Python numpy.asanyarray方法代码示例

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def format_mask(x):
    """
    Formats a mask into a readable string.
    Args:
        x (ndarray): an array with the mask;

    Returns:
        A readable string with the mask.
    """
    x = numpy.asanyarray(x)
    if len(x) == 0:
        return "(empty)"
    if x.dtype == bool:
        x = numpy.argwhere(x)[:, 0]
    grps = tuple(list(g) for _, g in groupby(x, lambda n, c=count(): n-next(c)))
    return ",".join("{:d}-{:d}".format(i[0], i[-1]) if len(i) > 1 else "{:d}".format(i[0]) for i in grps) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def image_copy(img, dataobj=Ellipsis, affine=Ellipsis, image_type=None):
    '''
    image_copy(image) copies the given image and returns the new object; the affine, header, and
      dataobj members are duplicated so that changes will not change the original image.
    
    The following optional arguments may be given to overwrites part of the new image; in each case,
    the default value (Ellipsis) specifies that no update should be made.
      * dataobj (default: Ellipsis) may overwrite the new image's dataobj object.
      * affine (default: Ellipsis) may overwrite the new image's affine transformation matrix.
    '''
    dataobj = np.array(img.dataobj) if dataobj is Ellipsis else np.asanyarray(dataobj)
    imspec = to_image_spec(img)
    imtype = to_image_type(img if image_type is None else image_type)
    affine = imspec['affine'] if affine is Ellipsis else affine
    imspec['affine'] = affine
    return imtype.create(dataobj, imspec) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def apply_affine(aff, coords):
    '''
    apply_affine(affine, coords) yields the result of applying the given affine transformation to
      the given coordinate or coordinates.

    This function expects coords to be a (dims X n) matrix but if the first dimension is neither 2
    nor 3, coords.T is used; i.e.:
      apply_affine(affine3x3, coords2xN) ==> newcoords2xN
      apply_affine(affine4x4, coords3xN) ==> newcoords3xN
      apply_affine(affine3x3, coordsNx2) ==> newcoordsNx2 (for N != 2)
      apply_affine(affine4x4, coordsNx3) ==> newcoordsNx3 (for N != 3)
    '''
    if aff is None: return coords
    (coords,tr) = (np.asanyarray(coords), False)
    if len(coords.shape) == 1: return np.squeeze(apply_affine(np.reshape(coords, (-1,1)), aff))
    elif len(coords.shape) > 2: raise ValueError('cannot apply affine to ND-array for N > 2')
    if   len(coords) == 2: aff = to_affine(aff, 2)
    elif len(coords) == 3: aff = to_affine(aff, 3)
    else: (coords,aff,tr) = (coords.T, to_affine(aff, coords.shape[1]), True)
    r = np.dot(aff, np.vstack([coords, np.ones([1,coords.shape[1]])]))[:-1]
    return r.T if tr else r 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def supercell_space_required(transform_oo, transform_vv, final_space):
    """
    For a given orbital transformation and a given `ov` mask in the transformed space, calculates a minimal `ov` mask
    in the original space required to achieve this transform.
    Args:
        transform_oo (ndarray): the transformation in the occupied space;
        transform_vv (ndarray): the transformation in the virtual space;
        final_space (ndarray): the final `ov` space. Basis order: [k_o, o, k_v, v];

    Returns:
        The initial active space. Basis order: [k_o, o, k_v, v].
    """
    final_space = numpy.asanyarray(final_space)
    final_space = final_space.reshape(final_space.shape[:-1] + (transform_oo.shape[1], transform_vv.shape[1]))
    result = einsum(
        "ao,bv,...ov->...ab",
        (transform_oo.toarray() != 0).astype(int),
        (transform_vv.toarray() != 0).astype(int),
        final_space.astype(int),
    ) != 0
    return result.reshape(result.shape[:-2] + (-1,)) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def orb2ov(space, nocc, nmo):
    """
    Converts orbital active space specification into ov-pairs space spec.
    Args:
        space (ndarray): the obital space. Basis order: [k, orb=o+v];
        nocc (Iterable): the numbers of occupied orbitals per k-point;
        nmo (Iterable): the total numbers of orbitals per k-point;

    Returns:
        The ov space specification. Basis order: [k_o, o, k_v, v].
    """
    space = numpy.asanyarray(space)
    m = ko_mask(nocc, nmo)  # [k, orb=o+v]
    o = space[...,  m]  # [k, o]
    v = space[..., ~m]  # [k, v]
    return (o[..., numpy.newaxis] * v[..., numpy.newaxis, :]).reshape(space.shape[:-1] + (-1,))  # [k_o, o, k_v, v] 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def vector_to_amplitudes(vectors, nocc, nmo):
    """
    Transforms (reshapes) and normalizes vectors into amplitudes.
    Args:
        vectors (numpy.ndarray): raw eigenvectors to transform;
        nocc (tuple): numbers of occupied orbitals;
        nmo (int): the total number of orbitals per k-point;

    Returns:
        Amplitudes with the following shape: (# of roots, 2 (x or y), # of kpts, # of occupied orbitals,
        # of virtual orbitals).
    """
    if not all(i == nocc[0] for i in nocc):
        raise NotImplementedError("Varying occupation numbers are not implemented yet")
    nk = len(nocc)
    nocc = nocc[0]
    if not all(i == nmo[0] for i in nmo):
        raise NotImplementedError("Varying AO spaces are not implemented yet")
    nmo = nmo[0]
    vectors = numpy.asanyarray(vectors)
    vectors = vectors.reshape(2, nk, nocc, nmo-nocc, vectors.shape[1])
    norm = (abs(vectors) ** 2).sum(axis=(1, 2, 3))
    norm = 2 * (norm[0] - norm[1])
    vectors /= norm ** .5
    return vectors.transpose(4, 0, 1, 2, 3) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def vector_to_amplitudes(vectors, nocc, nmo):
    """
    Transforms (reshapes) and normalizes vectors into amplitudes.
    Args:
        vectors (numpy.ndarray): raw eigenvectors to transform;
        nocc (tuple): numbers of occupied orbitals;
        nmo (tuple): the total numbers of AOs per k-point;

    Returns:
        Amplitudes with the following shape: (# of roots, 2 (x or y), # of kpts, # of kpts, # of occupied orbitals,
        # of virtual orbitals).
    """
    if not all(i == nocc[0] for i in nocc):
        raise NotImplementedError("Varying occupation numbers are not implemented yet")
    nk = len(nocc)
    nocc = nocc[0]
    if not all(i == nmo[0] for i in nmo):
        raise NotImplementedError("Varying AO spaces are not implemented yet")
    nmo = nmo[0]
    vectors = numpy.asanyarray(vectors)
    vectors = vectors.reshape(2, nk, nk, nocc, nmo-nocc, vectors.shape[1])
    norm = (abs(vectors) ** 2).sum(axis=(1, 2, 3, 4))
    norm = 2 * (norm[0] - norm[1])
    vectors /= norm ** .5
    return vectors.transpose(5, 0, 1, 2, 3, 4) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def vector_to_amplitudes(vectors, nocc, nmo):
    """
    Transforms (reshapes) and normalizes vectors into amplitudes.
    Args:
        vectors (numpy.ndarray): raw eigenvectors to transform;
        nocc (int): number of occupied orbitals;
        nmo (int): the total number of orbitals;

    Returns:
        Amplitudes with the following shape: (# of roots, 2 (x or y), # of occupied orbitals, # of virtual orbitals).
    """
    vectors = numpy.asanyarray(vectors)
    vectors = vectors.reshape(2, nocc, nmo-nocc, vectors.shape[1])
    norm = (abs(vectors) ** 2).sum(axis=(1, 2))
    norm = 2 * (norm[0] - norm[1])
    vectors /= norm ** .5
    return vectors.transpose(3, 0, 1, 2) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def nside_to_pixel_area(nside):
    """
    Find the area of HEALPix pixels given the pixel dimensions of one of
    the 12 'top-level' HEALPix tiles.

    Parameters
    ----------
    nside : int
        The number of pixels on the side of one of the 12 'top-level' HEALPix tiles.

    Returns
    -------
    pixel_area : :class:`~astropy.units.Quantity`
        The area of the HEALPix pixels
    """
    nside = np.asanyarray(nside, dtype=np.int64)
    _validate_nside(nside)
    npix = 12 * nside * nside
    pixel_area = 4 * math.pi / npix * u.sr
    return pixel_area 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def nside_to_pixel_resolution(nside):
    """
    Find the resolution of HEALPix pixels given the pixel dimensions of one of
    the 12 'top-level' HEALPix tiles.

    Parameters
    ----------
    nside : int
        The number of pixels on the side of one of the 12 'top-level' HEALPix tiles.

    Returns
    -------
    resolution : :class:`~astropy.units.Quantity`
        The resolution of the HEALPix pixels

    See also
    --------
    pixel_resolution_to_nside
    """
    nside = np.asanyarray(nside, dtype=np.int64)
    _validate_nside(nside)
    return (nside_to_pixel_area(nside) ** 0.5).to(u.arcmin) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def nside_to_npix(nside):
    """
    Find the number of pixels corresponding to a HEALPix resolution.

    Parameters
    ----------
    nside : int
        The number of pixels on the side of one of the 12 'top-level' HEALPix tiles.

    Returns
    -------
    npix : int
        The number of pixels in the HEALPix map.
    """
    nside = np.asanyarray(nside, dtype=np.int64)
    _validate_nside(nside)
    return 12 * nside ** 2 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def take(self, indexer, axis=1, verify=True, convert=True):
        """
        Take items along any axis.
        """
        self._consolidate_inplace()
        indexer = (np.arange(indexer.start, indexer.stop, indexer.step,
                             dtype='int64')
                   if isinstance(indexer, slice)
                   else np.asanyarray(indexer, dtype='int64'))

        n = self.shape[axis]
        if convert:
            indexer = maybe_convert_indices(indexer, n)

        if verify:
            if ((indexer == -1) | (indexer >= n)).any():
                raise Exception('Indices must be nonzero and less than '
                                'the axis length')

        new_labels = self.axes[axis].take(indexer)
        return self.reindex_indexer(new_axis=new_labels, indexer=indexer,
                                    axis=axis, allow_dups=True) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def apply_lut(in_dseg, lut, newpath=None):
    """Map the input discrete segmentation to a new label set (lookup table, LUT)."""
    import numpy as np
    import nibabel as nb
    from nipype.utils.filemanip import fname_presuffix

    if newpath is None:
        from os import getcwd
        newpath = getcwd()

    out_file = fname_presuffix(in_dseg, suffix='_dseg', newpath=newpath)
    lut = np.array(lut, dtype='int16')

    segm = nb.load(in_dseg)
    hdr = segm.header.copy()
    hdr.set_data_dtype('int16')
    segm.__class__(lut[np.asanyarray(segm.dataobj, dtype=int)].astype('int16'),
                   segm.affine, hdr).to_filename(out_file)

    return out_file 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def _call_series(self, a, inputs):
        if isinstance(self._q, TENSOR_TYPE):
            q_val = self._q
            index_val = pd.Index([], dtype=q_val.dtype)
            store_index_value = False
        else:
            q_val = np.asanyarray(self._q)
            index_val = pd.Index(q_val)
            store_index_value = True

        # get dtype by tensor
        a_t = astensor(a)
        self._dtype = dtype = tensor_quantile(
            a_t, self._q, interpolation=self._interpolation,
            handle_non_numeric=not self._numeric_only).dtype

        if q_val.ndim == 0:
            return self.new_scalar(inputs, dtype=dtype)
        else:
            return self.new_series(
                inputs, shape=q_val.shape, dtype=dtype,
                index_value=parse_index(index_val, a, q_val, self._interpolation,
                                        type(self).__name__, store_data=store_index_value),
                name=a.name) 

# 需要导入模块: import numpy [as 别名]
# 或者: from numpy import asanyarray [as 别名]
def cifti_split(cii, label=('lh', 'rh', 'rest'), subject=None, hemi=None, null=np.nan):
    '''
    cifti_split(cii, label) yields the rows or columns of the given cifti file that correspond to
      the given label (see below).
    cifti_split(cii) is equivalent to cifti_split(cii, ('lh', 'rh', 'rest')).

    The label argument may be any of the following:
      * a valid CIFTI label name such as 'CIFTI_STRUCTURE_CEREBELLUM' or
        'CIFTI_STRUCTURE_CORTEX_LEFT';
      * an abbreviated name such as 'cerebellum' for 'CIFTI_STRUCTURE_CEREBELLUM'.
      * the abbreviations 'lh' and 'rh' which stand for 'CIFTI_STRUCTURE_CORTEX_LEFT' and 
        'CIFTI_STRUCTURE_CORTEX_RIGHT';
      * the special keyword 'rest', which represents all the rows/columns not collected by any other
        instruction ('rest', by itself, results in the whole matrix being returned); or
      * A tuple of the above, indicating that each of the items listed should be returned
        sequentially in a tuple.

    The following optional arguments may be given:
      * subject (default: None) may specify the subject
      * hemi (default: None) can specify the hemisphere object that 
    '''
    dat = np.asanyarray(cii.dataobj if is_image(cii) else cii)
    n = dat.shape[-1]
    atlas = cifti_split._size_data.get(n, None)
    if atlas is None: raise ValueError('cannot split cifti with size %d' % n)
    if atlas not in cifti_split._atlas_cache:
        patt = os.path.join('data', 'fs_LR', '%s.atlasroi.%dk_fs_LR.shape.gii')
        lgii = nib.load(os.path.join(library_path(), patt % ('lh', atlas)))
        rgii = nib.load(os.path.join(library_path(), patt % ('rh', atlas)))
        cifti_split._atlas_cache[atlas] = tuple([pimms.imm_array(gii.darrays[0].data.astype('bool'))
                                                 for gii in (lgii, rgii)])
    (lroi,rroi) = cifti_split._atlas_cache[atlas]
    (ln,lN) = (np.sum(lroi), len(lroi))
    (rn,rN) = (np.sum(rroi), len(rroi))
    (ldat,rdat,sdat) = [np.full(dat.shape[:-1] + (k,), null) for k in [lN, rN, n - ln - rn]]
    ldat[..., lroi] = dat[..., :ln]
    rdat[..., rroi] = dat[..., ln:(ln+rn)]
    sdat[...] = dat[..., (ln+rn):]
    if ln + rn >= n: sdat = None
    return (ldat, rdat, sdat)