def __setitem__(self, key, x):
row, col = self._parse_indices(key)
if isinstance(row, _int_scalar_types) and\
isinstance(col, _int_scalar_types):
x = cupy.asarray(x, dtype=self.dtype)
if x.size != 1:
raise ValueError('Trying to assign a sequence to an item')
self._set_intXint(row, col, x.flat[0])
return
if isinstance(row, slice):
row = cupy.arange(*row.indices(self.shape[0]))[:, None]
else:
row = cupy.atleast_1d(row)
if isinstance(col, slice):
col = cupy.arange(*col.indices(self.shape[1]))[None, :]
if row.ndim == 1:
row = row[:, None]
else:
col = cupy.atleast_1d(col)
i, j = cupy.broadcast_arrays(row, col)
if i.shape != j.shape:
raise IndexError('number of row and column indices differ')
if isspmatrix(x):
if i.ndim == 1:
# Inner indexing, so treat them like row vectors.
i = i[None]
j = j[None]
broadcast_row = x.shape[0] == 1 and i.shape[0] != 1
broadcast_col = x.shape[1] == 1 and i.shape[1] != 1
if not ((broadcast_row or x.shape[0] == i.shape[0]) and
(broadcast_col or x.shape[1] == i.shape[1])):
raise ValueError('shape mismatch in assignment')
if x.size == 0:
return
x = x.tocoo(copy=True)
x.sum_duplicates()
self._set_arrayXarray_sparse(i, j, x)
else:
# Make x and i into the same shape
x = cupy.asarray(x, dtype=self.dtype)
x, _ = cupy.broadcast_arrays(x, i)
if x.size == 0:
return
x = x.reshape(i.shape)
self._set_arrayXarray(i, j, x)
def normal(loc=0.0, scale=1.0, size=None, dtype=float):
"""Returns an array of normally distributed samples.
Args:
loc (float or array_like of floats): Mean of the normal distribution.
scale (float or array_like of floats):
Standard deviation of the normal distribution.
size (int or tuple of ints): The shape of the array. If ``None``, a
zero-dimensional array is generated.
dtype: Data type specifier. Only :class:`numpy.float32` and
:class:`numpy.float64` types are allowed.
Returns:
cupy.ndarray: Normally distributed samples.
.. seealso:: :func:`numpy.random.normal`
"""
rs = _generator.get_random_state()
if size is None and any(isinstance(arg, cupy.ndarray)
for arg in [scale, loc]):
size = cupy.broadcast_arrays(loc, scale)[0].shape
x = rs.normal(0, 1, size, dtype)
cupy.multiply(x, scale, out=x)
cupy.add(x, loc, out=x)
return x
def _ndim_coords_from_arrays(points, ndim=None):
"""
Convert a tuple of coordinate arrays to a (..., ndim)-shaped array.
"""
if isinstance(points, tuple) and len(points) == 1:
# handle argument tuple
points = points[0]
if isinstance(points, tuple):
p = cp.broadcast_arrays(*points)
n = len(p)
for j in range(1, n):
if p[j].shape != p[0].shape:
raise ValueError(
"coordinate arrays do not have the same shape")
points = cp.empty(p[0].shape + (len(points), ), dtype=float)
for j, item in enumerate(p):
points[..., j] = item
else:
points = cp.asarray(points)
if points.ndim == 1:
if ndim is None:
points = points.reshape(-1, 1)
else:
points = points.reshape(-1, ndim)
return points
def rvs(self, a, b, loc, scale, size):
self.a, self.b = cp.broadcast_arrays(a, b)
H,N = size
U = cp.random.uniform(low=0, high=1, size=(H,N))
x = self._truncnorm_ppf(U, N)
x = x*scale + loc
return x
def broadcast_arrays(*arrays: Array) -> List[Array]:
"""
Array API compatible wrapper for :py:func:`np.broadcast_arrays <numpy.broadcast_arrays>`.
See its docstring for more information.
"""
from ._array_object import Array
return [
Array._new(array) for array in np.broadcast_arrays(*[a._array for a in arrays])
]
def __getitem__(self, key):
# For testing- Scipy >= 1.4.0 is needed to guarantee
# results match.
if scipy_available and numpy.lib.NumpyVersion(
scipy.__version__) < '1.4.0':
raise NotImplementedError(
"Sparse __getitem__() requires Scipy >= 1.4.0")
row, col = self._parse_indices(key)
# Dispatch to specialized methods.
if isinstance(row, _int_scalar_types):
if isinstance(col, _int_scalar_types):
return self._get_intXint(row, col)
elif isinstance(col, slice):
return self._get_intXslice(row, col)
elif col.ndim == 1:
return self._get_intXarray(row, col)
raise IndexError('index results in >2 dimensions')
elif isinstance(row, slice):
if isinstance(col, _int_scalar_types):
return self._get_sliceXint(row, col)
elif isinstance(col, slice):
if row == slice(None) and row == col:
return self.copy()
return self._get_sliceXslice(row, col)
elif col.ndim == 1:
return self._get_sliceXarray(row, col)
raise IndexError('index results in >2 dimensions')
elif row.ndim == 1:
if isinstance(col, _int_scalar_types):
return self._get_arrayXint(row, col)
elif isinstance(col, slice):
return self._get_arrayXslice(row, col)
else: # row.ndim == 2
if isinstance(col, _int_scalar_types):
return self._get_arrayXint(row, col)
elif isinstance(col, slice):
raise IndexError('index results in >2 dimensions')
elif row.shape[1] == 1 and (col.ndim == 1 or col.shape[0] == 1):
# special case for outer indexing
return self._get_columnXarray(row[:, 0], col.ravel())
# The only remaining case is inner (fancy) indexing
row, col = cupy.broadcast_arrays(row, col)
if row.shape != col.shape:
raise IndexError('number of row and column indices differ')
if row.size == 0:
return self.__class__(cupy.atleast_2d(row).shape, dtype=self.dtype)
return self._get_arrayXarray(row, col)
def reshape_backward(self):
dx_reshaped = cp.zeros_like(self.x_reshaped)
out_newaxis = self.output_tensor[:, :, :, cp.newaxis, :, cp.newaxis]
mask = (self.x_reshaped == out_newaxis)
dout_newaxis = self.grads[:, :, :, cp.newaxis, :, cp.newaxis]
dout_broadcast, _ = cp.broadcast_arrays(dout_newaxis, dx_reshaped)
dx_reshaped[mask] = dout_broadcast[mask]
dx_reshaped /= cp.sum(mask, axis=(3, 5), keepdims=True)
outputs = dx_reshaped.reshape(self.input_tensor.shape)
for layer in self.inbounds:
if layer.require_grads:
layer.grads += outputs
else:
layer.grads = self.grads
def polygamma(n, x):
"""Polygamma function n.
Args:
n (cupy.ndarray): The order of the derivative of `psi`.
x (cupy.ndarray): Where to evaluate the polygamma function.
Returns:
cupy.ndarray: The result.
.. seealso:: :data:`scipy.special.polygamma`
"""
n, x = cupy.broadcast_arrays(n, x)
fac2 = (-1.0)**(n + 1) * _gamma.gamma(n + 1.0) * _zeta.zeta(n + 1.0, x)
return cupy.where(n == 0, _digamma.digamma(x), fac2)
def zeta(x, q):
"""Hurwitz zeta function.
Args:
x (cupy.ndarray): Input data, must be real.
q (cupy.ndarray): Input data, must be real.
Returns:
cupy.ndarray: Values of zeta(x, q).
.. seealso:: :data:`scipy.special.zeta`
"""
if x.dtype.char in '?ebBhH':
x = x.astype(cupy.float32)
elif x.dtype.char in 'iIlLqQ':
x = x.astype(cupy.float64)
q = q.astype(x.dtype)
x, q = cupy.broadcast_arrays(x, q)
y = cupy.zeros_like(x)
_get_zeta_kernel()(x, q, y)
return y
def cupy_ravel_multi_index(multi_index, dims):
"""
Sadly CuPy 7.6.0 does not have ravel_multi_index function (only from 8 version)
Implement simple version of it.
:param multi_index: multi indexes
:param dims: dimension of target
"""
ndim = len(dims)
s = 1
ravel_strides = [1] * ndim
for i in range(ndim - 2, -1, -1):
s = s * dims[i + 1]
ravel_strides[i] = s
multi_index = cp.broadcast_arrays(*multi_index)
raveled_indices = cp.zeros(multi_index[0].shape, dtype=cp.int64)
for d, stride, idx in zip(dims, ravel_strides, multi_index):
idx = idx.astype(cp.int64, copy=False)
raveled_indices += stride * idx
return raveled_indices
def _select(input, labels=None, index=None, find_min=False, find_max=False,
find_min_positions=False, find_max_positions=False,
find_median=False):
"""Return one or more of: min, max, min position, max position, median.
If neither `labels` or `index` is provided, these are the global values
in `input`. If `index` is None, but `labels` is provided, a global value
across all non-zero labels is given. When both `labels` and `index` are
provided, lists of values are provided for each labeled region specified
in `index`. See further details in :func:`cupyx.scipy.ndimage.minimum`,
etc.
Used by minimum, maximum, minimum_position, maximum_position, extrema.
"""
find_positions = find_min_positions or find_max_positions
positions = None
if find_positions:
positions = cupy.arange(input.size).reshape(input.shape)
def single_group(vals, positions):
result = []
if find_min:
result += [vals.min()]
if find_min_positions:
result += [positions[vals == vals.min()][0]]
if find_max:
result += [vals.max()]
if find_max_positions:
result += [positions[vals == vals.max()][0]]
if find_median:
result += [cupy.median(vals)]
return result
if labels is None:
return single_group(input, positions)
# ensure input and labels match sizes
input, labels = cupy.broadcast_arrays(input, labels)
if index is None:
mask = labels > 0
masked_positions = None
if find_positions:
masked_positions = positions[mask]
return single_group(input[mask], masked_positions)
if cupy.isscalar(index):
mask = labels == index
masked_positions = None
if find_positions:
masked_positions = positions[mask]
return single_group(input[mask], masked_positions)
index = cupy.asarray(index)
safe_int = _safely_castable_to_int(labels.dtype)
min_label = labels.min()
max_label = labels.max()
# Remap labels to unique integers if necessary, or if the largest label is
# larger than the number of values.
if (not safe_int or min_label < 0 or max_label > labels.size):
# Remap labels, and indexes
unique_labels, labels = cupy.unique(labels, return_inverse=True)
idxs = cupy.searchsorted(unique_labels, index)
# Make all of idxs valid
idxs[idxs >= unique_labels.size] = 0
found = unique_labels[idxs] == index
else:
# Labels are an integer type, and there aren't too many
idxs = cupy.asanyarray(index, int).copy()
found = (idxs >= 0) & (idxs <= max_label)
idxs[~found] = max_label + 1
input = input.ravel()
labels = labels.ravel()
if find_positions:
positions = positions.ravel()
using_cub = _core._accelerator.ACCELERATOR_CUB in \
cupy._core.get_routine_accelerators()
if using_cub:
# Cutoff values below were determined empirically for relatively large
# input arrays.
if find_positions or find_median:
n_label_cutoff = 15
else:
n_label_cutoff = 30
else:
n_label_cutoff = 0
if n_label_cutoff and len(idxs) <= n_label_cutoff:
return _select_via_looping(
input, labels, idxs, positions, find_min, find_min_positions,
find_max, find_max_positions, find_median
)
order = cupy.lexsort(cupy.stack((input.ravel(), labels.ravel())))
input = input[order]
labels = labels[order]
if find_positions:
positions = positions[order]
# Determine indices corresponding to the min or max value for each label
label_change_index = cupy.searchsorted(labels,
cupy.arange(1, max_label + 2))
if find_min or find_min_positions or find_median:
# index corresponding to the minimum value at each label
min_index = label_change_index[:-1]
if find_max or find_max_positions or find_median:
# index corresponding to the maximum value at each label
max_index = label_change_index[1:] - 1
result = []
# the order below matches the order expected by cupy.ndimage.extrema
if find_min:
mins = cupy.zeros(int(labels.max()) + 2, input.dtype)
mins[labels[min_index]] = input[min_index]
result += [mins[idxs]]
if find_min_positions:
minpos = cupy.zeros(labels.max().item() + 2, int)
minpos[labels[min_index]] = positions[min_index]
result += [minpos[idxs]]
if find_max:
maxs = cupy.zeros(int(labels.max()) + 2, input.dtype)
maxs[labels[max_index]] = input[max_index]
result += [maxs[idxs]]
if find_max_positions:
maxpos = cupy.zeros(labels.max().item() + 2, int)
maxpos[labels[max_index]] = positions[max_index]
result += [maxpos[idxs]]
if find_median:
locs = cupy.arange(len(labels))
lo = cupy.zeros(int(labels.max()) + 2, int)
lo[labels[min_index]] = locs[min_index]
hi = cupy.zeros(int(labels.max()) + 2, int)
hi[labels[max_index]] = locs[max_index]
lo = lo[idxs]
hi = hi[idxs]
# lo is an index to the lowest value in input for each label,
# hi is an index to the largest value.
# move them to be either the same ((hi - lo) % 2 == 0) or next
# to each other ((hi - lo) % 2 == 1), then average.
step = (hi - lo) // 2
lo += step
hi -= step
if input.dtype.kind in 'iub':
# fix for https://github.com/scipy/scipy/issues/12836
result += [(input[lo].astype(float) + input[hi].astype(float)) /
2.0]
else:
result += [(input[lo] + input[hi]) / 2.0]
return result
def mean(input, labels=None, index=None):
"""Calculates the mean of the values of an n-D image array, optionally
at specified sub-regions.
Args:
input (cupy.ndarray): Nd-image data to process.
labels (cupy.ndarray or None): Labels defining sub-regions in `input`.
If not None, must be same shape as `input`.
index (cupy.ndarray or None): `labels` to include in output. If None
(default), all values where `labels` is non-zero are used.
Returns:
mean (cupy.ndarray): mean of values, for each sub-region if
`labels` and `index` are specified.
.. seealso:: :func:`scipy.ndimage.mean`
"""
if not isinstance(input, cupy.ndarray):
raise TypeError('input must be cupy.ndarray')
if input.dtype in (cupy.complex64, cupy.complex128):
raise TypeError("cupyx.scipy.ndimage.mean does not support %{}".format(
input.dtype.type))
use_kern = False
# There is constraints on types because of atomicAdd() in CUDA.
if input.dtype not in [cupy.int32, cupy.float16, cupy.float32,
cupy.float64, cupy.uint32, cupy.uint64,
cupy.ulonglong]:
warnings.warn(
'Using the slower implmentation as '
'cupyx.scipy.ndimage.mean supports int32, float16, '
'float32, float64, uint32, uint64 as data types '
'for the fast implmentation', _util.PerformanceWarning)
use_kern = True
def calc_mean_with_intermediate_float(input):
sum = input.sum()
count = input.size
# Does not use `ndarray.mean()` here to return the same results as
# SciPy does, especially in case `input`'s dtype is float16.
return sum / cupy.asanyarray(count).astype(float)
if labels is None:
return calc_mean_with_intermediate_float(input)
if not isinstance(labels, cupy.ndarray):
raise TypeError('label must be cupy.ndarray')
input, labels = cupy.broadcast_arrays(input, labels)
if index is None:
return calc_mean_with_intermediate_float(input[labels > 0])
if cupy.isscalar(index):
return calc_mean_with_intermediate_float(input[labels == index])
if not isinstance(index, cupy.ndarray):
if not isinstance(index, int):
raise TypeError('index must be cupy.ndarray or a scalar int')
else:
return (input[labels == index]).mean(dtype=cupy.float64)
return _mean_driver(input, labels, index, use_kern=use_kern)
def sum_labels(input, labels=None, index=None):
"""Calculates the sum of the values of an n-D image array, optionally
at specified sub-regions.
Args:
input (cupy.ndarray): Nd-image data to process.
labels (cupy.ndarray or None): Labels defining sub-regions in `input`.
If not None, must be same shape as `input`.
index (cupy.ndarray or None): `labels` to include in output. If None
(default), all values where `labels` is non-zero are used.
Returns:
sum (cupy.ndarray): sum of values, for each sub-region if
`labels` and `index` are specified.
.. seealso:: :func:`scipy.ndimage.sum_labels`
"""
if not isinstance(input, cupy.ndarray):
raise TypeError('input must be cupy.ndarray')
if input.dtype in (cupy.complex64, cupy.complex128):
raise TypeError("cupyx.scipy.ndimage.sum does not support %{}".format(
input.dtype.type))
use_kern = False
# There is constraints on types because of atomicAdd() in CUDA.
if input.dtype not in [cupy.int32, cupy.float16, cupy.float32,
cupy.float64, cupy.uint32, cupy.uint64,
cupy.ulonglong]:
warnings.warn(
'Using the slower implmentation as '
'cupyx.scipy.ndimage.sum supports int32, float16, '
'float32, float64, uint32, uint64 as data types'
'for the fast implmentation', _util.PerformanceWarning)
use_kern = True
if labels is None:
return input.sum()
if not isinstance(labels, cupy.ndarray):
raise TypeError('label must be cupy.ndarray')
input, labels = cupy.broadcast_arrays(input, labels)
if index is None:
return input[labels != 0].sum()
if not isinstance(index, cupy.ndarray):
if not isinstance(index, int):
raise TypeError('index must be cupy.ndarray or a scalar int')
else:
return (input[labels == index]).sum()
if index.size == 0:
return cupy.array([], dtype=cupy.int64)
out = cupy.zeros_like(index, dtype=cupy.float64)
# The following parameters for sum where determined using a Tesla P100.
if (input.size >= 262144 and index.size <= 4) or use_kern:
return _ndimage_sum_kernel_2(input, labels, index, out)
return _ndimage_sum_kernel(input, labels, index, index.size, out)
def variance(input, labels=None, index=None):
"""Calculates the variance of the values of an n-D image array, optionally
at specified sub-regions.
Args:
input (cupy.ndarray): Nd-image data to process.
labels (cupy.ndarray or None): Labels defining sub-regions in `input`.
If not None, must be same shape as `input`.
index (cupy.ndarray or None): `labels` to include in output. If None
(default), all values where `labels` is non-zero are used.
Returns:
cupy.ndarray: Values of variance, for each sub-region if
`labels` and `index` are specified.
.. seealso:: :func:`scipy.ndimage.variance`
"""
if not isinstance(input, cupy.ndarray):
raise TypeError('input must be cupy.ndarray')
if input.dtype in (cupy.complex64, cupy.complex128):
raise TypeError("cupyx.scipy.ndimage.variance doesn't support %{}"
"".format(input.dtype.type))
use_kern = False
# There are constraints on types because of atomicAdd() in CUDA.
if input.dtype not in [cupy.int32, cupy.float16, cupy.float32,
cupy.float64, cupy.uint32, cupy.uint64,
cupy.ulonglong]:
warnings.warn(
'Using the slower implementation because the provided '
f'type {input.dtype} is not supported by cupyx.scipy.ndimage.sum. '
'Consider using an array of type int32, float16, '
'float32, float64, uint32, uint64 as data types '
'for the fast implementation', _util.PerformanceWarning)
use_kern = True
def calc_var_with_intermediate_float(input):
vals_c = input - input.mean()
count = vals_c.size
# Does not use `ndarray.mean()` here to return the same results as
# SciPy does, especially in case `input`'s dtype is float16.
return cupy.square(vals_c).sum() / cupy.asanyarray(count).astype(float)
if labels is None:
return calc_var_with_intermediate_float(input)
if not isinstance(labels, cupy.ndarray):
raise TypeError('label must be cupy.ndarray')
input, labels = cupy.broadcast_arrays(input, labels)
if index is None:
return calc_var_with_intermediate_float(input[labels > 0])
if cupy.isscalar(index):
return calc_var_with_intermediate_float(input[labels == index])
if not isinstance(index, cupy.ndarray):
if not isinstance(index, int):
raise TypeError('index must be cupy.ndarray or a scalar int')
else:
return (input[labels == index]).var().astype(cupy.float64,
copy=False)
mean_val, count = _mean_driver(input, labels, index, True, use_kern)
if use_kern:
new_axis = (..., *(cupy.newaxis for _ in range(input.ndim)))
return cupy.where(labels[None, ...] == index[new_axis],
cupy.square(input - mean_val[new_axis]),
0).sum(tuple(range(1, input.ndim + 1))) / count
out = cupy.zeros_like(index, dtype=cupy.float64)
return _ndimage_variance_kernel(input, labels, index, index.size, mean_val,
out) / count
def labeled_comprehension(
input, labels, index, func, out_dtype, default, pass_positions=False
):
"""Array resulting from applying ``func`` to each labeled region.
Roughly equivalent to [func(input[labels == i]) for i in index].
Sequentially applies an arbitrary function (that works on array_like input)
to subsets of an N-D image array specified by `labels` and `index`.
The option exists to provide the function with positional parameters as the
second argument.
Args:
input (cupy.ndarray): Data from which to select `labels` to process.
labels (cupy.ndarray or None): Labels to objects in `input`. If not
None, array must be same shape as `input`. If None, `func` is
applied to raveled `input`.
index (int, sequence of ints or None): Subset of `labels` to which to
apply `func`. If a scalar, a single value is returned. If None,
`func` is applied to all non-zero values of `labels`.
func (callable): Python function to apply to `labels` from `input`.
out_dtype (dtype): Dtype to use for `result`.
default (int, float or None): Default return value when a element of
`index` does not exist in `labels`.
pass_positions (bool, optional): If True, pass linear indices to `func`
as a second argument.
Returns:
cupy.ndarray: Result of applying `func` to each of `labels` to `input`
in `index`.
.. seealso:: :func:`scipy.ndimage.labeled_comprehension`
"""
as_scalar = cupy.isscalar(index)
input = cupy.asarray(input)
if pass_positions:
positions = cupy.arange(input.size).reshape(input.shape)
if labels is None:
if index is not None:
raise ValueError('index without defined labels')
if not pass_positions:
return func(input.ravel())
else:
return func(input.ravel(), positions.ravel())
try:
input, labels = cupy.broadcast_arrays(input, labels)
except ValueError:
raise ValueError(
'input and labels must have the same shape '
'(excepting dimensions with width 1)'
)
if index is None:
if not pass_positions:
return func(input[labels > 0])
else:
return func(input[labels > 0], positions[labels > 0])
index = cupy.atleast_1d(index)
if cupy.any(index.astype(labels.dtype).astype(index.dtype) != index):
raise ValueError(
'Cannot convert index values from <%s> to <%s> '
'(labels.dtype) without loss of precision'
% (index.dtype, labels.dtype)
)
index = index.astype(labels.dtype)
# optimization: find min/max in index, and select those parts of labels,
# input, and positions
lo = index.min()
hi = index.max()
mask = (labels >= lo) & (labels <= hi)
# this also ravels the arrays
labels = labels[mask]
input = input[mask]
if pass_positions:
positions = positions[mask]
# sort everything by labels
label_order = labels.argsort()
labels = labels[label_order]
input = input[label_order]
if pass_positions:
positions = positions[label_order]
index_order = index.argsort()
sorted_index = index[index_order]
def do_map(inputs, output):
"""labels must be sorted"""
nidx = sorted_index.size
# Find boundaries for each stretch of constant labels
# This could be faster, but we already paid N log N to sort labels.
lo = cupy.searchsorted(labels, sorted_index, side='left')
hi = cupy.searchsorted(labels, sorted_index, side='right')
for i, low, high in zip(range(nidx), lo, hi):
if low == high:
continue
output[i] = func(*[inp[low:high] for inp in inputs])
if out_dtype == object:
temp = {i: default for i in range(index.size)}
else:
temp = cupy.empty(index.shape, out_dtype)
if default is None and temp.dtype.kind in 'fc':
default = numpy.nan # match NumPy floating-point None behavior
temp[:] = default
if not pass_positions:
do_map([input], temp)
else:
do_map([input, positions], temp)
if out_dtype == object:
# use a list of arrays since object arrays are not supported
index_order = cupy.asnumpy(index_order)
output = [temp[i] for i in index_order.argsort()]
else:
output = cupy.zeros(index.shape, out_dtype)
output[cupy.asnumpy(index_order)] = temp
if as_scalar:
output = output[0]
return output
def _set_arrayXarray_sparse(self, row, col, x):
# Fall back to densifying x
x = cupy.asarray(x.toarray(), dtype=self.dtype)
x, _ = cupy.broadcast_arrays(x, row)
self._set_arrayXarray(row, col, x)
def meshgrid(*xi, **kwargs):
"""Return coordinate matrices from coordinate vectors.
Given one-dimensional coordinate arrays ``x1, x2, ... , xn`` this
function makes N-D grids.
For one-dimensional arrays ``x1, x2, ... , xn`` with lengths
``Ni = len(xi)``, this function returns ``(N1, N2, N3, ..., Nn)`` shaped
arrays if indexing='ij' or ``(N2, N1, N3, ..., Nn)`` shaped arrays
if indexing='xy'.
Unlike NumPy, CuPy currently only supports 1-D arrays as inputs.
Args:
xi (tuple of ndarrays): 1-D arrays representing the coordinates
of a grid.
indexing ({'xy', 'ij'}, optional): Cartesian ('xy', default) or
matrix ('ij') indexing of output.
sparse (bool, optional): If ``True``, a sparse grid is returned in
order to conserve memory. Default is ``False``.
copy (bool, optional): If ``False``, a view
into the original arrays are returned. Default is ``True``.
Returns:
list of cupy.ndarray
.. seealso:: :func:`numpy.meshgrid`
"""
indexing = kwargs.pop('indexing', 'xy')
copy = bool(kwargs.pop('copy', True))
sparse = bool(kwargs.pop('sparse', False))
if kwargs:
raise TypeError(
'meshgrid() got an unexpected keyword argument \'{}\''.format(
list(kwargs)[0]))
if indexing not in ['xy', 'ij']:
raise ValueError('Valid values for `indexing` are \'xy\' and \'ij\'.')
for x in xi:
if x.ndim != 1:
raise ValueError('input has to be 1d')
if not isinstance(x, cupy.ndarray):
raise ValueError('input has to be cupy.ndarray')
if len(xi) <= 1:
return list(xi)
meshes = []
for i, x in enumerate(xi):
if indexing == 'xy' and i == 0:
left_none = 1
elif indexing == 'xy' and i == 1:
left_none = 0
else:
left_none = i
expand_slices = ((None, ) * left_none + (slice(None), ) + (None, ) *
(len(xi) - (left_none + 1)))
meshes.append(x[expand_slices])
if sparse:
meshes_br = meshes
else:
meshes_br = list(cupy.broadcast_arrays(*meshes))
if copy:
for i in range(len(meshes_br)):
meshes_br[i] = meshes_br[i].copy()
return meshes_br
def meshgrid(*xi, **kwargs):
"""Return coordinate matrices from coordinate vectors.
Given one-dimensional coordinate arrays x1, x2, ..., xn, this function
makes N-D grids.
For one-dimensional arrays x1, x2, ..., xn with lengths ``Ni = len(xi)``,
this function returns ``(N1, N2, N3, ..., Nn)`` shaped arrays
if indexing='ij' or ``(N2, N1, N3, ..., Nn)`` shaped arrays
if indexing='xy'.
Unlike NumPy, CuPy currently only supports 1-D arrays as inputs.
Also, CuPy does not support ``sparse`` option yet.
Args:
xi (tuple of ndarrays): 1-D arrays representing the coordinates
of a grid.
indexing ({'xy', 'ij'}, optional): Cartesian ('xy', default) or
matrix ('ij') indexing of output.
copy (bool, optional): If ``False``, a view
into the original arrays are returned. Default is True.
Returns:
list of cupy.ndarray
.. seealso:: :func:`numpy.meshgrid`
"""
indexing = kwargs.pop('indexing', 'xy')
copy = bool(kwargs.pop('copy', True))
if kwargs:
raise TypeError(
'meshgrid() got an unexpected keyword argument \'{}\''.format(
list(kwargs)[0]))
if indexing not in ['xy', 'ij']:
raise ValueError('Valid values for `indexing` are \'xy\' and \'ij\'.')
for x in xi:
if x.ndim != 1:
raise ValueError('input has to be 1d')
if not isinstance(x, cupy.ndarray):
raise ValueError('input has to be cupy.ndarray')
if len(xi) <= 1:
return list(xi)
meshes = []
for i, x in enumerate(xi):
if indexing == 'xy' and i == 0:
left_none = 1
elif indexing == 'xy' and i == 1:
left_none = 0
else:
left_none = i
expand_slices = ((None,) * left_none +
(slice(None),) +
(None,) * (len(xi) - (left_none + 1)))
meshes.append(x[expand_slices])
meshes_br = list(cupy.broadcast_arrays(*meshes))
if copy:
for i in range(len(meshes_br)):
meshes_br[i] = meshes_br[i].copy()
return meshes_br
def ravel_multi_index(multi_index, dims, mode='wrap', order='C'):
"""
Converts a tuple of index arrays into an array of flat indices, applying
boundary modes to the multi-index.
Args:
multi_index (tuple of cupy.ndarray) : A tuple of integer arrays, one
array for each dimension.
dims (tuple of ints): The shape of array into which the indices from
``multi_index`` apply.
mode ('raise', 'wrap' or 'clip'), optional: Specifies how out-of-bounds
indices are handled. Can specify either one mode or a tuple of
modes, one mode per index:
- *'raise'* -- raise an error
- *'wrap'* -- wrap around (default)
- *'clip'* -- clip to the range
In 'clip' mode, a negative index which would normally wrap will
clip to 0 instead.
order ('C' or 'F'), optional: Determines whether the multi-index should
be viewed as indexing in row-major (C-style) or column-major
(Fortran-style) order.
Returns:
raveled_indices (cupy.ndarray): An array of indices into the flattened
version of an array of dimensions ``dims``.
.. warning::
This function may synchronize the device when ``mode == 'raise'``.
Notes
-----
Note that the default `mode` (``'wrap'``) is different than in NumPy. This
is done to avoid potential device synchronization.
Examples
--------
>>> cupy.ravel_multi_index(cupy.asarray([[3,6,6],[4,5,1]]), (7,6))
array([22, 41, 37])
>>> cupy.ravel_multi_index(cupy.asarray([[3,6,6],[4,5,1]]), (7,6),
... order='F')
array([31, 41, 13])
>>> cupy.ravel_multi_index(cupy.asarray([[3,6,6],[4,5,1]]), (4,6),
... mode='clip')
array([22, 23, 19])
>>> cupy.ravel_multi_index(cupy.asarray([[3,6,6],[4,5,1]]), (4,4),
... mode=('clip', 'wrap'))
array([12, 13, 13])
>>> cupy.ravel_multi_index(cupy.asarray((3,1,4,1)), (6,7,8,9))
array(1621)
.. seealso:: :func:`numpy.ravel_multi_index`, :func:`unravel_index`
"""
ndim = len(dims)
if len(multi_index) != ndim:
raise ValueError(
"parameter multi_index must be a sequence of "
"length {}".format(ndim))
for d in dims:
if not isinstance(d, numbers.Integral):
raise TypeError(
"{} object cannot be interpreted as an integer".format(
type(d)))
if isinstance(mode, str):
mode = (mode, ) * ndim
if functools.reduce(operator.mul, dims) > cupy.iinfo(cupy.int64).max:
raise ValueError("invalid dims: array size defined by dims is larger "
"than the maximum possible size")
s = 1
ravel_strides = [1] * ndim
if order is None:
order = "C"
if order == "C":
for i in range(ndim - 2, -1, -1):
s = s * dims[i + 1]
ravel_strides[i] = s
elif order == "F":
for i in range(1, ndim):
s = s * dims[i - 1]
ravel_strides[i] = s
else:
raise TypeError("order not understood")
multi_index = cupy.broadcast_arrays(*multi_index)
raveled_indices = cupy.zeros(multi_index[0].shape, dtype=cupy.int64)
for d, stride, idx, _mode in zip(dims, ravel_strides, multi_index, mode):
if not isinstance(idx, cupy.ndarray):
raise TypeError("elements of multi_index must be cupy arrays")
if not cupy.can_cast(idx, cupy.int64, 'same_kind'):
raise TypeError(
'multi_index entries could not be cast from dtype(\'{}\') to '
'dtype(\'{}\') according to the rule \'same_kind\''.format(
idx.dtype, cupy.int64().dtype))
idx = idx.astype(cupy.int64, copy=False)
if _mode == "raise":
if cupy.any(cupy.logical_or(idx >= d, idx < 0)):
raise ValueError("invalid entry in coordinates array")
elif _mode == "clip":
idx = cupy.clip(idx, 0, d - 1)
elif _mode == 'wrap':
idx = idx % d
else:
raise TypeError("Unrecognized mode: {}".format(_mode))
raveled_indices += stride * idx
return raveled_indices
def labeled_comprehension(input,
labels,
index,
func,
out_dtype,
default,
pass_positions=False):
"""
Roughly equivalent to [func(input[labels == i]) for i in index].
Sequentially applies an arbitrary function (that works on array_like input)
to subsets of an N-D image array specified by `labels` and `index`.
The option exists to provide the function with positional parameters as the
second argument.
Parameters
----------
input : array_like
Data from which to select `labels` to process.
labels : array_like or None
Labels to objects in `input`.
If not None, array must be same shape as `input`.
If None, `func` is applied to raveled `input`.
index : int, sequence of ints or None
Subset of `labels` to which to apply `func`.
If a scalar, a single value is returned.
If None, `func` is applied to all non-zero values of `labels`.
func : callable
Python function to apply to `labels` from `input`.
out_dtype : dtype
Dtype to use for `result`.
default : int, float or None
Default return value when a element of `index` does not exist
in `labels`.
pass_positions : bool, optional
If True, pass linear indices to `func` as a second argument.
Default is False.
Returns
-------
result : ndarray
Result of applying `func` to each of `labels` to `input` in `index`.
Examples
--------
>>> import cupy as cp
>>> a = cp.array([[1, 2, 0, 0],
... [5, 3, 0, 4],
... [0, 0, 0, 7],
... [9, 3, 0, 0]])
>>> from cupyimg.scipy import ndimage
>>> lbl, nlbl = ndimage.label(a)
>>> lbls = cp.arange(1, nlbl+1)
>>> ndimage.labeled_comprehension(a, lbl, lbls, cp.mean, float, 0)
array([ 2.75, 5.5 , 6. ])
Falling back to `default`:
>>> lbls = cp.arange(1, nlbl+2)
>>> ndimage.labeled_comprehension(a, lbl, lbls, cp.mean, float, -1)
array([ 2.75, 5.5 , 6. , -1. ])
Passing positions:
>>> def fn(val, pos):
... print("fn says: %s : %s" % (val, pos))
... return (val.sum()) if (pos.sum() % 2 == 0) else (-val.sum())
...
>>> ndimage.labeled_comprehension(a, lbl, lbls, fn, float, 0, True)
fn says: [1 2 5 3] : [0 1 4 5]
fn says: [4 7] : [ 7 11]
fn says: [9 3] : [12 13]
array([ 11., 11., -12., 0.])
"""
as_scalar = cupy.isscalar(index)
input = cupy.asarray(input)
if pass_positions:
positions = cupy.arange(input.size).reshape(input.shape)
if labels is None:
if index is not None:
raise ValueError("index without defined labels")
if not pass_positions:
return func(input.ravel())
else:
return func(input.ravel(), positions.ravel())
try:
input, labels = cupy.broadcast_arrays(input, labels)
except ValueError:
raise ValueError("input and labels must have the same shape "
"(excepting dimensions with width 1)")
if index is None:
if not pass_positions:
return func(input[labels > 0])
else:
return func(input[labels > 0], positions[labels > 0])
index = cupy.atleast_1d(index)
if cupy.any(index.astype(labels.dtype).astype(index.dtype) != index):
raise ValueError("Cannot convert index values from <%s> to <%s> "
"(labels' type) without loss of precision" %
(index.dtype, labels.dtype))
index = index.astype(labels.dtype)
# optimization: find min/max in index, and select those parts of labels, input, and positions
lo = index.min()
hi = index.max()
mask = (labels >= lo) & (labels <= hi)
# this also ravels the arrays
labels = labels[mask]
input = input[mask]
if pass_positions:
positions = positions[mask]
# sort everything by labels
label_order = labels.argsort()
labels = labels[label_order]
input = input[label_order]
if pass_positions:
positions = positions[label_order]
index_order = index.argsort()
sorted_index = index[index_order]
def do_map(inputs, output):
"""labels must be sorted"""
nidx = sorted_index.size
# Find boundaries for each stretch of constant labels
# This could be faster, but we already paid N log N to sort labels.
lo = cupy.searchsorted(labels, sorted_index, side="left")
hi = cupy.searchsorted(labels, sorted_index, side="right")
for i, l, h in zip(range(nidx), lo, hi):
if l == h:
continue
output[i] = cupy.asnumpy(func(*[inp[l:h] for inp in inputs]))
temp = numpy.empty(index.shape, out_dtype)
temp[:] = default
if not pass_positions:
do_map([input], temp)
else:
do_map([input, positions], temp)
output = numpy.zeros(index.shape, out_dtype)
output[cupy.asnumpy(index_order)] = temp
if as_scalar:
output = output[0]
return output
def select(condlist, choicelist, default=0):
"""Return an array drawn from elements in choicelist, depending on conditions.
Args:
condlist (list of bool arrays): The list of conditions which determine
from which array in `choicelist` the output elements are taken.
When multiple conditions are satisfied, the first one encountered
in `condlist` is used.
choicelist (list of cupy.ndarray): The list of arrays from which the
output elements are taken. It has to be of the same length
as `condlist`.
default (scalar) : If provided, will fill element inserted in `output`
when all conditions evaluate to False. default value is 0.
Returns:
cupy.ndarray: The output at position m is the m-th element of the
array in `choicelist` where the m-th element of the corresponding
array in `condlist` is True.
.. seealso:: :func:`numpy.select`
"""
if len(condlist) != len(choicelist):
raise ValueError(
'list of cases must be same length as list of conditions')
if len(condlist) == 0:
raise ValueError("select with an empty condition list is not possible")
if not cupy.isscalar(default):
raise TypeError("default only accepts scalar values")
for i in range(len(choicelist)):
if not isinstance(choicelist[i], cupy.ndarray):
raise TypeError("choicelist only accepts lists of cupy ndarrays")
cond = condlist[i]
if cond.dtype.type is not cupy.bool_:
raise ValueError(
'invalid entry {} in condlist: should be boolean ndarray'.
format(i))
dtype = cupy.result_type(*choicelist)
condlist = cupy.broadcast_arrays(*condlist)
choicelist = cupy.broadcast_arrays(*choicelist, default)
if choicelist[0].ndim == 0:
result_shape = condlist[0].shape
else:
result_shape = cupy.broadcast_arrays(condlist[0],
choicelist[0])[0].shape
result = cupy.empty(result_shape, dtype)
cupy.copyto(result, default)
choicelist = choicelist[-2::-1]
condlist = condlist[::-1]
for choice, cond in zip(choicelist, condlist):
cupy.copyto(result, choice, where=cond)
return result