# biodivMapR v1.12.0

## Fix
- remove dependency to rgdal and rgeos (issue #18)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: biodivMapR
 Title: biodivMapR: an R package for a- and ß-diversity mapping using remotely-sensed images
-Version: 1.11.1
+Version: 1.12.0
 Authors@R: c(person(given = "Jean-Baptiste", 
 					family = "Feret", 
 					email = "jb.feret@teledetection.fr", 
@@ -18,28 +18,31 @@ Encoding: UTF-8
 License: GPL-3 + file LICENSE
 LazyData: true
 Imports: 
-    dissUtils,
+    ape,
+    cli,
     data.table,
+    dissUtils,
+    dplyr,
     fields,
     future,
     future.apply,
+    gdalUtilities,
     geometry,
+    jsonlite,
     labdsv,
+    magrittr,
     matlab,
     matrixStats,
     mmand,
+    progressr,
     raster,
-    rgdal,
     snow,
     stars,
     stringr,
+    terra,
     tools,
     vegan,
-    zip,
-    progressr,
-    cli,
-    ape,
-    terra
+    zip
 RoxygenNote: 7.2.3
 Suggests: 
     knitr,

NAMESPACE

@@ -40,7 +40,6 @@ export(exclude_spectral_domains)
 export(extract.big_raster)
 export(extract_pixels)
 export(extract_pixels_coordinates)
-export(extract_pixels_coordinates.From.OGR)
 export(extract_samples_from_image)
 export(filter_PCA)
 export(filter_prior_CR)
@@ -52,6 +51,7 @@ export(get_Shannon)
 export(get_Simpson)
 export(get_alpha_metrics)
 export(get_byte_order)
+export(get_gdal_info)
 export(get_image_bands)
 export(get_random_subset_from_image)
 export(get_sunlit_pixels)
@@ -99,19 +99,26 @@ export(write_PCA_raster)
 export(write_StarsStack)
 export(write_raster)
 import(cli)
+import(magrittr)
 import(stars)
 import(tools)
 importFrom(ape,mst)
 importFrom(data.table,data.table)
 importFrom(data.table,rbindlist)
 importFrom(data.table,setorder)
 importFrom(dissUtils,diss)
+importFrom(dplyr,group_by)
+importFrom(dplyr,group_split)
+importFrom(dplyr,mutate)
+importFrom(dplyr,select)
 importFrom(fields,rdist)
 importFrom(future,multisession)
 importFrom(future,plan)
 importFrom(future,sequential)
 importFrom(future.apply,future_lapply)
+importFrom(gdalUtilities,gdalinfo)
 importFrom(geometry,convhulln)
+importFrom(jsonlite,fromJSON)
 importFrom(labdsv,pco)
 importFrom(matlab,meshgrid)
 importFrom(matlab,ones)
@@ -123,22 +130,12 @@ importFrom(progressr,handlers)
 importFrom(progressr,progressor)
 importFrom(progressr,with_progress)
 importFrom(raster,brick)
-importFrom(raster,cellFromPolygon)
-importFrom(raster,cellFromXY)
-importFrom(raster,compareCRS)
 importFrom(raster,hdr)
 importFrom(raster,nbands)
 importFrom(raster,ncell)
-importFrom(raster,projection)
 importFrom(raster,raster)
 importFrom(raster,values)
 importFrom(raster,writeRaster)
-importFrom(rgdal,GDAL.close)
-importFrom(rgdal,GDAL.open)
-importFrom(rgdal,GDALinfo)
-importFrom(rgdal,getDriver)
-importFrom(rgdal,getDriverLongName)
-importFrom(rgdal,readOGR)
 importFrom(snow,splitCols)
 importFrom(snow,splitList)
 importFrom(snow,splitRows)
@@ -154,8 +151,13 @@ importFrom(stats,prcomp)
 importFrom(stats,quantile)
 importFrom(stats,sd)
 importFrom(stringr,str_count)
+importFrom(terra,cells)
+importFrom(terra,colFromCell)
 importFrom(terra,rast)
+importFrom(terra,rowFromCell)
+importFrom(terra,same.crs)
 importFrom(terra,values)
+importFrom(terra,vect)
 importFrom(tools,file_path_sans_ext)
 importFrom(utils,file.edit)
 importFrom(utils,read.table)

NEWS.md

@@ -1,3 +1,8 @@
+# biodivMapR v1.12.0
+
+## Fix
+- remove dependency to rgdal and rgeos (issue #18) 
+
 # biodivMapR v1.11.1
 
 ## Change

R/Lib_ImageProcess.R

@@ -534,8 +534,8 @@ extract.big_raster <- function(ImPath, rowcol, MaxRAM=.50){
     # stars data cube dimension order is x*y*band
     ipix_stars <- (rc$rowInBlock-min(rc$rowInBlock))*nXSize+rc$col
     # get driver
-    driver <- attr(rgdal::GDALinfo(ImPath,returnStats = FALSE), 'driver')
-    values <- read_stars(ImPath, RasterIO =list(nXSize=nXSize, nYOff=rr[1], nYSize=nYSize),proxy = FALSE, driver=driver)[[1]]
+    driver <- get_gdal_info(ImPath)$driverShortName
+    values <- read_stars(ImPath, RasterIO =list(nXSize=nXSize, nYOff=rr[1], nYSize=nYSize), proxy = FALSE, driver = driver)[[1]]
     values <- matrix(values, nrow=nYSize*nXSize)
     if (length(ipix_stars)>1){
       res <- cbind(rc$sampleIndex, values[ipix_stars, ])
@@ -689,6 +689,20 @@ get_byte_order <- function() {
   return(ByteOrder)
 }
 
+#' Get GDAL info as a nested list
+#' @param x character. Raster image path.
+#' @return list. Nested list of raster characteristics.
+#' @import magrittr
+#' @importFrom gdalUtilities gdalinfo
+#' @importFrom jsonlite fromJSON
+#' @export
+get_gdal_info <- function(x){
+  x <- normalizePath(x)
+  if(!file.exists(x))
+    stop("File not found: ", x)
+  gdalUtilities::gdalinfo(x, json = TRUE, quiet = TRUE) %>%
+    jsonlite::fromJSON()
+}
 #' get hdr name from image file name, assuming it is BIL format
 #'
 #' @param ImPath character. ath of the image

R/Lib_MapAlphaDiversity.R

@@ -542,7 +542,6 @@ compute_SSD <- function(Image_Chunk, window_size, nbclusters,
 #'
 #' @return list. includes Spectral_Species_Path
 #' @importFrom stars read_stars write_stars
-#' @importFrom rgdal GDALinfo
 #' @importFrom tools file_path_sans_ext
 #' @export
 
@@ -583,8 +582,9 @@ get_SSpath <- function(Output_Dir, Input_Image_File, TypePCA, ClassifMap, nbclus
     }
     # save classification map in proper format in output directory
     # if not expected file format for Spectral Species map
-    driver <- attr(rgdal::GDALinfo(ClassifMap,returnStats = FALSE), 'driver')
-    df <- unique(attr(rgdal::GDALinfo(ClassifMap,returnStats = FALSE),"df")$GDType)
+    info <- get_gdal_info(ClassifMap)
+    driver <- info$driverShortName
+    df <- unique(info$bands$type)
     if (driver=='ENVI' & df =='Byte'){
       if (Input_Image_File==FALSE){
         Input_Image_File <- tools::file_path_sans_ext(basename(ClassifMap))
@@ -726,7 +726,7 @@ compute_ALPHA_SSD_per_window <- function(listAlpha, nb_partitions, nbclusters,
     SimpsonAlpha <- NA*vector(length = nb_partitions)
     SSDMap <- NA*vector(length = nb_partitions*nbclusters)
   }
-  res <- list('shannonIter' = shannonIter, 'SimpsonAlpha' = SimpsonAlpha, 
+  res <- list('shannonIter' = shannonIter, 'SimpsonAlpha' = SimpsonAlpha,
               'FisherAlpha' = FisherAlpha, 'SSDMap' = SSDMap)
   return(res)
 }

R/Lib_MapFunctionalDiversity.R

@@ -116,8 +116,6 @@ map_functional_div <- function(Original_Image_File,Functional_File = FALSE,
 #' @importFrom future.apply future_lapply
 #' @importFrom stats sd
 #' @import cli
-#' @importFrom future plan multisession sequential
-#' @importFrom future.apply future_lapply
 #' @importFrom terra rast values
 #' @export
 

R/Lib_MapSpectralSpecies.R

@@ -28,7 +28,6 @@
 #'
 #' @return Kmeans_info
 #' @importFrom utils read.table
-#' @importFrom rgdal getDriverLongName getDriver GDAL.open GDAL.close
 #' @export
 map_spectral_species <- function(Input_Image_File, Output_Dir,
                                  SpectralSpace_Output,
@@ -40,12 +39,7 @@ map_spectral_species <- function(Input_Image_File, Output_Dir,
 
   # check if input mask file has expected format
   if (!Input_Mask_File==FALSE){
-    # driverMask_class <- new("GDALReadOnlyDataset", Input_Mask_File)
-    driverMask_class <- GDAL.open(filename = Input_Mask_File,
-                                  read.only = TRUE, silent=FALSE,
-                                  allowedDrivers = NULL, options=NULL)
-    driverMask <- rgdal::getDriverLongName(getDriver(driverMask_class))
-    GDAL.close(driverMask_class)
+    driverMask <- get_gdal_info(Input_Mask_File)$driverLongName
     if (driverMask == 'ENVI .hdr Labelled'){
       HDR <- read_ENVI_header(get_HDR_name(Input_Mask_File))
       if (!HDR$`data type`==1){
@@ -589,7 +583,3 @@ error_PC_sel <- function(Output_Dir_PCA){
   print("or in the 'SelectedPCs' variable of map_spectral_species")
   print("Image processing aborted")
 }
-
-
-
-