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import operator
import warnings
import numpy
import cupy
from cupy import _core
# rename builtin range for use in functions that take a range argument
_range = range
# TODO(unno): use searchsorted
_histogram_kernel = _core.ElementwiseKernel(
'S x, raw T bins, int32 n_bins',
'raw U y',
'''
if (x < bins[0] or bins[n_bins - 1] < x) {
return;
}
int high = n_bins - 1;
int low = 0;
while (high - low > 1) {
int mid = (high + low) / 2;
if (bins[mid] <= x) {
low = mid;
} else {
high = mid;
}
}
atomicAdd(&y[low], U(1));
''',
'cupy_histogram_kernel')
_weighted_histogram_kernel = _core.ElementwiseKernel(
'S x, raw T bins, int32 n_bins, raw W weights',
'raw Y y',
'''
if (x < bins[0] or bins[n_bins - 1] < x) {
return;
}
int high = n_bins - 1;
int low = 0;
while (high - low > 1) {
int mid = (high + low) / 2;
if (bins[mid] <= x) {
low = mid;
} else {
high = mid;
}
}
atomicAdd(&y[low], (Y)weights[i]);
''',
'cupy_weighted_histogram_kernel')
def _ravel_and_check_weights(a, weights):
""" Check a and weights have matching shapes, and ravel both """
# Ensure that the array is a "subtractable" dtype
if a.dtype == cupy.bool_:
warnings.warn('Converting input from {} to {} for compatibility.'
.format(a.dtype, cupy.uint8),
RuntimeWarning, stacklevel=3)
a = a.astype(cupy.uint8)
if weights is not None:
if not isinstance(weights, cupy.ndarray):
raise ValueError('weights must be a cupy.ndarray')
if weights.shape != a.shape:
raise ValueError(
'weights should have the same shape as a.')
weights = weights.ravel()
a = a.ravel()
return a, weights
def _get_outer_edges(a, range):
"""
Determine the outer bin edges to use, from either the data or the range
argument
"""
if range is not None:
first_edge, last_edge = range
if first_edge > last_edge:
raise ValueError(
'max must be larger than min in range parameter.')
if not (numpy.isfinite(first_edge) and numpy.isfinite(last_edge)):
raise ValueError(
'supplied range of [{}, {}] is not finite'.format(
first_edge, last_edge))
elif a.size == 0:
first_edge = 0.0
last_edge = 1.0
else:
first_edge = float(a.min())
last_edge = float(a.max())
if not (cupy.isfinite(first_edge) and cupy.isfinite(last_edge)):
raise ValueError(
'autodetected range of [{}, {}] is not finite'.format(
first_edge, last_edge))
# expand empty range to avoid divide by zero
if first_edge == last_edge:
first_edge = first_edge - 0.5
last_edge = last_edge + 0.5
return first_edge, last_edge
def _get_bin_edges(a, bins, range):
"""
Computes the bins used internally by `histogram`.
Args:
a (ndarray): Ravelled data array
bins (int or ndarray): Forwarded argument from `histogram`.
range (None or tuple): Forwarded argument from `histogram`.
Returns:
bin_edges (ndarray): Array of bin edges
"""
# parse the overloaded bins argument
n_equal_bins = None
bin_edges = None
if isinstance(bins, str):
raise NotImplementedError(
'only integer and array bins are implemented')
elif isinstance(bins, cupy.ndarray) or numpy.ndim(bins) == 1:
# TODO(okuta): After #3060 is merged, `if cupy.ndim(bins) == 1:`.
if isinstance(bins, cupy.ndarray):
bin_edges = bins
else:
bin_edges = numpy.asarray(bins)
if (bin_edges[:-1] > bin_edges[1:]).any(): # synchronize! when CuPy
raise ValueError(
'`bins` must increase monotonically, when an array')
if isinstance(bin_edges, numpy.ndarray):
bin_edges = cupy.asarray(bin_edges)
elif numpy.ndim(bins) == 0:
try:
n_equal_bins = operator.index(bins)
except TypeError:
raise TypeError(
'`bins` must be an integer, a string, or an array')
if n_equal_bins < 1:
raise ValueError('`bins` must be positive, when an integer')
first_edge, last_edge = _get_outer_edges(a, range)
else:
raise ValueError('`bins` must be 1d, when an array')
if n_equal_bins is not None:
# numpy's gh-10322 means that type resolution rules are dependent on
# array shapes. To avoid this causing problems, we pick a type now and
# stick with it throughout.
bin_type = cupy.result_type(first_edge, last_edge, a)
if cupy.issubdtype(bin_type, cupy.integer):
bin_type = cupy.result_type(bin_type, float)
# bin edges must be computed
bin_edges = cupy.linspace(
first_edge, last_edge, n_equal_bins + 1,
endpoint=True, dtype=bin_type)
return bin_edges
def histogram(x, bins=10, range=None, weights=None, density=False):
"""Computes the histogram of a set of data.
Args:
x (cupy.ndarray): Input array.
bins (int or cupy.ndarray): If ``bins`` is an int, it represents the
number of bins. If ``bins`` is an :class:`~cupy.ndarray`, it
represents a bin edges.
range (2-tuple of float, optional): The lower and upper range of the
bins. If not provided, range is simply ``(x.min(), x.max())``.
Values outside the range are ignored. The first element of the
range must be less than or equal to the second. `range` affects the
automatic bin computation as well. While bin width is computed to
be optimal based on the actual data within `range`, the bin count
will fill the entire range including portions containing no data.
density (bool, optional): If False, the default, returns the number of
samples in each bin. If True, returns the probability *density*
function at the bin, ``bin_count / sample_count / bin_volume``.
weights (cupy.ndarray, optional): An array of weights, of the same
shape as `x`. Each value in `x` only contributes its associated
weight towards the bin count (instead of 1).
Returns:
tuple: ``(hist, bin_edges)`` where ``hist`` is a :class:`cupy.ndarray`
storing the values of the histogram, and ``bin_edges`` is a
:class:`cupy.ndarray` storing the bin edges.
.. warning::
This function may synchronize the device.
.. seealso:: :func:`numpy.histogram`
"""
if x.dtype.kind == 'c':
# TODO(unno): comparison between complex numbers is not implemented
raise NotImplementedError('complex number is not supported')
if not isinstance(x, cupy.ndarray):
raise ValueError('x must be a cupy.ndarray')
x, weights = _ravel_and_check_weights(x, weights)
bin_edges = _get_bin_edges(x, bins, range)
if weights is None:
y = cupy.zeros(bin_edges.size - 1, dtype=cupy.int64)
# TODO(leofang): we temporarily remove CUB histogram support for now,
# see cupy/cupy#7698. When it's ready, revert the commit that checked
# in this comment to restore the support.
_histogram_kernel(x, bin_edges, bin_edges.size, y)
else:
simple_weights = (
cupy.can_cast(weights.dtype, cupy.float64) or
cupy.can_cast(weights.dtype, cupy.complex128)
)
if not simple_weights:
# object dtype such as Decimal are supported in NumPy, but not here
raise NotImplementedError(
'only weights with dtype that can be cast to float or complex '
'are supported')
if weights.dtype.kind == 'c':
y = cupy.zeros(bin_edges.size - 1, dtype=cupy.complex128)
_weighted_histogram_kernel(
x, bin_edges, bin_edges.size, weights.real, y.real)
_weighted_histogram_kernel(
x, bin_edges, bin_edges.size, weights.imag, y.imag)
else:
if weights.dtype.kind in 'bui':
y = cupy.zeros(bin_edges.size - 1, dtype=int)
else:
y = cupy.zeros(bin_edges.size - 1, dtype=cupy.float64)
_weighted_histogram_kernel(
x, bin_edges, bin_edges.size, weights, y)
if density:
db = cupy.array(cupy.diff(bin_edges), cupy.float64)
return y / db / y.sum(), bin_edges
return y, bin_edges
def histogramdd(sample, bins=10, range=None, weights=None, density=False):
"""Compute the multidimensional histogram of some data.
Args:
sample (cupy.ndarray): The data to be histogrammed. (N, D) or (D, N)
array
Note the unusual interpretation of sample when an array_like:
* When an array, each row is a coordinate in a D-dimensional
space - such as ``histogramdd(cupy.array([p1, p2, p3]))``.
* When an array_like, each element is the list of values for single
coordinate - such as ``histogramdd((X, Y, Z))``.
The first form should be preferred.
bins (int or tuple of int or cupy.ndarray): The bin specification:
* A sequence of arrays describing the monotonically increasing bin
edges along each dimension.
* The number of bins for each dimension (nx, ny, ... =bins)
* The number of bins for all dimensions (nx=ny=...=bins).
range (sequence, optional): A sequence of length D, each an optional
(lower, upper) tuple giving the outer bin edges to be used if the
edges are not given explicitly in `bins`. An entry of None in the
sequence results in the minimum and maximum values being used for
the corresponding dimension. The default, None, is equivalent to
passing a tuple of D None values.
weights (cupy.ndarray): An array of values `w_i` weighing each sample
`(x_i, y_i, z_i, ...)`. The values of the returned histogram are
equal to the sum of the weights belonging to the samples falling
into each bin.
density (bool, optional): If False, the default, returns the number of
samples in each bin. If True, returns the probability *density*
function at the bin, ``bin_count / sample_count / bin_volume``.
Returns:
tuple:
H (cupy.ndarray):
The multidimensional histogram of sample x. See
normed and weights for the different possible semantics.
edges (list of cupy.ndarray):
A list of D arrays describing the bin
edges for each dimension.
.. warning::
This function may synchronize the device.
.. seealso:: :func:`numpy.histogramdd`
"""
if isinstance(sample, cupy.ndarray):
# Sample is an ND-array.
if sample.ndim == 1:
sample = sample[:, cupy.newaxis]
nsamples, ndim = sample.shape
else:
sample = cupy.stack(sample, axis=-1)
nsamples, ndim = sample.shape
nbin = numpy.empty(ndim, int)
edges = ndim * [None]
dedges = ndim * [None]
if weights is not None:
weights = cupy.asarray(weights)
try:
nbins = len(bins)
if nbins != ndim:
raise ValueError(
'The dimension of bins must be equal to the dimension of the '
' sample x.'
)
except TypeError:
# bins is an integer
bins = ndim * [bins]
# normalize the range argument
if range is None:
range = (None,) * ndim
elif len(range) != ndim:
raise ValueError('range argument must have one entry per dimension')
# Create edge arrays
for i in _range(ndim):
if cupy.ndim(bins[i]) == 0:
if bins[i] < 1:
raise ValueError(
'`bins[{}]` must be positive, when an integer'.format(i)
)
smin, smax = _get_outer_edges(sample[:, i], range[i])
num = int(bins[i] + 1) # synchronize!
edges[i] = cupy.linspace(smin, smax, num)
elif cupy.ndim(bins[i]) == 1:
if not isinstance(bins[i], cupy.ndarray):
raise ValueError('array-like bins not supported')
edges[i] = bins[i]
if (edges[i][:-1] > edges[i][1:]).any(): # synchronize!
raise ValueError(
'`bins[{}]` must be monotonically increasing, when an '
'array'.format(i)
)
else:
raise ValueError(
'`bins[{}]` must be a scalar or 1d array'.format(i)
)
nbin[i] = len(edges[i]) + 1 # includes an outlier on each end
dedges[i] = cupy.diff(edges[i])
# Compute the bin number each sample falls into.
ncount = tuple(
# avoid cupy.digitize to work around NumPy issue gh-11022
cupy.searchsorted(edges[i], sample[:, i], side='right')
for i in _range(ndim)
)
# Using digitize, values that fall on an edge are put in the right bin.
# For the rightmost bin, we want values equal to the right edge to be
# counted in the last bin, and not as an outlier.
for i in _range(ndim):
# Find which points are on the rightmost edge.
on_edge = sample[:, i] == edges[i][-1]
# Shift these points one bin to the left.
ncount[i][on_edge] -= 1
# Compute the sample indices in the flattened histogram matrix.
# This raises an error if the array is too large.
xy = cupy.ravel_multi_index(ncount, nbin)
# Compute the number of repetitions in xy and assign it to the
# flattened histmat.
hist = cupy.bincount(xy, weights, minlength=numpy.prod(nbin))
# Shape into a proper matrix
hist = hist.reshape(nbin)
# This preserves the (bad) behavior observed in NumPy gh-7845, for now.
hist = hist.astype(float) # Note: NumPy uses casting='safe' here too
# Remove outliers (indices 0 and -1 for each dimension).
core = ndim * (slice(1, -1),)
hist = hist[core]
if density:
# calculate the probability density function
s = hist.sum()
for i in _range(ndim):
shape = [1] * ndim
shape[i] = nbin[i] - 2
hist = hist / dedges[i].reshape(shape)
hist /= s
if any(hist.shape != numpy.asarray(nbin) - 2):
raise RuntimeError('Internal Shape Error')
return hist, edges
def histogram2d(x, y, bins=10, range=None, weights=None, density=None):
"""Compute the bi-dimensional histogram of two data samples.
Args:
x (cupy.ndarray): The first array of samples to be histogrammed.
y (cupy.ndarray): The second array of samples to be histogrammed.
bins (int or tuple of int or cupy.ndarray): The bin specification:
* A sequence of arrays describing the monotonically increasing bin
edges along each dimension.
* The number of bins for each dimension (nx, ny)
* The number of bins for all dimensions (nx=ny=bins).
range (sequence, optional): A sequence of length two, each an optional
(lower, upper) tuple giving the outer bin edges to be used if the
edges are not given explicitly in `bins`. An entry of None in the
sequence results in the minimum and maximum values being used for
the corresponding dimension. The default, None, is equivalent to
passing a tuple of two None values.
weights (cupy.ndarray): An array of values `w_i` weighing each sample
`(x_i, y_i)`. The values of the returned histogram are equal to the
sum of the weights belonging to the samples falling into each bin.
density (bool, optional): If False, the default, returns the number of
samples in each bin. If True, returns the probability *density*
function at the bin, ``bin_count / sample_count / bin_volume``.
Returns:
tuple:
H (cupy.ndarray):
The multidimensional histogram of sample x. See
normed and weights for the different possible semantics.
edges0 (tuple of cupy.ndarray):
A list of D arrays describing the bin
edges for the first dimension.
edges1 (tuple of cupy.ndarray):
A list of D arrays describing the bin
edges for the second dimension.
.. warning::
This function may synchronize the device.
.. seealso:: :func:`numpy.histogram2d`
"""
try:
n = len(bins)
except TypeError:
n = 1
if n != 1 and n != 2:
if isinstance(bins, cupy.ndarray):
xedges = yedges = bins
bins = [xedges, yedges]
else:
raise ValueError('array-like bins not supported in CuPy')
hist, edges = histogramdd([x, y], bins, range, weights, density)
return hist, edges[0], edges[1]
_bincount_kernel = _core.ElementwiseKernel(
'S x', 'raw U bin',
'atomicAdd(&bin[x], U(1))',
'cupy_bincount_kernel')
_bincount_with_weight_kernel = _core.ElementwiseKernel(
'S x, T w', 'raw U bin',
'atomicAdd(&bin[x], w)',
'cupy_bincount_with_weight_kernel')
def bincount(x, weights=None, minlength=None):
"""Count number of occurrences of each value in array of non-negative ints.
Args:
x (cupy.ndarray): Input array.
weights (cupy.ndarray): Weights array which has the same shape as
``x``.
minlength (int): A minimum number of bins for the output array.
Returns:
cupy.ndarray: The result of binning the input array. The length of
output is equal to ``max(cupy.max(x) + 1, minlength)``.
.. warning::
This function may synchronize the device.
.. seealso:: :func:`numpy.bincount`
"""
if x.ndim > 1:
raise ValueError('object too deep for desired array')
if x.ndim < 1:
raise ValueError('object of too small depth for desired array')
if x.dtype.kind == 'f':
raise TypeError('x must be int array')
if (x < 0).any(): # synchronize!
raise ValueError('The first argument of bincount must be non-negative')
if weights is not None and x.shape != weights.shape:
raise ValueError('The weights and list don\'t have the same length.')
if minlength is not None:
minlength = int(minlength)
if minlength < 0:
raise ValueError('minlength must be non-negative')
size = int(cupy.max(x)) + 1 # synchronize!
if minlength is not None:
size = max(size, minlength)
if weights is None:
b = cupy.zeros((size,), dtype=numpy.intp)
# TODO(leofang): we temporarily remove CUB histogram support for now,
# see cupy/cupy#7698. When it's ready, revert the commit that checked
# in this comment to restore the support.
_bincount_kernel(x, b)
else:
b = cupy.zeros((size,), dtype=numpy.float64)
_bincount_with_weight_kernel(x, weights, b)
return b
def digitize(x, bins, right=False):
"""Finds the indices of the bins to which each value in input array belongs.
.. note::
In order to avoid device synchronization, digitize does not raise
an exception when the array is not monotonic
Args:
x (cupy.ndarray): Input array.
bins (cupy.ndarray): Array of bins.
It has to be 1-dimensional and monotonic increasing or decreasing.
right (bool):
Indicates whether the intervals include the right or the left bin
edge.
Returns:
cupy.ndarray: Output array of indices, of same shape as ``x``.
.. seealso:: :func:`numpy.digitize`
""" # NOQA
# This is for NumPy compat, although it works fine
if x.dtype.kind == 'c':
raise TypeError('x may not be complex')
if bins.ndim > 1:
raise ValueError('object too deep for desired array')
if bins.ndim < 1:
raise ValueError('object of too small depth for desired array')
# As the order of the arguments are reversed, the side must be too.
side = 'left' if right else 'right'
return cupy._sorting.search._searchsorted(bins, x, side, None, False)