Extracting pixel values in different bands for different points giving NAs and not pixel values

Question

I am working with R statistics. And I am trying to extract pixel values for each point in each Landsat bands, however, I am just getting NAs instead of getting pixel values

Does anyone have any other ideas about what I am doing wrong?

##point files
trainData_crs<- read.csv(file.csv)

##images loading and convert it to bricks
all_landsat_bands<-list.files ("file.tif")
img <- brick(all_landsat_bands)
##convert to same projection 

## conver~t csv to shp

coordinates(trainData_crs)<-~Latitude +Longitude
proj4string(trainData_crs) <- ("+proj=utm +zone=34 +south +a=6378249.145 +b=6356514.966398753 +towgs84=-138,-105,-289,0,0,0,0 +units=m
+no_defs ")
class(trainData_crs)

##extract pixel values 
trainData_bands<-raster::extract(x=img,y=trainData_sf, df=T)
View(trainData_bands)

---

I don't know how to supply my data, I don't see anywhere to attach it, but I am also new to posting here but I will try to give you the printout of the data.

##point files
trainData_crs<- read.csv(file.csv)                                                                       > class(trainData_crs)
[1] "data.frame"

> summary(trainData_crs)
       PlotType      Class          Latitude       Longitude    
 closedforest:22   Min.   :1.000   Min.   :17.81   Min.   :24.72  
 grass       :34   1st Qu.:2.000   1st Qu.:17.86   1st Qu.:24.98  
 lowforest   :24   Median :3.000   Median :17.92   Median :25.02  
 mediumforest:26   Mean   :2.904   Mean   :17.95   Mean   :25.02  
 shrubs      : 4   3rd Qu.:4.000   3rd Qu.:18.01   3rd Qu.:25.10  
 unknown     : 3   Max.   :7.000   Max.   :18.46   Max.   :25.16  
 water       : 1 

##images load and convert it to bricks
all_landsat_bands<-list.files ("file.tif")
img <- brick(all_landsat_bands)
> img <- brick(LandsatAprJune_2019_st)
> class(img)
[1] "RasterBrick"
attr(,"package")
[1] "raster"
> names(img)
[1] "B1"  "B2"  "B3"  "B4"  "B5"  "B6"  "B7"  "B10" "B11"
>


##convert to same projection 

coordinates(trainData_crs)<-~Latitude +Longitude
trainData_crs <- SpatialPoints(cbind(trainData_crs$Latitude, trainData_crs$Longitude), 
                            proj4string=CRS("+proj=utm +zone=34 +south +a=6378249.145 +b=6356514.966398753 +towgs84=-138,-105,-289,0,0,0,0 +units=m
+no_defs "))
trainData_crs_sp <- spTransform(trainData_crs, crs(img))

##confirm if points and image are in same coordinates
> crs(trainData_crs_sp)
CRS arguments:
 +proj=utm +zone=34 +south +a=6378249.145 +b=6356514.966398753 +towgs84=-138,-105,-289,0,0,0,0 +units=m
+no_defs 
> crs(img)
CRS arguments:
 +proj=utm +zone=34 +south +a=6378249.145 +b=6356514.966398753 +towgs84=-138,-105,-289,0,0,0,0 +units=m
+no_defs 

##summary on transformed points
> summary(trainData_crs_sp)
Object of class SpatialPoints
Coordinates:
                 min        max
coords.x1   177676.9   244145.4
coords.x2 12738109.3 12786443.7
Is projected: TRUE 
proj4string :
[+proj=utm +zone=34 +south +a=6378249.145 +b=6356514.966398753 +towgs84=-138,-105,-289,0,0,0,0 +units=m
+no_defs]
Number of points: 114

##extract pixel values 
trainData_bands<-raster::extract(img, trainData_crs_sp)

I have edited the code above to try using spTransform on the points but I am still getting NAs

---

Read data files

trainData_crs<- read.csv(".csv")

coordinates(trainData_crs)<-~Latitude +Longitude

set lat-long coordinate numbers

proj4string(trainData_crs) = CRS("+init=epsg:4326")

crs(trainData_crs) CRS arguments: +init=epsg:4326 +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0

ransform them to the CRS of the image

trainData_crs_sp <- spTransform(trainData_crs, crs(img))

plot images

plotRGB(img, r = 4, g = 3, b = 2, stretch = "lin", scale=1000, axes = TRUE, main = "RGB composite image\n Landsat Bands 7, 3, 2") box(col = "black"); plot(trainData_crs_sp, add=T)

plot(trainData_crs_sp)

crs(img) crs(trainData_crs_sp)

crs(trainData_crs_sp) CRS arguments: +proj=utm +zone=34 +south +a=6378249.145 +b=6356514.966398753 +towgs84=-138,-105,-289,0,0,0,0 +units=m +no_defs crs(img) CRS arguments: +proj=utm +zone=34 +south +a=6378249.145 +b=6356514.966398753 +towgs84=-138,-105,-289,0,0,0,0 +units=m +no_defs

They seem to be in the same coordinate but when I plot them , they are not appearing in the same spot/they are not overlapping. I think this is why I am getting NAs because there is no overlap. any idea of the possibilities Why they are not overlapping if they are in the same coordinates now?

Answer 1

The numbers in your point CSV look like degrees in lat-long. This is (999 times out of a 1000) EPSG coordinate system 4326. After reading the data in you need to assign that CRS to it before you transform it to anything else. Note there is a great difference between assigning a coordinate system to some data (which does not change the coordinate numbers) and transforming it to another system (which does change the numbers).

trainData_crs<- read.csv(file.csv)

## convert csv to shp

coordinates(trainData_crs)<-~Latitude +Longitude

at this point you've got a spatial data set with those lat-long coordinate numbers. Tell R these are in lat-long:

proj4string(trainData_crs) = CRS("+init=epsg:4326")

Now you should be able to transform them to the CRS of the image:

trainData_crs_sp <- spTransform(trainData_crs, crs(img))

Plot the image [plot(img)] and add the points [plot(trainData_crs_sp, add=TRUE)] to check the points overlap.