
if (progress_bar) {
utils::setTxtProgressBar(pb = pb, value = utils::getTxtProgressBar(pb) + 1)
}
return(result)
})
if (progress_bar) {
close(pb)
}
metadata <- do.call(rbind, metadata)
metadata <- tibble::as_tibble(metadata)
return(metadata)
}
#### fetch metadata ####
rasters <-
dplyr::tibble(product = products,
tile = tiles, collection = collection,
href = url, bands = bands, date = dates,
type = "image/tiff")
system.time(meta_data <- .files.metadata(rasters$href))
rasters <- dplyr::bind_cols(list(rasters, meta_data))
rasters <-
EOCubes::MOD13Q1_bands %>%
dplyr::mutate(band_long_name = paste0("250m_16_days_", band_long_name)) %>%
dplyr::right_join(rasters, by = c("band_long_name" = "bands"))
rasters$keywords <- list(c("MOD13Q1", "Test Sites"))
#### cubes functions ####
cub_list <- function(. = NULL, .by = NULL, .index = FALSE, ...) {
if (missing(.))
return(list(...))
dots <- substitute(list(...))[-1:0]
.by <- substitute(.by)
if (!is.data.frame(.))
stop("You must inform a data frame as data input.")
.by_values <- eval(.by, envir = ., enclos = environment())
if (length(.by_values) == 0)
.by_values <- rep(1, len = nrow(.))
partitions <- by(., tapply(seq_len(length(.by_values)), .by_values), list)
res <- lapply(partitions, function(.) {
lapply(dots, function(expr) {
eval(expr, envir = ., enclos = environment())
})
})
names(res) <- NULL
if (.index) {
names(res) <- sapply(partitions, function(.) {
eval(.by, envir = .[1,], enclos = environment())
}, USE.NAMES = FALSE)
}
return(res)
}
get_spatial_crs <- function(crs) {
list(type = "name",
properties = list(name = crs))
}
get_spatial_extent <- function(.,
.xmin = "xmin",
.ymin = "ymin",
.xmax = "xmax",
.ymax = "ymax") {
list(type = "Feature",
bbox = c(min(.[[.xmin]]),
min(.[[.ymin]]),
max(.[[.xmax]]),
max(.[[.ymax]])),
geometry = list(type = "Polygon",
coordinates = list(list(c(min(.[[.xmin]]),
min(.[[.ymin]])),
c(min(.[[.xmin]]),
min(.[[.ymax]])),
c(min(.[[.xmax]]),
min(.[[.ymax]])),
c(min(.[[.xmax]]),
min(.[[.ymin]])),
c(min(.[[.xmin]]),
min(.[[.ymin]]))))))
}
get_temporal_extent <- function(., .date = "date") {
.date <- substitute(.date)
if (is.name(.date))
.date <- deparse(.date)
c(min(.[[.date]]), max(.[[.date]]))
}
cub_unique <- function(x) {
res <- unique(x)
if (length(res) > 1)
stop(sprintf(paste("Field '%s's values have not unique values.",
"Values: %s\n", sep = "\n"),
deparse(substitute(x)), paste(res, collapse = ", ")), call. = FALSE)
return(res)
}
cub_node <- function(., .name = NULL, ...) {
dots <- substitute(list(...))[-1:0]
.name <- substitute(.name)
partitions <- .
res <- lapply(partitions, function(.) {
lapply(dots, function(expr) {
eval(expr, envir = ., enclos = environment())
})
})
if (!is.null(.name)) {
names(res) <- sapply(partitions, function(.) {
eval(.name, envir = ., enclos = environment())
}, USE.NAMES = FALSE)
}
return(res)
}
cub_write_json <- function(x, project_path) {
id <- x$id
if (is.null(id))
id <- "/"
project_path <- path.expand(project_path)
path <- paste(dirname(project_path), basename(project_path), id, sep = "/")
if (!dir.exists(path))
dir.create(path, showWarnings = FALSE, recursive = TRUE)
file_path <- paste(path, "catalog.json", sep = "/")
jsonlite::write_json(x, path = file_path, pretty = TRUE, auto_unbox = TRUE)
return(file_path)
}
cub_remote <- function(remotes = NULL, name, base, curators, keywords) {
res <- dplyr::tibble(name = name, base = base, curators = curators, keywords = list(unlist(keywords)))
if (!is.null(remotes))
res <- dplyr::bind_rows(list(remotes, res))
return(res)
}
cub_curator <- function(curators = NULL, name, email) {
res <- list(list(list(name = name, email = email)))
if (!is.null(curators))
res <- list(append(curators[[1]], res[[1]]))
return(res)
}
#### make cubes ####
#### >localhost ####
project_folder <- "~/Documents/EOCubes/localhost"
published_location <- "~/Documents/EOCubes/localhost" # "http://eocubes-test.s3.amazonaws.com"
# complete definition
cube_def <-
rasters %>%
cub_list(.by = paste(product, collection, sep = "/"), .index = TRUE,
id = cub_unique(paste(product, collection, sep = "/")),
meta = list(crs = get_spatial_crs(cub_unique(crs)),
bands = cub_list(., .by = band_short_name, .index = TRUE,
min = cub_unique(min),
max = cub_unique(max),
fill = cub_unique(fill),
scale = cub_unique(scale),
name = cub_unique(band_long_name))),
tiles = cub_list(., .by = tile, .index = TRUE,
id = cub_unique(paste(product, collection, tile, sep = "/")),
extent = get_spatial_extent(.),
meta = list(cube = cub_unique(paste(published_location, product, collection, "catalog.json", sep = "/"))),
bands = cub_list(., .by = band_short_name, .index = TRUE,
layers = cub_list(., .by = date, .index = FALSE,
href = cub_unique(href),
date = cub_unique(date)))))
# cube
cube_lst <-
cube_def %>%
cub_node(.,
id = id,
version = "0.6",
description = "",
keywords = c("USGS/NASA", "MOD13Q1", "Brazil"),
meta = meta,
tiles = cub_node(.$tiles,
href = paste(published_location, id, "catalog.json", sep = "/"),
extent = extent))
cube_lst %>%
lapply(cub_write_json, project_folder)
# tiles
tiles_lst <- unname(cub_node(cube_def[[1]]$tiles,
id = id,
extent = extent,
meta = meta,
bands = cub_node(.$bands,
layers = layers)))
tiles_lst %>%
lapply(cub_write_json, project_folder)
#### make remotes ####
#### >eocubes ####
eocubes_lst <-
cub_remote(name = "eocubes",
base = "http://eocubes-test.s3.amazonaws.com",
curators = cub_curator(name = "Rolf Simoes", email = "<rolf.simoes@inpe.br>") %>%
cub_curator(name = "Ricardo Cartaxo", email = "<ricardo.cartaxo@inpe.br>") %>%
cub_curator(name = "Alber Sanchez", email = "<alber.sanchez@inpe.br>"),
keywords = c("INPE", "EOCubes", "R Package")) %>%
cub_list(curators = unlist(curators, recursive = FALSE),
keywords = unlist(keywords, recursive = FALSE),
cubes = cub_node(list(), .name = id,
description = description,
href = paste(published_location, id, "catalog.json", sep = "/")))
eocubes_lst %>%
lapply(cub_write_json, project_folder)
#### >localhost ####
localhost_lst <-
cub_remote(name = "localhost",
base = project_folder,
curators = cub_curator(name = Sys.info()[["user"]], email = ""),
keywords = c("EOCubes", "Local")) %>%
cub_list(version = "0.6",
description = "Local maintained cubes",
keywords = unlist(keywords, recursive = FALSE),
curators = unlist(curators, recursive = FALSE),
cubes = cub_node(cube_lst, .name = id,
description = description,
keywords = keywords,
href = paste(published_location, id, "catalog.json", sep = "/")))
localhost_lst %>%
lapply(cub_write_json, project_folder)
localhost_lst %>%
jsonlite::toJSON(pretty = T)
##### >root #####
root_lst <-
cub_list(version = "0.6",
default = "localhost",
remotes = cub_node(localhost_lst,
.name = "localhost",
description = description,
keywords = unlist(keywords),
href = cub_unique(paste(project_folder, "catalog.json", sep = "/"))))
root_lst %>%
jsonlite::toJSON(pretty = T, auto_unbox = T)
root_lst %>% jsonlite::write_json(path = "~/.EOCubes/remotes.json", pretty = T)
# publish on AWS S3
input_folder <- path.expand(paste(project_folder, cube_name, sep = "/"))
files <- list.files(path = input_folder, recursive = T, full.names = T)
files_output <- gsub(sprintf("^%s/(.*)$", input_folder), paste0(cube_name, "/\\1"), files)
files <- c(path.expand(paste(project_folder, "catalog.json", sep = "/")), files)
files_output <- c("catalog.json", files_output)
sapply(seq_along(files), function(i) aws.s3::put_object(files[i], files_output[i], "eocubes-test", acl = "public-read"))
#### EOCubes use ####
mod13q1_006 <- cube("MOD13Q1/006")
cube_crs(mod13q1_006)
cube_bands(mod13q1_006)
cube_tiles(mod13q1_006)
city_shp <- sf::read_sf("~/Downloads/test.shp")
cube_tiles(mod13q1_006, which = tiles_intersects(mod13q1_006, city_shp))
h12v10_cube <- filter_tiles(mod13q1_006, which = tiles_intersects(mod13q1_006, city_shp))
test <- make_stacks(h12v10_cube,
bands = c("ndvi", "evi"),
start_dates = seq(as.Date("2000-01-01"), as.Date("2018-01-01"), by = "years"),
end_dates = seq(as.Date("2001-01-01"), as.Date("2019-01-01"), by = "years"),
count = 23)
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