Get sequence of adjacent cell numbers out of a raster

Question

I am currently working on a script, that loads a TIF file into a raster object, crops it and plots two points (starting point and point of destination; selected via the click-function) into that raster. I then want it to get the cell numbers of those two points. All of that hasn't caused any trouble but now I have tried to write a while-Loop which gets me the number of a random cell (which is adjacent to the current cell; beginning from the starting point) until that cell number equals the cell number of my point of destination. My idea behind that was to "walk" across the raster until I have reached my point of destination or at least the column containing it (to reduce computation time). The numbers of the cells i cross during that walk should be stored in a vector ("Path"). I select the adjacent cell (=choose my next step) by randomly sampling from a vector that contains numbers that, when added to the current cell number, lead to the number of an adjacent cell. I have multiple vectors from which to sample as the number of possible directions in which to "walk" differs depending on the position of the current cell (e.g. I can't "walk" to the cell to my lower rigth (=n + (ncol_dispersal + 1) if I am currently positioned at the bottom of the raster). The script looks like this so far:

library(gdistance)
library(raster)
library(rgdal)
library(sp)
setwd("C:/Users/Giaco/Dropbox/Random Walk")   
altdata <- raster("altitude.tif")        
plot(altdata)      
e <- extent(92760.79,93345.79,204017.5,204242.5)    
dispersal_area <- crop(altdata,e)               
plot(dispersal_area)
points(92790.79,204137.5,pch=16,cex=1)              
points(93300.79,204062.5,pch=16,cex=1) 
Pts <- matrix(c(92790.79,204137.5,93300.79,204062.5),nrow=2,ncol=2,byrow=TRUE)     
Start <- cellFromXY(dispersal_area,Pts[1,])    
End <- cellFromXY(dispersal_area,Pts[2,])
nrow_dispersal <- nrow(dispersal_area)     
ncol_dispersal <- ncol(dispersal_area)
col_start <- colFromCell(dispersal_area,Start)  
row_start <- rowFromCell(dispersal_area,Start)
col_end <- colFromCell(dispersal_area,End)
row_end <- rowFromCell(dispersal_area,End)
upper_left_corner <- cellFromRowCol(dispersal_area,1,1)     
lower_left_corner <- cellFromRowCol(dispersal_area,14,1)
sample_standard <- c(1,(ncol_dispersal+1),(ncol_dispersal*-1+1))   
sample_top <- c(1,ncol_dispersal,(ncol_dispersal+1))               
sample_bottom <- c(1,(ncol_dispersal*-1+1),(ncol_dispersal*-1))    
sample_left <- c(1,(ncol_dispersal+1),(ncol_dispersal*-1+1))       
sample_upper_left <- c(1,ncol_dispersal,(ncol_dispersal+1))        
sample_lower_left <- c(1,(ncol_dispersal*-1+1),(ncol_dispersal*-1))
Path <- c()
Path[1] <- Start    
n <- Start
counter <- 1




       while (n != End)                             
                {
                n = Start+sample(sample_standard,1) 
                   if (colFromCell(dispersal_area,n)==col_end) {
                   n=End
                   break
                   } else if (n==upper_left_corner) {
                   n = n+sample(sample_upper_left,1)
                   } else if(n==lower_left_corner){
                   n = n+sample(sample_lower_left,1)
                   } else if(colFromCell(dispersal_area,n)==1) {
                   n = n+sample(sample_left,1)
                   } else if(rowFromCell(dispersal_area,n)==1){
                   n = n+sample(sample_top,1)
                   } else if(rowFromCell(dispersal_area,n)==nrow_dispersal) {
                   n = n+sample(sample_bottom,1)
                   } 
                counter <- counter+1
                Path[counter] <- n
                }

When I run the script and print the path vector it returns a veeerryy long vector (I always have to stop it as it never finishes computing) which contains only a few different numbers. Why is that ? I have been staring at this all day but I simply can't figure out where i went wrong. There must be something wrong with the while Loop but I don't see it. If anyone of you guys could help me out with this I would be really really thankful. Thanks in advance !

Robert Hijmans Robert Hijmans · Accepted Answer · 2016-04-10T23:20:11

In the future, please provide a simple and reproducible example. Something like this (that also answers your question I think).

library(gdistance)

r <- raster(system.file("external/maungawhau.grd", package="gdistance"))
r <- aggregate(r, 5)
p <- matrix(c(2667531, 6478843, 2667731, 6479227), ncol=2, byrow=TRUE)     

start <- cellFromXY(r, p[1,])    
end <- cellFromXY(r, p[2,])

counter <- 1
cell <- start
path <- cell
while (cell != end)  {
    a <- adjacent(r, cell, pairs=F)
    cell <- sample(a, 1)
    path <- c(path, cell)
}
xy <- xyFromCell(r, path)

plot(r)
lines(xy)

or

cols <- rainbow(nrow(xy))
for (i in 1:nrow(xy)-1) { lines(xy[i:(i+1), ], col=cols[i]) }

This is pretty fast on this coarse raster, but it could indeed take a very long time to reach a particular cell on a large raster by random walk.

You are not stating why you do this. Perhaps there are function in gdistance that are more useful?

Get sequence of adjacent cell numbers out of a raster

1 Answers