AbsSpectrumBase

class quantarhei.spectroscopy.absbase.AbsSpectrumBase(axis=None, data=None)

Provides basic container for absorption spectrum

Examples

Methods

add_to_data(spect)	Performs addition on the data.
apply_to_data(func)	Applies a submitted function to the data
at(x[, approx])	Returns the function value at the argument x
change_axis(axis)	Replaces the axis object with a compatible one, zero pads or trims the values
clear_data()	Sets spectrum data to zero
copy()	Returns a shallow copy of the self
deepcopy()	Returns a deep copy of the self
fit_exponential([guess])	Exponential fit of the function
fit_gaussian([N, guess, Nsvf])	Performs a Gaussian fit of the spectrum based on an initial guess
get_Fourier_transform([window])	Returns Fourier transform of the DFunction
get_inverse_Fourier_transform()	Returns inverse Fourier transform of the DFunction
load(filename[, test])	Loads an object from a file and returns it
load_data(filename)	Loads data from file into this absorption spectrum
loaddir(dirname)	Returns a directory of objects saved into a directory
normalize()	Normalization to one
normalize2([norm])	Normalizes spectrum to a given value
plot(**kwargs)	Plotting absorption spectrum using the DFunction plot method
save(filename[, comment, test])	Saves the object with all its content into a file
save_data(filename)	Saves the data of this absorption spectrum
savedir(dirname[, tag, comment, test])	Saves an object into directory containing a file with unique name
savefig(filename)	Saves current figure into a file
scopy()	Creates a copy of the object by saving and loading it
set_axis(axis)	Sets axis atribute
set_by_interpolation(x, y[, xaxis])	Sets the data by interpolation with splines
set_data(data)	Sets data atribute
set_data_protected()	Implement this method to put protections on data property
set_data_writable()	Implement this method to lift existing protection of data property
subtract(val)	Subtracts a value from the spectrum to shift its base line

convert_2_current_u
convert_2_internal_u
unit_repr
unit_repr_latex

add_to_data(spect)

Performs addition on the data.

Expects a compatible object holding absorption spectrum and adds its data to the present absorption spectrum.

Parameters:spect (spectrum containing object) – This object should have a compatible axis and some data

Examples

Standard usage

>>> from quantarhei import energy_units
>>> abs = AbsSpectrumBase()
>>> other = AbsSpectrumBase()
>>> with energy_units("1/cm"):
...     w = FrequencyAxis(10000.0, 1000, 5.0)
...     y = numpy.exp(-(w.data-12500.0)**2/(200.0**2))
>>> other.set_axis(w)
>>> other.set_data(y)
>>> abs.add_to_data(other)

Axes have to be compatible (i.e. the same)

>>> yetanother = AbsSpectrumBase()
>>> yetanother.set_axis(FrequencyAxis(8000.0, 1000, 4.0))
>>> abs.add_to_data(yetanother)
Traceback (most recent call last):
    ...
Exception: Incompatible axis

An empty AbsSpectrumBase can be filled by add_to_data() method Axis is taken from the class that we add

>>> yetanother.set_axis(w)
>>> yetanother.add_to_data(abs)
>>> onemore = AbsSpectrumBase()
>>> onemore.add_to_data(other)

>>> numpy.testing.assert_allclose(onemore.data,abs.data)

clear_data()

Sets spectrum data to zero

load_data(filename)

Loads data from file into this absorption spectrum

normalize()

Normalization to one

normalize2(norm=1.0)

Normalizes spectrum to a given value

plot(**kwargs)

Plotting absorption spectrum using the DFunction plot method

save_data(filename)

Saves the data of this absorption spectrum

set_axis(axis)

Sets axis atribute

Parameters:axis (FrequencyAxis object) – Frequency axis object. This object has managed energy units

set_by_interpolation(x, y, xaxis='frequency')

Sets the data by interpolation with splines

When the spectrum is defined in wavelength, it is converted to an internal representation in frequency.

Examples

>>> from quantarhei import REAL
>>> from quantarhei import energy_units
>>> abs = AbsSpectrumBase()
>>> x = numpy.array([600.0 + 5.0*ii for ii in range(100)], dtype=REAL)
>>> y = numpy.exp(-(x-800.0)**2/(50**2))
>>> abs.set_by_interpolation(x, y, xaxis="wavelength")
>>> with energy_units("1/cm"):
...     print("%6.3f, %6.3f" % (abs.axis.min, abs.axis.max))
9132.420, 16591.324

set_data(data)

Sets data atribute

Parameters:data (array like object (numpy array)) – Sets the data of the absorption spectrum

subtract(val)

Subtracts a value from the spectrum to shift its base line