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Sandhill crane/10 Get shapefile from detection inference.R

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+
+library (raster)
+library (rgdal)
+library (sf)
+
+# Input: Set working dir for ortho/mosaics
+setwd(file.path('D:', 'SACR_mosaics_Mar18_19_final2'))
+
+# Inputs: pred1 = table from detection inference depicting predictions: xmin, ymin, w, h
+# output_csv = name of output table of georeferenced predictions 
+# output_gis = name of shapefile to output
+# gsd_cm = spatial resolution of image
+# crs1 = utm proj of mosaic-- 14N= 32614 or 15N = 32615
+pred1 <- read.table ("C:/Users/bpickens/Desktop/SACR_detection/demo1.csv", sep = ",", header=TRUE, fill=TRUE)
+output_predictions = "D:/test_Dec11.csv"
+export_spatial = "D:/test_Dec11.shp"
+gsd_m = 0.103 
+crs1 = 32614
+
+## List files in dir and get extents
+gridz <- list.files (pattern="*tif$")  
+gridz
+
+extents1 <- data.frame(raster_name=NA, xmin_extent=NA, xmax_extent=NA, ymin_extent=NA, ymax_extent=NA)
+
+for (f in gridz){
+  r1 <- raster(f)
+  e1 <- extent(r1)
+  raster_name <- f
+  xmin_extent <- e1[1,]
+  xmax_extent <- e1[2,]
+  ymin_extent <- e1[3,]
+  ymax_extent <- e1[4,]
+  vector1 <- c(raster_name, xmin_extent, xmax_extent, ymin_extent, ymax_extent)
+  print(vector1)
+  extents1 <- rbind(extents1, vector1)
+}
+
+extents1$unique_image_jpg <- extents1$raster_name
+extents1$raster_name <- NULL
+
+## Merge with predictions
+pred1$basename <- basename(pred1$unique_image_jpg)
+pred1$unique_image_jpg <- pred1$basename
+pred1$basename <- NULL
+
+merge1 <- merge(extents1, pred1, by="unique_image_jpg") 
+
+# m = abbreviated for meters
+merge1$xmin_m <- merge1$xmin*gsd_m
+merge1$ymin_m <- merge1$ymin*gsd_m
+merge1$h_m <- (merge1$h*gsd_m)/2
+merge1$w_m <- (merge1$w*gsd_m)/2
+
+# x_annot, y_annot = coordinates for annotations
+class(merge1$xmin_extent)
+
+merge1$xmin_extent <- as.numeric(merge1$xmin_extent)
+merge1$ymax_extent <- as.numeric(merge1$ymax_extent)
+
+merge1$x_annot <- merge1$xmin_extent + ((merge1$xmin_m)+ merge1$w_m)
+
+merge1$y_annot <- merge1$ymax_extent - ((merge1$ymin_m)+ merge1$h_m)
+merge1$y_annot_above <- merge1$y_annot + 0.40
+
+merge1$x_annot <- as.numeric(merge1$x_annot)
+merge1$y_annot <- as.numeric(merge1$y_annot)
+merge1$y_annot_above <- as.numeric(merge1$y_annot_above)
+merge1$xmax_extent <- NULL
+merge1$ymax_extent <- NULL
+
+merge1[0:5,]
+
+write.table(merge1, output_predictions, sep=",", row.names=FALSE)
+
+## Make shapefile
+# get rid of na's first
+merge2 <- merge1[complete.cases(merge1), ]
+
+# Projections, crs = 4326--WGS84
+new_sf <- st_as_sf(merge2, coords = c("x_annot", "y_annot_above"), crs= crs1)
+
+st_write(new_sf, export_spatial, driver = "ESRI Shapefile")  
+
+
+
+
+
+