void
test_transpose_readonly(MatrixT view)
{
typedef typename MatrixT::value_type T;
// Check that view is initialized
check_matrix(view, 0);
length_type const size1 = view.size(1);
typename MatrixT::const_transpose_type trans = view.transpose();
test_assert(trans.size(0) == view.size(1));
test_assert(trans.size(1) == view.size(0));
for (index_type idx0=0; idx0<trans.size(0); ++idx0)
for (index_type idx1=0; idx1<trans.size(1); ++idx1)
{
T expected = T(idx1 * size1 + idx0 + 0);
test_assert(equal(trans.get(idx0, idx1), expected));
test_assert(equal(trans.get(idx0, idx1),
view. get(idx1, idx0)));
}
// Check that view is unchanged
check_matrix(view, 0);
}
void convolute_3d_out_of_place(MatrixT& _image, MatrixT& _kernel) {
if (_image.size() != _kernel.size()) {
std::cerr << "received image and kernel of mismatching size!\n";
return;
}
unsigned M, N, K;
M = _image.shape()[0];
N = _image.shape()[1];
K = _image.shape()[2];
unsigned fft_size = M * N * (K / 2 + 1);
// setup fourier space arrays
fftwf_complex* image_fourier = static_cast<fftwf_complex*>(
fftwf_malloc(sizeof(fftwf_complex) * fft_size));
fftwf_complex* kernel_fourier = static_cast<fftwf_complex*>(
fftwf_malloc(sizeof(fftwf_complex) * fft_size));
float scale = 1.0 / (M * N * K);
// define+run forward plans
fftwf_plan image_fwd_plan = fftwf_plan_dft_r2c_3d(
M, N, K, _image.data(), image_fourier, FFTW_ESTIMATE);
fftwf_execute(image_fwd_plan);
fftwf_plan kernel_fwd_plan = fftwf_plan_dft_r2c_3d(
M, N, K, _kernel.data(), kernel_fourier, FFTW_ESTIMATE);
fftwf_execute(kernel_fwd_plan);
// multiply
for (unsigned index = 0; index < fft_size; ++index) {
float real = image_fourier[index][0] * kernel_fourier[index][0] -
image_fourier[index][1] * kernel_fourier[index][1];
float imag = image_fourier[index][0] * kernel_fourier[index][1] +
image_fourier[index][1] * kernel_fourier[index][0];
image_fourier[index][0] = real;
image_fourier[index][1] = imag;
}
fftwf_destroy_plan(kernel_fwd_plan);
fftwf_destroy_plan(image_fwd_plan);
fftwf_plan image_rev_plan = fftwf_plan_dft_c2r_3d(
M, N, K, image_fourier, _image.data(), FFTW_ESTIMATE);
fftwf_execute(image_rev_plan);
for (unsigned index = 0; index < _image.num_elements(); ++index) {
_image.data()[index] *= scale;
}
fftwf_destroy_plan(image_rev_plan);
fftwf_free(image_fourier);
fftwf_free(kernel_fourier);
}
void
fill_matrix(MatrixT view, int offset=0)
{
typedef typename MatrixT::value_type T;
length_type const size1 = view.size(1);
// Initialize view
for (index_type idx0=0; idx0<view.size(0); ++idx0)
for (index_type idx1=0; idx1<view.size(1); ++idx1)
view.put(idx0, idx1, T(idx0 * size1 + idx1 + offset));
}
void
check_matrix(MatrixT view, int offset=0)
{
typedef typename MatrixT::value_type T;
length_type const size1 = view.size(1);
for (index_type idx0=0; idx0<view.size(0); ++idx0)
for (index_type idx1=0; idx1<view.size(1); ++idx1)
{
test_assert(equal(view.get(idx0, idx1),
T(idx0 * size1 + idx1 + offset)));
}
}
void nodes_of_strongly_connected_component(MatrixT const & matrix,
std::vector<IndexT> & node_list)
{
std::vector<bool> node_visited_already(matrix.size(), false);
std::deque<IndexT> node_queue;
//
// Step 1: Push root nodes to queue:
//
for (typename std::vector<IndexT>::iterator it = node_list.begin();
it != node_list.end();
it++)
{
node_queue.push_back(*it);
}
node_list.resize(0);
//
// Step 2: Fill with remaining nodes of strongly connected compontent
//
while (!node_queue.empty())
{
vcl_size_t node_id = static_cast<vcl_size_t>(node_queue.front());
node_queue.pop_front();
if (!node_visited_already[node_id])
{
node_list.push_back(IndexT(node_id));
node_visited_already[node_id] = true;
for (typename MatrixT::value_type::const_iterator it = matrix[node_id].begin();
it != matrix[node_id].end();
it++)
{
vcl_size_t neighbor_node_id = static_cast<vcl_size_t>(it->first);
if (neighbor_node_id == node_id) continue;
if (node_visited_already[neighbor_node_id]) continue;
node_queue.push_back(IndexT(neighbor_node_id));
}
}
}
}
void generate_layering(MatrixT const & matrix,
std::vector< std::vector<IndexT> > & layer_list)
{
std::vector<bool> node_visited_already(matrix.size(), false);
//
// Step 1: Set root nodes to visited
//
for (vcl_size_t i=0; i<layer_list.size(); ++i)
{
for (typename std::vector<IndexT>::iterator it = layer_list[i].begin();
it != layer_list[i].end();
it++)
node_visited_already[*it] = true;
}
//
// Step 2: Fill next layers
//
while (layer_list.back().size() > 0)
{
vcl_size_t layer_index = layer_list.size(); //parent nodes are at layer 0
layer_list.push_back(std::vector<IndexT>());
for (typename std::vector<IndexT>::iterator it = layer_list[layer_index].begin();
it != layer_list[layer_index].end();
it++)
{
for (typename MatrixT::value_type::const_iterator it2 = matrix[*it].begin();
it2 != matrix[*it].end();
it2++)
{
if (it2->first == *it) continue;
if (node_visited_already[it2->first]) continue;
layer_list.back().push_back(it2->first);
node_visited_already[it2->first] = true;
}
}
}
// remove last (empty) nodelist:
layer_list.resize(layer_list.size()-1);
}
unsigned nrow(const MatrixT& mat) {
return mat.size();
}
void convolute_3d_in_place(MatrixT& _image, const MatrixT& _kernel,
const bool& _verbose = false) {
if (_image.size() == _kernel.size()) {
std::cerr << "received image and kernel of matching size, this makes "
"preparing the kernel impossible!\nExiting.\n";
return;
}
if (MatrixT::dimensionality != 3) {
std::cerr << "received image and kernel of dimension "
<< MatrixT::dimensionality
<< " that cannot be processed by convolute_3d_in_place!\n";
return;
}
std::vector<unsigned> origin_image_extents(MatrixT::dimensionality);
std::copy(_image.shape(), _image.shape() + MatrixT::dimensionality,
origin_image_extents.begin());
std::vector<unsigned> origin_kernel_extents(MatrixT::dimensionality);
std::copy(_kernel.shape(), _kernel.shape() + MatrixT::dimensionality,
origin_kernel_extents.begin());
if (_verbose) {
std::cout << "[convolute_3d_in_place]\timage:\n" << _image << "\n";
std::cout << "[convolute_3d_in_place]\tkernel:\n" << _kernel << "\n";
}
///////////////////////////////////////////////////////////////////////////
// CALCULATE PADDING EXTENT
std::vector<unsigned> common_extents(MatrixT::dimensionality);
std::transform(origin_image_extents.begin(), origin_image_extents.end(),
origin_kernel_extents.begin(), common_extents.begin(),
add_minus_1<unsigned>());
std::vector<unsigned> common_offsets(MatrixT::dimensionality);
std::transform(origin_kernel_extents.begin(), origin_kernel_extents.end(),
common_offsets.begin(), minus_1_div_2<unsigned>());
///////////////////////////////////////////////////////////////////////////
// PADD IMAGE
image_stack padded_image(common_extents, _image.storage_order());
image_stack_view subview_padded_image = padded_image
[boost::indices[range(common_offsets[0],
common_offsets[0] + origin_image_extents[0])]
[range(common_offsets[1],
common_offsets[1] + origin_image_extents[1])]
[range(common_offsets[2],
common_offsets[2] + origin_image_extents[2])]];
subview_padded_image = _image;
unsigned long size_of_transform = padded_image.num_elements();
///////////////////////////////////////////////////////////////////////////
// PADD KERNEL
image_stack padded_kernel(common_extents, _kernel.storage_order());
for (long z = 0; z < origin_kernel_extents[2]; ++z)
for (long y = 0; y < origin_kernel_extents[1]; ++y)
for (long x = 0; x < origin_kernel_extents[0]; ++x) {
long intermediate_x = x - origin_kernel_extents[0] / 2L;
long intermediate_y = y - origin_kernel_extents[1] / 2L;
long intermediate_z = z - origin_kernel_extents[2] / 2L;
intermediate_x = (intermediate_x < 0)
? intermediate_x + common_extents[0]
: intermediate_x;
intermediate_y = (intermediate_y < 0)
? intermediate_y + common_extents[1]
: intermediate_y;
intermediate_z = (intermediate_z < 0)
? intermediate_z + common_extents[2]
: intermediate_z;
padded_kernel[intermediate_x][intermediate_y][intermediate_z] =
_kernel[x][y][z];
}
///////////////////////////////////////////////////////////////////////////
// RESIZE ALL TO ALLOW FFTW INPLACE TRANSFORM
std::vector<unsigned> inplace_extents(3);
adapt_extents_for_fftw_inplace(common_extents, inplace_extents,
_image.storage_order());
padded_image.resize(boost::extents[inplace_extents[0]][inplace_extents[1]]
[inplace_extents[2]]);
padded_kernel.resize(boost::extents[inplace_extents[0]][inplace_extents[1]]
[inplace_extents[2]]);
if (_verbose) {
std::cout << "[convolute_3d_in_place]\t padded image:\n" << padded_image
<< "\n";
std::cout << "[convolute_3d_in_place]\t padded kernel:\n" << padded_kernel
<< "\n";
}
float scale = 1.0 / (size_of_transform);
fftwf_complex* complex_image_fourier = (fftwf_complex*)padded_image.data();
fftwf_complex* complex_kernel_fourier = (fftwf_complex*)padded_kernel.data();
// define+run forward plans
fftwf_plan image_fwd_plan = fftwf_plan_dft_r2c_3d(
common_extents[0], common_extents[1], common_extents[2],
padded_image.data(), complex_image_fourier, FFTW_ESTIMATE);
fftwf_execute(image_fwd_plan);
fftwf_plan kernel_fwd_plan = fftwf_plan_dft_r2c_3d(
common_extents[0], common_extents[1], common_extents[2],
padded_kernel.data(), complex_kernel_fourier, FFTW_ESTIMATE);
fftwf_execute(kernel_fwd_plan);
fftwf_destroy_plan(kernel_fwd_plan);
fftwf_destroy_plan(image_fwd_plan);
// multiply
unsigned fourier_num_elements = padded_image.num_elements() / 2;
for (unsigned index = 0; index < fourier_num_elements; ++index) {
float real =
complex_image_fourier[index][0] * complex_kernel_fourier[index][0] -
complex_image_fourier[index][1] * complex_kernel_fourier[index][1];
float imag =
complex_image_fourier[index][0] * complex_kernel_fourier[index][1] +
complex_image_fourier[index][1] * complex_kernel_fourier[index][0];
complex_image_fourier[index][0] = real;
complex_image_fourier[index][1] = imag;
}
fftwf_plan image_rev_plan = fftwf_plan_dft_c2r_3d(
common_extents[0], common_extents[1], common_extents[2],
complex_image_fourier, padded_image.data(), FFTW_ESTIMATE);
fftwf_execute(image_rev_plan);
for (unsigned index = 0; index < padded_image.num_elements(); ++index) {
padded_image.data()[index] *= scale;
}
fftwf_destroy_plan(image_rev_plan);
_image = padded_image
[boost::indices[range(common_offsets[0],
common_offsets[0] + origin_image_extents[0])]
[range(common_offsets[1],
common_offsets[1] + origin_image_extents[1])]
[range(common_offsets[2],
common_offsets[2] + origin_image_extents[2])]];
if (_verbose) {
std::cout << "[convolute_3d_in_place]\t padded result:\n" << padded_image
<< "\n";
std::cout << "[convolute_3d_in_place]\t result:\n" << _image << "\n";
}
}