Exemple #1
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/*
 * @brief           Create new vector
 *                  and copy the data into the new vector. If the target
 *                  is bigger, the remaining space is set 0. If it is
 *                  smaller data is truncted.
 *
 * @param   M       The matrix to resize
 * @param   sz      New length
 * @return          Resized vector
 */
template <class T> inline static Matrix<T> resize (const Matrix<T>& M, const size_t& s0,
        const size_t& s1, const size_t& s2, const size_t& s3, const size_t& s4) {
    assert (numel(M)==s0*s1*s2*s3*s4);
    Matrix<T> res (s0,s1,s2,s3,s4);
    res.Container() = M.Container();
    return res;
}
Exemple #2
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/**
 * @brief          FLip up down
 *
 * @param   M      Matrix
 * @return         Flipped matrix
 */
template <class T> inline static Matrix<T> flipud (const Matrix<T>& M)  {

    size_t scol = size(M,0), ncol = numel(M)/scol;
    Matrix<T> res = M;

    if (scol == 1) // trivial
        return res;

    typedef typename Vector<T>::iterator VI;
    for (VI i = res.Container().begin(); i < res.Container().end(); i += scol)
        std::reverse(i, i+scol);
    return res;

}
Exemple #3
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    /**
     * @brief           Elementwise multiplication with scalar (lhs)
     *
     * @param  s        Scalar lhs
     * @param  m        Matrix rhs
     * @return          m * s
     */
    inline friend Matrix<T,P>
    operator/  (const T s, const Matrix<T,P> &m) {

        Matrix<T,P> res = m;
#ifdef USE_VALARRAY
		res.Container() = s / res.Container();
#else
#ifdef EW_OMP
    #pragma omp parallel for
#endif
        for (size_t i = 0; i < m.Size(); ++i)
            res[i] = s / res[i];
#endif
        return res;

    }
Exemple #4
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/**
 * @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;

}
Exemple #5
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	/**
	 * @brief        Construct FFTW plans for forward and backward FT with credentials
	 * 
	 * @param  sl    Matrix of side length of the FT range
	 * @param  mask  K-Space mask (if left empty no mask is applied)
	 * @param  pc    Phase correction (or target phase)
	 * @param  b0    Field distortion
	 */
	explicit DFT         (const Matrix<size_t>& sl,
				 const Matrix<T>& mask = Matrix<T>(1),
				 const Matrix<CT>& pc = Matrix<CT>(1),
				 const Matrix<T>& b0 = Matrix<T>(1)) :
		m_N(1), m_have_mask (false), m_have_pc (false) {

		size_t rank = numel(sl);

		container<int> n (rank);
		
		if (numel(mask) > 1) {
			m_have_mask = true;	m_mask = mask;
		}
		
		if (numel(pc)   > 1) {
			m_have_pc = true; m_pc = pc; m_cpc = conj(pc);
		}
		
		for (int i = 0; i < rank; i++)
			n[i]  = (int) sl [rank-1-i];

		m_N = std::accumulate(n.begin(), n.end(), 1, std::multiplies<int>());

		Matrix<size_t> tmp = resize(sl,3,1);
		for (size_t i = 0; i < 3; ++i)
			tmp[i] = (tmp[i] > 0) ? tmp[i] : 1;

		d = tmp.Container(); // data side lengths
		c = (floor(tmp/2)).Container(); // center coords

 		Allocate (rank, &n[0]);

		m_initialised = true;

	}
Exemple #6
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	/**
	 * @brief          Construct NFFT plans for forward and backward FT with credentials
	 * 
	 * @param  imsize  Matrix of side length of the image space
	 * @param  nk      # k-space points
	 * @param  m       Spatial cut-off of FT
	 * @param  alpha   Oversampling factor
	 * @param  b0      Off-resonance maps if available
	 * @param  pc      Phase correction applied before forward or after adjoint transforms (default: empty)
	 * @param  eps     Convergence criterium for inverse transform (default: 1.0e-7)
	 * @param  maxit   Maximum # NFFT iterations (default: 3)
	 */
	NFFT        (const Matrix<size_t>& imsize, const size_t& nk, const size_t m = 1, 
				 const T alpha = 1.0, const Matrix<T> b0 = Matrix<T>(1),
				 const Matrix< std::complex<T> > pc = Matrix< std::complex<T> >(1),
				 const T eps = 7.0e-4, const size_t maxit = 1) : m_prepared (false) {
		
		m_M     = nk;
		m_imgsz = 1;
		m_m = m;
		
		m_N = imsize.Container();
		m_n = m_N;//ceil (alpha*m_N);

		m_rank = numel(imsize);
		
		m_imgsz = prod(m_N);

		m_epsilon = eps;
		m_maxit   = maxit;
		
		NFFTTraits<double>::Init (m_N, m_M, m_n, m_m, m_fplan, m_iplan);
		
        m_y = m_iplan.y;
        m_f = m_iplan.f_hat_iter;

		if (pc.Size() > 1)
			m_have_pc = true;
		
		m_pc   = pc;
		m_cpc  = conj(pc);
		
		m_initialised = true;
		
	}
Exemple #7
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/**
 * @brief       Uniformly random matrix
 *
 * @param  sz   Size vector
 * @return      Rand matrix
 *
 */
template <class T> inline static Matrix<T>
randn          (const Matrix<size_t>& sz) {

	Matrix<T> res (sz.Container());
    Random<T>::Normal(res);
 	return res;

}
Exemple #8
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/**
 * @brief       Which elements are Inf
 *
 * @param  M    Matrix
 * @return      Matrix of booleans true where inf
 */
template <class T> inline static  Matrix<cbool>
isnan (const Matrix<T>& M) {

    Matrix<cbool> res (M.Dim());
    for (size_t i = 0; i < res.Size(); ++i)
        res.Container()[i] = (is_nan(TypeTraits<T>::Imag(M[i]))||is_nan(TypeTraits<T>::Imag(M[i])));
    return res;

}
Exemple #9
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		template <class T> Matrix<T>
		Read (const std::string& uri = "") const {

			int dt;
			size_t  ns, n;
			std::vector<size_t> dim;
			std::vector<float>  res;
			char* name;
			Matrix<T> M;
			T t;

			// Read type
			if (!mread (&dt, 1, m_file, "data type"))
				return M;

			// Matrix and data type must fit as of now.
			if (CODTraits<T>::dt == dt) {

				if (!mread (&n, 1, m_file, "dimensions"))
					return M;
				dim = std::vector<size_t>(n,1);
				res = std::vector<float>(n,1.0);

				// Read dimensions and allocate matrix
				if (!mread (dim, m_file, "dimensions"))
					return M;

				//Read resolutions and assign
				if (!mread (res, m_file, "resolutions"))
					return M;
				M = Matrix<T>(dim,res);
				n = numel(M);

				// Name
				if (!mread (&n,  1, m_file, "name length"))
					return M;

				name = new char [n+1];

				if (!mread (name, n, m_file, "name"))
					return M;
				name[n] = '\0';
				M.SetClassName(name);

				// Read data
				if (!mread (M.Container(), m_file, "data"))
					return M;

				//Close and clean up;
				delete name;

			}

			return M;

		}
Exemple #10
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		template <class T> bool
		Write (const Matrix<T>& M, const std::string& uri = "") {

			assert (m_file != NULL);

			dtype dt = CODTraits<T>::dt;
			size_t n, l;

			// Dump type
			if (!mwrite(&dt,         1, m_file, "data type"))
				return false;

			n = M.NDim();
			if (!mwrite(&n,          1, m_file, "data dimensions"))
				return false;

			// Dump dimensions
			if (!mwrite(M.Dim(),        m_file, "dimensions"))
				return false;

			// Dump resolutions
			if (!mwrite(M.Res(),        m_file, "resolutions"))
				return false;

			// Size of name and name
			n = uri.size();
			if (!mwrite(&n,          1, m_file, "name length"))
				return false;

			// Dump name
			if (!mwrite(uri.c_str(), n, m_file, "name"))
				return false;

			// Dump data
			if (!mwrite(M.Container(),  m_file, "data"))
				return false;

			if (!mwrite(delim.c_str(), delim.length(), m_file, "delimiter"))
				return false;

			return true;

		}
Exemple #11
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	/**
	 * @brief        Construct FFTW plans for forward and backward FT with credentials for FT with identical side lengths
	 * 
	 * @param  rank  Rank (i.e. # FT directions)
	 * @param  sl    Side length of the slice, volume ...
	 * @param  mask  K-Space mask (if left empty no mask is applied)
	 * @param  pc    Phase correction (or target phase)
	 * @param  b0    Static field distortion
	 */
	DFT         (const size_t rank, const size_t sl, const Matrix<T>& mask = Matrix<T>(),
				 const Matrix<CT>& pc = Matrix<CT>(), const Matrix<T>& b0 = Matrix<T>()) :
		m_have_mask (false), m_have_pc (false) {

		std::vector<int> n (rank);
		
		size_t i;

		if (numel(mask) > 1) {
			m_have_mask = true;
			m_mask      = mask;
		}
		
		if (pc.Size() > 1) {
			m_have_pc   = true;
			m_pc   = pc;
			m_cpc  = conj(pc);
		}
		
		for (i = 0; i < rank; i++) {
			n[i]  = sl;
			m_N  *= n[i];
		}
		
		Matrix<size_t> tmp (3,1);
		for (i = 0; i < rank; ++i)
			tmp[i] = sl;
		for (     ; i < 3;    ++i)
			tmp[i] = 1;

		d = tmp.Container(); // data side lengths
		c = (floor(tmp/2)).Container(); // center coords

		Allocate (rank, &n[0]);
		
		m_initialised = true;
	
	}
Exemple #12
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/**
 * @brief           Create new vector
 *                  and copy the data into the new vector. If the target
 *                  is bigger, the remaining space is set 0. If it is
 *                  smaller data is truncted.
 *
 * @param   M       The matrix to resize
 * @param   sc      New height
 * @param   sl      New width
 * @return          Resized vector
 */
template <class T> inline static  Matrix<T> resize (const Matrix<T>& M, size_t sc, size_t sl) {
    assert(sl*sc==numel(M));
    Matrix<T> ret(sc,sl);
    ret.Container() = M.Container();
    return ret;
}
Exemple #13
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/**
 * @brief       Zero matrix
 *
 * @param  sz   Size vector
 * @return      Zero matrix
 *
 */
template <class T> inline static Matrix<T> 
zeros           (const Matrix<size_t>& sz) {

 	return Matrix<T> (sz.Container());

}