# Author: Carlos Xavier Hernandez <cxh@stanford.edu>
# Contributors: Christian Schwantes <schwancr@gmail.com>
# Copyright (c) 2015, Stanford University and the Authors
# All rights reserved.

# -----------------------------------------------------------------------------
# Imports
# -----------------------------------------------------------------------------

from __future__ import print_function, division, absolute_import

import numpy as np

from .tica import tICA
from .kernel_approximation import LandmarkNystroem

# -----------------------------------------------------------------------------
# Code
# -----------------------------------------------------------------------------


class KernelTICA(tICA):
    """Time-structure Independent Componenent Analysis (tICA) using the kernel trick.

    The kernel trick allows one to extend a linear method (e.g. tICA) to
    include non-linear solutions.

    Parameters
    ----------
    n_components : int, None
        Number of components to keep.
    lag_time : int
        Delay time forward or backward in the input data. The time-lagged
        correlations is computed between datas X[t] and X[t+lag_time].
    shrinkage : float, default=None
        The covariance shrinkage intensity (range 0-1). If shrinkage is not
        specified (the default) it is estimated using an analytic formula
        (the Rao-Blackwellized Ledoit-Wolf estimator) introduced in [5].
    kinetic_mapping : bool, default=False
        If True, weigh the projections by the tICA eigenvalues, yielding
         kinetic distances as described in [2].
    kernel : str or callable (default='rbf')
        Kernel map to be approximated using the Nystroem approximation.
        It must be one of:
            - 'linear' : linear kernel (dot product in the input space)
            - 'poly' : polynomial kernel
            - 'rbf' : radial basis function
            - 'sigmoid' : sigmoid kernel
            - 'laplacian' : laplacian kernel
            - 'cosine' : cosine similarity kernel
            - callable : A callable should accept two arguments
            and the keyword arguments passed to this object as kernel_params,
            and should return a floating point number.
    degree : int, optional (default=3)
        Degree of the polynomial kernel. This is only used if kernel
        is 'poly'.
    gamma : float, optional (default=None)
        Kernel coefficient for 'rbf', 'poly', and 'sigmoid'. If gamma == 0.0,
        then will use 1 / n_features.
    coef0 : float, optional (default=1.)
        Independent term in 'poly' and 'sigmoid'.
    landmarks : ndarray, optional (default=None)
        Custom landmark points for the Nyostroem approximation
    stride : int, optional (default=1)
        Only sample pairs of points from the data according to this stride

    Attributes
    ----------
    components_ : array-like, shape (n_components, n_features)
        Components with maximum autocorrelation.
    offset_correlation_ : array-like, shape (n_features, n_features)
        Symmetric time-lagged correlation matrix, :math:`C=E[(x_t)^T x_{t+lag}]`.
    eigenvalues_ : array-like, shape (n_features,)
        Eigenvalues of the tICA generalized eigenproblem, in decreasing
        order.
    eigenvectors_ : array-like, shape (n_components, n_features)
        Eigenvectors of the tICA generalized eigenproblem. The vectors
        give a set of "directions" through configuration space along
        which the system relaxes towards equilibrium. Each eigenvector
        is associated with characteritic timescale
        :math:`- \frac{lag_time}{ln \lambda_i}, where :math:`lambda_i` is
        the corresponding eigenvector. See [2] for more information.
    means_ : array, shape (n_features,)
        The mean of the data along each feature
    n_observations_ : int
        Total number of data points fit by the model. Note that the model
        is "reset" by calling `fit()` with new sequences, whereas
        `partial_fit()` updates the fit with new data, and is suitable for
        online learning.
    n_sequences_ : int
        Total number of sequences fit by the model. Note that the model
        is "reset" by calling `fit()` with new sequences, whereas
        `partial_fit()` updates the fit with new data, and is suitable for
         online learning.
    timescales_ : array-like, shape (n_features,)
        The implied timescales of the tICA model, given by
        -offset / log(eigenvalues)

    References
    ----------
    .. [1] Schwantes, Christian R., and Vijay S. Pande. J. Chem Theory Comput. 11.2 (2015): 600--608.
    .. [2] Noe, F. and Clementi, C. arXiv arXiv:1506.06259 [physics.comp-ph] (2015)
    """

    def __init__(self, n_components=None, lag_time=1, shrinkage=None,
                 kinetic_mapping=False, kernel='rbf', degree=3, gamma=None,
                 coef0=1., stride=1, landmarks=None, random_state=None,
                 kernel_params=None):
        self.n_components = n_components
        self.lag_time = lag_time
        self.shrinkage = shrinkage
        self.kinetic_mapping = kinetic_mapping
        self.kernel = kernel
        self.degree = degree
        self.gamma = gamma
        self.coef0 = coef0
        self.stride = 1
        self.landmarks = landmarks
        self.random_state = random_state
        self.kernel_params = kernel_params
        if kernel_params is None:
            self.kernel_params = {
                                  'kernel': self.kernel,
                                  'degree': self.degree,
                                  'gamma': self.gamma,
                                  'coef0': self.coef0,
                                  'random_state': self.random_state
                                  }
        super(KernelTICA, self).__init__(n_components=n_components,
                                         lag_time=lag_time,
                                         shrinkage=shrinkage,
                                         kinetic_mapping=kinetic_mapping)

    def _gen_landmarks(self, sequences):
        X = []
        for seq in sequences:
            u = np.arange(seq.shape[0])[self.lag_time::self.stride]
            v = np.arange(seq.shape[0])[::self.stride][:u.shape[0]]

            X.append(seq[np.unique((u, v))])

        return np.concatenate(X, axis=0)

    def fit(self, sequences, y=None):
        if self.landmarks is None:
            self.landmarks = self._gen_landmarks(sequences)
        self._nystroem = LandmarkNystroem(landmarks=self.landmarks,
                                          **self.kernel_params)
        ksequences = self._nystroem.fit_transform(sequences)

        super(KernelTICA, self).fit(ksequences, y=y)

    def partial_fit(self, X):
        if self.landmarks is None:
            self.landmarks = self._gen_landmarks([X])
        if self._nystroem is None:
            self._nystroem = LandmarkNystroem(landmarks=self.landmarks,
                                              **self.kernel_params)
            self._nystroem.partial_fit(X)

        Y = self._nystroem.partial_transform(X)

        super(KernelTICA, self).partial_fit(Y)

    def transform(self, sequences):
        ksequences = self._nystroem.transform(sequences)
        return super(KernelTICA, self).transform(ksequences)

@@ -5259,17 +5259,22 @@
 tride = 
-1
+stride
 %0A       

Update ktica.py