From 114dd8f03cb1db4930e8d0b03f6f04c8541686b6 Mon Sep 17 00:00:00 2001
From: Rob Marty <robmarty3@gmail.com>
Date: Wed, 20 Dec 2023 15:32:09 -0500
Subject: [PATCH] remove fill value

---
 R/blackmarbler.R | 47 ++++++++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 46 insertions(+), 1 deletion(-)

diff --git a/R/blackmarbler.R b/R/blackmarbler.R
index a6bb398..8ac7636 100644
--- a/R/blackmarbler.R
+++ b/R/blackmarbler.R
@@ -58,6 +58,46 @@ pad3 <- function(x){
 }
 pad3 <- Vectorize(pad3)
 
+remove_fill_value <- function(x, variable){
+  # Apply scaling factor to variables according to Black Marble user guide
+  
+  # https://viirsland.gsfc.nasa.gov/PDF/BlackMarbleUserGuide_v1.2_20220916.pdf
+  # * Table 3 (page 12)
+  # * Table 6 (page 16)
+  # * Table 9 (page 18)
+  
+  if(variable %in% c(
+    
+    # VNP46A1
+    "DNB_At_Sensor_Radiance",
+    
+    # VNP46A2
+    "DNB_BRDF-Corrected_NTL",
+    "Gap_Filled_DNB_BRDF-Corrected_NTL",
+    "DNB_Lunar_Irradiance",
+    
+    # VNP46A3/4
+    "AllAngle_Composite_Snow_Covered",
+    "AllAngle_Composite_Snow_Covered_Std",
+    "AllAngle_Composite_Snow_Free",
+    "AllAngle_Composite_Snow_Free_Std",
+    "NearNadir_Composite_Snow_Covered",
+    "NearNadir_Composite_Snow_Covered_Std",
+    "NearNadir_Composite_Snow_Free",
+    "NearNadir_Composite_Snow_Free_Std",
+    "OffNadir_Composite_Snow_Covered",
+    "OffNadir_Composite_Snow_Covered_Std",
+    "OffNadir_Composite_Snow_Free",
+    "OffNadir_Composite_Snow_Free_Std")
+  ){
+    
+    if(x == 65535) x <- NA
+    
+  }
+  
+  return(x)
+}
+
 apply_scaling_factor <- function(x, variable){
   # Apply scaling factor to variables according to Black Marble user guide
   
@@ -73,7 +113,7 @@ apply_scaling_factor <- function(x, variable){
     
     # VNP46A2
     "DNB_BRDF-Corrected_NTL",
-    "Gap_Filled_DNB_BRDFCorrected_NTL",
+    "Gap_Filled_DNB_BRDF-Corrected_NTL",
     "DNB_Lunar_Irradiance",
     
     # VNP46A3/4
@@ -90,7 +130,9 @@ apply_scaling_factor <- function(x, variable){
     "OffNadir_Composite_Snow_Free",
     "OffNadir_Composite_Snow_Free_Std")
   ){
+    
     x <- x * 0.1
+    
   }
   
   return(x)
@@ -224,6 +266,9 @@ file_to_raster <- function(f,
   #assign the extents to the raster
   extent(outr) <- rasExt
   
+  #set fill values to NA
+  outr <- remove_fill_value(outr, variable)
+  
   #apply scaling factor
   outr <- apply_scaling_factor(outr, variable)