void wotreplay::read_png(std::istream &is, boost::multi_array<uint8_t, 3> &image) {
png_structp png_ptr = png_create_read_struct(PNG_LIBPNG_VER_STRING, nullptr, nullptr, nullptr);
png_infop info_ptr = png_create_info_struct(png_ptr);
png_infop end_info = png_create_info_struct(png_ptr);
if (setjmp(png_jmpbuf(png_ptr))) {
png_destroy_read_struct(&png_ptr, &info_ptr, &end_info);
return;
}
png_set_read_fn(png_ptr, &is, &user_read_data);
png_read_info(png_ptr, info_ptr);
int width = png_get_image_width(png_ptr, info_ptr);
int height = png_get_image_height(png_ptr, info_ptr);
png_byte color_type = png_get_color_type(png_ptr, info_ptr);
if (color_type == PNG_COLOR_TYPE_RGB) {
// add alpha channel
png_set_add_alpha(png_ptr, 0xff, PNG_FILLER_AFTER);
} else if (color_type == PNG_COLOR_TYPE_RGB_ALPHA) {
// do nothing extra
} else {
throw std::runtime_error("Unsupported image type");
}
image.resize(boost::extents[height][width][4]);
std::vector<png_bytep> row_pointers;
get_row_pointers(image, row_pointers);
png_read_image(png_ptr, &row_pointers[0]);
png_read_end(png_ptr, info_ptr);
}
//-----------------------------------------------------------------------------
void DofMap::tabulate_coordinates(boost::multi_array<double, 2>& coordinates,
const ufc::cell& ufc_cell) const
{
// FIXME: This is a hack because UFC wants a double pointer for coordinates
dolfin_assert(_ufc_dofmap);
// Check dimensions
if (coordinates.shape()[0] != cell_dimension(ufc_cell.index) ||
coordinates.shape()[1] != _ufc_dofmap->geometric_dimension())
{
boost::multi_array<double, 2>::extent_gen extents;
const std::size_t cell_dim = cell_dimension(ufc_cell.index);
coordinates.resize(extents[cell_dim][_ufc_dofmap->geometric_dimension()]);
}
// Set vertex coordinates
const std::size_t num_points = coordinates.size();
std::vector<double*> coords(num_points);
for (std::size_t i = 0; i < num_points; ++i)
coords[i] = &(coordinates[i][0]);
// Tabulate coordinates
_ufc_dofmap->tabulate_coordinates(coords.data(),
&ufc_cell.vertex_coordinates[0]);
}
void load(input_archive& ar, boost::multi_array<T, N, Allocator>& marray, unsigned)
{
boost::array<std::size_t, N> shape;
ar & shape;
marray.resize(shape);
ar & make_array(marray.data(), marray.num_elements());
}
//-----------------------------------------------------------------------------
void HexahedronCell::create_entities(boost::multi_array<unsigned int, 2>& e,
std::size_t dim, const unsigned int* v) const
{
// We need to know how to create edges and faces
switch (dim)
{
case 1:
// Resize data structure
e.resize(boost::extents[12][2]);
// Create the 12 edges
e[0][0] = v[0]; e[0][1] = v[1];
e[1][0] = v[2]; e[1][1] = v[3];
e[2][0] = v[4]; e[2][1] = v[5];
e[3][0] = v[6]; e[3][1] = v[7];
e[4][0] = v[0]; e[4][1] = v[2];
e[5][0] = v[1]; e[5][1] = v[3];
e[6][0] = v[4]; e[6][1] = v[6];
e[7][0] = v[5]; e[7][1] = v[7];
e[8][0] = v[0]; e[8][1] = v[4];
e[9][0] = v[1]; e[9][1] = v[5];
e[10][0] = v[2]; e[10][1] = v[6];
e[11][0] = v[3]; e[11][1] = v[7];
break;
case 2:
// Resize data structure
e.resize(boost::extents[6][4]);
// Create the 6 faces
e[0][0] = v[0]; e[0][1] = v[2]; e[0][2] = v[4]; e[0][3] = v[6];
e[1][0] = v[1]; e[1][1] = v[3]; e[1][2] = v[5]; e[1][3] = v[7];
e[2][0] = v[0]; e[2][1] = v[1]; e[2][2] = v[4]; e[2][3] = v[5];
e[3][0] = v[2]; e[3][1] = v[3]; e[3][2] = v[6]; e[3][3] = v[7];
e[4][0] = v[0]; e[4][1] = v[1]; e[4][2] = v[2]; e[4][3] = v[3];
e[5][0] = v[4]; e[5][1] = v[5]; e[5][2] = v[6]; e[5][3] = v[7];
break;
default:
dolfin_error("HexahedronCell.cpp",
"create entities of tetrahedron cell",
"Don't know how to create entities of topological dimension %d", dim);
}
}
//-----------------------------------------------------------------------------
void IntervalCell::create_entities(boost::multi_array<unsigned int, 2>& e,
std::size_t dim, const unsigned int* v) const
{
// For completeness, IntervalCell has two 'edges'
dolfin_assert(dim == 0);
// Resize data structure
e.resize(boost::extents[2][1]);
// Create the three edges
e[0][0] = v[0]; e[1][0] = v[1];
}
void compute_Tnl_legendre(int n_matsubara, int n_legendre, boost::multi_array<std::complex<double>,2> &Tnl) {
double sign_tmp = 1.0;
Tnl.resize(boost::extents[n_matsubara][n_legendre]);
for (int im = 0; im < n_matsubara; ++im) {
std::complex<double> ztmp(0.0, 1.0);
for (int il = 0; il < n_legendre; ++il) {
Tnl[im][il] = sign_tmp * ztmp * std::sqrt(2 * il + 1.0) * boost::math::sph_bessel(il, 0.5 * (2 * im + 1) * M_PI);
ztmp *= std::complex<double>(0.0, 1.0);
}
sign_tmp *= -1;
}
}
void precompute(double distance, double scalex, double scaley)
{
double const radius2 = distance * distance;
width = 2* ceil(distance / scalex) + 1;
height = 2* ceil(distance / scaley) + 1;
in_distance.resize(boost::extents[height][width]);
std::fill(in_distance.data(), in_distance.data() + in_distance.num_elements(), false);
parents.resize(boost::extents[height][width]);
std::fill(parents.data(), parents.data() + parents.num_elements(), std::make_pair(-1, -1));
centerx = width / 2;
centery = height / 2;
parents[centery][centerx] = std::make_pair(-1, -1);
for (unsigned int y = 0; y < height; ++y)
{
for (unsigned int x = 0; x < width; ++x)
{
int dx = (centerx - x);
int dy = (centery - y);
if (dx == 0 && dy == 0) continue;
double d2 = dx * dx * scalex * scalex + dy * dy * scaley * scaley;
in_distance[y][x] = (d2 < radius2);
if (abs(dx) > abs(dy))
{
int parentx = x + dx / abs(dx);
int parenty = y + rint(static_cast<double>(dy) / abs(dx));
parents[y][x] = std::make_pair(parentx, parenty);
}
else
{
int parentx = x + rint(static_cast<double>(dx) / abs(dy));
int parenty = y + dy / abs(dy);
parents[y][x] = std::make_pair(parentx, parenty);
}
}
}
}
void load( Archive & ar,
boost::multi_array<double,2> & t,
const unsigned int file_version )
{
typedef boost::multi_array<double,2> multi_array_;
typedef typename multi_array_::size_type size_;
size_ n0;
ar >> BOOST_SERIALIZATION_NVP( n0 );
size_ n1;
ar >> BOOST_SERIALIZATION_NVP( n1 );
t.resize( boost::extents[n0][n1] );
ar >> make_array( t.data(), t.num_elements() );
}
void
resize_from_MultiArray(boost::multi_array<T,N>& marray, U& other) {
// U must be a model of MultiArray
boost::function_requires<
boost::multi_array_concepts::ConstMultiArrayConcept<U,U::dimensionality> >();
// U better have U::dimensionality == N
BOOST_STATIC_ASSERT(U::dimensionality == N);
boost::array<typename boost::multi_array<T,N>::size_type, N> shape;
std::copy(other.shape(), other.shape()+N, shape.begin());
marray.resize(shape);
}
//-----------------------------------------------------------------------------
void TriangleCell::create_entities(boost::multi_array<unsigned int, 2>& e,
std::size_t dim, const unsigned int* v) const
{
// We only need to know how to create edges
if (dim != 1)
{
dolfin_error("TriangleCell.cpp",
"create entities of triangle cell",
"Don't know how to create entities of topological dimension %d", dim);
}
// Resize data structure
e.resize(boost::extents[3][2]);
// Create the three edges
e[0][0] = v[1]; e[0][1] = v[2];
e[1][0] = v[0]; e[1][1] = v[2];
e[2][0] = v[0]; e[2][1] = v[1];
}
void wotreplay::resize(boost::multi_array<uint8_t, 3> &original, int width, int height, boost::multi_array<uint8_t, 3> &result) {
const size_t *shape = original.shape();
result.resize(boost::extents[height][width][shape[2]]);
float ty = ((float) shape[0] / height);
float tx = ((float) shape[1] / width);
for (int y = 0; y < height; ++y) {
for (int x = 0; x < width; ++x) {
int xx = (int) (tx * x);
int yy = (int) (ty * y);
float dx = (tx * x) - xx;
float dy = (ty * y) - yy;
for (int c = 0; c < shape[2]; ++c) {
result[y][x][c] = original[yy][xx][c]*(1-dy)*(1-dx) +
original[std::min(yy + 1, (int) shape[0] - 1)][xx][c]*dy*(1-dx) +
original[std::min(yy + 1, (int) shape[0] - 1)][std::min(xx + 1, (int) shape[1] - 1)][c]*dy*dx +
original[yy][std::min(xx + 1, (int) shape[1] - 1)][c]*(1-dy)*dx;
}
}
}
}
int main(int argc, char** argv){
ParseCommandLine(argc, argv);
ParseConfigFile(config_filename);
volume.resize(boost::extents[D][H][W]);
FILE* in = fopen(input_filename.c_str(), "r+b");
short *buff = new short[W];
for(int k=0; k<D; k++){
for(int j=0; j<H; j++){
fread(buff, W, sizeof(short), in);
for(int i=0; i<W; i++){
volume[k][j][i] = (float)buff[i];// -(float)log((double)buff[i]);
}
}
}
fclose(in);
string basename = split(input_filename, ".").at(0);
std::ofstream ofs;
ofs.open((basename + ".inr").c_str(), std::ios::binary);
stringstream header;
std::string headerEND = "##}\n";
//Header
header << "#INRIMAGE-4#{" << endl;
header << "XDIM="<< W << endl;
header << "YDIM="<< H << endl;
header << "ZDIM="<< D << endl;
header << "VDIM=" << 1 << endl;
header << "VX=" << VX << endl;
header << "VY=" << VY << endl;
header << "VZ=" << VZ << endl;
header << "TYPE=float" <<endl;
header << "PIXSIZE=" << pixel_size << " bits" << endl;
header << "CPU=decm" << endl;
int hlen = 256 - header.str().length() - headerEND.length();
for(int i=0; i<hlen; i++){
header << "\n";
}
header << headerEND;
ofs.write(header.str().c_str(), header.str().size());
float *buf = new float[W];
for(int i=0; i<D; i++){
for(int j=0; j<H; j++){
for(int k=0; k<W; k++){
//ofs << volume[i][j][k];
//buf[k] = volume[i][j][k];
ofs.write((char*)&volume[i][j][k], sizeof(float));
}
}
}
ofs.close();
}
//-----------------------------------------------------------------------------
void MeshPartitioning::distribute_vertices(const LocalMeshData& mesh_data,
const boost::multi_array<std::size_t, 2>& cell_vertices,
std::vector<std::size_t>& vertex_indices,
std::map<std::size_t, std::size_t>& vertex_global_to_local,
boost::multi_array<double, 2>& vertex_coordinates)
{
// This function distributes all vertices (coordinates and
// local-to-global mapping) according to the cells that are stored on
// each process. This happens in several stages: First each process
// figures out which vertices it needs (by looking at its cells)
// and where those vertices are located. That information is then
// distributed so that each process learns where it needs to send
// its vertices.
// Get number of processes
const std::size_t num_processes = MPI::num_processes();
// Get geometric dimension
const std::size_t gdim = mesh_data.gdim;
// Compute which vertices we need
std::set<std::size_t> needed_vertex_indices;
boost::multi_array<std::size_t, 2>::const_iterator vertices;
for (vertices = cell_vertices.begin(); vertices != cell_vertices.end();
++vertices)
{
needed_vertex_indices.insert(vertices->begin(), vertices->end());
}
// Compute where (process number) the vertices we need are located
std::vector<std::vector<std::size_t> > send_vertex_indices(num_processes);
std::vector<std::vector<std::size_t> > vertex_location(num_processes);
std::set<std::size_t>::const_iterator required_vertex;
for (required_vertex = needed_vertex_indices.begin();
required_vertex != needed_vertex_indices.end(); ++required_vertex)
{
// Get process that has required vertex
const std::size_t location
= MPI::index_owner(*required_vertex, mesh_data.num_global_vertices);
send_vertex_indices[location].push_back(*required_vertex);
vertex_location[location].push_back(*required_vertex);
}
// Send required vertices to other processes, and receive back vertices
// required by other processes.
std::vector<std::vector<std::size_t> > received_vertex_indices;
MPI::all_to_all(send_vertex_indices, received_vertex_indices);
// Distribute vertex coordinates
std::vector<std::vector<double> > send_vertex_coordinates(num_processes);
const std::pair<std::size_t, std::size_t> local_vertex_range
= MPI::local_range(mesh_data.num_global_vertices);
for (std::size_t p = 0; p < num_processes; ++p)
{
send_vertex_coordinates[p].reserve(received_vertex_indices[p].size()*gdim);
for (std::size_t i = 0; i < received_vertex_indices[p].size(); ++i)
{
dolfin_assert(received_vertex_indices[p][i] >= local_vertex_range.first
&& received_vertex_indices[p][i] < local_vertex_range.second);
const std::size_t location
= received_vertex_indices[p][i] - local_vertex_range.first;
for (std::size_t j = 0; j < gdim; ++j)
send_vertex_coordinates[p].push_back(mesh_data.vertex_coordinates[location][j]);
}
}
std::vector<std::vector<double> > received_vertex_coordinates;
MPI::all_to_all(send_vertex_coordinates, received_vertex_coordinates);
// Set index counters to first position in receive buffers
std::vector<std::size_t> index_counters(num_processes, 0);
// Clear data
vertex_indices.clear();
vertex_global_to_local.clear();
// Count number of local vertices
std::size_t num_local_vertices = 0;
for (std::size_t p = 0; p < num_processes; ++p)
num_local_vertices += received_vertex_coordinates[p].size()/gdim;
// Store coordinates and construct global to local mapping
vertex_coordinates.resize(boost::extents[num_local_vertices][gdim]);
vertex_indices.resize(num_local_vertices);
std::size_t v = 0;
for (std::size_t p = 0; p < num_processes; ++p)
{
for (std::size_t i = 0; i < received_vertex_coordinates[p].size();
i += gdim)
{
for (std::size_t j = 0; j < gdim; ++j)
vertex_coordinates[v][j] = received_vertex_coordinates[p][i + j];
const std::size_t global_vertex_index
= vertex_location[p][index_counters[p]++];
vertex_global_to_local[global_vertex_index] = v;
vertex_indices[v] = global_vertex_index;
++v;
}
}
}
//-----------------------------------------------------------------------------
void MeshPartitioning::distribute_cells(const LocalMeshData& mesh_data,
const std::vector<std::size_t>& cell_partition,
std::vector<std::size_t>& global_cell_indices,
boost::multi_array<std::size_t, 2>& cell_vertices)
{
// This function takes the partition computed by the partitioner
// (which tells us to which process each of the local cells stored in
// LocalMeshData on this process belongs. We use MPI::all_to_all to
// redistribute all cells (the global vertex indices of all cells).
// Number of MPI processes
const std::size_t num_processes = MPI::num_processes();
// Get dimensions of local mesh_data
const std::size_t num_local_cells = mesh_data.cell_vertices.size();
dolfin_assert(mesh_data.global_cell_indices.size() == num_local_cells);
const std::size_t num_cell_vertices = mesh_data.num_vertices_per_cell;
if (!mesh_data.cell_vertices.empty())
{
if (mesh_data.cell_vertices[0].size() != num_cell_vertices)
{
dolfin_error("MeshPartitioning.cpp",
"distribute cells",
"Mismatch in number of cell vertices (%d != %d) on process %d",
mesh_data.cell_vertices[0].size(), num_cell_vertices,
MPI::process_number());
}
}
// Build array of cell-vertex connectivity and partition vector
// Distribute the global cell number as well
std::vector<std::vector<std::size_t> > send_cell_vertices(num_processes);
for (std::size_t i = 0; i < num_local_cells; i++)
{
const std::size_t dest = cell_partition[i];
send_cell_vertices[dest].push_back(mesh_data.global_cell_indices[i]);
for (std::size_t j = 0; j < num_cell_vertices; j++)
send_cell_vertices[dest].push_back(mesh_data.cell_vertices[i][j]);
}
// Distribute cell-vertex connectivity
std::vector<std::vector<std::size_t> > received_cell_vertices(num_processes);
MPI::all_to_all(send_cell_vertices, received_cell_vertices);
// Count number of received cells
std::size_t num_new_local_cells = 0;
for (std::size_t p = 0; p < received_cell_vertices.size(); ++p)
{
num_new_local_cells
+= received_cell_vertices[p].size()/(num_cell_vertices + 1);
}
// Put mesh_data back into mesh_data.cell_vertices
cell_vertices.resize(boost::extents[num_new_local_cells][num_cell_vertices]);
global_cell_indices.resize(num_new_local_cells);
// Loop over new cells
std::size_t c = 0;
for (std::size_t p = 0; p < num_processes; ++p)
{
for (std::size_t i = 0; i < received_cell_vertices[p].size();
i += (num_cell_vertices + 1))
{
global_cell_indices[c] = received_cell_vertices[p][i];
for (std::size_t j = 0; j < num_cell_vertices; ++j)
cell_vertices[c][j] = received_cell_vertices[p][i + 1 + j];
++c;
}
}
}
void Octtree::find_cell_ranks( const boost::multi_array<Real,2>& coordinates, std::vector<Uint>& ranks )
{
ranks.resize(coordinates.size());
Handle< Elements > element_component;
Uint element_idx;
std::deque<Uint> missing_cells;
RealVector dummy(m_dim);
for(Uint i=0; i<coordinates.size(); ++i)
{
for (Uint d=0; d<m_dim; ++d)
dummy[d] = coordinates[i][d];
if( find_element(dummy,element_component,element_idx) )
{
ranks[i] = Comm::instance().rank();
}
else
{
ranks[i] = math::Consts::uint_max();
missing_cells.push_back(i);
}
}
std::vector<Real> send_coords(m_dim*missing_cells.size());
std::vector<Real> recv_coords;
Uint c(0);
boost_foreach(const Uint i, missing_cells)
{
for(Uint d=0; d<m_dim; ++d)
send_coords[c++]=coordinates[i][d];
}
for (Uint root=0; root<PE::Comm::instance().size(); ++root)
{
recv_coords.resize(0);
PE::Comm::instance().broadcast(send_coords,recv_coords,root,m_dim);
// size is only because it doesn't get resized for this rank
std::vector<Uint> send_found(missing_cells.size(),math::Consts::uint_max());
if (root!=Comm::instance().rank())
{
std::vector<RealVector> recv_coordinates(recv_coords.size()/m_dim) ;
boost_foreach(RealVector& realvec, recv_coordinates)
realvec.resize(m_dim);
c=0;
for (Uint i=0; i<recv_coordinates.size(); ++i)
{
for(Uint d=0; d<m_dim; ++d)
recv_coordinates[i][d]=recv_coords[c++];
}
send_found.resize(recv_coordinates.size());
for (Uint i=0; i<recv_coordinates.size(); ++i)
{
if( find_element(recv_coordinates[i],element_component,element_idx) )
{
send_found[i] = Comm::instance().rank();
}
else
send_found[i] = math::Consts::uint_max();
}
}
std::vector<Uint> recv_found(missing_cells.size()*Comm::instance().size());
PE::Comm::instance().gather(send_found,recv_found,root);
if( root==Comm::instance().rank())
{
const Uint stride = missing_cells.size();
for (Uint i=0; i<missing_cells.size(); ++i)
{
for(Uint p=0; p<Comm::instance().size(); ++p)
{
ranks[missing_cells[i]] = std::min(recv_found[i+p*stride] , ranks[missing_cells[i]]);
}
}
}
}
}
