Process Single Tree – Compute Convex Hulls


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Processing a terrestrial laser scan of a single tree… (TLS data)

#####might need to install the concaveman library
library("lidR")
library("rgdal")
library("concaveman")

#####Load Files
mypath<- "U:/FANR5640/Spring2019/labs/lab09Data"
myfile<- "SingleTree.laz"
infile<- file.path(mypath,myfile)
lastmp = readLAS(infile, select = "xyzirc")##, Intensity = F, ReturnNumber = F, NumberOfReturn = F, ScanAngle = F, EdgeOfFlightline = F, ScanDirectionFlag = F, UserData = F, PointSourceId = F, color = T)
summary(lastmp)
lasd<- lastmp
plot(lasd)
summary(lasd)

#####use for loop later on
valMinZ<- lasd@header@PHB$'Min Z'
valMaxZ<- lasd@header@PHB$'Max Z'
valDifZ<- valMaxZ - valMinZ
print(valMinZ)
print(valMaxZ)

#####manually set ground to valMinZ - 
#####the next line creates a 'ground' object whose raster values are not actually the ground
grnd<- grid_metrics(lasd,min(Z),0.05)
#####reset all cell values tothe minimum valMinZ value
grnd[grnd > valMinZ]<- valMinZ

#####Normalize lasd based on the grnd object created above
lasd_n<- lasnormalize(lasd,grnd)
summary(lasd_n)
plot(lasd_n)

#####maximum heigt
valMaxZNorm<- lasd_n@header@PHB$'Max Z'

col<- pastel.colors(250)

#####chm = surface model 
chm<- grid_canopy(lasd_n, res=0.5,p2r(0.3))
ker <- matrix(1,3,3)
#####smooth the canopy height mocel
chm <- raster::focal(chm, w = ker, fun = mean, na.rm = TRUE)
plot(chm)

####tree detection required for convex_hull procedures below
#tree_detection(lasd,lmf(ws=25,hmin=(65)))
ttops <- tree_detection(chm, lmf(4, 2))
lasd_n<- lastrees(lasd_n,mcwatershed(chm,ttops))
plot(lasd_n,color="treeID")

#####SLICE TREE
seqStep<- 3
for (i in seq(0,valMaxZNorm,seqStep)){
  charI<- as.character(i)
  lowval<- i
  highval<- i + seqStep
  #####the point cloud below stores the sliced point cloud and is overwritten each loop
  lasd_n_xxft<- lasfilter(lasd_n,((Z>=lowval) & (Z<highval)))
  #####https://rdrr.io/cran/lidR/man/tree_hulls.html
  convex_hulls<- tree_hulls(lasd_n_xxft)
  sp::plot(convex_hulls)
  bbox_hulls<- tree_hulls(lasd_n_xxft,"bbox")
  sp::plot(bbox_hulls)
  concave_hulls<- tree_hulls(lasd_n_xxft,"concave")
  sp::plot(concave_hulls)
  #####Export hulls to shapefile
  #####pattern to create output file name
  outshape<-(paste("convexhull_",charI))
  writeOGR(obj=convex_hulls,dsn=mypath, layer=outshape, driver="ESRI Shapefile", overwrite=TRUE)
}


 

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