EVOLUTION-MANAGER

Edit File: decomp_qr.py

"""QR decomposition functions."""
from __future__ import division, print_function, absolute_import

import numpy

# Local imports
from .lapack import get_lapack_funcs
from .misc import _datacopied

__all__ = ['qr', 'qr_multiply', 'rq']

def safecall(f, name, *args, **kwargs):
    """Call a LAPACK routine, determining lwork automatically and handling
    error return values"""
    lwork = kwargs.get("lwork", None)
    if lwork in (None, -1):
        kwargs['lwork'] = -1
        ret = f(*args, **kwargs)
        kwargs['lwork'] = ret[-2][0].real.astype(numpy.int)
    ret = f(*args, **kwargs)
    if ret[-1] < 0:
        raise ValueError("illegal value in %d-th argument of internal %s"
                         % (-ret[-1], name))
    return ret[:-2]

def qr(a, overwrite_a=False, lwork=None, mode='full', pivoting=False,
       check_finite=True):
    """
    Compute QR decomposition of a matrix.

Calculate the decomposition ``A = Q R`` where Q is unitary/orthogonal
    and R upper triangular.

Parameters
    ----------
    a : (M, N) array_like
        Matrix to be decomposed
    overwrite_a : bool, optional
        Whether data in a is overwritten (may improve performance)
    lwork : int, optional
        Work array size, lwork >= a.shape[1]. If None or -1, an optimal size
        is computed.
    mode : {'full', 'r', 'economic', 'raw'}, optional
        Determines what information is to be returned: either both Q and R
        ('full', default), only R ('r') or both Q and R but computed in
        economy-size ('economic', see Notes). The final option 'raw'
        (added in SciPy 0.11) makes the function return two matrices
        (Q, TAU) in the internal format used by LAPACK.
    pivoting : bool, optional
        Whether or not factorization should include pivoting for rank-revealing
        qr decomposition. If pivoting, compute the decomposition
        ``A P = Q R`` as above, but where P is chosen such that the diagonal
        of R is non-increasing.
    check_finite : bool, optional
        Whether to check that the input matrix contains only finite numbers.
        Disabling may give a performance gain, but may result in problems
        (crashes, non-termination) if the inputs do contain infinities or NaNs.

Returns
    -------
    Q : float or complex ndarray
        Of shape (M, M), or (M, K) for ``mode='economic'``.  Not returned
        if ``mode='r'``.
    R : float or complex ndarray
        Of shape (M, N), or (K, N) for ``mode='economic'``.  ``K = min(M, N)``.
    P : int ndarray
        Of shape (N,) for ``pivoting=True``. Not returned if
        ``pivoting=False``.

Raises
    ------
    LinAlgError
        Raised if decomposition fails

Notes
    -----
    This is an interface to the LAPACK routines dgeqrf, zgeqrf,
    dorgqr, zungqr, dgeqp3, and zgeqp3.

If ``mode=economic``, the shapes of Q and R are (M, K) and (K, N) instead
    of (M,M) and (M,N), with ``K=min(M,N)``.

Examples
    --------
    >>> from scipy import linalg
    >>> a = np.random.randn(9, 6)

>>> q, r = linalg.qr(a)
    >>> np.allclose(a, np.dot(q, r))
    True
    >>> q.shape, r.shape
    ((9, 9), (9, 6))

>>> r2 = linalg.qr(a, mode='r')
    >>> np.allclose(r, r2)
    True

>>> q3, r3 = linalg.qr(a, mode='economic')
    >>> q3.shape, r3.shape
    ((9, 6), (6, 6))

>>> q4, r4, p4 = linalg.qr(a, pivoting=True)
    >>> d = np.abs(np.diag(r4))
    >>> np.all(d[1:] <= d[:-1])
    True
    >>> np.allclose(a[:, p4], np.dot(q4, r4))
    True
    >>> q4.shape, r4.shape, p4.shape
    ((9, 9), (9, 6), (6,))

>>> q5, r5, p5 = linalg.qr(a, mode='economic', pivoting=True)
    >>> q5.shape, r5.shape, p5.shape
    ((9, 6), (6, 6), (6,))

"""
    # 'qr' was the old default, equivalent to 'full'. Neither 'full' nor
    # 'qr' are used below.
    # 'raw' is used internally by qr_multiply
    if mode not in ['full', 'qr', 'r', 'economic', 'raw']:
        raise ValueError("Mode argument should be one of ['full', 'r',"
                         "'economic', 'raw']")

if check_finite:
        a1 = numpy.asarray_chkfinite(a)
    else:
        a1 = numpy.asarray(a)
    if len(a1.shape) != 2:
        raise ValueError("expected 2D array")
    M, N = a1.shape
    overwrite_a = overwrite_a or (_datacopied(a1, a))

if pivoting:
        geqp3, = get_lapack_funcs(('geqp3',), (a1,))
        qr, jpvt, tau = safecall(geqp3, "geqp3", a1, overwrite_a=overwrite_a)
        jpvt -= 1  # geqp3 returns a 1-based index array, so subtract 1
    else:
        geqrf, = get_lapack_funcs(('geqrf',), (a1,))
        qr, tau = safecall(geqrf, "geqrf", a1, lwork=lwork,
                           overwrite_a=overwrite_a)

if mode not in ['economic', 'raw'] or M < N:
        R = numpy.triu(qr)
    else:
        R = numpy.triu(qr[:N, :])

if pivoting:
        Rj = R, jpvt
    else:
        Rj = R,

if mode == 'r':
        return Rj
    elif mode == 'raw':
        return ((qr, tau),) + Rj

gor_un_gqr, = get_lapack_funcs(('orgqr',), (qr,))

if M < N:
        Q, = safecall(gor_un_gqr, "gorgqr/gungqr", qr[:, :M], tau,
                      lwork=lwork, overwrite_a=1)
    elif mode == 'economic':
        Q, = safecall(gor_un_gqr, "gorgqr/gungqr", qr, tau, lwork=lwork,
                      overwrite_a=1)
    else:
        t = qr.dtype.char
        qqr = numpy.empty((M, M), dtype=t)
        qqr[:, :N] = qr
        Q, = safecall(gor_un_gqr, "gorgqr/gungqr", qqr, tau, lwork=lwork,
                      overwrite_a=1)

return (Q,) + Rj

def qr_multiply(a, c, mode='right', pivoting=False, conjugate=False,
                overwrite_a=False, overwrite_c=False):
    """
    Calculate the QR decomposition and multiply Q with a matrix.

Calculate the decomposition ``A = Q R`` where Q is unitary/orthogonal
    and R upper triangular. Multiply Q with a vector or a matrix c.

Parameters
    ----------
    a : (M, N), array_like
        Input array
    c : array_like
        Input array to be multiplied by ``q``.
    mode : {'left', 'right'}, optional
        ``Q @ c`` is returned if mode is 'left', ``c @ Q`` is returned if
        mode is 'right'.
        The shape of c must be appropriate for the matrix multiplications,
        if mode is 'left', ``min(a.shape) == c.shape[0]``,
        if mode is 'right', ``a.shape[0] == c.shape[1]``.
    pivoting : bool, optional
        Whether or not factorization should include pivoting for rank-revealing
        qr decomposition, see the documentation of qr.
    conjugate : bool, optional
        Whether Q should be complex-conjugated. This might be faster
        than explicit conjugation.
    overwrite_a : bool, optional
        Whether data in a is overwritten (may improve performance)
    overwrite_c : bool, optional
        Whether data in c is overwritten (may improve performance).
        If this is used, c must be big enough to keep the result,
        i.e. ``c.shape[0]`` = ``a.shape[0]`` if mode is 'left'.

Returns
    -------
    CQ : ndarray
        The product of ``Q`` and ``c``.
    R : (K, N), ndarray
        R array of the resulting QR factorization where ``K = min(M, N)``.
    P : (N,) ndarray
        Integer pivot array. Only returned when ``pivoting=True``.

Raises
    ------
    LinAlgError
        Raised if QR decomposition fails.

Notes
    -----
    This is an interface to the LAPACK routines ``?GEQRF``, ``?ORMQR``,
    ``?UNMQR``, and ``?GEQP3``.

.. versionadded:: 0.11.0

Examples
    --------
    >>> from scipy.linalg import qr_multiply, qr
    >>> A = np.array([[1, 3, 3], [2, 3, 2], [2, 3, 3], [1, 3, 2]])
    >>> qc, r1, piv1 = qr_multiply(A, 2*np.eye(4), pivoting=1)
    >>> qc
    array([[-1.,  1., -1.],
           [-1., -1.,  1.],
           [-1., -1., -1.],
           [-1.,  1.,  1.]])
    >>> r1
    array([[-6., -3., -5.            ],
           [ 0., -1., -1.11022302e-16],
           [ 0.,  0., -1.            ]])
    >>> piv1
    array([1, 0, 2], dtype=int32)
    >>> q2, r2, piv2 = qr(A, mode='economic', pivoting=1)
    >>> np.allclose(2*q2 - qc, np.zeros((4, 3)))
    True

"""
    if mode not in ['left', 'right']:
        raise ValueError("Mode argument can only be 'left' or 'right' but "
                         "not '{}'".format(mode))
    c = numpy.asarray_chkfinite(c)
    if c.ndim < 2:
        onedim = True
        c = numpy.atleast_2d(c)
        if mode == "left":
            c = c.T
    else:
        onedim = False

a = numpy.atleast_2d(numpy.asarray(a))  # chkfinite done in qr
    M, N = a.shape

if mode == 'left':
        if c.shape[0] != min(M, N + overwrite_c*(M-N)):
            raise ValueError('Array shapes are not compatible for Q @ c'
                             ' operation: {} vs {}'.format(a.shape, c.shape))
    else:
        if M != c.shape[1]:
            raise ValueError('Array shapes are not compatible for c @ Q'
                             ' operation: {} vs {}'.format(c.shape, a.shape))

raw = qr(a, overwrite_a, None, "raw", pivoting)
    Q, tau = raw[0]

gor_un_mqr, = get_lapack_funcs(('ormqr',), (Q,))
    if gor_un_mqr.typecode in ('s', 'd'):
        trans = "T"
    else:
        trans = "C"

Q = Q[:, :min(M, N)]
    if M > N and mode == "left" and not overwrite_c:
        if conjugate:
            cc = numpy.zeros((c.shape[1], M), dtype=c.dtype, order="F")
            cc[:, :N] = c.T
        else:
            cc = numpy.zeros((M, c.shape[1]), dtype=c.dtype, order="F")
            cc[:N, :] = c
            trans = "N"
        if conjugate:
            lr = "R"
        else:
            lr = "L"
        overwrite_c = True
    elif c.flags["C_CONTIGUOUS"] and trans == "T" or conjugate:
        cc = c.T
        if mode == "left":
            lr = "R"
        else:
            lr = "L"
    else:
        trans = "N"
        cc = c
        if mode == "left":
            lr = "L"
        else:
            lr = "R"
    cQ, = safecall(gor_un_mqr, "gormqr/gunmqr", lr, trans, Q, tau, cc,
                   overwrite_c=overwrite_c)
    if trans != "N":
        cQ = cQ.T
    if mode == "right":
        cQ = cQ[:, :min(M, N)]
    if onedim:
        cQ = cQ.ravel()

return (cQ,) + raw[1:]

def rq(a, overwrite_a=False, lwork=None, mode='full', check_finite=True):
    """
    Compute RQ decomposition of a matrix.

Calculate the decomposition ``A = R Q`` where Q is unitary/orthogonal
    and R upper triangular.

Returns
    -------
    R : float or complex ndarray
        Of shape (M, N) or (M, K) for ``mode='economic'``.  ``K = min(M, N)``.
    Q : float or complex ndarray
        Of shape (N, N) or (K, N) for ``mode='economic'``.  Not returned
        if ``mode='r'``.

Raises
    ------
    LinAlgError
        If decomposition fails.

Notes
    -----
    This is an interface to the LAPACK routines sgerqf, dgerqf, cgerqf, zgerqf,
    sorgrq, dorgrq, cungrq and zungrq.

If ``mode=economic``, the shapes of Q and R are (K, N) and (M, K) instead
    of (N,N) and (M,N), with ``K=min(M,N)``.

Examples
    --------
    >>> from scipy import linalg
    >>> a = np.random.randn(6, 9)
    >>> r, q = linalg.rq(a)
    >>> np.allclose(a, r @ q)
    True
    >>> r.shape, q.shape
    ((6, 9), (9, 9))
    >>> r2 = linalg.rq(a, mode='r')
    >>> np.allclose(r, r2)
    True
    >>> r3, q3 = linalg.rq(a, mode='economic')
    >>> r3.shape, q3.shape
    ((6, 6), (6, 9))

"""
    if mode not in ['full', 'r', 'economic']:
        raise ValueError(
                 "Mode argument should be one of ['full', 'r', 'economic']")

if check_finite:
        a1 = numpy.asarray_chkfinite(a)
    else:
        a1 = numpy.asarray(a)
    if len(a1.shape) != 2:
        raise ValueError('expected matrix')
    M, N = a1.shape
    overwrite_a = overwrite_a or (_datacopied(a1, a))

gerqf, = get_lapack_funcs(('gerqf',), (a1,))
    rq, tau = safecall(gerqf, 'gerqf', a1, lwork=lwork,
                       overwrite_a=overwrite_a)
    if not mode == 'economic' or N < M:
        R = numpy.triu(rq, N-M)
    else:
        R = numpy.triu(rq[-M:, -M:])

if mode == 'r':
        return R

gor_un_grq, = get_lapack_funcs(('orgrq',), (rq,))

if N < M:
        Q, = safecall(gor_un_grq, "gorgrq/gungrq", rq[-N:], tau, lwork=lwork,
                      overwrite_a=1)
    elif mode == 'economic':
        Q, = safecall(gor_un_grq, "gorgrq/gungrq", rq, tau, lwork=lwork,
                      overwrite_a=1)
    else:
        rq1 = numpy.empty((N, N), dtype=rq.dtype)
        rq1[-M:] = rq
        Q, = safecall(gor_un_grq, "gorgrq/gungrq", rq1, tau, lwork=lwork,
                      overwrite_a=1)

return R, Q