Good Morning, Sir can i get to know the codes for calculating all the indices specially the NDVI for a field trial.

[ImrAn Khan]

Good Morning, Sir can i get to know the codes for calculating all the indices specially the NDVI for a field trial.

[fmatias]

Hi there,

The code/equation/formula to calculate vegetation indices are described in this table: https://github.com/OpenDroneMap/FIELDimageR#P6

As you can see for NDVI is NDVI=(NIR-R)/(NIR+R)

Best,

Filipe

[ImrAn Khan]

Sir, this did not help me. I am facing aproblem in calculation of NDVI. Can i get all the codes please.

Regards

IMRAN KHAN

[fmatias]

I am not understanding your question. Could you send the error here?

About the code, the only code that I have is the code that you already have when you installed the package. 

In other words, I have the same code that everyone else has when installing the package. 

Filipe

[ImrAn Khan]

Sir i used these codes, what changes shall i make to calculate the other indices such as NDVI:

library(FIELDimageR)

library(raster)

 

EX1<-stack("C:/Users/dell/Downloads/EX2_RGB.tif")

plotRGB(EX1, r = 1, g = 2, b = 3)

EX1.Crop <- fieldCrop(mosaic = EX1)

EX1.Rotated<-fieldRotate(mosaic = EX1.Crop, clockwise = F, h=F)

EX1.Rotated<-fieldRotate(mosaic = EX1.Crop, theta = 2.3)

source(system.file("extdata", "fieldRotate.R", package = "FIELDimageR"))

EX1.Rotated<-fieldRotate(mosaic = EX1.Crop, theta = 2.3, extentGIS=TRUE)

EX1.Indices<- fieldIndex(mosaic = EX1.RemSoil$newMosaic, Red = 1, Green = 2, Blue = 3, index = c("NGRDI","BGI"), myIndex = c("(Red-Blue)/Green"))

EX1.Indices.myIndex<- fieldIndex(mosaic = EX1.RemSoil$newMosaic, Red = 1, Green = 2, Blue = 3, index = c("NGRDI","BGI"), myIndex = c("(Red-Blue)/Green","Red/Green","Blue/Green"))

So sir how can i get the NDVI??

Regards 

IMRAN KHAN                           

[fmatias]

Hi Imran Khan,

To calculate indices as NDVI or NDRE it is necessary a multispectral image/mosaic (with RedEdge and/or NIR bands besides the traditional RGB). First, you need to inform the function fieldIndex() which layer in your mosaic represents the RedEdge (e.g., layer 4 in the mosaic) and NIR (e.g., layer 5 in the mosaic). Then on the parameter "index", you can write any index (e.g., NDVI and NDRE) from the table available in this link: https://github.com/OpenDroneMap/FIELDimageR#P6

Here is an example of code to calculate NDVI and NDRE:

EX1.Indices<- fieldIndex(mosaic = EX1.RemSoil$newMosaic,

                                            Red=1,Green=2,Blue=3,

                                            RedEdge=4,

                                            NIR=5, 

                                            index = c("NGRDI","BGI","NDVI","NDRE"))

Also, there is more information about multispectral in this link: https://github.com/OpenDroneMap/FIELDimageR#P14

Best,

Filipe

[Prasanth Chigurupati]

Hello Imran,

Here is the YouTube link (https://youtu.be/2khnveYFov8), where you can clear your confusion.

Thank you

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[ImrAn Khan]

  Error in fieldIndex(mosaic = EX1.RemSoil$newMosaic, Red = 1, Green = 2,  :
  RedEdge and/or NIR is/are not available in your mosaic

Sir i'm facing this error while executing this particular query.

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[fmatias]

Imran,

You need to inform which bands are the RedEdge and NIR. The easy solution, if you have a multispectral image (5 bands order: R, G, B, RedEdge, and NIR), is to include RedEdge=4 and NIR=5 in the function fieldIndex().

EX1.Indices<- fieldIndex(mosaic = EX1.RemSoil$newMosaic,

                                            Red=1,

                                            Green=2,

                                            Blue=3,

                                            RedEdge=4,

                                            NIR=5, 

                                            index = c("NGRDI","BGI","NDVI","NDRE"))

Best,

Filipe

[ImrAn Khan]

Sir how to inform which bands are the RedEdge and NIR.

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[ImrAn Khan]

Sir the same error is being prompted again:

Error in fieldIndex(mosaic = EX1.RemSoil$newMosaic, Red = 1, Green = 2,  :
  RedEdge and/or NIR is/are not available in your mosaic

[fmatias]

Imran,

The number (e.g., 1, 2, 3, 4, and 5) in front of the band's name in the function fieldIndex() means the sequence of those bands in your picture. Imagine a multispectral image with 5 bands (e.g, Red, Green, Blue, RedEdge, and NIR) each band is represented for example by:

Red=1

Green=2

Blue=3

RedEdge=4

NIR=5 

Where Red=1 means that the first layer/band of your multispectral image (with 5 layers) represents the region RED (e.g., 600-680 nm) of the spectrum capture by your sensor/camera.  Green=2 means the region GREEN (e.g., 480-600 nm). Blue=3 means the region BLUE (e.g., 400-480 nm). RedEdge=4 means the region RED-EDGE (e.g., 680-750 nm). And NIR=5 means the region NIR (e.g., >750 nm).

Hope it makes sense.

Best,

Filipe

[ImrAn Khan]

Sir, i couldn't get you. I need some more help in this.

May i share the image so that you can help me with the index calculation??

[fmatias]

Hi Imran,

Sure... Please send your image here and we will try to figure out what's going on.

Best,

Filipe

[ImrAn Khan]

Sir, i'm attaching the image of the trial plot below. Please find the attached image. Will be waiting for you response to my problems. thank you sir.

[fmatias]

Hi Imran,

Unfortunately, you can’t calculate NDVI.

 The image that you shared is an RGB image with three layers (Red, Green, and Blue). To calculate NDVI or NDRE you need a Multispectral image with Red-Edge and NIR layers besides the RGB.

 Here, there are some nice reviews to help you to understand the difference:

·       https://doi.org/10.3389/fpls.2017.01111

·       https://doi.org/10.1016/j.tplants.2013.09.008

·       https://doi.org/10.1016/j.tplants.2018.11.007

 Using FIELDimageR and your image you can calculate other RGB indices as “BI”, “SCI”, “GLI”, “HI”, “NGRDI”, “SI”, “VARI”, “HUE”, and “BGI” (https://github.com/OpenDroneMap/FIELDimageR#P6). For example, using the code below:

  

### START ###

 library(FIELDimageR)

library(raster)

EX1<-stack("EX6_RGB.JPG")

plotRGB(EX1)

EX1.Indices<- fieldIndex(mosaic = EX1, Red = 1, Green = 2, Blue = 3, index = c("NGRDI","BGI"))

 ### END ###

  

Hope this explanation helps you.

Best,

Filipe

[ImrAn Khan]

Good Morning sir, Sir i had a query. Sir how can i generate a CSV table for the image for this particular image?