Signal1D Tools

The methods described in this section are only available for one-dimensional signals in the Signal1D class.

Cropping

The crop_signal1D() crops the spectral energy range in-place. If no parameter is passed, a user interface appears in which to crop the one dimensional signal. For example:

s = hs.datasets.example_signals.EDS_TEM_Spectrum()
s.crop_signal1D(5, 15) # s is cropped in place

Additionally, cropping in HyperSpy can be performed using the Signal indexing syntax. For example, the following crops a spectrum to the 5 keV-15 keV region:

s = hs.datasets.example_signals.EDS_TEM_Spectrum()
sc = s.isig[5.:15.] # s is not cropped, sc is a "cropped view" of s

It is possible to crop interactively using Region Of Interest (ROI). For example:

s = hs.datasets.example_signals.EDS_TEM_Spectrum()
roi = hs.roi.SpanROI(left=5, right=15)
s.plot()
sc = roi.interactive(s)
../_images/interactive_signal1d_cropping.png

Interactive spectrum cropping using a ROI.

Background removal

New in version 1.4: zero_fill and plot_remainder keyword arguments and big speed improvements.

The remove_background() method provides background removal capabilities through both a CLI and a GUI. The GUI displays an interactive preview of the remainder after background subtraction. Current background type supported are power law, offset, polynomial and gaussian. By default the background parameters are estimated using analytical approximations (keyword argument fast=True). For better accuracy, but higher processing time, the parameters can be estimated by curve fitting by setting fast=False.

Example of usage:

s = hs.datasets.artificial_data.get_core_loss_eels_signal(add_powerlaw=True)
s.remove_background(zero_fill=False)
../_images/signal_1d_remove_background.png

Interactive background removal. In order to select the region used to estimate the background parameters (red area in the figure) click inside the axes of the figure and drag to the right without releasing the button.

Calibration

The calibrate() method provides a user interface to calibrate the spectral axis.

Alignment

The following methods use sub-pixel cross-correlation or user-provided shifts to align spectra. They support applying the same transformation to multiple files.

  • align1D()
  • shift1D()

Integration

Deprecated since version 1.3: integrate_in_range(). It will be removed in 2.0. Use integrate1D() instead, possibly in combination with a Region Of Interest (ROI) if interactivity is required.

Data smoothing

The following methods (that include user interfaces when no arguments are passed) can perform data smoothing with different algorithms:

  • smooth_lowess() (requires statsmodels to be installed)
  • smooth_tv()
  • smooth_savitzky_golay()

Spike removal

New in version 0.5.

spikes_removal_tool() provides an user interface to remove spikes from spectra.

../_images/spikes_removal_tool.png

Spikes removal tool.

Peak finding

A peak finding routine based on the work of T. O’Haver is available in HyperSpy through the find_peaks1D_ohaver() method.

Other methods

  • Interpolate the spectra in between two positions interpolate_in_between()
  • Convolve the spectra with a gaussian gaussian_filter()
  • Apply a hanning taper to the spectra hanning_taper()