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import operator |
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import warnings |
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import numpy |
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import cupy |
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from cupy import _core |
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_range = range |
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_histogram_kernel = _core.ElementwiseKernel( |
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'S x, raw T bins, int32 n_bins', |
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'raw U y', |
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''' |
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if (x < bins[0] or bins[n_bins - 1] < x) { |
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return; |
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} |
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int high = n_bins - 1; |
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int low = 0; |
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while (high - low > 1) { |
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int mid = (high + low) / 2; |
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if (bins[mid] <= x) { |
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low = mid; |
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} else { |
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high = mid; |
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} |
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} |
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atomicAdd(&y[low], U(1)); |
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''', |
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'cupy_histogram_kernel') |
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_weighted_histogram_kernel = _core.ElementwiseKernel( |
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'S x, raw T bins, int32 n_bins, raw W weights', |
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'raw Y y', |
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''' |
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if (x < bins[0] or bins[n_bins - 1] < x) { |
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return; |
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} |
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int high = n_bins - 1; |
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int low = 0; |
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while (high - low > 1) { |
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int mid = (high + low) / 2; |
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if (bins[mid] <= x) { |
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low = mid; |
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} else { |
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high = mid; |
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} |
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} |
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atomicAdd(&y[low], (Y)weights[i]); |
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''', |
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'cupy_weighted_histogram_kernel') |
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def _ravel_and_check_weights(a, weights): |
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""" Check a and weights have matching shapes, and ravel both """ |
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if a.dtype == cupy.bool_: |
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warnings.warn('Converting input from {} to {} for compatibility.' |
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.format(a.dtype, cupy.uint8), |
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RuntimeWarning, stacklevel=3) |
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a = a.astype(cupy.uint8) |
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if weights is not None: |
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if not isinstance(weights, cupy.ndarray): |
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raise ValueError('weights must be a cupy.ndarray') |
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if weights.shape != a.shape: |
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raise ValueError( |
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'weights should have the same shape as a.') |
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weights = weights.ravel() |
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a = a.ravel() |
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return a, weights |
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def _get_outer_edges(a, range): |
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""" |
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Determine the outer bin edges to use, from either the data or the range |
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argument |
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""" |
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if range is not None: |
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first_edge, last_edge = range |
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if first_edge > last_edge: |
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raise ValueError( |
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'max must be larger than min in range parameter.') |
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if not (numpy.isfinite(first_edge) and numpy.isfinite(last_edge)): |
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raise ValueError( |
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'supplied range of [{}, {}] is not finite'.format( |
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first_edge, last_edge)) |
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elif a.size == 0: |
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first_edge = 0.0 |
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last_edge = 1.0 |
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else: |
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first_edge = float(a.min()) |
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last_edge = float(a.max()) |
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if not (cupy.isfinite(first_edge) and cupy.isfinite(last_edge)): |
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raise ValueError( |
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'autodetected range of [{}, {}] is not finite'.format( |
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first_edge, last_edge)) |
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if first_edge == last_edge: |
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first_edge = first_edge - 0.5 |
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last_edge = last_edge + 0.5 |
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return first_edge, last_edge |
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def _get_bin_edges(a, bins, range): |
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""" |
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Computes the bins used internally by `histogram`. |
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Args: |
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a (ndarray): Ravelled data array |
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bins (int or ndarray): Forwarded argument from `histogram`. |
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range (None or tuple): Forwarded argument from `histogram`. |
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Returns: |
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bin_edges (ndarray): Array of bin edges |
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""" |
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n_equal_bins = None |
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bin_edges = None |
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if isinstance(bins, str): |
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raise NotImplementedError( |
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'only integer and array bins are implemented') |
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elif isinstance(bins, cupy.ndarray) or numpy.ndim(bins) == 1: |
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if isinstance(bins, cupy.ndarray): |
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bin_edges = bins |
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else: |
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bin_edges = numpy.asarray(bins) |
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if (bin_edges[:-1] > bin_edges[1:]).any(): |
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raise ValueError( |
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'`bins` must increase monotonically, when an array') |
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if isinstance(bin_edges, numpy.ndarray): |
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bin_edges = cupy.asarray(bin_edges) |
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elif numpy.ndim(bins) == 0: |
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try: |
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n_equal_bins = operator.index(bins) |
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except TypeError: |
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raise TypeError( |
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'`bins` must be an integer, a string, or an array') |
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if n_equal_bins < 1: |
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raise ValueError('`bins` must be positive, when an integer') |
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first_edge, last_edge = _get_outer_edges(a, range) |
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else: |
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raise ValueError('`bins` must be 1d, when an array') |
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if n_equal_bins is not None: |
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bin_type = cupy.result_type(first_edge, last_edge, a) |
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if cupy.issubdtype(bin_type, cupy.integer): |
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bin_type = cupy.result_type(bin_type, float) |
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bin_edges = cupy.linspace( |
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first_edge, last_edge, n_equal_bins + 1, |
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endpoint=True, dtype=bin_type) |
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return bin_edges |
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def histogram(x, bins=10, range=None, weights=None, density=False): |
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"""Computes the histogram of a set of data. |
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Args: |
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x (cupy.ndarray): Input array. |
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bins (int or cupy.ndarray): If ``bins`` is an int, it represents the |
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number of bins. If ``bins`` is an :class:`~cupy.ndarray`, it |
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represents a bin edges. |
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range (2-tuple of float, optional): The lower and upper range of the |
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bins. If not provided, range is simply ``(x.min(), x.max())``. |
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Values outside the range are ignored. The first element of the |
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range must be less than or equal to the second. `range` affects the |
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automatic bin computation as well. While bin width is computed to |
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be optimal based on the actual data within `range`, the bin count |
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will fill the entire range including portions containing no data. |
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density (bool, optional): If False, the default, returns the number of |
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samples in each bin. If True, returns the probability *density* |
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function at the bin, ``bin_count / sample_count / bin_volume``. |
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weights (cupy.ndarray, optional): An array of weights, of the same |
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shape as `x`. Each value in `x` only contributes its associated |
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weight towards the bin count (instead of 1). |
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Returns: |
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tuple: ``(hist, bin_edges)`` where ``hist`` is a :class:`cupy.ndarray` |
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storing the values of the histogram, and ``bin_edges`` is a |
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:class:`cupy.ndarray` storing the bin edges. |
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.. warning:: |
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This function may synchronize the device. |
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.. seealso:: :func:`numpy.histogram` |
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""" |
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if x.dtype.kind == 'c': |
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raise NotImplementedError('complex number is not supported') |
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if not isinstance(x, cupy.ndarray): |
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raise ValueError('x must be a cupy.ndarray') |
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x, weights = _ravel_and_check_weights(x, weights) |
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bin_edges = _get_bin_edges(x, bins, range) |
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if weights is None: |
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y = cupy.zeros(bin_edges.size - 1, dtype=cupy.int64) |
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_histogram_kernel(x, bin_edges, bin_edges.size, y) |
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else: |
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simple_weights = ( |
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cupy.can_cast(weights.dtype, cupy.float64) or |
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cupy.can_cast(weights.dtype, cupy.complex128) |
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) |
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if not simple_weights: |
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raise NotImplementedError( |
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'only weights with dtype that can be cast to float or complex ' |
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'are supported') |
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if weights.dtype.kind == 'c': |
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y = cupy.zeros(bin_edges.size - 1, dtype=cupy.complex128) |
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_weighted_histogram_kernel( |
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x, bin_edges, bin_edges.size, weights.real, y.real) |
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_weighted_histogram_kernel( |
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x, bin_edges, bin_edges.size, weights.imag, y.imag) |
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else: |
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if weights.dtype.kind in 'bui': |
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y = cupy.zeros(bin_edges.size - 1, dtype=int) |
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else: |
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y = cupy.zeros(bin_edges.size - 1, dtype=cupy.float64) |
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_weighted_histogram_kernel( |
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x, bin_edges, bin_edges.size, weights, y) |
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if density: |
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db = cupy.array(cupy.diff(bin_edges), cupy.float64) |
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return y / db / y.sum(), bin_edges |
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return y, bin_edges |
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def histogramdd(sample, bins=10, range=None, weights=None, density=False): |
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"""Compute the multidimensional histogram of some data. |
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Args: |
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sample (cupy.ndarray): The data to be histogrammed. (N, D) or (D, N) |
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array |
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Note the unusual interpretation of sample when an array_like: |
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* When an array, each row is a coordinate in a D-dimensional |
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space - such as ``histogramdd(cupy.array([p1, p2, p3]))``. |
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* When an array_like, each element is the list of values for single |
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coordinate - such as ``histogramdd((X, Y, Z))``. |
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The first form should be preferred. |
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bins (int or tuple of int or cupy.ndarray): The bin specification: |
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* A sequence of arrays describing the monotonically increasing bin |
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edges along each dimension. |
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* The number of bins for each dimension (nx, ny, ... =bins) |
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* The number of bins for all dimensions (nx=ny=...=bins). |
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range (sequence, optional): A sequence of length D, each an optional |
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(lower, upper) tuple giving the outer bin edges to be used if the |
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edges are not given explicitly in `bins`. An entry of None in the |
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sequence results in the minimum and maximum values being used for |
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the corresponding dimension. The default, None, is equivalent to |
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passing a tuple of D None values. |
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weights (cupy.ndarray): An array of values `w_i` weighing each sample |
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`(x_i, y_i, z_i, ...)`. The values of the returned histogram are |
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equal to the sum of the weights belonging to the samples falling |
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into each bin. |
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density (bool, optional): If False, the default, returns the number of |
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samples in each bin. If True, returns the probability *density* |
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function at the bin, ``bin_count / sample_count / bin_volume``. |
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Returns: |
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tuple: |
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H (cupy.ndarray): |
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The multidimensional histogram of sample x. See |
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normed and weights for the different possible semantics. |
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edges (list of cupy.ndarray): |
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A list of D arrays describing the bin |
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edges for each dimension. |
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.. warning:: |
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This function may synchronize the device. |
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.. seealso:: :func:`numpy.histogramdd` |
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""" |
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if isinstance(sample, cupy.ndarray): |
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if sample.ndim == 1: |
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sample = sample[:, cupy.newaxis] |
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nsamples, ndim = sample.shape |
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else: |
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sample = cupy.stack(sample, axis=-1) |
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nsamples, ndim = sample.shape |
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nbin = numpy.empty(ndim, int) |
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edges = ndim * [None] |
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dedges = ndim * [None] |
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if weights is not None: |
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weights = cupy.asarray(weights) |
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try: |
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nbins = len(bins) |
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if nbins != ndim: |
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raise ValueError( |
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'The dimension of bins must be equal to the dimension of the ' |
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' sample x.' |
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) |
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except TypeError: |
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bins = ndim * [bins] |
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if range is None: |
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range = (None,) * ndim |
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elif len(range) != ndim: |
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raise ValueError('range argument must have one entry per dimension') |
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for i in _range(ndim): |
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if cupy.ndim(bins[i]) == 0: |
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if bins[i] < 1: |
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raise ValueError( |
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'`bins[{}]` must be positive, when an integer'.format(i) |
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) |
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smin, smax = _get_outer_edges(sample[:, i], range[i]) |
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num = int(bins[i] + 1) |
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edges[i] = cupy.linspace(smin, smax, num) |
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elif cupy.ndim(bins[i]) == 1: |
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if not isinstance(bins[i], cupy.ndarray): |
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raise ValueError('array-like bins not supported') |
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edges[i] = bins[i] |
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if (edges[i][:-1] > edges[i][1:]).any(): |
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raise ValueError( |
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'`bins[{}]` must be monotonically increasing, when an ' |
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'array'.format(i) |
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) |
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else: |
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raise ValueError( |
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'`bins[{}]` must be a scalar or 1d array'.format(i) |
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) |
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nbin[i] = len(edges[i]) + 1 |
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dedges[i] = cupy.diff(edges[i]) |
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ncount = tuple( |
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cupy.searchsorted(edges[i], sample[:, i], side='right') |
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for i in _range(ndim) |
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) |
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for i in _range(ndim): |
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on_edge = sample[:, i] == edges[i][-1] |
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ncount[i][on_edge] -= 1 |
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xy = cupy.ravel_multi_index(ncount, nbin) |
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hist = cupy.bincount(xy, weights, minlength=numpy.prod(nbin)) |
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hist = hist.reshape(nbin) |
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hist = hist.astype(float) |
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core = ndim * (slice(1, -1),) |
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hist = hist[core] |
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if density: |
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s = hist.sum() |
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for i in _range(ndim): |
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shape = [1] * ndim |
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shape[i] = nbin[i] - 2 |
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hist = hist / dedges[i].reshape(shape) |
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hist /= s |
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if any(hist.shape != numpy.asarray(nbin) - 2): |
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raise RuntimeError('Internal Shape Error') |
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return hist, edges |
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|
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def histogram2d(x, y, bins=10, range=None, weights=None, density=None): |
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"""Compute the bi-dimensional histogram of two data samples. |
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|
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Args: |
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x (cupy.ndarray): The first array of samples to be histogrammed. |
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y (cupy.ndarray): The second array of samples to be histogrammed. |
|
|
bins (int or tuple of int or cupy.ndarray): The bin specification: |
|
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|
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|
* 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 |
|
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(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:: |
|
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|
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|
This function may synchronize the device. |
|
|
|
|
|
.. seealso:: :func:`numpy.histogram2d` |
|
|
""" |
|
|
try: |
|
|
n = len(bins) |
|
|
except TypeError: |
|
|
n = 1 |
|
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|
|
|
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') |
|
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|
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|
hist, edges = histogramdd([x, y], bins, range, weights, density) |
|
|
return hist, edges[0], edges[1] |
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|
|
|
|
|
|
_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') |
|
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|
|
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|
|
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 |
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``x``. |
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minlength (int): A minimum number of bins for the output array. |
|
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|
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|
Returns: |
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|
cupy.ndarray: The result of binning the input array. The length of |
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output is equal to ``max(cupy.max(x) + 1, minlength)``. |
|
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|
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|
.. warning:: |
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|
|
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|
This function may synchronize the device. |
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|
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|
.. seealso:: :func:`numpy.bincount` |
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|
|
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""" |
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if x.ndim > 1: |
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raise ValueError('object too deep for desired array') |
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if x.ndim < 1: |
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raise ValueError('object of too small depth for desired array') |
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|
if x.dtype.kind == 'f': |
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|
raise TypeError('x must be int array') |
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|
if (x < 0).any(): |
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raise ValueError('The first argument of bincount must be non-negative') |
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if weights is not None and x.shape != weights.shape: |
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|
raise ValueError('The weights and list don\'t have the same length.') |
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|
if minlength is not None: |
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|
minlength = int(minlength) |
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|
if minlength < 0: |
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raise ValueError('minlength must be non-negative') |
|
|
|
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|
size = int(cupy.max(x)) + 1 |
|
|
if minlength is not None: |
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|
size = max(size, minlength) |
|
|
|
|
|
if weights is None: |
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|
b = cupy.zeros((size,), dtype=numpy.intp) |
|
|
|
|
|
|
|
|
|
|
|
_bincount_kernel(x, b) |
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else: |
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|
b = cupy.zeros((size,), dtype=numpy.float64) |
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|
_bincount_with_weight_kernel(x, weights, b) |
|
|
|
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|
return b |
|
|
|
|
|
|
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|
def digitize(x, bins, right=False): |
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|
"""Finds the indices of the bins to which each value in input array belongs. |
|
|
|
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|
.. 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` |
|
|
""" |
|
|
|
|
|
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') |
|
|
|
|
|
|
|
|
side = 'left' if right else 'right' |
|
|
return cupy._sorting.search._searchsorted(bins, x, side, None, False) |
|
|
|