SOM ANN R script -edited

somPEs <- 36   # user defined constant specific to dataset dimensionality
inputPEs <- 6; # arbitrary constant specific to dataset dimensionality
hm <- matrix(c(c(1:8),rep(0,somPEs-length(c(1:8)))), nrow=sqrt(somPEs), ncol=sqrt(somPEs))
hm2 <- as.vector(matrix(hm, byrow=TRUE))
initial_w <- matrix(1, nrow=somPEs, ncol=inputPEs)
w <- t(apply(initial_w, 1, function(i) runif(i)));

# Do fences, weight distances.
fence_edges = matrix(0, nrow=somPEs, ncol=4); # cols are top, bottom, left, right borders of each somPE
fence_diagonals = matrix(0, nrow=somPEs, ncol=4); # cols are top left, top right, bottom left, bottom right
# Reshape w to a 3D matrix of dimension: c(sqrt(somPEs), sqrt(somPEs), inputPEs)
dim(w) <- c(sqrt(somPEs), sqrt(somPEs), inputPEs)
w <- aperm(w, c(2, 1, 3))

# Plot weight distance between adjacent somPEs in all directions in grayscale
it = 1;
for (i in 1:sqrt(somPEs)) {
  for (j in 1:sqrt(somPEs)) {
    if (i>1 && i<sqrt(somPEs)) {
      if (j>1 && j<sqrt(somPEs)) {
        for (k in 1:inputPEs) {
          fence_edges[it,1] = fence_edges[it,1] + dist(rbind(w[i,j,k], w[i-1,j,k]));
          fence_edges[it,2] = fence_edges[it,2] + dist(rbind(w[i,j,k], w[i+1,j,k]));
          fence_edges[it,3] = fence_edges[it,3] + dist(rbind(w[i,j,k], w[i,j-1,k]));
          fence_edges[it,4] = fence_edges[it,4] + dist(rbind(w[i,j,k], w[i,j+1,k]));
          fence_diagonals[it,1] = fence_diagonals[it,1] + dist(rbind(w[i,j,k], w[i-1,j-1,k]));
          fence_diagonals[it,2] = fence_diagonals[it,2] + dist(rbind(w[i,j,k], w[i-1,j+1,k]));
          fence_diagonals[it,3] = fence_diagonals[it,3] + dist(rbind(w[i,j,k], w[i+1,j-1,k]));
          fence_diagonals[it,4] = fence_diagonals[it,4] + dist(rbind(w[i,j,k], w[i+1,j+1,k]));
        }
      } else if (j==1) {
        for (k in 1:inputPEs) {
          fence_edges[it,1] = fence_edges[it,1] + dist(rbind(w[i,j,k], w[i-1,j,k]));
          fence_edges[it,2] = fence_edges[it,2] + dist(rbind(w[i,j,k], w[i+1,j,k]));
          fence_edges[it,4] = fence_edges[it,4] + dist(rbind(w[i,j,k], w[i,j+1,k]));
          fence_diagonals[it,2] = fence_diagonals[it,2] + dist(rbind(w[i,j,k], w[i-1,j+1,k]));
          fence_diagonals[it,4] = fence_diagonals[it,4] + dist(rbind(w[i,j,k], w[i+1,j+1,k]));
        }
      } else { # j==10
        for (k in 1:inputPEs) {
          fence_edges[it,1] = fence_edges[it,1] + dist(rbind(w[i,j,k], w[i-1,j,k]));
          fence_edges[it,2] = fence_edges[it,2] + dist(rbind(w[i,j,k], w[i+1,j,k]));
          fence_edges[it,3] = fence_edges[it,3] + dist(rbind(w[i,j,k], w[i,j-1,k]));
          fence_diagonals[it,1] = fence_diagonals[it,1] + dist(rbind(w[i,j,k], w[i-1,j-1,k]));
          fence_diagonals[it,3] = fence_diagonals[it,3] + dist(rbind(w[i,j,k], w[i+1,j-1,k]));
        }
      }
    } else if (i==1) {
      if (j>1 && j<sqrt(somPEs)) {
        for (k in 1:inputPEs) {
          fence_edges[it,2] = fence_edges[it,2] + dist(rbind(w[i,j,k], w[i+1,j,k]));
          fence_edges[it,3] = fence_edges[it,3] + dist(rbind(w[i,j,k], w[i,j-1,k]));
          fence_edges[it,4] = fence_edges[it,4] + dist(rbind(w[i,j,k], w[i,j+1,k]));
          fence_diagonals[it,3] = fence_diagonals[it,3] + dist(rbind(w[i,j,k], w[i+1,j-1,k]));
          fence_diagonals[it,4] = fence_diagonals[it,4] + dist(rbind(w[i,j,k], w[i+1,j+1,k]));
        }
      } else if (j==1) {
        for (k in 1:inputPEs) {
          fence_edges[it,2] = fence_edges[it,2] + dist(rbind(w[i,j,k], w[i+1,j,k]));
          fence_edges[it,4] = fence_edges[it,4] + dist(rbind(w[i,j,k], w[i,j+1,k]));
          fence_diagonals[it,4] = fence_diagonals[it,4] + dist(rbind(w[i,j,k], w[i+1,j+1,k]));
        }
      } else { # j==10
        for (k in 1:inputPEs) {
          fence_edges[it,2] = fence_edges[it,2] + dist(rbind(w[i,j,k], w[i+1,j,k]));
          fence_edges[it,3] = fence_edges[it,3] + dist(rbind(w[i,j,k], w[i,j-1,k]));
          fence_diagonals[it,3] = fence_diagonals[it,3] + dist(rbind(w[i,j,k], w[i+1,j-1,k]));
        }
      }
    } else { # i==10
      if (j>1 && j<sqrt(somPEs)) {
        for (k in 1:inputPEs) {
          fence_edges[it,1] = fence_edges[it,1] + dist(rbind(w[i,j,k], w[i-1,j,k]));
          fence_edges[it,3] = fence_edges[it,3] + dist(rbind(w[i,j,k], w[i,j-1,k]));
          fence_edges[it,4] = fence_edges[it,4] + dist(rbind(w[i,j,k], w[i,j+1,k]));
          fence_diagonals[it,1] = fence_diagonals[it,1] + dist(rbind(w[i,j,k], w[i-1,j-1,k]));
          fence_diagonals[it,2] = fence_diagonals[it,2] + dist(rbind(w[i,j,k], w[i-1,j+1,k]));
        }
      } else if (j==1) {
        for (k in 1:inputPEs) {
          fence_edges[it,1] = fence_edges[it,1] + dist(rbind(w[i,j,k], w[i-1,j,k]));
          fence_edges[it,4] = fence_edges[it,4] + dist(rbind(w[i,j,k], w[i,j+1,k]));
          fence_diagonals[it,2] = fence_diagonals[it,2] + dist(rbind(w[i,j,k], w[i-1,j+1,k]));
        }
      } else { # j==10
        for (k in 1:inputPEs) {
          fence_edges[it,1] = fence_edges[it,1] + dist(rbind(w[i,j,k], w[i-1,j,k]));
          fence_edges[it,3] = fence_edges[it,3] + dist(rbind(w[i,j,k], w[i,j-1,k]));
          fence_diagonals[it,1] = fence_diagonals[it,1] + dist(rbind(w[i,j,k], w[i-1,j-1,k]));
        }
      }
    }
    it=it+1;
  }
}
mxEdges = max(max(fence_edges));
mxDiagonals = max(max(fence_diagonals));
fence_edges = fence_edges/mxEdges;
fence_diagonals = fence_diagonals/mxDiagonals;