PROTOLIDAR (version 0.1)

Extract_plant_3D_function: Extract plant 3D (grapevine).

Description

This function move the axes x,y,z to the center of the plant. This output could be exported and transformed in GRASS GIS in 3D maps.

Usage

Extract_plant_3D_function(out, z_min, z_max, y_min, y_max, distance_left, distance_right)

Arguments

out

out is a data frame output from Extract_plant_grapevine_function.

z_min

the minimum position of the stem in z measured in meters.

z_max

the maximum position of the stem in z measured in meters.

y_min

the minimum position of the stem in y measured in meters.

y_max

the maximum position of the stem in y measured in meters.

distance_left

the left distance of the plant, generally here we can write the half of the distance between plants, but is better the real distance from the center of the plant. Measured in meters.

distance_right

the right distance of the plant, generally here we can write the half of the distance between plants, but is better the real distance from the center of the plant. Measured in meters.

Examples

## Should be DIRECTLY executable !!
## out come from Extract_plant_grapevine_function. The other parameters or inputs are needed to write before.
## For example:
   data (LIDAR_data)
   x <- LIDAR_data[,1]
   y <- LIDAR_data[,2]
   z <- LIDAR_data[,3]
   zdistance <- 190 # total LIDAR scan distance measured in cm.
   miny <- 0 # minimum height of the plant measured in cm.
   maxy <- 2000 # maximum height of the plant measured in cm.
   minx <- 450 # minimum width from where LIDAR starts to measure (cm).
   maxx <- 1470# maximum width from where LIDAR starts to measure (cm).
   minz <- 0 # the beginning of the LIDAR scan measured in cm.
   maxz <- 186 # the end of the LIDAR scan measured in cm (length of interest).
   out <- Extract_plant_grapevine_function(x,y,z,zdistance,miny,maxy,minx,maxx,minz,maxz)
   z_min <- 1.1 
   z_max <- 1.13
   y_min <- 0.4
   y_max <- 0.5
   distance_left <- -0.6
   distance_right <- 0.51
   

## The function is currently defined as

Extract_plant_3D_function <- function(out,z_min,z_max,y_min,y_max,distance_left,distance_right){ 
  x_cm <- y_cm <- z_cm <- NULL
  data_stem <- subset(out,out$y_cm > y_min & out$y_cm<= y_max & out$z_cm >= z_min  & out$z_cm <= z_max,select=c(x_cm,y_cm,z_cm))
  x_c       <- out$x_cm - min(data_stem$x_cm)
  y_c       <- out$y_cm
  z_c       <- out$z_cm - min(data_stem$z_cm)
  data_cero <- data.frame(x_c,y_c,z_c)
  data_plant <- subset(data_cero, data_cero$z_c >= distance_left & data_cero$z_c <= distance_right,select=c(x_c,y_c,z_c))
  x_plant <- data_plant[,1]
  y_plant <- data_plant[,2]
  z_plant <- data_plant[,3]
  return(data.frame(x_plant,y_plant,z_plant))
  }
  data_3D <- Extract_plant_3D_function(out,z_min,z_max,y_min,y_max,distance_left,distance_right)
  x_plant <- data_3D[,1]
  y_plant <- data_3D[,2]
  z_plant <- data_3D[,3]
  # plot
  par(mfcol=c(2,2))
    plot(x_plant,y_plant,pch=20,cex=.4)
    plot(x_plant,z_plant,pch=20,cex=.4)
    plot(z_plant,y_plant,pch=20,cex=.4)