Utility functions

This section summarizes various useful functions implemented in LumiSpy.

Join spectra

In case several spectra (or spectral images) where subsequently recorded for different, but overlapping spectral windows, LumiSpy provides a utility join_spectra() to merge these into a single spectrum. The main argument is a list of two or more spectral objects. Spectra are joined at the centre of the overlapping range along the signal axis. To avoid steps in the intensity, several parameters (see docstring: join_spectra()) allow to tune the scaling of the later signals with respect to the previous ones. By default, the scaling parameter is determined as average ratio between the two signals in the range of +/- 50 pixels around the centre of the overlapping region.

>>> import lumispy as lum
>>> s = lum.join_spectra([s1,s2])

Exporting text files

LumiSpy includes a function savetxt() that exports the data of a signal object (with not more than two axes) to a simple .txt (or .csv) file. Can facilitate data transfer to other programs, but no metadata is included. By default, the axes are saved as first column (and row in 2d case). Set axes=False to save the data object only. The function can also transpose (default False) the dataset or take a custom fmt (default %.5f) or delimiter (default \t) string.

>>> import lumispy as lum
>>> import numpy as np
...
>>> # Spectrum:
>>> S = lum.signals.LumiSpectrum(np.arange(5))
>>> lum.savetxt(S, 'spectrum.txt')
0.00000     0.00000
1.00000     1.00000
2.00000     2.00000
3.00000     3.00000
4.00000     4.00000
...
>>> # Linescan:
>>> L = lum.signals.LumiSpectrum(np.arange(25).reshape((5,5)))
>>> lum.savetxt(L, 'linescan.txt')
0.00000     0.00000 1.00000 2.00000 3.00000 4.00000
0.00000     0.00000 5.00000 10.00000        15.00000        20.00000
1.00000     1.00000 6.00000 11.00000        16.00000        21.00000
2.00000     2.00000 7.00000 12.00000        17.00000        22.00000
3.00000     3.00000 8.00000 13.00000        18.00000        23.00000
4.00000     4.00000 9.00000 14.00000        19.00000        24.00000

Mathematical routines

Unit conversion

For convenience, LumiSpy provides functions that convert between different units commonly used for the signal axis. Namely,

For the energy axis, the conversion uses the wavelength-dependent refractive index of air.

Solving the grating equation

The function solve_grating_equation() (relationship between wavelength and pixel position in the detector plane) follows the conventions described in the tutorial from Horiba Scientific.

Cropping multiple signals in the navigation axis

The function crop_edges() removes a specified amount from the edges of a spectral map, from the edges inwards. The amount can be given as an integer (pixels), a float (converted to indices), or a string using HyperSpy’s fancy indexing syntax (e.g. rel0.1 for 10% or 100 nm for 100 nm). See HyperSpy’s indexing guide for details. It takes a list of Signals and cropping can happen uniformly on all sides or by individually specifying the cropping range for each axis or each side. If the navigation axes shape across the list of signals is different, all signals can be rebinned to match the shape of the first signal in the list. It is a convenience wrapper for the inav method in HyperSpy. The function can also be called as s.crop_edges() on a single signal object.

>>> signals = [cl_map, sem_image]
>>> signals
[CLSpectrum <256,256|1024>, Signal1D <128,128|1>]
>>> signals_cropped = lum.utils.crop_edges(signals, crop_range=5, rebin_nav=True)
>>> signals_cropped
[CLSpectrum <246,246|1024>, Signal1D <246,246|1>]

Note

Many scanning luminescence techniques result in artefacts at the edges of the scanned region. This function enables the same cropping of the navigation axis for a list of signals recorded in the same region to correct for such defect.