def to_invcm_relative(self, laser, inplace=True, jacobian=True):
"""Converts signal axis of 1D signal to non-linear wavenumber axis
(cm^-1) relative to the exciting laser wavelength (Stokes/Anti-Stokes
shift). Assumes wavelength in units of nm unless the axis units are
specifically set to µm.
The intensity is converted from counts/nm (counts/µm) to counts/cm^-1
by doing a Jacobian transformation, see e.g. Wang and Townsend,
J. Lumin. 142, 202 (2013), which ensures that integrated signals are
correct also in the energy domain.
Input parameters
----------------
laser : float
Laser wavelength in same units as signal axes (nm or µm).
inplace : boolean
If `False`, a new signal object is created and returned. Otherwise
(default) the operation is performed on the existing signal object.
jacobian : boolean
The default is to do the Jacobian transformation (recommended at
least for luminescence signals), but the transformation can be
suppressed by setting this option to `False`.
Examples
--------
> import numpy as np
> from lumispy import LumiSpectrum
> S1 = LumiSpectrum(np.ones(20), DataAxis(axis = np.arange(200,400,10)), ))
> S1.to_invcm()
Note
----
Using a non-linear axis works only for the non_uniform_axis development
branch of HyperSpy.
"""
# Check if non_uniform_axis is available in hyperspy version
if not "axis" in getfullargspec(DataAxis)[0]:
raise ImportError(
"Conversion to wavenumber axis works only"
" if the non_uniform_axis branch of HyperSpy is used.")
invcmaxis, factor = axis2invcm(self.axes_manager.signal_axes[0])
# convert to relative wavenumber scale
if self.axes_manager.signal_axes[0].units == "µm":
invcmlaser = nm2invcm(1000 * laser)
else:
invcmlaser = nm2invcm(laser)
absaxis = invcmaxis.axis[::-1]
invcmaxis.axis = invcmlaser - absaxis
# in place conversion
if inplace:
if jacobian:
self.data = data2invcm(self.data, factor,
self.axes_manager.signal_axes[0].axis,
absaxis)
# else:
# self.data = self.isig[::-1].data
self.axes_manager.remove(-1)
self.axes_manager._axes.append(invcmaxis)
# create and return new signal
else:
if jacobian:
s2data = data2invcm(self.data, factor,
self.axes_manager.signal_axes[0].axis,
absaxis)
else:
s2data = self.data
if self.data.ndim == 1:
s2 = LumiSpectrum(s2data,
axes=(invcmaxis.get_axis_dictionary(), ))
elif self.data.ndim == 2:
s2 = LumiSpectrum(
s2data,
axes=(
self.axes_manager.navigation_axes[0].
get_axis_dictionary(),
invcmaxis.get_axis_dictionary(),
),
)
else:
s2 = LumiSpectrum(
s2data,
axes=(
self.axes_manager.navigation_axes[1].
get_axis_dictionary(),
self.axes_manager.navigation_axes[0].
get_axis_dictionary(),
invcmaxis.get_axis_dictionary(),
),
)
s2.set_signal_type(self.metadata.Signal.signal_type)
s2.metadata = self.metadata
return s2
def test_nm2invcm():
assert nm2invcm(250) == 4e4
assert nm2invcm(400) == 25e3