Finding the NaN boundary of a matrix in MATLAB - matlab

Question

I have a very large (2019x1678 double) DEM (digital elevation model) file put as a matrix in MATLAB. The edges of it contain NaN values. In order to account for edge effects in my code, I have to put a 1 cell buffer (same value as adjacent cell) around my DEM. Where NaNs are present, I need to find the edge of the NaN values in order to build that buffer. I have tried doing this two ways:
In the first I get the row and column coordinates all non-NaN DEM values, and find the first and last row numbers for each column to get the north and south boundaries, then find the first and last column numbers for each row to get the east and west boundaries. I use these in the sub2ind() to create my buffer.
[r, c] = find(~isnan(Zb_ext)); %Zb is my DEM matrix
idx = accumarray(c, r, [], #(x) {[min(x) max(x)]});
idx = vertcat(idx{:});
NorthBoundary_row = transpose(idx(:,1)); % the values to fill my buffer with
NorthBoundary_row_ext = transpose(idx(:,1) - 1); % My buffer cells
columnmax = length(NorthBoundary_row);
column1 = min(c);
Boundary_Colu = linspace(column1,column1+columnmax-1,columnmax);
SouthBoundary_row = (transpose(idx(:,2))); % Repeat for south Boundary
SouthBoundary_row_ext = transpose(idx(:,2) + 1);
SouthB_Ind = sub2ind(size(Zb_ext),SouthBoundary_row,Boundary_Colu);
SouthB_Ind_ext = sub2ind(size(Zb_ext),SouthBoundary_row_ext, Boundary_Colu);
NorthB_Ind = sub2ind(size(Zb_ext),NorthBoundary_row, Boundary_Colu);
NorthB_Ind_ext = sub2ind(size(Zb_ext),NorthBoundary_row_ext, Boundary_Colu);
Zb_ext(NorthB_Ind_ext) = Zb_ext(NorthB_Ind);
Zb_ext(SouthB_Ind_ext) = Zb_ext(SouthB_Ind);
% Repeat above for East and West Boundary by reversing the roles of row and
% column
[r, c] = find(~isnan(Zb_ext));
idx = accumarray(r, c, [], #(x) {[min(x) max(x)]});
idx = vertcat(idx{:});
EastBoundary_colu = transpose(idx(:,1)); % Repeat for east Boundary
EastBoundary_colu_ext = transpose(idx(:,1) - 1);
row1 = min(r);
rowmax = length(EastBoundary_colu);
Boundary_row = linspace(row1,row1+rowmax-1,rowmax);
WestBoundary_colu = transpose(idx(:,2)); % Repeat for west Boundary
WestBoundary_colu_ext = transpose(idx(:,2) + 1);
EastB_Ind = sub2ind(size(Zb_ext),Boundary_row, EastBoundary_colu);
EastB_Ind_ext = sub2ind(size(Zb_ext),Boundary_row, EastBoundary_colu_ext);
WestB_Ind = sub2ind(size(Zb_ext),Boundary_row, WestBoundary_colu);
WestB_Ind_ext = sub2ind(size(Zb_ext),Boundary_row, WestBoundary_colu_ext);
Zb_ext(NorthB_Ind_ext) = Zb_ext(NorthB_Ind);
Zb_ext(SouthB_Ind_ext) = Zb_ext(SouthB_Ind);
Zb_ext(EastB_Ind_ext) = Zb_ext(EastB_Ind);
Zb_ext(WestB_Ind_ext) = Zb_ext(WestB_Ind);
This works well on my small development matrix, but fails on my full sized DEM. I do not understand the behavior of my code, but looking at the data there are gaps in my boundary. I wonder if I need to better control the order of max/min row/column values, though in my test on a smaller dataset, all seemed in order....
The second method I got from a similar question to this and basically uses a dilation method. However, when I transition to my full dataset, it takes hours to calculate ZbDilated. Although my first method does not work, it at least calculates within seconds.
[m, n] = size(Zb); %
Zb_ext = nan(size(Zb)+2);
Zb_ext(2:end-1, 2:end-1) = Zb; % pad Zb with zeroes on each side
ZbNANs = ~isnan(Zb_ext);
ZbDilated = zeros(m + 2, n + 2); % this will hold the dilated shape.
for i = 1:(m+2)
if i == 1 %handling boundary situations during dilation
i_f = i;
i_l = i+1;
elseif i == m+2
i_f = i-1;
i_l = i;
else
i_f = i-1;
i_l = i+1;
end
for j = 1:(n+2)
mask = zeros(size(ZbNANs));
if j == 1 %handling boundary situations again
j_f = j;
j_l = j+1;
elseif j == n+2
j_f = j-1;
j_l = j;
else
j_f = j-1;
j_l = j+1;
end
mask(i_f:i_l, j_f:j_l) = 1; % this places a 3x3 square of 1's around (i, j)
ZbDilated(i, j) = max(ZbNANs(logical(mask)));
end
end
Zb_ext(logical(ZbDilated)) = fillmissing(Zb_ext(logical(ZbDilated)),'nearest');
Does anyone have any ideas on making either of these usable?
Here is what I start out with:
NaN NaN 2 5 39 55 44 8 NaN NaN
NaN NaN NaN 7 33 48 31 66 17 NaN
NaN NaN NaN 28 NaN 89 NaN NaN NaN NaN
Here is the matrix buffered on the limits with NaNs:
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
NaN NaN NaN 2 5 39 55 44 8 NaN NaN NaN
NaN NaN NaN NaN 7 33 48 31 66 17 NaN NaN
NaN NaN NaN NaN 28 NaN 89 NaN NaN NaN NaN NaN
NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
Here is what I want to get after using fillmissing (though I have noticed some irregularities with how buffer values are filled...):
NaN NaN 2 2 5 39 55 44 8 17 NaN NaN
NaN NaN 2 2 5 39 55 44 8 17 17 NaN
NaN NaN 2 2 7 33 48 31 66 17 17 NaN
NaN NaN NaN 2 28 33 89 31 66 17 17 NaN
NaN NaN NaN 5 28 55 89 8 NaN NaN NaN NaN
To try and clear up any confusion about what I am doing, here is the logical I get from dilation I use for fillmissing
0 0 1 1 1 1 1 1 1 1 0 0
0 0 1 1 1 1 1 1 1 1 1 0
0 0 1 1 1 1 1 1 1 1 1 0
0 0 0 1 1 1 1 1 1 1 1 0
0 0 0 1 1 1 1 1 0 0 0 0

Answer 1

A faster way to apply a 3x3 dilation would be as follows. This does involve some large intermediate matrices, which make it less efficient than, say applying imdilate.
[m, n] = size(Zb); %
Zb_ext = nan(size(Zb)+2);
Zb_ext(2:end-1, 2:end-1) = Zb; % pad A with zeroes on each side
ZbNANs = ~isnan(Zb_ext);
ZbDilated = ZbNANs; % this will hold the dilated shape.
% up and down neighbors
ZbDilated(2:end, :) = max(ZbDilated(2:end, :), ZbNANs(1:end-1, :));
ZbDilated(1:end-1, :) = max(ZbDilated(1:end-1, :), ZbNANs(2:end, :));
% left and right neighbors
ZbDilated(:, 2:end) = max(ZbDilated(:, 2:end), ZbNANs(:, 1:end-1));
ZbDilated(:, 1:end-1) = max(ZbDilated(:, 1:end-1), ZbNANs(:, 2:end));
% and 4 diagonal neighbors
ZbDilated(2:end, 2:end) = max(ZbDilated(2:end, 2:end), ZbNANs(1:end-1, 1:end-1));
ZbDilated(1:end-1, 2:end) = max(ZbDilated(1:end-1, 2:end), ZbNANs(2:end, 1:end-1));
ZbDilated(2:end, 1:end-1) = max(ZbDilated(2:end, 1:end-1), ZbNANs(1:end-1, 2:end));
ZbDilated(1:end-1, 1:end-1) = max(ZbDilated(1:end-1, 1:end-1), ZbNANs(2:end, 2:end));
This is a tedious way to write it, I'm sure there's a loop that can be written that is shorter, but this I think makes the intention clearer.
[Edit: Because we're dealing with a logical array here, instead of max(A,B) we could also do A | B. I'm not sure if there would be any difference in time.]
What #beaker said in a comment was to not use
mask = zeros(size(ZbNANs));
mask(i_f:i_l, j_f:j_l) = 1; % this places a 3x3 square of 1's around (i, j)
ZbDilated(i, j) = max(ZbNANs(logical(mask)));
but rather do
ZbDilated(i, j) = max(ZbNANs(i_f:i_l, j_f:j_l), [], 'all');
[Edit: Because we're dealing with a logical array here, instead of max(A,[],'all') we could also do any(A,'all'), which should be faster. See #beaker's other comment.]