# 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 numpy as np
from . import core, stump, config
from .aampi import aampi
[docs]@core.non_normalized(aampi)
class stumpi:
"""
Compute an incremental z-normalized matrix profile for streaming data
This is based on the on-line STOMPI and STAMPI algorithms.
Parameters
----------
T : ndarray
The time series or sequence for which the matrix profile and matrix profile
indices will be returned
m : int
Window size
egress : bool, default True
If set to `True`, the oldest data point in the time series is removed and
the time series length remains constant rather than forever increasing
normalize : bool, default True
When set to `True`, this z-normalizes subsequences prior to computing distances.
Otherwise, this class gets re-routed to its complementary non-normalized
equivalent set in the `@core.non_normalized` class decorator.
Attributes
----------
P_ : ndarray
The updated matrix profile for `T`
I_ : ndarray
The updated matrix profile indices for `T`
left_P_ : ndarray
The updated left matrix profile for `T`
left_I_ : ndarray
The updated left matrix profile indices for `T`
T_ : ndarray
The updated time series or sequence for which the matrix profile and matrix
profile indices are computed
Methods
-------
update(t)
Append a single new data point, `t`, to the time series, `T`, and update the
matrix profile
Notes
-----
`DOI: 10.1007/s10618-017-0519-9 \
<https://www.cs.ucr.edu/~eamonn/MP_journal.pdf>`__
See Table V
Note that line 11 is missing an important `sqrt` operation!
"""
def __init__(self, T, m, egress=True, normalize=True):
"""
Initialize the `stumpi` object
Parameters
----------
T : ndarray
The time series or sequence for which the matrix profile and matrix profile
indices will be returned
m : int
Window size
egress : bool, default True
If set to `True`, the oldest data point in the time series is removed and
the time series length remains constant rather than forever increasing
normalize : bool, default True
When set to `True`, this z-normalizes subsequences prior to computing
distances. Otherwise, this class gets re-routed to its complementary
non-normalized equivalent set in the `@core.non_normalized` class decorator.
"""
self._T = T.copy()
self._T = np.asarray(self._T)
core.check_dtype(self._T)
self._m = m
self._n = self._T.shape[0]
self._excl_zone = int(np.ceil(self._m / config.STUMPY_EXCL_ZONE_DENOM))
self._T_isfinite = np.isfinite(self._T)
self._egress = egress
mp = stump(self._T, self._m)
self._P = mp[:, 0].astype(np.float64)
self._I = mp[:, 1].astype(np.int64)
self._left_I = mp[:, 2].astype(np.int64)
self._left_P = np.empty(self._P.shape)
self._left_P[:] = np.inf
self._T, self._M_T, self._Σ_T = core.preprocess(self._T, self._m)
# Retrieve the left matrix profile values
for i, j in enumerate(self._left_I):
if j >= 0:
D = core.mass(self._T[i : i + self._m], self._T[j : j + self._m])
self._left_P[i] = D[0]
Q = self._T[-m:]
self._QT = core.sliding_dot_product(Q, self._T)
if self._egress:
self._QT_new = np.empty(self._QT.shape[0])
self._n_appended = 0
def update(self, t):
"""
Append a single new data point, `t`, to the existing time series `T` and update
the matrix profile and matrix profile indices.
Parameters
----------
t : float
A single new data point to be appended to `T`
Notes
-----
`DOI: 10.1007/s10618-017-0519-9 \
<https://www.cs.ucr.edu/~eamonn/MP_journal.pdf>`__
See Table V
Note that line 11 is missing an important `sqrt` operation!
"""
if self._egress:
self._update_egress(t)
else:
self._update(t)
def _update_egress(self, t):
"""
Ingress a new data point, egress the oldest data point, and update the matrix
profile and matrix profile indices
"""
self._n = self._T.shape[0]
l = self._n - self._m + 1 - 1 # Subtract 1 due to egress
self._T[:-1] = self._T[1:]
self._T[-1] = t
self._n_appended += 1
self._QT[:-1] = self._QT[1:]
S = self._T[l:]
t_drop = self._T[l - 1]
self._T_isfinite[:-1] = self._T_isfinite[1:]
self._I[:-1] = self._I[1:]
self._P[:-1] = self._P[1:]
self._left_I[:-1] = self._left_I[1:]
self._left_P[:-1] = self._left_P[1:]
if np.isfinite(t):
self._T_isfinite[-1] = True
else:
self._T_isfinite[-1] = False
t = 0
self._T[-1] = 0
S[-1] = 0
if np.any(~self._T_isfinite[-self._m :]):
μ_Q = np.inf
σ_Q = np.nan
else:
μ_Q, σ_Q = core.compute_mean_std(S, self._m)
μ_Q = μ_Q[0]
σ_Q = σ_Q[0]
self._M_T[:-1] = self._M_T[1:]
self._Σ_T[:-1] = self._Σ_T[1:]
self._M_T[-1] = μ_Q
self._Σ_T[-1] = σ_Q
self._QT_new[1:] = self._QT[:l] - self._T[:l] * t_drop + self._T[self._m :] * t
self._QT_new[0] = np.sum(self._T[: self._m] * S[: self._m])
D = core.calculate_distance_profile(
self._m, self._QT_new, μ_Q, σ_Q, self._M_T, self._Σ_T
)
if np.any(~self._T_isfinite[-self._m :]):
D[:] = np.inf
core.apply_exclusion_zone(D, D.shape[0] - 1, self._excl_zone)
update_idx = np.argwhere(D < self._P).flatten()
self._I[update_idx] = D.shape[0] + self._n_appended - 1 # D.shape[0] is base-1
self._P[update_idx] = D[update_idx]
I_last = np.argmin(D)
if np.isinf(D[I_last]):
self._I[-1] = -1
self._P[-1] = np.inf
else:
self._I[-1] = I_last + self._n_appended
self._P[-1] = D[I_last]
self._left_I[-1] = I_last + self._n_appended
self._left_P[-1] = D[I_last]
self._QT[:] = self._QT_new
def _update(self, t):
"""
Ingress a new data point and update the matrix profile and matrix profile
indices without egressing the oldest data point
"""
n = self._T.shape[0]
l = n - self._m + 1
T_new = np.append(self._T, t)
QT_new = np.empty(self._QT.shape[0] + 1)
S = T_new[l:]
t_drop = T_new[l - 1]
if np.isfinite(t):
self._T_isfinite = np.append(self._T_isfinite, True)
else:
self._T_isfinite = np.append(self._T_isfinite, False)
t = 0
T_new[-1] = 0
S[-1] = 0
if np.any(~self._T_isfinite[-self._m :]):
μ_Q = np.inf
σ_Q = np.nan
else:
μ_Q, σ_Q = core.compute_mean_std(S, self._m)
μ_Q = μ_Q[0]
σ_Q = σ_Q[0]
M_T_new = np.append(self._M_T, μ_Q)
Σ_T_new = np.append(self._Σ_T, σ_Q)
QT_new[1:] = self._QT[:l] - T_new[:l] * t_drop + T_new[self._m :] * t
QT_new[0] = np.sum(T_new[: self._m] * S[: self._m])
D = core.calculate_distance_profile(self._m, QT_new, μ_Q, σ_Q, M_T_new, Σ_T_new)
if np.any(~self._T_isfinite[-self._m :]):
D[:] = np.inf
core.apply_exclusion_zone(D, D.shape[0] - 1, self._excl_zone)
update_idx = np.argwhere(D[:l] < self._P[:l]).flatten()
self._I[update_idx] = l
self._P[update_idx] = D[update_idx]
I_last = np.argmin(D)
if np.isinf(D[I_last]):
I_new = np.append(self._I, -1)
P_new = np.append(self._P, np.inf)
else:
I_new = np.append(self._I, I_last)
P_new = np.append(self._P, D[I_last])
left_I_new = np.append(self._left_I, I_last)
left_P_new = np.append(self._left_P, D[I_last])
self._T = T_new
self._P = P_new
self._I = I_new
self._left_I = left_I_new
self._left_P = left_P_new
self._QT = QT_new
self._M_T = M_T_new
self._Σ_T = Σ_T_new
@property
def P_(self):
"""
Get the matrix profile
"""
return self._P.astype(np.float64)
@property
def I_(self):
"""
Get the matrix profile indices
"""
return self._I.astype(np.int64)
@property
def left_P_(self):
"""
Get the left matrix profile
"""
return self._left_P.astype(np.float64)
@property
def left_I_(self):
"""
Get the left matrix profile indices
"""
return self._left_I.astype(np.int64)
@property
def T_(self):
"""
Get the time series
"""
return self._T