def function_to_sin(fctn: Function):
psi = fctn.get_domain()
theta = fctn.eval()
sinsqrd = np.fromiter(map(lambda x: np.sin(np.deg2rad(x)) ** 2, psi), float)
dy = fctn.dy
if dy is not None:
dy = Function.to_function(sinsqrd, dy.eval())
return Function.to_function(sinsqrd, theta, dy=dy)
def to_function(cls, domain, feval, x_err=None, y_err=None):
f = Function.to_function(domain, feval)
if x_err is not None:
x_err = Function.to_function(domain, x_err)
if y_err is not None:
y_err = Function.to_function(domain, y_err)
return cls(f, x_err, y_err)
def _to_sin_sqr(self, fctn):
psi = fctn.get_domain()
theta = fctn.eval()
sinsqrd = np.fromiter(map(lambda x: np.sin(np.deg2rad(x))**2, psi),
float)
dy = fctn.dy
if not dy.is_null():
dy = Function.to_function(sinsqrd, dy.eval())
return Function.to_function(sinsqrd, theta, dy=dy)
def test_exp():
domain = np.linspace(-5, 5, 100)
w_space = np.linspace(-10, 10, 1000)
a = 2
f = Function.to_function(domain, lambda x: np.exp(-a * x ** 2))
F_analytical = Function.to_function(w_space, lambda x: np.sqrt(np.pi / a) * np.exp(-x ** 2 / (4 * a)))
F = FourierTransform.from_function(w_space, f)
assert_equal(F, F_analytical)
def from_file(self):
from numpy import loadtxt
q, R, dq, dR = loadtxt(self._file).T
f = Function.to_function(q, R)
df = Function.to_function(q, dR)
dx = Function.to_function(q, dq)
f.set_dy(df)
f.set_dx(dx)
return f
def from_file(self):
from numpy import loadtxt
q, dq, R, dR = loadtxt(self._file, usecols=(0, 1, 2, 3)).T
f = Function.to_function(q, R)
dx = Function.to_function(q, dq)
dy = Function.to_function(q, dR)
f.set_dy(dy)
f.set_dx(dx)
return f
def test_identity_matrix():
x_space = np.linspace(-10, 10, 1000)
w_space = np.linspace(-10, 10, 1000)
fun = Function(x_space, lambda x: np.exp(-x**2 / 2))
trafo = fourier_matrix(x_space, w_space)
f = Function.to_function(w_space, np.dot(trafo, fun(x_space)))
trafo = invfourier_matrix(w_space, x_space)
fun2 = Function.to_function(x_space, np.dot(trafo, f(w_space)))
assert_equal(fun, fun2)
def merge_group(self, group):
multi_merge = MultiMerger(MeasurementMerger())
merged = {}
for psi, mss in group.items():
merge = multi_merge.merge(mss)
merge = ErrorCalculation().manipulate(
merge, self._c._settings_controller.get_measurement_context())
theta, dtheta, counts, dcounts = zip(*merge.get_data())
theta = np.array(theta)
dx = Function.to_function(theta, dtheta)
dy = Function.to_function(theta, dcounts)
merged[psi] = Function.to_function(theta, counts, dx=dx, dy=dy)
return merged
def remesh(self, interpolation=1, interpolation_kind=None):
"""
Re-meshes the loaded data onto a common grid by interpolation.
Usually, the reflectivity data is not measured at the very same q points. Also the min/max range of
the q values might vary. But, to reconstruct the phase, the reflectivity needs to be measured at
the same q values. This method achieves this goal.
The new grid is the coarsest possible grid. The min/max values are chosen such that every reflectivity
measurement contains the min/max values.
:param interpolation: integer number. Defines the number of additional interpolations between
two q-grid points
:param interpolation_kind: interpolation of the function between the point (linear/quadratic/etc..)
See scipy.interp1d for possible values
:return: None
"""
# coarsest possible grid
qmin = max([ms['Qin'][0] for ms in self._measurements])
qmax = min([ms['Qin'][-1] for ms in self._measurements])
npts = min([len(ms['Qin']) for ms in self._measurements])
new_mesh = np.linspace(qmin, qmax, npts + 1)
for measurement in self._measurements:
q, R, dR = measurement['Qin'], measurement['Rin'], measurement[
'dRin']
try:
from skipi.function import Function
f = Function.to_function(
q, R, interpolation=interpolation_kind).remesh(
new_mesh).oversample(interpolation)
if dR is not None:
df = Function.to_function(
q, dR, interpolation=interpolation_kind).remesh(
new_mesh).oversample(interpolation)
dR = df.eval()
measurement['Qin'], measurement['Rin'], measurement[
'dRin'] = f.get_domain(), f.eval(), dR
except:
# Fallback if skipi is not available
q, R = remesh([q, R], qmin, qmax, npts, left=0, right=0)
if dR is not None:
q, dR = remesh([q, dR], qmin, qmax, npts, left=0, right=0)
measurement['Qin'], measurement['Rin'], measurement[
'dRin'] = q, R, dR
def from_functions(cls, functions: [Function], domain=None, avg_fun=None):
if domain is None:
domain = functions[0].get_domain()
if avg_fun is None:
avg_fun = cls.avg
return Function.to_function(domain, lambda x: avg_fun([f(x) for f in functions]))
def to_function(cls, frequency_domain, feval, x_domain):
dx = Domain.get_dx(frequency_domain)
w = numpy.array(x_domain).reshape((len(x_domain), 1))
domain = numpy.array(frequency_domain).reshape(
(1, len(frequency_domain)))
feval = evaluate(domain, feval)
F = trapz(feval * numpy.cos(numpy.dot(w, domain)), dx=dx)
return Function.to_function(x_domain, F)
def test_compare_matrix_with_fourier_function():
x_space = np.linspace(-10, 10, 1000)
fun = Function(x_space, lambda x: np.exp(-x**2 / 2))
w_space = np.linspace(-10, 10, 1000)
f1 = FourierTransform.from_function(w_space, fun)
trafo = fourier_matrix(x_space, w_space)
f2 = Function.to_function(w_space, np.dot(trafo, fun(x_space)))
assert_equal(f1, f2, 1e-14)
def test_compare_InverseFourier_matrix():
x_space = np.linspace(-10, 10, 1000)
w_space = np.linspace(-10, 10, 1000)
fun = Function(x_space, lambda x: np.exp(-x**2 / 2))
f = FourierTransform.from_function(w_space, fun)
trafo = invfourier_matrix(x_space, w_space)
fun2 = Function.to_function(w_space, np.dot(trafo, f(x_space)))
assert_equal(fun, fun2)
def to_function(cls, frequency_domain, feval, x_domain):
# TODO: frequency_domain as Domain?
w = numpy.array(x_domain).reshape((len(x_domain), 1))
domain = numpy.array(frequency_domain).reshape(
(1, len(frequency_domain)))
feval = evaluate(domain, feval)
integrand = feval * numpy.exp(1j * numpy.dot(w, domain))
F = 1 / (2 * numpy.pi) * trapz(integrand,
dx=Domain.get_dx(frequency_domain))
return Function.to_function(x_domain, F)
def from_function(cls, function: Function):
dy = function.dy
if dy is None:
return function
value = numpy.random.normal(function.eval().real, dy.eval().real)
if function.is_complex():
value = value + 1j * numpy.random.normal(function.eval().imag, dy.eval().imag)
return Function.to_function(function.get_dom(), value)
def test_gauss():
domain = Domain(-1, 1, 10000)
#domain = np.linspace(-1, 1, 10000)
f = Function.to_function(domain, lambda x: rect(1 / (2 * np.pi) * x))
freq_dom = np.linspace(-20, 20, 1000)
F = FourierTransform.from_function(freq_dom, f)
fourier_trafo = Function(domain, lambda x: 2 * sinc(x / np.pi))
import pylab
pylab.plot(domain.get(), [fourier_trafo(x) for x in domain])
Function.to_function(domain, lambda x: 2*sinc(x/np.pi)).plot()
pylab.show()
#f.plot()
#fourier_trafo.plot()
#(f - fourier_trafo).plot(show=True)
assert_equal(F, fourier_trafo, TOL=1e-6, do_print=True)
def to_function(cls, domain, feval, frequency_domain):
#TODO: frequency_domain as Domain?
#domain = Domain.from_domain(domain)
#frequency_domain = Domain.from_domain(frequency_domain)
#dom = domain.get()
#freq_dom = frequency_domain.get()
w = numpy.array(frequency_domain).reshape((len(frequency_domain), 1))
feval = evaluate(domain, feval)
t_domain = numpy.array(domain).reshape((1, len(domain)))
integrand = feval * numpy.exp(-1j * numpy.dot(w, t_domain))
F = trapz(integrand, dx=Domain.get_dx(domain))
return Function.to_function(frequency_domain, F)
def from_functions(cls, functions: [Function], domain=None, std_fun=None):
"""
Computes the standard deviation (pointwise) using all functions
If domain is None, the domain from the first function will be used
If std_fun is None, the "complex" standard deviation will be used, see the method cstd.
:param functions: A list of functions from which the std should be calculated
:param domain: A domain
:param std_fun: A function calculating the std
:return: new Function
"""
if domain is None:
domain = functions[0].get_domain()
if std_fun is None:
std_fun = cls.cstd
return Function.to_function(domain, lambda x: std_fun([f(x) for f in functions]))
dmax.append((psi, f.argmax()))
print(fit.fit_report(show_correl=False))
pylab.show()
def function_to_sin(fctn: Function):
psi = fctn.get_domain()
theta = fctn.eval()
sinsqrd = np.fromiter(map(lambda x: np.sin(np.deg2rad(x)) ** 2, psi), float)
dy = fctn.dy
if dy is not None:
dy = Function.to_function(sinsqrd, dy.eval())
return Function.to_function(sinsqrd, theta, dy=dy)
def function_to_d(fctn: Function):
return fctn.transform(lambda sin, theta: wavelength_k1 / (2*np.sin(np.deg2rad(theta))))
# data = dmax
psi, theta = zip(*data)
psi = np.array(psi)
f = Function.to_function(psi, theta)
fpos = function_to_d(function_to_sin(f.vremesh((0, None), dstart=-1)))
fneg = function_to_d(function_to_sin(f.vremesh((None, 0))))
pylab.xlabel(xlabel="$\sin^2 \psi")
fpos.plot(label='$\psi > 0$')
fneg.plot(show=True, label='$\psi < 0$', )
def from_function(cls, fun: Function, **kwargs):
domain = fun.get_domain()
conv = numpy.convolve(fun(domain),
cls.get_kernel(fun, **kwargs),
mode='same')
return Function.to_function(domain, conv)
def analyze(self):
measurements = self._c.measurements # type: uxdconverter.measurement.Measurements
psi_measurement_dict = self.merge_group(
self.group_measurements_by_psi(measurements))
wavelength_k1 = 0.70931724
wavelength_k2 = 0.71360728
psis = []
thetas = []
for psi, fctn in psi_measurement_dict.items():
if not (psi in self._fitters.keys()):
self._fitters[psi] = CorrelatedTwoPeakFit(
fctn, wavelength_k1, wavelength_k2)
fitter = self._fitters[psi]
fit = fitter.get_fit()
fitter.plot()
print(fit.fit_report(show_correl=False))
if fit.redchi > 1000:
continue
psis.append(psi)
thetas.append(fitter.get_peak_position())
pylab.show()
pylab.figure()
pylab.xlabel("$sin^2(\psi)$")
pylab.ylabel("lattice spacing $[\AA]$")
f = Function.to_function(psis, np.array(thetas))
trafo_to_lattice = lambda psi, theta: wavelength_k1 / (2 * np.sin(
np.deg2rad(theta)))
dy_traf = lambda psi, theta: np.abs(
trafo_to_lattice(psi, theta) / np.tan(np.deg2rad(theta)))
dy_scale = f.transform(dy_traf)
dy_traf = lambda psi, dtheta: dtheta * dy_scale(psi)
f = f.transform(trafo_to_lattice, trafo_dy=dy_traf)
if f.get_dom().min() < 0:
fneg = self._to_sin_sqr(f.vremesh((None, 0)))
else:
fneg = NullFunction(f.get_dom())
if f.get_dom().max() > 0:
fpos = self._to_sin_sqr(f.vremesh((0, None), dstart=-1))
else:
fpos = NullFunction(f.get_dom())
fpos.plot(label='$\psi \geq 0$')
fneg.plot(label='$\psi < 0$')
self.analyze_psi(fpos)
self.analyze_psi(fneg)
pylab.show()
return f
def from_functions(cls, functions: [Function]):
return Function.to_function(functions[0].get_dom(), lambda x: numpy.min([f(x) for f in functions]))
