[WIP] Fixed #639 Top-K Nearest Neighbors to Matrix Profile (normalize…

…=False) (#714)

* Add support for top-k to naive aamp

* Add test function for TopK. Expect Error.

* Add TopK support to aamp. Error Resolved

* Add TopK test function for AB_join

* (Temporarily) fix scraamp to adapt the changes in _aamp

* fix calling function _aamp

* (Temporarily) fixed aamped

* Avoid unnecessary passing k and minor changes

* fix docstring in aamped

* Add support for top-k to naive prescraamp

* Add test function for prescraamp top-k. Expect Error

* Add top-k support for prescraamp

* Add top-k test function for AB_join prescraamp

* Add top-k support to scraamp and update test function

* Add new test functions and minor fixes

* update test function to adapt to new changes

* update test function to adapt to new changes

* Add Top-K support to gpu_aamp

* fix import

* fix minor bug

* minor fixes

* Add test function for top-k

* Empty Commit

* Add top-k support to naive

* fix issues to pass existing unit tests aampi

* Add top-k test. Expect Error

* Add top-k support to performant aampi

* Add top-k test function to aampi with egress

* minor changes

* Revised signature

* replace param with class attribute

* fixed style

* fixed typo

* Move device function to core to fix circular import error

* Update test functions

* fix bug

* replace wrong variable with the correct one

* fix docstring

* fix docstrings

* Empty commit

stumpy/aamp.py

@@ -15,7 +15,7 @@
 
 @njit(
     # "(f8[:], f8[:], i8, b1[:], b1[:], f8, i8[:], i8, i8, i8, f8[:, :, :],"
-    # "i8[:, :, :], b1)",
+    # "f8[:, :], f8[:, :], i8[:, :, :], i8[:, :], i8[:, :], b1)",
     fastmath=True,
 )
 def _compute_diagonal(
@@ -30,12 +30,17 @@ def _compute_diagonal(
     diags_stop_idx,
     thread_idx,
     P,
+    PL,
+    PR,
     I,
+    IL,
+    IR,
     ignore_trivial,
 ):
     """
-    Compute (Numba JIT-compiled) and update P, I along a single diagonal using a single
-    thread and avoiding race conditions
+    Compute (Numba JIT-compiled) and update the (top-k) matrix profile P,
+    PL, PR, I, IL, and IR sequentially along individual diagonals using a single
+    thread and avoiding race conditions.
 
     Parameters
     ----------
@@ -49,12 +54,6 @@ def _compute_diagonal(
     m : int
         Window size
 
-    P : numpy.ndarray
-        Matrix profile
-
-    I : numpy.ndarray
-        Matrix profile indices
-
     T_A_subseq_isfinite : numpy.ndarray
         A boolean array that indicates whether a subsequence in `T_A` contains a
         `np.nan`/`np.inf` value (False)
@@ -78,6 +77,24 @@ def _compute_diagonal(
     thread_idx : int
         The thread index
 
+    P : numpy.ndarray
+        The (top-k) matrix profile, sorted in ascending order per row
+
+    PL : numpy.ndarray
+        The top-1 left marix profile
+
+    PR : numpy.ndarray
+        The top-1 right marix profile
+
+    I : numpy.ndarray
+        The (top-k) matrix profile indices
+
+    IL : numpy.ndarray
+        The top-1 left matrix profile indices
+
+    IR : numpy.ndarray
+        The top-1 right matrix profile indices
+
     ignore_trivial : bool
         Set to `True` if this is a self-join. Otherwise, for AB-join, set this to
         `False`. Default is `True`.
@@ -92,16 +109,16 @@ def _compute_diagonal(
     uint64_1 = np.uint64(1)
 
     for diag_idx in range(diags_start_idx, diags_stop_idx):
-        k = diags[diag_idx]
+        g = diags[diag_idx]
 
-        if k >= 0:
-            iter_range = range(0, min(n_A - m + 1, n_B - m + 1 - k))
+        if g >= 0:
+            iter_range = range(0, min(n_A - m + 1, n_B - m + 1 - g))
         else:
-            iter_range = range(-k, min(n_A - m + 1, n_B - m + 1 - k))
+            iter_range = range(-g, min(n_A - m + 1, n_B - m + 1 - g))
 
         for i in iter_range:
             uint64_i = np.uint64(i)
-            uint64_j = np.uint64(i + k)
+            uint64_j = np.uint64(i + g)
 
             if uint64_i == 0 or uint64_j == 0:
                 p_norm = (
@@ -129,36 +146,59 @@ def _compute_diagonal(
 
             if T_A_subseq_isfinite[uint64_i] and T_B_subseq_isfinite[uint64_j]:
                 # Neither subsequence contains NaNs
-                if p_norm < P[thread_idx, uint64_i, 0]:
-                    P[thread_idx, uint64_i, 0] = p_norm
-                    I[thread_idx, uint64_i, 0] = uint64_j
 
-                if ignore_trivial:
-                    if p_norm < P[thread_idx, uint64_j, 0]:
-                        P[thread_idx, uint64_j, 0] = p_norm
-                        I[thread_idx, uint64_j, 0] = uint64_i
+                # `P[thread_idx, i, :]` is sorted ascendingly and MUST be updated
+                # when the newly-calculated `p_norm` value becomes smaller than the
+                # last (i.e. greatest) element in this array. Note that the goal
+                # is to have top-k smallest distancs for each subsequence.
+                if p_norm < P[thread_idx, uint64_i, -1]:
+                    idx = np.searchsorted(P[thread_idx, uint64_i], p_norm)
+                    core._shift_insert_at_index(
+                        P[thread_idx, uint64_i], idx, p_norm, shift="right"
+                    )
+                    core._shift_insert_at_index(
+                        I[thread_idx, uint64_i], idx, uint64_j, shift="right"
+                    )
+
+                if ignore_trivial:  # self-joins only
+                    if p_norm < P[thread_idx, uint64_j, -1]:
+                        idx = np.searchsorted(P[thread_idx, uint64_j], p_norm)
+                        core._shift_insert_at_index(
+                            P[thread_idx, uint64_j], idx, p_norm, shift="right"
+                        )
+                        core._shift_insert_at_index(
+                            I[thread_idx, uint64_j], idx, uint64_i, shift="right"
+                        )
 
                     if uint64_i < uint64_j:
                         # left matrix profile and left matrix profile index
-                        if p_norm < P[thread_idx, uint64_j, 1]:
-                            P[thread_idx, uint64_j, 1] = p_norm
-                            I[thread_idx, uint64_j, 1] = uint64_i
+                        if p_norm < PL[thread_idx, uint64_j]:
+                            PL[thread_idx, uint64_j] = p_norm
+                            IL[thread_idx, uint64_j] = uint64_i
 
                         # right matrix profile and right matrix profile index
-                        if p_norm < P[thread_idx, uint64_i, 2]:
-                            P[thread_idx, uint64_i, 2] = p_norm
-                            I[thread_idx, uint64_i, 2] = uint64_j
+                        if p_norm < PR[thread_idx, uint64_i]:
+                            PR[thread_idx, uint64_i] = p_norm
+                            IR[thread_idx, uint64_i] = uint64_j
 
     return
 
 
 @njit(
-    # "(f8[:], f8[:], i8, b1[:], b1[:], i8[:], b1)",
+    # "(f8[:], f8[:], i8, b1[:], b1[:], i8[:], b1, i8)",
     parallel=True,
     fastmath=True,
 )
 def _aamp(
-    T_A, T_B, m, T_A_subseq_isfinite, T_B_subseq_isfinite, p, diags, ignore_trivial
+    T_A,
+    T_B,
+    m,
+    T_A_subseq_isfinite,
+    T_B_subseq_isfinite,
+    p,
+    diags,
+    ignore_trivial,
+    k,
 ):
     """
     A Numba JIT-compiled version of AAMP for parallel computation of the matrix
@@ -194,13 +234,30 @@ def _aamp(
         Set to `True` if this is a self-join. Otherwise, for AB-join, set this to
         `False`. Default is `True`.
 
+    k : int
+        The number of top `k` smallest distances used to construct the matrix profile.
+        Note that this will increase the total computational time and memory usage
+        when k > 1.
+
     Returns
     -------
-    P : numpy.ndarray
-        Matrix profile
+    out1 : numpy.ndarray
+        The (top-k) matrix profile
 
-    I : numpy.ndarray
-        Matrix profile indices
+    out2 : numpy.ndarray
+        The (top-1) left matrix profile
+
+    out3 : numpy.ndarray
+        The (top-1) right matrix profile
+
+    out4 : numpy.ndarray
+        The (top-k) matrix profile indices
+
+    out5 : numpy.ndarray
+        The (top-1) left matrix profile indices
+
+    out6 : numpy.ndarray
+        The (top-1) right matrix profile indices
 
     Notes
     -----
@@ -213,8 +270,15 @@ def _aamp(
     n_B = T_B.shape[0]
     l = n_A - m + 1
     n_threads = numba.config.NUMBA_NUM_THREADS
-    P = np.full((n_threads, l, 3), np.inf, dtype=np.float64)
-    I = np.full((n_threads, l, 3), -1, dtype=np.int64)
+
+    P = np.full((n_threads, l, k), np.inf, dtype=np.float64)
+    I = np.full((n_threads, l, k), -1, dtype=np.int64)
+
+    PL = np.full((n_threads, l), np.inf, dtype=np.float64)
+    IL = np.full((n_threads, l), -1, dtype=np.int64)
+
+    PR = np.full((n_threads, l), np.inf, dtype=np.float64)
+    IR = np.full((n_threads, l), -1, dtype=np.int64)
 
     ndist_counts = core._count_diagonal_ndist(diags, m, n_A, n_B)
     diags_ranges = core._get_array_ranges(ndist_counts, n_threads, False)
@@ -233,26 +297,37 @@ def _aamp(
             diags_ranges[thread_idx, 1],
             thread_idx,
             P,
+            PL,
+            PR,
             I,
+            IL,
+            IR,
             ignore_trivial,
         )
 
     # Reduction of results from all threads
     for thread_idx in range(1, n_threads):
-        for i in prange(l):
-            if P[0, i, 0] > P[thread_idx, i, 0]:
-                P[0, i, 0] = P[thread_idx, i, 0]
-                I[0, i, 0] = I[thread_idx, i, 0]
-            # left matrix profile and left matrix profile indices
-            if P[0, i, 1] > P[thread_idx, i, 1]:
-                P[0, i, 1] = P[thread_idx, i, 1]
-                I[0, i, 1] = I[thread_idx, i, 1]
-            # right matrix profile and right matrix profile indices
-            if P[0, i, 2] > P[thread_idx, i, 2]:
-                P[0, i, 2] = P[thread_idx, i, 2]
-                I[0, i, 2] = I[thread_idx, i, 2]
-
-    return np.power(P[0, :, :], 1.0 / p), I[0, :, :]
+        # update top-k arrays
+        core._merge_topk_PI(P[0], P[thread_idx], I[0], I[thread_idx])
+
+        # update left matrix profile and matrix profile indices
+        mask = PL[0] > PL[thread_idx]
+        PL[0][mask] = PL[thread_idx][mask]
+        IL[0][mask] = IL[thread_idx][mask]
+
+        # update right matrix profile and matrix profile indices
+        mask = PR[0] > PR[thread_idx]
+        PR[0][mask] = PR[thread_idx][mask]
+        IR[0][mask] = IR[thread_idx][mask]
+
+    return (
+        np.power(P[0], 1.0 / p),
+        np.power(PL[0], 1.0 / p),
+        np.power(PR[0], 1.0 / p),
+        I[0],
+        IL[0],
+        IR[0],
+    )
 
 
 def aamp(T_A, m, T_B=None, ignore_trivial=True, p=2.0, k=1):
@@ -291,8 +366,16 @@ def aamp(T_A, m, T_B=None, ignore_trivial=True, p=2.0, k=1):
     Returns
     -------
     out : numpy.ndarray
-        The first column consists of the matrix profile, the second column
-        consists of the matrix profile indices.
+        When k = 1 (default), the first column consists of the matrix profile,
+        the second column consists of the matrix profile indices, the third column
+        consists of the left matrix profile indices, and the fourth column consists
+        of the right matrix profile indices. However, when k > 1, the output array
+        will contain exactly 2 * k + 2 columns. The first k columns (i.e., out[:, :k])
+        consists of the top-k matrix profile, the next set of k columns
+        (i.e., out[:, k:2k]) consists of the corresponding top-k matrix profile
+        indices, and the last two columns (i.e., out[:, 2k] and out[:, 2k+1] or,
+        equivalently, out[:, -2] and out[:, -1]) correspond to the top-1 left
+        matrix profile indices and the top-1 right matrix profile indices, respectively.
 
     Notes
     -----
@@ -331,19 +414,26 @@ def aamp(T_A, m, T_B=None, ignore_trivial=True, p=2.0, k=1):
     l = n_A - m + 1
 
     excl_zone = int(np.ceil(m / config.STUMPY_EXCL_ZONE_DENOM))
-    out = np.empty((l, 4), dtype=object)
-
     if ignore_trivial:
         diags = np.arange(excl_zone + 1, n_A - m + 1, dtype=np.int64)
     else:
         diags = np.arange(-(n_A - m + 1) + 1, n_B - m + 1, dtype=np.int64)
 
-    P, I = _aamp(
-        T_A, T_B, m, T_A_subseq_isfinite, T_B_subseq_isfinite, p, diags, ignore_trivial
+    P, PL, PR, I, IL, IR = _aamp(
+        T_A,
+        T_B,
+        m,
+        T_A_subseq_isfinite,
+        T_B_subseq_isfinite,
+        p,
+        diags,
+        ignore_trivial,
+        k,
     )
 
-    out[:, 0] = P[:, 0]
-    out[:, 1:] = I[:, :]
+    out = np.empty((l, 2 * k + 2), dtype=object)
+    out[:, :k] = P
+    out[:, k:] = np.column_stack((I, IL, IR))
 
     core._check_P(out[:, 0])
 

stumpy/aamped.py

@@ -55,8 +55,16 @@ def aamped(dask_client, T_A, m, T_B=None, ignore_trivial=True, p=2.0, k=1):
     Returns
     -------
     out : numpy.ndarray
-        The first column consists of the matrix profile, the second column
-        consists of the matrix profile indices.
+        When k = 1 (default), the first column consists of the matrix profile,
+        the second column consists of the matrix profile indices, the third column
+        consists of the left matrix profile indices, and the fourth column consists
+        of the right matrix profile indices. However, when k > 1, the output array
+        will contain exactly 2 * k + 2 columns. The first k columns (i.e., out[:, :k])
+        consists of the top-k matrix profile, the next set of k columns
+        (i.e., out[:, k:2k]) consists of the corresponding top-k matrix profile
+        indices, and the last two columns (i.e., out[:, 2k] and out[:, 2k+1] or,
+        equivalently, out[:, -2] and out[:, -1]) correspond to the top-1 left
+        matrix profile indices and the top-1 right matrix profile indices, respectively.
 
     Notes
     -----
@@ -94,12 +102,10 @@ def aamped(dask_client, T_A, m, T_B=None, ignore_trivial=True, p=2.0, k=1):
     n_B = T_B.shape[0]
     l = n_A - m + 1
 
-    excl_zone = int(np.ceil(m / config.STUMPY_EXCL_ZONE_DENOM))
-    out = np.empty((l, 4), dtype=object)
-
     hosts = list(dask_client.ncores().keys())
     nworkers = len(hosts)
 
+    excl_zone = int(np.ceil(m / config.STUMPY_EXCL_ZONE_DENOM))
     if ignore_trivial:
         diags = np.arange(excl_zone + 1, n_A - m + 1, dtype=np.int64)
     else:
@@ -141,20 +147,30 @@ def aamped(dask_client, T_A, m, T_B=None, ignore_trivial=True, p=2.0, k=1):
                 p,
                 diags_futures[i],
                 ignore_trivial,
+                k,
             )
         )
 
     results = dask_client.gather(futures)
-    profile, indices = results[0]
+    profile, profile_L, profile_R, indices, indices_L, indices_R = results[0]
     for i in range(1, len(hosts)):
-        P, I = results[i]
-        for col in range(P.shape[1]):  # pragma: no cover
-            cond = P[:, col] < profile[:, col]
-            profile[:, col] = np.where(cond, P[:, col], profile[:, col])
-            indices[:, col] = np.where(cond, I[:, col], indices[:, col])
-
-    out[:, 0] = profile[:, 0]
-    out[:, 1:4] = indices
+        P, PL, PR, I, IL, IR = results[i]
+        # Update top-k matrix profile and matrix profile indices
+        core._merge_topk_PI(profile, P, indices, I)
+
+        # Update top-1 left matrix profile and matrix profile index
+        mask = PL < profile_L
+        profile_L[mask] = PL[mask]
+        indices_L[mask] = IL[mask]
+
+        # Update top-1 right matrix profile and matrix profile index
+        mask = PR < profile_R
+        profile_R[mask] = PR[mask]
+        indices_R[mask] = IR[mask]
+
+    out = np.empty((l, 2 * k + 2), dtype=object)
+    out[:, :k] = profile
+    out[:, k : 2 * k + 2] = np.column_stack((indices, indices_L, indices_R))
 
     core._check_P(out[:, 0])