mex - matlab coder: cannot transpose a matrix that is incorrectly deemed to be 3-D when it should always be 2-D -

mex - matlab coder: cannot transpose a matrix that is incorrectly deemed to be 3-D when it should always be 2-D -

i have function (with code given below) wish convert mex file. trying utilize matlab coder 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 calls function = 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 %% phone call function potential_mat = func_test(i,coordfile_mat,radii_mat,stat_mat,... ind_cr,len_stat_atoms,num_stat_atoms,num_coord_atoms,... counter,num_divs,dof); end %% function code function potential_mat = func_test(i,coordfile_mat,radii_mat,stat_mat,... ind_cr,len_stat_atoms,num_stat_atoms,num_coord_atoms,... counter,num_divs,dof); potential_mat = zeros(num_coord_atoms,num_divs^dof); j = 1:size(coordfile_mat,3) %% compute distances = zeros(3,len_stat_atoms(i)); = coordfile_mat(:,1:len_stat_atoms(i),j); b = zeros(3,len_stat_atoms(i),num_stat_atoms(i)); b = repmat(a,[1 1 num_stat_atoms(i)]); c = zeros(1,len_stat_atoms(i),num_stat_atoms(i)); c = sqrt(sum((b - stat_mat).^2,1)); d = zeros(len_stat_atoms(i),num_stat_atoms(i)); d = shiftdim(c,1); distances = zeros(num_stat_atoms(i),len_stat_atoms(i)); distances = d'; %% compute clashes , 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 on 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 end

the problem occurs @ sec line below, throws error because cannot transpose nd matrix.

d = shiftdim(c,1); distances = d';

matlab coder identifies c of size 1 x :? x :?, correct. d = shiftdim(c,1) line should yield 2d matrix of size :? x :?, transpose. however, fails correctly shift dimensions of d, , gives size of :? x :? x :?. causes transpose error. how can resolve problem? furthermore, own edification, why matlab coder unable correctly assign dimensions of variables, a, b, c, d, , distances?

the docs describe incompatibility matlab in determining size of variable-size n-d arrays (d created in loop, seems variable size):

for variable-size n-d arrays, size function can homecoming different result in generated code in matlab. in generated code, size(a) returns fixed-length output because it not drop trailing singleton dimensions of variable-size n-d arrays. contrast, size(a) in matlab returns variable-length output because drops trailing singleton dimensions.

for example, if shape of array a :?x:?x:? , size(a,3)==1, size(a) returns:

three-element vector in generated code two-element vector in matlab code

the issue addressed in above documentation pertains utilize of size function. however, in case, want able transpose. workaround utilize permute, since transpose general case of permute:

% after shiftdim: distances = permute(d,[2 1 3]) % same d' 2d array, handles 3d

you cutting out shiftdim entirely:

distances = permute(c,[2 3 1])

also, don't have much experience coder, require initializations zeros? seem unnecessary.

mex matlab-coder