MATLAB Coder: Help with input matrices that are not of constant size

I have a function (with the code given below) that I wish to convert into a MEX file. I am trying to use matlab coder to do so.

    %%Inputs
    dof = 3;
    num_divs = 72;
    ind_cr =
         0     0
         1     1
         1     2
         2     2
         1     3
         2     3
         3     3
    ind_switch =
         1
         1
         1
         0
         1
         0
         0
    len_stat_atoms =
               1
              72
            5184
              72
          373248
            5184
              72
    num_stat_atoms =
       108
       111
       111
         3
       111
         3
         3
    coordFile = 
        [3x1        double]
        [3x1        double]
        [3x72x3     double]
        [3x5184x3   double]
        [3x373248x4 double]
    radii_cell = 
        [108x1x3      double]
        [111x72x3     double]
        [111x5184x3   double]
        [  3x72x3     double]
        [111x373248x4 double]
        [  3x5184x4   double]
        [  3x72x4     double]
    stat_cell = 
        [3x1x108      double]
        [3x72x111     double]
        [3x5184x111   double]
        [3x72x3       double]
        [3x373248x111 double]
        [3x5184x3     double]
        [3x72x3       double]    
    %%Code that calls function
    for i = 1:(dof*(dof+1)/2+1)
        %%Load matrices
        radii_mat = radii_cell{i,1};
        stat_mat = stat_cell{i,1};
        if ind_switch(i)
            coordFile_mat = coordFile{ind_cr(i,2)+2};
        end
        %%Call the function
        function [output] = foo(appropriate inputs)
    end
    %%Function code
    potential_mat = zeros(num_coord_atoms,num_divs^dof);
    for j = 1:size(coordFile_mat,3)
        %%Compute distances
        temp_coordFile = coordFile_mat(:,1:len_stat_atoms(i),j);
        temp_coordFile = repmat(temp_coordFile,[1 1 num_stat_atoms(i)]);
        distances = shiftdim(sqrt(sum((temp_coordFile - stat_mat).^2)),1)';
        %%Compute clashes and potentials
        clashes = distances < radii_mat(:,:,j);
        potentials = zeros(size(distances));
        potentials(clashes) = (1-(distances(clashes)./radii_mat(find(clashes)+numel(clashes)*(j-1))).^6).^2;
        %%Iterate over nodes
        col = ind_cr(i,1); row = ind_cr(i,2);
        if col == 1
            ind_kron = repmat(1:size(potentials,2),[num_divs^(dof-row) 1]);
            potentials = potentials(:,ind_kron(:)');
        elseif row == dof
            vec_repmat = [1 num_divs^(col-1)];
            potentials = repmat(potentials,vec_repmat);
        elseif col > 0
            vec_repmat = [1 num_divs^(col-1)];
            ind_kron = repmat(1:size(potentials,2),[num_divs^(dof-row) 1]);
            potentials = repmat(potentials(:,ind_kron(:)'),vec_repmat);
        else
            potentials = repmat(sum(potentials),[1 num_divs^dof]);
        end
        counter = counter+1;
        potential_mat(counter,:) = sum(potentials,1);
    end

The main problem that arises while converting the function code into MEX occurs at this line, where it throws an error because it cannot transpose an ND matrix.

    shiftdim(sqrt(sum((temp_coordFile - stat_mat).^2)),1)'

My regular matlab function works fine, and I believe the above error occurs because, when I use the 'autodefine types' GUI option, Coder imposes upper bounds and uses these max bounds to compute the sizes of the intermediary variables.

    coordFile_mat  double (3 x :373248 x :4) 
    radii_mat      double (:111 x :373248 x :4) 
    stat_mat       double (3 x :373248 x :111)

I think using these variable sizes gives rise to the transpose error. I want Coder to use the dimensions at a given instance, i.e.

    temp_coordFile =            radii_mat =                  stat_mat = 
        [3x1x108      double]        [108x1x3      double]         [3x1x108      double]
        [3x72x111     double]        [111x72x3     double]         [3x72x111     double]
        [3x5184x111   double]        [111x5184x3   double]         [3x5184x111   double]
        [3x72x3       double]        [  3x72x3     double]         [3x72x3       double]
        [3x373248x111 double]        [111x373248x4 double]         [3x373248x111 double]
        [3x5184x3     double]        [  3x5184x4   double]         [3x5184x3     double]
        [3x72x3       double]        [  3x72x4     double]         [3x72x3       double]

and not the max bounds. Is there any way to resolve this issue? If so, can you provide clear instructions/examples using my code? Thanks!

[Geoff Hayes]

Alejandro - it may be helpful to include the error message that is being thrown.

Answer 1

[Fred Smith]

Alejandro,

The problem is most likely not the upper bounds but rather the number of dimensions. Without the specific error message it is hard to be sure. If you know one of the dimensions has a single element but MATLAB Coder does not you can use indexing to force the number of dimensions to drop: A(:,:,1).

Hope this helps,

Fred