/**
* @brief FFT shift
*
* @param m TO be shifted
* @return Shifted
*/
template <class T> inline Matrix<T>
fftshift (const Matrix<T>& m, const bool& fw = true) {
assert (isvec(m) || is2d(m) || is3d(m));
Matrix<size_t> tmp = resize(size(m),ndims(m),1);
for (size_t i = 0; i<ndims(m); i++)
if (tmp[i] == 0)
tmp[i] = 1;
container<size_t> d = tmp.Container(); // data side lengths
container<size_t> c = floor(tmp/2).Container(); // center coords
Matrix<T> res (vsize(m));
size_t oi[3];
size_t si[3];
for (oi[0] = 0; oi[0] < d[0]; oi[0]++) {
si[0] = (oi[0] + c[0]) % d[0];
for (oi[1] = 0; oi[1] < d[1]; oi[1]++) {
si[1] = (oi[1] + c[1]) % d[1];
for (oi[2] = 0; oi[2] < d[2]; oi[2]++) {
si[2] = (oi[2] + c[2]) % d[2];
if (fw)
res(si[0],si[1],si[2]) = m(oi[0],oi[1],oi[2]);
else
res(oi[0],oi[1],oi[2]) = m(si[0],si[1],si[2]);
}
}
}
return res;
}
mxArray* KDTree::to_matlab_matrix(){
/// Create an empty 1x1 struct
const char* fieldnames[] = {"points", "nodes"};
mxArray* matstruct = mxCreateStructMatrix(1,1,2,fieldnames);
/// Sticks datapoints into a mxArray
{
/// Create memory
mxArray* points_mex = mxCreateDoubleMatrix(npoints, ndims(), mxREAL);
double* points_data = mxGetPr(points_mex);
/// Fill data
for( int i=0; i<npoints; i++ )
for( int j=0; j<ndims(); j++ )
points_data[ i + j*npoints ] = points[i][j];
/// Add it to struct
mxSetField(matstruct, 0, "points", points_mex);
}
/// Sticks tree nodes into an
{
/// Create memory
mxArray* nodes_mex = mxCreateNumericMatrix(nodesPtrs.size(), 4, mxDOUBLE_CLASS, mxREAL);
double* nodes_data = (double*) mxGetData(nodes_mex);
/// Fill data
for( int i=0,off=0; i<nodesPtrs.size(); i++,off+=4 ){
nodes_data[off+0] = (double) nodesPtrs[i]->LIdx;
nodes_data[off+1] = (double) nodesPtrs[i]->RIdx;
nodes_data[off+2] = (double) nodesPtrs[i]->pIdx;
nodes_data[off+3] = (double) nodesPtrs[i]->key;
}
mxSetField(matstruct, 0, "nodes", nodes_mex);
}
return matstruct;
}
/**
* @brief Assign k-space trajectory
*
* @param k K-space trajectory
*/
void KSpace (const Matrix<RT>& k) {
m_k = k;
if (size(k,1) == KSpaceSize() && m_nmany == 1) {
#pragma omp parallel num_threads (m_fts.size())
{
m_fts[omp_get_thread_num()].KSpace(k);
}
} else if (size(m_k,2) == m_nmany) {
#pragma omp parallel num_threads (m_fts.size())
{
size_t i = omp_get_thread_num();
if (ndims(k)==3)
m_fts[i].KSpace(k(CR(),CR(),CR(i)));
else if (ndims(k) == 4)
m_fts[i].KSpace(k(CR(),CR(),CR(),CR(i)));
else
throw NCSENSE_KSPACE_DIMENSIONS;
}
} else if (size(m_k,2)*size(m_k,3) == m_nmany) {
#pragma omp parallel num_threads (m_fts.size())
{
size_t i = omp_get_thread_num(), l=i%size(m_k,2), n = i/size(m_k,2);
if (ndims(k)==4)
m_fts[i].KSpace(k(CR(),CR(),CR(l),CR(n)));
else if (ndims(k) == 5)
m_fts[i].KSpace(k(CR(),CR(),CR(),CR(l),CR(n)));
else
throw NCSENSE_KSPACE_DIMENSIONS;
}
} else {
throw NCSENSE_KSPACE_DIMENSIONS;
}
}
/**
* @brief Sum of squares over a dimension
*
* Usage:
* @code
* Matrix<cxfl> m = rand<double> (8,7,6);
* m = sos (M,1); // dims (8,6);
* @endcode
*
* @param M Matrix
* @param d Dimension
* @return Sum of squares
*/
template <class T> inline static Matrix<typename TypeTraits<T>::RT>
sos (const Matrix<T>& M, long d = -1) {
typedef typename TypeTraits<T>::RT real_type;
if (d == -1)
d = ndims(M)-1;
assert (d <= ndims(M)-1);
const real_type* rt = (real_type*)&M[0];
Matrix<real_type> res(size(M));
for (size_t i = 0; i < numel(M); ++i)
res[i] = rt[2*i]*rt[2*i]+rt[2*i+1]*rt[2*i+1];
return sum (res, d);
}
cv::MatND MxArray::toMatND(int depth, bool transpose) const
{
// Create cv::Mat object.
std::vector<int> d(dims(), dims()+ndims());
std::swap(d[0], d[1]);
cv::MatND m(ndims(), &d[0], CV_MAKETYPE(DepthOf[classID()], 1),
mxGetData(p_));
// Copy.
cv::MatND mat;
depth = (depth==CV_USRTYPE1) ? CV_MAKETYPE(DepthOf[classID()], 1) : depth;
m.convertTo(mat, CV_MAKETYPE(depth, 1));
return (mat.dims==2 && transpose) ? cv::Mat(mat.t()) : mat;
}
void ZArray::printInfo()
{
if (m_data == NULL) {
std::cout << "Empty array: null data" << std::endl;
} else {
if (ndims() == 0) {
std::cout << "Empty array: 0-dimentional" << std::endl;
} else {
std::cout << "Array(#): " << mylib::Array_Refcount(m_data) << std::endl;
std::cout << " size: " << dim(0);
for (int i = 1; i < ndims(); i++) {
std::cout << " x " << dim(i);
}
std::cout << std::endl;
switch (valueType()) {
case mylib::UINT8_TYPE:
std::cout << " uint8" << std::endl;
break;
case mylib::UINT16_TYPE:
std::cout << " uint16" << std::endl;
break;
case mylib::UINT32_TYPE:
std::cout << " uint32" << std::endl;
break;
case mylib::UINT64_TYPE:
std::cout << " uint64" << std::endl;
break;
case mylib::INT8_TYPE:
std::cout << " int8" << std::endl;
break;
case mylib::INT16_TYPE:
std::cout << " int16" << std::endl;
break;
case mylib::INT32_TYPE:
std::cout << " int32" << std::endl;
break;
case mylib::INT64_TYPE:
std::cout << " int64" << std::endl;
break;
case mylib::FLOAT32_TYPE:
std::cout << " single float" << std::endl;
case mylib::FLOAT64_TYPE:
std::cout << " double float" << std::endl;
default:
std::cout << " unknown type" << std::endl;
}
}
}
}
bool validposition(const position& pos) const {
if (ndims() != pos.nd_) return false;
for (int i=0; i != pos.nd_; ++i) {
if (pos.position_[i] < 0 || pos.position_[i] >= this->dim(i)) return false;
}
return true;
}
cv::Mat MxArray::toMat(int depth, bool transpose) const
{
// Create cv::Mat object.
std::vector<int> d(dims(), dims()+ndims());
int ndims = (d.size()>2) ? d.size()-1 : d.size();
int nchannels = (d.size()>2) ? *(d.end()-1) : 1;
depth = (depth==CV_USRTYPE1) ? DepthOf[classID()] : depth;
std::swap(d[0], d[1]);
cv::Mat mat(ndims, &d[0], CV_MAKETYPE(depth, nchannels));
// Copy each channel.
std::vector<cv::Mat> channels(nchannels);
std::vector<mwSize> si(d.size(), 0); // subscript index
int type = CV_MAKETYPE(DepthOf[classID()], 1); // Source type
for (int i = 0; i<nchannels; ++i)
{
si[d.size()-1] = i;
void *pd = reinterpret_cast<void*>(
reinterpret_cast<size_t>(mxGetData(p_))+
mxGetElementSize(p_)*subs(si));
cv::Mat m(ndims, &d[0], type, pd);
// Read from mxArray through m
m.convertTo(channels[i], CV_MAKETYPE(depth, 1));
}
cv::merge(channels, mat);
return (mat.dims==2 && transpose) ? cv::Mat(mat.t()) : mat;
}
std::vector<int>
cartesian_communicator::coordinates(int rk) const {
std::vector<int> cbuf(ndims());
BOOST_MPI_CHECK_RESULT(MPI_Cart_coords,
(MPI_Comm(*this), rk, cbuf.size(), c_data(cbuf) ));
return cbuf;
}
cv::Mat MxArray::toMat(int depth, bool transpose) const
{
// Create cv::Mat object (of the specified depth), equivalent to mxArray
std::vector<int> d(dims(), dims()+ndims());
const mwSize ndims = (d.size()>2) ? d.size()-1 : d.size();
const mwSize nchannels = (d.size()>2) ? d.back() : 1;
depth = (depth == CV_USRTYPE1) ? DepthOf[classID()] : depth;
std::swap(d[0], d[1]);
cv::Mat mat(ndims, &d[0], CV_MAKETYPE(depth, nchannels));
// Copy each channel from mxArray to Mat (converting to specified depth),
// as in: channels[i] <- cast_to_mat_depth(p_(:,:,i))
std::vector<cv::Mat> channels(nchannels);
std::vector<mwSize> si(d.size(), 0); // subscript index
const int type = CV_MAKETYPE(DepthOf[classID()], 1); // Source type
for (mwIndex i = 0; i<nchannels; ++i) {
si[si.size() - 1] = i; // last dim is a channel idx
void *pd = reinterpret_cast<void*>(
reinterpret_cast<size_t>(mxGetData(p_)) +
mxGetElementSize(p_)*subs(si)); // ptr to i-th channel data
const cv::Mat m(ndims, &d[0], type, pd); // only creates Mat headers
// Read from mxArray through m, writing into channels[i]
m.convertTo(channels[i], CV_MAKETYPE(depth, 1));
}
// Merge channels back into one cv::Mat array
cv::merge(channels, mat);
// transpose cv::Mat if needed
if (mat.dims==2 && transpose)
mat = mat.t();
return mat;
}
cartesian_topology
cartesian_communicator::topology() const {
cartesian_topology topo(ndims());
std::vector<int> coords;
topology(topo, coords);
return topo;
}
std::pair<int, int>
cartesian_communicator::shifted_ranks(int dim, int disp) const {
std::pair<int, int> r(-1,-1);
assert(0 <= dim && dim < ndims());
BOOST_MPI_CHECK_RESULT(MPI_Cart_shift,
(MPI_Comm(*this), dim, disp, &(r.first), &(r.second)));
return r;
}
result_type operator()(Expr& e) const
{
sz0 const& size0 = boost::proto::child_c<0>(e).extent();
sz1 const& size1 = boost::proto::child_c<1>(e).extent();
BOOST_ASSERT_MSG( ndims(size0) <= 2 && ndims(size1) <= 2
, "Inputs must be 2-D, or at least one input must be scalar"
);
BOOST_ASSERT_MSG( boost::fusion::at_c<1>(size0) == boost::fusion::at_c<0>(size1)
, "Inner dimensions must agree"
);
return result_type( boost::fusion::at_c<0>(size0)
, boost::fusion::at_c<1>(size1)
);
}
int
cartesian_communicator::rank(const std::vector<int>& coords ) const {
int r = -1;
assert(int(coords.size()) == ndims());
BOOST_MPI_CHECK_RESULT(MPI_Cart_rank,
(MPI_Comm(*this), c_data(const_cast<std::vector<int>&>(coords)),
&r));
return r;
}
cv::MatND MxArray::toMatND(int depth, bool transpose) const
{
// Create cv::MatND object (of the specified depth), equivalent to mxArray
std::vector<int> d(dims(), dims()+ndims());
std::swap(d[0], d[1]);
depth = (depth == CV_USRTYPE1) ? DepthOf[classID()] : depth;
cv::MatND mat(d.size(), &d[0], CV_MAKETYPE(depth, 1));
// Copy from mxArray to cv::MatND (converting to specified depth)
const int type = CV_MAKETYPE(DepthOf[classID()], 1); // source type
const cv::MatND m(d.size(), &d[0], type, mxGetData(p_)); // only Mat header
// Read from mxArray through m, writing into mat
m.convertTo(mat, CV_MAKETYPE(depth, 1));
// transpose cv::MatND if needed
if (mat.dims==2 && transpose)
mat = mat.t();
return mat;
}
//#include "Print.hpp"
template <class T> inline static Matrix<T> permute (const Matrix<T>& M, const Vector<size_t>& perm) {
// Check that perm only includes one number between 0 and INVALID_DIM once
size_t ndnew = perm.size(), i = 0;
size_t ndold = ndims (M);
// Must have same number of dimensions
assert (ndnew == ndold);
// Every number between 0 and ndnew must appear exactly once
Vector<cbool> occupied;
occupied.resize(ndnew);
for (i = 0; i < ndnew; ++i) {
assert (!occupied[perm[i]]);
occupied [perm[i]] = true;
}
// Old and new sizes
Vector<size_t> so = size (M);
Vector<size_t> sn (16,1);
for (i = 0; i < ndnew; ++i)
sn[i] = so[perm[i]];
// Allocate new matrix with permuted dimensions
Matrix<T> res(sn);
// Relation of old to new indices
Vector<size_t> d(16), od(16);
for (i = 0; i < ndnew; ++i) od[i] = perm[i];
for ( ; i < 16; ++i) od[i] = i;
// Copy data accordingly
for (d[15] = 0; d[15] < size(M,15); d[15]++)
for (d[14] = 0; d[14] < size(M,14); d[14]++)
for (d[13] = 0; d[13] < size(M,13); d[13]++)
for (d[12] = 0; d[12] < size(M,12); d[12]++)
for (d[11] = 0; d[11] < size(M,11); d[11]++)
for (d[10] = 0; d[10] < size(M,10); d[10]++)
for (d[ 9] = 0; d[ 9] < size(M, 9); d[ 9]++)
for (d[ 8] = 0; d[ 8] < size(M, 8); d[ 8]++)
for (d[ 7] = 0; d[ 7] < size(M, 7); d[ 7]++)
for (d[ 6] = 0; d[ 6] < size(M, 6); d[ 6]++)
for (d[ 5] = 0; d[ 5] < size(M, 5); d[ 5]++)
for (d[ 4] = 0; d[ 4] < size(M, 4); d[ 4]++)
for (d[ 3] = 0; d[ 3] < size(M, 3); d[ 3]++)
for (d[ 2] = 0; d[ 2] < size(M, 2); d[ 2]++)
for (d[ 1] = 0; d[ 1] < size(M, 1); d[ 1]++)
for (d[ 0] = 0; d[ 0] < size(M, 0); d[ 0]++)
res (d[od[ 0]],d[od[ 1]],d[od[ 2]],d[od[ 3]],
d[od[ 4]],d[od[ 5]],d[od[ 6]],d[od[ 7]],
d[od[ 8]],d[od[ 9]],d[od[10]],d[od[11]],
d[od[12]],d[od[13]],d[od[14]],d[od[15]]) =
M (d[ 0],d[ 1],d[ 2],d[ 3],d[ 4],d[ 5],
d[ 6],d[ 7],d[ 8],d[ 9],d[10],d[11],
d[12],d[13],d[14],d[15]);
// Remove trailing singelton dimensions
sn.erase(sn.begin()+ndnew, sn.begin()+16);
return resize(res, sn);
}
template<class T> bool
Write (const Matrix<T>& M, const std::string& uri) {
T t;
Group group, *tmp;
std::string path;
boost::tokenizer<> tok(uri);
std::vector<std::string> sv (Split (uri, "/"));
std::string name = sv[sv.size() - 1];
sv.pop_back(); // data name not part of path
if (sv.size() == 0)
path = "/";
else
for (size_t i = 0; i < sv.size(); i++) {
if (sv[i].compare(""))
path += "/";
path += sv[i];
}
if (this->m_verb)
printf ("Creating dataset %s at path (%s)\n", name.c_str(), path.c_str());
try {
group = m_file.openGroup(path);
if (this->m_verb)
printf ("Group %s opened for writing\n", path.c_str()) ;
} catch (const Exception& e) {
for (size_t i = 0, depth = 0; i < sv.size(); i++) {
if (sv[i].compare("")) {
try {
group = (depth) ? (*tmp).openGroup(sv[i]) : m_file.openGroup(sv[i]);
} catch (const Exception& e) {
group = (depth) ? (*tmp).createGroup(sv[i]) : m_file.createGroup(sv[i]);
}
tmp = &group;
depth++;
}
}
}
// One more field for complex numbers
size_t tmpdim = ndims(M);
std::vector<hsize_t> dims (tmpdim);
for (size_t i = 0; i < tmpdim; i++)
dims[i] = M.Dim(tmpdim-1-i);
if (is_complex(t)) {
dims.push_back(2);
tmpdim++;
}
DataSpace space (tmpdim, &dims[0]);
PredType* type = HDF5Traits<T>::PType();
DataSet set = group.createDataSet(name, (*type), space);
set.write (M.Ptr(), (*type));
set.close ();
space.close ();
return true;
}
