Back to msmbuilder-3.8.0

Author: bojunliu0818

msmbuilder/cluster/base.py

@@ -171,162 +171,4 @@ def partial_transform(self, X):
     def fit_transform(self, sequences, y=None):
         """Alias for fit_predict"""
         return self.fit_predict(sequences, y)
-
-# Add sample_weight for methods
-class MultiSequenceClusterMixin_update(object):
-
-    # The API for the scikit-learn Cluster object is, in fit(), that
-    # they take a single 2D array of shape (n_data_points, n_features).
-    #
-    # For clustering a collection of timeseries, we need to preserve
-    # the structure of which data_point came from which sequence. If
-    # we concatenate the sequences together, we lose that information.
-    #
-    # This mixin is basically a little "adaptor" that changes fit()
-    # so that it accepts a list of sequences. Its implementation
-    # concatenates the sequences, calls the superclass fit(), and
-    # then splits the labels_ back into the sequenced form.
-
-    _allow_trajectory = False
-
-    def fit(self, sequences, y=None, sample_weight=None):
-        """Fit the  clustering on the data
-
-        Parameters
-        ----------
-        sequences : list of array-like, each of shape [sequence_length, n_features]
-            A list of multivariate timeseries. Each sequence may have
-            a different length, but they all must have the same number
-            of features.
-
-        Returns
-        -------
-        self
-        """
-        check_iter_of_sequences(sequences, allow_trajectory=self._allow_trajectory)
-        super(MultiSequenceClusterMixin_update, self).fit(self._concat(sequences))
-
-        if hasattr(self, 'labels_'):
-            self.labels_ = self._split(self.labels_)
-
-        return self
-
-    def _concat(self, sequences):
-        self.__lengths = [len(s) for s in sequences]
-        if len(sequences) > 0 and isinstance(sequences[0], np.ndarray):
-            concat = np.ascontiguousarray(np.concatenate(sequences))
-        elif isinstance(sequences[0], md.Trajectory):
-            # if the input sequences are not numpy arrays, we need to guess
-            # how to concatenate them. this operation below works for mdtraj
-            # trajectories (which is the use case that I want to be sure to
-            # support), but in general the python container protocol doesn't
-            # give us a generic way to make sure we merged sequences
-            concat = sequences[:][0]
-            if len(sequences) > 1:
-                concat = concat.join(sequences[:][1:])
-            concat.center_coordinates()
-        else:
-            raise TypeError('sequences must be a list of numpy arrays '
-                            'or ``md.Trajectory``s')
-
-        assert sum(self.__lengths) == len(concat)
-        return concat
-
-    def _split(self, concat):
-        return [concat[cl - l: cl] for (cl, l) in zip(np.cumsum(self.__lengths), self.__lengths)]
-
-    def _split_indices(self, concat_inds):
-        """Take indices in 'concatenated space' and return as pairs
-        of (traj_i, frame_i)
-        """
-        clengths = np.append([0], np.cumsum(self.__lengths))
-        mapping = np.zeros((clengths[-1], 2), dtype=int)
-        for traj_i, (start, end) in enumerate(zip(clengths[:-1], clengths[1:])):
-            mapping[start:end, 0] = traj_i
-            mapping[start:end, 1] = np.arange(end - start)
-        return mapping[concat_inds]
-
-    def predict(self, sequences, y=None, sample_weight=None):
-        """Predict the closest cluster each sample in each sequence in
-        sequences belongs to.
-
-        In the vector quantization literature, `cluster_centers_` is called
-        the code book and each value returned by `predict` is the index of
-        the closest code in the code book.
-
-        Parameters
-        ----------
-        sequences : list of array-like, each of shape [sequence_length, n_features]
-            A list of multivariate timeseries. Each sequence may have
-            a different length, but they all must have the same number
-            of features.
-
-        Returns
-        -------
-        Y : list of arrays, each of shape [sequence_length,]
-            Index of the closest center each sample belongs to.
-        """
-        predictions = []
-        check_iter_of_sequences(sequences, allow_trajectory=self._allow_trajectory)
-        for X in sequences:
-            predictions.append(self.partial_predict(X, sample_weight))
-        return predictions
-
-    def partial_predict(self, X, y=None, sample_weight=None):
-        """Predict the closest cluster each sample in X belongs to.
-
-        In the vector quantization literature, `cluster_centers_` is called
-        the code book and each value returned by `predict` is the index of
-        the closest code in the code book.
-
-        Parameters
-        ----------
-        X : array-like shape=(n_samples, n_features)
-            A single timeseries.
-
-        Returns
-        -------
-        Y : array, shape=(n_samples,)
-            Index of the cluster that each sample belongs to
-        """
-        if isinstance(X, md.Trajectory):
-            X.center_coordinates()
-        return super(MultiSequenceClusterMixin_update, self).predict(X)
-
-    def fit_predict(self, sequences, y=None, sample_weight=None):
-        """Performs clustering on X and returns cluster labels.
-
-        Parameters
-        ----------
-        sequences : list of array-like, each of shape [sequence_length, n_features]
-            A list of multivariate timeseries. Each sequence may have
-            a different length, but they all must have the same number
-            of features.
-
-        Returns
-        -------
-        Y : list of ndarray, each of shape [sequence_length, ]
-            Cluster labels
-        """
-        if hasattr(super(MultiSequenceClusterMixin_update, self), 'fit_predict'):
-            check_iter_of_sequences(sequences, allow_trajectory=self._allow_trajectory)
-            labels = super(MultiSequenceClusterMixin_update, self).fit_predict(sequences)
-        else:
-            self.fit(sequences)
-            labels = self.predict(sequences)
-
-        if not isinstance(labels, list):
-            labels = self._split(labels)
-        return labels
-
-    def transform(self, sequences):
-        """Alias for predict"""
-        return self.predict(sequences)
-
-    def partial_transform(self, X):
-        """Alias for partial_predict"""
-        return self.partial_predict(X)
-
-    def fit_transform(self, sequences, y=None, sample_weight=None):
-        """Alias for fit_predict"""
-        return self.fit_predict(sequences, y)
+