<reponame>pauldmccarthy/fslpy
#!/usr/bin/env python
#
# affine.py - Utility functions for working with affine transformations.
#
# Author: <NAME> <<EMAIL>>
#
"""This module contains utility functions for working with affine
transformations. The following functions are available:

.. autosummary::
   :nosignatures:

   transform
   scaleOffsetXform
   invert
   concat
   compose
   decompose
   rotMatToAffine
   rotMatToAxisAngles
   axisAnglesToRotMat
   axisBounds
   rmsdev
   rescale

And a few more functions are provided for working with vectors:

.. autosummary::
   :nosignatures:

   veclength
   normalise
   transformNormal
"""


import collections.abc as abc
import numpy           as np
import numpy.linalg    as linalg


def invert(x):
    """Inverts the given matrix using ``numpy.linalg.inv``. """
    return linalg.inv(x)


def concat(*xforms):
    """Combines the given matrices (returns the dot product)."""

    result = xforms[0]

    for i in range(1, len(xforms)):
        result = np.dot(result, xforms[i])

    return result


def veclength(vec):
    """Returns the length of the given vector(s).

    Multiple vectors may be passed in, with a shape of ``(n, 3)``.
    """
    vec = np.array(vec, copy=False).reshape(-1, 3)
    return np.sqrt(np.einsum('ij,ij->i', vec, vec))


def normalise(vec):
    """Normalises the given vector(s) to unit length.

    Multiple vectors may be passed in, with a shape of ``(n, 3)``.
    """
    vec = np.array(vec, copy=False).reshape(-1, 3)
    n   = (vec.T / veclength(vec)).T

    if n.size == 3:
        n = n[0]

    return n


def scaleOffsetXform(scales, offsets):
    """Creates and returns an affine transformation matrix which encodes
    the specified scale(s) and offset(s).


    :arg scales:  A tuple of up to three values specifying the scale factors
                  for each dimension. If less than length 3, is padded with
                  ``1.0``.

    :arg offsets: A tuple of up to three values specifying the offsets for
                  each dimension. If less than length 3, is padded with
                  ``0.0``.

    :returns:     A ``numpy.float32`` array of size :math:`4 \\times 4`.
    """

    oktypes = (abc.Sequence, np.ndarray)

    if not isinstance(scales,  oktypes): scales  = [scales]
    if not isinstance(offsets, oktypes): offsets = [offsets]
    if not isinstance(scales,  list):    scales  = list(scales)
    if not isinstance(offsets, list):    offsets = list(offsets)

    lens = len(scales)
    leno = len(offsets)

    if lens < 3: scales  = scales  + [1.0] * (3 - lens)
    if leno < 3: offsets = offsets + [0.0] * (3 - leno)

    xform = np.eye(4, dtype=np.float64)

    xform[0, 0] = scales[0]
    xform[1, 1] = scales[1]
    xform[2, 2] = scales[2]

    xform[0, 3] = offsets[0]
    xform[1, 3] = offsets[1]
    xform[2, 3] = offsets[2]

    return xform


def compose(scales, offsets, rotations, origin=None, shears=None):
    """Compose a transformation matrix out of the given scales, offsets
    and axis rotations.

    :arg scales:    Sequence of three scale values.

    :arg offsets:   Sequence of three offset values.

    :arg rotations: Sequence of three rotation values, in radians, or
                    a rotation matrix of shape ``(3, 3)``.

    :arg origin:    Origin of rotation - must be scaled by the ``scales``.
                    If not provided, the rotation origin is ``(0, 0, 0)``.

    :arg shears:    Sequence of three shear values
    """

    preRotate  = np.eye(4)
    postRotate = np.eye(4)

    rotations = np.array(rotations)

    if rotations.shape == (3,):
        rotations = axisAnglesToRotMat(*rotations)

    if origin is not None:
        preRotate[ 0, 3] = -origin[0]
        preRotate[ 1, 3] = -origin[1]
        preRotate[ 2, 3] = -origin[2]
        postRotate[0, 3] =  origin[0]
        postRotate[1, 3] =  origin[1]
        postRotate[2, 3] =  origin[2]

    scale  = np.eye(4, dtype=np.float64)
    offset = np.eye(4, dtype=np.float64)
    rotate = np.eye(4, dtype=np.float64)
    shear  = np.eye(4, dtype=np.float64)

    scale[  0,  0] = scales[ 0]
    scale[  1,  1] = scales[ 1]
    scale[  2,  2] = scales[ 2]
    offset[ 0,  3] = offsets[0]
    offset[ 1,  3] = offsets[1]
    offset[ 2,  3] = offsets[2]

    rotate[:3, :3] = rotations

    if shears is not None:
        shear[0, 1] = shears[0]
        shear[0, 2] = shears[1]
        shear[1, 2] = shears[2]

    return concat(offset, postRotate, rotate, preRotate, scale, shear)


def decompose(xform, angles=True, shears=False):
    """Decomposes the given transformation matrix into separate offsets,
    scales, and rotations, according to the algorithm described in:

    <NAME>, Decomposing a matrix into simple transformations, pp
    320-323 in *Graphics Gems II*, <NAME> (editor), Academic Press, 1991,
    ISBN: 0120644819.

    It is assumed that the given transform has no perspective components.

    :arg xform:  A ``(3, 3)`` or ``(4, 4)`` affine transformation matrix.

    :arg angles: If ``True`` (the default), the rotations are returned
                 as axis-angles, in radians. Otherwise, the rotation matrix
                 is returned.

    :arg shears: Defaults to ``False``. If ``True``, shears are returned.

    :returns: The following:

               - A sequence of three scales
               - A sequence of three translations (all ``0`` if ``xform``
                 was a ``(3, 3)`` matrix)
               - A sequence of three rotations, in radians. Or, if
                 ``angles is False``, a rotation matrix.
               - If ``shears is True``, a sequence of three shears.
    """

    # The inline comments in the code below are taken verbatim from
    # the referenced article, [except for notes in square brackets].

    # The next step is to extract the translations. This is trivial;
    # we find t_x = M_{4,1}, t_y = M_{4,2}, and t_z = M_{4,3}. At this
    # point we are left with a 3*3 matrix M' = M_{1..3,1..3}.
    xform = np.array(xform).T

    if xform.shape == (4, 4):
        translations = xform[ 3, :3]
        xform        = xform[:3, :3]
    else:
        translations = np.array([0, 0, 0])

    M1 = xform[0]
    M2 = xform[1]
    M3 = xform[2]

    # The process of finding the scaling factors and shear parameters
    # is interleaved. First, find s_x = |M'_1|.
    sx = np.sqrt(np.dot(M1, M1))
    M1 = M1 / sx

    # Then, compute an initial value for the xy shear factor,
    # s_xy = M'_1 * M'_2. (this is too large by the y scaling factor).
    sxy = np.dot(M1, M2)

    # The second row of the matrix is made orthogonal to the first by
    # setting M'_2 = M'_2 - s_xy * M'_1.
    M2 = M2 - sxy * M1

    # Then the y scaling factor, s_y, is the length of the modified
    # second row.
    sy = np.sqrt(np.dot(M2, M2))

    # The second row is normalized, and s_xy is divided by s_y to
    # get its final value.
    M2  = M2  / sy
    sxy = sxy / sx

    # The xz and yz shear factors are computed as in the preceding,
    sxz = np.dot(M1, M3)
    syz = np.dot(M2, M3)

    # the third row is made orthogonal to the first two rows,
    M3 = M3 - sxz * M1 - syz * M2

    # the z scaling factor is computed,
    sz = np.sqrt(np.dot(M3, M3))

    # the third row is normalized, and the xz and yz shear factors are
    # rescaled.
    M3  = M3  / sz
    sxz = sxz / sx
    syz = syz / sy

    # The resulting matrix now is a pure rotation matrix, except that it
    # might still include a scale factor of -1. If the determinant of the
    # matrix is -1, negate the matrix and all three scaling factors. Call
    # the resulting matrix R.
    #
    # [We do things different here - if the rotation matrix has negative
    #  determinant, the flip is encoded in the x scaling factor.]
    R = np.array([M1, M2, M3])
    if linalg.det(R) < 0:
        R[0] = -R[0]
        sx   = -sx

    # Finally, we need to decompose the rotation matrix into a sequence
    # of rotations about the x, y, and z axes. [This is done in the
    # rotMatToAxisAngles function]
    if angles: rotations = rotMatToAxisAngles(R.T)
    else:      rotations = R.T

    retval = [np.array([sx, sy, sz]), translations, rotations]

    if shears:
        retval.append(np.array((sxy, sxz, syz)))

    return tuple(retval)



def rotMatToAffine(rotmat, origin=None):
    """Convenience function which encodes the given ``(3, 3)`` rotation
    matrix into a ``(4, 4)`` affine.
    """
    return compose([1, 1, 1], [0, 0, 0], rotmat, origin)


def rotMatToAxisAngles(rotmat):
    """Given a ``(3, 3)`` rotation matrix, decomposes the rotations into
    an angle in radians about each axis.
    """

    yrot = np.sqrt(rotmat[0, 0] ** 2 + rotmat[1, 0] ** 2)

    if np.isclose(yrot, 0):
        xrot = np.arctan2(-rotmat[1, 2], rotmat[1, 1])
        yrot = np.arctan2(-rotmat[2, 0], yrot)
        zrot = 0
    else:
        xrot = np.arctan2( rotmat[2, 1], rotmat[2, 2])
        yrot = np.arctan2(-rotmat[2, 0], yrot)
        zrot = np.arctan2( rotmat[1, 0], rotmat[0, 0])

    return [xrot, yrot, zrot]


def axisAnglesToRotMat(xrot, yrot, zrot):
    """Constructs a ``(3, 3)`` rotation matrix from the given angles, which
    must be specified in radians.
    """

    xmat = np.eye(3)
    ymat = np.eye(3)
    zmat = np.eye(3)

    xmat[1, 1] =  np.cos(xrot)
    xmat[1, 2] = -np.sin(xrot)
    xmat[2, 1] =  np.sin(xrot)
    xmat[2, 2] =  np.cos(xrot)

    ymat[0, 0] =  np.cos(yrot)
    ymat[0, 2] =  np.sin(yrot)
    ymat[2, 0] = -np.sin(yrot)
    ymat[2, 2] =  np.cos(yrot)

    zmat[0, 0] =  np.cos(zrot)
    zmat[0, 1] = -np.sin(zrot)
    zmat[1, 0] =  np.sin(zrot)
    zmat[1, 1] =  np.cos(zrot)

    return concat(zmat, ymat, xmat)


def axisBounds(shape,
               xform,
               axes=None,
               origin='centre',
               boundary='high',
               offset=1e-4):
    """Returns the ``(lo, hi)`` bounds of the specified axis/axes in the
    world coordinate system defined by ``xform``.

    If the ``origin`` parameter is set to  ``centre`` (the default),
    this function assumes that voxel indices correspond to the voxel
    centre. For example, the voxel at ``(4, 5, 6)`` covers the space:

      ``[3.5 - 4.5, 4.5 - 5.5, 5.5 - 6.5]``

    So the bounds of the specified shape extends from the corner at

      ``(-0.5, -0.5, -0.5)``

    to the corner at

      ``(shape[0] - 0.5, shape[1] - 0.5, shape[1] - 0.5)``

    If the ``origin`` parameter is set to ``corner``, this function
    assumes that voxel indices correspond to the voxel corner. In this
    case, a voxel  at ``(4, 5, 6)`` covers the space:

      ``[4 - 5, 5 - 6, 6 - 7]``

    So the bounds of the specified shape extends from the corner at

      ``(0, 0, 0)``

    to the corner at

      ``(shape[0], shape[1], shape[1])``.


    If the ``boundary`` parameter is set to ``high``, the high voxel bounds
    are reduced by a small amount (specified by the ``offset`` parameter)
    before they are transformed to the world coordinate system.  If
    ``boundary`` is set to ``low``, the low bounds are increased by a small
    amount.  The ``boundary`` parameter can also be set to ``'both'``, or
    ``None``. This option is provided so that you can ensure that the
    resulting bounds will always be contained within the image space.

    :arg shape:    The ``(x, y, z)`` shape of the data.

    :arg xform:    Transformation matrix which transforms voxel coordinates
                   to the world coordinate system.

    :arg axes:     The world coordinate system axis bounds to calculate.

    :arg origin:   Either ``'centre'`` (the default) or ``'corner'``.

    :arg boundary: Either ``'high'`` (the default), ``'low'``, ''`both'``,
                   or ``None``.

    :arg offset:   Amount by which the boundary voxel coordinates should be
                   offset. Defaults to ``1e-4``.

    :returns:      A tuple containing the ``(low, high)`` bounds for each
                   requested world coordinate system axis.
    """

    origin = origin.lower()

    # lousy US spelling
    if origin == 'center':
        origin = 'centre'

    if origin not in ('centre', 'corner'):
        raise ValueError('Invalid origin value: {}'.format(origin))
    if boundary not in ('low', 'high', 'both', None):
        raise ValueError('Invalid boundary value: {}'.format(boundary))

    scalar = False

    if axes is None:
        axes = [0, 1, 2]

    elif not isinstance(axes, abc.Iterable):
        scalar = True
        axes   = [axes]

    x, y, z = shape[:3]

    points = np.zeros((8, 3), dtype=np.float32)

    if origin == 'centre':
        x0 = -0.5
        y0 = -0.5
        z0 = -0.5
        x -=  0.5
        y -=  0.5
        z -=  0.5
    else:
        x0 = 0
        y0 = 0
        z0 = 0

    if boundary in ('low', 'both'):
        x0 += offset
        y0 += offset
        z0 += offset

    if boundary in ('high', 'both'):
        x  -= offset
        y  -= offset
        z  -= offset

    points[0, :] = [x0, y0, z0]
    points[1, :] = [x0, y0,  z]
    points[2, :] = [x0,  y, z0]
    points[3, :] = [x0,  y,  z]
    points[4, :] = [x,  y0, z0]
    points[5, :] = [x,  y0,  z]
    points[6, :] = [x,   y, z0]
    points[7, :] = [x,   y,  z]

    tx = transform(points, xform)

    lo = tx[:, axes].min(axis=0)
    hi = tx[:, axes].max(axis=0)

    if scalar: return (lo[0], hi[0])
    else:      return (lo,    hi)


def transform(p, xform, axes=None, vector=False):
    """Transforms the given set of points ``p`` according to the given affine
    transformation ``xform``.


    :arg p:      A sequence or array of points of shape :math:`N \\times  3`.

    :arg xform:  A ``(4, 4)`` affine transformation matrix with which to
                 transform the points in ``p``.

    :arg axes:   If you are only interested in one or two axes, and the source
                 axes are orthogonal to the target axes (see the note below),
                 you may pass in a 1D, ``N*1``, or ``N*2`` array as ``p``, and
                 use this argument to specify which axis/axes that the data in
                 ``p`` correspond to.

    :arg vector: Defaults to ``False``. If ``True``, the points are treated
                 as vectors - the translation component of the transformation
                 is not applied. If you set this flag, you pass in a ``(3, 3)``
                 transformation matrix.

    :returns:    The points in ``p``, transformed by ``xform``, as a ``numpy``
                 array with the same data type as the input.


    .. note:: The ``axes`` argument should only be used if the source
              coordinate system (the points in ``p``) axes are orthogonal
              to the target coordinate system (defined by the ``xform``).

              In other words, you can only use the ``axes`` argument if
              the ``xform`` matrix consists solely of translations and
              scalings.
    """

    p  = _fillPoints(p, axes)
    t  = np.dot(xform[:3, :3], p.T).T

    if not vector:
        t = t + xform[:3, 3]

    if axes is not None:
        t = t[:, axes]

    if t.size == 1: return t[0]
    else:           return t


def transformNormal(p, xform, axes=None):
    """Transforms the given point(s), under the assumption that they
    are normal vectors. In this case, the points are transformed by
    ``invert(xform[:3, :3]).T``.
    """
    return transform(p, invert(xform[:3, :3]).T, axes, vector=True)


def _fillPoints(p, axes):
    """Used by the :func:`transform` function. Turns the given array p into
    a ``N*3`` array of ``x,y,z`` coordinates. The array p may be a 1D array,
    or an ``N*2`` or ``N*3`` array.
    """

    if not isinstance(p, abc.Iterable): p = [p]

    p = np.array(p)

    if axes is None: return p

    if not isinstance(axes, abc.Iterable): axes = [axes]

    if p.ndim == 1:
        p = p.reshape((len(p), 1))

    if p.ndim != 2:
        raise ValueError('Points array must be either one or two '
                         'dimensions')

    if len(axes) != p.shape[1]:
        raise ValueError('Points array shape does not match specified '
                         'number of axes')

    newp = np.zeros((len(p), 3), dtype=p.dtype)

    for i, ax in enumerate(axes):
        newp[:, ax] = p[:, i]

    return newp


def rmsdev(T1, T2, R=None, xc=None):
    """Calculates the RMS deviation of the given affine transforms ``T1`` and
    ``T2``. This can be used as a measure of the 'distance' between two
    affines.

    The ``T1`` and ``T2`` arguments may be either full ``(4, 4)`` affines, or
    ``(3, 3)`` rotation matrices.

    See FMRIB technical report TR99MJ1, available at:

    https://www.fmrib.ox.ac.uk/datasets/techrep/

    :arg T1:  First affine
    :arg T2:  Second affine
    :arg R:   Sphere radius
    :arg xc:  Sphere centre
    :returns: The RMS deviation between ``T1`` and ``T2``.
    """

    if R is None:
        R = 1

    if xc is None:
        xc = np.zeros(3)

    # rotations only
    if T1.shape == (3, 3):
        M = np.dot(T2, invert(T1)) - np.eye(3)
        A = M[:3, :3]
        t = np.zeros(3)

    # full affine
    else:
        M = np.dot(T2, invert(T1)) - np.eye(4)
        A = M[:3, :3]
        t = M[:3,  3]

    Axc = np.dot(A, xc)

    erms = np.dot((t + Axc).T, t + Axc)
    erms = 0.2 * R ** 2 * np.dot(A.T, A).trace() + erms
    erms = np.sqrt(erms)

    return erms


def rescale(oldShape, newShape, origin=None):
    """Calculates an affine matrix to use for resampling.

    This function generates an affine transformation matrix that can be used
    to resample an N-D array from ``oldShape`` to ``newShape`` using, for
    example, ``scipy.ndimage.affine_transform``.

    The matrix will contain scaling factors derived from the ``oldShape /
    newShape`` ratio, and an offset determined by the ``origin``.

    The default value for ``origin`` (``'centre'``) causes the corner voxel of
    the output to have the same centre as the corner voxel of the input. If
    the origin is ``'corner'``, we apply an offset which effectively causes
    the voxel grid corners of the input and output to be aligned.

    :arg oldShape: Shape of input data
    :arg newShape: Shape to resample data to
    :arg origin:   Voxel grid alignment - either ``'centre'`` (the default) or
                   ``'corner'``
    :returns:      An affine resampling matrix
    """

    if origin is None:
        origin = 'centre'

    oldShape = np.array(oldShape, dtype=float)
    newShape = np.array(newShape, dtype=float)
    ndim     = len(oldShape)

    if len(oldShape) != len(newShape):
        raise ValueError('Shape mismatch')

    # shapes are the same - no rescaling needed
    if np.all(np.isclose(oldShape, newShape)):
        return np.eye(ndim + 1)

    # Otherwise we calculate a scaling
    # matrix from the old/new shape
    # ratio, and specify an offset
    # according to the origin
    ratio = oldShape / newShape
    scale = np.diag(ratio)

    # Calculate an offset from the origin
    if   origin == 'centre': offset = [0] * ndim
    elif origin == 'corner': offset = (ratio - 1) / 2

    # combine the scales and translations
    # to form thte final affine
    xform               = np.eye(ndim + 1)
    xform[:ndim, :ndim] = scale
    xform[:ndim, -1]    = offset

    return xform

#!/usr/bin/env python
#
# affine.py - Utility functions for working with affine transformations.
#
# Author: <NAME> <<EMAIL>>
#
"""This module contains utility functions for working with affine
transformations. The following functions are available:

.. autosummary::
   :nosignatures:

   transform
   scaleOffsetXform
   invert
   concat
   compose
   decompose
   rotMatToAffine
   rotMatToAxisAngles
   axisAnglesToRotMat
   axisBounds
   rmsdev
   rescale

And a few more functions are provided for working with vectors:

.. autosummary::
   :nosignatures:

   veclength
   normalise
   transformNormal
"""


import collections.abc as abc
import numpy           as np
import numpy.linalg    as linalg


def invert(x):
    """Inverts the given matrix using ``numpy.linalg.inv``. """
    return linalg.inv(x)


def concat(*xforms):
    """Combines the given matrices (returns the dot product)."""

    result = xforms[0]

    for i in range(1, len(xforms)):
        result = np.dot(result, xforms[i])

    return result


def veclength(vec):
    """Returns the length of the given vector(s).

    Multiple vectors may be passed in, with a shape of ``(n, 3)``.
    """
    vec = np.array(vec, copy=False).reshape(-1, 3)
    return np.sqrt(np.einsum('ij,ij->i', vec, vec))


def normalise(vec):
    """Normalises the given vector(s) to unit length.

    Multiple vectors may be passed in, with a shape of ``(n, 3)``.
    """
    vec = np.array(vec, copy=False).reshape(-1, 3)
    n   = (vec.T / veclength(vec)).T

    if n.size == 3:
        n = n[0]

    return n


def scaleOffsetXform(scales, offsets):
    """Creates and returns an affine transformation matrix which encodes
    the specified scale(s) and offset(s).


    :arg scales:  A tuple of up to three values specifying the scale factors
                  for each dimension. If less than length 3, is padded with
                  ``1.0``.

    :arg offsets: A tuple of up to three values specifying the offsets for
                  each dimension. If less than length 3, is padded with
                  ``0.0``.

    :returns:     A ``numpy.float32`` array of size :math:`4 \\times 4`.
    """

    oktypes = (abc.Sequence, np.ndarray)

    if not isinstance(scales,  oktypes): scales  = [scales]
    if not isinstance(offsets, oktypes): offsets = [offsets]
    if not isinstance(scales,  list):    scales  = list(scales)
    if not isinstance(offsets, list):    offsets = list(offsets)

    lens = len(scales)
    leno = len(offsets)

    if lens < 3: scales  = scales  + [1.0] * (3 - lens)
    if leno < 3: offsets = offsets + [0.0] * (3 - leno)

    xform = np.eye(4, dtype=np.float64)

    xform[0, 0] = scales[0]
    xform[1, 1] = scales[1]
    xform[2, 2] = scales[2]

    xform[0, 3] = offsets[0]
    xform[1, 3] = offsets[1]
    xform[2, 3] = offsets[2]

    return xform


def compose(scales, offsets, rotations, origin=None, shears=None):
    """Compose a transformation matrix out of the given scales, offsets
    and axis rotations.

    :arg scales:    Sequence of three scale values.

    :arg offsets:   Sequence of three offset values.

    :arg rotations: Sequence of three rotation values, in radians, or
                    a rotation matrix of shape ``(3, 3)``.

    :arg origin:    Origin of rotation - must be scaled by the ``scales``.
                    If not provided, the rotation origin is ``(0, 0, 0)``.

    :arg shears:    Sequence of three shear values
    """

    preRotate  = np.eye(4)
    postRotate = np.eye(4)

    rotations = np.array(rotations)

    if rotations.shape == (3,):
        rotations = axisAnglesToRotMat(*rotations)

    if origin is not None:
        preRotate[ 0, 3] = -origin[0]
        preRotate[ 1, 3] = -origin[1]
        preRotate[ 2, 3] = -origin[2]
        postRotate[0, 3] =  origin[0]
        postRotate[1, 3] =  origin[1]
        postRotate[2, 3] =  origin[2]

    scale  = np.eye(4, dtype=np.float64)
    offset = np.eye(4, dtype=np.float64)
    rotate = np.eye(4, dtype=np.float64)
    shear  = np.eye(4, dtype=np.float64)

    scale[  0,  0] = scales[ 0]
    scale[  1,  1] = scales[ 1]
    scale[  2,  2] = scales[ 2]
    offset[ 0,  3] = offsets[0]
    offset[ 1,  3] = offsets[1]
    offset[ 2,  3] = offsets[2]

    rotate[:3, :3] = rotations

    if shears is not None:
        shear[0, 1] = shears[0]
        shear[0, 2] = shears[1]
        shear[1, 2] = shears[2]

    return concat(offset, postRotate, rotate, preRotate, scale, shear)


def decompose(xform, angles=True, shears=False):
    """Decomposes the given transformation matrix into separate offsets,
    scales, and rotations, according to the algorithm described in:

    <NAME>, Decomposing a matrix into simple transformations, pp
    320-323 in *Graphics Gems II*, <NAME> (editor), Academic Press, 1991,
    ISBN: 0120644819.

    It is assumed that the given transform has no perspective components.

    :arg xform:  A ``(3, 3)`` or ``(4, 4)`` affine transformation matrix.

    :arg angles: If ``True`` (the default), the rotations are returned
                 as axis-angles, in radians. Otherwise, the rotation matrix
                 is returned.

    :arg shears: Defaults to ``False``. If ``True``, shears are returned.

    :returns: The following:

               - A sequence of three scales
               - A sequence of three translations (all ``0`` if ``xform``
                 was a ``(3, 3)`` matrix)
               - A sequence of three rotations, in radians. Or, if
                 ``angles is False``, a rotation matrix.
               - If ``shears is True``, a sequence of three shears.
    """

    # The inline comments in the code below are taken verbatim from
    # the referenced article, [except for notes in square brackets].

    # The next step is to extract the translations. This is trivial;
    # we find t_x = M_{4,1}, t_y = M_{4,2}, and t_z = M_{4,3}. At this
    # point we are left with a 3*3 matrix M' = M_{1..3,1..3}.
    xform = np.array(xform).T

    if xform.shape == (4, 4):
        translations = xform[ 3, :3]
        xform        = xform[:3, :3]
    else:
        translations = np.array([0, 0, 0])

    M1 = xform[0]
    M2 = xform[1]
    M3 = xform[2]

    # The process of finding the scaling factors and shear parameters
    # is interleaved. First, find s_x = |M'_1|.
    sx = np.sqrt(np.dot(M1, M1))
    M1 = M1 / sx

    # Then, compute an initial value for the xy shear factor,
    # s_xy = M'_1 * M'_2. (this is too large by the y scaling factor).
    sxy = np.dot(M1, M2)

    # The second row of the matrix is made orthogonal to the first by
    # setting M'_2 = M'_2 - s_xy * M'_1.
    M2 = M2 - sxy * M1

    # Then the y scaling factor, s_y, is the length of the modified
    # second row.
    sy = np.sqrt(np.dot(M2, M2))

    # The second row is normalized, and s_xy is divided by s_y to
    # get its final value.
    M2  = M2  / sy
    sxy = sxy / sx

    # The xz and yz shear factors are computed as in the preceding,
    sxz = np.dot(M1, M3)
    syz = np.dot(M2, M3)

    # the third row is made orthogonal to the first two rows,
    M3 = M3 - sxz * M1 - syz * M2

    # the z scaling factor is computed,
    sz = np.sqrt(np.dot(M3, M3))

    # the third row is normalized, and the xz and yz shear factors are
    # rescaled.
    M3  = M3  / sz
    sxz = sxz / sx
    syz = syz / sy

    # The resulting matrix now is a pure rotation matrix, except that it
    # might still include a scale factor of -1. If the determinant of the
    # matrix is -1, negate the matrix and all three scaling factors. Call
    # the resulting matrix R.
    #
    # [We do things different here - if the rotation matrix has negative
    #  determinant, the flip is encoded in the x scaling factor.]
    R = np.array([M1, M2, M3])
    if linalg.det(R) < 0:
        R[0] = -R[0]
        sx   = -sx

    # Finally, we need to decompose the rotation matrix into a sequence
    # of rotations about the x, y, and z axes. [This is done in the
    # rotMatToAxisAngles function]
    if angles: rotations = rotMatToAxisAngles(R.T)
    else:      rotations = R.T

    retval = [np.array([sx, sy, sz]), translations, rotations]

    if shears:
        retval.append(np.array((sxy, sxz, syz)))

    return tuple(retval)



def rotMatToAffine(rotmat, origin=None):
    """Convenience function which encodes the given ``(3, 3)`` rotation
    matrix into a ``(4, 4)`` affine.
    """
    return compose([1, 1, 1], [0, 0, 0], rotmat, origin)


def rotMatToAxisAngles(rotmat):
    """Given a ``(3, 3)`` rotation matrix, decomposes the rotations into
    an angle in radians about each axis.
    """

    yrot = np.sqrt(rotmat[0, 0] ** 2 + rotmat[1, 0] ** 2)

    if np.isclose(yrot, 0):
        xrot = np.arctan2(-rotmat[1, 2], rotmat[1, 1])
        yrot = np.arctan2(-rotmat[2, 0], yrot)
        zrot = 0
    else:
        xrot = np.arctan2( rotmat[2, 1], rotmat[2, 2])
        yrot = np.arctan2(-rotmat[2, 0], yrot)
        zrot = np.arctan2( rotmat[1, 0], rotmat[0, 0])

    return [xrot, yrot, zrot]


def axisAnglesToRotMat(xrot, yrot, zrot):
    """Constructs a ``(3, 3)`` rotation matrix from the given angles, which
    must be specified in radians.
    """

    xmat = np.eye(3)
    ymat = np.eye(3)
    zmat = np.eye(3)

    xmat[1, 1] =  np.cos(xrot)
    xmat[1, 2] = -np.sin(xrot)
    xmat[2, 1] =  np.sin(xrot)
    xmat[2, 2] =  np.cos(xrot)

    ymat[0, 0] =  np.cos(yrot)
    ymat[0, 2] =  np.sin(yrot)
    ymat[2, 0] = -np.sin(yrot)
    ymat[2, 2] =  np.cos(yrot)

    zmat[0, 0] =  np.cos(zrot)
    zmat[0, 1] = -np.sin(zrot)
    zmat[1, 0] =  np.sin(zrot)
    zmat[1, 1] =  np.cos(zrot)

    return concat(zmat, ymat, xmat)


def axisBounds(shape,
               xform,
               axes=None,
               origin='centre',
               boundary='high',
               offset=1e-4):
    """Returns the ``(lo, hi)`` bounds of the specified axis/axes in the
    world coordinate system defined by ``xform``.

    If the ``origin`` parameter is set to  ``centre`` (the default),
    this function assumes that voxel indices correspond to the voxel
    centre. For example, the voxel at ``(4, 5, 6)`` covers the space:

      ``[3.5 - 4.5, 4.5 - 5.5, 5.5 - 6.5]``

    So the bounds of the specified shape extends from the corner at

      ``(-0.5, -0.5, -0.5)``

    to the corner at

      ``(shape[0] - 0.5, shape[1] - 0.5, shape[1] - 0.5)``

    If the ``origin`` parameter is set to ``corner``, this function
    assumes that voxel indices correspond to the voxel corner. In this
    case, a voxel  at ``(4, 5, 6)`` covers the space:

      ``[4 - 5, 5 - 6, 6 - 7]``

    So the bounds of the specified shape extends from the corner at

      ``(0, 0, 0)``

    to the corner at

      ``(shape[0], shape[1], shape[1])``.


    If the ``boundary`` parameter is set to ``high``, the high voxel bounds
    are reduced by a small amount (specified by the ``offset`` parameter)
    before they are transformed to the world coordinate system.  If
    ``boundary`` is set to ``low``, the low bounds are increased by a small
    amount.  The ``boundary`` parameter can also be set to ``'both'``, or
    ``None``. This option is provided so that you can ensure that the
    resulting bounds will always be contained within the image space.

    :arg shape:    The ``(x, y, z)`` shape of the data.

    :arg xform:    Transformation matrix which transforms voxel coordinates
                   to the world coordinate system.

    :arg axes:     The world coordinate system axis bounds to calculate.

    :arg origin:   Either ``'centre'`` (the default) or ``'corner'``.

    :arg boundary: Either ``'high'`` (the default), ``'low'``, ''`both'``,
                   or ``None``.

    :arg offset:   Amount by which the boundary voxel coordinates should be
                   offset. Defaults to ``1e-4``.

    :returns:      A tuple containing the ``(low, high)`` bounds for each
                   requested world coordinate system axis.
    """

    origin = origin.lower()

    # lousy US spelling
    if origin == 'center':
        origin = 'centre'

    if origin not in ('centre', 'corner'):
        raise ValueError('Invalid origin value: {}'.format(origin))
    if boundary not in ('low', 'high', 'both', None):
        raise ValueError('Invalid boundary value: {}'.format(boundary))

    scalar = False

    if axes is None:
        axes = [0, 1, 2]

    elif not isinstance(axes, abc.Iterable):
        scalar = True
        axes   = [axes]

    x, y, z = shape[:3]

    points = np.zeros((8, 3), dtype=np.float32)

    if origin == 'centre':
        x0 = -0.5
        y0 = -0.5
        z0 = -0.5
        x -=  0.5
        y -=  0.5
        z -=  0.5
    else:
        x0 = 0
        y0 = 0
        z0 = 0

    if boundary in ('low', 'both'):
        x0 += offset
        y0 += offset
        z0 += offset

    if boundary in ('high', 'both'):
        x  -= offset
        y  -= offset
        z  -= offset

    points[0, :] = [x0, y0, z0]
    points[1, :] = [x0, y0,  z]
    points[2, :] = [x0,  y, z0]
    points[3, :] = [x0,  y,  z]
    points[4, :] = [x,  y0, z0]
    points[5, :] = [x,  y0,  z]
    points[6, :] = [x,   y, z0]
    points[7, :] = [x,   y,  z]

    tx = transform(points, xform)

    lo = tx[:, axes].min(axis=0)
    hi = tx[:, axes].max(axis=0)

    if scalar: return (lo[0], hi[0])
    else:      return (lo,    hi)


def transform(p, xform, axes=None, vector=False):
    """Transforms the given set of points ``p`` according to the given affine
    transformation ``xform``.


    :arg p:      A sequence or array of points of shape :math:`N \\times  3`.

    :arg xform:  A ``(4, 4)`` affine transformation matrix with which to
                 transform the points in ``p``.

    :arg axes:   If you are only interested in one or two axes, and the source
                 axes are orthogonal to the target axes (see the note below),
                 you may pass in a 1D, ``N*1``, or ``N*2`` array as ``p``, and
                 use this argument to specify which axis/axes that the data in
                 ``p`` correspond to.

    :arg vector: Defaults to ``False``. If ``True``, the points are treated
                 as vectors - the translation component of the transformation
                 is not applied. If you set this flag, you pass in a ``(3, 3)``
                 transformation matrix.

    :returns:    The points in ``p``, transformed by ``xform``, as a ``numpy``
                 array with the same data type as the input.


    .. note:: The ``axes`` argument should only be used if the source
              coordinate system (the points in ``p``) axes are orthogonal
              to the target coordinate system (defined by the ``xform``).

              In other words, you can only use the ``axes`` argument if
              the ``xform`` matrix consists solely of translations and
              scalings.
    """

    p  = _fillPoints(p, axes)
    t  = np.dot(xform[:3, :3], p.T).T

    if not vector:
        t = t + xform[:3, 3]

    if axes is not None:
        t = t[:, axes]

    if t.size == 1: return t[0]
    else:           return t


def transformNormal(p, xform, axes=None):
    """Transforms the given point(s), under the assumption that they
    are normal vectors. In this case, the points are transformed by
    ``invert(xform[:3, :3]).T``.
    """
    return transform(p, invert(xform[:3, :3]).T, axes, vector=True)


def _fillPoints(p, axes):
    """Used by the :func:`transform` function. Turns the given array p into
    a ``N*3`` array of ``x,y,z`` coordinates. The array p may be a 1D array,
    or an ``N*2`` or ``N*3`` array.
    """

    if not isinstance(p, abc.Iterable): p = [p]

    p = np.array(p)

    if axes is None: return p

    if not isinstance(axes, abc.Iterable): axes = [axes]

    if p.ndim == 1:
        p = p.reshape((len(p), 1))

    if p.ndim != 2:
        raise ValueError('Points array must be either one or two '
                         'dimensions')

    if len(axes) != p.shape[1]:
        raise ValueError('Points array shape does not match specified '
                         'number of axes')

    newp = np.zeros((len(p), 3), dtype=p.dtype)

    for i, ax in enumerate(axes):
        newp[:, ax] = p[:, i]

    return newp


def rmsdev(T1, T2, R=None, xc=None):
    """Calculates the RMS deviation of the given affine transforms ``T1`` and
    ``T2``. This can be used as a measure of the 'distance' between two
    affines.

    The ``T1`` and ``T2`` arguments may be either full ``(4, 4)`` affines, or
    ``(3, 3)`` rotation matrices.

    See FMRIB technical report TR99MJ1, available at:

    https://www.fmrib.ox.ac.uk/datasets/techrep/

    :arg T1:  First affine
    :arg T2:  Second affine
    :arg R:   Sphere radius
    :arg xc:  Sphere centre
    :returns: The RMS deviation between ``T1`` and ``T2``.
    """

    if R is None:
        R = 1

    if xc is None:
        xc = np.zeros(3)

    # rotations only
    if T1.shape == (3, 3):
        M = np.dot(T2, invert(T1)) - np.eye(3)
        A = M[:3, :3]
        t = np.zeros(3)

    # full affine
    else:
        M = np.dot(T2, invert(T1)) - np.eye(4)
        A = M[:3, :3]
        t = M[:3,  3]

    Axc = np.dot(A, xc)

    erms = np.dot((t + Axc).T, t + Axc)
    erms = 0.2 * R ** 2 * np.dot(A.T, A).trace() + erms
    erms = np.sqrt(erms)

    return erms


def rescale(oldShape, newShape, origin=None):
    """Calculates an affine matrix to use for resampling.

    This function generates an affine transformation matrix that can be used
    to resample an N-D array from ``oldShape`` to ``newShape`` using, for
    example, ``scipy.ndimage.affine_transform``.

    The matrix will contain scaling factors derived from the ``oldShape /
    newShape`` ratio, and an offset determined by the ``origin``.

    The default value for ``origin`` (``'centre'``) causes the corner voxel of
    the output to have the same centre as the corner voxel of the input. If
    the origin is ``'corner'``, we apply an offset which effectively causes
    the voxel grid corners of the input and output to be aligned.

    :arg oldShape: Shape of input data
    :arg newShape: Shape to resample data to
    :arg origin:   Voxel grid alignment - either ``'centre'`` (the default) or
                   ``'corner'``
    :returns:      An affine resampling matrix
    """

    if origin is None:
        origin = 'centre'

    oldShape = np.array(oldShape, dtype=float)
    newShape = np.array(newShape, dtype=float)
    ndim     = len(oldShape)

    if len(oldShape) != len(newShape):
        raise ValueError('Shape mismatch')

    # shapes are the same - no rescaling needed
    if np.all(np.isclose(oldShape, newShape)):
        return np.eye(ndim + 1)

    # Otherwise we calculate a scaling
    # matrix from the old/new shape
    # ratio, and specify an offset
    # according to the origin
    ratio = oldShape / newShape
    scale = np.diag(ratio)

    # Calculate an offset from the origin
    if   origin == 'centre': offset = [0] * ndim
    elif origin == 'corner': offset = (ratio - 1) / 2

    # combine the scales and translations
    # to form thte final affine
    xform               = np.eye(ndim + 1)
    xform[:ndim, :ndim] = scale
    xform[:ndim, -1]    = offset

    return xform
#!/usr/bin/env python # # affine.py - Utility functions for working with affine transformations. # # Author: <NAME> <<EMAIL>> # This module contains utility functions for working with affine transformations. The following functions are available:  .. autosummary::    :nosignatures:     transform    scaleOffsetXform    invert    concat    compose    decompose    rotMatToAffine    rotMatToAxisAngles    axisAnglesToRotMat    axisBounds    rmsdev    rescale  And a few more functions are provided for working with vectors:  .. autosummary::    :nosignatures:     veclength    normalise    transformNormal Inverts the given matrix using ``numpy.linalg.inv``. Combines the given matrices (returns the dot product). Returns the length of the given vector(s).      Multiple vectors may be passed in, with a shape of ``(n, 3)``. Normalises the given vector(s) to unit length.      Multiple vectors may be passed in, with a shape of ``(n, 3)``. Creates and returns an affine transformation matrix which encodes     the specified scale(s) and offset(s).       :arg scales:  A tuple of up to three values specifying the scale factors                   for each dimension. If less than length 3, is padded with                   ``1.0``.      :arg offsets: A tuple of up to three values specifying the offsets for                   each dimension. If less than length 3, is padded with                   ``0.0``.      :returns:     A ``numpy.float32`` array of size :math:`4 \\times 4`. Compose a transformation matrix out of the given scales, offsets     and axis rotations.      :arg scales:    Sequence of three scale values.      :arg offsets:   Sequence of three offset values.      :arg rotations: Sequence of three rotation values, in radians, or                     a rotation matrix of shape ``(3, 3)``.      :arg origin:    Origin of rotation - must be scaled by the ``scales``.                     If not provided, the rotation origin is ``(0, 0, 0)``.      :arg shears:    Sequence of three shear values Decomposes the given transformation matrix into separate offsets,     scales, and rotations, according to the algorithm described in:      <NAME>, Decomposing a matrix into simple transformations, pp     320-323 in *Graphics Gems II*, <NAME> (editor), Academic Press, 1991,     ISBN: 0120644819.      It is assumed that the given transform has no perspective components.      :arg xform:  A ``(3, 3)`` or ``(4, 4)`` affine transformation matrix.      :arg angles: If ``True`` (the default), the rotations are returned                  as axis-angles, in radians. Otherwise, the rotation matrix                  is returned.      :arg shears: Defaults to ``False``. If ``True``, shears are returned.      :returns: The following:                 - A sequence of three scales                - A sequence of three translations (all ``0`` if ``xform``                  was a ``(3, 3)`` matrix)                - A sequence of three rotations, in radians. Or, if                  ``angles is False``, a rotation matrix.                - If ``shears is True``, a sequence of three shears. # The inline comments in the code below are taken verbatim from # the referenced article, [except for notes in square brackets]. # The next step is to extract the translations. This is trivial; # we find t_x = M_{4,1}, t_y = M_{4,2}, and t_z = M_{4,3}. At this # point we are left with a 3*3 matrix M' = M_{1..3,1..3}. # The process of finding the scaling factors and shear parameters # is interleaved. First, find s_x = |M'_1|. # Then, compute an initial value for the xy shear factor, # s_xy = M'_1 * M'_2. (this is too large by the y scaling factor). # The second row of the matrix is made orthogonal to the first by # setting M'_2 = M'_2 - s_xy * M'_1. # Then the y scaling factor, s_y, is the length of the modified # second row. # The second row is normalized, and s_xy is divided by s_y to # get its final value. # The xz and yz shear factors are computed as in the preceding, # the third row is made orthogonal to the first two rows, # the z scaling factor is computed, # the third row is normalized, and the xz and yz shear factors are # rescaled. # The resulting matrix now is a pure rotation matrix, except that it # might still include a scale factor of -1. If the determinant of the # matrix is -1, negate the matrix and all three scaling factors. Call # the resulting matrix R. # # [We do things different here - if the rotation matrix has negative #  determinant, the flip is encoded in the x scaling factor.] # Finally, we need to decompose the rotation matrix into a sequence # of rotations about the x, y, and z axes. [This is done in the # rotMatToAxisAngles function] Convenience function which encodes the given ``(3, 3)`` rotation     matrix into a ``(4, 4)`` affine. Given a ``(3, 3)`` rotation matrix, decomposes the rotations into     an angle in radians about each axis. Constructs a ``(3, 3)`` rotation matrix from the given angles, which     must be specified in radians. Returns the ``(lo, hi)`` bounds of the specified axis/axes in the     world coordinate system defined by ``xform``.      If the ``origin`` parameter is set to  ``centre`` (the default),     this function assumes that voxel indices correspond to the voxel     centre. For example, the voxel at ``(4, 5, 6)`` covers the space:        ``[3.5 - 4.5, 4.5 - 5.5, 5.5 - 6.5]``      So the bounds of the specified shape extends from the corner at        ``(-0.5, -0.5, -0.5)``      to the corner at        ``(shape[0] - 0.5, shape[1] - 0.5, shape[1] - 0.5)``      If the ``origin`` parameter is set to ``corner``, this function     assumes that voxel indices correspond to the voxel corner. In this     case, a voxel  at ``(4, 5, 6)`` covers the space:        ``[4 - 5, 5 - 6, 6 - 7]``      So the bounds of the specified shape extends from the corner at        ``(0, 0, 0)``      to the corner at        ``(shape[0], shape[1], shape[1])``.       If the ``boundary`` parameter is set to ``high``, the high voxel bounds     are reduced by a small amount (specified by the ``offset`` parameter)     before they are transformed to the world coordinate system.  If     ``boundary`` is set to ``low``, the low bounds are increased by a small     amount.  The ``boundary`` parameter can also be set to ``'both'``, or     ``None``. This option is provided so that you can ensure that the     resulting bounds will always be contained within the image space.      :arg shape:    The ``(x, y, z)`` shape of the data.      :arg xform:    Transformation matrix which transforms voxel coordinates                    to the world coordinate system.      :arg axes:     The world coordinate system axis bounds to calculate.      :arg origin:   Either ``'centre'`` (the default) or ``'corner'``.      :arg boundary: Either ``'high'`` (the default), ``'low'``, ''`both'``,                    or ``None``.      :arg offset:   Amount by which the boundary voxel coordinates should be                    offset. Defaults to ``1e-4``.      :returns:      A tuple containing the ``(low, high)`` bounds for each                    requested world coordinate system axis. # lousy US spelling Transforms the given set of points ``p`` according to the given affine     transformation ``xform``.       :arg p:      A sequence or array of points of shape :math:`N \\times  3`.      :arg xform:  A ``(4, 4)`` affine transformation matrix with which to                  transform the points in ``p``.      :arg axes:   If you are only interested in one or two axes, and the source                  axes are orthogonal to the target axes (see the note below),                  you may pass in a 1D, ``N*1``, or ``N*2`` array as ``p``, and                  use this argument to specify which axis/axes that the data in                  ``p`` correspond to.      :arg vector: Defaults to ``False``. If ``True``, the points are treated                  as vectors - the translation component of the transformation                  is not applied. If you set this flag, you pass in a ``(3, 3)``                  transformation matrix.      :returns:    The points in ``p``, transformed by ``xform``, as a ``numpy``                  array with the same data type as the input.       .. note:: The ``axes`` argument should only be used if the source               coordinate system (the points in ``p``) axes are orthogonal               to the target coordinate system (defined by the ``xform``).                In other words, you can only use the ``axes`` argument if               the ``xform`` matrix consists solely of translations and               scalings. Transforms the given point(s), under the assumption that they     are normal vectors. In this case, the points are transformed by     ``invert(xform[:3, :3]).T``. Used by the :func:`transform` function. Turns the given array p into     a ``N*3`` array of ``x,y,z`` coordinates. The array p may be a 1D array,     or an ``N*2`` or ``N*3`` array. Calculates the RMS deviation of the given affine transforms ``T1`` and     ``T2``. This can be used as a measure of the 'distance' between two     affines.      The ``T1`` and ``T2`` arguments may be either full ``(4, 4)`` affines, or     ``(3, 3)`` rotation matrices.      See FMRIB technical report TR99MJ1, available at:      https://www.fmrib.ox.ac.uk/datasets/techrep/      :arg T1:  First affine     :arg T2:  Second affine     :arg R:   Sphere radius     :arg xc:  Sphere centre     :returns: The RMS deviation between ``T1`` and ``T2``. # rotations only # full affine Calculates an affine matrix to use for resampling.      This function generates an affine transformation matrix that can be used     to resample an N-D array from ``oldShape`` to ``newShape`` using, for     example, ``scipy.ndimage.affine_transform``.      The matrix will contain scaling factors derived from the ``oldShape /     newShape`` ratio, and an offset determined by the ``origin``.      The default value for ``origin`` (``'centre'``) causes the corner voxel of     the output to have the same centre as the corner voxel of the input. If     the origin is ``'corner'``, we apply an offset which effectively causes     the voxel grid corners of the input and output to be aligned.      :arg oldShape: Shape of input data     :arg newShape: Shape to resample data to     :arg origin:   Voxel grid alignment - either ``'centre'`` (the default) or                    ``'corner'``     :returns:      An affine resampling matrix # shapes are the same - no rescaling needed # Otherwise we calculate a scaling # matrix from the old/new shape # ratio, and specify an offset # according to the origin # Calculate an offset from the origin # combine the scales and translations # to form thte final affine