def least(func, x, y, sy=None, beta0=[]):
linear = odrpack.Model(func)
#mydata = odrpack.Data(x, z[1], wd=1./np.power(z[2],2), we=1./np.power(sy,2))
if not sy == None:
mydata = odrpack.RealData(x, y, sy=sy)
else:
mydata = odrpack.RealData(x, y)
myodr = odrpack.ODR(mydata, linear, beta0=beta0)
myodr.set_job(fit_type=2)
myoutput = myodr.run()
myoutput.pprint()
return myodr.output
def bilinear_Q_regression(freqs_log, Q_list_log):
freqs_log = array(freqs_log)
#data = odrpack.RealData(x[12:], y[12:])
data = odrpack.RealData(freqs_log, Q_list_log)
#x_range = arange(-0.5, 1.0, step=0.01) # x range
bilin_reg = odrpack.Model(bilinear_reg_free)
odr = odrpack.ODR(data, bilin_reg, beta0=[0.4, 3.0, 0.3, -0.5])
odr.set_job(
fit_type=2) #if set fit_type=2, returns the same as least squares
out = odr.run()
#print('\nbilinear auto\n')
#out.pprint()
a = out.beta[0]
b = out.beta[1]
c = out.beta[2]
hx = out.beta[3] # x hinge point
log_q_fit = b + a * freqs_log # get y values from bilinear
yhinge = b + a * hx
idx = freqs_log > hx
log_q_fit[idx] = c * (freqs_log[idx] - hx) + yhinge
return log_q_fit
def bilinear_regression(x, y):
data = odrpack.RealData(x[12:], y[12:])
x_range = np.arange(-0.5, 1.0, step=0.01) # x range
bilin_reg = odrpack.Model(bilinear_reg_free)
odr = odrpack.ODR(data, bilin_reg, beta0=[0.4, 3.0, 0.3, -0.5])
odr.set_job(fit_type=2) #if set fit_type=2, returns the same as least squares
out = odr.run()
print('\nbilinear auto\n')
out.pprint()
a = out.beta[0]
b = out.beta[1]
c = out.beta[2]
hx = out.beta[3] # x hinge point
y_range = b + a * x_range # get y values from bilinear
yhinge = b + a * hx
idx = x_range > hx
y_range[idx] = c * (x_range[idx]-hx) + yhinge
return y_range, x_range
def least(func, x, y, sy=None, beta0=None, ifixb=None, fjacb=None):
linear = odrpack.Model(func, fjacb=fjacb)
#mydata = odrpack.Data(x, z[1], wd=1./np.power(z[2],2), we=1./np.power(sy,2))
mydata = odrpack.RealData(x, y, sy=sy)
myodr = odrpack.ODR(mydata, linear, beta0=beta0, ifixb=ifixb)
myodr.set_job(fit_type=2)
myoutput = myodr.run()
# myoutput.pprint()
return myodr.output
def ws_correlation_orthoginal_distance_model(data, ref_ws_col='ref', site_ws_col='site', force_through_origin=False):
"""Calculate the slope and offset between two wind speed columns using orthoganal distance regression.
https://docs.scipy.org/doc/scipy-0.18.1/reference/odr.html
:Parameters:
data: DataFrame
DataFrame with wind speed columns ref and site, and direction data dir
ref_ws_col: string, default None (primary anemometer assumed)
Reference anemometer data to use. Extracted from MetMast.data
site_ws_col: string, default None (primary anemometer assumed)
Site anemometer data to use. Extracted from MetMast.data
force_through_origin: boolean, default False
Force the correlation through the origin (offset equal to zero)
:Returns:
out: DataFrame
slope, offset, R2, uncert, points
"""
data = data.loc[:, [ref_ws_col, site_ws_col]].dropna().astype(np.float)
results = return_correlation_results_frame(ref_label=ref_ws_col, site_label=site_ws_col)
if not valid_ws_correlation_data(data=data, ref_ws_col=ref_ws_col, site_ws_col=site_ws_col):
return results
points = data.shape[0]
R2 = calculate_R2(data=data, ref_ws_col=ref_ws_col, site_ws_col=site_ws_col)
uncert = calculate_IEC_uncertainty(data=data, ref_ws_col=ref_ws_col, site_ws_col=site_ws_col)
X = data.loc[:, ref_ws_col].values
Y = data.loc[:, site_ws_col].values
data_mean = data.mean()
slope_estimate_via_ratio = data_mean[site_ws_col] / data_mean[ref_ws_col]
realdata = odrpack.RealData(X, Y)
if force_through_origin:
linear = odrpack.Model(f_without_offset)
odr = odrpack.ODR(realdata, linear, beta0=[slope_estimate_via_ratio])
slope = odr.run().beta[0]
offset = 0
else:
linear = odrpack.Model(f_with_offset)
odr = odrpack.ODR(realdata, linear, beta0=[slope_estimate_via_ratio, 0.0])
slope, offset = odr.run().beta[0], odr.run().beta[1]
results.loc[pd.IndexSlice[ref_ws_col, site_ws_col], ['slope', 'offset', 'R2', 'uncert', 'points']] = np.array(
[slope, offset, R2, uncert, points])
return results
def fitScipyODR(xdata, ydata, xerr, yerr, func, pInit):
""" Fit a series of data points with ODR (function must be in from f(beta[n], x))
"""
model = odrpack.Model(func)
data = odrpack.RealData(xdata, ydata, sx=xerr, sy=yerr)
odr = odrpack.ODR(data, model, beta0=pInit)
out = odr.run()
popt = out.beta
pcov = out.cov_beta
out.pprint()
print('Chi square = %f' % out.sum_square)
return popt, pcov
def do_odr(f, x, xe, y, ye, estimates):
model = odrpack.Model(f)
# sx and sy should be the covariances
data = odrpack.RealData(x, y, sx=xe, sy=ye)
# need to hard-code in estimates for parameters
odr = odrpack.ODR(data, model, estimates)
output = odr.run()
return output
def estimate_spectra(self):
from scipy.odr import odrpack as odr
def ofunc(pars, x, sp_sens, nu, el):
a, b, dkalpha, tele = pars
spectra = a * Kalpha_profile(el, nu, dkalpha) + b * ff_profile(
nu, tele)
spectra /= np.trapz(spectra, nu)
spectra = np.tile(spectra, (sp_sens.shape[0], 1))
comp_tr = np.trapz(sp_sens * spectra, nu, axis=-1)
return comp_tr
def ofunc2(pars, thick, nu, el):
spectra = compute_spectra(pars, nu)
sp_tr_filters = np.ones(nu.shape)
for filt_el, filt_thick in self.filters.iteritems():
sp_tr_filters *= np.exp(-cold_opacity(filt_el, nu=nu) *
filt_thick)
ip_sens = ip_sensitivity(nu)
comp_tr = []
for this_thick in thick:
sp_sens = np.exp(-cold_opacity(el, nu=nu)*this_thick)\
* sp_tr_filters * ip_sens * spectra
comp_tr.append(np.trapz(sp_sens, nu, axis=0))
return np.array(comp_tr).reshape((1, -1))
#return ((comp_tr - exp_tr)**2).sum()
beta0 = [1, 1, 100, 1000]
my_data = odr.RealData(self.thick,
self.exp_tr,
sy=0.05 * np.ones(self.exp_tr.shape))
my_model = odr.Model(ofunc2, extra_args=(self.nu, 'polystyrene'))
my_odr = odr.ODR(my_data, my_model, beta0=beta0)
my_odr.set_job(fit_type=2)
my_odr.set_iprint(final=2, iter=1, iter_step=1)
fit = my_odr.run()
self.beta = fit.beta #[::-1]
self.sdbeta = fit.sd_beta #[::-1]
print(ofunc2(self.beta, self.thick, self.nu, 'polystyrene'))
print(self.exp_tr)
print('\n')
print(beta0)
print(self.beta)
def nominal_AB(self, K, N, T, explore_mag=10, res_time=100):
'''
Estimates matrices A and B
Args:
K: The controller gain
N: number of iterations to be consistent with iterative methods
T: Rollout length
explore_mag: noise magnitude for excitement
res_time: when to reset the dynamics to its initial condition
Returns: A_nom, B_nom
'''
Lin_gain = LinK(K)
Lin_gain.make_sampling_on(explore_mag)
if T >= res_time:
N = int(np.ceil(N * T / res_time))
T = res_time
A_nom = np.zeros((self.n, self.n))
B_nom = np.zeros((self.n, self.m))
# storage matrices
states_batch = np.zeros((self.n, N, T))
next_states_batch = np.zeros((self.n, N, T))
actions_batch = np.zeros((self.m, N, T))
# simulate
for k in range(N):
# Do one rollout to save data for model estimation
states, actions, _, next_states = self.dyn.one_rollout(Lin_gain.sample_lin_policy, T)
states_batch[:, k, :] = states.T
actions_batch[:, k, :] = actions.T
next_states_batch[:, k, :] = next_states.T
for i in range(self.n):
linear = odrpack.Model(linear_func)
data = odrpack.RealData(
x=np.vstack((states_batch.reshape(self.n, N * T), actions_batch.reshape(self.m, N * T))),
y=next_states_batch[i, :, :].reshape(1, N * T))
Myodr = odrpack.ODR(data, linear, np.zeros(self.n + self.m))
out = Myodr.run()
tmp = out.beta
A_nom[i, :] = tmp[0:self.n]
B_nom[i, :] = tmp[self.n:]
return A_nom, B_nom
def fitSingleCrystalBallPeak(self):
params = np.array([
self.peak1_paramsEdits[0].value(),
self.peak1_paramsEdits[1].value(),
self.peak1_paramsEdits[2].value(),
self.peak1_paramsEdits[3].value(), 0.9, 4
])
model = odr.Model(lineshape.Single_Crystalball)
odr_data = odr.RealData(self.x_cut,
self.y_cut) #, sy = np.sqrt(self.y_cut))
myodr = odr.ODR(odr_data, model, beta0=params)
myodr.set_job(fit_type=0)
myoutput = myodr.run()
self.params = myoutput.beta
params_cov = myoutput.cov_beta
params_output = []
params_red_chi2 = myoutput.res_var
content, error = integrate.quad(lineshape.Single_Crystalball_integrand,
self.x_fit[0],
self.x_fit[-1],
args=tuple(self.params))
params_output.append(content)
params_output.append(params_red_chi2)
self.params_outputs = np.array(params_output)
for i in range(len(self.peak1_paramsEdits)):
self.peak1_paramsEdits[i].setValue(self.params[i])
self.peak1_contentEdit.setText(str(self.params_outputs[0]))
self.peak1_chi2Edit.setText(str(self.params_outputs[1]))
self.plotWidget.plot(clear=True)
self.plotWidget.plot(self.x, self.y[:-1], stepMode=True)
fitPen = pg.mkPen(color=(204, 0, 0), width=2)
self.plotWidget.plot(self.x_fit,
lineshape.Single_Crystalball(
self.params, self.x_fit),
pen=fitPen)
self.plotWidget.addItem(self.vLine, ignoreBounds=True)
self.plotWidget.addItem(self.hLine, ignoreBounds=True)
def fit2(data,interval,init):
interval.sort()
nData = data[(data[:,0] > interval[0])&(data[:,0] < interval[1])]
x=nData[:,0]
y=nData[:,1]
sx=None
sy=None
try:
sx = nData[:,2]
sy = nData[:,3]
except:
pass
def func(B,x):
return (1/B[0]) * x
linear = odrpack.Model(func)
mydata = odrpack.RealData(x, y, sx=sx, sy=sy)
myodr = odrpack.ODR(mydata, linear, beta0=[init])
myoutput = myodr.run()
myoutput.pprint()
return [myoutput.beta[0],myoutput.sd_beta[0]]
def fit_tls(x: np.ndarray, y: np.ndarray) -> float: """Fit total least squares model to data This function fits a total least squares (also known as orthogonal distance regression) model to 2-dimensional data. The model has the form `y = m * x`, where m is the "slope". (It has an intercept at y==0). See Also: At its core, the function uses scipy's `Orthogonal Distance Regression`_ module .. _Orthogonal Distance Regression: https://docs.scipy.org/doc/scipy/reference/odr.html Args: x: 1-dimensional Numpy array y: 1-dimensional Numpy array of the same size as `x` Returns: The slope of the fitted model """ odr_data = odrpack.RealData(x, y) model = odrpack.Model(lambda beta, x_: beta[0] * x_) odr_container = odrpack.ODR(odr_data, model, beta0=[1.0]) slope = odr_container.run().beta[0] #TODO PLOT SECTOR 0 some pairs (weird results) return slope
def ODRfit(model, X, Y, p0, verbose=False):
if type(p0) != 'numpy.ndarray':
try:
p0, up0 = unpack_unarray(p0)
except TypeError:
pass
x, ux = unpack_unarray(X)
y, uy = unpack_unarray(Y)
modello = odrpack.Model(model)
data = odrpack.RealData(x, y, sx=ux, sy=uy)
engine = odrpack.ODR(data, modello, beta0=p0)
output = engine.run()
P = unc.correlated_values(output.beta, output.cov_beta)
if verbose:
output.pprint()
return P, output.sum_square
infile = sys.argv[1]
outfile = sys.argv[2]
dataframe = pd.read_pickle(infile)
def f(params, x):
rho_per, rho_par, shift = params
return rho_per + (rho_par - rho_per) * np.cos(x - shift)**2
slice = dataframe.loc[dataframe.current == CURRENT]
R_S = "Sample Resistance, R_S (Ohmns)"
R_S_E = "Error in R_S, alpha_R_S (Ohms)"
A = "Angle, theta (degrees)"
A_E = "Error in theta, alpha_theta (degrees)"
xs = slice[A] * np.pi / 180
ys = slice[R_S]
sx = slice[A_E] * np.pi / 180
sy = slice[R_S_E]
beta0 = [0., 2., 0.]
linear = odrpack.Model(f)
mydata = odrpack.RealData(xs, ys, sx=sx, sy=sy)
myodr = odrpack.ODR(mydata, linear, beta0, maxit=100)
myoutput = myodr.run()
fig, ax = plt.subplots()
ax.scatter(xs, ys, marker="+")
ax.plot(xs, f(myoutput.beta, xs))
fig.savefig(outfile)
##
## Test orth. regression
##
################################################################################
def f(B, theta1):
return B[0] * (np.cos((2*np.pi)/360*theta1))**2 + B[1]
x = theta1
y = a1
sx = theta2
sy = a2
linear = odrpack.Model(f)
myData = odrpack.RealData(x, y, sx=sx, sy=sy)
myOdr = odrpack.ODR(myData, linear , beta0=[1,1])
myOdr.set_job(fit_type=2) #if set fit_type=2, returns the same as leastsq
out = myOdr.run()
#out.pprint()
coeff = out.beta[::-1]
err = out.sd_beta[::-1]
print(coeff[0], err[0])
print(coeff[1], err[1])
################################################################################
stdp[x, :, :] = np.std(np.fft.ifft(np.fft.fft(temp) * noise_mask), -1)
# Reshape variables into a single column
mag = np.reshape(
mag, (-1, nt)) # Reshapes variable intro 2D matrix of voxels x timepoints
ph = np.reshape(ph, (-1, nt))
stdm = np.reshape(
stdm, (-1, )) # Reshapes variable intro array of length = number of voxels
stdp = np.reshape(stdp, (-1, ))
mask = np.reshape(mask, (-1, ))
for x in range(mag.shape[0]):
if mask[x]:
design = ph[x, :]
ests = [stdm[x] / stdp[x], 1.0]
mydata = odr.RealData(design, mag[x, :], sx=stdp[x], sy=stdm[x])
odr_obj = odr.ODR(mydata, linearfit, beta0=ests, maxit=600)
res = odr_obj.run()
est = res.y
r2[x] = 1.0 - (np.sum((mag[x, :] - est)**2) / np.sum((mag[x, :])**2))
# take out scaled phase signal and re-mean may need correction
sim[x, :] = ph[x, :] * res.beta[0]
filt[x, :] = mag[x, :] - est
# estimate residuals
residuals[x, :] = np.sign(mag[x, :] - est) * (
np.sum(res.delta**2, axis=0) + res.eps**2)
delta[x, :] = np.sum(
res.delta, axis=0
) # res.delta --> Array of estimated errors in input variables (same shape as x)
print(linfit3)
#[ 2.34733290e-07 -6.08446455e-05]
#[ 2.62854976e-07 -8.24342656e-05]
#[ 2.58426791e-07 -7.77971621e-05]
def f(B, x):
return B[0] * x + B[1]
linear = odrpack.Model(f)
#for i in range(0):
mydata1 = odrpack.RealData(druck[0],
brechungsindex[0],
sx=Er_druck[0],
sy=Er_brech[0])
mydata2 = odrpack.RealData(druck[1],
brechungsindex[1],
sx=Er_druck[1],
sy=Er_brech[1])
mydata3 = odrpack.RealData(druck[2],
brechungsindex[2],
sx=Er_druck[2],
sy=Er_brech[2])
myodr1 = odrpack.ODR(mydata1, linear, beta0=[1., 2.])
myodr2 = odrpack.ODR(mydata2, linear, beta0=[1., 2.])
myodr3 = odrpack.ODR(mydata3, linear, beta0=[1., 2.])
myoutput1 = myodr1.run()
myoutput2 = myodr2.run()
myoutput3 = myodr3.run()
def peak_fit(xdata, ydata, iparams=[], peaktype='Gauss', maxit=300,
background='constant', plot=False, func_out=False, debug=False):
"""
fit function using odr-pack wrapper in scipy similar to
https://github.com/tiagopereira/python_tips/wiki/Scipy%3A-curve-fitting
for Gauss, Lorentz or Pseudovoigt-functions
Parameters
----------
xdata: xcoordinates of the data to be fitted
ydata: ycoordinates of the data which should be fit
keyword parameters:
iparams: initial paramters for the fit,
determined automatically if not specified
peaktype: type of peak to fit: 'Gauss', 'Lorentz', 'PseudoVoigt',
'PseudoVoigtAsym'
maxit: maximal iteration number of the fit
background: type of background, either 'constant' or 'linear'
plot: flag to ask for a plot to visually judge the fit.
If plot is a string it will be used as figure name, which
makes reusing the figures easier.
func_out: returns the fitted function, which takes the independent
variables as only argument (f(x))
Returns
-------
params,sd_params,itlim[,fitfunc]
the parameters as defined in function Gauss1d/Lorentz1d/PseudoVoigt1d/
PseudoVoigt1dasym(x, *param). In the case of linear background one more
parameter is included! For every parameter the corresponding errors of the
fit 'sd_params' are returned. A boolean flag 'itlim', which is False in
the case of a successful fit is added by default. Further the function
used in the fit can be returned (see func_out).
"""
if plot:
try:
from matplotlib import pyplot as plt
except ImportError:
if config.VERBOSITY >= config.INFO_ALL:
print("XU.math.peak_fit: Warning: plot "
"functionality not available")
plot = False
gfunc, gfunc_dx, gfunc_dp = _getfit_func(peaktype, background)
# determine initial parameters
_check_iparams(iparams, peaktype, background)
if not any(iparams):
iparams = _guess_iparams(xdata, ydata, peaktype, background)
if config.VERBOSITY >= config.DEBUG:
print("XU.math.peak_fit: iparams: %s" % str(tuple(iparams)))
# set up odr fitting
peak = odr.Model(gfunc, fjacd=gfunc_dx, fjacb=gfunc_dp)
sy = numpy.sqrt(ydata)
sy[sy == 0] = 1
mydata = odr.RealData(xdata, ydata, sy=sy)
myodr = odr.ODR(mydata, peak, beta0=iparams, maxit=maxit)
myodr.set_job(fit_type=2) # use least-square fit
fit = myodr.run()
if config.VERBOSITY >= config.DEBUG:
print('XU.math.peak_fit:')
fit.pprint() # prints final message from odrpack
fparam = fit.beta
if peaktype in ('PseudoVoigt', 'PseudoVoigtAsym'):
if background == 'linear':
etaidx = -2
else:
etaidx = -1
fparam[etaidx] = 0 if fparam[etaidx] < 0 else fparam[etaidx]
fparam[etaidx] = 1 if fparam[etaidx] > 1 else fparam[etaidx]
itlim = False
if fit.stopreason[0] == 'Iteration limit reached':
itlim = True
if config.VERBOSITY >= config.INFO_LOW:
print("XU.math.peak_fit: Iteration limit reached, "
"do not trust the result!")
if plot:
if isinstance(plot, basestring):
plt.figure(plot)
else:
plt.figure('XU:peak_fit')
plt.plot(xdata, ydata, 'ko', label='data', mew=2)
if debug:
plt.plot(xdata, gfunc(iparams, xdata), '-', color='0.5',
label='estimate')
plt.plot(xdata, gfunc(fparam, xdata), 'r-',
label='%s-fit' % peaktype)
plt.legend()
if func_out:
return fparam, fit.sd_beta, itlim, lambda x: gfunc(fparam, x)
else:
return fparam, fit.sd_beta, itlim
medbin = delete(medbin, delidx)
binstrp = delete(binstrp, delidx)
stdbin = delete(stdbin, delidx)
'''
if mb == 4.25:
print(len(mmi[idx]))
print(log10(rrup[idx]))
print(medbin, binstrp)
print(eqname[idx])
crash
'''
if len(medbin < 2) and mb != 4.25:
# get intercept
data = odrpack.RealData(binstrp, medbin)
intfit = odrpack.Model(linear_fixed_slope)
odr = odrpack.ODR(data, intfit, beta0=[5.0])
#data = odrpack.RealData(10**binstrp, medbin, meta={'mag':mb})
#intfit = odrpack.Model(near_src_trunc_fixed_slope)
#odr = odrpack.ODR(data, intfit, beta0=[5.0])
odr.set_job(fit_type=2) #if set fit_type=2, returns the same as leastsq, 0=ODR
out = odr.run()
intercept = out.beta
intercepts.append(intercept[0])
meanmagbin.append(mean(mmi[idx]))
meanmws.append(mean(mw[idx]))
else:
intercepts.append(nan)
def peak_fit(xdata, ydata, iparams=[], peaktype='Gauss', maxit=300,
background='constant', plot=False, func_out=False, debug=False):
"""
fit function using odr-pack wrapper in scipy similar to
https://github.com/tiagopereira/python_tips/wiki/Scipy%3A-curve-fitting
for Gauss, Lorentz or Pseudovoigt-functions
Parameters
----------
xdata : array_like
x-coordinates of the data to be fitted
ydata : array_like
y-coordinates of the data which should be fit
iparams : list, optional
initial paramters, determined automatically if not specified
peaktype : {'Gauss', 'Lorentz', 'PseudoVoigt', 'PseudoVoigtAsym', 'PseudoVoigtAsym2'}, optional
type of peak to fit
maxit : int, optional
maximal iteration number of the fit
background : {'constant', 'linear'}, optional
type of background function
plot : bool or str, optional
flag to ask for a plot to visually judge the fit. If plot is a string
it will be used as figure name, which makes reusing the figures easier.
func_out : bool, optional
returns the fitted function, which takes the independent variables as
only argument (f(x))
Returns
-------
params : list
the parameters as defined in function `Gauss1d/Lorentz1d/PseudoVoigt1d/
PseudoVoigt1dasym`. In the case of linear background one more parameter
is included!
sd_params : list
For every parameter the corresponding errors are returned.
itlim : bool
flag to tell if the iteration limit was reached, should be False
fitfunc : function, optional
the function used in the fit can be returned (see func_out).
"""
if plot:
plot, plt = utilities.import_matplotlib_pyplot('XU.math.peak_fit')
gfunc, gfunc_dx, gfunc_dp = _getfit_func(peaktype, background)
# determine initial parameters
_check_iparams(iparams, peaktype, background)
if not any(iparams):
iparams = _guess_iparams(xdata, ydata, peaktype, background)
if config.VERBOSITY >= config.DEBUG:
print("XU.math.peak_fit: iparams: %s" % str(tuple(iparams)))
# set up odr fitting
peak = odr.Model(gfunc, fjacd=gfunc_dx, fjacb=gfunc_dp)
sy = numpy.sqrt(ydata)
sy[sy == 0] = 1
mydata = odr.RealData(xdata, ydata, sy=sy)
myodr = odr.ODR(mydata, peak, beta0=iparams, maxit=maxit)
myodr.set_job(fit_type=2) # use least-square fit
fit = myodr.run()
if config.VERBOSITY >= config.DEBUG:
print('XU.math.peak_fit:')
fit.pprint() # prints final message from odrpack
fparam = fit.beta
etaidx = []
if peaktype in ('PseudoVoigt', 'PseudoVoigtAsym'):
if background == 'linear':
etaidx = [-2, ]
else:
etaidx = [-1, ]
elif peaktype == 'PseudoVoigtAsym2':
etaidx = [5, 6]
for e in etaidx:
fparam[e] = 0 if fparam[e] < 0 else fparam[e]
fparam[e] = 1 if fparam[e] > 1 else fparam[e]
itlim = False
if fit.stopreason[0] == 'Iteration limit reached':
itlim = True
if config.VERBOSITY >= config.INFO_LOW:
print("XU.math.peak_fit: Iteration limit reached, "
"do not trust the result!")
if plot:
if isinstance(plot, str):
plt.figure(plot)
else:
plt.figure('XU:peak_fit')
plt.plot(xdata, ydata, 'ok', label='data', mew=2)
if debug:
plt.plot(xdata, gfunc(iparams, xdata), '-', color='0.5',
label='estimate')
plt.plot(xdata, gfunc(fparam, xdata), '-r',
label='%s-fit' % peaktype)
plt.legend()
if func_out:
return fparam, fit.sd_beta, itlim, lambda x: gfunc(fparam, x)
else:
return fparam, fit.sd_beta, itlim
ang = np.array([20, 40, 60, 80, 100, 120, 140, 160, 180])
x = np.round(np.sin(np.radians(ang / 2)), 2)
y = (41, 48, 63, 76, 107, 111, 137, 162, 172)
error = np.round(np.sqrt(y), 2)
yerr1 = np.array(error)
def f(p, x):
B, c = p
return B * x + c
linear = odrpack.Model(f)
mydata = odrpack.RealData(x, y, sy=yerr1)
myodr = odrpack.ODR(mydata, linear, beta0=[0., 1.])
myoutput = myodr.run()
myoutput.pprint()
x_fit = np.linspace(x[0], x[-1], 100)
y_fit = f(myoutput.beta, x_fit)
plt.plot(x_fit, y_fit, label='ODR', lw=3, color='purple')
plt.xlabel('Sin(Theta/2)[Degrees]')
plt.ylabel('dN')
def multPeakFit(x, data, peakpos, peakwidth, dranges=None,
peaktype='Gaussian'):
"""
function to fit multiple Gaussian/Lorentzian peaks with linear background
to a set of data
Parameters
----------
x: x-coordinate of the data
data: data array with same length as x
peakpos: initial parameters for the peak positions
peakwidth: initial values for the peak width
dranges: list of tuples with (min,max) value of the data ranges to use.
does not need to have the same number of entries as peakpos
peaktype: type of peaks to be used: can be either 'Gaussian' or
'Lorentzian'
Returns
-------
pos,sigma,amp,background
pos: list of peak positions derived by the fit
sigma: list of peak width derived by the fit
amp: list of amplitudes of the peaks derived by the fit
background: array of background values at positions x
"""
if peaktype == 'Gaussian':
pfunc = Gauss1d
pfunc_derx = Gauss1d_der_x
elif peaktype == 'Lorentzian':
pfunc = Lorentz1d
pfunc_derx = Lorentz1d_der_x
else:
raise ValueError('wrong value for parameter peaktype was given')
def deriv_x(p, x):
"""
function to calculate the derivative of the signal of multiple peaks
and background w.r.t. the x-coordinate
p: list of parameters, for every peak there needs to be position,
sigma, amplitude and at the end two values for the linear background
function (b0,b1)
x: x-coordinate
"""
derx = numpy.zeros(x.size)
# sum up peak functions contributions
for i in range(len(p) // 3):
ldx = pfunc_derx(x, p[3 * i], p[3 * i + 1], p[3 * i + 2], 0)
derx += ldx
# background contribution
k = p[-2]
d = p[-1]
b = numpy.ones(x.size) * k
return derx + b
def deriv_p(p, x):
"""
function to calculate the derivative of the signal of multiple peaks
and background w.r.t. the parameters
p: list of parameters, for every peak there needs to be position,
sigma, amplitude and at the end two values for the linear background
function (b0,b1)
x: x-coordinate
returns derivative w.r.t. all the parameters with shape (len(p),x.size)
"""
derp = numpy.empty(0)
# peak functions contributions
for i in range(len(p) // 3):
lp = (p[3 * i], p[3 * i + 1], p[3 * i + 2], 0)
if peaktype == 'Gaussian':
derp = numpy.append(derp, -2 * (lp[0] - x) * pfunc(x, *lp))
derp = numpy.append(
derp, (lp[0] - x) ** 2 / (2 * lp[1] ** 3) * pfunc(x, *lp))
derp = numpy.append(derp, pfunc(x, *lp) / lp[2])
else: # Lorentzian
derp = numpy.append(derp, 4 * (x - lp[0]) * lp[2] / lp[1] /
(1 + (2 * (x - lp[0]) / lp[1]) ** 2) ** 2)
derp = numpy.append(derp, 4 * (lp[0] - x) * lp[2] /
lp[1] ** 2 / (1 + (2 * (x - lp[0]) /
lp[1]) ** 2) ** 2)
derp = numpy.append(derp,
1 / (1 + (2 * (x - p[0]) / p[1]) ** 2))
# background contributions
derp = numpy.append(derp, x)
derp = numpy.append(derp, numpy.ones(x.size))
# reshape output
derp.shape = (len(p),) + x.shape
return derp
def fsignal(p, x):
"""
function to calculate the signal of multiple peaks and background
p: list of parameters, for every peak there needs to be position,
sigma, amplitude and at the end two values for the linear background
function (k,d)
x: x-coordinate
"""
f = numpy.zeros(x.size)
# sum up peak functions
for i in range(len(p) // 3):
lf = pfunc(x, p[3 * i], p[3 * i + 1], p[3 * i + 2], 0)
f += lf
# background
k = p[-2]
d = p[-1]
b = numpy.polyval((k, d), x)
return f + b
##########################
# create local data set (extract data ranges)
if dranges:
mask = numpy.array([False] * x.size)
for i in range(len(dranges)):
lrange = dranges[i]
lmask = numpy.logical_and(x > lrange[0], x < lrange[1])
mask = numpy.logical_or(mask, lmask)
lx = x[mask]
ldata = data[mask]
else:
lx = x
ldata = data
# create initial parameter list
p = []
# background
k, d = numpy.polyfit(lx, ldata, 1)
# peak parameters
for i in range(len(peakpos)):
amp = ldata[(lx - peakpos[i]) >= 0][0] - \
numpy.polyval((k, d), lx)[(lx - peakpos[i]) >= 0][0]
p += [peakpos[i], peakwidth[i], amp]
# background parameters
p += [k, d]
if(config.VERBOSITY >= config.DEBUG):
print("XU.math.multGaussFit: intial parameters")
print(p)
##########################
# fit with odrpack
model = odr.Model(fsignal, fjacd=deriv_x, fjacb=deriv_p)
odata = odr.RealData(lx, ldata)
my_odr = odr.ODR(odata, model, beta0=p)
# fit type 2 for least squares
my_odr.set_job(fit_type=2)
fit = my_odr.run()
if(config.VERBOSITY >= config.DEBUG):
print("XU.math.multPeakFit: fitted parameters")
print(fit.beta)
try:
if fit.stopreason[0] not in ['Sum of squares convergence']:
print("XU.math.multPeakFit: fit NOT converged (%s)"
% fit.stopreason[0])
return None, None, None, None
except:
print("XU.math.multPeakFit: fit most probably NOT converged (%s)"
% str(fit.stopreason))
return None, None, None, None
# prepare return values
fpos = fit.beta[:-2:3]
fwidth = numpy.abs(fit.beta[1:-2:3])
famp = fit.beta[2::3]
background = numpy.polyval((fit.beta[-2], fit.beta[-1]), x)
return fpos, fwidth, famp, background
def multPeakFit(x, data, peakpos, peakwidth, dranges=None,
peaktype='Gaussian', returnerror=False):
"""
function to fit multiple Gaussian/Lorentzian peaks with linear background
to a set of data
Parameters
----------
x : array-like
x-coordinate of the data
data : array-like
data array with same length as `x`
peakpos : list
initial parameters for the peak positions
peakwidth : list
initial values for the peak width
dranges : list of tuples
list of tuples with (min, max) value of the data ranges to use. does
not need to have the same number of entries as peakpos
peaktype : {'Gaussian', 'Lorentzian'}
type of peaks to be used
returnerror : bool
decides if the fit errors of pos, sigma, and amp are returned (default:
False)
Returns
-------
pos : list
peak positions derived by the fit
sigma : list
peak width derived by the fit
amp : list
amplitudes of the peaks derived by the fit
background : array-like
background values at positions `x`
if returnerror == True:
sd_pos : list
standard error of peak positions as returned by scipy.odr.Output
sd_sigma : list
standard error of the peak width
sd_amp : list
standard error of the peak amplitude
"""
warnings.warn("deprecated function -> use the lmfit Python packge instead",
DeprecationWarning)
if peaktype == 'Gaussian':
pfunc = Gauss1d
pfunc_derx = Gauss1d_der_x
elif peaktype == 'Lorentzian':
pfunc = Lorentz1d
pfunc_derx = Lorentz1d_der_x
else:
raise ValueError('wrong value for parameter peaktype was given')
def deriv_x(p, x):
"""
function to calculate the derivative of the signal of multiple peaks
and background w.r.t. the x-coordinate
Parameters
----------
p : list
parameters, for every peak there needs to be position, sigma,
amplitude and at the end two values for the linear background
function (b0, b1)
x : array-like
x-coordinate
"""
derx = numpy.zeros(x.size)
# sum up peak functions contributions
for i in range(len(p) // 3):
ldx = pfunc_derx(x, p[3 * i], p[3 * i + 1], p[3 * i + 2], 0)
derx += ldx
# background contribution
k = p[-2]
b = numpy.ones(x.size) * k
return derx + b
def deriv_p(p, x):
"""
function to calculate the derivative of the signal of multiple peaks
and background w.r.t. the parameters
Parameters
----------
p : list
parameters, for every peak there needs to be position, sigma,
amplitude and at the end two values for the linear background
function (b0, b1)
x : array-like
x-coordinate
returns derivative w.r.t. all the parameters with shape (len(p),x.size)
"""
derp = numpy.empty(0)
# peak functions contributions
for i in range(len(p) // 3):
lp = (p[3 * i], p[3 * i + 1], p[3 * i + 2], 0)
if peaktype == 'Gaussian':
derp = numpy.append(derp, -2 * (lp[0] - x) * pfunc(x, *lp))
derp = numpy.append(
derp, (lp[0] - x) ** 2 / (2 * lp[1] ** 3) * pfunc(x, *lp))
derp = numpy.append(derp, pfunc(x, *lp) / lp[2])
else: # Lorentzian
derp = numpy.append(derp, 4 * (x - lp[0]) * lp[2] / lp[1] /
(1 + (2 * (x - lp[0]) / lp[1]) ** 2) ** 2)
derp = numpy.append(derp, 4 * (lp[0] - x) * lp[2] /
lp[1] ** 2 / (1 + (2 * (x - lp[0]) /
lp[1]) ** 2) ** 2)
derp = numpy.append(derp,
1 / (1 + (2 * (x - p[0]) / p[1]) ** 2))
# background contributions
derp = numpy.append(derp, x)
derp = numpy.append(derp, numpy.ones(x.size))
# reshape output
derp.shape = (len(p),) + x.shape
return derp
def fsignal(p, x):
"""
function to calculate the signal of multiple peaks and background
Parameters
----------
p : list
list of parameters, for every peak there needs to be position,
sigma, amplitude and at the end two values for the linear
background function (k, d)
x : array-like
x-coordinate
"""
f = numpy.zeros(x.size)
# sum up peak functions
for i in range(len(p) // 3):
lf = pfunc(x, p[3 * i], p[3 * i + 1], p[3 * i + 2], 0)
f += lf
# background
k = p[-2]
d = p[-1]
b = numpy.polyval((k, d), x)
return f + b
##########################
# create local data set (extract data ranges)
if dranges:
mask = numpy.array([False] * x.size)
for i in range(len(dranges)):
lrange = dranges[i]
lmask = numpy.logical_and(x > lrange[0], x < lrange[1])
mask = numpy.logical_or(mask, lmask)
lx = x[mask]
ldata = data[mask]
else:
lx = x
ldata = data
# create initial parameter list
p = []
# background
# exclude +/-2 peakwidth around the peaks
bmask = numpy.ones_like(lx, dtype=bool)
for pp, pw in zip(peakpos, peakwidth):
bmask = numpy.logical_and(bmask, numpy.logical_or(lx < (pp-2*pw),
lx > (pp+2*pw)))
if numpy.any(bmask):
k, d = numpy.polyfit(lx[bmask], ldata[bmask], 1)
else:
if(config.VERBOSITY >= config.DEBUG):
print("XU.math.multPeakFit: no data outside peak regions!")
k, d = (0, ldata.min())
# peak parameters
for i in range(len(peakpos)):
amp = ldata[(lx - peakpos[i]) >= 0][0] - \
numpy.polyval((k, d), lx)[(lx - peakpos[i]) >= 0][0]
p += [peakpos[i], peakwidth[i], amp]
# background parameters
p += [k, d]
if(config.VERBOSITY >= config.DEBUG):
print("XU.math.multPeakFit: intial parameters")
print(p)
##########################
# fit with odrpack
model = odr.Model(fsignal, fjacd=deriv_x, fjacb=deriv_p)
odata = odr.RealData(lx, ldata)
my_odr = odr.ODR(odata, model, beta0=p)
# fit type 2 for least squares
my_odr.set_job(fit_type=2)
fit = my_odr.run()
if(config.VERBOSITY >= config.DEBUG):
print("XU.math.multPeakFit: fitted parameters")
print(fit.beta)
try:
if fit.stopreason[0] not in ['Sum of squares convergence']:
print("XU.math.multPeakFit: fit NOT converged (%s)"
% fit.stopreason[0])
return Nono, None, None, None
except IndexError:
print("XU.math.multPeakFit: fit most probably NOT converged (%s)"
% str(fit.stopreason))
return None, None, None, None
# prepare return values
fpos = fit.beta[:-2:3]
fwidth = numpy.abs(fit.beta[1:-2:3])
famp = fit.beta[2::3]
background = numpy.polyval((fit.beta[-2], fit.beta[-1]), x)
if returnerror:
sd_pos = fit.sd_beta[:-2:3]
sd_width = fit.sd_beta[1:-2:3]
sd_amp = fit.sd_beta[2::3]
return fpos, fwidth, famp, background, sd_pos, sd_width, sd_amp
return fpos, fwidth, famp, background
mb = np.array(mb)
mw = np.array(mw)
idx_src = np.array(idx)
# Mw = np.array([x[3] for x in cat])
# Ml_pre = np.array([x[4] for x in cat])
# Ml_rev = np.array([x[5] for x in cat])
# Mw_ref = np.array([x[6] for x in cat])
#
# idx1 = np.where(Mw_ref=='HG')[0]
# idx2 = np.where(Mw_ref=='TA-SEA')[0]
# idx3 = np.where(Mw_ref=='TA-WA')[0]
# idx4 = np.where(Mw_ref=='other')[0]
############### bilinear auto
data = odrpack.RealData(mb[mb >= 3.5], mw[mb >= 3.5])
sx = np.interp(mw, [min(mw), max(mw)], [0.3, 0.1])
sy = sx
data = odrpack.RealData(mb[mb >= 3.5],
mw[mb >= 3.5],
sx=sx[mb >= 3.5],
sy=sy[mb >= 3.5])
xrng = np.arange(3.5, 6.0, step=0.01)
bilin_reg = odrpack.Model(bilinear_reg_free)
odr = odrpack.ODR(data, bilin_reg, beta0=[0.7, 1.0, 1.0, 3.5])
odr.set_job(fit_type=0) #if set fit_type=2, returns the same as least squares
out = odr.run()
out.pprint()
#d1_array.append(d1)
#d2_array.append(d2)
#d3_array.append(d3)
plt.semilogx(10**medx, logmedamp, 'rs', ms=6)
ax.set_xscale('log')
###############################################################################
# fit data
###############################################################################
def fit_site_amp(c, x):
return c[0] + c[1] / (x - log10(150))
#data = odrpack.RealData(medx, logmedamp)
idx = where(isfinite(Yres))[0]
data = odrpack.RealData(log10(vs30[idx]), Yres[idx])
sitefit = odrpack.Model(fit_site_amp)
odr = odrpack.ODR(data, sitefit, beta0=[0.1, 0.])
odr.set_job(
fit_type=2) #if set fit_type=2, returns the same as leastsq, 0=ODR
out = odr.run()
c = out.beta
print(c)
coefs1.append(c)
# plot fit
dx = arange(2., 3, 0.01)
dy = c[0] + c[1] / (dx - log10(150))
#dy = d0 + d1*dx**3 + d2*dx**2 + d3*dx
# plot bi-linear interface
cinter_len = 10**(lenc + lengrd1*mrng)
idx = mrng > lenhmag
ylen = lenc + lengrd1 * lenhmag
cinter_len[idx] = 10**(lengrd2 * (mrng[idx]-lenhmag) + ylen)
'''
h = plt.semilogy(mrng, cinter_len, 'k-', lw=2.0)
hh = [h[0]]
# fit lengths
savec = []
tabtxt = 'Length\nType,a,SEa,b,sig,Range\n'
for i in range(0, len(fmag)):
data = odrpack.RealData(array(fmag[i]),log10(array(flen[i])))
grad = grads[0]
lin = odrpack.Model(linear_reg_fix_slope)
odr = odrpack.ODR(data, lin, beta0=[-2.])
odr.set_job(fit_type=0) #if set fit_type=2, returns the same as leastsq
out = odr.run()
out.pprint()
c = out.beta[0]
savec.append(c)
regmrng = arange(min(fmag[i]), max(fmag[i])+0.01, 0.01)
clen = 10**(c + grad * regmrng)
print i
h = plt.semilogy(regmrng, clen, '-', color=cs2[i+1], lw=2.0)
hh.append(h[0])
def fit_function(w, F0, w0, gamma):
#gamma = 0.01515
return F0 / pylab.sqrt((w0**2 - w**2)**2 + 4.0 * (gamma**2) * (w**2))
def fit_function_ODR(pars, w):
#pars[2] = 0.01515
return pars[0] / pylab.sqrt((pars[1]**2 - w**2)**2 + 4.0 * (pars[2]**2) *
(w**2))
# Run the actual ODR.
model = odrpack.Model(fit_function_ODR)
data = odrpack.RealData(s, x)
odr = odrpack.ODR(data, model, beta0=(53.7, 4.7, 0.064))
out = odr.run()
popt, pcov = out.beta, out.cov_beta
F0, w0, gamma = popt
dF0, dw0, dgamma = numpy.sqrt(pcov.diagonal())
chisq = out.sum_square
# !Run the actual ODR.
# Run the actual ODR.
model = odrpack.Model(fit_function_ODR)
data = odrpack.RealData(s, x)
odr = odrpack.ODR(data, model, beta0=(F0, w0, gamma))
out = odr.run()
popt, pcov = out.beta, out.cov_beta
F0, w0, gamma = popt
dF0, dw0, dgamma = numpy.sqrt(pcov.diagonal())
def fitDoubleCrystalBallPeak(self):
params = np.array([
self.peak1_paramsEdits[0].value(),
self.peak1_paramsEdits[1].value(),
self.peak1_paramsEdits[2].value(),
self.peak1_paramsEdits[3].value(),
self.peak2_paramsEdits[0].value(),
self.peak2_paramsEdits[1].value(),
self.peak2_paramsEdits[2].value(), 0.9, 4
])
model = odr.Model(lineshape.Double_Crystalball)
odr_data = odr.RealData(self.x_cut,
self.y_cut) #, sy = np.sqrt(self.y_cut))
myodr = odr.ODR(odr_data, model, beta0=params)
myodr.set_job(fit_type=0)
myoutput = myodr.run()
self.params = myoutput.beta
params_cov = myoutput.cov_beta
params_output = []
params_red_chi2 = myoutput.res_var
single_index = [0, 1, 2, 3, 7, 8]
params_single = self.params[single_index]
double_index = [4, 5, 6, 3, 7, 8]
params_double = self.params[double_index]
content1, error1 = integrate.quad(
lineshape.Single_Crystalball_integrand,
self.x_fit[0],
self.x_fit[-1],
args=tuple(params_single))
content2, error2 = integrate.quad(
lineshape.Single_Crystalball_integrand,
self.x_fit[0],
self.x_fit[-1],
args=tuple(params_double))
params_output.append(content1)
params_output.append(params_red_chi2)
params_output.append(content2)
self.params_outputs = np.array(params_output)
for i in range(len(self.params)):
if i < 4:
self.peak1_paramsEdits[i].setValue(self.params[i])
if 3 < i < 7:
self.peak2_paramsEdits[i - 4].setValue(self.params[i])
self.peak1_contentEdit.setText(str(self.params_outputs[0]))
self.peak1_chi2Edit.setText(str(self.params_outputs[1]))
self.peak2_contentEdit.setText(str(self.params_outputs[2]))
self.plotWidget.plot(clear=True)
histo = pg.PlotCurveItem(self.x, self.y[:-1], stepMode=True)
self.plotWidget.addItem(histo)
if self.PeaksButton.isChecked() == False:
fitPen = pg.mkPen(color=(204, 0, 0), width=2)
self.plotWidget.plot(self.x_fit,
lineshape.Double_Crystalball(
self.params, self.x_fit),
pen=fitPen)
if self.PeaksButton.isChecked() == True:
fitPen = pg.mkPen(color=(204, 0, 0),
width=2,
style=QtCore.Qt.DashLine)
params1 = np.array([
self.peak1_paramsEdits[0].value(),
self.peak1_paramsEdits[1].value(),
self.peak1_paramsEdits[2].value(),
self.peak1_paramsEdits[3].value(), 0.9, 4
])
params2 = np.array([
self.peak2_paramsEdits[0].value(),
self.peak2_paramsEdits[1].value(),
self.peak2_paramsEdits[2].value(),
self.peak1_paramsEdits[3].value(), 0.9, 4
])
self.plotWidget.plot(self.x_fit,
lineshape.Single_Crystalball(
params1, self.x_fit),
pen=fitPen)
self.plotWidget.plot(self.x_fit,
lineshape.Single_Crystalball(
params2, self.x_fit),
pen=fitPen)
self.plotWidget.addItem(self.vLine, ignoreBounds=True)
self.plotWidget.addItem(self.hLine, ignoreBounds=True)
if len(nidx) > 0:
namps = log10(mamps) - logmedamp[nidx]
if len(log_norm_amps) == 0:
log_norm_amps = namps
norm_rhyps = mrhyps
else:
log_norm_amps = hstack((log_norm_amps, namps))
norm_rhyps = hstack((norm_rhyps, mrhyps))
# regress mag-dependent data and get intercept
didx = where((medx >= 2) & (medx <= 3.35))[0]
data = odrpack.RealData(medx[didx], logmedamp[didx])
intfit = odrpack.Model(linear_fixed_slope)
odr = odrpack.ODR(data, intfit, beta0=[5.0])
odr.set_job(
fit_type=2) #if set fit_type=2, returns the same as leastsq, 0=ODR
out = odr.run()
intercept = out.beta
if round(m, 1) != 4.9 and round(m, 1) != 5.5: #or round(m,1) > 6.6
m_intercept.append(intercept[0])
m_reg.append(m)
xplt = array([2, 3])
yplt = meanslope * xplt + intercept[0]
def main():
# make output directory
if not os.path.exists("output"):
os.makedirs("output")
# get data and caluclate reflectance
n_pix = np.genfromtxt(s_filename, delimiter=",")[:, 0]
i_s = np.genfromtxt(s_filename, delimiter=",")[:, 1]
i_p = np.genfromtxt(p_filename, delimiter=",")[:, 1]
i_bg = np.genfromtxt(bg_filename, delimiter=",")[:, 1]
ref = (i_p - i_bg) / (i_s - i_bg)
# find beam edges
popt, pcov = curve_fit(gaus, n_pix, i_s, p0=[1, 1000, 50])
i_width = gaus(popt[1], *popt) / np.e**2
i_max = int(popt[1])
beam_lim = np.argmax(
i_s[:i_max] -
i_width > 0), len(n_pix) - np.argmax(i_s[:-i_max:-1] - i_width > 0)
idx_centre = int(np.diff(beam_lim) / 2) + beam_lim[0] - 1
# plot raw data and threshold limits
plt.figure(figsize=(8, 6))
plt.plot(n_pix, i_s, label="S polarised")
plt.plot(n_pix, i_p, label="P polarised")
plt.plot(n_pix, i_bg, label="Background")
plt.plot(n_pix, gaus(n_pix, *popt), label="Gaussian")
plt.plot(n_pix[idx_centre], i_width, "kx", ms=8)
plt.plot((n_pix[beam_lim[1]], n_pix[beam_lim[0]]),
(i_s[beam_lim[1]], i_s[beam_lim[0]]),
"kx",
ms=8)
plt.text(n_pix[beam_lim[0]] + 20,
i_width - 0.01,
r"$n_{edge, low}$",
ha="left",
va="top")
plt.text(n_pix[beam_lim[1]] + 20,
i_width - 0.01,
r"$n_{edge, up}$",
ha="left",
va="top")
plt.text(n_pix[idx_centre] + 20,
i_width - 0.01,
r"$n_{centre}$",
ha="left",
va="top")
plt.xlabel("Pixel number")
plt.ylabel("Intensity")
plt.title("S and P polarised intensities for sample 21")
plt.legend()
plt.show()
# get range of angles and error
n_pix_shift = np.arange(0, 2048, 1) - idx_centre
correct = angle_offset(5)
theta_range = beam_angle(n_pix_shift) + (t_prism * correct[0] + correct[1])
n_err = err_edge(np.sqrt(np.diagonal(pcov)), popt, i_width)
theta_err = err_angle(n_pix_shift, n_err)
err_red = theta_err[beam_lim[0]:beam_lim[1]]
ref_red_ = ref[beam_lim[0]:beam_lim[1]]
theta_red = theta_range[beam_lim[0]:beam_lim[1]]
ref_red = ref_red_ / max(ref_red_[500:-500])
# moving average
ref_av = moving_average(ref_red, n=n_av)
theta_av = np.linspace(min(theta_red), max(theta_red), len(ref_av))
# fit whole reflectivity to asymmetric
asymm = odr.Model(asymmetric)
data_full = odr.RealData(theta_red, ref_red, sx=err_red)
fit_asy_full = odr.ODR(data_full,
asymm,
beta0=[0.9, 0.4, 0.4, t_prism + 6, -0.6],
maxit=100).run()
ref_max = argrelextrema(asymmetric(fit_asy_full.beta, theta_red),
np.greater)[0][0]
# fit right side of reflectivity to asymmetric
idx_asy = ref_max + delta_3
data_right = odr.RealData(theta_red[idx_asy:-400],
ref_red[idx_asy:-400],
sx=err_red[idx_asy:-400])
fit_asy = odr.ODR(data_right,
asymm,
beta0=[0.9, 0.4, 0.4, t_prism + 6, -0.6],
maxit=100).run()
r_sq_asy = 1 - fit_asy.res_var / np.var(ref_red[idx_asy:], ddof=1)
data_asy = asymmetric(fit_asy.beta, theta_red)
# fit left side of reflectivity to sigmoid
sig = odr.Model(sigmoid)
idx_sig = ref_max + delta_2
data_left = odr.RealData(theta_red[delta_1:idx_sig],
ref_red[delta_1:idx_sig],
sx=err_red[delta_1:idx_sig])
fit_sig = odr.ODR(data_left,
sig,
beta0=[0.15, -2.3, t_prism + 4, 0.8],
maxit=100).run()
r_sq_sig = 1 - fit_sig.res_var / np.var(ref_red[delta_1:idx_sig], ddof=1)
data_sig = sigmoid(fit_sig.beta, theta_red)
data_sig_asy = sig_asy(
(*fit_asy.beta, *fit_sig.beta[:-1]), theta_red) - fit_sig.beta[0]
# first derrivative of asymmetric-sigmoid
a, b, c, d, e, f, g, h, x = sym.symbols("a b c d e f g h x")
sym_fit = a * (1 - (b + c * (x - d)) /
((x - d)**2 + e**2)) + (f / (1 + sym.exp(g * (x - h))))
fit = sym.lambdify((a, b, c, d, e, f, g, h, x), sym_fit.diff(x), "numpy")
d_fit = fit(*(*fit_asy.beta, *fit_sig.beta[:-1]), theta_red)
# spr, critical angle, min reflectance and FWHM
idx_spr = argrelextrema(data_sig_asy, np.less)[0][0]
idx_crit = argrelextrema(d_fit, np.greater)[0][0]
theta_spr = theta_red[idx_spr]
spr_err = np.sqrt(err_red[idx_spr]**2)
theta_crit = theta_red[idx_crit]
crit_err = np.sqrt(err_red[idx_crit]**2)
min_ref = data_sig_asy[idx_spr]
err_min_ref = min_ref * np.linalg.norm(
(*fit_sig.sd_beta / fit_sig.beta, *fit_asy.sd_beta / fit_asy.beta))
fwhm_1 = find_nearest(data_sig_asy[ref_max:idx_spr],
data_sig_asy[ref_max] / 2) + ref_max
fwhm_2 = find_nearest(data_sig_asy[idx_spr:],
data_sig_asy[ref_max] / 2) + idx_spr
fwhm = np.abs(theta_red[fwhm_2] - theta_red[fwhm_1])
err_fwhm = np.sqrt(err_red[fwhm_1]**2 + err_red[fwhm_2]**2)
# plot ratio of s and p intensities, moving average and fitted curves
if isinstance(prism_no, float):
prism_no_str = str(int(prism_no)) + "a"
else:
prism_no_str = prism_no
plt.figure(figsize=(8, 6))
plt.plot(theta_red, ref_red, "silver", label="Reflectance data")
plt.plot(theta_red, data_sig_asy, label="Asymmetric-sigmoid")
if details:
plt.plot(theta_av, ref_av, label="Moving average, $n={}$".format(n_av))
plt.plot(theta_red, data_asy, label="Asymmetric")
plt.plot(theta_red, data_sig, label="Sigmoid")
plt.plot(theta_red,
d_fit,
label="1st derivative of \n asymmetric-sigmoid")
plt.plot((theta_red[delta_1], theta_red[idx_sig]),
(ref_red[delta_1], ref_red[idx_sig]),
"s",
label="Sigmoid data range")
plt.plot((theta_red[idx_asy], theta_red[-1]),
(ref_red[idx_asy], ref_red[-1]),
"s",
label="Asymmetric data range")
plt.plot((theta_red[fwhm_1], theta_red[fwhm_2]),
(ref_red[fwhm_1], ref_red[fwhm_2]),
"s",
label="FWHM limits")
plt.plot(theta_crit, d_fit[idx_crit], "kx", ms=8)
plt.plot(theta_spr, data_asy[idx_spr], "kx", ms=8)
plt.plot(theta_red[ref_max],
asymmetric(fit_asy.beta, theta_red)[ref_max],
"kx",
ms=8)
plt.text(theta_crit + 0.2, d_fit[idx_crit] - 0.02, r"$\theta_{crit}$")
plt.text(theta_spr + 0.2, data_asy[idx_spr] - 0.02, r"$\theta_{spr}$")
plt.text(theta_red[ref_max] - 0.2,
asymmetric(fit_asy.beta, theta_red)[ref_max] - 0.08,
r"$\theta_{max}$")
plt.xlim(theta_red[0], theta_red[-1])
plt.ylim(-0.1, 1.1)
plt.xlabel(r"Incidence angle /$^\circ$")
plt.ylabel("Normalised reflectance")
plt.title("Reflectance plot for sample {}".format(prism_no_str))
plt.legend(loc=7)
# formatted string containing the parameters
text = """Sample {} on {}: \nprism angle {} deg\nsensor distance {} m\nSPR angle = {} +/- {} deg
Critical angle = {} +/- {} deg \nR squared (asymmetric)= {} \nR squared (sigmoid)= {}
Asymmetric parameters: {} \nAsymmetric parameter errors: {} \nSigmoid parameters: {}
Sigmoid parameter errors: {} \nMinimum reflectance {} +/- {} \nFWHM {} +/- {} deg
delta (1, 2, 3): {}, {}, {}
\n""".format(prism_no_str,
datetime.datetime.now().strftime("%d/%m/%y %H:%M"), t_prism,
d_sens, theta_spr, spr_err, theta_crit, crit_err, r_sq_asy,
r_sq_sig, fit_asy.beta, fit_asy.sd_beta, fit_sig.beta,
fit_sig.sd_beta, min_ref, err_min_ref, fwhm, err_fwhm, delta_1,
delta_2, delta_3)
if export:
# save figure
plt.savefig(plotname, dpi=100, bbox_inches="tight")
# log parameters
file = open("log.txt", "w")
file = open("output/log.txt", "a")
file.write(text)
file.close()
# write data to csv
np.savetxt(txtname,
np.vstack((theta_red, ref_red)).T,
delimiter=",",
fmt="%f",
header="theta,R")
# write parameters to csv
arr = [
prism_no, theta_spr, spr_err, theta_crit, crit_err, r_sq_asy,
r_sq_sig, min_ref, err_min_ref, fwhm, err_fwhm
]
with open("output/param.csv", "ab") as f:
np.savetxt(f, arr, delimiter=",", newline=",", fmt="%f")
f.write(b'\n')
plt.show()
print(text)
