Commit c8773202 authored by Philipp Arras's avatar Philipp Arras
Browse files

Add polynomial fitting demo and fix spelling mistake

parent fcbd1ea9
......@@ -111,3 +111,12 @@ run_bernoulli:
- '*.png'
stage: demo_runs
- python demos/
- python3 demos/
- '*.png'
import matplotlib.pyplot as plt
import numpy as np
import nifty5 as ift
def polynomial(coefficients, sampling_points):
"""Computes values of polynomial whose coefficients are stored in
coefficients at sampling points. This is a quick version of the
coefficients: Model
sampling_points: Numpy array
if not (isinstance(coefficients, ift.Model)
and isinstance(sampling_points, np.ndarray)):
raise TypeError
params = coefficients.value.to_global_data()
out = np.zeros_like(sampling_points)
for ii in range(len(params)):
out += params[ii] * sampling_points**ii
return out
class PolynomialResponse(ift.LinearOperator):
"""Calculates values of a polynomial parameterized by input at sampling points.
domain: UnstructuredDomain
The domain on which the coefficients of the polynomial are defined.
sampling_points: Numpy array
x-values of the sampling points.
def __init__(self, domain, sampling_points):
super(PolynomialResponse, self).__init__()
if not (isinstance(domain, ift.UnstructuredDomain)
and isinstance(x, np.ndarray)):
raise TypeError
self._domain = ift.DomainTuple.make(domain)
tgt = ift.UnstructuredDomain(sampling_points.shape)
self._target = ift.DomainTuple.make(tgt)
sh = (, domain.size)
self._mat = np.empty(sh)
for d in range(domain.size):
self._mat.T[d] = sampling_points**d
def apply(self, x, mode):
self._check_input(x, mode)
val = x.to_global_data()
if mode == self.TIMES:
# FIXME Use polynomial() here
out =
# FIXME Can this be optimized?
out = self._mat.conj()
return ift.from_global_data(self._tgt(mode), out)
def domain(self):
return self._domain
def target(self):
return self._target
def capability(self):
return self.TIMES | self.ADJOINT_TIMES
# Generate some mock data
N_params = 10
N_samples = 100
size = (12,)
x = np.random.random(size) * 10
y = np.sin(x**2) * x**3
var = np.full_like(y, y.var() / 10)
var[-2] *= 4
var[5] /= 2
y[5] -= 0
# Set up minimization problem
p_space = ift.UnstructuredDomain(N_params)
params = ift.Variable(ift.MultiField.from_dict(
{'params': ift.full(p_space, 0.)}))['params']
R = PolynomialResponse(p_space, x)
d_space =
d = ift.from_global_data(d_space, y)
N = ift.DiagonalOperator(ift.from_global_data(d_space, var))
IC = ift.GradientNormController(tol_abs_gradnorm=1e-8)
H = ift.Hamiltonian(ift.GaussianEnergy(R(params), d, N), IC)
H = H.make_invertible(IC)
# Minimize
minimizer = ift.RelaxedNewton(IC)
H, _ = minimizer(H)
# Draw posterior samples
samples = [H.metric.draw_sample(from_inverse=True) + H.position
for _ in range(N_samples)]
# Plotting
plt.errorbar(x, y, np.sqrt(var), fmt='ko', label='Data with error bars')
xmin, xmax = x.min(), x.max()
xs = np.linspace(xmin, xmax, 100)
sc = ift.StatCalculator()
for ii in range(len(samples)):
ys = polynomial([ii]), xs)
if ii == 0:
plt.plot(xs, ys, 'k', alpha=.05, label='Posterior samples')
plt.plot(xs, ys, 'k', alpha=.05)
ys = polynomial(, xs)
plt.plot(xs, ys, 'r', linewidth=2., label='Interpolation')
# Print parameters
mean = sc.mean.to_global_data()
sigma = np.sqrt(sc.var.to_global_data())
for ii in range(len(mean)):
print('Coefficient x**{}: {:.2E} +/- {:.2E}'.format(ii, mean[ii],
......@@ -54,7 +54,7 @@ class HartleyOperator(LinearOperator):
of the result field, respectivey.
In many contexts the Hartley transform is a perfect substitute for the
Fourier transform, but in some situations (e.g. convolution with a general,
non-symmetrc kernel, the full FFT must be used instead.
non-symmetric kernel, the full FFT must be used instead.
def __init__(self, domain, target=None, space=None):
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