Merge branch 'save_samplepoints' into 'master'

Save samplepoints

See merge request !18

R-package/R/WriteOutSamples.r

 #' Sample Collection for Habitat Types
 #'
-#'Writes out a set of samples (SpatialPointsDataFrame) into an ESRI shapefile for a selected habitat type. Each point represents a valid sample location that identifies the selected habitat type.
+#'Writes out a set of samples (SpatialPointsDataFrame) into ESRI shapefiles or a GeoJSON file for a selected habitat type. Each point represents a valid sample location that identifies the selected habitat type.
 #'
 #' @param inPath 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 className name (character) of habitat type for which samples should be selected
+#' @param output_format format (character) of output; whether shp (default) or geojson
 #'
-#' @return ESRI shapefile with name: RefHaSa_className_step.shp
+#' @return ESRI shapefiles/GeoJSON with name: RefHaSa_step_classname.shp/RefHaSa_step_classname.geojson
 #' 1) Point Shape represents pixel that belong to selected habitat type and can be used as reference for further model building
 #'
 #'
 #' @export
 
-###write out selected samples for step = 6 using
-write_Out_Samples <- function (inPath, step, className) {
+###write out selected samples
+write_Out_Samples <- function (inPath, step, className, output_format = c("shp", "geojson")) {
+
   paste(inPath, "step_", step, "_", className, ".tif", sep = "")
   run1 <- get(load(paste(inPath, "Run", step, sep = "")))
   load(paste(inPath, "threshold_step_", step, sep = ""))
-  dummy <-
+  dummy_sample <-
     raster::raster(paste(inPath, "step_", step, "_", className, ".tif", sep =
                            ""))
-  thres <- threshold[6]
-  dummy[dummy < thres] <- NA
-  dummy[dummy >= thres] <- 1
+
+  length_threshold <- length(threshold)
+  thres <- threshold[length_threshold]
+  dummy_sample[dummy_sample < thres] <- NA
+  dummy_sample[dummy_sample >= thres] <- 1
 
   collect <- list()
   j <- 0
@@ -43,17 +47,41 @@ write_Out_Samples <- function (inPath, step, className) {
       }
     }
   }
+  
   result <- do.call(rbind, collect)
 
-  res <- raster::extract(dummy, result)
+  res <- raster::extract(dummy_sample, result)
   if (length(which(is.na(res))) > 0) {
     res <- result[-which(is.na(res)), ]
   }
   
+  output_format <- match.arg(output_format)
+  
+  if (output_format == "geojson") {
+    crs_dummy <- sp::proj4string(dummy_sample)
+    crs(res) <- crs_dummy
+    res <- sp::spTransform(res, CRS("+proj=longlat +datum=WGS84 +init=epsg:4326"))
+    
     rgdal::writeOGR(
       res,
-    layer = "result",
+      layer = paste("RefHaSa_step_", step, "_", className, sep = ""),
+      dsn = paste(inPath, "RefHaSa_step_", step, "_", className, ".geojson", sep = ""),
+      driver = "GeoJSON",
+      check_exists = TRUE,
+      overwrite_layer = TRUE
+    ) 
+   } else {
+      crs_dummy <- sp::proj4string(dummy_sample)
+      crs(res) <- crs_dummy
+      res <- sp::spTransform(res, CRS("+proj=longlat +datum=WGS84 +init=epsg:4326"))
+
+      rgdal::writeOGR(
+        res,
+        layer = paste("RefHaSa_step_", step, "_", className, sep = ""),
         dsn = paste(inPath, "RefHaSa_", className, "_", step, ".shp", sep = ""),
-    driver = "ESRI Shapefile"
+        driver = "ESRI Shapefile",
+        check_exists = TRUE,
+        overwrite_layer = TRUE
       )
+     }
 }

R-package/man/write_Out_Samples.Rd

@@ -4,7 +4,7 @@
 \alias{write_Out_Samples}
 \title{Sample Collection for Habitat Types}
 \usage{
-write_Out_Samples(inPath, step, className)
+write_Out_Samples(inPath, step, className, output_format = c("shp", "geojson"))
 }
 \arguments{
 \item{inPath}{file path (character) for results of habitat type sampling and probability mapping (same as outPath from function multi_Class_Sampling)}
@@ -12,13 +12,15 @@ write_Out_Samples(inPath, step, className)
 \item{step}{step number (numeric)}
 
 \item{className}{name (character) of habitat type for which samples should be selected}
+
+\item{output_format}{format (character) of output; whether shp (default) or geojson}
 }
 \value{
-ESRI shapefile with name: RefHaSa_className_step.shp
+ESRI shapefiles/GeoJSON with name: RefHaSa_step_classname.shp/RefHaSa_step_classname.geojson
 \enumerate{
 \item Point Shape represents pixel that belong to selected habitat type and can be used as reference for further model building
 }
 }
 \description{
-Writes out a set of samples (SpatialPointsDataFrame) into an ESRI shapefile for a selected habitat type. Each point represents a valid sample location that identifies the selected habitat type.
+Writes out a set of samples (SpatialPointsDataFrame) into ESRI shapefiles or a GeoJSON file for a selected habitat type. Each point represents a valid sample location that identifies the selected habitat type.
 }