def _binary_clf_curve(y_true, y_score):
if y_true.dtype.kind == 'f' and np.any(y_true != y_true.astype(int)):
raise ValueError("Continuous format of y_true " "is not supported.")
ids = cp.argsort(-y_score)
sorted_score = y_score[ids]
ones = y_true[ids].astype('float32') # for calculating true positives
zeros = 1 - ones # for calculating predicted positives
# calculate groups
group = _group_same_scores(sorted_score)
num = int(group[-1])
tps = cp.zeros(num, dtype='float32')
fps = cp.zeros(num, dtype='float32')
tps = _addup_x_in_group(group, ones, tps)
fps = _addup_x_in_group(group, zeros, fps)
tps = cp.cumsum(tps)
fps = cp.cumsum(fps)
thresholds = cp.unique(y_score)
return fps, tps, thresholds
def _csr_row_index(rows, Ap, Aj, Ax):
"""Populate indices and data arrays from the given row index
Args:
rows (cupy.ndarray): index array of rows to populate
Ap (cupy.ndarray): indptr array from input sparse matrix
Aj (cupy.ndarray): indices array from input sparse matrix
Ax (cupy.ndarray): data array from input sparse matrix
Returns:
Bp (cupy.ndarray): indptr array for output sparse matrix
Bj (cupy.ndarray): indices array of output sparse matrix
Bx (cupy.ndarray): data array of output sparse matrix
"""
row_nnz = cupy.diff(Ap)
Bp = cupy.empty(rows.size + 1, dtype=Ap.dtype)
Bp[0] = 0
cupy.cumsum(row_nnz[rows], out=Bp[1:])
nnz = int(Bp[-1])
out_rows = cupy.empty(nnz, dtype=numpy.int32)
# Build a COO row array from output CSR indptr.
# Calling backend cusparse API directly to avoid
# constructing a whole COO object.
handle = device.get_cusparse_handle()
cusparse.xcsr2coo(handle, Bp.data.ptr, nnz, Bp.size - 1, out_rows.data.ptr,
cusparse.CUSPARSE_INDEX_BASE_ZERO)
Bj, Bx = _csr_row_index_ker(out_rows, rows, Ap, Aj, Ax, Bp)
return Bp, Bj, Bx
def _major_slice(self, idx, copy=False):
"""Index along the major axis where idx is a slice object.
"""
if idx == slice(None):
return self.copy() if copy else self
M, N = self._swap(*self.shape)
start, stop, step = idx.indices(M)
M = len(range(start, stop, step))
new_shape = self._swap(M, N)
if M == 0:
return self.__class__(new_shape)
row_nnz = cupy.diff(self.indptr)
idx_dtype = self.indices.dtype
res_indptr = cupy.zeros(M + 1, dtype=idx_dtype)
cupy.cumsum(row_nnz[idx], out=res_indptr[1:])
if step == 1:
idx_start = self.indptr[start]
idx_stop = self.indptr[stop]
res_indices = cupy.array(self.indices[idx_start:idx_stop],
copy=copy)
res_data = cupy.array(self.data[idx_start:idx_stop], copy=copy)
else:
res_indices, res_data = _index._csr_row_slice(
start, step, self.indptr, self.indices, self.data, res_indptr)
return self.__class__((res_data, res_indices, res_indptr),
shape=new_shape,
copy=False)
def _get_csr_submatrix_minor_axis(Ap, Aj, Ax, start, stop):
"""Return a submatrix of the input sparse matrix by slicing minor axis.
Args:
Ap (cupy.ndarray): indptr array from input sparse matrix
Aj (cupy.ndarray): indices array from input sparse matrix
Ax (cupy.ndarray): data array from input sparse matrix
start (int): starting index of minor axis
stop (int): ending index of minor axis
Returns:
Bp (cupy.ndarray): indptr array of output sparse matrix
Bj (cupy.ndarray): indices array of output sparse matrix
Bx (cupy.ndarray): data array of output sparse matrix
"""
mask = (start <= Aj) & (Aj < stop)
mask_sum = cupy.empty(Aj.size + 1, dtype=Aj.dtype)
mask_sum[0] = 0
mask_sum[1:] = mask
cupy.cumsum(mask_sum, out=mask_sum)
Bp = mask_sum[Ap]
Bj = Aj[mask] - start
Bx = Ax[mask]
return Bp, Bj, Bx
def _perform_insert(self, indices_inserts, data_inserts,
rows, row_counts, idx_dtype):
"""Insert new elements into current sparse matrix in sorted order"""
indptr_diff = cupy.diff(self.indptr)
indptr_diff[rows] += row_counts
new_indptr = cupy.empty(self.indptr.shape, dtype=idx_dtype)
new_indptr[0] = idx_dtype(0)
new_indptr[1:] = indptr_diff
# Build output arrays
cupy.cumsum(new_indptr, out=new_indptr)
out_nnz = int(new_indptr[-1])
new_indices = cupy.empty(out_nnz, dtype=idx_dtype)
new_data = cupy.empty(out_nnz, dtype=self.data.dtype)
# Build an indexed indptr that contains the offsets for each
# row but only for in i, j, and x.
new_indptr_lookup = cupy.zeros(new_indptr.size, dtype=idx_dtype)
new_indptr_lookup[1:][rows] = row_counts
cupy.cumsum(new_indptr_lookup, out=new_indptr_lookup)
_index._insert_many_populate_arrays(
indices_inserts, data_inserts, new_indptr_lookup,
self.indptr, self.indices, self.data, new_indptr, new_indices,
new_data, size=self.indptr.size-1)
self.indptr = new_indptr
self.indices = new_indices
self.data = new_data
def sinhm(arr):
"""Hyperbolic Sine calculation for a given nXn matrix
Args:
arr(cupy.ndarray) :
Square matrix with dimension nXn.
Returns:
(cupy.ndarray):
Hyperbolic sine of given square matrix as input.
..seealso:: :func: 'scipy.linalg.sinhm'
"""
arr = cupy.array(arr)
# Checking whether the input is a 2D matrix or not
if (len(arr.shape) != 2):
raise ValueError("Dimensions of matrix should be 2")
# Checking whether the input matrix is square matrix or not
if (arr.shape[0] != arr.shape[1]):
raise ValueError("Input matrix should be a square matrix")
# Checking whether the input matrix elements are nan or not
if (cupy.isnan(cupy.cumsum(arr)[2 * arr.shape[0] - 1])):
raise ValueError("Input matrix elements cannot be nan")
# Checking whether the input matrix elements are infinity or not
if (cupy.isinf(cupy.cumsum(arr)[2 * arr.shape[0] - 1])):
raise ValueError("Input matrix elements cannot be infinity")
return 0.5 * (cupy.exp(arr) - cupy.exp(-1 * arr))
def threshold_yen(image=None, nbins=256, *, hist=None):
"""Return threshold value based on Yen's method.
Either image or hist must be provided. In case hist is given, the actual
histogram of the image is ignored.
Parameters
----------
image : (N, M) ndarray, optional
Input image.
nbins : int, optional
Number of bins used to calculate histogram. This value is ignored for
integer arrays.
hist : array, or 2-tuple of arrays, optional
Histogram from which to determine the threshold, and optionally a
corresponding array of bin center intensities.
An alternative use of this function is to pass it only hist.
Returns
-------
threshold : float
Upper threshold value. All pixels with an intensity higher than
this value are assumed to be foreground.
References
----------
.. [1] Yen J.C., Chang F.J., and Chang S. (1995) "A New Criterion
for Automatic Multilevel Thresholding" IEEE Trans. on Image
Processing, 4(3): 370-378. :DOI:`10.1109/83.366472`
.. [2] Sezgin M. and Sankur B. (2004) "Survey over Image Thresholding
Techniques and Quantitative Performance Evaluation" Journal of
Electronic Imaging, 13(1): 146-165, :DOI:`10.1117/1.1631315`
http://www.busim.ee.boun.edu.tr/~sankur/SankurFolder/Threshold_survey.pdf
.. [3] ImageJ AutoThresholder code, http://fiji.sc/wiki/index.php/Auto_Threshold
Examples
--------
>>> from skimage.data import camera
>>> image = camera()
>>> thresh = threshold_yen(image)
>>> binary = image <= thresh
"""
counts, bin_centers = _validate_image_histogram(image, hist, nbins)
# On blank images (e.g. filled with 0) with int dtype, `histogram()`
# returns ``bin_centers`` containing only one value. Speed up with it.
if bin_centers.size == 1:
return bin_centers[0]
# Calculate probability mass function
pmf = counts.astype(cp.float32) / counts.sum()
P1 = cp.cumsum(pmf) # Cumulative normalized histogram
P1_sq = cp.cumsum(pmf * pmf)
# Get cumsum calculated from end of squared array:
P2_sq = cp.cumsum(pmf[::-1]**2)[::-1]
# P2_sq indexes is shifted +1. I assume, with P1[:-1] it's help avoid
# '-inf' in crit. ImageJ Yen implementation replaces those values by zero.
crit = cp.log(
((P1_sq[:-1] * P2_sq[1:])**-1) * (P1[:-1] * (1.0 - P1[:-1]))**2)
return bin_centers[crit.argmax()]
def update(self):
with cuda.gpus[self.gpu]:
self.d_cell_counts.fill(0)
self.cu_cell_list[self.bpg_part,
self.tpb](self.system.d_x, self.system.d_box,
self.d_ibox, self.d_cells,
self.d_cell_counts)
cupy.cumsum(self.d_cell_counts, out=self.d_cell_counts)
self.d_cell_list = cupy.argsort(self.d_cells)
def moving_mean_std_gpu(a, w):
s = cp.concatenate([cp.array([0]), cp.cumsum(a)])
sSq = cp.concatenate([cp.array([0]), cp.cumsum(a**2)])
segSum = s[w:] - s[:-w]
segSumSq = sSq[w:] - sSq[:-w]
movmean = segSum / w
movstd = cp.sqrt(segSumSq / w - (segSum / w)**2)
return (movmean, movstd)
def _window_sum_2d(image, window_shape):
window_sum = cp.cumsum(image, axis=0)
window_sum = (window_sum[window_shape[0]:-1] -
window_sum[:-window_shape[0] - 1])
window_sum = cp.cumsum(window_sum, axis=1)
window_sum = (window_sum[:, window_shape[1]:-1] -
window_sum[:, :-window_shape[1] - 1])
return window_sum
def set_attractivities(self, attractivities):
self.square_sampling_probas = get_square_sampling_probas(attractivities,
self.square_ids_cells,
self.coords_squares,
self.dscale)
mask_eligible = cp.where(attractivities > 0)[0] # only cells with attractivity > 0 are eligible for a move
self.eligible_cells = self.cell_ids[mask_eligible]
# Compute square to cell transition matrix
self.cell_sampling_probas, self.cell_index_shift = get_cell_sampling_probas(attractivities[mask_eligible], self.square_ids_cells[mask_eligible])
# Compute upfront cumulated sum of sampling matrices
self.square_sampling_probas = cp.cumsum(self.square_sampling_probas, axis=1)
self.cell_sampling_probas = cp.cumsum(self.cell_sampling_probas, axis=1)
def _window_sum_2d(image, window_shape):
# TODO: remove copy in line below once the following issue is resolved
# https://github.com/cupy/cupy/issues/4456
window_sum = cp.cumsum(image, axis=0)
window_sum = (window_sum[window_shape[0]:-1] -
window_sum[:-window_shape[0] - 1])
window_sum = cp.cumsum(window_sum, axis=1)
window_sum = (window_sum[:, window_shape[1]:-1] -
window_sum[:, :-window_shape[1] - 1])
return window_sum
def perform_cumsum(input_array, use_cuda):
"""
Return an array containing the cumulative sum of the 1darray `input_array`
(The returned array has one more element than `input_array`; its first
element is 0 and its last element is the total sum of `input_array`)
"""
if use_cuda:
cumulative_array = cupy.zeros(len(input_array) + 1, dtype=cupy.int64)
cupy.cumsum(input_array, out=cumulative_array[1:])
else:
cumulative_array = np.zeros(len(input_array) + 1, dtype=np.int64)
np.cumsum(input_array, out=cumulative_array[1:])
return (cumulative_array)
def sum_by_group(values1, values2, groups):
order = cp.argsort(groups)
groups = groups[order]
values1 = values1[order]
values2 = values2[order]
cp.cumsum(values1, out=values1, axis=0)
cp.cumsum(values2, out=values2, axis=0)
index = cp.ones(len(groups), 'bool')
index[:-1] = groups[1:] != groups[:-1]
values1 = values1[index]
values2 = values2[index]
groups = groups[index]
values1[1:] = values1[1:] - values1[:-1]
values2[1:] = values2[1:] - values2[:-1]
return values1, values2, groups
def dense2csr(a):
if a.dtype.char in 'fdFD':
return cusparse.dense2csr(a)
m, n = a.shape
a = cupy.ascontiguousarray(a)
indptr = cupy.zeros(m + 1, dtype=numpy.int32)
info = cupy.zeros(m * n + 1, dtype=numpy.int32)
cupy_dense2csr_step1()(m, n, a, indptr, info)
indptr = cupy.cumsum(indptr, dtype=numpy.int32)
info = cupy.cumsum(info, dtype=numpy.int32)
nnz = int(indptr[-1])
indices = cupy.empty(nnz, dtype=numpy.int32)
data = cupy.empty(nnz, dtype=a.dtype)
cupy_dense2csr_step2()(m, n, a, info, indices, data)
return csr_matrix((data, indices, indptr), shape=(m, n))
def create_cats(self, size, cats_rep, entries=False):
"""
size = number of rows
num_cols = how many columns you want produced
cat_rep = a list of tuple values (cardinality, min, max) representing the cardinality,
minimum and maximum categorical string length
"""
# should alpha also be exposed? related to dist... should be part of that
df = cudf.DataFrame()
for col in cats_rep:
# if mh resets size
col_size = size
offs = None
dist = col.distro or self.dist
if col.multi_min and col.multi_max:
entrys_lens = dist.create_col(
col_size + 1, dtype=np.long, min_val=col.multi_min, max_val=col.multi_max
).ceil()
# sum returns numpy dtype
col_size = int(entrys_lens.sum())
offs = cupy.cumsum(entrys_lens.values)
ser = dist.create_col(
col_size, dtype=np.long, min_val=0, max_val=col.cardinality
).ceil()
if entries:
cat_names = self.create_cat_entries(
col.cardinality, min_size=col.min_entry_size, max_size=col.max_entry_size
)
ser, _ = self.merge_cats_encoding(ser, cat_names)
if offs is not None:
# create multi_column from offs and ser
ser = self.create_multihot_col(offs, ser)
ser.name = col.name
df = cudf.concat([df, ser], axis=1)
return df
def _match_cumulative_cdf(source, template):
"""
Return modified source array so that the cumulative density function of
its values matches the cumulative density function of the template.
"""
src_values, src_unique_indices, src_counts = cp.unique(source.ravel(),
return_inverse=True,
return_counts=True)
tmpl_values, tmpl_counts = cp.unique(template.ravel(), return_counts=True)
# calculate normalized quantiles for each array
src_quantiles = cp.cumsum(src_counts) / source.size
tmpl_quantiles = cp.cumsum(tmpl_counts) / template.size
interp_a_values = cp.interp(src_quantiles, tmpl_quantiles, tmpl_values)
return interp_a_values[src_unique_indices].reshape(source.shape)
def unwrap(p, discont=numpy.pi, axis=-1):
"""Unwrap by changing deltas between values to 2*pi complement.
Args:
p (cupy.ndarray): Input array.
discont (float): Maximum discontinuity between values, default is
``pi``.
axis (int): Axis along which unwrap will operate, default is the last
axis.
Returns:
cupy.ndarray: The result array.
.. seealso:: :func:`numpy.unwrap`
"""
p = cupy.asarray(p)
nd = p.ndim
dd = sumprod.diff(p, axis=axis)
slice1 = [slice(None, None)]*nd # full slices
slice1[axis] = slice(1, None)
slice1 = tuple(slice1)
ph_correct = _unwrap_correct(dd, discont)
up = cupy.array(p, copy=True, dtype='d')
up[slice1] = p[slice1] + cupy.cumsum(ph_correct, axis=axis)
return up
def tocsc(self, copy=False):
"""Converts the matrix to Compressed Sparse Column format.
Args:
copy (bool): If ``False``, it shares data arrays as much as
possible. Actually this option is ignored because all
arrays in a matrix cannot be shared in dia to csc conversion.
Returns:
cupy.sparse.csc_matrix: Converted matrix.
"""
if self.data.size == 0:
return csc.csc_matrix(self.shape, dtype=self.dtype)
num_rows, num_cols = self.shape
num_offsets, offset_len = self.data.shape
row, mask = core.ElementwiseKernel(
'int32 offset_len, int32 offsets, int32 num_rows, '
'int32 num_cols, T data', 'int32 row, bool mask', '''
int offset_inds = i % offset_len;
row = offset_inds - offsets;
mask = (row >= 0 && row < num_rows && offset_inds < num_cols
&& data != 0);
''', 'dia_tocsc')(offset_len, self.offsets[:, None], num_rows,
num_cols, self.data)
indptr = cupy.zeros(num_cols + 1, dtype='i')
indptr[1:offset_len + 1] = cupy.cumsum(mask.sum(axis=0))
indptr[offset_len + 1:] = indptr[offset_len]
indices = row.T[mask.T].astype('i', copy=False)
data = self.data.T[mask.T]
return csc.csc_matrix((data, indices, indptr),
shape=self.shape,
dtype=self.dtype)
def test_args(self):
dx = cp.cumsum(cp.ones(5))
dx_uneven = [1.0, 2.0, 5.0, 9.0, 11.0]
f_2d = cp.arange(25).reshape(5, 5)
# distances must be scalars or have size equal to gradient[axis]
gradient(cp.arange(5), 3.0)
gradient(cp.arange(5), cp.array(3.0))
gradient(cp.arange(5), dx)
# dy is set equal to dx because scalar
gradient(f_2d, 1.5)
gradient(f_2d, cp.array(1.5))
gradient(f_2d, dx_uneven, dx_uneven)
# mix between even and uneven spaces and
# mix between scalar and vector
gradient(f_2d, dx, 2)
# 2D but axis specified
gradient(f_2d, dx, axis=1)
# 2d coordinate arguments are not yet allowed
assert_raises_regex(
ValueError,
".*scalars or 1d",
gradient,
f_2d,
cp.stack([dx] * 2, axis=-1),
1,
)
def pricepaths(S, tau, r, q, v, M, N):
dt = tau / M
g1 = (r - q - v / 2) * dt
g2 = math.sqrt(v * dt)
aux = math.log(S) + cp.cumsum(
g1 + g2 * cp.random.randn(M, N, dtype=cp.float32), 0)
return cp.exp(aux)
def transform(self, columns: ColumnNames, df: DataFrameType) -> DataFrameType:
on_cpu = _is_cpu_object(df)
ret = type(df)()
for col in columns:
# handle CPU via normal python slicing (not very efficient)
if on_cpu:
ret[col] = [row[self.start : self.end] for row in df[col]]
else:
# figure out the size of each row from the list offsets
c = df[col]._column
offsets = c.offsets.values
elements = c.elements.values
# figure out the size of each row after slicing start/end
new_offsets = cp.zeros(offsets.size, dtype=offsets.dtype)
threads = 32
blocks = (offsets.size + threads - 1) // threads
# calculate new row offsets after slicing
_calculate_row_sizes[blocks, threads](self.start, self.end, offsets, new_offsets)
new_offsets = cp.cumsum(new_offsets).astype(offsets.dtype)
# create a new array for the sliced elements
new_elements = cp.zeros(new_offsets[-1].item(), dtype=elements.dtype)
if new_elements.size:
_slice_rows[blocks, threads](
self.start, offsets, elements, new_offsets, new_elements
)
# build up a list column with the sliced values
ret[col] = _build_cudf_list_column(new_elements, new_offsets)
return ret
def rank_order(image):
"""Return an image of the same shape where each pixel is the
index of the pixel value in the ascending order of the unique
values of ``image``, aka the rank-order value.
Parameters
----------
image : ndarray
Returns
-------
labels : ndarray of type np.uint32, of shape image.shape
New array where each pixel has the rank-order value of the
corresponding pixel in ``image``. Pixel values are between 0 and
n - 1, where n is the number of distinct unique values in
``image``.
original_values : 1-D ndarray
Unique original values of ``image``
Examples
--------
>>> a = cp.asarray([[1, 4, 5], [4, 4, 1], [5, 1, 1]])
>>> a
array([[1, 4, 5],
[4, 4, 1],
[5, 1, 1]])
>>> rank_order(a)
(array([[0, 1, 2],
[1, 1, 0],
[2, 0, 0]], dtype=uint32), array([1, 4, 5]))
>>> b = cp.asarray([-1., 2.5, 3.1, 2.5])
>>> rank_order(b)
(array([0, 1, 2, 1], dtype=uint32), array([-1. , 2.5, 3.1]))
"""
flat_image = image.ravel()
sort_order = flat_image.argsort().astype(cp.uint32)
flat_image = flat_image[sort_order]
sort_rank = cp.zeros_like(sort_order)
is_different = flat_image[:-1] != flat_image[1:]
cp.cumsum(is_different, out=sort_rank[1:])
original_values = cp.zeros((sort_rank[-1].get() + 1, ), image.dtype)
original_values[0] = flat_image[0]
original_values[1:] = flat_image[1:][is_different]
int_image = cp.zeros_like(sort_order)
int_image[sort_order] = sort_rank
return (int_image.reshape(image.shape), original_values)
def _get_indices(self, sample, upper_limit, cond):
dtype = numpy.uint32 if sample.size < 2**32 else numpy.uint64
flags = (sample <= upper_limit) if cond else (sample > upper_limit)
csum = cupy.cumsum(flags, dtype=dtype)
del flags
indices = cupy.empty((int(csum[-1]), ), dtype=dtype)
self._kernel_get_indices(csum, indices, size=csum.size)
return indices
def assemble_sparse(self, ke, tri, perm, n_pts, ref=0):
'''
function that assembles the global stiffness matrix from all element stiffness matrices
takes:
ke - stiffness on each element matrix - array shape (n_triangles, n_vertices, n_vertices)
tri - array with all indices (in pts array) of triangle vertices - shape (num_triangles, 3)
perm - array with permittivity in each element - array shape (num_triangles,)
n_pts - number of nodes - int
ref - electrode on which reference value is placed
returns:
K - global stiffness matrix - (n_pts, n_pts)
'''
n_tri, n_vertices = tri.shape
row = cp.tile(tri, (1, n_vertices))
i = cp.array([0, 3, 6, 1, 4, 7, 2, 5, 8])
row = row[:, i].ravel()
col = cp.tile(tri, (n_vertices)).reshape(
(tri.shape[0] * tri.shape[1] * n_vertices))
admittanceMatrixC2 = self.admittanceMatrixC2()
data = cp.multiply(ke[:], perm[:, None, None])
indexElectrode = cp.sort(self.tri[self.twoFromElectrode][self.isValid],
axis=1)[:, 0] // self.n_per_el
data[self.twoFromElectrode][self.isValid] = (
data[self.twoFromElectrode][self.isValid] +
((1 / self.z[indexElectrode]))[:, None, None] * admittanceMatrixC2)
data = data.ravel()
ind = cp.argsort(row)
row = row[ind]
col = col[ind]
data = data[ind]
unique, counts = cp.unique(row, return_counts=True)
index_pointer = cp.zeros(n_pts + 1)
sum_count = cp.cumsum(counts)
index_pointer[unique[:] + 1] = sum_count[:]
K = sp.csr_matrix((data, col, index_pointer),
shape=(n_pts, n_pts),
dtype=perm.dtype)
K = K.toarray()
A = cp.empty((self.n_pts + self.ne, self.n_pts + self.ne), dtype='f8')
if 0 <= self.ref < n_pts:
K[self.ref, :] = 0.
K[:, self.ref] = 0.
K[self.ref, self.ref] = 1.
A[:self.n_pts, :self.n_pts] = K[:]
admittanceMatrixE = self.admittanceMatrixE()
A[self.n_pts:, :self.n_pts] = admittanceMatrixE.T
A[:self.n_pts, self.n_pts:] = admittanceMatrixE
A[self.n_pts:, self.n_pts:] = self.admittanceMatrixD()
return A
def sum_duplicates(self):
"""Eliminate duplicate matrix entries by adding them together.
.. seealso::
:func:`scipy.sparse.coo_matrix.sum_duplicates`
"""
if self._has_canonical_format:
return
if self.data.size == 0:
self._has_canonical_format = True
return
keys = cupy.stack([self.row, self.col])
order = cupy.lexsort(keys)
src_data = self.data[order]
src_row = self.row[order]
src_col = self.col[order]
diff = cupy.ElementwiseKernel(
'raw int32 row, raw int32 col',
'int32 diff',
'''
int index;
if (i == 0 || row[i - 1] == row[i] && col[i - 1] == col[i]) {
diff = 0;
} else {
diff = 1;
}
''',
'sum_duplicates_diff'
)(src_row, src_col, size=self.row.size)
if diff[1:].all():
# All elements have different indices.
data = src_data
row = src_row
col = src_col
else:
index = cupy.cumsum(diff, dtype='i')
size = int(index[-1]) + 1
data = cupy.zeros(size, dtype=self.data.dtype)
row = cupy.empty(size, dtype='i')
col = cupy.empty(size, dtype='i')
cupy.ElementwiseKernel(
'T src_data, int32 src_row, int32 src_col, int32 index',
'raw T data, raw int32 row, raw int32 col',
'''
atomicAdd(&data[index], src_data);
row[index] = src_row;
col[index] = src_col;
''',
'sum_duplicates_assign',
preamble=util._preamble_atomic_add
)(src_data, src_row, src_col, index, data, row, col)
self.data = data
self.row = row
self.col = col
self._has_canonical_format = True
def sample(self, n_samples=1, random_state=None):
"""
Generate random samples from the model.
Currently, this is implemented only for gaussian and tophat kernels,
and the Euclidean metric.
Parameters
----------
n_samples : int, default=1
Number of samples to generate.
random_state : int, cupy RandomState instance or None, default=None
Returns
-------
X : cupy array of shape (n_samples, n_features)
List of samples.
"""
if not hasattr(self, "X_"):
raise NotFittedError()
supported_kernels = ["gaussian", "tophat"]
if (self.kernel not in supported_kernels
or self.metric != "euclidean"):
raise NotImplementedError(
"Only {} kernels, and the euclidean"
" metric are supported.".format(supported_kernels))
if isinstance(random_state, cp.random.RandomState):
rng = random_state
else:
rng = cp.random.RandomState(random_state)
u = rng.uniform(0, 1, size=n_samples)
if self.sample_weight_ is None:
i = (u * self.X_.shape[0]).astype(np.int64)
else:
cumsum_weight = cp.cumsum(self.sample_weight_)
sum_weight = cumsum_weight[-1]
i = cp.searchsorted(cumsum_weight, u * sum_weight)
if self.kernel == "gaussian":
return cp.atleast_2d(rng.normal(self.X_[i], self.bandwidth))
elif self.kernel == "tophat":
# we first draw points from a d-dimensional normal distribution,
# then use an incomplete gamma function to map them to a uniform
# d-dimensional tophat distribution.
has_scipy(raise_if_unavailable=True)
dim = self.X_.shape[1]
X = rng.normal(size=(n_samples, dim))
s_sq = cp.einsum("ij,ij->i", X, X).get()
# do this on the CPU becaause we don't have
# a gammainc function readily available
correction = cp.array(
gammainc(0.5 * dim, 0.5 * s_sq)**(1.0 / dim) * self.bandwidth /
np.sqrt(s_sq))
return self.X_[i] + X * correction[:, np.newaxis]
def _window_sum_3d(image, window_shape):
window_sum = _window_sum_2d(image, window_shape)
window_sum = cp.cumsum(window_sum, axis=2)
window_sum = (window_sum[:, :, window_shape[2]:-1] -
window_sum[:, :, :-window_shape[2] - 1])
return window_sum
def cumulative_distribution(data, bins):
assert cup.min(data) >= 0.0 and cup.max(data) <= 1.0
hg_av, hg_a = cup.unique(cup.floor(data * (bins - 1)), return_index=True)
hg_a = cup.float32(hg_a)
hgs = cup.sum(hg_a)
hg_a /= hgs
res = cup.zeros((bins, ))
res[cup.int64(hg_av)] = hg_a
return cup.cumsum(res)
def multiply_by_csr(a, b):
a_m, a_n = a.shape
b_m, b_n = b.shape
if not (a_m == b_m or a_m == 1 or b_m == 1):
raise ValueError('inconsistent shape')
if not (a_n == b_n or a_n == 1 or b_n == 1):
raise ValueError('inconsistent shape')
m, n = max(a_m, b_m), max(a_n, b_n)
a_nnz = a.nnz * (m // a_m) * (n // a_n)
b_nnz = b.nnz * (m // b_m) * (n // b_n)
if a_nnz > b_nnz:
return multiply_by_csr(b, a)
c_nnz = a_nnz
dtype = numpy.promote_types(a.dtype, b.dtype)
c_data = cupy.empty(c_nnz, dtype=dtype)
c_indices = cupy.empty(c_nnz, dtype=a.indices.dtype)
if m > a_m:
if n > a_n:
c_indptr = cupy.arange(0, c_nnz+1, n, dtype=a.indptr.dtype)
else:
c_indptr = cupy.arange(0, c_nnz+1, a.nnz, dtype=a.indptr.dtype)
else:
c_indptr = a.indptr.copy()
if n > a_n:
c_indptr *= n
flags = cupy.zeros(c_nnz+1, dtype=a.indices.dtype)
nnz_each_row = cupy.zeros(m+1, dtype=a.indptr.dtype)
# compute c = a * b where necessary and get sparsity pattern of matrix d
cupy_multiply_by_csr_step1()(
a.data, a.indptr, a.indices, a_m, a_n,
b.data, b.indptr, b.indices, b_m, b_n,
c_indptr, m, n, c_data, c_indices, flags, nnz_each_row)
flags = cupy.cumsum(flags, dtype=a.indptr.dtype)
d_indptr = cupy.cumsum(nnz_each_row, dtype=a.indptr.dtype)
d_nnz = int(d_indptr[-1])
d_data = cupy.empty(d_nnz, dtype=dtype)
d_indices = cupy.empty(d_nnz, dtype=a.indices.dtype)
# remove zero elements in matric c
cupy_multiply_by_csr_step2()(c_data, c_indices, flags, d_data, d_indices)
return csr_matrix((d_data, d_indices, d_indptr), shape=(m, n))