How to use the pyglm.components.component.Component function in pyglm

return self._log_p

    def get_variables(self):
        """ Get the theano variables associated with this model.
        """
        return {'A' : self.A}


    def sample(self, acc):
        N = self.model['N']
        A = np.random.rand(N, N) < self.rho
        A = A.astype(np.int)
        return {'A' : A}


class StochasticBlockGraphModel(Component):
    def __init__(self, model, latent):
        """ Initialize the stochastic block model for the adjacency matrix
        """
        self.model = model
        self.latent = latent
        self.prms = model['network']['graph']
        self.N = model['N']

        # Get the number of latent types (R) and the latent type vector (Y)
        self.type_name = self.prms['types']
        self.R = self.latent[self.type_name].R
        self.Y = self.latent[self.type_name].Y

        # A RxR matrix of connection probabilities per pair of clusters
        self.B = T.dmatrix('B')

nT,Ns = data["S"].shape
        assert Ns == self.N, "ERROR: Spike train must be (TxN) " \
                             "dimensional where N=%d" % self.N
        fS = convolve_with_basis(data["S"], ibasis)

        # Flatten this manually to be safe
        # (there's surely a way to do this with numpy)
        (nT,Nc,B) = fS.shape
        assert Nc == self.N, "ERROR: Convolution with spike train " \
                             "resulted in incorrect shape: %s" % str(fS.shape)
        data['fS'] = fS

    def set_data(self, data):
        self.ir.set_value(data['fS'])

class DirichletImpulses(Component):
    """ Normalized impulse response functions using a Dirichlet prior.
        Here we separate out the parameters of each impulse response
        so that they may be sampled separately.
    """
    def __init__(self, model):
        self.model = model
        self.imp_model = model['impulse']

        # Number of presynaptic neurons
        self.N = model['N']

        # Get parameters of the prior
        self.alpha = self.imp_model['alpha']

        # Create a basis for the impulse responses response
        self.basis = create_basis(self.imp_model['basis'])

def set_hyperparameters(self, model):
        """ Set the hyperparameters of the model
        """
        # TODO Fix me
        self.mu.set_value(model['mu'])
        self.sigma.set_value(model['sigma'])

    def sample(self, acc):
        """ Sample from the prior
                """
        # TODO Use size
        v = self.mu.get_value() + self.sigma.get_value() * np.random.randn(self.D)
        return {str(self.value): v}

class GroupLasso(Component):
    """ Wrapper for a scalar random variable with a Normal distribution
    """
    def __init__(self, model, name='gaussian'):
        self.prms = model
        self.lam = theano.shared(name='lam', value=self.prms['lam'])
        self.mu = theano.shared(name='mu', value=self.prms['mu'])
        self.sigma = theano.shared(name='sigma', value=self.prms['sigma'])
    
    def log_p(self, value):
        """ Compute log prob of the given value under this prior
            Value should be NxB where N is the number of groups and
            B is the number of parameters per group.
        """
        return -1.0*self.lam * T.sum(T.sqrt(T.sum(((value-self.mu)/self.sigma)**2, axis=1)))

type = model['bkgd']['type'].lower()
    if type == 'no_stimulus' or \
       type == 'none' or \
       type == 'nostimulus':
       bkgd = NoStimulus(model)
    elif type == 'basis':
        bkgd = BasisStimulus(model)
    elif type == 'spatiotemporal':
        bkgd = SpatiotemporalStimulus(model)
    elif type == 'sharedtuningcurve':
        bkgd = SharedTuningCurveStimulus(model, glm, latent)
    else:
        raise Exception("Unrecognized backgound model: %s" % type)
    return bkgd

class NoStimulus(Component):
    """ No stimulus dependence. Constant biases are handled by the 
        bias component. 
    """

    def __init__(self, model):
        """ No stimulus.
        """        
        # Log probability
        self.log_p = T.constant(0.0)

        # Due a theano quirk, I_stim cannot directly be a constant
        self.stim = T.constant(0.0)
        # Expose outputs to the Glm class
        self.I_stim = T.dot(T.constant(1.0), self.stim)
    
class BasisStimulus(Component):

lp += -np.Inf * T.lt(value, self.min)
        lp += -np.Inf * T.gt(value, self.max)
        lp += self.p[value]
        return lp

    def get_variables(self):
        return {}

    def sample(self, acc, size=(1,)):
        """ Sample from the prior
        """
        v = np.random.choice(self.p, size=size)
        return v


class JointCategorical(Component):
    """
    Wrapper for a discrete random variable from a product distribution of
    two categorical distributions.
    """
    def __init__(self, model):
        self.prms = model
        self.p0 = theano.shared(name='p0', value=self.prms['p0'])
        self.p1 = theano.shared(name='p1', value=self.prms['p1'])
        self.min0 = self.prms['min0']
        self.max0 = self.prms['max0']
        self.min1 = self.prms['min1']
        self.max1 = self.prms['max1']

    def ravel_index(self, value):
        return (self.max1-self.min1+1)*(value[0]-self.min0) + (value[1]-self.min1)

return JointCategorical(model, **kwargs)
    elif typ == 'spherical_gaussian':
        return SphericalGaussian(model, **kwargs)
    elif typ == 'group_lasso' or \
         typ == 'grouplasso':
        return GroupLasso(model, **kwargs)
    elif typ == 'dpp':
        return DeterminenalPointProcess(model, **kwargs)
    elif typ == 'dirichlet':
        return Dirichlet(model)
    else:
        raise Exception("Unrecognized prior type: %s" % typ)



class Categorical(Component):
    """ Wrapper for a discrete random variable from a Categorical distribution
    """
    def __init__(self, model):
        self.prms = model
        self.p = theano.shared(name='p', value=self.prms['p'])
        self.min = self.prms['min']
        self.max = self.prms['max']

    def ravel_index(self,value):
        return value - self.min

    def log_p(self, value):
        """ Compute log prob of the given value under this prior
        """
        lp = T.constant(0.)
        lp += -np.Inf * T.lt(value, self.min)

B = np.random.beta(self.b0, self.b1, (self.R, self.R))

        # We need a sample of Y in order to evaluate pA!
        Y = acc['latent'][self.type_name]['Y']
        pA = self.pA.eval({self.B: B})

        A = np.random.rand(N, N) < pA
        A = A.astype(np.int8)
        return {str(self.A): A,
                str(self.B): B}

    def get_state(self):
        return {str(self.A): self.A,
                str(self.B): self.B}

class LatentDistanceGraphModel(Component):
    def __init__(self, model, latent):
        """ Initialize the stochastic block model for the adjacency matrix
        """
        self.model = model
        self.prms = model['network']['graph']
        self.N = model['N']
        self.N_dims = self.prms['N_dims']

        # Get the latent location
        self.location = latent[self.prms['locations']]
        self.Lm = self.location.Lm
        # self.location_prior = create_prior(self.prms['location_prior'])
        #
        # # Latent distance model has NxR matrix of locations L
        # self.L = T.dvector('L')
        # self.Lm = T.reshape(self.L, (self.N, self.N_dims))

def set_hyperparameters(self, model):
        """ Set the hyperparameters of the model
        """
        self.mu.set_value(model['mu'])
        self.sigma.set_value(model['sigma'])

    def sample(self, acc, size=(1,)):
        """ Sample from the prior
                """
        v = self.mu.get_value() + self.sigma.get_value() * np.random.randn(*size)

        return v

class SphericalGaussian(Component):
    """ Wrapper for a vector random variable with a spherical distribution
    """
    def __init__(self, model, name='spherical_gaussian', D=1):
        self.prms = model
        self.D = D
        self.value = T.dvector(name=name)
        self.mu = theano.shared(name='mu', value=self.prms['mu'])
        self.sigma = theano.shared(name='sigma', value=self.prms['sigma'])
        self.log_p = -0.5/self.sigma**2 *T.sum((self.value-self.mu)**2)

    def get_variables(self):
        return {str(self.value): self.value}

    def set_hyperparameters(self, model):
        """ Set the hyperparameters of the model
        """

graph = LatentDistanceGraphModel(model, latent)
    else:
        raise Exception("Unrecognized graph model: %s" % type)
    return graph

def create_kayak_graph_component(model, latent):
    type = model['network']['graph']['type'].lower()
    if type == 'complete':
        graph = KayakCompleteGraphModel(model)
    elif type == 'erdos_renyi' or \
         type == 'erdosrenyi':
        graph = KayakErdosRenyiGraphModel(model)
    return graph


class _GraphModelBase(Component):
    @property
    def A(self):
        raise NotImplementedError()

    def get_state(self):
        return {'A': self.A}

class TheanoCompleteGraphModel(_GraphModelBase):
    def __init__(self, model):
        """ Initialize the filtered stim model
        """
        self.model = model
        N = model['N']

        # Define complete adjacency matrix
        self._A = T.ones((N, N))

""" Initialize the component with the parameters from the given model,
        the vector of symbolic variables, vars, and the offset into that vector, offset.
        """
        self._log_p = T.constant(0.)

    @property
    def log_p(self):
        return self._log_p

    def nlin(self, x):
        return T.log(1.0+T.exp(x))

    def f_nlin(self, x):
        return np.log(1.0 + np.exp(x))

class KayakExpLinearNonlinearity(Component):
    """ Exponential nonlinearity (\lambda=e^x) for x<0,
        Linear (\lambda=1+x) for x>0.
        This is nice because it satisfies a Lipschitz bound of 1.
    """

    def __init__(self, model):
        """ Initialize the component with the parameters from the given model,
        the vector of symbolic variables, vars, and the offset into that vector, offset.
        """
        self._log_p = kyk.Constant(0.)

    @property
    def log_p(self):
        return self._log_p

    def nlin(self, x):