python类toeplitz()的实例源码

def lpfls(N,wp,ws,W):
    M = (N-1)/2
    nq = np.arange(0,2*M+1)
    nb = np.arange(0,M+1)
    q = (wp/np.pi)*np.sinc((wp/np.pi)*nq) - W*(ws/np.pi)*np.sinc((ws/np.pi)*nq)
    b = (wp/np.pi)*np.sinc((wp/np.pi)*nb)
    b[0] = wp/np.pi
    q[0] = wp/np.pi + W*(1-ws/np.pi) # since sin(pi*n)/pi*n = 1, not 0
    b = b.transpose()

    Q1 = ln.toeplitz(q[0:M+1])
    Q2 = ln.hankel(q[0:M+1],q[M:])
    Q = Q1+Q2

    a = ln.solve(Q,b)
    h = list(nq)
    for i in nb:
        h[i] = 0.5*a[M-i]
        h[N-1-i] = h[i]
    h[M] = 2*h[M]
    hmax = max(np.absolute(h))
    for i in nq:
        h[i] = (8191/hmax)*h[i]
    return h

def bpfls(N,ws1,wp1,wp2,ws2,W):
    M = (N-1)/2
    nq = np.arange(0,2*M+1)
    nb = np.arange(0,M+1)
    q = W*np.sinc(nq) - (W*ws2/np.pi) * np.sinc(nq* (ws2/np.pi)) + (wp2/np.pi) * np.sinc(nq*(wp2/np.pi)) - (wp1/np.pi) * np.sinc(nq*(wp1/np.pi)) + (W*ws1/np.pi) * np.sinc(nq*(ws1/np.pi))
    b = (wp2/np.pi)*np.sinc((wp2/np.pi)*nb) - (wp1/np.pi)*np.sinc((wp1/np.pi)*nb)
    b[0] = wp2/np.pi - wp1/np.pi
    q[0] = W - W*ws2/np.pi + wp2/np.pi - wp1/np.pi + W*ws1/np.pi # since sin(pi*n)/pi*n = 1, not 0
    b = b.transpose()

    Q1 = ln.toeplitz(q[0:M+1])
    Q2 = ln.hankel(q[0:M+1],q[M:])
    Q = Q1+Q2

    a = ln.solve(Q,b)
    h = list(nq)
    for i in nb:
        h[i] = 0.5*a[M-i]
        h[N-1-i] = h[i]
    h[M] = 2*h[M]
    hmax = max(np.absolute(h))
    for i in nq:
        h[i] = (8191/hmax)*h[i]
    return h

def hpfls(N,ws,wp,W):
    M = (N-1)/2
    nq = np.arange(0,2*M+1)
    nb = np.arange(0,M+1)
    b = 1 - (wp/np.pi)* np.sinc(nb * wp/np.pi)
    b[0] = 1- wp/np.pi
    q = 1 - (wp/np.pi)* np.sinc(nq * wp/np.pi) + W * (ws/np.pi) * np.sinc(nq * ws/np.pi) # since sin(pi*n)/pi*n = 1, not 0
    q[0] = b[0] + W* ws/np.pi
    b = b.transpose()

    Q1 = ln.toeplitz(q[0:M+1])
    Q2 = ln.hankel(q[0:M+1],q[M:])
    Q = Q1+Q2

    a = ln.solve(Q,b)
    h = list(nq)
    for i in nb:
        h[i] = 0.5*a[M-i]
        h[N-1-i] = h[i]
    h[M] = 2*h[M]
    hmax = max(np.absolute(h))
    for i in nq:
        h[i] = (8191/hmax)*h[i]
    return h

def corrmtx(x,m):
    """
    from https://github.com/cokelaer/spectrum/
    like matlab corrmtx(x,'mod'), with a different normalization factor.
    """
    x = np.asarray(x, dtype=float)
    assert x.ndim == 1, '1-D only'

    N = x.size

    Tp = toeplitz(x[m:N], x[m::-1])

    C = np.zeros((2*(N-m), m+1), dtype=x.dtype)

    for i in range(0, N-m):
        C[i] = Tp[i]

    Tp = np.fliplr(Tp.conj())
    for i in range(N-m, 2*(N-m)):
        C[i] = Tp[i-N+m]

    return C

def aryule(c, k):
    """Solve Yule-Walker equation.

    Args:
        c (numpy array): Coefficients (i.e. autocorrelation)
        k (int): Assuming the AR(k) model

    Returns:
        numpy array: k model parameters
            Some formulations solve: C a = -c,
            but we actually solve C a = c.

    """
    a = np.zeros(k)

    # ignore a singular matrix
    C = toeplitz(c[:k])
    if not np.all(C == 0.0) and np.isfinite(ln.cond(C)):
        a = np.dot(ln.inv(C), c[1:])

    return a

def toepz(self):
        cormat = np.zeros((self.nkdim, self.nkdim))

        epsilon = (1 - np.max(self.rho)) / (1 + np.max(self.rho)) - .01

        for i in np.arange(self.k):
            t = np.insert(np.power(self.rho[i], np.arange(1, self.nk[i])), 0, 1)
            cor = toeplitz(t)
            if i == 0:
                cormat[0:self.nk[0], 0:self.nk[0]] = cor
            if i != 0:
                cormat[np.sum(self.nk[0:i]):np.sum(self.nk[0:i + 1]),
                np.sum(self.nk[0:i]):np.sum(self.nk[0:i + 1])] = cor

        np.fill_diagonal(cormat, 1 - epsilon)

        cormat = self._generate_noise(cormat, self.nkdim, self.M, epsilon)

        return cormat

def hub(self):
        cormat = np.zeros((self.nkdim, self.nkdim))

        for i in np.arange(self.k):
            cor = toeplitz(self._fill_hub_matrix(self.rho[i,0],self.rho[i,1], self.power, self.nk[i]))
            if i == 0:
                cormat[0:self.nk[0], 0:self.nk[0]] = cor
            if i != 0:
                cormat[np.sum(self.nk[0:i]):np.sum(self.nk[0:i + 1]),
                np.sum(self.nk[0:i]):np.sum(self.nk[0:i + 1])] = cor
            tau = (np.max(self.rho[i]) - np.min(self.rho[i])) / (self.nk[i] - 2)

        epsilon = 0.08 #(1 - np.min(rho) - 0.75 * np.min(tau)) - 0.01

        np.fill_diagonal(cormat, 1 - epsilon)

        cormat = self._generate_noise(cormat, self.nkdim, self.M, epsilon)

        return cormat

def aryule(c, k):
    """Solve Yule-Walker equation.

    Args:
        c (numpy array): Coefficients (i.e. autocorrelation)
        k (int): Assuming the AR(k) model

    Returns:
        numpy array: k model parameters
            Some formulations solve: C a = -c,
            but we actually solve C a = c.

    """
    a = np.zeros(k)

    # ignore a singular matrix
    C = toeplitz(c[:k])
    if not np.all(C == 0.0) and np.isfinite(ln.cond(C)):
        a = np.dot(ln.inv(C), c[1:])

    return a

def lpfls2notch(N,wp,ws,wn1,wn2,W):
    M = (N-1)/2
    nq = np.arange(0,2*M+1)
    nb = np.arange(0,M+1)
    q = (wp/np.pi)*np.sinc((wp/np.pi)*nq) - W*(ws/np.pi)*np.sinc((ws/np.pi)*nq)
    b = (wp/np.pi)*np.sinc((wp/np.pi)*nb)
    q[0] = wp/np.pi + W*(1-ws/np.pi) # since sin(pi*n)/pi*n = 1, not 0
    b = np.asmatrix(b)
    b = b.transpose()

    Q1 = ln.toeplitz(q[0:M+1])
    Q2 = ln.hankel(q[0:M+1],q[M:])
    Q = Q1+Q2

    G1 = np.cos(wn1*nb)
    G2 = np.cos(wn2*nb)
    G = np.matrix([G1,G2])

    d = np.array([0,0])
    d = np.asmatrix(d)
    d = d.transpose()

    c = np.asmatrix(ln.solve(Q,b))

    mu = ln.solve(G*ln.inv(Q)*G.transpose(),G*c - d)

    a = c - ln.solve(Q,G.transpose()*mu)
    h = np.zeros(N)
    for i in nb:
        h[i] = 0.5*a[M-i]
        h[N-1-i] = h[i]
    h[M] = 2*h[M]
    hmax = max(np.absolute(h))
    for i in nq:
        h[i] = (8191/hmax)*h[i]
    return h

def lpfls1notch(N,wp,ws,wn1,W):
    M = (N-1)/2
    nq = np.arange(0,2*M+1)
    nb = np.arange(0,M+1)
    q = (wp/np.pi)*np.sinc((wp/np.pi)*nq) - W*(ws/np.pi)*np.sinc((ws/np.pi)*nq)
    b = (wp/np.pi)*np.sinc((wp/np.pi)*nb)
    q[0] = wp/np.pi + W*(1-ws/np.pi) # since sin(pi*n)/pi*n = 1, not 0
    b = np.asmatrix(b)
    b = b.transpose()

    Q1 = ln.toeplitz(q[0:M+1])
    Q2 = ln.hankel(q[0:M+1],q[M:])
    Q = Q1+Q2

    G1 = np.cos(wn1*nb)
    G = np.matrix([G1])

    d = np.array([0])
    d = np.asmatrix(d)

    c = np.asmatrix(ln.solve(Q,b))

    mu = ln.solve(G*ln.inv(Q)*G.transpose(),G*c - d)

    a = c - ln.solve(Q,G.transpose()*mu)
    h = np.zeros(N)
    for i in nb:
        h[i] = 0.5*a[M-i]
        h[N-1-i] = h[i]
    h[M] = 2*h[M]
    hmax = max(np.absolute(h))
    for i in nq:
        h[i] = (8191/hmax)*h[i]
    return h

def solve_random_qp(n, solver):
    M, b = random.random((n, n)), random.random(n)
    P, q = dot(M.T, M), dot(b, M).reshape((n,))
    G = toeplitz([1., 0., 0.] + [0.] * (n - 3), [1., 2., 3.] + [0.] * (n - 3))
    h = ones(n)
    return solve_qp(P, q, G, h, solver=solver)

def damped_lstsq(a,b,damping=1.0,plot=False,return_G=False):
    '''
    Gm = d
       G : discrete convolution matrix
       m : signal we are trying to recover (receiver function)
       d : the convolved data (signal a)

       m = (G^T G)^(-1)G^T * d
    '''

    #build G
    padding = np.zeros(a.shape[0] - 1, a.dtype)
    first_col = np.r_[a, padding]
    first_row = np.r_[a[0], padding]
    G = toeplitz(first_col, first_row)

    #reshape b
    shape = G.shape
    shape = shape[0]
    len_b = len(b)
    zeros = np.zeros((shape-len_b))
    b = np.append(b,zeros)

    #solve system (use either lsmr or scipy solve)
    #sol = lsmr(G,b,damp=damping)
    sol = np.linalg.solve(G+damping*np.eye(G.shape[0]),b,overwrite_a=False,overwrite_b=False)
    m_est = sol[0]
    rf = m_est

    if plot==True:
       fig,axes = plt.subplots(3,sharex=True)
       axes[0].plot(a)
       axes[1].plot(b)
       axes[2].plot(rf)
       plt.show()

    if return_G==True:
       return G
    else:
       return rf

def damped_lstsq(a,b,damping=1.0,plot=False):
    '''
    Gm = d
       G : discrete convolution matrix
       m : signal we are trying to recover (receiver function)
       d : the convolved data (signal a)

       m = (G^T G)^(-1)G^T * d
    '''

    #build G
    padding = np.zeros(a.shape[0] - 1, a.dtype)
    first_col = np.r_[a, padding]
    first_row = np.r_[a[0], padding]
    G = toeplitz(first_col, first_row)

    #reshape b
    shape = G.shape
    shape = shape[0]
    len_b = len(b)
    zeros = np.zeros((shape-len_b))
    b = np.append(b,zeros)

    #solve with scipy.sparse.linalg.lsmr
    sol = lsmr(G,b,damp=damping)
    m_est = sol[0]
    rf = m_est

    if plot==True:
       fig,axes = plt.subplots(3,sharex=True)
       axes[0].plot(a)
       axes[1].plot(b)
       axes[2].plot(rf)
       plt.show()

    return rf

def damped_lstsq(a,b,damping=1.0,plot=False):
    '''
    Gm = d
       G : discrete convolution matrix
       m : signal we are trying to recover (receiver function)
       d : the convolved data (signal a)

       m = (G^T G)^(-1)G^T * d
    '''

    #build G
    padding = np.zeros(a.shape[0] - 1, a.dtype)
    first_col = np.r_[a, padding]
    first_row = np.r_[a[0], padding]
    G = toeplitz(first_col, first_row)

    #reshape b
    shape = G.shape
    shape = shape[0]
    len_b = len(b)
    zeros = np.zeros((shape-len_b))
    b = np.append(b,zeros)

    #solve with scipy.sparse.linalg.lsmr
    sol = lsmr(G,b,damp=damping)
    m_est = sol[0]
    rf = m_est

    if plot==True:
       fig,axes = plt.subplots(3,sharex=True)
       axes[0].plot(a)
       axes[1].plot(b)
       axes[2].plot(rf)
       plt.show()

    return rf

def generate_data(n_samples, n_features, size_groups, rho=0.5,
                  random_state=24):
    """ Data generation process with Toplitz like correlated features:
        this correspond to the synthetic dataset used in our paper
        "GAP Safe Screening Rules for Sparse-Group Lasso".

    """

    rng = check_random_state(random_state)
    n_groups = len(size_groups)
    # g_start = np.zeros(n_groups, order='F', dtype=np.intc)
    # for i in range(1, n_groups):
    #     g_start[i] = size_groups[i - 1] + g_start[i - 1]
    g_start = np.cumsum(size_groups, dtype=np.intc) - size_groups[0]

    # 10% of groups are actives
    gamma1 = int(np.ceil(n_groups * 0.1))
    selected_groups = rng.random_integers(0, n_groups - 1, gamma1)
    true_beta = np.zeros(n_features)

    for i in selected_groups:

        begin = g_start[i]
        end = g_start[i] + size_groups[i]
        # 10% of features are actives
        gamma2 = int(np.ceil(size_groups[i] * 0.1))
        selected_features = rng.random_integers(begin, end - 1, gamma2)

        ns = len(selected_features)
        s = 2 * rng.rand(ns) - 1
        u = rng.rand(ns)
        true_beta[selected_features] = np.sign(s) * (10 * u + (1 - u) * 0.5)

    vect = rho ** np.arange(n_features)
    covar = toeplitz(vect, vect)

    X = rng.multivariate_normal(np.zeros(n_features), covar, n_samples)
    y = np.dot(X, true_beta) + 0.01 * rng.normal(0, 1, n_samples)

    return X, y

def Tmtx_ri(b_ri, K, D, L):
    """
    build convolution matrix associated with b_ri
    :param b_ri: a real-valued vector
    :param K: number of Diracs
    :param D1: expansion matrix for the real-part
    :param D2: expansion matrix for the imaginary-part
    :return:
    """
    b_ri = np.dot(D, b_ri)
    b_r = b_ri[:L]
    b_i = b_ri[L:]
    Tb_r = linalg.toeplitz(b_r[K:], b_r[K::-1])
    Tb_i = linalg.toeplitz(b_i[K:], b_i[K::-1])
    return np.vstack((np.hstack((Tb_r, -Tb_i)), np.hstack((Tb_i, Tb_r))))

def Rmtx_ri(coef_ri, K, D, L):
    coef_ri = np.squeeze(coef_ri)
    coef_r = coef_ri[:K + 1]
    coef_i = coef_ri[K + 1:]
    R_r = linalg.toeplitz(np.concatenate((np.array([coef_r[-1]]),
                                          np.zeros(L - K - 1))),
                          np.concatenate((coef_r[::-1],
                                          np.zeros(L - K - 1)))
                          )
    R_i = linalg.toeplitz(np.concatenate((np.array([coef_i[-1]]),
                                          np.zeros(L - K - 1))),
                          np.concatenate((coef_i[::-1],
                                          np.zeros(L - K - 1)))
                          )
    return np.dot(np.vstack((np.hstack((R_r, -R_i)), np.hstack((R_i, R_r)))), D)

def estimate(self, nbcorr=np.nan, numpsd=-1):
        fft_length, _ = self.check_params()
        if np.isnan((nbcorr)):
            nbcorr = self.ordar

        # -------- estimate correlation from psd
        full_psd = self.psd[numpsd]
        full_psd = np.c_[full_psd, np.conjugate(full_psd[:, :0:-1])]
        correl = fftpack.ifft(full_psd[0], fft_length, 0).real

        # -------- estimate AR part
        col1 = correl[self.ordma:self.ordma + nbcorr]
        row1 = correl[np.abs(
            np.arange(self.ordma, self.ordma - self.ordar, -1))]
        R = linalg.toeplitz(col1, row1)
        r = -correl[self.ordma + 1:self.ordma + nbcorr + 1]
        AR = linalg.solve(R, r)
        self.AR_ = AR

        # -------- estimate correlation of MA part

        # -------- estimate MA part
        if self.ordma == 0:
            sigma2 = correl[0] + np.dot(AR, correl[1:self.ordar + 1])
            self.MA = np.ones(1) * np.sqrt(sigma2)
        else:
            raise NotImplementedError(
                'arma: estimation of the MA part not yet implemented')

def least_square_evoked(epochs, return_toeplitz=False):
    """Least square estimation of evoked response from a Epochs instance.

    Parameters
    ----------
    epochs : Epochs instance
        An instance of Epochs.
    return_toeplitz : bool (default False)
        If true, compute the toeplitz matrix.

    Returns
    -------
    evokeds : dict of evoked instance
        An dict of evoked instance for each event type in epochs.event_id.
    toeplitz : dict of ndarray
        If return_toeplitz is true, return the toeplitz matrix for each event
        type in epochs.event_id.
    """
    if not isinstance(epochs, _BaseEpochs):
        raise ValueError('epochs must be an instance of `mne.Epochs`')

    events = epochs.events.copy()
    events[:, 0] -= (np.min(events[:, 0]) +
                     int(epochs.tmin * epochs.info['sfreq']))
    data = _construct_signal_from_epochs(epochs)
    evoked_data, toeplitz = _least_square_evoked(data, events, epochs.event_id,
                                                 tmin=epochs.tmin,
                                                 tmax=epochs.tmax,
                                                 sfreq=epochs.info['sfreq'])
    evokeds = dict()
    info = cp.deepcopy(epochs.info)
    for name, data in evoked_data.items():
        n_events = len(events[events[:, 2] == epochs.event_id[name]])
        evoked = EvokedArray(data, info, tmin=epochs.tmin,
                             comment=name, nave=n_events)
        evokeds[name] = evoked

    if return_toeplitz:
        return evokeds, toeplitz

    return evokeds

def roots(self):
        """
        Utilises Boyd's O(n^2) recursive subdivision algorithm. The chebfun
        is recursively subsampled until it is successfully represented to
        machine precision by a sequence of piecewise interpolants of degree
        100 or less. A colleague matrix eigenvalue solve is then applied to
        each of these pieces and the results are concatenated.
        See:
        J. P. Boyd, Computing zeros on a real interval through Chebyshev
        expansion and polynomial rootfinding, SIAM J. Numer. Anal., 40
        (2002), pp. 1666–1682.
        """
        if self.size() == 1:
            return np.array([])

        elif self.size() <= 100:
            ak = self.coefficients()
            v = np.zeros_like(ak[:-1])
            v[1] = 0.5
            C1 = linalg.toeplitz(v)
            C2 = np.zeros_like(C1)
            C1[0,1] = 1.
            C2[-1,:] = ak[:-1]
            C = C1 - .5/ak[-1] * C2
            eigenvalues = linalg.eigvals(C)
            roots = [eig.real for eig in eigenvalues
                    if np.allclose(eig.imag,0,atol=1e-10)
                        and np.abs(eig.real) <=1]
            scaled_roots = self._ui_to_ab(np.array(roots))
            return scaled_roots
        else:
            # divide at a close-to-zero split-point
            split_point = self._ui_to_ab(0.0123456789)
            return np.concatenate(
                (self.restrict([self._domain[0],split_point]).roots(),
                 self.restrict([split_point,self._domain[1]]).roots())
            )

    # ----------------------------------------------------------------
    # Interpolation and evaluation (go from values to coefficients)
    # ----------------------------------------------------------------

def _create_Toeplitz(data, npts_stf):
    # Desired dimensions: len(data) + npts_stf - 1 x npts_stf
    nrows = npts_stf + len(data) - 1
    data_col = data
    first_col = np.r_[data_col,
                      np.zeros(nrows - len(data_col))]

    ncols = npts_stf
    first_row = np.r_[data[0], np.zeros(ncols - 1)]
    return toeplitz(first_col, first_row)

def pade(time,dipole):
    damp_const = 100.0
    dipole = np.asarray(dipole) - dipole[0]

    stepsize = time[1] - time[0]
    #print dipole
    damp = np.exp(-(stepsize*np.arange(len(dipole)))/float(damp_const))
    dipole *= damp
    M = len(dipole)
    N = int(np.floor(M / 2))

    #print "N = ", N
    num_pts = 20000
    if N > num_pts:
        N = num_pts
    #print "Trimmed points to: ", N

    # G and d are (N-1) x (N-1)
    # d[k] = -dipole[N+k] for k in range(1,N)
    d = -dipole[N+1:2*N]

    try:
        from scipy.linalg import toeplitz, solve_toeplitz
    except ImportError:
        print("You'll need SciPy version >= 0.17.0")

    try:
        # Instead, form G = (c,r) as toeplitz
        #c = dipole[N:2*N-1]
        #r = np.hstack((dipole[1],dipole[N-1:1:-1]))
        b = solve_toeplitz((dipole[N:2*N-1],\
            np.hstack((dipole[1],dipole[N-1:1:-1]))),d,check_finite=False)
    except np.linalg.linalg.LinAlgError:  
        # OLD CODE: sometimes more stable
        # G[k,m] = dipole[N - m + k] for m,k in range(1,N)
        G = dipole[N + np.arange(1,N)[:,None] - np.arange(1,N)]
        b = np.linalg.solve(G,d)

    # Now make b Nx1 where b0 = 1
    b = np.hstack((1,b))

    # b[m]*dipole[k-m] for k in range(0,N), for m in range(k)
    a = np.dot(np.tril(toeplitz(dipole[0:N])),b)
    p = np.poly1d(a)
    q = np.poly1d(b)

    # If you want energies greater than 2*27.2114 eV, you'll need to change
    # the default frequency range to something greater.

    #frequency = np.arange(0.00,2.0,0.00005)
    frequency = np.arange(0.3,0.75,0.0002)

    W = np.exp(-1j*frequency*stepsize)

    fw = p(W)/q(W)

    return fw, frequency

def _project(reference_sources, estimated_source, flen):
    """Least-squares projection of estimated source on the subspace spanned by
    delayed versions of reference sources, with delays between 0 and flen-1
    """
    nsrc = reference_sources.shape[0]
    nsampl = reference_sources.shape[1]

    # computing coefficients of least squares problem via FFT ##
    # zero padding and FFT of input data
    reference_sources = np.hstack((reference_sources,
                                   np.zeros((nsrc, flen - 1))))
    estimated_source = np.hstack((estimated_source, np.zeros(flen - 1)))
    n_fft = int(2**np.ceil(np.log2(nsampl + flen - 1.)))
    sf = scipy.fftpack.fft(reference_sources, n=n_fft, axis=1)
    sef = scipy.fftpack.fft(estimated_source, n=n_fft)
    # inner products between delayed versions of reference_sources
    G = np.zeros((nsrc * flen, nsrc * flen))
    for i in range(nsrc):
        for j in range(nsrc):
            ssf = sf[i] * np.conj(sf[j])
            ssf = np.real(scipy.fftpack.ifft(ssf))
            ss = toeplitz(np.hstack((ssf[0], ssf[-1:-flen:-1])),
                          r=ssf[:flen])
            G[i * flen: (i+1) * flen, j * flen: (j+1) * flen] = ss
            G[j * flen: (j+1) * flen, i * flen: (i+1) * flen] = ss.T
    # inner products between estimated_source and delayed versions of
    # reference_sources
    D = np.zeros(nsrc * flen)
    for i in range(nsrc):
        ssef = sf[i] * np.conj(sef)
        ssef = np.real(scipy.fftpack.ifft(ssef))
        D[i * flen: (i+1) * flen] = np.hstack((ssef[0], ssef[-1:-flen:-1]))

    # Computing projection
    # Distortion filters
    try:
        C = np.linalg.solve(G, D).reshape(flen, nsrc, order='F')
    except np.linalg.linalg.LinAlgError:
        C = np.linalg.lstsq(G, D)[0].reshape(flen, nsrc, order='F')
    # Filtering
    sproj = np.zeros(nsampl + flen - 1)
    for i in range(nsrc):
        sproj += fftconvolve(C[:, i], reference_sources[i])[:nsampl + flen - 1]
    return sproj

def estimate_time_constant(Y, sn, p = None, lags = 5, include_noise = False, pixels = None):
    """
    Estimating global time constants for the dataset Y through the autocovariance function (optional).
    The function is no longer used in the standard setting of the algorithm since every trace has its own
    time constant.
    Inputs:
    Y: np.ndarray (2D)
        input movie data with time in the last axis
    p: positive integer
        order of AR process, default: 2
    lags: positive integer
        number of lags in the past to consider for determining time constants. Default 5
    include_noise: Boolean
        Flag to include pre-estimated noise value when determining time constants. Default: False
    pixels: np.ndarray
        Restrict estimation to these pixels (e.g., remove saturated pixels). Default: All pixels

    Output:
    g:  np.ndarray (p x 1)
        Discrete time constants
    """
    if p is None:
        raise Exception("You need to define p")

    if pixels is None:
        pixels = np.arange(np.size(Y)/np.shape(Y)[-1])

    from scipy.linalg import toeplitz

    npx = len(pixels)
    g = 0
    lags += p
    XC = np.zeros((npx,2*lags+1))
    for j in range(npx):
        XC[j,:] = np.squeeze(axcov(np.squeeze(Y[pixels[j],:]),lags))

    gv = np.zeros(npx*lags)
    if not include_noise:
        XC = XC[:,np.arange(lags-1,-1,-1)]
        lags -= p

    A = np.zeros((npx*lags,p))
    for i in range(npx):
        if not include_noise:
            A[i*lags+np.arange(lags),:] = toeplitz(np.squeeze(XC[i,np.arange(p-1,p+lags-1)]),np.squeeze(XC[i,np.arange(p-1,-1,-1)]))
        else:
            A[i*lags+np.arange(lags),:] = toeplitz(np.squeeze(XC[i,lags+np.arange(lags)]),np.squeeze(XC[i,lags+np.arange(p)])) - (sn[i]**2)*np.eye(lags,p)
            gv[i*lags+np.arange(lags)] = np.squeeze(XC[i,lags+1:])

    if not include_noise:
        gv = XC[:,p:].T
        gv = np.squeeze(np.reshape(gv,(np.size(gv),1),order='F'))

    g = np.dot(np.linalg.pinv(A),gv)

    return g

def solve_unit_norm_dual(lhs, rhs, lambd0, factr=1e7, debug=False,
                         lhs_is_toeplitz=False):
    if np.all(rhs == 0):
        return np.zeros(lhs.shape[0]), 0.

    n_atoms = lambd0.shape[0]
    n_times_atom = lhs.shape[0] // n_atoms

    # precompute SVD
    # U, s, V = linalg.svd(lhs)

    if lhs_is_toeplitz:
        # first column of the toeplitz matrix lhs
        lhs_c = lhs[0, :]

        # lhs will not stay toeplitz if we add different lambd on the diagonal
        assert n_atoms == 1

        def x_star(lambd):
            lambd += 1e-14  # avoid numerical issues
            # lhs_inv = np.dot(V.T / (s + np.repeat(lambd, n_times_atom)), U.T)
            # return np.dot(lhs_inv, rhs)
            lhs_c_copy = lhs_c.copy()
            lhs_c_copy[0] += lambd
            return linalg.solve_toeplitz(lhs_c_copy, rhs)

    else:

        def x_star(lambd):
            lambd += 1e-14  # avoid numerical issues
            # lhs_inv = np.dot(V.T / (s + np.repeat(lambd, n_times_atom)), U.T)
            # return np.dot(lhs_inv, rhs)
            return linalg.solve(lhs + np.diag(np.repeat(lambd, n_times_atom)),
                                rhs)

    def dual(lambd):
        x_hats = x_star(lambd)
        norms = linalg.norm(x_hats.reshape(-1, n_times_atom), axis=1)
        return (x_hats.T.dot(lhs).dot(x_hats) - 2 * rhs.T.dot(x_hats) + np.dot(
            lambd, norms ** 2 - 1.))

    def grad_dual(lambd):
        x_hats = x_star(lambd).reshape(-1, n_times_atom)
        return linalg.norm(x_hats, axis=1) ** 2 - 1.

    def func(lambd):
        return -dual(lambd)

    def grad(lambd):
        return -grad_dual(lambd)

    bounds = [(0., None) for idx in range(0, n_atoms)]
    if debug:
        assert optimize.check_grad(func, grad, lambd0) < 1e-5
    lambd_hats, _, _ = optimize.fmin_l_bfgs_b(func, x0=lambd0, fprime=grad,
                                              bounds=bounds, factr=factr)
    x_hat = x_star(lambd_hats)
    return x_hat, lambd_hats

def fit(self, X, Y):
        X = np.asarray(X)
        Y = np.asarray(Y)
        assert X.shape[1] == self.num_feat
        assert Y.shape[1] == self.num_pred
        assert X.shape[0] == Y.shape[0]

        # Store output minimum and maximum values
        self._output_range = np.max(Y, axis = 0) - np.min(Y, axis = 0)
        self._output_max = np.max(Y, axis = 0)
        self._output_min = np.min(Y, axis = 0)


        # Center and standardize inputs
        X  = self._center_input(X)
        X = self._standardize_input(X)
        #  Center and standardize outputs
        Y = self._center_output(Y)
        Y = self._standardize_output(Y)

        numio = self.total_io
        R =  self._covf(np.hstack((X,Y)),self.num_lags)
        PHI = np.empty((2*self.num_lags-1,numio**2), dtype = float,  order='C')

        for ii in xrange(numio):
            for jj in xrange(numio):
                PHI[:,ii+jj*numio] = np.hstack((R[jj+ii*numio,np.arange(self.num_lags-1,0,-1)], R[ii+jj*numio,:]))

        Nxxr = np.arange(self.num_lags-1, 2*(self.num_lags-1)+1,1)
        Nxxc = np.arange(self.num_lags-1,-1,-1)
        Nxy = np.arange(self.num_lags-1, 2*(self.num_lags-1)+1)


        # Solve matrix equations to identify filters
        PX = np.empty((self.num_feat*self.num_lags,self.num_feat*self.num_lags), dtype=float, order='C')
        for ii in xrange(self.num_feat):
            for jj in xrange(self.num_feat):
                c_start = ii*self.num_lags
                c_end = (ii+1)*self.num_lags
                r_start = jj*self.num_lags
                r_end = (jj+1)*self.num_lags
                PX[r_start:r_end,c_start:c_end] = toeplitz(PHI[Nxxc,ii+(jj)*numio],PHI[Nxxr,ii+(jj)*numio])

        PXY = np.empty((self.num_feat*self.num_lags, self.num_pred), dtype=float, order='C')
        for ii in xrange(self.num_feat):
            for jj in xrange(self.num_feat,self.num_feat+self.num_pred,1):
                r_start = ii*self.num_lags
                r_end = (ii+1)*self.num_lags
                c_ind = jj-self.num_feat
                PXY[r_start:r_end,c_ind] = PHI[Nxy,ii+(jj)*numio]

        self.H = np.linalg.solve((PX + self.reg_lambda*np.ones_like(PX)), PXY)

def _least_square_evoked(data, events, event_id, tmin, tmax, sfreq):
    """Least square estimation of evoked response from data.

    Parameters
    ----------
    data : ndarray, shape (n_channels, n_times)
        The data to estimates evoked
    events : ndarray, shape (n_events, 3)
        The events typically returned by the read_events function.
        If some events don't match the events of interest as specified
        by event_id, they will be ignored.
    event_id : dict
        The id of the events to consider
    tmin : float
        Start time before event.
    tmax : float
        End time after event.
    sfreq : float
        Sampling frequency.

    Returns
    -------
    evokeds_data : dict of ndarray
        A dict of evoked data for each event type in event_id.
    toeplitz : dict of ndarray
        A dict of toeplitz matrix for each event type in event_id.
    """
    nmin = int(tmin * sfreq)
    nmax = int(tmax * sfreq)

    window = nmax - nmin
    n_samples = data.shape[1]
    toeplitz_mat = dict()
    full_toep = list()
    for eid in event_id:
        # select events by type
        ix_ev = events[:, -1] == event_id[eid]

        # build toeplitz matrix
        trig = np.zeros((n_samples, 1))
        ix_trig = (events[ix_ev, 0]) + nmin
        trig[ix_trig] = 1
        toep_mat = linalg.toeplitz(trig[0:window], trig)
        toeplitz_mat[eid] = toep_mat
        full_toep.append(toep_mat)

    # Concatenate toeplitz
    full_toep = np.concatenate(full_toep)

    # least square estimation
    predictor = np.dot(linalg.pinv(np.dot(full_toep, full_toep.T)), full_toep)
    all_evokeds = np.dot(predictor, data.T)
    all_evokeds = np.vsplit(all_evokeds, len(event_id))

    # parse evoked response
    evoked_data = dict()
    for idx, eid in enumerate(event_id):
        evoked_data[eid] = all_evokeds[idx].T

    return evoked_data, toeplitz_mat