initial upload

contains only some native gdal utils and metadata readers

Author: edzer

DESCRIPTION

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+Package: stars
+Version: 0.0
+Title: Scalable, Spatiotemporal Tidy Arrays for R
+Description: Support for Scalable, Spatiotemporal Arrays in R, using GDAL bindings.
+Authors@R: c(person("Edzer", "Pebesma", role = c("aut", "cre"), email = "edzer.pebesma@uni-muenster.de"),
+	person("Michael", "Sumner", role = "ctb"),
+	person("Etienne", "Racine", role = "ctb"))
+Depends:
+    R (>= 3.3.0)
+Imports: 
+    Rcpp, 
+	magrittr,
+	sf
+Suggests: 
+    testthat, 
+    knitr, 
+    tibble, 
+    dplyr, 
+    tidyr, 
+    geosphere (>= 1.5-5), 
+    maptools, 
+    maps
+LinkingTo: Rcpp, sf
+VignetteBuilder: knitr
+SystemRequirements: GDAL (>= 2.1.0), PROJ.4 (>= 4.8.0)
+License: Apache License
+URL: https://github.com/edzer/stars/
+BugReports: https://github.com/edzer/stars/issues/
+Collate:
+	init.R
+	dataset.R
+	utils.R
+	RcppExports.R
+RoxygenNote: 6.0.1

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export("%>%")
+export(st_gdalinfo)
+export(st_gdalrasterize)
+export(st_gdalwarp)
+export(st_get_metadata)
+export(st_get_subdatasets)
+export(st_read_crs)
+export(stars_extSoftVersion)
+importFrom(Rcpp,evalCpp)
+importFrom(magrittr,"%>%")
+importFrom(sf,sf_extSoftVersion)
+useDynLib(stars)

R/RcppExports.R

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+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+CPL_GetMetadata <- function(obj, domain_item, options) {
+    .Call('stars_CPL_GetMetadata', PACKAGE = 'stars', obj, domain_item, options)
+}
+
+CPL_get_crs <- function(obj, options) {
+    .Call('stars_CPL_get_crs', PACKAGE = 'stars', obj, options)
+}
+
+CPL_add_one <- function(inv) {
+    .Call('stars_CPL_add_one', PACKAGE = 'stars', inv)
+}
+
+CPL_gdal_init <- function() {
+    invisible(.Call('stars_CPL_gdal_init', PACKAGE = 'stars'))
+}
+
+CPL_gdal_cleanup_all <- function() {
+    invisible(.Call('stars_CPL_gdal_cleanup_all', PACKAGE = 'stars'))
+}
+
+CPL_gdal_version <- function(what = "RELEASE_NAME") {
+    .Call('stars_CPL_gdal_version', PACKAGE = 'stars', what)
+}
+
+CPL_proj_version <- function(b = FALSE) {
+    .Call('stars_CPL_proj_version', PACKAGE = 'stars', b)
+}
+
+CPL_proj_is_valid <- function(proj4string) {
+    .Call('stars_CPL_proj_is_valid', PACKAGE = 'stars', proj4string)
+}
+
+CPL_proj_info <- function(type) {
+    .Call('stars_CPL_proj_info', PACKAGE = 'stars', type)
+}
+
+CPL_gdalinfo <- function(obj, options) {
+    .Call('stars_CPL_gdalinfo', PACKAGE = 'stars', obj, options)
+}
+
+CPL_gdalwarp <- function(src, dst, options) {
+    .Call('stars_CPL_gdalwarp', PACKAGE = 'stars', src, dst, options)
+}
+
+CPL_gdalrasterize <- function(src, dst, options) {
+    .Call('stars_CPL_gdalrasterize', PACKAGE = 'stars', src, dst, options)
+}
+

R/dataset.R

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+#' get metadata of a raster layer
+#'
+#' get metadata of a raster layer
+#' @name get_get_metadata
+#' @export
+#' @param file file name
+#' @param domain_item character vector of length 0, 1 (with domain), or 2 (with domain and item); use \code{""} for the default domain, use \code{NA_character_} to query the domain names.
+#' @param options character; character vector with data open options
+#' @param parse logical; should metadata be parsed into a named list (\code{TRUE}) or returned as character data?
+#' @return named list with metadata items
+#' @examples
+#' f = system.file("tif/L7_ETMs.tif", package="stars")
+#' st_get_metadata(f)
+#' st_get_metadata(f, NA_character_)
+#' # try(st_get_metadata(f, "wrongDomain"))
+#' # st_get_metadata(f, c("", "AREA_OR_POINT"))
+st_get_metadata = function(file, domain_item = character(0), options = character(0), parse = TRUE) {
+	stopifnot(is.character(file))
+	stopifnot(is.character(domain_item))
+	stopifnot(length(domain_item) <= 2)
+	stopifnot(is.character(options))
+	if (length(domain_item) >= 1 && !is.na(domain_item[1]) &&
+			!(domain_item[1] %in% CPL_GetMetadata(file, NA_character_, options)))
+		stop("domain_item[1] not found in available metadata domains")
+	p = CPL_GetMetadata(file, domain_item, options)
+	if (!is.na(domain_item[1]) && parse)
+		parse_metadata(p)
+	else
+		p
+}
+
+parse_metadata = function(md) {
+	lst = lapply(strsplit(md, "="), function(x) x[[2]])
+	names(lst) = sapply(strsplit(md, "="), function(x) x[[1]])
+	structure(lst, class = "gdal_metadata")
+}
+
+#' @name get_get_metadata
+#' @param name logical; retrieve name of subdataset? If \code{FALSE}, retrieve description
+#' @export
+#' @return \code{st_get_subdatasets} returns a zero-length list if \code{file} does not have subdatasets.
+st_get_subdatasets = function(file, options = character(0), name = TRUE) {
+	if (!("SUBDATASETS" %in% CPL_GetMetadata(file, NA_character_, options)))
+		list()
+	else {
+		md = st_get_metadata(file, "SUBDATASETS", options, TRUE)
+		if (name)
+			md[seq(1, length(md), by = 2)]
+		else
+			md[seq(2, length(md), by = 2)]
+	}
+}
+
+#' read coordinate reference system from GDAL data set
+#' @param file character; file name
+#' @param options character; raster layer read options
+#' @return object of class \code{crs}, see \link[sf]{st_crs}.
+#' @export
+st_read_crs = function(file, options = character(0)) {
+	ret = CPL_get_crs(file, options)
+	ret$crs = sf::st_crs(wkt = ret$crs)
+	ret
+}

R/init.R

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+#' @importFrom sf sf_extSoftVersion
+#' @importFrom Rcpp evalCpp
+#' @useDynLib stars
+NULL
+
+#' @importFrom magrittr %>%
+#' @export
+magrittr::`%>%`
+
+.stars_cache <- new.env(FALSE, parent=globalenv())
+
+.onLoad = function(libname, pkgname) {
+	if (file.exists(system.file("proj/nad.lst", package = "stars")[1])) {
+		# nocov start
+  		assign(".stars.PROJ_LIB", Sys.getenv("PROJ_LIB"), envir=.stars_cache)
+		prj = system.file("proj", package = "stars")[1]
+		Sys.setenv("PROJ_LIB" = prj)
+		assign(".stars.GDAL_DATA", Sys.getenv("GDAL_DATA"), envir=.stars_cache)
+		gdl = system.file("gdal", package = "stars")[1]
+		Sys.setenv("GDAL_DATA" = gdl)
+		# nocov end
+	}
+	CPL_gdal_init()
+}
+
+.onUnload = function(libname, pkgname) {
+	CPL_gdal_cleanup_all()
+	if (file.exists(system.file("proj/nad.lst", package = "stars")[1])) {
+		# nocov start
+		Sys.setenv("PROJ_LIB"=get(".stars.PROJ_LIB", envir=.stars_cache))
+		Sys.setenv("GDAL_DATA"=get(".stars.GDAL_DATA", envir=.stars_cache))
+		# nocov end
+	}
+}
+
+.onAttach = function(libname, pkgname) {
+	m = paste0("Linking to GDAL ", CPL_gdal_version(), ", proj.4 ", CPL_proj_version())
+	packageStartupMessage(m)
+}
+
+#' Provide the external dependencies versions of the libraries linked to stars
+#' 
+#' Provide the external dependencies versions of the libraries linked to stars
+#' @export
+stars_extSoftVersion = function() {
+	structure(c(CPL_gdal_version(), CPL_proj_version()),
+		names = c("GDAL", "proj.4"))
+}
+
+.x = sf_extSoftVersion()

R/utils.R

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+#' Native interface to gdal utils
+#' @name gdal_utils
+#' @param name character; name of input layer
+#' @param source character; name(s) of input layer(s)
+#' @param destination character; name of output layer
+#' @param quiet logical; suppress printed output
+#' @param options layer opening options
+#' @return \code{st_gdalwarp} and \code{st_gdalrasterize} return \code{NULL} (invisibly) on success, an error message on failure.
+#' \code{st_gdalinfo} returns the raster metadata
+#' @export
+st_gdalinfo = function(name, options, quiet = FALSE) {
+	ret = CPL_gdalinfo(name, options)
+	if (! quiet)
+		cat(ret)
+	invisible(ret)
+}
+
+#' @name gdal_utils
+#' @export
+st_gdalwarp = function(source, destination, options) {
+	if (! CPL_gdalwarp(source, destination, options))
+		stop("st_gdalwarp: an error occured")
+	else
+		invisible(NULL)
+}
+
+#' @name gdal_utils
+#' @export
+st_gdalrasterize = function(source, destination, options) {
+	if (! CPL_gdalrasterize(source, destination, options))
+		stop("st_gdalrasterize: an error occured")
+	else
+		invisible(NULL)
+}

cleanup

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+#!/bin/sh
+
+# rm -fr man R/Rcpp*R src/Rcpp*cpp 
+rm -fr src/Makevars config.log config.status autom4te.cache src/*.o src/*.so
+rm -fr vignette/*html
+rm -fr proj_conf_test*
+rm -fr */Rplots.pdf