OpenDroneMap/FIELDimageR

# Uploading file (EX_Obj.tif)
EX.Obj <- stack("EX_Obj.jpg")
plotRGB(EX.Obj)
EX.Obj <- aggregate(EX.Obj,4)
EX.shapeFile<-fieldPolygon(EX.Obj,extent = T)

# Removing the background
EX.Obj.M<- fieldMask(mosaic = EX.Obj, index = "BGI",cropValue = 0.7,cropAbove = T)
dev.off()

# Taking measurements (Remove artifacts by changing the parameter *minArea* and observing the values on EX.Obj.D$Dimension$area)
EX.Obj.D<-fieldObject(mosaic = EX.Obj.M$mask, watershed = T, minArea = 0.01)

# Measurement Output:
EX.Obj.D$numObjects
EX.Obj.D$Dimension
plotRGB(EX.Obj)
plot(EX.shapeFile$fieldShape, add=T)
plot(EX.Obj.D$Objects, add=T, border="red")
plot(EX.Obj.D$Polygons, add=T, border="blue")
plot(EX.Obj.D$single.obj[[1]], add=T, col="yellow")
lines(EX.Obj.D$x.position[[1]], col="red", lty=2)
lines(EX.Obj.D$y.position[[1]], col="red", lty=2)
EX.Obj.I<- fieldIndex(mosaic = EX.Obj,index = c("SI","BGI","BI"))
EX.Obj.Data<-fieldInfo(mosaic = EX.Obj.I[[c("SI","BGI","BI")]], fieldShape = EX.Obj.D$Objects, projection = F)
EX.Obj.Data$fieldShape@data

# Perimeter:
# install.packages("spatialEco")
library(spatialEco)
perimeter<-polyPerimeter(EX.Obj.D$Objects)
box<-polyPerimeter(EX.Obj.D$Polygons)
Data.Obj<-cbind(EX.Obj.Data$fieldShape@data,EX.Obj.D$Dimension,perimeter=perimeter,box=box)
Data.Obj

# Uploading file (EX_RemObj.tif)
EX.RemObj <- stack("EX_RemObj.tif")

# Selecting the object boundaries to be removed (nPoint = 10)
EX.RemObj.Crop <- fieldCrop(mosaic = EX.RemObj, remove = T, nPoint = 10) # Selecting the plant in plot 13

# Removing the soil
EX.RemObj.RemSoil<- fieldMask(mosaic = EX.RemObj.Crop,index = "HUE")

# Building the plot shapefile (ncols = 8 and nrows = 4)
EX.RemObj.Shape<-fieldShape(mosaic = EX.RemObj.RemSoil,ncols = 8, nrows = 4)

# Building indice (NGRDI)
EX.RemObj.Indices<- fieldIndex(mosaic = EX.RemObj.RemSoil$newMosaic,index = c("NGRDI"))

# Extracting data (NGRDI)
EX.RemObj.Info<- fieldInfo(mosaic = EX.RemObj.Indices$NGRDI,
                      fieldShape = EX.RemObj.Shape$fieldShape,
                      n.core = 3)
                      
# Comparing plots values (the plant in plot 13 was removed and its value must be lower than plot 12 and 14)                      
EX.RemObj.Info$plotValue[c(12,13,14),]

# Uploading file (EX_RemObj.tif)
EX.Dist <- stack("EX_RemObj.tif")

# vegetation indices
EX.Dist.Ind <- fieldIndex(mosaic = EX.Dist,index = c("NGRDI"))

# Removing the soil
EX.Dist.RemSoil <- fieldMask(mosaic = EX.Dist.Ind)

# Evaluating distance between plants. Remember to press ESC when finished to draw the line.
EX.Dist.Draw <- fieldDraw(mosaic = EX.Dist.RemSoil$mask, 
                          dist = T,
                          value = 1, # Use the number to identify the object to be measured (1 for space and 0 for plants)
                          distSel = 0.4) 
EX.Dist.Draw$drawDist # Distance between plants
                          
# Making plots                         
plot(EX.Dist.Ind$NGRDI)
points(EX.Dist.Draw$drawData$x,EX.Dist.Draw$drawData$y, col="red",pch=16,cex=0.7)
points(EX.Dist.Draw$drawSegments$x,EX.Dist.Draw$drawSegments$y, col="blue",pch=16,cex=0.7)
lines(EX.Dist.Draw$drawDist[1,c("x1","x2")],EX.Dist.Draw$drawDist[1,c("y1","y2")], col="green",lwd=5)

# Evaluating an specific layer profile (e.g. NGRDI)
EX.Dist.Draw.2 <- fieldDraw(mosaic = EX.Dist.Ind,
                            ndraw = 4, # Making 4 lines (press ESC to conclude each line)
                            lwd = 5)
EX.Data<-EX.Dist.Draw.2$Draw1$drawData
dev.off()
plot(x = EX.Data$x, y = EX.Data$NGRDI, type="l", col="red",lwd=2,xlab="Distance (m)", ylab="NGRDI")
abline(h=0.0,col="blue", lty=2, lwd=3)

# Making polygons and extracting data per cell
EX.Dist.Draw.3 <- fieldDraw(mosaic = EX.Dist.Ind,
                            line = F, # Making 2 polygons (press ESC to conclude each polygon)
                            ndraw = 2,
                            lwd = 5)
plotRGB(EX.Dist.RemSoil$newMosaic)
plot(EX.Dist.Draw.3$Draw1$drawObject, col="red",add=T)