add NDVI formula

NEONScience · Feb 15, 2024 · 975546a · 975546a
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diff --git a/...perspectral/RasterStack-RGB-Images-in-R-Using-HSI/RasterStack-RGB-Images-in-R-Using-HSI.R b/...perspectral/RasterStack-RGB-Images-in-R-Using-HSI/RasterStack-RGB-Images-in-R-Using-HSI.R
@@ -1,16 +1,16 @@
-## ----load-libraries----------------------------------------------------------------------------------------------------------------------------------------
+## ----load-libraries, results="hide"-----------------------------------------------------------------------------------------------------------------------------
 library(terra)
 library(rhdf5)
 library(neonUtilities)
 
 
-## ----set-wd------------------------------------------------------------------------------------------------------------------------------------------------
+## ----set-wd-----------------------------------------------------------------------------------------------------------------------------------------------------
 # set working directory (this will depend on your local environment)
 wd <- "~/data/"
 setwd(wd)
 
 
-## ----download-refl, eval=FALSE-----------------------------------------------------------------------------------------------------------------------------
+## ----download-refl, eval=FALSE----------------------------------------------------------------------------------------------------------------------------------
 ## byTileAOP(dpID = 'DP3.30006.001',
 ##           site = 'SJER',
 ##           year = '2021',
@@ -19,16 +19,16 @@ setwd(wd)
 ##           savepath = wd)
 
 
-## ----define-h5, results="hide"-----------------------------------------------------------------------------------------------------------------------------
+## ----define-h5, results="hide"----------------------------------------------------------------------------------------------------------------------------------
 # Define the h5 file name to be opened
 h5_file <- paste0(wd,"DP3.30006.001/neon-aop-products/2021/FullSite/D17/2021_SJER_5/L3/Spectrometer/Reflectance/NEON_D17_SJER_DP3_257000_4112000_reflectance.h5")
 
 
-## ----view-file-structure, eval=FALSE, comment=NA-----------------------------------------------------------------------------------------------------------
+## ----view-file-structure, eval=FALSE, comment=NA----------------------------------------------------------------------------------------------------------------
 View(h5ls(h5_file,all=T))
 
 
-## ----get-spatial-attributes--------------------------------------------------------------------------------------------------------------------------------
+## ----get-spatial-attributes-------------------------------------------------------------------------------------------------------------------------------------
 
 # define coordinate reference system from the EPSG code provided in the HDF5 file
 h5EPSG <- h5read(h5_file,"/SJER/Reflectance/Metadata/Coordinate_System/EPSG Code" )
@@ -54,7 +54,7 @@ h5NoDataValue <- as.integer(reflInfo$Data_Ignore_Value)
 cat('No Data Value:',h5NoDataValue)
 
 
-## ----function-read-refl-data-------------------------------------------------------------------------------------------------------------------------------
+## ----function-read-refl-data------------------------------------------------------------------------------------------------------------------------------------
 
 # file: the hdf5 file
 # band: the band you want to process
@@ -85,7 +85,7 @@ band2Raster <- function(file, band, noDataValue, extent, CRS){
 
 
 
-## ----create-raster-list------------------------------------------------------------------------------------------------------------------------------------
+## ----create-raster-list-----------------------------------------------------------------------------------------------------------------------------------------
 
 # create a list of the bands (R,G,B) we want to include in our stack
 rgb <- list(58,34,19)
@@ -97,11 +97,11 @@ rgb_rast <- lapply(rgb,FUN=band2Raster, file = h5_file,
                    CRS=h5CRS)
 
 
-## ----rgb-rast-properties-----------------------------------------------------------------------------------------------------------------------------------
+## ----rgb-rast-properties----------------------------------------------------------------------------------------------------------------------------------------
 rgb_rast
 
 
-## ----raster-stack------------------------------------------------------------------------------------------------------------------------------------------
+## ----raster-stack-----------------------------------------------------------------------------------------------------------------------------------------------
 rgbStack <- rast(rgb_rast)
 
 
@@ -117,7 +117,7 @@ names(rgbStack) <- bandNames
 rgbStack
 
 
-## ----scale-plot-refl---------------------------------------------------------------------------------------------------------------------------------------
+## ----scale-plot-refl--------------------------------------------------------------------------------------------------------------------------------------------
 # scale the data as specified in the reflInfo$Scale Factor
 rgbStack <- rgbStack/as.integer(reflInfo$Scale_Factor)
 
@@ -147,7 +147,7 @@ plotRGB(rgbStack,
         stretch = "lin")
 
 
-## ----save-raster-geotiff, eval=FALSE, comment=NA-----------------------------------------------------------------------------------------------------------
+## ----save-raster-geotiff, eval=FALSE, comment=NA----------------------------------------------------------------------------------------------------------------
 # Write out final raster	
 # Note: if you set overwrite to TRUE, then you will overwrite (and lose) any older version of the tif file! 
 writeRaster(rgbStack, file=paste0(wd,"NEON_hyperspectral_tutorial_example_RGB_image.tif"), overwrite=TRUE)

diff --git a/...rspectral/RasterStack-RGB-Images-in-R-Using-HSI/RasterStack-RGB-Images-in-R-Using-HSI.Rmd b/...rspectral/RasterStack-RGB-Images-in-R-Using-HSI/RasterStack-RGB-Images-in-R-Using-HSI.Rmd
@@ -93,7 +93,7 @@ These steps included loading required packages, downloading the data (optionally
 
 First, let's load the required R packages, `terra` and `rhdf5`.
 
-```{r load-libraries}
+```{r load-libraries, results="hide"}
 library(terra)
 library(rhdf5)
 library(neonUtilities)
@@ -342,7 +342,13 @@ In this last part, we will calculate some vegetation indices using raster math i
 
 ### About NDVI
 
-NDVI is  a ratio between the near infrared (NIR) portion of the electromagnetic spectrum and the red portion of the spectrum. Please keep in mind that there are different ways to aggregate bands when using hyperspectral data. This example is using individual bands to perform the NDVI calculation. Using individual bands is not necessarily the best way to calculate NDVI from hyperspectral data! 
+NDVI is  a ratio between the near infrared (NIR) portion of the electromagnetic spectrum and the red portion of the spectrum. 
+
+$$
+NDVI = \frac{NIR-RED}{NIR+RED}
+$$
+
+Please keep in mind that there are different ways to aggregate bands when using hyperspectral data. This example is using individual bands to perform the NDVI calculation. Using individual bands is not necessarily the best way to calculate NDVI from hyperspectral data.
 
 ```{r create-NDVI, fig.cap=c("Raster plot of a portion of the SJER field site showing calculated NDVI values. The x-axis and y-axis values represent the extent, which range from 257500 to 258000 meters easting, and 4112500 to 4113000 meters northing, respectively. Plot legend goes from -1 to 1.","Raster plot of a portion of the SJER field site showing calculated NDVI values with predefined breaks at 0, 0.25, 0.5, 05, and 1. The x-axis and y-axis values represent the extent, which range from 257500 to 258000 meters easting, and 4112500 to 4113000 meters northing, respectively. Plot legend goes from 0 to 1.")  }
 
@@ -392,7 +398,7 @@ Try the following on your own:
 1. Calculate the Normalized Difference Nitrogen Index (NDNI) using the following equation: 
 
 $$
-\frac{log(\frac{1}{p_{1510}}) - log(\frac{1}{p_{1680}})}{log(\frac{1}{p_{1510}}) + log(\frac{1}{p_{1680}})}
+NDNI = \frac{log(\frac{1}{p_{1510}}) - log(\frac{1}{p_{1680}})}{log(\frac{1}{p_{1510}}) + log(\frac{1}{p_{1680}})}
 $$
 2. Calculate the Enhanced Vegetation Index (EVI). Hint: Look up the formula, and apply the appropriate NEON bands. Hint: You can look at satellite datasets, such as <a href="https://www.usgs.gov/landsat-missions/landsat-enhanced-vegetation-index" target="_blank">USGS Landsat EVI.</a>  
 

diff --git a/...spectral/RasterStack-RGB-Images-in-R-Using-HSI/RasterStack-RGB-Images-in-R-Using-HSI.html b/...spectral/RasterStack-RGB-Images-in-R-Using-HSI/RasterStack-RGB-Images-in-R-Using-HSI.html
@@ -417,7 +417,11 @@ <h3 id="challenge-other-band-combinations">Challenge: Other band combinations</h
 <h2 id="raster-math-creating-ndvi-and-other-vegetation-indices-in-r">Raster Math - Creating NDVI and other Vegetation Indices in R</h2>
 <p>In this last part, we will calculate some vegetation indices using raster math in R! We will start by creating NDVI or Normalized Difference Vegetation Index.</p>
 <h3 id="about-ndvi">About NDVI</h3>
-<p>NDVI is  a ratio between the near infrared (NIR) portion of the electromagnetic spectrum and the red portion of the spectrum. Please keep in mind that there are different ways to aggregate bands when using hyperspectral data. This example is using individual bands to perform the NDVI calculation. Using individual bands is not necessarily the best way to calculate NDVI from hyperspectral data!</p>
+<p>NDVI is  a ratio between the near infrared (NIR) portion of the electromagnetic spectrum and the red portion of the spectrum.</p>
+<p>$$
+NDVI = \frac{NIR-RED}{NIR+RED}
+$$</p>
+<p>Please keep in mind that there are different ways to aggregate bands when using hyperspectral data. This example is using individual bands to perform the NDVI calculation. Using individual bands is not necessarily the best way to calculate NDVI from hyperspectral data.</p>
 <pre><code># Calculate NDVI
 
 # select bands to use in calculation (red, NIR)
@@ -493,7 +497,7 @@ <h3 id="challenge-work-with-indices">Challenge: Work with Indices</h3>
 <li>Calculate the Normalized Difference Nitrogen Index (NDNI) using the following equation:</li>
 </ol>
 <p>$$
-\frac{log(\frac{1}{p_{1510}}) - log(\frac{1}{p_{1680}})}{log(\frac{1}{p_{1510}}) + log(\frac{1}{p_{1680}})}
+NDNI = \frac{log(\frac{1}{p_{1510}}) - log(\frac{1}{p_{1680}})}{log(\frac{1}{p_{1510}}) + log(\frac{1}{p_{1680}})}
 $$
 2. Calculate the Enhanced Vegetation Index (EVI). Hint: Look up the formula, and apply the appropriate NEON bands. Hint: You can look at satellite datasets, such as <a href="https://www.usgs.gov/landsat-missions/landsat-enhanced-vegetation-index" target="_blank">USGS Landsat EVI.</a></p>
 <ol start="3">

diff --git a/.../RasterStack-RGB-Images-in-R-Using-HSI/RasterStack-RGB-Images-in-R-Using-HSI.md b/.../RasterStack-RGB-Images-in-R-Using-HSI/RasterStack-RGB-Images-in-R-Using-HSI.md
@@ -433,7 +433,13 @@ In this last part, we will calculate some vegetation indices using raster math i
 
 ### About NDVI
 
-NDVI is  a ratio between the near infrared (NIR) portion of the electromagnetic spectrum and the red portion of the spectrum. Please keep in mind that there are different ways to aggregate bands when using hyperspectral data. This example is using individual bands to perform the NDVI calculation. Using individual bands is not necessarily the best way to calculate NDVI from hyperspectral data! 
+NDVI is  a ratio between the near infrared (NIR) portion of the electromagnetic spectrum and the red portion of the spectrum. 
+
+$$
+NDVI = \frac{NIR-RED}{NIR+RED}
+$$
+
+Please keep in mind that there are different ways to aggregate bands when using hyperspectral data. This example is using individual bands to perform the NDVI calculation. Using individual bands is not necessarily the best way to calculate NDVI from hyperspectral data.
 
 
     # Calculate NDVI
@@ -517,7 +523,7 @@ Try the following on your own:
 1. Calculate the Normalized Difference Nitrogen Index (NDNI) using the following equation: 
 
 $$
-\frac{log(\frac{1}{p_{1510}}) - log(\frac{1}{p_{1680}})}{log(\frac{1}{p_{1510}}) + log(\frac{1}{p_{1680}})}
+NDNI = \frac{log(\frac{1}{p_{1510}}) - log(\frac{1}{p_{1680}})}{log(\frac{1}{p_{1510}}) + log(\frac{1}{p_{1680}})}
 $$
 2. Calculate the Enhanced Vegetation Index (EVI). Hint: Look up the formula, and apply the appropriate NEON bands. Hint: You can look at satellite datasets, such as <a href="https://www.usgs.gov/landsat-missions/landsat-enhanced-vegetation-index" target="_blank">USGS Landsat EVI.</a>