Merge branch 'dev'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: biodivMapR
 Title: biodivMapR: an R package for a- and ß-diversity mapping using remotely-sensed images
-Version: 1.9.10
+Version: 1.9.11
 Authors@R: c(person(given = "Jean-Baptiste", 
 					family = "Feret", 
 					email = "jb.feret@teledetection.fr", 
@@ -42,7 +42,8 @@ Imports:
     sf,
     rgeos,
     progress,
-    progressr
+    progressr,
+    cli
 RoxygenNote: 7.2.3
 Suggests: 
     knitr,

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(Compute_ALPHA_SSD_per_window)
+export(Compute_ALPHA_SSD_per_window_list)
+export(Compute_ALPHA_per_window)
 export(ContinuumRemoval)
 export(ENVI_type2bytes)
 export(IQR_outliers)
@@ -20,6 +23,8 @@ export(compute_BCdiss)
 export(compute_BETA_FromPlots)
 export(compute_FUNCT)
 export(compute_NN_from_ordination)
+export(compute_SSD)
+export(compute_alpha_metrics)
 export(compute_beta_metrics)
 export(compute_spectral_species)
 export(compute_spectral_species_FieldPlots)
@@ -42,6 +47,9 @@ export(get_BB)
 export(get_BB_from_Vector)
 export(get_BB_from_fullImage)
 export(get_HDR_name)
+export(get_SSpath)
+export(get_Shannon)
+export(get_Simpson)
 export(get_alpha_metrics)
 export(get_byte_order)
 export(get_image_bands)
@@ -51,6 +59,7 @@ export(get_sunlit_pixels)
 export(ind2sub)
 export(ind2sub2)
 export(init_kmeans)
+export(kmeans_progressr)
 export(list_shp)
 export(map_alpha_div)
 export(map_beta_div)
@@ -60,8 +69,8 @@ export(mean_filter)
 export(minmax)
 export(mnf)
 export(noise)
-export(ordination_parallel)
 export(ordination_to_NN)
+export(ordination_to_NN_list)
 export(pca)
 export(perform_PCA)
 export(perform_radiometric_filtering)
@@ -89,6 +98,7 @@ export(write_ENVI_header)
 export(write_PCA_raster)
 export(write_StarsStack)
 export(write_raster)
+import(cli)
 import(stars)
 import(tools)
 importFrom(data.table,data.table)
@@ -129,12 +139,15 @@ importFrom(raster,projection)
 importFrom(raster,raster)
 importFrom(raster,values)
 importFrom(raster,writeRaster)
+importFrom(rgdal,GDALinfo)
 importFrom(rgdal,readOGR)
 importFrom(rgdal,writeOGR)
 importFrom(rgeos,gBuffer)
 importFrom(sf,st_bbox)
 importFrom(sf,st_crop)
 importFrom(sf,st_read)
+importFrom(snow,splitCols)
+importFrom(snow,splitList)
 importFrom(snow,splitRows)
 importFrom(sp,SpatialPoints)
 importFrom(sp,spTransform)

NEWS.md

@@ -1,3 +1,11 @@
+# biodivMapR v1.9.11
+
+## Addition
+- optimized codes for the computation of spectral species, alpha and beta diversity
+- addition of progress bars during the different steps of the computation of spectral species, alpha and beta diversity maps
+- addition of functions Compute_ALPHA_SSD_per_window_list, Compute_ALPHA_SSD_per_window, Compute_ALPHA_per_window, prepare_HDR_SSD, prepare_HDR_Sunlit, RW_bytes_all, RW_bytes
+- use multisession instead of multiprocess where it was forgotten
+
 # biodivMapR v1.9.10
 
 ## Addition

R/Lib_ContinuumRemoval.R

@@ -33,21 +33,25 @@ apply_continuum_removal <- function(Spectral_Data, Spectral, nbCPU = 1) {
     # corresponds to ~ 40 Mb data, but CR tends to requires ~ 10 times memory
     # avoids memory crash
     Max.nb.Values <- 2e6
-    nb.CR <- ceiling(nb.Values / Max.nb.Values)
-    Spectral_Data <- snow::splitRows(Spectral_Data, nb.CR)
+    nb_CR <- ceiling(nb.Values / Max.nb.Values)
+    Spectral_Data <- snow::splitRows(Spectral_Data, nb_CR)
     # perform multithread continuum removal
     if (nbCPU>1){
-      future::plan(multiprocess, workers = nbCPU) ## Parallelize using four cores
-      Schedule_Per_Thread <- ceiling(nb.CR / nbCPU)
-      Spectral_Data_tmp <- future.apply::future_lapply(Spectral_Data, FUN = ContinuumRemoval,
-                                                       Spectral_Bands = Spectral$Wavelength,
-                                                       future.scheduling = Schedule_Per_Thread)
+      future::plan(multisession, workers = nbCPU)
+      handlers(global = TRUE)
+      handlers("cli")
+      with_progress({
+        p <- progressr::progressor(steps = nb_CR)
+        Spectral_Data_tmp <- future.apply::future_lapply(Spectral_Data,
+                                                         FUN = ContinuumRemoval,
+                                                         Spectral_Bands = Spectral$Wavelength,
+                                                         p = p)
+      })
       future::plan(sequential)
     } else {
       Spectral_Data_tmp <- lapply(Spectral_Data, FUN = ContinuumRemoval,
                                   Spectral_Bands = Spectral$Wavelength)
     }
-
     Spectral_Data <- do.call("rbind", Spectral_Data_tmp)
     rm(Spectral_Data_tmp)
   } else {
@@ -66,11 +70,12 @@ apply_continuum_removal <- function(Spectral_Data, Spectral, nbCPU = 1) {
 #'
 #' @param Minit numeric. initial data matrix (nb samples x nb bands)
 #' @param Spectral_Bands numeric. central wavelength for the spectral bands
+#' @param p list. progressor object for progress bar
 #
 #' @return samples from image and updated number of pixels to sampel if necessary
 #' @export
 
-ContinuumRemoval <- function(Minit, Spectral_Bands) {
+ContinuumRemoval <- function(Minit, Spectral_Bands, p = NULL) {
 
   # Filter and prepare data prior to continuum removal
   CR_data <- filter_prior_CR(Minit, Spectral_Bands)