// Volumetric 2D Convolution
mat conv2d(cube image, cube kernel){
dbg_assert(image.n_rows == image.n_cols);
dbg_assert(kernel.n_rows == kernel.n_cols);
dbg_assert(kernel.n_rows <= image.n_rows);
dbg_assert(kernel.n_slices == image.n_slices);
int kernel_size = kernel.n_rows;
int image_size = image.n_rows;
int result_size = image_size - kernel_size + 1;
mat result = zeros<mat>(result_size, result_size);
for(int row=0; row < result_size; row++){
for(int col=0; col < result_size; col++){
result(row, col) = accu(
image.tube(
row,
col,
row + kernel_size - 1,
col + kernel_size - 1
) % kernel
);
}
}
return(result);
}
// converts a cube to a board by filling board(i,j) with the index
// of the largest index of Q(i,j,:)
Board cube2Board(const cube& Q){
int n = Q.n_rows;
Board solvedBoard(n);
uword ix;
vec A;
for(int i = 0; i < n; i++)
for(int j = 0; j < n; j++){
A = Q.tube(i,j);
A.max(ix);
solvedBoard(i,j) = (int)ix + 1;
}
return solvedBoard;
}
void setupDX_io(cube& xio, const mat& x, const mat& xion, icube& shiftio, const unsigned numMols, const unsigned numIons, const rowvec& box)
{
rowvec x_row(DIMS);
irowvec shift_row(DIMS);
for (unsigned i1=0; i1<numIons; i1++)
for (unsigned i2=0; i2<numMols; i2++)
{
findDx(x_row, xion.row(i1), x.row(i2), box, shift_row);
xio.tube(i1,i2) = x_row;
shiftio.tube(i1,i2) = shift_row;
}
}
void setupDX(cube& xoo, cube& xio, cube& xii, mat& roo2, mat& rio2, mat& rii2, const mat& x, const mat& xion, icube& shiftoo,
icube& shiftio, icube& shiftii, const unsigned numMols, const unsigned numIons, const rowvec& box)
{
rowvec x_row(DIMS);
irowvec shift_row(DIMS);
for (unsigned i1=0; i1<numMols; i1++)
for (unsigned i2=i1+1; i2<numMols; i2++)
{
findDx(x_row, x.row(i1), x.row(i2), box, shift_row);
xoo.tube(i1,i2) = x_row;
shiftoo.tube(i1,i2) = shift_row;
xoo.tube(i2,i1) = -1.0*x_row;
shiftoo.tube(i2,i1) = -1*shift_row;
roo2(i2,i1) = roo2(i1,i2) = dot(x_row,x_row);
}
for (unsigned i1=0; i1<numIons; i1++)
{
for (unsigned i2=0; i2<numMols; i2++)
{
findDx(x_row, xion.row(i1), x.row(i2), box, shift_row);
xio.tube(i1,i2) = x_row;
shiftio.tube(i1,i2) = shift_row;
rio2(i2,i1) = rio2(i1,i2) = dot(x_row,x_row);
}
for (unsigned i2=i1+1; i2<numIons; i2++)
{
findDx(x_row, xion.row(i1), xion.row(i2), box, shift_row);
xii.tube(i1,i2) = x_row;
shiftii.tube(i1,i2) = shift_row;
xii.tube(i2,i1) = -1.0*x_row;
shiftii.tube(i2,i1) = -1*shift_row;
rii2(i2,i1) = rii2(i1,i2) = dot(x_row,x_row);
}
}
}