cimport cython from cython cimport Py_ssize_t from libc.math cimport ( fabs, sqrt, ) from libc.stdlib cimport ( free, malloc, ) from libc.string cimport memmove import numpy as np cimport numpy as cnp from numpy cimport ( NPY_FLOAT64, NPY_INT8, NPY_INT16, NPY_INT32, NPY_INT64, NPY_OBJECT, NPY_UINT64, float32_t, float64_t, int8_t, int16_t, int32_t, int64_t, intp_t, ndarray, uint8_t, uint16_t, uint32_t, uint64_t, ) cnp.import_array() cimport pandas._libs.util as util from pandas._libs.dtypes cimport ( numeric_object_t, numeric_t, ) from pandas._libs.khash cimport ( kh_destroy_int64, kh_get_int64, kh_init_int64, kh_int64_t, kh_put_int64, kh_resize_int64, khiter_t, ) from pandas._libs.missing cimport ( checknull, isnaobj, ) from pandas._libs.util cimport get_nat cdef: float64_t FP_ERR = 1e-13 float64_t NaN = np.nan int64_t NPY_NAT = get_nat() tiebreakers = { "average": TIEBREAK_AVERAGE, "min": TIEBREAK_MIN, "max": TIEBREAK_MAX, "first": TIEBREAK_FIRST, "dense": TIEBREAK_DENSE, } cdef bint are_diff(object left, object right): try: return fabs(left - right) > FP_ERR except TypeError: return left != right class Infinity: """ Provide a positive Infinity comparison method for ranking. """ def __lt__(self, other): return False def __le__(self, other): return isinstance(other, Infinity) def __eq__(self, other): return isinstance(other, Infinity) def __ne__(self, other): return not isinstance(other, Infinity) def __gt__(self, other): return (not isinstance(other, Infinity) and not checknull(other)) def __ge__(self, other): return not checknull(other) class NegInfinity: """ Provide a negative Infinity comparison method for ranking. """ def __lt__(self, other): return (not isinstance(other, NegInfinity) and not checknull(other)) def __le__(self, other): return not checknull(other) def __eq__(self, other): return isinstance(other, NegInfinity) def __ne__(self, other): return not isinstance(other, NegInfinity) def __gt__(self, other): return False def __ge__(self, other): return isinstance(other, NegInfinity) @cython.wraparound(False) @cython.boundscheck(False) cpdef ndarray[int64_t, ndim=1] unique_deltas(const int64_t[:] arr): """ Efficiently find the unique first-differences of the given array. Parameters ---------- arr : ndarray[int64_t] Returns ------- ndarray[int64_t] An ordered ndarray[int64_t] """ cdef: Py_ssize_t i, n = len(arr) int64_t val khiter_t k kh_int64_t *table int ret = 0 list uniques = [] ndarray[int64_t, ndim=1] result table = kh_init_int64() kh_resize_int64(table, 10) for i in range(n - 1): val = arr[i + 1] - arr[i] k = kh_get_int64(table, val) if k == table.n_buckets: kh_put_int64(table, val, &ret) uniques.append(val) kh_destroy_int64(table) result = np.array(uniques, dtype=np.int64) result.sort() return result @cython.wraparound(False) @cython.boundscheck(False) def is_lexsorted(list_of_arrays: list) -> bool: cdef: Py_ssize_t i Py_ssize_t n, nlevels int64_t k, cur, pre ndarray arr bint result = True nlevels = len(list_of_arrays) n = len(list_of_arrays[0]) cdef int64_t **vecs = malloc(nlevels * sizeof(int64_t*)) for i in range(nlevels): arr = list_of_arrays[i] assert arr.dtype.name == "int64" vecs[i] = cnp.PyArray_DATA(arr) # Assume uniqueness?? with nogil: for i in range(1, n): for k in range(nlevels): cur = vecs[k][i] pre = vecs[k][i -1] if cur == pre: continue elif cur > pre: break else: result = False break if not result: break free(vecs) return result @cython.boundscheck(False) @cython.wraparound(False) def groupsort_indexer(const intp_t[:] index, Py_ssize_t ngroups): """ Compute a 1-d indexer. The indexer is an ordering of the passed index, ordered by the groups. Parameters ---------- index: np.ndarray[np.intp] Mappings from group -> position. ngroups: int64 Number of groups. Returns ------- ndarray[intp_t, ndim=1] Indexer ndarray[intp_t, ndim=1] Group Counts Notes ----- This is a reverse of the label factorization process. """ cdef: Py_ssize_t i, label, n intp_t[::1] indexer, where, counts counts = np.zeros(ngroups + 1, dtype=np.intp) n = len(index) indexer = np.zeros(n, dtype=np.intp) where = np.zeros(ngroups + 1, dtype=np.intp) with nogil: # count group sizes, location 0 for NA for i in range(n): counts[index[i] + 1] += 1 # mark the start of each contiguous group of like-indexed data for i in range(1, ngroups + 1): where[i] = where[i - 1] + counts[i - 1] # this is our indexer for i in range(n): label = index[i] + 1 indexer[where[label]] = i where[label] += 1 return indexer.base, counts.base cdef Py_ssize_t swap(numeric_t *a, numeric_t *b) noexcept nogil: cdef: numeric_t t # cython doesn't allow pointer dereference so use array syntax t = a[0] a[0] = b[0] b[0] = t return 0 cdef numeric_t kth_smallest_c(numeric_t* arr, Py_ssize_t k, Py_ssize_t n) noexcept nogil: """ See kth_smallest.__doc__. The additional parameter n specifies the maximum number of elements considered in arr, needed for compatibility with usage in groupby.pyx """ cdef: Py_ssize_t i, j, left, m numeric_t x left = 0 m = n - 1 while left < m: x = arr[k] i = left j = m while 1: while arr[i] < x: i += 1 while x < arr[j]: j -= 1 if i <= j: swap(&arr[i], &arr[j]) i += 1 j -= 1 if i > j: break if j < k: left = i if k < i: m = j return arr[k] @cython.boundscheck(False) @cython.wraparound(False) def kth_smallest(numeric_t[::1] arr, Py_ssize_t k) -> numeric_t: """ Compute the kth smallest value in arr. Note that the input array will be modified. Parameters ---------- arr : numeric[::1] Array to compute the kth smallest value for, must be contiguous k : Py_ssize_t Returns ------- numeric The kth smallest value in arr """ cdef: numeric_t result with nogil: result = kth_smallest_c(&arr[0], k, arr.shape[0]) return result # ---------------------------------------------------------------------- # Pairwise correlation/covariance @cython.boundscheck(False) @cython.wraparound(False) @cython.cdivision(True) def nancorr(const float64_t[:, :] mat, bint cov=False, minp=None): cdef: Py_ssize_t i, xi, yi, N, K int64_t minpv float64_t[:, ::1] result ndarray[uint8_t, ndim=2] mask int64_t nobs = 0 float64_t vx, vy, dx, dy, meanx, meany, divisor, ssqdmx, ssqdmy, covxy N, K = (mat).shape if minp is None: minpv = 1 else: minpv = minp result = np.empty((K, K), dtype=np.float64) mask = np.isfinite(mat).view(np.uint8) with nogil: for xi in range(K): for yi in range(xi + 1): # Welford's method for the variance-calculation # https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance nobs = ssqdmx = ssqdmy = covxy = meanx = meany = 0 for i in range(N): if mask[i, xi] and mask[i, yi]: vx = mat[i, xi] vy = mat[i, yi] nobs += 1 dx = vx - meanx dy = vy - meany meanx += 1. / nobs * dx meany += 1. / nobs * dy ssqdmx += (vx - meanx) * dx ssqdmy += (vy - meany) * dy covxy += (vx - meanx) * dy if nobs < minpv: result[xi, yi] = result[yi, xi] = NaN else: divisor = (nobs - 1.0) if cov else sqrt(ssqdmx * ssqdmy) if divisor != 0: result[xi, yi] = result[yi, xi] = covxy / divisor else: result[xi, yi] = result[yi, xi] = NaN return result.base # ---------------------------------------------------------------------- # Pairwise Spearman correlation @cython.boundscheck(False) @cython.wraparound(False) def nancorr_spearman(ndarray[float64_t, ndim=2] mat, Py_ssize_t minp=1) -> ndarray: cdef: Py_ssize_t i, xi, yi, N, K ndarray[float64_t, ndim=2] result ndarray[float64_t, ndim=2] ranked_mat ndarray[float64_t, ndim=1] rankedx, rankedy float64_t[::1] maskedx, maskedy ndarray[uint8_t, ndim=2] mask int64_t nobs = 0 bint no_nans float64_t vx, vy, sumx, sumxx, sumyy, mean, divisor N, K = (mat).shape # Handle the edge case where we know all results will be nan # to keep conditional logic inside loop simpler if N < minp: result = np.full((K, K), np.nan, dtype=np.float64) return result result = np.empty((K, K), dtype=np.float64) mask = np.isfinite(mat).view(np.uint8) no_nans = mask.all() ranked_mat = np.empty((N, K), dtype=np.float64) # Note: we index into maskedx, maskedy in loops up to nobs, but using N is safe # here since N >= nobs and values are stored contiguously maskedx = np.empty(N, dtype=np.float64) maskedy = np.empty(N, dtype=np.float64) for i in range(K): ranked_mat[:, i] = rank_1d(mat[:, i]) with nogil: for xi in range(K): for yi in range(xi + 1): sumx = sumxx = sumyy = 0 # Fastpath for data with no nans/infs, allows avoiding mask checks # and array reassignments if no_nans: mean = (N + 1) / 2. # now the cov numerator for i in range(N): vx = ranked_mat[i, xi] - mean vy = ranked_mat[i, yi] - mean sumx += vx * vy sumxx += vx * vx sumyy += vy * vy else: nobs = 0 # Keep track of whether we need to recompute ranks all_ranks = True for i in range(N): all_ranks &= not (mask[i, xi] ^ mask[i, yi]) if mask[i, xi] and mask[i, yi]: maskedx[nobs] = ranked_mat[i, xi] maskedy[nobs] = ranked_mat[i, yi] nobs += 1 if nobs < minp: result[xi, yi] = result[yi, xi] = NaN continue else: if not all_ranks: with gil: # We need to slice back to nobs because rank_1d will # require arrays of nobs length rankedx = rank_1d(np.asarray(maskedx)[:nobs]) rankedy = rank_1d(np.asarray(maskedy)[:nobs]) for i in range(nobs): maskedx[i] = rankedx[i] maskedy[i] = rankedy[i] mean = (nobs + 1) / 2. # now the cov numerator for i in range(nobs): vx = maskedx[i] - mean vy = maskedy[i] - mean sumx += vx * vy sumxx += vx * vx sumyy += vy * vy divisor = sqrt(sumxx * sumyy) if divisor != 0: result[xi, yi] = result[yi, xi] = sumx / divisor else: result[xi, yi] = result[yi, xi] = NaN return result # ---------------------------------------------------------------------- def validate_limit(nobs: int | None, limit=None) -> int: """ Check that the `limit` argument is a positive integer. Parameters ---------- nobs : int limit : object Returns ------- int The limit. """ if limit is None: lim = nobs else: if not util.is_integer_object(limit): raise ValueError("Limit must be an integer") if limit < 1: raise ValueError("Limit must be greater than 0") lim = limit return lim # TODO: overlap with libgroupby.group_fillna_indexer? @cython.boundscheck(False) @cython.wraparound(False) def get_fill_indexer(const uint8_t[:] mask, limit=None): """ Find an indexer to use for ffill to `take` on the array being filled. """ cdef: ndarray[intp_t, ndim=1] indexer Py_ssize_t i, N = len(mask), last_valid int lim # fill_count is the number of consecutive NAs we have seen. # If it exceeds the given limit, we stop padding. int fill_count = 0 lim = validate_limit(N, limit) indexer = np.empty(N, dtype=np.intp) last_valid = -1 # haven't yet seen anything non-NA for i in range(N): if not mask[i]: indexer[i] = i last_valid = i fill_count = 0 else: if fill_count < lim: indexer[i] = last_valid else: indexer[i] = -1 fill_count += 1 return indexer @cython.boundscheck(False) @cython.wraparound(False) def pad( ndarray[numeric_object_t] old, ndarray[numeric_object_t] new, limit=None ) -> ndarray: # -> ndarray[intp_t, ndim=1] cdef: Py_ssize_t i, j, nleft, nright ndarray[intp_t, ndim=1] indexer numeric_object_t cur, next_val int lim, fill_count = 0 nleft = len(old) nright = len(new) indexer = np.empty(nright, dtype=np.intp) indexer[:] = -1 lim = validate_limit(nright, limit) if nleft == 0 or nright == 0 or new[nright - 1] < old[0]: return indexer i = j = 0 cur = old[0] while j <= nright - 1 and new[j] < cur: j += 1 while True: if j == nright: break if i == nleft - 1: while j < nright: if new[j] == cur: indexer[j] = i elif new[j] > cur and fill_count < lim: indexer[j] = i fill_count += 1 j += 1 break next_val = old[i + 1] while j < nright and cur <= new[j] < next_val: if new[j] == cur: indexer[j] = i elif fill_count < lim: indexer[j] = i fill_count += 1 j += 1 fill_count = 0 i += 1 cur = next_val return indexer @cython.boundscheck(False) @cython.wraparound(False) def pad_inplace(numeric_object_t[:] values, uint8_t[:] mask, limit=None): cdef: Py_ssize_t i, N numeric_object_t val uint8_t prev_mask int lim, fill_count = 0 N = len(values) # GH#2778 if N == 0: return lim = validate_limit(N, limit) val = values[0] prev_mask = mask[0] for i in range(N): if mask[i]: if fill_count >= lim: continue fill_count += 1 values[i] = val mask[i] = prev_mask else: fill_count = 0 val = values[i] prev_mask = mask[i] @cython.boundscheck(False) @cython.wraparound(False) def pad_2d_inplace(numeric_object_t[:, :] values, uint8_t[:, :] mask, limit=None): cdef: Py_ssize_t i, j, N, K numeric_object_t val int lim, fill_count = 0 K, N = (values).shape # GH#2778 if N == 0: return lim = validate_limit(N, limit) for j in range(K): fill_count = 0 val = values[j, 0] for i in range(N): if mask[j, i]: if fill_count >= lim or i == 0: continue fill_count += 1 values[j, i] = val mask[j, i] = False else: fill_count = 0 val = values[j, i] @cython.boundscheck(False) @cython.wraparound(False) def backfill( ndarray[numeric_object_t] old, ndarray[numeric_object_t] new, limit=None ) -> ndarray: # -> ndarray[intp_t, ndim=1] """ Backfilling logic for generating fill vector Diagram of what's going on Old New Fill vector Mask . 0 1 . 0 1 . 0 1 A A 0 1 . 1 1 . 1 1 . 1 1 . 1 1 . 1 1 B B 1 1 . 2 1 . 2 1 . 2 1 C C 2 1 . 0 . 0 D """ cdef: Py_ssize_t i, j, nleft, nright ndarray[intp_t, ndim=1] indexer numeric_object_t cur, prev int lim, fill_count = 0 nleft = len(old) nright = len(new) indexer = np.empty(nright, dtype=np.intp) indexer[:] = -1 lim = validate_limit(nright, limit) if nleft == 0 or nright == 0 or new[0] > old[nleft - 1]: return indexer i = nleft - 1 j = nright - 1 cur = old[nleft - 1] while j >= 0 and new[j] > cur: j -= 1 while True: if j < 0: break if i == 0: while j >= 0: if new[j] == cur: indexer[j] = i elif new[j] < cur and fill_count < lim: indexer[j] = i fill_count += 1 j -= 1 break prev = old[i - 1] while j >= 0 and prev < new[j] <= cur: if new[j] == cur: indexer[j] = i elif new[j] < cur and fill_count < lim: indexer[j] = i fill_count += 1 j -= 1 fill_count = 0 i -= 1 cur = prev return indexer def backfill_inplace(numeric_object_t[:] values, uint8_t[:] mask, limit=None): pad_inplace(values[::-1], mask[::-1], limit=limit) def backfill_2d_inplace(numeric_object_t[:, :] values, uint8_t[:, :] mask, limit=None): pad_2d_inplace(values[:, ::-1], mask[:, ::-1], limit) @cython.boundscheck(False) @cython.wraparound(False) def is_monotonic(ndarray[numeric_object_t, ndim=1] arr, bint timelike): """ Returns ------- tuple is_monotonic_inc : bool is_monotonic_dec : bool is_strict_monotonic : bool """ cdef: Py_ssize_t i, n numeric_object_t prev, cur bint is_monotonic_inc = 1 bint is_monotonic_dec = 1 bint is_unique = 1 bint is_strict_monotonic = 1 n = len(arr) if n == 1: if arr[0] != arr[0] or (numeric_object_t is int64_t and timelike and arr[0] == NPY_NAT): # single value is NaN return False, False, True else: return True, True, True elif n < 2: return True, True, True if timelike and arr[0] == NPY_NAT: return False, False, True if numeric_object_t is not object: with nogil: prev = arr[0] for i in range(1, n): cur = arr[i] if timelike and cur == NPY_NAT: is_monotonic_inc = 0 is_monotonic_dec = 0 break if cur < prev: is_monotonic_inc = 0 elif cur > prev: is_monotonic_dec = 0 elif cur == prev: is_unique = 0 else: # cur or prev is NaN is_monotonic_inc = 0 is_monotonic_dec = 0 break if not is_monotonic_inc and not is_monotonic_dec: is_monotonic_inc = 0 is_monotonic_dec = 0 break prev = cur else: # object-dtype, identical to above except we cannot use `with nogil` prev = arr[0] for i in range(1, n): cur = arr[i] if timelike and cur == NPY_NAT: is_monotonic_inc = 0 is_monotonic_dec = 0 break if cur < prev: is_monotonic_inc = 0 elif cur > prev: is_monotonic_dec = 0 elif cur == prev: is_unique = 0 else: # cur or prev is NaN is_monotonic_inc = 0 is_monotonic_dec = 0 break if not is_monotonic_inc and not is_monotonic_dec: is_monotonic_inc = 0 is_monotonic_dec = 0 break prev = cur is_strict_monotonic = is_unique and (is_monotonic_inc or is_monotonic_dec) return is_monotonic_inc, is_monotonic_dec, is_strict_monotonic # ---------------------------------------------------------------------- # rank_1d, rank_2d # ---------------------------------------------------------------------- cdef numeric_object_t get_rank_nan_fill_val( bint rank_nans_highest, numeric_object_t val, bint is_datetimelike=False, ): """ Return the value we'll use to represent missing values when sorting depending on if we'd like missing values to end up at the top/bottom. (The second parameter is unused, but needed for fused type specialization) """ if numeric_object_t is int64_t and is_datetimelike and not rank_nans_highest: return NPY_NAT + 1 if rank_nans_highest: if numeric_object_t is object: return Infinity() elif numeric_object_t is int64_t: return util.INT64_MAX elif numeric_object_t is int32_t: return util.INT32_MAX elif numeric_object_t is int16_t: return util.INT16_MAX elif numeric_object_t is int8_t: return util.INT8_MAX elif numeric_object_t is uint64_t: return util.UINT64_MAX elif numeric_object_t is uint32_t: return util.UINT32_MAX elif numeric_object_t is uint16_t: return util.UINT16_MAX elif numeric_object_t is uint8_t: return util.UINT8_MAX else: return np.inf else: if numeric_object_t is object: return NegInfinity() elif numeric_object_t is int64_t: # Note(jbrockmendel) 2022-03-15 for reasons unknown, using util.INT64_MIN # instead of NPY_NAT here causes build warnings and failure in # test_cummax_i8_at_implementation_bound return NPY_NAT elif numeric_object_t is int32_t: return util.INT32_MIN elif numeric_object_t is int16_t: return util.INT16_MIN elif numeric_object_t is int8_t: return util.INT8_MIN elif numeric_object_t is uint64_t: return 0 elif numeric_object_t is uint32_t: return 0 elif numeric_object_t is uint16_t: return 0 elif numeric_object_t is uint8_t: return 0 else: return -np.inf @cython.wraparound(False) @cython.boundscheck(False) def rank_1d( ndarray[numeric_object_t, ndim=1] values, const intp_t[:] labels=None, bint is_datetimelike=False, ties_method="average", bint ascending=True, bint pct=False, na_option="keep", const uint8_t[:] mask=None, ): """ Fast NaN-friendly version of ``scipy.stats.rankdata``. Parameters ---------- values : array of numeric_object_t values to be ranked labels : np.ndarray[np.intp] or None Array containing unique label for each group, with its ordering matching up to the corresponding record in `values`. If not called from a groupby operation, will be None. is_datetimelike : bool, default False True if `values` contains datetime-like entries. ties_method : {'average', 'min', 'max', 'first', 'dense'}, default 'average' * average: average rank of group * min: lowest rank in group * max: highest rank in group * first: ranks assigned in order they appear in the array * dense: like 'min', but rank always increases by 1 between groups ascending : bool, default True False for ranks by high (1) to low (N) na_option : {'keep', 'top', 'bottom'}, default 'keep' pct : bool, default False Compute percentage rank of data within each group na_option : {'keep', 'top', 'bottom'}, default 'keep' * keep: leave NA values where they are * top: smallest rank if ascending * bottom: smallest rank if descending mask : np.ndarray[bool], optional, default None Specify locations to be treated as NA, for e.g. Categorical. """ cdef: TiebreakEnumType tiebreak Py_ssize_t N int64_t[::1] grp_sizes intp_t[:] lexsort_indexer float64_t[::1] out ndarray[numeric_object_t, ndim=1] masked_vals numeric_object_t[:] masked_vals_memview bint keep_na, nans_rank_highest, check_labels, check_mask numeric_object_t nan_fill_val tiebreak = tiebreakers[ties_method] if tiebreak == TIEBREAK_FIRST: if not ascending: tiebreak = TIEBREAK_FIRST_DESCENDING keep_na = na_option == "keep" N = len(values) if labels is not None: # TODO(cython3): cast won't be necessary (#2992) assert len(labels) == N out = np.empty(N) grp_sizes = np.ones(N, dtype=np.int64) # If we don't care about labels, can short-circuit later label # comparisons check_labels = labels is not None # For cases where a mask is not possible, we can avoid mask checks check_mask = ( numeric_object_t is float32_t or numeric_object_t is float64_t or numeric_object_t is object or (numeric_object_t is int64_t and is_datetimelike) ) check_mask = check_mask or mask is not None # Copy values into new array in order to fill missing data # with mask, without obfuscating location of missing data # in values array if numeric_object_t is object and values.dtype != np.object_: masked_vals = values.astype("O") else: masked_vals = values.copy() if mask is not None: pass elif numeric_object_t is object: mask = isnaobj(masked_vals) elif numeric_object_t is int64_t and is_datetimelike: mask = (masked_vals == NPY_NAT).astype(np.uint8) elif numeric_object_t is float64_t or numeric_object_t is float32_t: mask = np.isnan(masked_vals).astype(np.uint8) else: mask = np.zeros(shape=len(masked_vals), dtype=np.uint8) # If `na_option == 'top'`, we want to assign the lowest rank # to NaN regardless of ascending/descending. So if ascending, # fill with lowest value of type to end up with lowest rank. # If descending, fill with highest value since descending # will flip the ordering to still end up with lowest rank. # Symmetric logic applies to `na_option == 'bottom'` nans_rank_highest = ascending ^ (na_option == "top") nan_fill_val = get_rank_nan_fill_val(nans_rank_highest, 0) if nans_rank_highest: order = [masked_vals, mask] else: order = [masked_vals, ~(np.asarray(mask))] if check_labels: order.append(labels) np.putmask(masked_vals, mask, nan_fill_val) # putmask doesn't accept a memoryview, so we assign as a separate step masked_vals_memview = masked_vals # lexsort using labels, then mask, then actual values # each label corresponds to a different group value, # the mask helps you differentiate missing values before # performing sort on the actual values lexsort_indexer = np.lexsort(order).astype(np.intp, copy=False) if not ascending: lexsort_indexer = lexsort_indexer[::-1] with nogil: rank_sorted_1d( out, grp_sizes, lexsort_indexer, masked_vals_memview, mask, check_mask=check_mask, N=N, tiebreak=tiebreak, keep_na=keep_na, pct=pct, labels=labels, ) return np.asarray(out) @cython.wraparound(False) @cython.boundscheck(False) cdef void rank_sorted_1d( float64_t[::1] out, int64_t[::1] grp_sizes, const intp_t[:] sort_indexer, # TODO(cython3): make const (https://github.com/cython/cython/issues/3222) numeric_object_t[:] masked_vals, const uint8_t[:] mask, bint check_mask, Py_ssize_t N, TiebreakEnumType tiebreak=TIEBREAK_AVERAGE, bint keep_na=True, bint pct=False, # https://github.com/cython/cython/issues/1630, only trailing arguments can # currently be omitted for cdef functions, which is why we keep this at the end const intp_t[:] labels=None, ) noexcept nogil: """ See rank_1d.__doc__. Handles only actual ranking, so sorting and masking should be handled in the caller. Note that `out` and `grp_sizes` are modified inplace. Parameters ---------- out : float64_t[::1] Array to store computed ranks grp_sizes : int64_t[::1] Array to store group counts, only used if pct=True. Should only be None if labels is None. sort_indexer : intp_t[:] Array of indices which sorts masked_vals masked_vals : numeric_object_t[:] The values input to rank_1d, with missing values replaced by fill values mask : uint8_t[:] Array where entries are True if the value is missing, False otherwise. check_mask : bool If False, assumes the mask is all False to skip mask indexing N : Py_ssize_t The number of elements to rank. Note: it is not always true that N == len(out) or N == len(masked_vals) (see `nancorr_spearman` usage for why) tiebreak : TiebreakEnumType, default TIEBREAK_AVERAGE See rank_1d.__doc__ for the different modes keep_na : bool, default True Whether or not to keep nulls pct : bool, default False Compute percentage rank of data within each group labels : See rank_1d.__doc__, default None. None implies all labels are the same. """ cdef: Py_ssize_t i, j, dups=0, sum_ranks=0, Py_ssize_t grp_start=0, grp_vals_seen=1, grp_na_count=0 bint at_end, next_val_diff, group_changed, check_labels int64_t grp_size check_labels = labels is not None # Loop over the length of the value array # each incremental i value can be looked up in the lexsort_indexer # array that we sorted previously, which gives us the location of # that sorted value for retrieval back from the original # values / masked_vals arrays # TODO(cython3): de-duplicate once cython supports conditional nogil if numeric_object_t is object: with gil: for i in range(N): at_end = i == N - 1 # dups and sum_ranks will be incremented each loop where # the value / group remains the same, and should be reset # when either of those change. Used to calculate tiebreakers dups += 1 sum_ranks += i - grp_start + 1 next_val_diff = at_end or are_diff(masked_vals[sort_indexer[i]], masked_vals[sort_indexer[i+1]]) # We'll need this check later anyway to determine group size, so just # compute it here since shortcircuiting won't help group_changed = at_end or (check_labels and (labels[sort_indexer[i]] != labels[sort_indexer[i+1]])) # Update out only when there is a transition of values or labels. # When a new value or group is encountered, go back #dups steps( # the number of occurrence of current value) and assign the ranks # based on the starting index of the current group (grp_start) # and the current index if (next_val_diff or group_changed or (check_mask and (mask[sort_indexer[i]] ^ mask[sort_indexer[i+1]]))): # If keep_na, check for missing values and assign back # to the result where appropriate if keep_na and check_mask and mask[sort_indexer[i]]: grp_na_count = dups for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = NaN elif tiebreak == TIEBREAK_AVERAGE: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = sum_ranks / dups elif tiebreak == TIEBREAK_MIN: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = i - grp_start - dups + 2 elif tiebreak == TIEBREAK_MAX: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = i - grp_start + 1 # With n as the previous rank in the group and m as the number # of duplicates in this stretch, if TIEBREAK_FIRST and ascending, # then rankings should be n + 1, n + 2 ... n + m elif tiebreak == TIEBREAK_FIRST: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = j + 1 - grp_start # If TIEBREAK_FIRST and descending, the ranking should be # n + m, n + (m - 1) ... n + 1. This is equivalent to # (i - dups + 1) + (i - j + 1) - grp_start elif tiebreak == TIEBREAK_FIRST_DESCENDING: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = 2 * i - j - dups + 2 - grp_start elif tiebreak == TIEBREAK_DENSE: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = grp_vals_seen # Look forward to the next value (using the sorting in # lexsort_indexer). If the value does not equal the current # value then we need to reset the dups and sum_ranks, knowing # that a new value is coming up. The conditional also needs # to handle nan equality and the end of iteration. If group # changes we do not record seeing a new value in the group if not group_changed and (next_val_diff or (check_mask and (mask[sort_indexer[i]] ^ mask[sort_indexer[i+1]]))): dups = sum_ranks = 0 grp_vals_seen += 1 # Similar to the previous conditional, check now if we are # moving to a new group. If so, keep track of the index where # the new group occurs, so the tiebreaker calculations can # decrement that from their position. Fill in the size of each # group encountered (used by pct calculations later). Also be # sure to reset any of the items helping to calculate dups if group_changed: # If not dense tiebreak, group size used to compute # percentile will be # of non-null elements in group if tiebreak != TIEBREAK_DENSE: grp_size = i - grp_start + 1 - grp_na_count # Otherwise, it will be the number of distinct values # in the group, subtracting 1 if NaNs are present # since that is a distinct value we shouldn't count else: grp_size = grp_vals_seen - (grp_na_count > 0) for j in range(grp_start, i + 1): grp_sizes[sort_indexer[j]] = grp_size dups = sum_ranks = 0 grp_na_count = 0 grp_start = i + 1 grp_vals_seen = 1 else: for i in range(N): at_end = i == N - 1 # dups and sum_ranks will be incremented each loop where # the value / group remains the same, and should be reset # when either of those change. Used to calculate tiebreakers dups += 1 sum_ranks += i - grp_start + 1 next_val_diff = at_end or (masked_vals[sort_indexer[i]] != masked_vals[sort_indexer[i+1]]) # We'll need this check later anyway to determine group size, so just # compute it here since shortcircuiting won't help group_changed = at_end or (check_labels and (labels[sort_indexer[i]] != labels[sort_indexer[i+1]])) # Update out only when there is a transition of values or labels. # When a new value or group is encountered, go back #dups steps( # the number of occurrence of current value) and assign the ranks # based on the starting index of the current group (grp_start) # and the current index if (next_val_diff or group_changed or (check_mask and (mask[sort_indexer[i]] ^ mask[sort_indexer[i+1]]))): # If keep_na, check for missing values and assign back # to the result where appropriate if keep_na and check_mask and mask[sort_indexer[i]]: grp_na_count = dups for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = NaN elif tiebreak == TIEBREAK_AVERAGE: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = sum_ranks / dups elif tiebreak == TIEBREAK_MIN: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = i - grp_start - dups + 2 elif tiebreak == TIEBREAK_MAX: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = i - grp_start + 1 # With n as the previous rank in the group and m as the number # of duplicates in this stretch, if TIEBREAK_FIRST and ascending, # then rankings should be n + 1, n + 2 ... n + m elif tiebreak == TIEBREAK_FIRST: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = j + 1 - grp_start # If TIEBREAK_FIRST and descending, the ranking should be # n + m, n + (m - 1) ... n + 1. This is equivalent to # (i - dups + 1) + (i - j + 1) - grp_start elif tiebreak == TIEBREAK_FIRST_DESCENDING: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = 2 * i - j - dups + 2 - grp_start elif tiebreak == TIEBREAK_DENSE: for j in range(i - dups + 1, i + 1): out[sort_indexer[j]] = grp_vals_seen # Look forward to the next value (using the sorting in # lexsort_indexer). If the value does not equal the current # value then we need to reset the dups and sum_ranks, knowing # that a new value is coming up. The conditional also needs # to handle nan equality and the end of iteration. If group # changes we do not record seeing a new value in the group if not group_changed and (next_val_diff or (check_mask and (mask[sort_indexer[i]] ^ mask[sort_indexer[i+1]]))): dups = sum_ranks = 0 grp_vals_seen += 1 # Similar to the previous conditional, check now if we are # moving to a new group. If so, keep track of the index where # the new group occurs, so the tiebreaker calculations can # decrement that from their position. Fill in the size of each # group encountered (used by pct calculations later). Also be # sure to reset any of the items helping to calculate dups if group_changed: # If not dense tiebreak, group size used to compute # percentile will be # of non-null elements in group if tiebreak != TIEBREAK_DENSE: grp_size = i - grp_start + 1 - grp_na_count # Otherwise, it will be the number of distinct values # in the group, subtracting 1 if NaNs are present # since that is a distinct value we shouldn't count else: grp_size = grp_vals_seen - (grp_na_count > 0) for j in range(grp_start, i + 1): grp_sizes[sort_indexer[j]] = grp_size dups = sum_ranks = 0 grp_na_count = 0 grp_start = i + 1 grp_vals_seen = 1 if pct: for i in range(N): if grp_sizes[i] != 0: out[i] = out[i] / grp_sizes[i] def rank_2d( ndarray[numeric_object_t, ndim=2] in_arr, int axis=0, bint is_datetimelike=False, ties_method="average", bint ascending=True, na_option="keep", bint pct=False, ): """ Fast NaN-friendly version of ``scipy.stats.rankdata``. """ cdef: Py_ssize_t k, n, col float64_t[::1, :] out # Column-major so columns are contiguous int64_t[::1] grp_sizes ndarray[numeric_object_t, ndim=2] values numeric_object_t[:, :] masked_vals intp_t[:, :] sort_indexer uint8_t[:, :] mask TiebreakEnumType tiebreak bint check_mask, keep_na, nans_rank_highest numeric_object_t nan_fill_val tiebreak = tiebreakers[ties_method] if tiebreak == TIEBREAK_FIRST: if not ascending: tiebreak = TIEBREAK_FIRST_DESCENDING keep_na = na_option == "keep" # For cases where a mask is not possible, we can avoid mask checks check_mask = ( numeric_object_t is float32_t or numeric_object_t is float64_t or numeric_object_t is object or (numeric_object_t is int64_t and is_datetimelike) ) if axis == 1: values = np.asarray(in_arr).T.copy() else: values = np.asarray(in_arr).copy() if numeric_object_t is object: if values.dtype != np.object_: values = values.astype("O") nans_rank_highest = ascending ^ (na_option == "top") if check_mask: nan_fill_val = get_rank_nan_fill_val(nans_rank_highest, 0) if numeric_object_t is object: mask = isnaobj(values).view(np.uint8) elif numeric_object_t is float64_t or numeric_object_t is float32_t: mask = np.isnan(values).view(np.uint8) else: # i.e. int64 and datetimelike mask = (values == NPY_NAT).view(np.uint8) np.putmask(values, mask, nan_fill_val) else: mask = np.zeros_like(values, dtype=np.uint8) if nans_rank_highest: order = (values, mask) else: order = (values, ~np.asarray(mask)) n, k = (values).shape out = np.empty((n, k), dtype="f8", order="F") grp_sizes = np.ones(n, dtype=np.int64) # lexsort is slower, so only use if we need to worry about the mask if check_mask: sort_indexer = np.lexsort(order, axis=0).astype(np.intp, copy=False) else: kind = "stable" if ties_method == "first" else None sort_indexer = values.argsort(axis=0, kind=kind).astype(np.intp, copy=False) if not ascending: sort_indexer = sort_indexer[::-1, :] # putmask doesn't accept a memoryview, so we assign in a separate step masked_vals = values with nogil: for col in range(k): rank_sorted_1d( out[:, col], grp_sizes, sort_indexer[:, col], masked_vals[:, col], mask[:, col], check_mask=check_mask, N=n, tiebreak=tiebreak, keep_na=keep_na, pct=pct, ) if axis == 1: return np.asarray(out.T) else: return np.asarray(out) ctypedef fused diff_t: float64_t float32_t int8_t int16_t int32_t int64_t ctypedef fused out_t: float32_t float64_t int64_t @cython.boundscheck(False) @cython.wraparound(False) def diff_2d( ndarray[diff_t, ndim=2] arr, # TODO(cython3) update to "const diff_t[:, :] arr" ndarray[out_t, ndim=2] out, Py_ssize_t periods, int axis, bint datetimelike=False, ): cdef: Py_ssize_t i, j, sx, sy, start, stop bint f_contig = arr.flags.f_contiguous # bint f_contig = arr.is_f_contig() # TODO(cython3) diff_t left, right # Disable for unsupported dtype combinations, # see https://github.com/cython/cython/issues/2646 if (out_t is float32_t and not (diff_t is float32_t or diff_t is int8_t or diff_t is int16_t)): raise NotImplementedError # pragma: no cover elif (out_t is float64_t and (diff_t is float32_t or diff_t is int8_t or diff_t is int16_t)): raise NotImplementedError # pragma: no cover elif out_t is int64_t and diff_t is not int64_t: # We only have out_t of int64_t if we have datetimelike raise NotImplementedError # pragma: no cover else: # We put this inside an indented else block to avoid cython build # warnings about unreachable code sx, sy = (arr).shape with nogil: if f_contig: if axis == 0: if periods >= 0: start, stop = periods, sx else: start, stop = 0, sx + periods for j in range(sy): for i in range(start, stop): left = arr[i, j] right = arr[i - periods, j] if out_t is int64_t and datetimelike: if left == NPY_NAT or right == NPY_NAT: out[i, j] = NPY_NAT else: out[i, j] = left - right else: out[i, j] = left - right else: if periods >= 0: start, stop = periods, sy else: start, stop = 0, sy + periods for j in range(start, stop): for i in range(sx): left = arr[i, j] right = arr[i, j - periods] if out_t is int64_t and datetimelike: if left == NPY_NAT or right == NPY_NAT: out[i, j] = NPY_NAT else: out[i, j] = left - right else: out[i, j] = left - right else: if axis == 0: if periods >= 0: start, stop = periods, sx else: start, stop = 0, sx + periods for i in range(start, stop): for j in range(sy): left = arr[i, j] right = arr[i - periods, j] if out_t is int64_t and datetimelike: if left == NPY_NAT or right == NPY_NAT: out[i, j] = NPY_NAT else: out[i, j] = left - right else: out[i, j] = left - right else: if periods >= 0: start, stop = periods, sy else: start, stop = 0, sy + periods for i in range(sx): for j in range(start, stop): left = arr[i, j] right = arr[i, j - periods] if out_t is int64_t and datetimelike: if left == NPY_NAT or right == NPY_NAT: out[i, j] = NPY_NAT else: out[i, j] = left - right else: out[i, j] = left - right # generated from template include "algos_common_helper.pxi" include "algos_take_helper.pxi"