small code cleaning

I allowed to remove NA when extracting. The output folder is fixed but can be easily changed.

r/extract/extract_from_raster_based_on_polygon_zones.R

@@ -1,5 +1,5 @@
 ###################################################################################
-#### Script to extract the values from multiband rasters based on vector zones ####
+#### Script to extract the values from multiband rasters (Tif, Tiff and BSQ) based on vector zones ####
 #### Recopilado por Lorena González,  Septiembre 2019                          ####
 ####___________________________________________________________________________####
 #### There are two options for the Inputs: 
@@ -21,13 +21,24 @@
 ####  + individual file per raster with all statistics
 ####  + datafile with all the bands and dates extracted per field
 
-#### setwd() You can set the Working directory to the source file location
+
 #### Get functions and libraries
-source("functions_extract.R") #Check that this file is in the working directory
+source("F:\\Dropbox\\Software\\Scripts\\r\\extract\\functions_extract.R") #Check that this file is in the working directory
 #require(raster)
 
+## Ask user where to put the output tables
+#outFolder <- choose.dir(caption = "Select folder to save output tables")
+outFolder <- ("C:\\temp\\r") # Set path fix
+
+#summarize using the selected function
+func <- "median" #mean #min #max
+
+#Field in the shp table to use as identifier of the extracting features
+ID_field <- "Name"
+
 tryCatch({ ## Put it all inside a handle error function
 
+    ## Shapefile
     ## Ask user the list of rasters and zone vectors
     in_mode <- menu(c("CSV list of inputs", "Raster Folder and vector file","Raster File and Vector File"), title="How do you want to give the inputs?",graphics = TRUE);
 
@@ -36,10 +47,11 @@ tryCatch({ ## Put it all inside a handle error function
 
       #Select the CSV file with the list of inputs
       inputList <- askCSV() # read list from file
-      #Extract for every input in the list
+      ####EXTRACT####
+      # run for every item in te list
       for (i in 1:nrow(inputList)) {
         print(paste("Processing... ",i))
-        extractThis(inputList[i,1],shapefile(inputList[i,2]), inputList[i,3], inputList[i,4],mean,as.double(inputList[i,5])) ## r_file,zones, outFolder, ID_field, fun=mean, buf
+        extractThis(inputList[i,1],shapefile(inputList[i,2]), inputList[i,3], inputList[i,4],func,as.double(inputList[i,5])) ## r_file,zones, outFolder, ID_field, fun=mean, buf
       }
 
     } else if (in_mode == 2 || in_mode == 3){ ## Enter inputs
@@ -54,37 +66,36 @@ tryCatch({ ## Put it all inside a handle error function
         #Ask for the buffer size
         ##TODO: Add filters to deal with entering other than numbers for the buffer
 
-        buf <- as.double(readline(prompt = "Type the buffer size (+Positive to grow, -negative to shrink the feature)"));
+        buf <- as.double(readline(prompt = "ACTION: Type the buffer size in meters (+Positive to grow, -negative to shrink the feature)"));
       }
 
-      ## Ask user where to put the output tables
-      #tFolder <- "C:\\" Set path fix
-      outFolder <- choose.dir(caption = "Select folder to save output tables")
-
+
       if (in_mode == 2){ #### Process all rasters in a folder ####
         ## Ask user for Raster folder
         rFolder <- choose.dir(caption = "Select folder that contains the rasters to extract")
-        #list the rasters inside the folder
-        r_list <- list.files(path = rFolder, full.names= TRUE, pattern = "*.tif$") # Select only Tif files, for example
+        #list the rasters inside the folder. Return full path name
+        r_list <- list.files(path = rFolder, full.names= TRUE, pattern = "\\.tif$|\\.bsq$|\\.tiff$") # Select Tif and BSQ for example
         ## Extract each raster
         for (r_file in r_list) {
           ####EXTRACT#### 
-          print(paste("Processing...using =Name= as ID field... ",r_file))
-          extractThis(r_file,zones, outFolder,ID_field ="Name",fun = mean,buf)
+          print(paste("Processing... ",r_file))
+          extractThis(r_file,zones, outFolder,ID_field,fun = func,buf)
         }
       }
 
       if (in_mode == 3){ #### Ask for Raster file ####
         ####EXTRACT####
         r_file <- askRaster() #Get th raster name
-        print(paste("Processing...using =Name= as ID field... ",r_file))
+        print(paste("Processing... ",r_file))
         ## Run extraction and saves output, indicate statistic
-        extractThis(r_file,zones, outFolder,ID_field ="Name", fun = mean,buf)
+        extractThis(r_file,zones, outFolder,ID_field, fun = func,buf)
 
       }
     }
-    print("Finish")
+    print("Finish extracting")
   },
-  error = function(e){print(c("Se produjo un error: ",e$message))},
-  warning = function(e){print(paste("Hay advertencias: ", e$message))}
+  #In case of halting error:
+  error = function(e){print(c("Se produjo un error: ",e$message))}#,
+  # In case of warnings:
+  #warning = function(e){print(paste("Hay advertencias: ", e$message))}
 )

r/extract/functions_extract.R

@@ -48,7 +48,7 @@ extractThis <- function(r_file,zones, outFolder, ID_field ="Name",fun=mean,buf=0
     zones <- buffer(zones, width = buf, dissolve= FALSE)
   }
   ## With this we get a table with the values for all the plots and bands
-  table <- r$extract(zones, df=TRUE, fun=fun) #Perform the extraction with the selected statistic function
+  table <- r$extract(zones, df=TRUE, fun= function(x) fun(x, na.rm = TRUE)) #Perform the extraction with the selected statistic function, remove NA values
   ## Set ID names from the shapefile
   table$ID_sp <- zones@data[,ID_field] 
   #Save to disk