Add function to saveSamplePoints directly from the memory objects.

R-package/NAMESPACE

@@ -9,6 +9,7 @@ export(multi_Class_Sampling)
 export(plot_configuration)
 export(plot_results)
 export(sample_nb)
+export(saveSamplePoints)
 export(save_class_tiff)
 export(save_kml)
 export(save_run)

R-package/R/save_files.r

@@ -54,3 +54,80 @@ save_kml <- function(outPath, step, raster, overwrite) {
   
   raster::KML(kml, paste(outPath, paste("step_", step, sep = ""), sep = ""), overwrite = overwrite, zip = '')
 }
+
+
+#' Save Sample Points
+#'
+#' Saves the reference sample points
+#'
+#' @param in_path file path (character) for results of habitat type sampling and probability mapping (same as outPath from function multi_Class_Sampling)
+#' @param step step number (numeric)
+#' @param class_name name (character) of habitat type for which samples should be selected
+#' @param output_format format (character) of output; whether shp (default) or geojson
+#' @param ref_samples list of reference sample points
+#' @param ref_switch vector with switch values
+#' @param dummy_raster raster with classified pixels marked as 1
+#'
+#' @return ESRI shapefiles/GeoJSON with name: SamplePoints_step_classname.shp/SamplePoints_step_classname.geojson
+#' 1) Point Shape/GeoJSON represents pixel that belong to selected habitat type and can be used as reference for further model building.
+#'    ESRI shapefiles have the same CRS as the input raster. GeoJSON files are in the standard CRS of GeoJSON (EPSG:4326).
+#'
+#'
+#' @export
+saveSamplePoints <-
+  function(in_path,
+           step,
+           class_name,
+           output_format = c("shp", "geojson"),
+           ref_samples,
+           ref_switch,
+           dummy_raster) {
+    collect <- list()
+    j <- 0
+    
+    ###extract only class samples
+    for (i in 1:length(ref_samples)) {
+      if (length(dim(ref_samples[[i]])) != 0)
+      {
+        if (is.na(ref_switch[i]) == F) {
+          j = j + 1
+          collect[[j]] <-
+            ref_samples[[i]][which(ref_samples[[i]]@data == 1), ]
+        } else
+        {
+          j = j + 1
+          collect[[j]] <-
+            ref_samples[[i]][which(ref_samples[[i]]@data == 2), ]
+        }
+      }
+    }
+    
+    result <- do.call(rbind, collect)
+    
+    res <- raster::extract(dummy_raster, result)
+    if (length(which(is.na(res))) > 0) {
+      res <- result[-which(is.na(res)), ]
+    }
+    raster::crs(res) <- raster::crs(dummy_raster)
+    output_format <- match.arg(output_format)
+    if (output_format == "geojson") {
+      res <- sp::spTransform(res, sp::CRS("+init=epsg:4326"))
+      rgdal::writeOGR(
+        obj = res,
+        layer = paste("SamplePoints_step_", step, "_", class_name, sep = ""),
+        dsn = paste(in_path, "SamplePoints_step_", step, "_", class_name, ".geojson", sep = ""),
+        driver = "GeoJSON",
+        check_exists = TRUE,
+        overwrite_layer = TRUE
+      ) 
+    } else {
+      rgdal::writeOGR(
+        obj = res,
+        layer = paste("SamplePoints_step_", step, "_", class_name, sep = ""),
+        dsn = paste(in_path, "SamplePoints_step_", step, "_", class_name, ".shp", sep = ""),
+        driver = "ESRI Shapefile",
+        check_exists = TRUE,
+        overwrite_layer = TRUE
+      )
+    }
+}
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