update repo

CodeR/03_Compute_angles_cone.r

+rm(list=ls())
+gc()
+
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+## packages functions
+rm(list=ls())
+
+library("rlas")
+library("rgl")
+library("stringr")
+library("VoxR")
+library("data.table")
+
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+## DataR and CodeR
+## DataR <- paste0("/home/nibio/REPOS/holger_tower_pov/DataR")
+## DataR <- paste0("/home/pepito/Documents/holger_tower_pov/DataR")
+DataR <- paste0("/home/nica/Documents/Holger_tower_pov/DataR")
+
+CodeR <- paste0("/home/nica/Documents/Holger_tower_pov/CodeR")
+
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+## Functions
+source(paste0(CodeR, "/Functions/Functions.r"))
+
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+## plot data - full path
+DataPaths <- list.files(DataR,
+                        pattern = "plot_",
+                        ## pattern = "Plot_",
+                        ## pattern = "merg",
+                        ## pattern = ".rds",
+                        ## pattern = "Tower",
+                        full.names = T)
+
+Data <- read.las(DataPaths)
+Data[, 1:3]
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+
+
+## Data <- Data[sample(1:nrow(Data), nrow(Data)*0.10), ]
+Data[, X := Scale(Data$X)]
+Data[, Y := Scale(Data$Y)]
+Data[, Z := Scale(Data$Z)]
+
+Data[, X := X-mean(X)]
+Data[, Y := Y-mean(Y)]
+
+
+plot3d(Data, aspect = "iso", size = 0.5)
+pan3d(3)
+
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+## Create an artificial tower. Just the corners
+## CornA <- data.table(X = 3, Y = 3, Z = 40)
+## CornA <- Data[identify3d(Data, n = 1), ]
+spheres3d(CornA, radius = 1, col = "yellow")
+
+
+
+
+
+## Left click on a ground point in the point cloud
+## Right click  to scape
+## CornB <- Data[identify3d(Data, n = 1), ]
+spheres3d(CornB, radius = 1, col = "red")
+## rgl.pop()
+
+Data[, Dista := dist3d(X, Y, Z,
+                       CornA$X, CornA$Y, CornA$Z,
+                       CornB$X, CornB$Y, CornB$Z),
+     by = seq_len(nrow(Data))]
+setnames(Data, "Dista", "CO")
+
+## plot3d(Data, aspect = "iso", size = 0.5, col = "grey21")
+## plot3d(Data[CO < 5 , ], aspect = "iso", size = 4, col = "red", add = T)
+## spheres3d(CornA, radius = 1, col = "yellow")
+## spheres3d(CornB, radius = 1, col = "red")
+## pan3d(3)
+
+Data[, H := dist3d2(X, Y, Z,
+                   CornA$X, CornA$Y, CornA$Z),
+     by = seq_len(nrow(Data))]
+
+Data[, Angle := CO/H]
+Data[, Angle := (asin(Angle))*180/pi]
+
+plot3d(Data[Angle > 28, ], aspect = "iso", size = 0.5, col = "grey21")
+spheres3d(CornA, radius = 1, col = "yellow")
+spheres3d(CornB, radius = 1, col = "red")
+plot3d(Data[Angle < 28, ], aspect = "iso", size = 0.5, col = "red", add = T)
+pan3d(3)
+
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+## Select closest point by angle
+Data2 <- Data[Angle < 15, ]
+Data2[, min(H), by = Angle]
+
+
+
+
+

CodeR/03_Compute_angles_cone.r~

+rm(list=ls())
+gc()
+
+## system("gio mount -u smb://int.nibio.no/Databank")
+## system(paste0("gio mount smb://int.nibio.no/Databank ",
+##               "< /home/nibio/.craden"))
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+## Move the scan to have a local copy.
+## Origin <- paste0("/run/user/1003/gvfs",
+##                  "/smb-share:server=int.nibio.no,",
+##                  "share=databank/Prosjekter",
+##                  "/51160_IMPRINT/Forest_projections",
+##                  "/DataR/to_map/merged_22_classified.las")
+## Dest <- "/home/nibio/DATA"
+## cmd <- paste("cp", Origin, Dest) 
+## system(cmd)
+
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+## packages and functions
+rm(list=ls())
+
+library("rlas")
+library("rgl")
+library("stringr")
+library("VoxR")
+library("data.table")
+
+load("/home/nibio/REPOS/holger_tower_pov/DataR/pan3d.RData")
+## load("/home/pepito/Documents/holger_tower_pov/DataR/pan3d.RData")
+
+## this function scale points coordinate
+## between 0 and (max-min) values
+Scale <- function(Vector){
+    ((Vector - min(Vector))/
+     (max(Vector)-min(Vector)))*
+        (max(Vector)-min(Vector))}
+
+## Distances
+cross3d_prod <- function(v1,v2){
+  v3 <- vector()
+  v3[1] <- v1[2]*v2[3]-v1[3]*v2[2]
+  v3[2] <- v1[3]*v2[1]-v1[1]*v2[3]
+  v3[3] <- v1[1]*v2[2]-v1[2]*v2[1]
+  return(v3)
+}
+
+dist3d <- function(xa, ya, za, xb, yb, zb, xc, yc, zc) {
+    a <- c(xa, ya, za)
+    b <- c(xb, yb, zb, xc)
+    c <- c(xc, yc, zc)
+    
+    v1 <- b - c
+    v2 <- a - b      
+    v3 <- cross3d_prod(v1,v2)
+    area <- sqrt(sum(v3*v3))/2
+    d <- 2*area/sqrt(sum(v1*v1))
+    return(d)
+}
+
+dist3d2 <- function(xa, ya, za, xb, yb, zb) {
+    d <- sqrt(((xa - xb)^2) + ((ya - yb)^2) + ((za - zb)^2))
+    return(d)}
+
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+## DataR
+DataR <- paste0("/home/nibio/REPOS/holger_tower_pov/DataR")
+## DataR <- paste0("/home/pepito/Documents/holger_tower_pov/DataR")
+
+
+
+
+## plot data - full path
+DataPaths <- list.files(DataR,
+                        ## pattern = "plot_",
+                        ## pattern = "Plot_",
+                        ## pattern = "merg",
+                        ## pattern = ".rds",
+                        pattern = "Tower",
+                        full.names = T)
+
+Data <- read.las(DataPaths)
+Data[, 1:3]
+## Data <- fst::read_fst(DataPaths, as.data.table = T)
+
+Data <- Data[sample(1:nrow(Data), nrow(Data)*0.10), ]
+Data[, X := Scale(Data$X)]
+Data[, Y := Scale(Data$Y)]
+Data[, Z := Scale(Data$Z)]
+
+Data[, X := X-mean(X)]
+Data[, Y := Y-mean(Y)]
+
+
+HGSTPoint <- Data[max(Z), ]
+
+Data[, Dist := dist3d2(X, Y, 0,
+                   HGSTPoint$X, HGSTPoint$Y, 0),
+     by = seq_len(nrow(Data))]
+
+
+## open3d()
+Data <- Data[Dist < 10,]
+plot3d(Data, aspect = "iso", size = 3)
+spheres3d(HGSTPoint, radius = 1, col = "yellow")
+
+pan3d(3)
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+## Create an artificial tower. Just the corners
+## CornA <- data.table(X = 3, Y = 3, Z = 40)
+## CornA <- Data[identify3d(Data, n = 1), ]
+spheres3d(CornA, radius = 1, col = "yellow")
+
+## Left click on a ground point in the point cloud
+## Right click  to scape
+## CornB <- Data[identify3d(Data, n = 1), ]
+spheres3d(CornB, radius = 1, col = "red")
+## rgl.pop()
+
+Data[, Dista := dist3d(X, Y, Z,
+                       CornA$X, CornA$Y, CornA$Z,
+                       CornB$X, CornB$Y, CornB$Z),
+     by = seq_len(nrow(Data))]
+setnames(Data, "Dista", "CO")
+
+## plot3d(Data, aspect = "iso", size = 0.5, col = "grey21")
+## plot3d(Data[CO < 5 , ], aspect = "iso", size = 4, col = "red", add = T)
+## spheres3d(CornA, radius = 1, col = "yellow")
+## spheres3d(CornB, radius = 1, col = "red")
+## pan3d(3)
+
+Data[, H := dist3d2(X, Y, Z,
+                   CornA$X, CornA$Y, CornA$Z),
+     by = seq_len(nrow(Data))]
+
+Data[, Angle := CO/H]
+Data[, Angle := (asin(Angle))*180/pi]
+
+plot3d(Data[Angle > 28, ], aspect = "iso", size = 0.5, col = "grey21")
+spheres3d(CornA, radius = 1, col = "yellow")
+spheres3d(CornB, radius = 1, col = "red")
+plot3d(Data[Angle < 28, ], aspect = "iso", size = 0.5, col = "red", add = T)
+pan3d(3)
+
+## @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+## Select closest point by angle
+Data2 <- Data[Angle < 15, ]
+Data2[, min(H), by = Angle]
+
+
+
+
+

CodeR/Functions/Functions.r

+Scale <- function(Vector){
+    ((Vector - min(Vector))/
+     (max(Vector)-min(Vector)))*
+        (max(Vector)-min(Vector))}
+
+cross3d_prod <- function(v1,v2){
+  v3 <- vector()
+  v3[1] <- v1[2]*v2[3]-v1[3]*v2[2]
+  v3[2] <- v1[3]*v2[1]-v1[1]*v2[3]
+  v3[3] <- v1[1]*v2[2]-v1[2]*v2[1]
+  return(v3)
+}
+
+dist3d <- function(xa, ya, za, xb, yb, zb, xc, yc, zc) {
+    a <- c(xa, ya, za)
+    b <- c(xb, yb, zb, xc)
+    c <- c(xc, yc, zc)
+    
+    v1 <- b - c
+    v2 <- a - b      
+    v3 <- cross3d_prod(v1,v2)
+    area <- sqrt(sum(v3*v3))/2
+    d <- 2*area/sqrt(sum(v1*v1))
+    return(d)
+}
+
+dist3d2 <- function(xa, ya, za, xb, yb, zb) {
+    d <- sqrt(((xa - xb)^2) + ((ya - yb)^2) + ((za - zb)^2))
+    return(d)}
+
+
+pan3d <- function(button) {
+    library("rgl")
+    start <- list()
+    begin <- function(x, y) {
+        start$userMatrix <<- par3d("userMatrix")
+        start$viewport <<- par3d("viewport")
+        start$scale <<- par3d("scale")
+        start$projection <<- rgl.projection()
+        start$pos <<- rgl.window2user( x/start$viewport[3],
+                                      1 - y/start$viewport[4], 0.5,
+                                      projection = start$projection)
+    }
+
+    update <- function(x, y) {
+        xlat <- (rgl.window2user( x/start$viewport[3],
+                                 1 - y/start$viewport[4], 0.5,
+                                 projection = start$projection) -
+                 start$pos)*start$scale
+
+        mouseMatrix <- translationMatrix(xlat[1], xlat[2], xlat[3])
+        par3d(userMatrix = start$userMatrix %*% t(mouseMatrix) )
+    }
+
+    rgl.setMouseCallbacks(button, begin, update)
+    cat("Callbacks set on button", button, "of rgl device", rgl.cur(), "\n")
+}

CodeR/Functions/Functions.r~

+Scale <- function(Vector){
+    ((Vector - min(Vector))/
+     (max(Vector)-min(Vector)))*
+        (max(Vector)-min(Vector))}
+
+cross3d_prod <- function(v1,v2){
+  v3 <- vector()
+  v3[1] <- v1[2]*v2[3]-v1[3]*v2[2]
+  v3[2] <- v1[3]*v2[1]-v1[1]*v2[3]
+  v3[3] <- v1[1]*v2[2]-v1[2]*v2[1]
+  return(v3)
+}
+
+dist3d <- function(xa, ya, za, xb, yb, zb, xc, yc, zc) {
+    a <- c(xa, ya, za)
+    b <- c(xb, yb, zb, xc)
+    c <- c(xc, yc, zc)
+    
+    v1 <- b - c
+    v2 <- a - b      
+    v3 <- cross3d_prod(v1,v2)
+    area <- sqrt(sum(v3*v3))/2
+    d <- 2*area/sqrt(sum(v1*v1))
+    return(d)
+}
+
+dist3d2 <- function(xa, ya, za, xb, yb, zb) {
+    d <- sqrt(((xa - xb)^2) + ((ya - yb)^2) + ((za - zb)^2))
+    return(d)}
+