Source code for stumpy.mstumped

# STUMPY
# Copyright 2019 TD Ameritrade. Released under the terms of the 3-Clause BSD license.
# STUMPY is a trademark of TD Ameritrade IP Company, Inc. All rights reserved.

import logging

import numpy as np

from .mstump import (
    _mstump,
    _get_first_mstump_profile,
    _get_multi_QT,
    _preprocess_include,
)
from . import core
from .maamped import maamped
from .config import STUMPY_EXCL_ZONE_DENOM

logger = logging.getLogger(__name__)


[docs]@core.non_normalized(maamped) def mstumped(dask_client, T, m, include=None, discords=False, normalize=True): """ Compute the multi-dimensional z-normalized matrix profile with a distributed dask cluster This is a highly distributed implementation around the Numba JIT-compiled parallelized `_mstump` function which computes the multi-dimensional matrix profile according to STOMP. Note that only self-joins are supported. Parameters ---------- dask_client : client A Dask Distributed client that is connected to a Dask scheduler and Dask workers. Setting up a Dask distributed cluster is beyond the scope of this library. Please refer to the Dask Distributed documentation. T : ndarray The time series or sequence for which to compute the multi-dimensional matrix profile. Each row in `T` represents data from a different dimension while each column in `T` represents data from the same dimension. m : int Window size include : list, ndarray, default None A list of (zero-based) indices corresponding to the dimensions in `T` that must be included in the constrained multidimensional motif search. For more information, see Section IV D in: `DOI: 10.1109/ICDM.2017.66 \ <https://www.cs.ucr.edu/~eamonn/Motif_Discovery_ICDM.pdf>`__ discords : bool, default False When set to `True`, this reverses the distance matrix which results in a multi-dimensional matrix profile that favors larger matrix profile values (i.e., discords) rather than smaller values (i.e., motifs). Note that indices in `include` are still maintained and respected. normalize : bool, default True When set to `True`, this z-normalizes subsequences prior to computing distances. Otherwise, this function gets re-routed to its complementary non-normalized equivalent set in the `@core.non_normalized` function decorator. Returns ------- P : ndarray The multi-dimensional matrix profile. Each row of the array corresponds to each matrix profile for a given dimension (i.e., the first row is the 1-D matrix profile and the second row is the 2-D matrix profile). I : ndarray The multi-dimensional matrix profile index where each row of the array corresponds to each matrix profile index for a given dimension. Notes ----- `DOI: 10.1109/ICDM.2017.66 \ <https://www.cs.ucr.edu/~eamonn/Motif_Discovery_ICDM.pdf>`__ See mSTAMP Algorithm """ T_A = T T_B = T_A T_A, M_T, Σ_T = core.preprocess(T_A, m) T_B, μ_Q, σ_Q = core.preprocess(T_B, m) if T_A.ndim <= 1: # pragma: no cover err = f"T is {T_A.ndim}-dimensional and must be at least 1-dimensional" raise ValueError(f"{err}") core.check_window_size(m, max_size=min(T_A.shape[1], T_B.shape[1])) if include is not None: include = _preprocess_include(include) d, n = T_B.shape k = n - m + 1 excl_zone = int( np.ceil(m / STUMPY_EXCL_ZONE_DENOM) ) # See Definition 3 and Figure 3 P = np.empty((d, k), dtype="float64") I = np.empty((d, k), dtype="int64") hosts = list(dask_client.ncores().keys()) nworkers = len(hosts) step = 1 + k // nworkers for i, start in enumerate(range(0, k, step)): P[:, start], I[:, start] = _get_first_mstump_profile( start, T_A, T_B, m, excl_zone, M_T, Σ_T, μ_Q, σ_Q, include, discords ) # Scatter data to Dask cluster T_A_future = dask_client.scatter(T_A, broadcast=True, hash=False) M_T_future = dask_client.scatter(M_T, broadcast=True, hash=False) Σ_T_future = dask_client.scatter(Σ_T, broadcast=True, hash=False) μ_Q_future = dask_client.scatter(μ_Q, broadcast=True, hash=False) σ_Q_future = dask_client.scatter(σ_Q, broadcast=True, hash=False) QT_futures = [] QT_first_futures = [] for i, start in enumerate(range(0, k, step)): QT, QT_first = _get_multi_QT(start, T_A, m) QT_future = dask_client.scatter(QT, workers=[hosts[i]], hash=False) QT_first_future = dask_client.scatter(QT_first, workers=[hosts[i]], hash=False) QT_futures.append(QT_future) QT_first_futures.append(QT_first_future) futures = [] for i, start in enumerate(range(0, k, step)): stop = min(k, start + step) futures.append( dask_client.submit( _mstump, T_A_future, m, stop, excl_zone, M_T_future, Σ_T_future, QT_futures[i], QT_first_futures[i], μ_Q_future, σ_Q_future, k, start + 1, include, discords, ) ) results = dask_client.gather(futures) for i, start in enumerate(range(0, k, step)): stop = min(k, start + step) P[:, start + 1 : stop], I[:, start + 1 : stop] = results[i] # Delete data from Dask cluster dask_client.cancel(T_A_future) dask_client.cancel(M_T_future) dask_client.cancel(Σ_T_future) dask_client.cancel(μ_Q_future) dask_client.cancel(σ_Q_future) for QT_future in QT_futures: dask_client.cancel(QT_future) for QT_first_future in QT_first_futures: dask_client.cancel(QT_first_future) for future in futures: dask_client.cancel(future) return P, I