Ejemplo n.º 1
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def invert_legendre_polynomial(wavemin,
                               wavemax,
                               ycoef,
                               xcoef,
                               sigmacoef,
                               fiber,
                               npix_y,
                               wave_of_y,
                               width=7):

    #   Wavelength array used in 'invert_legendre_polynomial'
    wave = np.linspace(wavemin, wavemax, 100)
    #   Determines value of Y, so we can know its coeficient and then its position
    y_of_wave = legval(u(wave, wavemin, wavemax), ycoef[fiber])
    coef = legfit(u(y_of_wave, 0, npix_y), wave, deg=ycoef[fiber].size)
    wave_of_y[fiber] = legval(u(np.arange(npix_y).astype(float), 0, npix_y),
                              coef)
    #   Determines wavelength intensity (x) based on Y
    x_of_y = legval(u(wave_of_y[fiber], wavemin, wavemax), xcoef[fiber])
    sigma_of_y = legval(u(wave_of_y[fiber], wavemin, wavemax),
                        sigmacoef[fiber])

    #   Ascertain X by using low and high uncertainty
    x1_of_y = np.floor(x_of_y).astype(int) - width / 2
    x2_of_y = np.floor(x_of_y).astype(int) + width / 2 + 2
    return (x1_of_y, x_of_y, x2_of_y, sigma_of_y)
Ejemplo n.º 2
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def leggauss(n, x0=None):
    """
    Abscissa and weights for Gauss-Legendre quadrature.

    Parameters
    ----------
    n : int

    Returns
    -------
    x : ndarray
    weights : ndarray
    """

    J = legjacobi(n)
    if x0 is None:
        x, vec = np.linalg.eigh(J)
        return x, vec[0]**2 * 2
    else:
        from numpy.polynomial.legendre import legval
        J[-1,
          -1] = x0 - J[-1, -2]**2 * legval(x0, [0] * (n - 2) + [1]) / legval(
              x0, [0] * (n - 1) + [1])
        x, vec = np.linalg.eigh(J)
        return x, vec[0]**2 * 2
Ejemplo n.º 3
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def hamiltonian_matrix(BASIS_SIZE=BASIS_SIZE,
                       BASIS_FUNC=BASIS_FUNC,
                       DOMAIN=DOMAIN,
                       C=C,
                       V=V):
    '''Calculates the hamiltonian matrix <psi|H|psi>'''
    if BASIS_FUNC == 'legendre':
        hmat = np.zeros((BASIS_SIZE, BASIS_SIZE))
        for i in range(BASIS_SIZE):
            for j in range(BASIS_SIZE):
                coefs_i = [0] * (i) + [1]
                coefs_j = [0] * (j) + [1]
                inside = L.legmul(coefs_i, list(hamiltonian(coefs_j)))
                integ = L.legint(inside)
                val = L.legval(DOMAIN[1], integ) - L.legval(DOMAIN[0], integ)
                hmat[i, j] = val
    if BASIS_FUNC == 'fourier':
        a = DOMAIN[
            1]  #restrict the domain to be symmetric about origin for simplicity
        hmat = np.zeros((BASIS_SIZE, BASIS_SIZE))
        for i in range(BASIS_SIZE):
            for j in range(BASIS_SIZE):
                p1 = 2 * V * np.sin(a * j) / j  #cos V0 term
                p2 = 0  #cos cos term cancels due to parity if i != j
                if i == j:
                    p2 = C * (j**2) * (a + np.sin(2 * a * j) / (2 * j))
                hmat[i, j] = p1 + p2
    return hmat
Ejemplo n.º 4
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    def evaluate_basis_gauss(self):
        """Evaluate the basis at the Gaussian quadrature nodes.

        phi will be used to transform Legendre solution coefficients
        to the solution evaluated at the Gaussian quadrature nodes.

        dphi_w will be used for the interior flux integral

        """
        phi = np.zeros((len(self.x), self.N_s))
        dphi_w = np.zeros((len(self.x), self.N_s))

        for n in range(self.N_s):

            # Get the Legendre polynomial of order n and its gradient
            l = L.basis(n)
            dl = l.deriv()

            # Evaluate the basis at the Gaussian nodes
            phi[:, n] = leg.legval(self.x, l.coef)

            # Evaluate the gradient at the Gaussian nodes and multiply by the
            # weights
            dphi_w[n, :] = leg.legval(self.x, dl.coef) * self.w

        return phi, dphi_w
Ejemplo n.º 5
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Archivo: basis.py Proyecto: wo6677/dg1d
    def evaluate_basis_gauss(self):
        """Evaluate the basis at the Gaussian quadrature nodes.

        phi will be used to transform Legendre solution coefficients
        to the solution evaluated at the Gaussian quadrature nodes.

        dphi_w will be used for the interior flux integral

        """
        phi = np.zeros((len(self.x), self.N_s))
        dphi_w = np.zeros((len(self.x), self.N_s))

        for n in range(self.N_s):

            # Get the Legendre polynomial of order n and its gradient
            l = L.basis(n)
            dl = l.deriv()

            # Evaluate the basis at the Gaussian nodes
            phi[:, n] = leg.legval(self.x, l.coef)

            # Evaluate the gradient at the Gaussian nodes and multiply by the
            # weights
            dphi_w[n, :] = leg.legval(self.x, dl.coef) * self.w

        return phi, dphi_w
Ejemplo n.º 6
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def fitcont(wave, flux, sigup, fitidx, maxorder=6):
    wavepts = wave[fitidx]
    fluxpts = flux[fitidx]
    sigpts = sigup[fitidx]
    ### Cycle through fits of several orders and decide the appropriate order by F-test
    coeffs = []
    covmtxs = []
    fits = []
    chisqs = []
    dfs = []
    fprob = 0.
    i = 0
    order = 1
    while (fprob <= 0.95) & (order <= maxorder):
        order = i + 1
        coeff, covmtx = fitlegendre(wavepts, fluxpts, sigpts, order)
        coeffs.append(coeff)
        covmtxs.append(covmtx)
        fit = L.legval(wavepts, coeff, order)
        fits.append(fit)
        chisq, df = redchisq(fluxpts, fit, sigpts, order)
        chisqs.append(chisq), dfs.append(df)
        if i > 0:
            fval = chisqs[i] / chisqs[i - 1]
            fprob = stats.f.cdf(fval, dfs[i], dfs[i - 1])
        i += 1
    ### Choose fit of order just prior to where F-test indicates no improvement
    fitcoeff = coeffs[i - 2]
    fitcovmtx = covmtxs[i - 2]
    wrange = range(fitidx[0], fitidx[-1])
    cont = L.legval(wave[wrange], fitcoeff)
    return fitcoeff, fitcovmtx
Ejemplo n.º 7
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 def term_ijk(self, index):
     i, j, k = index
     ci = np.zeros(i + 1)
     cj = np.zeros(j + 1)
     ck = np.zeros(k + 1)
     ci[-1] = cj[-1] = ck[-1] = 1
     return legval(self.r[0], ci) * legval(self.r[1], cj) * legval(
         self.r[2], ck)
Ejemplo n.º 8
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def genericLegVal(locations, coeffs):
    if len(locations.shape)==1:
        return leg.legval(locations,coeffs)
    else: # assume dim 0 is points, dim 1 is dimensions
        c=leg.legval(locations[:,0], coeffs)
        for i in range(1, locations.shape[1]):
            c=leg.legval(locations[:,i],c, tensor=False)
        return c
Ejemplo n.º 9
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def gaussian_latitudes(n):
    """Construct latitudes and latitude bounds for a Gaussian grid.

    Args:

    * n:
        The Gaussian grid number (half the number of latitudes in the
        grid.

    Returns:
        A 2-tuple where the first element is a length `n` array of
        latitudes (in degrees) and the second element is an `(n, 2)`
        array of bounds.

    """
    if abs(int(n)) != n:
        raise ValueError('n must be a non-negative integer')
    nlat = 2 * n
    # Create the coefficients of the Legendre polynomial and construct the
    # companion matrix:
    cs = np.array([0] * nlat + [1], dtype=np.int)
    cm = legcompanion(cs)
    # Compute the eigenvalues of the companion matrix (the roots of the
    # Legendre polynomial) taking advantage of the fact that the matrix is
    # symmetric:
    roots = la.eigvalsh(cm)
    roots.sort()
    # Improve the roots by one application of Newton's method, using the
    # solved root as the initial guess:
    fx = legval(roots, cs)
    fpx = legval(roots, legder(cs))
    roots -= fx / fpx
    # The roots should exhibit symmetry, but with a sign change, so make sure
    # this is the case:
    roots = (roots - roots[::-1]) / 2.
    # Compute the Gaussian weights for each interval:
    fm = legval(roots, cs[1:])
    fm /= np.abs(fm).max()
    fpx /= np.abs(fpx).max()
    weights = 1. / (fm * fpx)
    # Weights should be symmetric and sum to two (unit weighting over the
    # interval [-1, 1]):
    weights = (weights + weights[::-1]) / 2.
    weights *= 2. / weights.sum()
    # Calculate the bounds from the weights, still on the interval [-1, 1]:
    bounds1d = np.empty([nlat + 1])
    bounds1d[0] = -1
    bounds1d[1:-1] = -1 + weights[:-1].cumsum()
    bounds1d[-1] = 1
    # Convert the bounds to degrees of latitude on [-90, 90]:
    bounds1d = np.rad2deg(np.arcsin(bounds1d))
    bounds2d = np.empty([nlat, 2])
    bounds2d[:, 0] = bounds1d[:-1]
    bounds2d[:, 1] = bounds1d[1:]
    # Convert the roots from the interval [-1, 1] to latitude values on the
    # interval [-90, 90] degrees:
    latitudes = np.rad2deg(np.arcsin(roots))
    return latitudes, bounds2d
Ejemplo n.º 10
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def gaussian_latitudes(n):
    """Construct latitudes and latitude bounds for a Gaussian grid.
    
    Args:
    
    * n:
        The Gaussian grid number (half the number of latitudes in the
        grid.

    Returns:
        A 2-tuple where the first element is a length `n` array of
        latitudes (in degrees) and the second element is an `(n, 2)`
        array of bounds.

    """
    if abs(int(n)) != n:
        raise ValueError('n must be a non-negative integer')
    nlat = 2 * n
    # Create the coefficients of the Legendre polynomial and construct the
    # companion matrix:
    cs = np.array([0] * nlat + [1], dtype=np.int)
    cm = legcompanion(cs)
    # Compute the eigenvalues of the companion matrix (the roots of the
    # Legendre polynomial) taking advantage of the fact that the matrix is
    # symmetric:
    roots = la.eigvalsh(cm)
    roots.sort()
    # Improve the roots by one application of Newton's method, using the
    # solved root as the initial guess:
    fx = legval(roots, cs)
    fpx = legval(roots, legder(cs))
    roots -= fx / fpx
    # The roots should exhibit symmetry, but with a sign change, so make sure
    # this is the case:
    roots = (roots - roots[::-1]) / 2.
    # Compute the Gaussian weights for each interval:
    fm = legval(roots, cs[1:])
    fm /= np.abs(fm).max()
    fpx /= np.abs(fpx).max()
    weights = 1. / (fm * fpx)
    # Weights should be symmetric and sum to two (unit weighting over the
    # interval [-1, 1]):
    weights = (weights + weights[::-1]) / 2.
    weights *= 2. / weights.sum()
    # Calculate the bounds from the weights, still on the interval [-1, 1]:
    bounds1d = np.empty([nlat + 1])
    bounds1d[0] = -1
    bounds1d[1:-1] = -1 + weights[:-1].cumsum()
    bounds1d[-1] = 1
    # Convert the bounds to degrees of latitude on [-90, 90]:
    bounds1d = np.rad2deg(np.arcsin(bounds1d))
    bounds2d = np.empty([nlat, 2])
    bounds2d[:, 0] = bounds1d[:-1]
    bounds2d[:, 1] = bounds1d[1:]
    # Convert the roots from the interval [-1, 1] to latitude values on the
    # interval [-90, 90] degrees:
    latitudes = np.rad2deg(np.arcsin(roots))
    return latitudes, bounds2d
Ejemplo n.º 11
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 def eval(self, x, u, output_array=None):
     if output_array is None:
         output_array = np.zeros(x.shape)
     x = self.map_reference_domain(x)
     w_hat = work[(u, 0, True)]
     self.set_factor_array(u)
     output_array[:] = leg.legval(x, u[:-2])
     w_hat[2:] = self._factor * u[:-2]
     output_array -= leg.legval(x, w_hat)
     return output_array
Ejemplo n.º 12
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    def parallels_transitions(turbine,
                              joints_parallel,
                              joints_vel_parallel,
                              joints_acc_parallel,
                              times_parallel,
                              step=.1,
                              number_of_points=8.):
        """ Given all parallels solutions, i.e., joints solutions for all waypoints split in parallels (lists),
        this method computes cubic polynomials to interpolate the two points: end of a parallel - begin of the next
        parallel, in joint space, considering velocities. It will return the parallels and the computed transition
        paths between them.
        Obs.: This is taking too long. No improvements are being made since plates can be used on the transition part.
        Args:
            turbine: (@ref Turbine) turbine object
            joints_parallel: (float[m][n<SUB>i</SUB>][nDOF]) list of joints for all parallels
            times_parallel: (float[m][n<SUB>i</SUB>]) list of deltatimes for all parallels
            step: distance (meters) between points
            number_of_points: minimal number of points
            max_acc: maximum permitted acceleration (percentage)
        Returns:
            Modifies the current joints_parallel and times_parallel with the computed transitions.
        """

        robot = turbine.robot

        for i in range(len(joints_parallel) - 1):
            joint_0 = joints_parallel[2 * i][-1]
            vel_0 = joints_vel_parallel[2 * i][-1]
            joint_1 = joints_parallel[2 * i + 1][0]
            vel_1 = joints_vel_parallel[2 * i + 1][0]

            c = mathtools.legn_path(3, [joint_0, joint_1], [vel_0, vel_1])
            joints = []
            joints_vel = []
            joints_acc = []
            times = []
            dt = min([step, 1. / number_of_points])
            for t in linspace(0, 1., max([1. / step, number_of_points])):
                joints.append(legendre.legval(t, c))
                joints_vel.append(legendre.legval(t, legendre.legder(c, 1)))
                joints_acc.append(legendre.legval(t, legendre.legder(c, 2)))
                times.append(dt)

            joints = joints[1:-1]
            joints_vel = joints_vel[1:-1]
            joints_acc = joints_acc[1:-1]
            times_parallel[2 * i + 1][0] = times[-1]
            times = times[1:-1]

            joints_parallel.insert(2 * i + 1, joints)
            joints_vel_parallel.insert(2 * i + 1, joints_vel)
            joints_acc_parallel.insert(2 * i + 1, joints_acc)
            times_parallel.insert(2 * i + 1, times)

        return joints_parallel, joints_vel_parallel, joints_acc_parallel, times_parallel
Ejemplo n.º 13
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 def eval(self, ispec, x):
     xx = self._xnorm(x)
     
     if isinstance(ispec, int):
         return legval(xx, self._coeff[ispec])
     else:
         if ispec is None:
             ispec = range(self._coeff.shape[0])
         
         y = [legval(xx, self._coeff[i]) for i in ispec]
         return np.array(y)
Ejemplo n.º 14
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def inner_product():  #do I even need this?
    if BASIS_FUNC == 'legendre':
        pmat = np.zeros((BASIS_SIZE, BASIS_SIZE))
        for i in range(BASIS_SIZE):
            for j in range(BASIS_SIZE):
                coefs_i = [0] * (i) + [1]
                coefs_j = [0] * (j) + [1]
                inside = L.legmul(coefs_i, coefs_j)
                integ = L.legint(inside)
                val = L.legval(DOMAIN[1], integ) - L.legval(DOMAIN[0], integ)
                pmat[i, j] = val
Ejemplo n.º 15
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 def eval(self, x, u, output_array=None):
     if output_array is None:
         output_array = np.zeros(x.shape)
     x = self.map_reference_domain(x)
     w_hat = work[(u, 0, True)]
     self.set_factor_array(u)
     output_array[:] = leg.legval(x, u[:-2]*self._factor)
     w_hat[2:] = u[:-2]*self._factor
     output_array -= leg.legval(x, w_hat)
     output_array += 0.5*(u[-1]*(1-x)+u[-2]*(1+x))
     return output_array
Ejemplo n.º 16
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    def term_ijk(self, index):
        if len(index) == 2:
            i, j = index
            ci = np.diag(np.ones(i + 1))[i]
            cj = np.diag(np.ones(j + 1))[j]
            return legval(self.r[2], ci) * legval(self.r[1], cj)

        elif len(index) == 1:
            k = index[0]
            ck = np.diag(np.ones(k + 1))[k]
            return legval(self.r[0], ck)
Ejemplo n.º 17
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def diffxsec_legendre_eval(sig, mu, coeff):
    c = coeff.T
    ans = np.zeros_like(mu)
    if (len(mu.shape) == 1):
        ans = sig * legval(mu, c, tensor=False)
    elif (len(mu.shape) == 2):
        ans = sig * legval(mu, c[:, None, :], tensor=False)
    elif (len(mu.shape) == 3):
        ans = sig * legval(mu, c[:, None, None, :], tensor=False)
    ans[np.abs(mu) > 1.0] = 0.0
    return ans
Ejemplo n.º 18
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    def eval(self, ispec, x):
        xx = self._xnorm(x)
        
        if isinstance(ispec, numbers.Integral):
            return legval(xx, self._coeff[ispec])
        else:
            if ispec is None:
                ispec = list(range(self._coeff.shape[0]))

            y = [legval(xx, self._coeff[i]) for i in ispec]
            return np.array(y)
Ejemplo n.º 19
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def weights_roots(order, rules='Gauss-Lobatto'):
    c_leg = [1] if order == 0 else [i//order for i in xrange(order+1)]
    c_dleg = lgd.legder(c_leg)

    if rules == 'Gauss-Lobatto':
        xs = np.array( [-1] + list( lgd.legroots(c_dleg) ) + [1] )
        ws = 2 / ( order * (order + 1) * (lgd.legval(xs, c_leg)**2) )

    elif rules == 'Gauss-Legendre':
        xs = lgd.legroots(c_leg)
        ws = 2 / ( (1 - xs**2) * (lgd.legval(xs, c_dleg)**2) )

    return xs, ws
Ejemplo n.º 20
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 def test_legmul(self) :
     # check values of result
     for i in range(5) :
         pol1 = [0]*i + [1]
         val1 = leg.legval(self.x, pol1)
         for j in range(5) :
             msg = "At i=%d, j=%d" % (i,j)
             pol2 = [0]*j + [1]
             val2 = leg.legval(self.x, pol2)
             pol3 = leg.legmul(pol1, pol2)
             val3 = leg.legval(self.x, pol3)
             assert_(len(pol3) == i + j + 1, msg)
             assert_almost_equal(val3, val1*val2, err_msg=msg)
Ejemplo n.º 21
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 def eval(self, x, fk, output_array=None):
     if output_array is None:
         output_array = np.zeros(x.shape)
     x = self.map_reference_domain(x)
     w_hat = work[(fk, 0)]
     self.set_factor_arrays(fk)
     output_array[:] = leg.legval(x, fk[:-4])
     w_hat[2:-2] = self._factor1 * fk[:-4]
     output_array += leg.legval(x, w_hat[:-2])
     w_hat[4:] = self._factor2 * fk[:-4]
     w_hat[:4] = 0
     output_array += leg.legval(x, w_hat)
     return output_array
Ejemplo n.º 22
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 def test_legmul(self) :
     # check values of result
     for i in range(5) :
         pol1 = [0]*i + [1]
         val1 = leg.legval(self.x, pol1)
         for j in range(5) :
             msg = "At i=%d, j=%d" % (i, j)
             pol2 = [0]*j + [1]
             val2 = leg.legval(self.x, pol2)
             pol3 = leg.legmul(pol1, pol2)
             val3 = leg.legval(self.x, pol3)
             assert_(len(pol3) == i + j + 1, msg)
             assert_almost_equal(val3, val1*val2, err_msg=msg)
Ejemplo n.º 23
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def invert_legendre_polynomial(wavemin, wavemax, ycoef, xcoef, fiber, npix_y, wave_of_y) :
 
    #   Wavelength array used in 'invert_legendre_polynomial'
    wave                = np.linspace(wavemin, wavemax, 100)
    #   Determines value of Y, so we can know its coeficient and then its position
    y_of_wave           = legval(u(wave, wavemin, wavemax), ycoef[fiber])
    coef                = legfit(u(y_of_wave, 0, npix_y), wave, deg=ycoef[fiber].size)
    wave_of_y[fiber]    = legval(u(np.arange(npix_y).astype(float), 0, npix_y), coef)
    #   Determines wavelength intensity (x) based on Y
    x_of_y              = legval(u(wave_of_y[fiber], wavemin, wavemax), xcoef[fiber])
    #   Ascertain X by using low and high uncertainty
    x1_of_y             = np.floor(x_of_y).astype(int) - 3
    x2_of_y             = np.floor(x_of_y).astype(int) + 4
    return (x1_of_y, x2_of_y)
Ejemplo n.º 24
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    def vizualize(self, x_left, x_right, points, coefs):
        y_interp = legndr.legval(points[0], coefs)
        self.q_residual.setText(str(np.linalg.norm(points[1] - y_interp)))

        x_interp = np.linspace(-1, 1, len(points[0])*20)
        x_interp = np.concatenate((x_interp, points[0]))
        x_interp = np.sort(x_interp)
        y_interp = legndr.legval(x_interp, coefs)
        x_interp = (x_left + x_right) / 2 + (x_right - x_left) / 2 * x_interp

        points[0] = (x_left + x_right) / 2 + (x_right - x_left) / 2 * points[0]
        plt.plot(points[0], points[1], 'ro')
        plt.plot(x_interp, y_interp)
        plt.show()
Ejemplo n.º 25
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    def build_spatial_flux(self):

        """ Calculates the flux across all nodes.
        Uses current flux_coefficients values.
        """

        for node in xrange(self.nodes):
            for index in xrange(self.solution_cells):
                normalized_index = self.normalized_index(index)
                flux_index = self.solution_cells*node+index
                coeff_start = self.order*node
                coeff_end = self.order*(node+1)
                self.flux[0, 1, flux_index] = legval(normalized_index, self.flux_coefficients[1, coeff_start:coeff_end])
                self.flux[0, 0, flux_index] = legval(normalized_index, self.flux_coefficients[0, coeff_start:coeff_end])
Ejemplo n.º 26
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def Hamiltonian_Legendre_polynomial(c, potential, domain, N):
    #potential is a constant in this case

    x = np.linspace(-domain / 2, domain / 2, N)
    delta_x = domain / (N - 1)

    #here, the normalized legendre polynomical has been used
    # for the nth polynomials, normalization constant is sqrt(2/(2n + 1))

    #kinetic term
    K = np.zeros((N, N))

    for ii in range(N):
        legen_left = np.zeros(N)
        legen_left[ii] = mt.sqrt((2 * ii + 1) / 2)
        for jj in range(N):
            deriva_array = np.zeros(N + 2)
            deriva_array[jj] = mt.sqrt((2 * jj + 1) / 2)
            legen_right_deriva = legen.legder(deriva_array, 2)

            #multiply them
            legen_multiply = legen.legmul(legen_left, legen_right_deriva)

            #integral
            legen_integral = legen.legint(legen_multiply)

            #calculate the matrix elements
            K[ii][jj] = legen.legval(domain / 2, legen_integral) - \
                        legen.legval(-domain / 2, legen_integral)

    #the S matrix, inside the [-1, 1] domain, the legendre ploynomial can be treatedas basis and satisfying <xi|xj> = delta ij, thus S matrix is a identity matrix
    S = np.zeros((N, N))

    for ii in range(N):
        legen_left_S = np.zeros(N)
        legen_left_S[ii] = mt.sqrt((2 * ii + 1) / 2)
        legen_multiply_S = legen.legmul(legen_left_S, legen_left_S)
        legen_integral_S = legen.legint(legen_multiply_S)
        S[ii][ii] = legen.legval(domain / 2, legen_integral_S) - \
                    legen.legval(-domain / 2, legen_integral_S)

    K = K * -1 * c

    #because the potential is just a constant here, we can calculate the V matrix   simply by multiply the matrix S a constant potential value

    V = potential * S

    ##divide the obtained Hamiltonian by the S matrix
    H = K + V
    return H
Ejemplo n.º 27
0
def icb_interface_flux_matrix(p, K, T):
    """The interface flux matrices for the ICB schemes, we use upwinding
     to get the fluxes.  Denote T the translation necessary to
     evaluate the flux from the other cell.

    """

    # Enhanced polynomial degree
    phat = p + len(K)

    G0 = smp.zeros(p + 1, phat + 1)
    G1 = smp.zeros(p + 1, phat + 1)
    for i in range(0, p + 1):
        for j in range(0, phat + 1):
            li = L.basis(i)
            lj = L.basis(j)
            G0[i, j] = leg.legval(-1, li.coef) * \
                leg.legval(1, lj.coef) * (T**-1)
            G1[i, j] = leg.legval(1, li.coef) * leg.legval(1, lj.coef)

    # Enhancement matrix
    A, Ainv, B, Binv = enhance.enhancement_matrices(p, K)

    # Using the enhanced function in the flux (see notes 21/4/15)
    BL = smp.zeros(phat + 1, phat + 1)
    BR = smp.zeros(phat + 1, phat + 1)
    for i in range(p + 1):
        li = L.basis(i)
        BL[i, i] = 1  # basis.integrate_legendre_product(li,li)
        BR[i, i] = 1  # BL[i,i]
    for i, k in enumerate(K):
        lk = L.basis(k)
        int_lklk = basis.integrate_legendre_product(lk, lk)
        BL[i + p + 1, i + p + 1] = T  # * int_lklk
        BR[i + p + 1, i + p + 1] = (T**(-1))  # * int_lklk

    # reduction matrix
    R = smp.zeros(phat + 1, p + 1)
    for i in range(p + 1):
        R[i, i] = 1
    for i, k in enumerate(K):
        for j in range(p + 1):
            R[i + p + 1, j] = auxf.delta(k, j)

    # Convert to sympy matrices
    G0 = smp.Matrix(G0) * smp.Matrix(Ainv) * BL * R
    G1 = smp.Matrix(G1) * smp.Matrix(Ainv) * BL * R

    return G0, G1
Ejemplo n.º 28
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def icb_interface_flux_matrix(p, K, T):
    """The interface flux matrices for the ICB schemes, we use upwinding
     to get the fluxes.  Denote T the translation necessary to
     evaluate the flux from the other cell.

    """

    # Enhanced polynomial degree
    phat = p + len(K)

    G0 = smp.zeros(p + 1, phat + 1)
    G1 = smp.zeros(p + 1, phat + 1)
    for i in range(0, p + 1):
        for j in range(0, phat + 1):
            li = L.basis(i)
            lj = L.basis(j)
            G0[i, j] = leg.legval(-1, li.coef) * \
                leg.legval(1, lj.coef) * (T**-1)
            G1[i, j] = leg.legval(1, li.coef) * leg.legval(1, lj.coef)

    # Enhancement matrix
    A, Ainv, B, Binv = enhance.enhancement_matrices(p, K)

    # Using the enhanced function in the flux (see notes 21/4/15)
    BL = smp.zeros(phat + 1, phat + 1)
    BR = smp.zeros(phat + 1, phat + 1)
    for i in range(p + 1):
        li = L.basis(i)
        BL[i, i] = 1  # basis.integrate_legendre_product(li,li)
        BR[i, i] = 1  # BL[i,i]
    for i, k in enumerate(K):
        lk = L.basis(k)
        int_lklk = basis.integrate_legendre_product(lk, lk)
        BL[i + p + 1, i + p + 1] = T  # * int_lklk
        BR[i + p + 1, i + p + 1] = (T**(-1))  # * int_lklk

    # reduction matrix
    R = smp.zeros(phat + 1, p + 1)
    for i in range(p + 1):
        R[i, i] = 1
    for i, k in enumerate(K):
        for j in range(p + 1):
            R[i + p + 1, j] = auxf.delta(k, j)

    # Convert to sympy matrices
    G0 = smp.Matrix(G0) * smp.Matrix(Ainv) * BL * R
    G1 = smp.Matrix(G1) * smp.Matrix(Ainv) * BL * R

    return G0, G1
def legplot(nterms=6):
    """
  Purpose:
    calculate (2l+1)/4pi * Pl and plot
  Procedure:
    
  Inputs:
    nterms: the number of Pl to plot, starting from 0
  Returns:
    theta values and scaled legendre polynomials
  """
    coefs = np.zeros([nterms, nterms])
    for coef in range(nterms):
        coefs[coef, coef] = ((2 * coef) + 1) / (4 * np.pi)
    npoints = 1801
    thetavals = np.linspace(0, 180, npoints)
    xvals = np.cos(thetavals * np.pi / 180.)
    print 'x vals: ', xvals
    Pl = np.empty([nterms, npoints])
    for ell in range(nterms):
        Pl[ell] = legval(xvals, coefs[ell])
        #print 'l = ',ell,', scaled Pl = ',Pl[ell]
        plt.plot(thetavals, Pl[ell], label='l = ' + str(ell))
    plt.xlabel('angle (degrees)')
    plt.ylabel('P_l * (2*l+1)/4pi')
    plt.title('scaled legendre polynomials')
    #plt.legend()
    plt.show()

    return thetavals, Pl
Ejemplo n.º 30
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def get_chi(blorder_max, ydata, xdata, blindex, noise):
    """
 Returns the best-fit Legendre polynomial to an input spectra, 
 based on a comparison of the reduced chi-squared values for each order 
 of the polynomial.     
   
 blorder_max = maximum order of polynomial to fit
 ydata = spectrum y values
 xdata = spectrum x values
 blindex = the indices of the spectra to include in baseline fitting
 noise = rms noise of spectrum"""
    opts = lsq(legendreLoss, np.zeros(blorder_max + 1), args=(ydata[blindex],
                                                          xdata[blindex],
                                                        noise), loss='arctan')
    chis = [] # first entry is order=1, second is order=2, ..., up to order=blorder
    ymods = []
    # Loop through each order of polynomial and create model baseline
    # and calculate that model's chi-squared values
    for i in np.arange(blorder_max)+1:
	# i is the polynomial order
    	ymod = legendre.legval(xdata, np.array(opts.x)[0:i+1]) #+1 to get last term
	ymods.append(ymod)
    	chi = redchisqg(ydata,ymod,deg=i+1)
	chis.append(chi)
    # Find the model with the lowest chi-squared value
    find_low = np.where(np.array(chis)==min(chis))
    low_model = np.array(ymods)[find_low]
    return ymod
Ejemplo n.º 31
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    def test_legvander(self) :
        # check for 1d x
        x = np.arange(3)
        v = leg.legvander(x, 3)
        assert_(v.shape == (3, 4))
        for i in range(4) :
            coef = [0]*i + [1]
            assert_almost_equal(v[..., i], leg.legval(x, coef))

        # check for 2d x
        x = np.array([[1, 2], [3, 4], [5, 6]])
        v = leg.legvander(x, 3)
        assert_(v.shape == (3, 2, 4))
        for i in range(4) :
            coef = [0]*i + [1]
            assert_almost_equal(v[..., i], leg.legval(x, coef))
Ejemplo n.º 32
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def leg_l(l_index, numgrid):
	leg_access = np.zeros(l_index + 1)
	leg_access[l_index] = 1
	#print leg_access
	x = np.linspace(0,1,numgrid)
	y = LG.legval(x, leg_access)
	return x,y
Ejemplo n.º 33
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def cheb_fitcurve(x, y, order):
    x = cheb.chebpts2(len(x))
    order = 64
    coef = legend.legfit(x, y, order)
    assert_equal(len(coef), order + 1)
    y1 = legend.legval(x, coef)
    err_1 = np.linalg.norm(y1 - y) / np.linalg.norm(y)

    coef = cheb.chebfit(x, y, order)
    assert_equal(len(coef), order + 1)
    thrsh = abs(coef[0] / 1000)
    for i in range(len(coef)):
        if abs(coef[i]) < thrsh:
            coef = coef[0:i + 1]
            break

    y2 = cheb.chebval(x, coef)
    err_2 = np.linalg.norm(y2 - y) / np.linalg.norm(y)

    plt.plot(x, y2, '.')
    plt.plot(x, y, '-')
    plt.title("nPt={} order={} err_cheby={:.6g} err_legend={:.6g}".format(
        len(x), order, err_2, err_1))
    plt.show()
    assert_almost_equal(cheb.chebval(x, coef), y)
    #
    return coef
Ejemplo n.º 34
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 def _sph_coefs_to_corr( self ):
     """
     computes correlation from legendre polynomial coefficients computed from spherical
     harmonic coefficients
 
     sets coefficients of order-l polynomials to zero
     """
     self.corr = np.zeros( (self.n_q, self.n_q, self.n_psi) )
     self.cospsi = np.linspace(-1,1, self.n_psi, endpoint=True)
     # Cl = Cl[:(Lmax+1),:,:]
 
     for i in range(self.n_q):
         for j in range(i, self.n_q):
             coefs = self.cl[:,i,j]
 #             even_coefs = Cl[:int(Lmax/2),i,j]
             # even_coefs= self.cl[::2,i,j]
             # for idx in range(even_coefs.size * 2):
             #     if idx%2 ==0:
             #         coefs.append(even_coefs[idx/2])
             #     else:
             #         coefs.append(0)
             # coefs = np.array(coefs)
         
             self.corr[i,j,:] = legval( self.cospsi, coefs )
             self.corr[j,i,:] = self.corr[i,j,:]  # copy it to the lower triangle too
Ejemplo n.º 35
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    def test_legvander(self) :
        # check for 1d x
        x = np.arange(3)
        v = leg.legvander(x, 3)
        assert_(v.shape == (3, 4))
        for i in range(4) :
            coef = [0]*i + [1]
            assert_almost_equal(v[..., i], leg.legval(x, coef))

        # check for 2d x
        x = np.array([[1, 2], [3, 4], [5, 6]])
        v = leg.legvander(x, 3)
        assert_(v.shape == (3, 2, 4))
        for i in range(4) :
            coef = [0]*i + [1]
            assert_almost_equal(v[..., i], leg.legval(x, coef))
Ejemplo n.º 36
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    def _get_weights(num_points, inner_nodes):
        from numpy.polynomial import legendre

        base_weight = 2.0 / (num_points * (num_points - 1))
        p_n_minus1 = [0] * (num_points - 1) + [1]
        p_n_minus1_at_nodes = legendre.legval(inner_nodes, p_n_minus1)
        return base_weight / p_n_minus1_at_nodes**2
Ejemplo n.º 37
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def baselineWithAmmonia(y,
                        v,
                        baselineIndex,
                        freqthrow=4.11 * u.MHz,
                        v0=8.5,
                        sigmav=1.0 * u.km / u.s,
                        line='oneone',
                        blorder=5,
                        noiserms=None):
    x = np.linspace(-1, 1, len(y))
    chthrow = (freqthrow.to(u.Hz).value / acons.freq_dict[line] * 299792.458 /
               np.abs(v[0] - v[1]))
    chthrow = (np.round(chthrow)).astype(np.int)
    if noiserms is None:
        noiserms = mad1d((y - np.roll(y, -2))[baselineIndex])

    opts = lsq(
        ammoniaLoss,
        np.r_[[
            np.nanmax(y[baselineIndex]), v[np.nanargmax(y[baselineIndex])], 1.0
        ],
              np.zeros(blorder + 1)],
        args=(y[baselineIndex], x[baselineIndex], v[baselineIndex], noiserms),
        kwargs={'chthrow': chthrow},
        loss='soft_l1')
    return y - legendre.legval(x, opts.x[3:])
Ejemplo n.º 38
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def chisq_leg(p, x, y, w, flag_call):
	ind = np.where(flag_call==1)[0]
	y_c = y[ind]
	x_c = x[ind]
	w_c = w[ind]
	chisq = np.sum( (1/(w_c)**2)*(leg.legval(x_c, p) - y_c)**2 ) / np.sum(1/w_c**2)
	return chisq
Ejemplo n.º 39
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def basisMatrixLegendre(x,order):
    '''
    Builds (order+1,x) 2-d array of Legendre polynomials evaluated at x

    Parameters
    ----------
    x: numpy 1-d array
        Points at which to evaluate basis functions
    order:
        Maximum order of polynomial set

    Returns
    -------
    legmtx: numpy 2d array of shape (order+1,x)
        Legendre polynomials evaluated at x
    '''

    ### Construct matrix of Legendre polynomials
    legmtx = np.zeros((order+1,len(x)))

    ### Prepare matrix of Leg. poly. basis functions evaluated at x
    for i in range(order+1):
        coeffs=np.zeros(i+1)
        coeffs[i]=1.
        legmtx[i,:]=L.legval(x, coeffs)

    return legmtx
Ejemplo n.º 40
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def Likelihood_Sph(vertex, *args):
    coeff, PMT_pos, event_pe, cut = args
    y = event_pe
    # fixed axis
    z = np.sqrt(np.sum(vertex[1:4]**2)) / shell
    if (np.abs(z) > 1):
        z = np.sign(z)
    cos_theta = np.sum(vertex[1:4]*PMT_pos,axis=1)\
        /np.sqrt(np.sum(vertex[1:4]**2)*np.sum(PMT_pos**2,axis=1))
    # accurancy and nan value
    cos_theta = np.nan_to_num(cos_theta)
    cos_theta[cos_theta > 1] = 1
    cos_theta[cos_theta < -1] = -1
    size = np.size(PMT_pos[:, 0])
    x = np.zeros((size, cut))
    # legendre coeff
    for i in np.arange(0, cut):
        c = np.zeros(cut)
        c[i] = 1
        x[:, i] = LG.legval(cos_theta, c)

    k = np.zeros(cut)
    for i in np.arange(cut):
        # cubic interp
        k[i] = np.sum(np.polynomial.legendre.legval(z, coeff[i, :]))

    #k[0] = k[0] + np.log(vertex[0])
    k[0] = vertex[0]
    expect = np.exp(np.dot(x, k))
    L = -np.sum(np.sum(np.log((expect**y) * np.exp(-expect))))
    return L
Ejemplo n.º 41
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def baselineSpectrum(spectrum,order=1,baselineIndex=()):
    x=np.arange(len(spectrum))
    coeffs = legendre.legfit(x[baselineIndex],spectrum[baselineIndex],order)
#    pdb.set_trace()
    spectrum -= legendre.legval(x,coeffs)
    
    return(spectrum)
Ejemplo n.º 42
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def baselineSpectrum(spectrum,order=1,baselineIndex=()):
    x=np.arange(len(spectrum))
    coeffs = legendre.legfit(x[baselineIndex],spectrum[baselineIndex],order)
#    pdb.set_trace()
    spectrum -= legendre.legval(x,coeffs)
    
    return(spectrum)
Ejemplo n.º 43
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 def work(j):
     i, order = annotation[j]
     c = numpy.zeros(5)
     c[order] = 1
     # watch out the eigenmode is wikipedia
     # no negative phase on 2nd order pole!
     eigenmode = eigenmodes[j]
     eigenmode[i].xi[...] = \
             powerspec.pole(eigenmode[i].r, order=order)[:, None] \
             * legval(eigenmode[i].mu, c)[None, :]
Ejemplo n.º 44
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def robustBaseline(y, baselineIndex, blorder=1, noiserms=None):
    x = np.linspace(-1, 1, len(y))
    if noiserms is None:
        noiserms = mad1d((y - np.roll(y, -2))[baselineIndex])
    opts = lsq(legendreLoss, np.zeros(blorder + 1), args=(y[baselineIndex],
                                                          x[baselineIndex],
                                                          noiserms),
               loss='arctan')

    return y - legendre.legval(x, opts.x)
Ejemplo n.º 45
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    def test_legfit(self) :
        def f(x) :
            return x*(x - 1)*(x - 2)

        # Test exceptions
        assert_raises(ValueError, leg.legfit, [1],    [1],     -1)
        assert_raises(TypeError,  leg.legfit, [[1]],  [1],      0)
        assert_raises(TypeError,  leg.legfit, [],     [1],      0)
        assert_raises(TypeError,  leg.legfit, [1],    [[[1]]],  0)
        assert_raises(TypeError,  leg.legfit, [1, 2], [1],      0)
        assert_raises(TypeError,  leg.legfit, [1],    [1, 2],   0)
        assert_raises(TypeError,  leg.legfit, [1],    [1],   0, w=[[1]])
        assert_raises(TypeError,  leg.legfit, [1],    [1],   0, w=[1, 1])

        # Test fit
        x = np.linspace(0, 2)
        y = f(x)
        #
        coef3 = leg.legfit(x, y, 3)
        assert_equal(len(coef3), 4)
        assert_almost_equal(leg.legval(x, coef3), y)
        #
        coef4 = leg.legfit(x, y, 4)
        assert_equal(len(coef4), 5)
        assert_almost_equal(leg.legval(x, coef4), y)
        #
        coef2d = leg.legfit(x, np.array([y, y]).T, 3)
        assert_almost_equal(coef2d, np.array([coef3, coef3]).T)
        # test weighting
        w = np.zeros_like(x)
        yw = y.copy()
        w[1::2] = 1
        y[0::2] = 0
        wcoef3 = leg.legfit(x, yw, 3, w=w)
        assert_almost_equal(wcoef3, coef3)
        #
        wcoef2d = leg.legfit(x, np.array([yw, yw]).T, 3, w=w)
        assert_almost_equal(wcoef2d, np.array([coef3, coef3]).T)
        # test scaling with complex values x points whose square
        # is zero when summed.
        x = [1, 1j, -1, -1j]
        assert_almost_equal(leg.legfit(x, x, 1), [0, 1])
Ejemplo n.º 46
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 def test_legfromroots(self) :
     res = leg.legfromroots([])
     assert_almost_equal(trim(res), [1])
     for i in range(1,5) :
         roots = np.cos(np.linspace(-np.pi, 0, 2*i + 1)[1::2])
         pol = leg.legfromroots(roots)
         res = leg.legval(roots, pol)
         tgt = 0
         assert_(len(pol) == i + 1)
         assert_almost_equal(leg.leg2poly(pol)[-1], 1)
         assert_almost_equal(res, tgt)
Ejemplo n.º 47
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    def test_legval(self):
        #check empty input
        assert_equal(leg.legval([], [1]).size, 0)

        #check normal input)
        x = np.linspace(-1, 1)
        y = [polyval(x, c) for c in Llist]
        for i in range(10):
            msg = "At i=%d" % i
            tgt = y[i]
            res = leg.legval(x, [0]*i + [1])
            assert_almost_equal(res, tgt, err_msg=msg)

        #check that shape is preserved
        for i in range(3):
            dims = [2]*i
            x = np.zeros(dims)
            assert_equal(leg.legval(x, [1]).shape, dims)
            assert_equal(leg.legval(x, [1, 0]).shape, dims)
            assert_equal(leg.legval(x, [1, 0, 0]).shape, dims)
Ejemplo n.º 48
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def dg_interface_flux_matrix(p, T):
    """The interface flux matrices, we use upwinding to get the fluxes
     Denote T the translation necessary to evaluate the flux from the
     other cell.

    There are also analytical expressions for these. See my thesis page 73.

    """

    G0 = smp.zeros(p + 1)
    G1 = smp.zeros(p + 1)
    for i in range(0, p + 1):
        for j in range(0, p + 1):
            li = L.basis(i)
            lj = L.basis(j)
            G0[i, j] = leg.legval(-1, li.coef) * \
                leg.legval(1, lj.coef) * (T**-1)
            G1[i, j] = leg.legval(1, li.coef) * leg.legval(1, lj.coef)

    return G0, G1
Ejemplo n.º 49
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        def __worker(rbin):
            rr = r[rbin]

            # Axis distribution beta parameters
            beta_axis = beta_coeffs_point(
                rr, self.coef, self.kmax, self.rkstep,
                self.sigma, self.lmax, oddl, truncate)

            # Detection function beta parameters in the detection frame
            beta_df = beta_coeffs_point(
                rr, df.coef, df.kmax, df.rkstep,
                df.sigma, df.lmax, df_oddl, truncate)

            # Detection function beta parameters in the lab frame
            beta_df = beta_df[0:lmax + 1] * plbeta

            # The following is too slow
            # res = scipy.optimize.basinhopping(
            #     lambda x: -legendre.legval(x, beta_df),
            #     [0.0], stepsize = 1.0/lmax, T=1.0,
            #     minimizer_kwargs=dict(method='TNC', bounds=((-1.0,1.0),))
            #     )

            # Find approximate position of maxmimum. Note that there
            # are lmax maxima/minima between -1..1, so this value of
            # Ns should suffice.
            res = scipy.optimize.brute(
                lambda x, *args: -legendre.legval(x, beta_df),
                ((-1.0, 1.0),), Ns=5.0 * lmax,
            )

            # Refine position of maximum - note that the 'finish'
            # option of optimize.brute doesn't work with fmin_tnc etc
            respolish = scipy.optimize.minimize(lambda x: -legendre.legval(x, beta_df),
                                                [res[0]], bounds=((-1.0,1.0),), method='TNC')

            maxval = -respolish.fun

            beta = beta_axis[0:lmax + 1] * beta_df[0:lmax + 1] * wt

            overlap[rbin] = beta.sum() / maxval
Ejemplo n.º 50
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def get_basis(deg, dofset=None):
    # Legendre polynomials are used as the basis of polynomials. In the basis of
    # Legendre polynomials is row of eye
    polyset = np.eye(deg+1)
   
    if dofset is None: dofset = np.linspace(-1, 1, deg+1)
    # Reatange dofs to have external first
    dofset = np.r_[dofset[0], dofset[-1], dofset[1:-1]]
    # Compute the nodal matrix
    A = np.array([legval(dofset, base) for base in polyset])
    # New coefficients
    B = np.linalg.inv(A) 

    # Combine the basis according to new weights
    basis = [lambda x, c=c: legval(x, c) for c in B]
    # Check that the basis is nodal
    assert np.allclose(np.array([f(dofset) for f in basis]), polyset)
    # First deriv
    dbasis = [lambda x, c=legder(c): legval(x, c) for c in B]
    
    return basis, dbasis
Ejemplo n.º 51
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    def test_legval(self) :
        def f(x) :
            return x*(x**2 - 1)

        #check empty input
        assert_equal(leg.legval([], [1]).size, 0)

        #check normal input)
        for i in range(10) :
            msg = "At i=%d" % i
            ser = np.zeros
            tgt = self.y[i]
            res = leg.legval(self.x, [0]*i + [1])
            assert_almost_equal(res, tgt, err_msg=msg)

        #check that shape is preserved
        for i in range(3) :
            dims = [2]*i
            x = np.zeros(dims)
            assert_equal(leg.legval(x, [1]).shape, dims)
            assert_equal(leg.legval(x, [1,0]).shape, dims)
            assert_equal(leg.legval(x, [1,0,0]).shape, dims)
Ejemplo n.º 52
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def leg_proj_legguass(x, signal, weights,lmax):
    """projection into legendre polynomial using gauss-legendre polynomial
    """
    coefs = np.zeros(lmax + 1)
    weights_sum = np.sum(weights)

    for l in range(lmax + 1):
        if l%2==0:
            cc = np.zeros(l+1)
            cc[l] = 1
            coefs[l] = np.sum( weights*legval(x,cc)*signal) / weights_sum*(2*l+1)

    return coefs
Ejemplo n.º 53
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def eval(pname,fiber,wavelength,verbose=False) :
    legdeg=hdulist[1].header["LEGDEG"]
    table=hdulist[1].data
    paramindex=numpy.where(table["PARAM"]==pname)[0][0]
    wavemin=table["WAVEMIN"][paramindex]
    wavemax=table["WAVEMAX"][paramindex]
    fiber_coeffs=table["COEFF"][paramindex][fiber]
    
    
    wr=2*(wavelength-(wavemin+wavemax)/2)/(wavemax-wavemin)
    val=legval(wr,fiber_coeffs)
    if verbose :
        print pname,"fiber=",fiber,"wave=",wavelength,"wrange=",wavemin,wavemax,"coefs=",fiber_coeffs,"val=",val
    return val
Ejemplo n.º 54
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def coeff_fig():
    """Plots a sorted degree sequence and its polynomial fit (used in lifting/restriction diagram). Also plots evolution of coefficients over time for both a cpi routine and a direct simulation (currently not included in manuscript).

    **To generate data:**::

        mpirun -n 50 ./pref_attach -n 100 -m 50000 -nms 1000000 -omw 100000 -ci 10000 -pStep 500000
        mpirun -n 50 ./pref_attach -n 100 -m 50000 -nms 1000000 -omw 100000 -ci 10000 -pStep 500000 -noinit
        cp ./paper-data/other-runs/withinitfitted_coeffs0.csv ./manuscript-materials/data
        cp ./paper-data/other-runs/withinitpre_proj_degs0.csv ./manuscript-materials/data
        cp ./paper-data/other-runs/withinittimes0.csv ./manuscript-materials/data
        cp ./paper-data/other-runs/noinittimes0.csv ./manuscript-materials/data
        cp ./paper-data/other-runs/noinitfitted_coeffs0.csv ./manuscript-materials/data
        cp ./paper-data/other-runs/noinitpre_proj_degs0.csv ./manuscript-materials/data

    """
    init = "noinit"
    times = np.genfromtxt(data_directory + init + 'times0.csv', delimiter=',', skip_header=True)
    degs = np.genfromtxt(data_directory + init + 'pre_proj_degs0.csv', delimiter=',', skip_header=True)
    fitted_coeffs = np.genfromtxt(data_directory + init + 'fitted_coeffs0.csv', delimiter=',', skip_header=True)

    init = "withinit"
    times_cpi = np.genfromtxt(data_directory + init + 'times0.csv', delimiter=',', skip_header=True)
    degs_cpi = np.genfromtxt(data_directory + init + 'pre_proj_degs0.csv', delimiter=',', skip_header=True)
    fitted_coeffs_cpi = np.genfromtxt(data_directory + init + 'fitted_coeffs0.csv', delimiter=',', skip_header=True)

    gsize = degs.shape[1]

    fig = plt.figure()
    ax = fig.add_subplot(111)
    index = 50 # arbitrary index, should show some curvature
    ax.scatter(np.arange(gsize), degs[index], label='Sorted degree sequence')
    ax.plot(np.arange(gsize), npl.legval(np.arange(gsize), fitted_coeffs[index]), c='r', label='Polynomial fit')
    ax.set_xlim((0,gsize))
    ax.set_xlabel('Vertex')
    ax.set_ylabel('Degree')
    ax.legend(loc=4, fontsize=42)
    fig.subplots_adjust(left=0.1, bottom=0.11)

    ncoeffs = fitted_coeffs.shape[1]
    for i in range(ncoeffs):
        fig = plt.figure()
        ax = fig.add_subplot(111)
        ax.scatter(times, fitted_coeffs[:,i], label='Direct simulation')
        ax.scatter(times_cpi, fitted_coeffs_cpi[:,i], label='CPI')
        ax.set_xlabel('Step')
        ax.set_ylabel(r'$c_' + str(i) + '$')
        ax.legend()

    plt.show()
def test_legendre_val():
    """Test Legendre polynomial (derivative) equivalence
    """
    rng = np.random.RandomState(0)
    # check table equiv
    xs = np.linspace(-1., 1., 1000)
    n_terms = 100

    # True, numpy
    vals_np = legendre.legvander(xs, n_terms - 1)

    # Table approximation
    for fun, nc in zip([_get_legen_lut_fast, _get_legen_lut_accurate],
                       [100, 50]):
        lut, n_fact = _get_legen_table('eeg', n_coeff=nc, force_calc=True)
        vals_i = fun(xs, lut)
        # Need a "1:" here because we omit the first coefficient in our table!
        assert_allclose(vals_np[:, 1:vals_i.shape[1] + 1], vals_i,
                        rtol=1e-2, atol=5e-3)

        # Now let's look at our sums
        ctheta = rng.rand(20, 30) * 2.0 - 1.0
        beta = rng.rand(20, 30) * 0.8
        lut_fun = partial(fun, lut=lut)
        c1 = _comp_sum_eeg(beta.flatten(), ctheta.flatten(), lut_fun, n_fact)
        c1.shape = beta.shape

        # compare to numpy
        n = np.arange(1, n_terms, dtype=float)[:, np.newaxis, np.newaxis]
        coeffs = np.zeros((n_terms,) + beta.shape)
        coeffs[1:] = (np.cumprod([beta] * (n_terms - 1), axis=0) *
                      (2.0 * n + 1.0) * (2.0 * n + 1.0) / n)
        # can't use tensor=False here b/c it isn't in old numpy
        c2 = np.empty((20, 30))
        for ci1 in range(20):
            for ci2 in range(30):
                c2[ci1, ci2] = legendre.legval(ctheta[ci1, ci2],
                                               coeffs[:, ci1, ci2])
        assert_allclose(c1, c2, 1e-2, 1e-3)  # close enough...

    # compare fast and slow for MEG
    ctheta = rng.rand(20 * 30) * 2.0 - 1.0
    beta = rng.rand(20 * 30) * 0.8
    lut, n_fact = _get_legen_table('meg', n_coeff=10, force_calc=True)
    fun = partial(_get_legen_lut_fast, lut=lut)
    coeffs = _comp_sums_meg(beta, ctheta, fun, n_fact, False)
    lut, n_fact = _get_legen_table('meg', n_coeff=20, force_calc=True)
    fun = partial(_get_legen_lut_accurate, lut=lut)
    coeffs = _comp_sums_meg(beta, ctheta, fun, n_fact, False)
Ejemplo n.º 56
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def recompute_legendre_coefficients(xcoef,ycoef,wavemin,wavemax,degxx,degxy,degyx,degyy,dx_coeff,dy_coeff) :
    """
    Modifies legendre coefficients of an input trace set using polynomial coefficents (as defined by the routine monomials)

    Args:
        xcoef : 2D np.array of shape (nfibers,ncoef) containing Legendre coefficents for each fiber to convert wavelenght to XCCD
        ycoef : 2D np.array of shape (nfibers,ncoef) containing Legendre coefficents for each fiber to convert wavelenght to YCCD
        wavemin : float
        wavemax : float. wavemin and wavemax are used to define a reduced variable legx(wave,wavemin,wavemax)=2*(wave-wavemin)/(wavemax-wavemin)-1
                  used to compute the traces, xccd=legval(legx(wave,wavemin,wavemax),xtrace[fiber])
        degxx : int, degree of polynomial for x shifts as a function of x (x is axis=1 in numpy image array, AXIS=0 in FITS, cross-dispersion axis = fiber number direction)
        degxy : int, degree of polynomial for x shifts as a function of y (y is axis=0 in numpy image array, AXIS=1 in FITS, wavelength dispersion axis)
        degyx : int, degree of polynomial for y shifts as a function of x
        degyy : int, degree of polynomial for y shifts as a function of y
        dx_coeff : 1D np.array of polynomial coefficients of size (degxx*degxy) as defined by the routine monomials.
        dy_coeff : 1D np.array of polynomial coefficients of size (degyx*degyy) as defined by the routine monomials.

    Returns:
        xcoef : 2D np.array of shape (nfibers,ncoef) with modified Legendre coefficents
        ycoef : 2D np.array of shape (nfibers,ncoef) with modified Legendre coefficents
    """
    wave=np.linspace(wavemin,wavemax,100)
    nfibers=xcoef.shape[0]
    rw=legx(wave,wavemin,wavemax)
    for fiber in range(nfibers) :
        x = legval(rw,xcoef[fiber])
        y = legval(rw,ycoef[fiber])

        m=monomials(x,y,degxx,degxy)
        dx=m.T.dot(dx_coeff)
        xcoef[fiber]=legfit(rw,x+dx,deg=xcoef.shape[1]-1)

        m=monomials(x,y,degyx,degyy)
        dy=m.T.dot(dy_coeff)
        ycoef[fiber]=legfit(rw,y+dy,deg=ycoef.shape[1]-1)
    return xcoef,ycoef
Ejemplo n.º 57
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    def test_evenly_spaced(self):
        import numpy as np
        from numpy.polynomial import legendre
        import six

        num_points = 17
        points = np.linspace(0, 1, num_points)
        result = self._call_func_under_test(points)
        self.assertEqual(result.shape, (num_points, num_points))
        self.assertTrue(result.flags.f_contiguous)
        expected_result = np.zeros((num_points, num_points))
        for n in six.moves.xrange(num_points):
            leg_coeffs = [0] * n + [1]
            expected_result[:, n] = legendre.legval(points, leg_coeffs)
        self.assertTrue(np.allclose(result, expected_result))
        frob_err = np.linalg.norm(result - expected_result, ord='fro')
        self.assertTrue(frob_err < 1e-13)
Ejemplo n.º 58
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def _calc_h(cosang, stiffness=4, num_lterms=50):
    """Calculate spherical spline h function between points on a sphere.

    Parameters
    ----------
    cosang : array-like of float, shape(n_channels, n_channels)
        cosine of angles between pairs of points on a spherical surface. This
        is equivalent to the dot product of unit vectors.
    stiffness : float
        stiffness of the spline. Also referred to as `m`.
    num_lterms : int
        number of Legendre terms to evaluate.
    H : np.ndrarray of float, shape(n_channels, n_channels)
        The H matrix.
    """
    factors = [(2 * n + 1) /
               (n ** (stiffness - 1) * (n + 1) ** (stiffness - 1) * 4 * np.pi)
               for n in range(1, num_lterms + 1)]
    return legval(cosang, [0] + factors)
Ejemplo n.º 59
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def contFitLegendreAboutLine(wave,flux,err,restlam,z,velfitregions,uniform=True,**kwargs):
    '''
    Fits a continuum over a spectral region using the formalism of Sembach
    & Savage 1992, estimating the uncertainty at each point of the continuum.

    Parameters
    ----------
    wave
    flux
    err
    restlam
    z
    velfitregions
    uniform

    Returns
    -------

    '''
    vels=joebgoodies.veltrans(z,wave,restlam)

    ### Find indices corresponding to velocities defined in velfitregions
    fitidxs=[]
    for reg in velfitregions:
        thesevels=np.where((vels>=reg[0])&(vels<=reg[1]))[0]
        fitidxs.extend(thesevels)

    if uniform != True:
        fitsol,err,parsol,errmtx,scalefac = fitLegendre(vels[fitidxs],flux[fitidxs],
                                           sig=err[fitidxs],**kwargs)
    else:
        fitsol,err,parsol,errmtx,scalefac = fitLegendre(vels[fitidxs],flux[fitidxs],**kwargs)

    ### Normalize x so that domain of fit is -1 to +1
    vscale = vels/scalefac # must scale to fitted domain

    ### Evaluate continuum using all points, not just those in fit regions
    continuum = L.legval(vels/scalefac,parsol)
    err = errorsLegendre(vscale,errmtx)

    return wave,continuum,err