def das(tup, x0, from_t=0.4, uniform_fil=None, plot_result=True, fit_kws=None):
out = namedtuple('das_result', field_names=[
'fitter', 'result', 'minimizer'])
ti = dv.make_fi(tup.t)
if uniform_fil is not None:
tupf = filter.uniform_filter(tup, uniform_fil)
else:
tupf = tup
if fit_kws is None:
fit_kws = {}
import numpy as np
#ct = dv.tup(np.hstack((wl, wl)), tup.t[ti(t0):], np.hstack((pa[ti(t0):, :], se[ti(t0):, :])))
ct = dv.tup(tup.wl, tup.t[ti(from_t):], tupf.data[ti(from_t):, :])
f = fitter.Fitter(ct, model_coh=0, model_disp=0)
f.lsq_method = 'ridge'
kws = dict(full_model=0, lower_bound=0.2, fixed_names=['w'])
kws.update(fit_kws)
lm = f.start_lmfit(x0, **kws)
res = lm.leastsq()
import lmfit
lmfit.report_fit(res)
if plot_result:
plt.figure(figsize=(4, 7))
plt.subplot(211)
if is_montone(f.wl):
monotone = False
# Assume wl is repeated
N = len(f.wl)
else:
monotone = True
N = len(f.wl) // 2
print(N)
l = plt.plot(f.wl[:N], f.c[:N, :], lw=3)
if monotone:
l2 = plt.plot(f.wl[:N], f.c[N:, :], lw=1)
for i, j in zip(l, l2):
j.set_color(i.get_color())
plot_helpers.lbl_spec()
lbls = ['%.1f' % i for i in f.last_para[1:-1]] + ['const']
plt.legend(lbls)
plt.subplot(212)
wi = dv.make_fi(tup.wl)
for i in range(N)[::6]:
l, = plt.plot(tup.t, tupf.data[:, i], '-o', lw=0.7,
alpha=0.5, label='%.1f cm-1' % f.wl[i], mec='None', ms=3)
plt.plot(f.t, f.model[:, i], lw=3, c=l.get_color())
if monotone:
l, = plt.plot(tup.t, tupf.data[:, i+N], '-o', lw=0.7,
alpha=0.5, label='%.1f cm-1' % f.wl[i], mec='None', ms=3)
plt.plot(f.t, f.model[:, i+N], lw=3, c=l.get_color())
plt.xlim(-1)
plt.xscale('symlog', linthreshx=1, linscalex=0.5)
plot_helpers.lbl_trans()
plt.legend(loc='best')
return out(f, res, lm)
def plot_freqs(tup, wl, from_t, to_t, taus=[1]):
ti = dv.make_fi(tup.t)
wi = dv.make_fi(tup.wl)
tl = tup.t[ti(from_t):ti(to_t)]
trans = tup.data[ti(from_t):ti(to_t), wi(wl)]
#ax1 = plt.subplot(311)
#ax1.plot(tl, trans)
dt = dv.exp_detrend(trans, tl, taus)
#ax1.plot(tl, -dt+trans)
#ax2 = plt.subplot(312)
ax3 = plt.subplot(111)
f = abs(np.fft.fft(np.kaiser(2 * dt.size, 2) * dt, dt.size * 2))**2
freqs = np.fft.fftfreq(dt.size * 2, tup.t[ti(from_t) + 1] - tup.t[ti(from_t)])
n = freqs.size // 2
ax3.plot(dv.fs2cm(1000 / freqs[1:n]), f[1:n])
ax3.set_xlabel('freq / cm$^{-1}$')
return dv.fs2cm(1000 / freqs[1:n]), f[1:n]
def plot_freqs(tup, wl, from_t, to_t, taus=[1]):
ti = dv.make_fi(tup.t)
wi = dv.make_fi(tup.wl)
tl = tup.t[ti(from_t):ti(to_t)]
trans = tup.data[ti(from_t):ti(to_t), wi(wl)]
#ax1 = plt.subplot(311)
#ax1.plot(tl, trans)
dt = dv.exp_detrend(trans, tl, taus)
#ax1.plot(tl, -dt+trans)
#ax2 = plt.subplot(312)
ax3 = plt.subplot(111)
f = abs(np.fft.fft(np.kaiser(2*dt.size, 2)*dt, dt.size*2))**2
freqs = np.fft.fftfreq(dt.size*2, tup.t[ti(from_t)+1]-tup.t[ti(from_t)])
n = freqs.size//2
ax3.plot(dv.fs2cm(1000/freqs[1:n]), f[1:n])
ax3.set_xlabel('freq / cm$^{-1}$')
return dv.fs2cm(1000/freqs[1:n]), f[1:n]
def __init__(
self,
fname,
invert_data=False,
is_pol_resolved=False,
pol_first_scan="unknown",
valid_channel=None,
):
"""Class for working with data files from MessPy v1.
Parameters
----------
fname : str
Filename to open.
invert_data : bool (optional)
If True, invert the sign of the data. `False` by default.
is_pol_resolved : bool (optional)
If the dataset was recorded polarization resolved.
pol_first_scan : {'magic', 'para', 'perp', 'unknown'}
Polarization between the pump and the probe in the first scan. If
`valid_channel` is 'both', this corresponds to the zeroth channel.
valid_channel : `0`, `1`, 'both'
Indicates which channels contains a real signal. For recently
recorded data, it is 0 for the visible setup and 1 for the IR
setup. Older IR data uses both. If `None` it guesses the valid
channel from the data, assuming recent data.
"""
with np.load(fname) as f:
self.wl = f["wl"]
self.initial_wl = self.wl.copy()
self.t = f["t"] / 1000.0
self.data = f["data"]
if invert_data:
self.data *= -1
self.wavenumbers = 1e7 / self.wl
self.pol_first_scan = pol_first_scan
self.is_pol_resolved = is_pol_resolved
if valid_channel is not None:
self.valid_channel = valid_channel
else:
self.valid_channel = 1 if self.wl.shape[0] > 32 else 0
self.num_cwl = self.data.shape[0]
self.plot = MessPyPlotter(self)
self.t_idx = make_fi(self.t)
def plot_coef_spec(taus, wl, coefs, div):
tau_coefs = coefs[:, :len(taus)]
div.append(taus.max() + 1)
ti = dv.make_fi(taus)
last_idx = 0
non_zeros = ~(coefs.sum(0) == 0)
for i in div:
idx = ti(i)
cur_taus = taus[last_idx:idx]
cur_nonzeros = non_zeros[last_idx:idx]
lbl = "%.1f - %.1f ps" % (taus[last_idx], taus[idx])
plt.plot(wl, tau_coefs[:, last_idx:idx].sum(-1), label=lbl)
last_idx = ti(i)
plt.plot(wl, coefs[:, -1])
plt.legend(title='Decay regions', loc='best')
lbl_spec()
plt.title("Spectrum of lft-parts")
def plot_coef_spec(taus, wl, coefs, div):
tau_coefs = coefs[:, :len(taus)]
div.append(taus.max()+1)
ti = dv.make_fi(taus)
last_idx = 0
non_zeros = ~(coefs.sum(0) == 0)
for i in div:
idx = ti(i)
cur_taus = taus[last_idx:idx]
cur_nonzeros = non_zeros[last_idx:idx]
lbl = "%.1f - %.1f ps"%(taus[last_idx], taus[idx])
plt.plot(wl, tau_coefs[:, last_idx:idx].sum(-1), label=lbl)
last_idx = ti(i)
plt.plot(wl, coefs[:, -1])
plt.legend(title='Decay regions', loc='best')
lbl_spec()
plt.title("Spectrum of lft-parts")
def __init__(self, frequency, signal, unit_freq='nm', unit_signal='OD'):
"""
Class for working with steady state spectra.
Parameters
----------
frequency : ndarray
The frequencies of the spectrum
signal : ndarray
Array containing the signal.
unit_freq : str
Unit type of the frequencies.
unit_signal : str
Unit type of the signal.
"""
assert (frequency.shape[0] == signal.shape[0])
idx = np.argsort(frequency)
self.x = frequency[idx]
self.y = signal[idx, ...]
self.unit_freq = unit_freq
self.unit_signal = unit_signal
self.back = np.zeros_like(self.x)
self.fi = dv.make_fi(self.x)
def das(tup, x0, from_t=0.4, uniform_fil=None, plot_result=True, fit_kws=None):
out = namedtuple('das_result',
field_names=['fitter', 'result', 'minimizer'])
ti = dv.make_fi(tup.t)
if uniform_fil is not None:
tupf = filter.uniform_filter(tup, uniform_fil)
else:
tupf = tup
if fit_kws is None:
fit_kws = {}
#ct = dv.tup(np.hstack((wl, wl)), tup.t[ti(t0):], np.hstack((pa[ti(t0):, :], se[ti(t0):, :])))
ct = dv.tup(tup.wl, tup.t[ti(from_t):], tupf.data[ti(from_t):, :])
f = fitter.Fitter(ct, model_coh=0, model_disp=0)
f.lsq_method = 'ridge'
kws = dict(full_model=0, lower_bound=0.2, fixed_names=['w'])
kws.update(fit_kws)
lm = f.start_lmfit(x0, **kws)
res = lm.leastsq()
import lmfit
lmfit.report_fit(res)
if plot_result:
plt.figure(figsize=(4, 7))
plt.subplot(211)
if is_montone(f.wl):
monotone = False
# Assume wl is repeated
N = len(f.wl)
else:
monotone = True
N = len(f.wl) // 2
print(N)
l = plt.plot(f.wl[:N], f.c[:N, :], lw=3)
if monotone:
l2 = plt.plot(f.wl[:N], f.c[N:, :], lw=1)
for i, j in zip(l, l2):
j.set_color(i.get_color())
plot_helpers.lbl_spec()
lbls = ['%.1f' % i for i in f.last_para[1:-1]] + ['const']
plt.legend(lbls)
plt.subplot(212)
wi = dv.make_fi(tup.wl)
for i in range(N)[::6]:
l, = plt.plot(tup.t,
tupf.data[:, i],
'-o',
lw=0.7,
alpha=0.5,
label='%.1f cm-1' % f.wl[i],
mec='None',
ms=3)
plt.plot(f.t, f.model[:, i], lw=3, c=l.get_color())
if monotone:
l, = plt.plot(tup.t,
tupf.data[:, i + N],
'-o',
lw=0.7,
alpha=0.5,
label='%.1f cm-1' % f.wl[i],
mec='None',
ms=3)
plt.plot(f.t, f.model[:, i + N], lw=3, c=l.get_color())
plt.xlim(-1)
plt.xscale('symlog', linthreshx=1, linscalex=0.5)
plot_helpers.lbl_trans()
plt.legend(loc='best')
return out(f, res, lm)
def __init__(self,
wl,
t,
data,
err=None,
name=None,
freq_unit='nm',
disp_freq_unit=None,
auto_plot=True):
"""
Class for working with time-resolved spectra. If offers methods for
analyzing and pre-processing the data. To visualize the data,
each `TimeResSpec` object has an instance of an `DataSetPlotter` object
accessible under `plot`.
Parameters
----------
wl : array of shape(n)
Array of the spectral dimension
t : array of shape(m)
Array with the delay times.
data : array of shape(n, m)
Array with the data for each point.
err : array of shape(n, m) or None (optional)
Contains the std err of the data, can be `None`.
name : str (optional)
Identifier for data set.
freq_unit : 'nm' or 'cm' (optional)
Unit of the wavelength array, default is 'nm'.
disp_freq_unit : 'nm','cm' or None (optional)
Unit which is used by default for plotting, masking and cutting
the dataset. If `None`, it defaults to `freq_unit`.
Attributes
----------
wavelengths, wavenumbers, t, data : ndarray
Arrays with the data itself.
plot : TimeResSpecPlotter
Helper class which can plot the dataset using `matplotlib`.
t_idx : function
Helper function to find the nearest index in t for a given time.
wl_idx : function
Helper function to search for the nearest wavelength index for a
given wavelength.
wn_idx : function
Helper function to search for the nearest wavelength index for a
given wavelength.
auto_plot : bool
When True, some function will display their result automatically.
"""
assert ((t.shape[0], wl.shape[0]) == data.shape)
t = t.copy()
wl = wl.copy()
data = data.copy()
if freq_unit == 'nm':
self.wavelengths = wl
self.wavenumbers = 1e7 / wl
self.wl = self.wavelengths
else:
self.wavelengths = 1e7 / wl
self.wavenumbers = wl
self.wl = self.wavenumbers
self.t = t
self.data = data
self.err = err
if name is not None:
self.name = name
# Sort wavelenths and data.
idx = np.argsort(self.wavelengths)
self.wavelengths = self.wavelengths[idx]
self.wavenumbers = self.wavenumbers[idx]
self.data = self.data[:, idx]
self.auto_plot = auto_plot
self.plot = TimeResSpecPlotter(self)
self.t_idx = dv.make_fi(self.t)
self.wl_idx = dv.make_fi(self.wavelengths)
self.wn_idx = dv.make_fi(self.wavenumbers)
if disp_freq_unit is None:
self.disp_freq_unit = freq_unit
else:
self.disp_freq_unit = disp_freq_unit
self.plot.freq_unit = self.disp_freq_unit
def __init__(
self,
wl,
t,
data,
err=None,
name=None,
freq_unit="nm",
disp_freq_unit=None,
auto_plot=True,
):
"""
Class for working with time-resolved spectra. If offers methods for
analyzing and pre-processing the data. To visualize the data,
each `TimeResSpec` object has an instance of an `DataSetPlotter` object
accessible under `plot`.
Parameters
----------
wl : array of shape(n)
Array of the spectral dimension
t : array of shape(m)
Array with the delay times.
data : array of shape(n, m)
Array with the data for each point.
err : array of shape(n, m) or None (optional)
Contains the std err of the data, can be `None`.
name : str (optional)
Identifier for data set.
freq_unit : 'nm' or 'cm' (optional)
Unit of the wavelength array, default is 'nm'.
disp_freq_unit : 'nm','cm' or None (optional)
Unit which is used by default for plotting, masking and cutting
the dataset. If `None`, it defaults to `freq_unit`.
Attributes
----------
wavelengths, wavenumbers, t, data : ndarray
Arrays with the data itself.
plot : TimeResSpecPlotter
Helper class which can plot the dataset using `matplotlib`.
t_idx : function
Helper function to find the nearest index in t for a given time.
wl_idx : function
Helper function to search for the nearest wavelength index for a
given wavelength.
wn_idx : function
Helper function to search for the nearest wavelength index for a
given wavelength.
auto_plot : bool
When True, some function will display their result automatically.
"""
assert (t.shape[0], wl.shape[0]) == data.shape
t = t.copy()
wl = wl.copy()
data = data.copy()
if freq_unit == "nm":
self.wavelengths = wl
self.wavenumbers = 1e7 / wl
self.wl = self.wavelengths
else:
self.wavelengths = 1e7 / wl
self.wavenumbers = wl
self.wl = self.wavenumbers
self.t = t
self.data = data
self.err = err
if name is not None:
self.name = name
# Sort wavelenths and data.
idx = np.argsort(self.wavelengths)
self.wavelengths = self.wavelengths[idx]
self.wavenumbers = self.wavenumbers[idx]
self.data = self.data[:, idx]
self.auto_plot = auto_plot
self.plot = TimeResSpecPlotter(self)
self.t_idx = dv.make_fi(self.t)
self.wl_idx = dv.make_fi(self.wavelengths)
self.wn_idx = dv.make_fi(self.wavenumbers)
if disp_freq_unit is None:
self.disp_freq_unit = freq_unit
else:
self.disp_freq_unit = disp_freq_unit
self.plot.freq_unit = self.disp_freq_unit