Devel (v. 1.3.3.9003) RC 1.3.4 (#304)

## New functions - `gdalUtil()`: function used to perform GDAL operations, calling C-based GDAL utilities using `sf::gdal_utils()`, and Python-based ones through system calls (a standalone GDAL environment is request to do it, as it was in previous versions). ## Documentation - Improve documentation of vignette "Output file structure", including the description of output products. ## New dependency - **`rgdal`** is now an explicit dependency (this because it is used by **`raster`** but it is not a mandatory dependency). ## Minor changes - GDAL C-based utilities are called using internal GDAL routines in package **`sf`** (see `gdalUtil()`). This allows reducing the use of external runtime dependencies. - GDAL messages are suppressed if the suggested dependency **`sys`** is installed (#257). - The new section of the vignette "Output file documentation" regarding products is linked in the GUI. ## Bug fixes - Fix #308.
ranghetti · Apr 22, 2020 · 7f0b41b · 7f0b41b
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diff --git a/.travis.yml b/.travis.yml
@@ -10,6 +10,10 @@ r_packages:
   - RPostgreSQL
   - covr
 
+r_github_packages:
+  - r-spatial/lwgeom
+  - r-spatial/sf
+
 apt_packages:
   - libgdal-dev
   - libproj-dev

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: sen2r
 Type: Package
 Title: Find, Download and Process Sentinel-2 Data
-Version: 1.3.3.9001
+Version: 1.3.4
 Authors@R: c(person("Luigi", "Ranghetti",
                     email = "[email protected]",
                     role = c("aut", "cre"),
@@ -23,10 +23,11 @@ BugReports: https://github.com/ranghetti/sen2r/issues
 Depends: R (>= 3.5.0)
 Imports:
   methods,
-  sf,
-  stars,
+  sf (>= 0.9.2),
+  stars (>= 0.4.1),
   data.table,
   raster,
+  rgdal,
   XML,
   jsonlite,
   geojsonio,
@@ -44,7 +45,6 @@ Imports:
   httr,
   RcppTOML
 Suggests:
-  rgdal,
   spelling,
   geojsonlint,
   httptest,
@@ -58,5 +58,5 @@ SystemRequirements: GDAL (>= 2.1.2), PROJ (>= 4.9.1), GEOS (>= 3.4.2),
   Cairo, Curl, NetCDF, jq, Protocol Buffers, V8, OpenSSL, Libxml2.
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
 Language: en-GB
diff --git a/Dockerfile b/Dockerfile
@@ -12,9 +12,6 @@ RUN apt-get update && apt-get install -y \
     apt-get autoremove -y && \
     rm -rf /var/lib/apt/lists/*
 
-# Install lwgeom from remote (https://github.com/rocker-org/geospatial/issues/17)
-RUN R -e "remotes::install_github('r-spatial/lwgeom', dependencies = TRUE)"
-
 # Install the package
 RUN R -e "remotes::install_github('ranghetti/sen2r', ref = 'master', dependencies = TRUE)"
 

diff --git a/NAMESPACE b/NAMESPACE
@@ -17,6 +17,7 @@ export(check_scihub_login)
 export(check_sen2r_deps)
 export(comsub)
 export(expand_path)
+export(gdalUtil)
 export(gdal_abs2rel)
 export(gdal_rel2abs)
 export(gdal_warp)
@@ -123,6 +124,7 @@ importFrom(raster,values)
 importFrom(raster,writeStart)
 importFrom(raster,writeStop)
 importFrom(raster,writeValues)
+importFrom(rgdal,GDALinfo)
 importFrom(sf,gdal_crs)
 importFrom(sf,gdal_utils)
 importFrom(sf,sf_extSoftVersion)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,24 @@
+# Version 1.3.4
+
+## New functions
+- `gdalUtil()`: function used to perform GDAL operations, calling C-based GDAL utilities using `sf::gdal_utils()`, and Python-based ones through system calls (a standalone GDAL environment is request to do it, as it was in previous versions).
+
+## Documentation
+- Improve documentation of vignette "Output file structure", including the description of output products.
+
+## New dependency
+- **`rgdal`** is now an explicit dependency (this because it is used by **`raster`** but it is not a mandatory dependency).
+
+## Minor changes
+- GDAL C-based utilities are called using internal GDAL routines in package **`sf`** (see `gdalUtil()`). This allows reducing the use of external runtime dependencies.
+- GDAL messages are suppressed if the suggested dependency **`sys`** is installed (#257).
+- The new section of the vignette "Output file documentation" regarding products is linked in the GUI.
+
+## Bug fixes
+- Re-fix #292.
+- Fix #308.
+
+
 # Version 1.3.3
 
 ## Major changes
@@ -12,7 +33,7 @@
 - Improve the installation page.
 
 ## Bug fixes
-- Support for `sf` >= 0.9 (#260)
+- Support for **`sf`** >= 0.9 (#260)
 - Patch for **`stars`** issue, made to resolve the temporary incompatibility with **`sf`** >= 0.9 (see issue #295)
 - Fix #292 
 - Small improvements
@@ -283,7 +304,7 @@ First stable release of package **sen2r**! See the announcement [here](https://l
 ### Bug fixing:
 * Fix bug in SciHub login
 * Fix maps (tiles were hidden)
-* Fix:missing dependency lwgeom
+* Fix:missing dependency **`lwgeom`**
 * Various fixes (#140, #141, #142, etc.)
 
 

diff --git a/R/check_gdal.R b/R/check_gdal.R
@@ -278,11 +278,6 @@ check_gdal <- function(abort = TRUE, gdal_path = NULL, force = FALSE, full_scan
   gdal_version <- gdal_versions[1]
   bin_ext <- ifelse(Sys.info()["sysname"] == "Windows", ".exe", "")
   binpaths$gdalinfo <- normalize_path(file.path(gdal_dir,paste0("gdalinfo",bin_ext)))
-  binpaths$ogrinfo <- normalize_path(file.path(gdal_dir,paste0("ogrinfo",bin_ext)))
-  binpaths$gdal_translate <- normalize_path(file.path(gdal_dir,paste0("gdal_translate",bin_ext)))
-  binpaths$gdalwarp <- normalize_path(file.path(gdal_dir,paste0("gdalwarp",bin_ext)))
-  binpaths$gdalbuildvrt <- normalize_path(file.path(gdal_dir,paste0("gdalbuildvrt",bin_ext)))
-  binpaths$gdaldem <- normalize_path(file.path(gdal_dir,paste0("gdaldem",bin_ext)))
   if (Sys.info()["sysname"] == "Windows") {
     binpaths$python <- normalize_path(file.path(gdal_dir,paste0("python",bin_ext)))
   }
@@ -291,11 +286,6 @@ check_gdal <- function(abort = TRUE, gdal_path = NULL, force = FALSE, full_scan
   } else {
     normalize_path(file.path(gdal_py_dir,"gdal_calc.py"))
   }
-  binpaths$gdal_polygonize <- if (Sys.info()["sysname"] == "Windows") {
-    paste0(binpaths$python," ",normalize_path(file.path(gdal_py_dir,"gdal_polygonize.py")))
-  } else {
-    normalize_path(file.path(gdal_py_dir,"gdal_polygonize.py"))
-  }
   binpaths$gdal_fillnodata <- if (Sys.info()["sysname"] == "Windows") {
     paste0(binpaths$python," ",normalize_path(file.path(gdal_py_dir,"gdal_fillnodata.py")))
   } else {

diff --git a/R/dontuse.R b/R/dontuse.R
@@ -0,0 +1,15 @@
+#' @title Don't use
+#' @description Don't use this function.
+#' @details This function simply call an `rgdal` function, so to be able to
+#'  include package `rgdal` among imported dependencies.
+#'  This is necessary since using `raster` without having `rgdal` installed
+#'  causes troublings in R 4.
+#' @importFrom rgdal GDALinfo
+#' @return NULL
+dontuse <- function() {
+  suppressWarnings(GDALinfo(
+    system.file("extdata/out/S2A2A_20190723_022_Barbellino_SCL_10.tif", package = "sen2r")
+  ))
+  message("Disobedient.")
+  invisible(NULL)
+}
diff --git a/R/expect_equal_crs.R b/R/expect_equal_crs.R
@@ -0,0 +1,20 @@
+#' @title Compare two non-null CRS
+#' @description Internal function: convenience function to compare two non-null
+#'  CRS in tests without using EPSG (so usable with rgdal >= 1.5).
+#' @param crs1 CRS 1 to compare
+#' @param crs2 CRS 2 to compare
+#' @return `testthat::expect_equal()` output.
+#' @importFrom sf st_geometry st_read st_coordinates st_transform
+#' @author Luigi Ranghetti, phD (2020) \email{luigi@@ranghetti.info}
+#' @note License: GPL 3.0
+
+expect_equal_crs <- function(crs1, crs2) {
+  ref_vec <- st_geometry(st_read(
+    system.file("extdata/vector/barbellino.geojson", package = "sen2r"), 
+    quiet = TRUE
+  ))
+  testthat::expect_equal(
+    as.integer(st_coordinates(st_transform(ref_vec, crs1))[,c("X","Y")]),
+    as.integer(st_coordinates(st_transform(ref_vec, crs2))[,c("X","Y")])
+  )
+}
diff --git a/R/gdalUtil.R b/R/gdalUtil.R
@@ -0,0 +1,217 @@
+#' @title Interface to GDAL Python-based utilities
+#' @description This accessory function interfaces with GDAL 
+#'  utilities (sen2r must be interfaced with a runtime GDAL
+#'  environment, see `check_gdal()`).
+#'  Python-based utilities are always called from a runtime GDAL;
+#'  C-based ones are called using `sf::gdal_utils()`.
+#' @param util Character: one among `"info"`, `"translate"`, `"warp"`, 
+#'  `"demprocessing"` ,`"buildvrt"` (C-based),
+#'  `"calc"` and `"fillnodata"` (Python-based).
+#'  Other utilities were not implemented, since they are not used by sen2r.
+#' @param source path of input layer(s); for `calc` this can be more than one.
+#' @param destination Path of the output layer.
+#' @param options Character vector with GDAL options.
+#' @param quiet Logical: if TRUE, suppress printing of output for info
+#'  (this argument is ignored in case package `sys` is not installed).
+#' @param formula (for `util = "calc"`) Calculation in `gdalnumeric` syntax using
+#'  `+`, `-`, `/`, `*`, or any `numpy` array functions (i.e. `log10()`).
+#' @param processing Character: processing options for `util = "demprocessing"`.
+#' @param colorfilename Character: name of colour file for `util = "demprocessing"`
+#'  (mandatory if `processing="color-relief"`).
+#' @return A logical (invisible) indicating success (i.e., TRUE); 
+#'  in case of failure, an error is raised and FALSE is returned (in case of 
+#'  Python-based utilities).
+#' @importFrom sf gdal_utils
+#' @export
+#' @author Luigi Ranghetti, phD (2020) \email{luigi@@ranghetti.info}
+#' @note License: GPL 3.0
+#' @examples 
+#' # Define product names
+#' examplename <- system.file(
+#'   "extdata/out/S2A2A_20190723_022_Barbellino_BOA_10.tif",
+#'   package = "sen2r"
+#' )
+#' 
+#' \donttest{
+#' ## gdalinfo
+#' out0 <- gdalUtil("info", examplename, quiet = TRUE)
+#' message(out0)
+#' 
+#' ## gdal_translate
+#' outname1 <- tempfile(fileext = ".tif")
+#' gdalUtil(
+#'   "translate", 
+#'   examplename, outname1,
+#'   options = c("-tr", "2", "2", "-r", "cubicspline", "-co", "COMPRESS=DEFLATE")
+#' )
+#' oldpar <- par(mfrow = c(1,2), mar = rep(0,4))
+#' image(stars::read_stars(examplename), rgb = c(11,8,4))
+#' image(stars::read_stars(outname1), rgb = c(11,8,4))
+
+#' 
+#' ## gdalwarp
+#' outname2 <- tempfile(fileext = ".tif")
+#' gdalUtil(
+#'   "warp", 
+#'   examplename, outname2,
+#'   options = c("-t_srs", "EPSG:32633", "-co", "COMPRESS=DEFLATE")
+#' )
+#' oldpar <- par(mfrow = c(1,2), mar = rep(0,4))
+#' image(stars::read_stars(examplename), rgb = c(11,8,4))
+#' image(stars::read_stars(outname2), rgb = c(11,8,4))
+#' 
+#' ## gdal_calc
+#' outname3 <- tempfile(fileext = ".tif")
+#' ndvirefname <- system.file(
+#'   "extdata/out/S2A2A_20190723_022_Barbellino_NDVI_10.tif",
+#'   package = "sen2r"
+#' )
+#' gdalUtil(
+#'   "calc", 
+#'   rep(examplename,2), outname3,
+#'   formula = "10000*(A.astype(float)-B)/(A+B)",
+#'   options = c("--A_band", "8", "--B_band", "4", "--type", "Int16")
+#' )
+#' oldpar <- par(mfrow = c(1,2), mar = rep(0,4))
+#' image(stars::read_stars(ndvirefname))
+#' image(stars::read_stars(outname3))
+#' }
+
+
+
+gdalUtil <-function(
+  util = "info",
+  source,
+  destination = character(0),
+  options = character(0),
+  quiet = FALSE,
+  formula = character(0),
+  processing = character(0),
+  colorfilename = character(0)
+) {
+
+  # Check "util"
+  utils <- c(
+    "info" = "gdalinfo",
+    "translate" = "gdal_translate",
+    "warp" = "gdalwarp", 
+    "demprocessing" = "gdaldem" , 
+    "buildvrt" = "gdalbuildvrt",
+    "calc" = "gdal_calc", 
+    "fillnodata" = "gdal_fillnodata"
+  )
+  if (!util %in% names(utils)) {
+    print_message(
+      type = "error", 
+      "Currently, method '",util,"' is not implemented."
+    )
+  }
+
+  # Check additional arguments
+  if (util != "info" && missing(destination)) {
+    print_message(
+      type = "error",
+      "Argument \"destination\" is missing, with no default."
+    )
+  }
+  if (util == "calc" && missing(formula)) {
+    print_message(
+      type = "error",
+      "Argument \"formula\" is required for gdal_calc."
+    )
+  }
+  if (util == "demprocessing" && missing(processing)) {
+    print_message(
+      type = "error",
+      "Argument \"processing\" is required for gdaldem."
+    )
+  }
+  if (util == "demprocessing" && processing == "color-relief" && missing(colorfilename)) {
+    print_message(
+      type = "error",
+      "Argument \"colorfilename\" is required for gdaldem with mode 'color-relief'."
+    )
+  }
+
+  # Choose the modality to proceed (sf::gdal_utils or system call)
+  if (util %in% c("calc", "fillnodata")) {
+
+    ## System call mode
+
+    # Load GDAL paths
+    binpaths <- load_binpaths("gdal")
+    init_python()
+
+    # Normalise paths
+    source <- normalize_path(source, mustWork = TRUE)
+    destination <- normalize_path(destination, mustWork = FALSE)
+
+    # Define arguments
+    gdal_args <- if (util %in% c("fillnodata")) {
+      list(
+        "sys" = c(options, source, destination),
+        "base" = paste0(
+          paste(options, collapse = " ")," ",
+          source," ",destination
+        )
+      )
+    } else if (util %in% c("calc")) {
+      list(
+        "sys" = c(
+          unlist(lapply(seq_along(source), function(i) {c(paste0("-",LETTERS[i]), source[i])})),
+          "--outfile", destination,
+          "--calc", formula,
+          options
+        ),
+        "base" = paste0(
+          paste(paste0("-",LETTERS[seq_along(source)]," \"",source,"\""), collapse = " ")," ",
+          "--outfile=\"",destination,"\" ",
+          "--calc=\"",formula,"\" ",
+          paste(options, collapse = " ")
+        )
+      )
+    }
+
+    # use exec_wait if sys is installed, system otherwise
+    gdal_out <- if (requireNamespace("sys", quietly = TRUE)) {
+      sel_log_output <- if (quiet) {
+        tempfile(pattern = "stdout_", fileext = ".txt")
+      } else {NA}
+      sys::exec_wait(
+        binpaths[[utils[util]]],
+        args = gdal_args$sys,
+        std_out = sel_log_output
+      )
+    } else {
+      system(
+        paste(binpaths[[utils[util]]], gdal_args$base),
+        intern = Sys.info()["sysname"] == "Windows"
+      )
+    }
+    invisible(gdal_out == 0)
+
+    # end of system call modality
+
+  } else {
+
+    ## Use gdal_utils()
+
+    # Normalise paths
+    # (use canonical instead than short form to avoid problems with 
+    # ENVI header files)
+    source <- normalizePath(source, mustWork = TRUE)
+    destination <- normalizePath(destination, mustWork = FALSE)
+
+    gdal_utils(
+      util = util,
+      source = source,
+      destination = destination,
+      options = options,
+      quiet = quiet,
+      processing = processing,
+      colorfilename = colorfilename
+    )
+
+  }
+
+}