PaddleSpeech/paddlespeech/vector/cluster/diarization.py

# Copyright (c) 2022 PaddlePaddle and SpeechBrain Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# Modified from speechbrain(https://github.com/speechbrain/speechbrain)
"""
This script contains basic functions used for speaker diarization.
This script has an optional dependency on open source sklearn library.
A few sklearn functions are modified in this script as per requirement.
"""
import argparse
import copy
import warnings

import numpy as np
import scipy
import sklearn
from distutils.util import strtobool
from scipy import linalg
from scipy import sparse
from scipy.sparse.csgraph import connected_components
from scipy.sparse.csgraph import laplacian as csgraph_laplacian
from scipy.sparse.linalg import eigsh
from sklearn.cluster import SpectralClustering
from sklearn.cluster._kmeans import k_means
from sklearn.neighbors import kneighbors_graph


def _graph_connected_component(graph, node_id):
    """
    Find the largest graph connected components that contains one
    given node.

    Arguments
    ---------
    graph : array-like, shape: (n_samples, n_samples)
        Adjacency matrix of the graph, non-zero weight means an edge
        between the nodes.
    node_id : int
        The index of the query node of the graph.

    Returns
    -------
    connected_components_matrix : array-like
        shape - (n_samples,).
        An array of bool value indicating the indexes of the nodes belonging
        to the largest connected components of the given query node.
    """

    n_node = graph.shape[0]
    if sparse.issparse(graph):
        # speed up row-wise access to boolean connection mask
        graph = graph.tocsr()
    connected_nodes = np.zeros(n_node, dtype=bool)
    nodes_to_explore = np.zeros(n_node, dtype=bool)
    nodes_to_explore[node_id] = True
    for _ in range(n_node):
        last_num_component = connected_nodes.sum()
        np.logical_or(connected_nodes, nodes_to_explore, out=connected_nodes)
        if last_num_component >= connected_nodes.sum():
            break
        indices = np.where(nodes_to_explore)[0]
        nodes_to_explore.fill(False)
        for i in indices:
            if sparse.issparse(graph):
                neighbors = graph[i].toarray().ravel()
            else:
                neighbors = graph[i]
            np.logical_or(nodes_to_explore, neighbors, out=nodes_to_explore)
    return connected_nodes


def _graph_is_connected(graph):
    """
    Return whether the graph is connected (True) or Not (False)

    Arguments
    ---------
    graph : array-like or sparse matrix, shape: (n_samples, n_samples)
        Adjacency matrix of the graph, non-zero weight means an edge between the nodes.

    Returns
    -------
    is_connected : bool
        True means the graph is fully connected and False means not.
    """

    if sparse.isspmatrix(graph):
        # sparse graph, find all the connected components
        n_connected_components, _ = connected_components(graph)
        return n_connected_components == 1
    else:
        # dense graph, find all connected components start from node 0
        return _graph_connected_component(graph, 0).sum() == graph.shape[0]


def _set_diag(laplacian, value, norm_laplacian):
    """
    Set the diagonal of the laplacian matrix and convert it to a sparse
    format well suited for eigenvalue decomposition.

    Arguments
    ---------
    laplacian : array or sparse matrix
        The graph laplacian.
    value : float
        The value of the diagonal.
    norm_laplacian : bool
        Whether the value of the diagonal should be changed or not.

    Returns
    -------
    laplacian : array or sparse matrix
        An array of matrix in a form that is well suited to fast eigenvalue
        decomposition, depending on the bandwidth of the matrix.
    """

    n_nodes = laplacian.shape[0]
    # We need all entries in the diagonal to values
    if not sparse.isspmatrix(laplacian):
        if norm_laplacian:
            laplacian.flat[::n_nodes + 1] = value
    else:
        laplacian = laplacian.tocoo()
        if norm_laplacian:
            diag_idx = laplacian.row == laplacian.col
            laplacian.data[diag_idx] = value
        # If the matrix has a small number of diagonals (as in the
        # case of structured matrices coming from images), the
        # dia format might be best suited for matvec products:
        n_diags = np.unique(laplacian.row - laplacian.col).size
        if n_diags <= 7:
            # 3 or less outer diagonals on each side
            laplacian = laplacian.todia()
        else:
            # csr has the fastest matvec and is thus best suited to
            # arpack
            laplacian = laplacian.tocsr()
    return laplacian


def _deterministic_vector_sign_flip(u):
    """
    Modify the sign of vectors for reproducibility. Flips the sign of
    elements of all the vectors (rows of u) such that the absolute
    maximum element of each vector is positive.

    Arguments
    ---------
    u : ndarray
        Array with vectors as its rows.

    Returns
    -------
    u_flipped : ndarray
        Array with the sign flipped vectors as its rows. The same shape as `u`.
    """

    max_abs_rows = np.argmax(np.abs(u), axis=1)
    signs = np.sign(u[range(u.shape[0]), max_abs_rows])
    u *= signs[:, np.newaxis]
    return u


def _check_random_state(seed):
    """
    Turn seed into a np.random.RandomState instance.

    Arguments
    ---------
    seed : None | int | instance of RandomState
        If seed is None, return the RandomState singleton used by np.random.
        If seed is an int, return a new RandomState instance seeded with seed.
        If seed is already a RandomState instance, return it.
        Otherwise raise ValueError.
    """

    if seed is None or seed is np.random:
        return np.random.mtrand._rand
    if isinstance(seed, numbers.Integral):
        return np.random.RandomState(seed)
    if isinstance(seed, np.random.RandomState):
        return seed
    raise ValueError("%r cannot be used to seed a np.random.RandomState"
                     " instance" % seed)


def spectral_embedding(
        adjacency,
        n_components=8,
        norm_laplacian=True,
        drop_first=True, ):
    """
    Returns spectral embeddings.

    Arguments
    ---------
    adjacency : array-like or sparse graph
        shape - (n_samples, n_samples)
        The adjacency matrix of the graph to embed.
    n_components : int
        The dimension of the projection subspace.
    norm_laplacian : bool
        If True, then compute normalized Laplacian.
    drop_first : bool
        Whether to drop the first eigenvector.

    Returns
    -------
    embedding : array
        Spectral embeddings for each sample.

    Example
    -------
    >>> import numpy as np
    >>> import diarization as diar
    >>> affinity = np.array([[1, 1, 1, 0.5, 0, 0, 0, 0, 0, 0.5],
    ... [1, 1, 1, 0, 0, 0, 0, 0, 0, 0],
    ... [1, 1, 1, 0, 0, 0, 0, 0, 0, 0],
    ... [0.5, 0, 0, 1, 1, 1, 0, 0, 0, 0],
    ... [0, 0, 0, 1, 1, 1, 0, 0, 0, 0],
    ... [0, 0, 0, 1, 1, 1, 0, 0, 0, 0],
    ... [0, 0, 0, 0, 0, 0, 1, 1, 1, 1],
    ... [0, 0, 0, 0, 0, 0, 1, 1, 1, 1],
    ... [0, 0, 0, 0, 0, 0, 1, 1, 1, 1],
    ... [0.5, 0, 0, 0, 0, 0, 1, 1, 1, 1]])
    >>> embs = diar.spectral_embedding(affinity, 3)
    >>> # Notice similar embeddings
    >>> print(np.around(embs , decimals=3))
    [[ 0.075  0.244  0.285]
     [ 0.083  0.356 -0.203]
     [ 0.083  0.356 -0.203]
     [ 0.26  -0.149  0.154]
     [ 0.29  -0.218 -0.11 ]
     [ 0.29  -0.218 -0.11 ]
     [-0.198 -0.084 -0.122]
     [-0.198 -0.084 -0.122]
     [-0.198 -0.084 -0.122]
     [-0.167 -0.044  0.316]]
    """

    # Whether to drop the first eigenvector
    if drop_first:
        n_components = n_components + 1

    if not _graph_is_connected(adjacency):
        warnings.warn("Graph is not fully connected, spectral embedding"
                      " may not work as expected.")

    laplacian, dd = csgraph_laplacian(
        adjacency, normed=norm_laplacian, return_diag=True)

    laplacian = _set_diag(laplacian, 1, norm_laplacian)

    laplacian *= -1

    vals, diffusion_map = eigsh(
        laplacian,
        k=n_components,
        sigma=1.0,
        which="LM", )

    embedding = diffusion_map.T[n_components::-1]

    if norm_laplacian:
        embedding = embedding / dd

    embedding = _deterministic_vector_sign_flip(embedding)
    if drop_first:
        return embedding[1:n_components].T
    else:
        return embedding[:n_components].T


def spectral_clustering(
        affinity,
        n_clusters=8,
        n_components=None,
        random_state=None,
        n_init=10, ):
    """
    Performs spectral clustering.

    Arguments
    ---------
    affinity : matrix
        Affinity matrix.
    n_clusters : int
        Number of clusters for kmeans.
    n_components : int
        Number of components to retain while estimating spectral embeddings.
    random_state : int
        A pseudo random number generator used by kmeans.
     n_init : int
        Number of time the k-means algorithm will be run with different centroid seeds.

    Returns
    -------
    labels : array
        Cluster label for each sample.

    Example
    -------
    >>> import numpy as np
    >>> diarization as diar
    >>> affinity = np.array([[1, 1, 1, 0.5, 0, 0, 0, 0, 0, 0.5],
    ... [1, 1, 1, 0, 0, 0, 0, 0, 0, 0],
    ... [1, 1, 1, 0, 0, 0, 0, 0, 0, 0],
    ... [0.5, 0, 0, 1, 1, 1, 0, 0, 0, 0],
    ... [0, 0, 0, 1, 1, 1, 0, 0, 0, 0],
    ... [0, 0, 0, 1, 1, 1, 0, 0, 0, 0],
    ... [0, 0, 0, 0, 0, 0, 1, 1, 1, 1],
    ... [0, 0, 0, 0, 0, 0, 1, 1, 1, 1],
    ... [0, 0, 0, 0, 0, 0, 1, 1, 1, 1],
    ... [0.5, 0, 0, 0, 0, 0, 1, 1, 1, 1]])
    >>> labs = diar.spectral_clustering(affinity, 3)
    >>> # print (labs) # [2 2 2 1 1 1 0 0 0 0]
    """

    random_state = _check_random_state(random_state)
    n_components = n_clusters if n_components is None else n_components

    maps = spectral_embedding(
        affinity,
        n_components=n_components,
        drop_first=False, )

    _, labels, _ = k_means(
        maps, n_clusters, random_state=random_state, n_init=n_init)

    return labels


class EmbeddingMeta:
    """
    A utility class to pack deep embeddings and meta-information in one object.

    Arguments
    ---------
    segset : list
        List of session IDs as an array of strings.
    modelset : list
        List of model IDs as an array of strings.
    stats : tensor
        An ndarray of float64. Each line contains embedding
        from the corresponding session.
    """

    def __init__(
            self,
            segset=None,
            modelset=None,
            stats=None, ):

        if segset is None:
            self.segset = np.empty(0, dtype="|O")
            self.modelset = np.empty(0, dtype="|O")
            self.stats = np.array([], dtype=np.float64)
        else:
            self.segset = segset
            self.modelset = modelset
            self.stats = stats

        self.stat0 = np.array([[1.0]] * self.stats.shape[0])

    def norm_stats(self):
        """
        Divide all first-order statistics by their Euclidean norm.
        """

        vect_norm = np.clip(np.linalg.norm(self.stats, axis=1), 1e-08, np.inf)
        self.stats = (self.stats.transpose() / vect_norm).transpose()

    def get_mean_stats(self):
        """
        Return the mean of first order statistics.
        """
        mu = np.mean(self.stats, axis=0)
        return mu

    def get_total_covariance_stats(self):
        """
        Compute and return the total covariance matrix of the first-order statistics.
        """
        C = self.stats - self.stats.mean(axis=0)
        return np.dot(C.transpose(), C) / self.stats.shape[0]

    def get_model_stat0(self, mod_id):
        """Return zero-order statistics of a given model

        Arguments
        ---------
        mod_id : str
            ID of the model which stat0 will be returned.
        """
        S = self.stat0[self.modelset == mod_id, :]
        return S

    def get_model_stats(self, mod_id):
        """Return first-order statistics of a given model.

        Arguments
        ---------
        mod_id : str
            ID of the model which stat1 will be returned.
        """
        return self.stats[self.modelset == mod_id, :]

    def sum_stat_per_model(self):
        """
        Sum the zero- and first-order statistics per model and store them
        in a new EmbeddingMeta.
        Returns a EmbeddingMeta object with the statistics summed per model
        and a numpy array with session_per_model.
        """

        sts_per_model = EmbeddingMeta()
        sts_per_model.modelset = np.unique(
            self.modelset)  # nd: get uniq spkr ids
        sts_per_model.segset = copy.deepcopy(sts_per_model.modelset)
        sts_per_model.stat0 = np.zeros(
            (sts_per_model.modelset.shape[0], self.stat0.shape[1]),
            dtype=np.float64, )
        sts_per_model.stats = np.zeros(
            (sts_per_model.modelset.shape[0], self.stats.shape[1]),
            dtype=np.float64, )

        session_per_model = np.zeros(np.unique(self.modelset).shape[0])

        # For each model sum the stats
        for idx, model in enumerate(sts_per_model.modelset):
            sts_per_model.stat0[idx, :] = self.get_model_stat0(model).sum(
                axis=0)
            sts_per_model.stats[idx, :] = self.get_model_stats(model).sum(
                axis=0)
            session_per_model[idx] += self.get_model_stats(model).shape[0]
        return sts_per_model, session_per_model

    def center_stats(self, mu):
        """
        Center first order statistics.

        Arguments
        ---------
        mu : array
            Array to center on.
        """

        dim = self.stats.shape[1] / self.stat0.shape[1]
        index_map = np.repeat(np.arange(self.stat0.shape[1]), dim)
        self.stats = self.stats - (self.stat0[:, index_map] *
                                   mu.astype(np.float64))

    def rotate_stats(self, R):
        """
        Rotate first-order statistics by a right-product.

        Arguments
        ---------
        R : ndarray
            Matrix to use for right product on the first order statistics.
        """
        self.stats = np.dot(self.stats, R)

    def whiten_stats(self, mu, sigma, isSqrInvSigma=False):
        """
        Whiten first-order statistics
        If sigma.ndim == 1, case of a diagonal covariance.
        If sigma.ndim == 2, case of a single Gaussian with full covariance.
        If sigma.ndim == 3, case of a full covariance UBM.

        Arguments
        ---------
        mu : array
            Mean vector to be subtracted from the statistics.
        sigma : narray
            Co-variance matrix or covariance super-vector.
        isSqrInvSigma : bool
            True if the input Sigma matrix is the inverse of the square root of a covariance matrix.
        """

        if sigma.ndim == 1:
            self.center_stats(mu)
            self.stats = self.stats / np.sqrt(sigma.astype(np.float64))

        elif sigma.ndim == 2:
            # Compute the inverse square root of the co-variance matrix Sigma
            sqr_inv_sigma = sigma

            if not isSqrInvSigma:
                # eigen_values, eigen_vectors = scipy.linalg.eigh(sigma)
                eigen_values, eigen_vectors = linalg.eigh(sigma)
                ind = eigen_values.real.argsort()[::-1]
                eigen_values = eigen_values.real[ind]
                eigen_vectors = eigen_vectors.real[:, ind]

                sqr_inv_eval_sigma = 1 / np.sqrt(eigen_values.real)
                sqr_inv_sigma = np.dot(eigen_vectors,
                                       np.diag(sqr_inv_eval_sigma))
            else:
                pass

            # Whitening of the first-order statistics
            self.center_stats(mu)  # CENTERING
            self.rotate_stats(sqr_inv_sigma)

        elif sigma.ndim == 3:
            # we assume that sigma is a 3D ndarray of size D x n x n
            # where D is the number of distributions and n is the dimension of a single distribution
            n = self.stats.shape[1] // self.stat0.shape[1]
            sess_nb = self.stat0.shape[0]
            self.center_stats(mu)
            self.stats = (np.einsum("ikj,ikl->ilj",
                                    self.stats.T.reshape(-1, n, sess_nb), sigma)
                          .reshape(-1, sess_nb).T)

        else:
            raise Exception("Wrong dimension of Sigma, must be 1 or 2")

    def align_models(self, model_list):
        """
        Align models of the current EmbeddingMeta to match a list of models
            provided as input parameter. The size of the StatServer might be
            reduced to match the input list of models.

        Arguments
        ---------
        model_list : ndarray of strings
            List of models to match.
        """
        indx = np.array(
            [np.argwhere(self.modelset == v)[0][0] for v in model_list])
        self.segset = self.segset[indx]
        self.modelset = self.modelset[indx]
        self.stat0 = self.stat0[indx, :]
        self.stats = self.stats[indx, :]

    def align_segments(self, segment_list):
        """
        Align segments of the current EmbeddingMeta to match a list of segment
            provided as input parameter. The size of the StatServer might be
            reduced to match the input list of segments.

        Arguments
        ---------
        segment_list: ndarray of strings
            list of segments to match
        """
        indx = np.array(
            [np.argwhere(self.segset == v)[0][0] for v in segment_list])
        self.segset = self.segset[indx]
        self.modelset = self.modelset[indx]
        self.stat0 = self.stat0[indx, :]
        self.stats = self.stats[indx, :]


class SpecClustUnorm:
    """
    This class implements the spectral clustering with unnormalized affinity matrix.
    Useful when affinity matrix is based on cosine similarities.

    Reference
    ---------
    Von Luxburg, U. A tutorial on spectral clustering. Stat Comput 17, 395–416 (2007).
    https://doi.org/10.1007/s11222-007-9033-z

    Example
    -------
    >>> import diarization as diar
    >>> clust = diar.SpecClustUnorm(min_num_spkrs=2, max_num_spkrs=10)
    >>> emb = [[ 2.1, 3.1, 4.1, 4.2, 3.1],
    ... [ 2.2, 3.1, 4.2, 4.2, 3.2],
    ... [ 2.0, 3.0, 4.0, 4.1, 3.0],
    ... [ 8.0, 7.0, 7.0, 8.1, 9.0],
    ... [ 8.1, 7.1, 7.2, 8.1, 9.2],
    ... [ 8.3, 7.4, 7.0, 8.4, 9.0],
    ... [ 0.3, 0.4, 0.4, 0.5, 0.8],
    ... [ 0.4, 0.3, 0.6, 0.7, 0.8],
    ... [ 0.2, 0.3, 0.2, 0.3, 0.7],
    ... [ 0.3, 0.4, 0.4, 0.4, 0.7],]
    >>> # Estimating similarity matrix
    >>> sim_mat = clust.get_sim_mat(emb)
    >>> print (np.around(sim_mat[5:,5:], decimals=3))
    [[1.    0.957 0.961 0.904 0.966]
     [0.957 1.    0.977 0.982 0.997]
     [0.961 0.977 1.    0.928 0.972]
     [0.904 0.982 0.928 1.    0.976]
     [0.966 0.997 0.972 0.976 1.   ]]
    >>> # Prunning
    >>> prunned_sim_mat = clust.p_pruning(sim_mat, 0.3)
    >>> print (np.around(prunned_sim_mat[5:,5:], decimals=3))
    [[1.    0.    0.    0.    0.   ]
     [0.    1.    0.    0.982 0.997]
     [0.    0.977 1.    0.    0.972]
     [0.    0.982 0.    1.    0.976]
     [0.    0.997 0.    0.976 1.   ]]
    >>> # Symmetrization
    >>> sym_prund_sim_mat = 0.5 * (prunned_sim_mat + prunned_sim_mat.T)
    >>> print (np.around(sym_prund_sim_mat[5:,5:], decimals=3))
    [[1.    0.    0.    0.    0.   ]
     [0.    1.    0.489 0.982 0.997]
     [0.    0.489 1.    0.    0.486]
     [0.    0.982 0.    1.    0.976]
     [0.    0.997 0.486 0.976 1.   ]]
    >>> # Laplacian
    >>> laplacian = clust.get_laplacian(sym_prund_sim_mat)
    >>> print (np.around(laplacian[5:,5:], decimals=3))
    [[ 1.999  0.     0.     0.     0.   ]
     [ 0.     2.468 -0.489 -0.982 -0.997]
     [ 0.    -0.489  0.975  0.    -0.486]
     [ 0.    -0.982  0.     1.958 -0.976]
     [ 0.    -0.997 -0.486 -0.976  2.458]]
    >>> # Spectral Embeddings
    >>> spec_emb, num_of_spk = clust.get_spec_embs(laplacian, 3)
    >>> print(num_of_spk)
    3
    >>> # Clustering
    >>> clust.cluster_embs(spec_emb, num_of_spk)
    >>> # print (clust.labels_) # [0 0 0 2 2 2 1 1 1 1]
    >>> # Complete spectral clustering
    >>> clust.do_spec_clust(emb, k_oracle=3, p_val=0.3)
    >>> # print(clust.labels_) # [0 0 0 2 2 2 1 1 1 1]
    """

    def __init__(self, min_num_spkrs=2, max_num_spkrs=10):

        self.min_num_spkrs = min_num_spkrs
        self.max_num_spkrs = max_num_spkrs

    def do_spec_clust(self, X, k_oracle, p_val):
        """
        Function for spectral clustering.

        Arguments
        ---------
        X : array
            (n_samples, n_features).
            Embeddings extracted from the model.
        k_oracle : int
            Number of speakers (when oracle number of speakers).
        p_val : float
            p percent value to prune the affinity matrix.
        """

        # Similarity matrix computation
        sim_mat = self.get_sim_mat(X)

        # Refining similarity matrix with p_val
        prunned_sim_mat = self.p_pruning(sim_mat, p_val)

        # Symmetrization
        sym_prund_sim_mat = 0.5 * (prunned_sim_mat + prunned_sim_mat.T)

        # Laplacian calculation
        laplacian = self.get_laplacian(sym_prund_sim_mat)

        # Get Spectral Embeddings
        emb, num_of_spk = self.get_spec_embs(laplacian, k_oracle)

        # Perform clustering
        self.cluster_embs(emb, num_of_spk)

    def get_sim_mat(self, X):
        """
        Returns the similarity matrix based on cosine similarities.

        Arguments
        ---------
        X : array
            (n_samples, n_features).
            Embeddings extracted from the model.

        Returns
        -------
        M : array
            (n_samples, n_samples).
            Similarity matrix with cosine similarities between each pair of embedding.
        """

        # Cosine similarities
        M = sklearn.metrics.pairwise.cosine_similarity(X, X)
        return M

    def p_pruning(self, A, pval):
        """
        Refine the affinity matrix by zeroing less similar values.

        Arguments
        ---------
        A : array
            (n_samples, n_samples).
            Affinity matrix.
        pval : float
            p-value to be retained in each row of the affinity matrix.

        Returns
        -------
        A : array
            (n_samples, n_samples).
            Prunned affinity matrix based on p_val.
        """

        n_elems = int((1 - pval) * A.shape[0])

        # For each row in a affinity matrix
        for i in range(A.shape[0]):
            low_indexes = np.argsort(A[i, :])
            low_indexes = low_indexes[0:n_elems]

            # Replace smaller similarity values by 0s
            A[i, low_indexes] = 0

        return A

    def get_laplacian(self, M):
        """
        Returns the un-normalized laplacian for the given affinity matrix.

        Arguments
        ---------
        M : array
            (n_samples, n_samples)
            Affinity matrix.

        Returns
        -------
        L : array
            (n_samples, n_samples)
            Laplacian matrix.
        """

        M[np.diag_indices(M.shape[0])] = 0
        D = np.sum(np.abs(M), axis=1)
        D = np.diag(D)
        L = D - M
        return L

    def get_spec_embs(self, L, k_oracle=4):
        """
        Returns spectral embeddings and estimates the number of speakers
        using maximum Eigen gap.

        Arguments
        ---------
        L : array (n_samples, n_samples)
            Laplacian matrix.
        k_oracle : int
            Number of speakers when the condition is oracle number of speakers,
            else None.

        Returns
        -------
        emb : array (n_samples, n_components)
            Spectral embedding for each sample with n Eigen components.
        num_of_spk : int
            Estimated number of speakers. If the condition is set to the oracle
            number of speakers then returns k_oracle.
        """

        lambdas, eig_vecs = scipy.linalg.eigh(L)

        # if params["oracle_n_spkrs"] is True:
        if k_oracle is not None:
            num_of_spk = k_oracle
        else:
            lambda_gap_list = self.get_eigen_gaps(lambdas[1:self.max_num_spkrs])

            num_of_spk = (np.argmax(
                lambda_gap_list[:min(self.max_num_spkrs, len(lambda_gap_list))])
                          + 2)

            if num_of_spk < self.min_num_spkrs:
                num_of_spk = self.min_num_spkrs

        emb = eig_vecs[:, 0:num_of_spk]

        return emb, num_of_spk

    def cluster_embs(self, emb, k):
        """
        Clusters the embeddings using kmeans.

        Arguments
        ---------
        emb : array (n_samples, n_components)
            Spectral embedding for each sample with n Eigen components.
        k : int
            Number of clusters to kmeans.

        Returns
        -------
        self.labels_ : self
            Labels for each sample embedding.
        """
        _, self.labels_, _ = k_means(emb, k)

    def get_eigen_gaps(self, eig_vals):
        """
        Returns the difference (gaps) between the Eigen values.

        Arguments
        ---------
        eig_vals : list
            List of eigen values

        Returns
        -------
        eig_vals_gap_list : list
            List of differences (gaps) between adjacent Eigen values.
        """

        eig_vals_gap_list = []
        for i in range(len(eig_vals) - 1):
            gap = float(eig_vals[i + 1]) - float(eig_vals[i])
            eig_vals_gap_list.append(gap)

        return eig_vals_gap_list


class SpecCluster(SpectralClustering):
    def perform_sc(self, X, n_neighbors=10):
        """
        Performs spectral clustering using sklearn on embeddings.

        Arguments
        ---------
        X : array (n_samples, n_features)
            Embeddings to be clustered.
        n_neighbors : int
            Number of neighbors in estimating affinity matrix.
        """

        # Computation of affinity matrix
        connectivity = kneighbors_graph(
            X,
            n_neighbors=n_neighbors,
            include_self=True, )
        self.affinity_matrix_ = 0.5 * (connectivity + connectivity.T)

        # Perform spectral clustering on affinity matrix
        self.labels_ = spectral_clustering(
            self.affinity_matrix_,
            n_clusters=self.n_clusters, )
        return self


def is_overlapped(end1, start2):
    """
    Returns True if segments are overlapping.

    Arguments
    ---------
    end1 : float
        End time of the first segment.
    start2 : float
        Start time of the second segment.

    Returns
    -------
    overlapped : bool
        True of segments overlapped else False.

    Example
    -------
    >>> import diarization as diar
    >>> diar.is_overlapped(5.5, 3.4)
    True
    >>> diar.is_overlapped(5.5, 6.4)
    False
    """

    if start2 > end1:
        return False
    else:
        return True


def merge_ssegs_same_speaker(lol):
    """
    Merge adjacent sub-segs from the same speaker.

    Arguments
    ---------
    lol : list of list
        Each list contains [rec_id, seg_start, seg_end, spkr_id].

    Returns
    -------
    new_lol : list of list
        new_lol contains adjacent segments merged from the same speaker ID.

    Example
    -------
    >>> import diarization as diar
    >>> lol=[['r1', 5.5, 7.0, 's1'],
    ... ['r1', 6.5, 9.0, 's1'],
    ... ['r1', 8.0, 11.0, 's1'],
    ... ['r1', 11.5, 13.0, 's2'],
    ... ['r1', 14.0, 15.0, 's2'],
    ... ['r1', 14.5, 15.0, 's1']]
    >>> diar.merge_ssegs_same_speaker(lol)
    [['r1', 5.5, 11.0, 's1'], ['r1', 11.5, 13.0, 's2'], ['r1', 14.0, 15.0, 's2'], ['r1', 14.5, 15.0, 's1']]
    """

    new_lol = []

    # Start from the first sub-seg
    sseg = lol[0]
    flag = False
    for i in range(1, len(lol)):
        next_sseg = lol[i]

        # IF sub-segments overlap AND has same speaker THEN merge
        if is_overlapped(sseg[2], next_sseg[1]) and sseg[3] == next_sseg[3]:
            sseg[2] = next_sseg[2]  # just update the end time
            # This is important. For the last sseg, if it is the same speaker the merge
            # Make sure we don't append the last segment once more. Hence, set FLAG=True
            if i == len(lol) - 1:
                flag = True
                new_lol.append(sseg)
        else:
            new_lol.append(sseg)
            sseg = next_sseg

    # Add last segment only when it was skipped earlier.
    if flag is False:
        new_lol.append(lol[-1])

    return new_lol


def write_ders_file(ref_rttm, DER, out_der_file):
    """Write the final DERs for individual recording.

    Arguments
    ---------
    ref_rttm : str
        Reference RTTM file.
    DER : array
        Array containing DER values of each recording.
    out_der_file : str
        File to write the DERs.
    """

    rttm = read_rttm(ref_rttm)
    spkr_info = list(filter(lambda x: x.startswith("SPKR-INFO"), rttm))

    rec_id_list = []
    count = 0

    with open(out_der_file, "w") as f:
        for row in spkr_info:
            a = row.split(" ")
            rec_id = a[1]
            if rec_id not in rec_id_list:
                r = [rec_id, str(round(DER[count], 2))]
                rec_id_list.append(rec_id)
                line_str = " ".join(r)
                f.write("%s\n" % line_str)
                count += 1
        r = ["OVERALL ", str(round(DER[count], 2))]
        line_str = " ".join(r)
        f.write("%s\n" % line_str)


def get_oracle_num_spkrs(rec_id, spkr_info):
    """
    Returns actual number of speakers in a recording from the ground-truth.
    This can be used when the condition is oracle number of speakers.

    Arguments
    ---------
    rec_id : str
        Recording ID for which the number of speakers have to be obtained.
    spkr_info : list
        Header of the RTTM file. Starting with `SPKR-INFO`.

    Example
    -------
    >>> from speechbrain.processing import diarization as diar
    >>> spkr_info = ['SPKR-INFO ES2011a 0 <NA> <NA> <NA> unknown ES2011a.A <NA> <NA>',
    ... 'SPKR-INFO ES2011a 0 <NA> <NA> <NA> unknown ES2011a.B <NA> <NA>',
    ... 'SPKR-INFO ES2011a 0 <NA> <NA> <NA> unknown ES2011a.C <NA> <NA>',
    ... 'SPKR-INFO ES2011a 0 <NA> <NA> <NA> unknown ES2011a.D <NA> <NA>',
    ... 'SPKR-INFO ES2011b 0 <NA> <NA> <NA> unknown ES2011b.A <NA> <NA>',
    ... 'SPKR-INFO ES2011b 0 <NA> <NA> <NA> unknown ES2011b.B <NA> <NA>',
    ... 'SPKR-INFO ES2011b 0 <NA> <NA> <NA> unknown ES2011b.C <NA> <NA>']
    >>> diar.get_oracle_num_spkrs('ES2011a', spkr_info)
    4
    >>> diar.get_oracle_num_spkrs('ES2011b', spkr_info)
    3
    """

    num_spkrs = 0
    for line in spkr_info:
        if rec_id in line:
            # Since rec_id is prefix for each speaker
            num_spkrs += 1

    return num_spkrs


def distribute_overlap(lol):
    """
    Distributes the overlapped speech equally among the adjacent segments
    with different speakers.

    Arguments
    ---------
    lol : list of list
        It has each list structure as [rec_id, seg_start, seg_end, spkr_id].

    Returns
    -------
    new_lol : list of list
        It contains the overlapped part equally divided among the adjacent
        segments with different speaker IDs.

    Example
    -------
    >>> import diarization as diar
    >>> lol = [['r1', 5.5, 9.0, 's1'],
    ... ['r1', 8.0, 11.0, 's2'],
    ... ['r1', 11.5, 13.0, 's2'],
    ... ['r1', 12.0, 15.0, 's1']]
    >>> diar.distribute_overlap(lol)
    [['r1', 5.5, 8.5, 's1'], ['r1', 8.5, 11.0, 's2'], ['r1', 11.5, 12.5, 's2'], ['r1', 12.5, 15.0, 's1']]
    """

    new_lol = []
    sseg = lol[0]

    # Add first sub-segment here to avoid error at: "if new_lol[-1] != sseg:" when new_lol is empty
    # new_lol.append(sseg)

    for i in range(1, len(lol)):
        next_sseg = lol[i]
        # No need to check if they are different speakers.
        # Because if segments are overlapped then they always have different speakers.
        # This is because similar speaker's adjacent sub-segments are already merged by "merge_ssegs_same_speaker()"

        if is_overlapped(sseg[2], next_sseg[1]):

            # Get overlap duration.
            # Now this overlap will be divided equally between adjacent segments.
            overlap = sseg[2] - next_sseg[1]

            # Update end time of old seg
            sseg[2] = sseg[2] - (overlap / 2.0)

            # Update start time of next seg
            next_sseg[1] = next_sseg[1] + (overlap / 2.0)

            if len(new_lol) == 0:
                # For first sub-segment entry
                new_lol.append(sseg)
            else:
                # To avoid duplicate entries
                if new_lol[-1] != sseg:
                    new_lol.append(sseg)

            # Current sub-segment is next sub-segment
            sseg = next_sseg

        else:
            # For the first sseg
            if len(new_lol) == 0:
                new_lol.append(sseg)
            else:
                # To avoid duplicate entries
                if new_lol[-1] != sseg:
                    new_lol.append(sseg)

            # Update the current sub-segment
            sseg = next_sseg

    # Add the remaining last sub-segment
    new_lol.append(next_sseg)

    return new_lol


def read_rttm(rttm_file_path):
    """
    Reads and returns RTTM in list format.

    Arguments
    ---------
    rttm_file_path : str
        Path to the RTTM file to be read.

    Returns
    -------
    rttm : list
        List containing rows of RTTM file.
    """

    rttm = []
    with open(rttm_file_path, "r") as f:
        for line in f:
            entry = line[:-1]
            rttm.append(entry)
    return rttm


def write_rttm(segs_list, out_rttm_file):
    """
    Writes the segment list in RTTM format (A standard NIST format).

    Arguments
    ---------
    segs_list : list of list
        Each list contains [rec_id, seg_start, seg_end, spkr_id].
    out_rttm_file : str
        Path of the output RTTM file.
    """

    rttm = []
    rec_id = segs_list[0][0]

    for seg in segs_list:
        new_row = [
            "SPEAKER",
            rec_id,
            "0",
            str(round(seg[1], 4)),
            str(round(seg[2] - seg[1], 4)),
            "<NA>",
            "<NA>",
            seg[3],
            "<NA>",
            "<NA>",
        ]
        rttm.append(new_row)

    with open(out_rttm_file, "w") as f:
        for row in rttm:
            line_str = " ".join(row)
            f.write("%s\n" % line_str)


def do_AHC(diary_obj, out_rttm_file, rec_id, k_oracle=4, p_val=0.3):
    """
    Performs Agglomerative Hierarchical Clustering on embeddings.

    Arguments
    ---------
    diary_obj : EmbeddingMeta type
        Contains embeddings in diary_obj.stats and segment IDs in diary_obj.segset.
    out_rttm_file : str
        Path of the output RTTM file.
    rec_id : str
        Recording ID for the recording under processing.
    k : int
        Number of speaker (None, if it has to be estimated).
    pval : float
        `pval` for prunning affinity matrix. Used only when number of speakers
        are unknown. Note that this is just for experiment. Prefer Spectral clustering
        for better clustering results.
    """

    from sklearn.cluster import AgglomerativeClustering

    # p_val is the threshold_val (for AHC)
    diary_obj.norm_stats()

    # processing
    if k_oracle is not None:
        num_of_spk = k_oracle

        clustering = AgglomerativeClustering(
            n_clusters=num_of_spk,
            affinity="cosine",
            linkage="average", ).fit(diary_obj.stats)
        labels = clustering.labels_

    else:
        # Estimate num of using max eigen gap with `cos` affinity matrix.
        # This is just for experimentation.
        clustering = AgglomerativeClustering(
            n_clusters=None,
            affinity="cosine",
            linkage="average",
            distance_threshold=p_val, ).fit(diary_obj.stats)
        labels = clustering.labels_

    # Convert labels to speaker boundaries
    subseg_ids = diary_obj.segset
    lol = []

    for i in range(labels.shape[0]):
        spkr_id = rec_id + "_" + str(labels[i])

        sub_seg = subseg_ids[i]

        splitted = sub_seg.rsplit("_", 2)
        rec_id = str(splitted[0])
        sseg_start = float(splitted[1])
        sseg_end = float(splitted[2])

        a = [rec_id, sseg_start, sseg_end, spkr_id]
        lol.append(a)

    # Sorting based on start time of sub-segment
    lol.sort(key=lambda x: float(x[1]))

    # Merge and split in 2 simple steps: (i) Merge sseg of same speakers then (ii) split different speakers
    # Step 1: Merge adjacent sub-segments that belong to same speaker (or cluster)
    lol = merge_ssegs_same_speaker(lol)

    # Step 2: Distribute duration of adjacent overlapping sub-segments belonging to different speakers (or cluster)
    # Taking mid-point as the splitting time location.
    lol = distribute_overlap(lol)

    # logger.info("Completed diarizing " + rec_id)
    write_rttm(lol, out_rttm_file)


def do_spec_clustering(diary_obj, out_rttm_file, rec_id, k, pval, affinity_type,
                       n_neighbors):
    """
    Performs spectral clustering on embeddings. This function calls specific
    clustering algorithms as per affinity.

    Arguments
    ---------
    diary_obj : EmbeddingMeta type
        Contains embeddings in diary_obj.stats and segment IDs in diary_obj.segset.
    out_rttm_file : str
        Path of the output RTTM file.
    rec_id : str
        Recording ID for the recording under processing.
    k : int
        Number of speaker (None, if it has to be estimated).
    pval : float
        `pval` for prunning affinity matrix.
    affinity_type : str
        Type of similarity to be used to get affinity matrix (cos or nn).
    """

    if affinity_type == "cos":
        clust_obj = SpecClustUnorm(min_num_spkrs=2, max_num_spkrs=10)
        k_oracle = k  # use it only when oracle num of speakers
        clust_obj.do_spec_clust(diary_obj.stats, k_oracle, pval)
        labels = clust_obj.labels_
    else:
        clust_obj = SpecCluster(
            n_clusters=k,
            assign_labels="kmeans",
            random_state=1234,
            affinity="nearest_neighbors", )
        clust_obj.perform_sc(diary_obj.stats, n_neighbors)
        labels = clust_obj.labels_

    # Convert labels to speaker boundaries
    subseg_ids = diary_obj.segset
    lol = []

    for i in range(labels.shape[0]):
        spkr_id = rec_id + "_" + str(labels[i])

        sub_seg = subseg_ids[i]

        splitted = sub_seg.rsplit("_", 2)
        rec_id = str(splitted[0])
        sseg_start = float(splitted[1])
        sseg_end = float(splitted[2])

        a = [rec_id, sseg_start, sseg_end, spkr_id]
        lol.append(a)

    # Sorting based on start time of sub-segment
    lol.sort(key=lambda x: float(x[1]))

    # Merge and split in 2 simple steps: (i) Merge sseg of same speakers then (ii) split different speakers
    # Step 1: Merge adjacent sub-segments that belong to same speaker (or cluster)
    lol = merge_ssegs_same_speaker(lol)

    # Step 2: Distribute duration of adjacent overlapping sub-segments belonging to different speakers (or cluster)
    # Taking mid-point as the splitting time location.
    lol = distribute_overlap(lol)

    # logger.info("Completed diarizing " + rec_id)
    write_rttm(lol, out_rttm_file)


if __name__ == '__main__':

    parser = argparse.ArgumentParser(
        prog='python diarization.py --backend AHC', description='diarizing')
    parser.add_argument(
        '--sys_rttm_dir',
        required=False,
        help='Directory to store system RTTM files')
    parser.add_argument(
        '--ref_rttm_dir',
        required=False,
        help='Directory to store reference RTTM files')
    parser.add_argument(
        '--backend', default="AHC", help='type of backend, AHC or SC or kmeans')
    parser.add_argument(
        '--oracle_n_spkrs',
        default=True,
        type=strtobool,
        help='Oracle num of speakers')
    parser.add_argument(
        '--mic_type',
        default="Mix-Headset",
        help='Type of microphone to be used')
    parser.add_argument(
        '--affinity', default="cos", help='affinity matrix, cos or nn')
    parser.add_argument(
        '--max_subseg_dur',
        default=3.0,
        type=float,
        help='Duration in seconds of a subsegments to be prepared from larger segments'
    )
    parser.add_argument(
        '--overlap',
        default=1.5,
        type=float,
        help='Overlap duration in seconds between adjacent subsegments')

    args = parser.parse_args()

    pval = 0.3
    rec_id = "utt0001"
    n_neighbors = 10
    out_rttm_file = "./out.rttm"

    embeddings = np.empty(shape=[0, 32], dtype=np.float64)
    segset = []

    for i in range(10):
        seg = [rec_id + "_" + str(i) + "_" + str(i + 1)]
        segset = segset + seg
        emb = np.random.rand(1, 32)
        embeddings = np.concatenate((embeddings, emb), axis=0)

    segset = np.array(segset, dtype="|O")
    stat_obj = EmbeddingMeta(segset, embeddings)
    if args.oracle_n_spkrs is True:
        num_spkrs = 2

    if args.backend == "SC":
        print("begin SC ")
        do_spec_clustering(
            stat_obj,
            out_rttm_file,
            rec_id,
            num_spkrs,
            pval,
            args.affinity,
            n_neighbors, )
    if args.backend == "AHC":
        print("begin AHC ")
        do_AHC(stat_obj, out_rttm_file, rec_id, num_spkrs, pval)