Available actions

Most menu entries and toolbar buttons trigger an action when clicked. This is a rather loose definition, but actions are different from Tools and Widgets.

The list below is sorted on category, which roughly corresponds to the toolbar/menu in which they appear.

File

Open

Open a dialog to let the user interactively browse for files. It then loads these files using hyperspy.io.load() before plotting the loaded signals.

Open Stack

Open files and combine the loaded signals into one signal (stacked).

Close

Close the selected signal(s).

Save

Save the selected signal(s).

Save figure

Save the currently active figure using matplotlib’s savefig(). Note that this does not care about how the figure was produced, or the underlying resolution of the data.

New editor

Opens a new Code editor widget.

Close All (signals)

Close all signals. This can sometimes help clear out signals that get stuck in an invalid state.

Exit

Close the application.

Signal

Signal type

Changes the signal type using a combination of methods on hyperspy.signal.Signal:

  • set_signal_type()
  • set_signal_origin()
  • and by converting with as_signal2D() and as_signal1D().

Signal data type

Change the data type use to store the signal data internally. See the numpy docs for details. The operation is performed by change_dtype().

Manual align

Interactively align the signal. Navigate through the signal stack, and shift each point individually. This will also shift all the following points by the same amount. During input, the images are simply looped around the edges, but for final processing the signal dimensions will be expanded to fit the aligned signal.

Statistics

Print the signal statistics to the console. See print_summary_statistics() for details.

Histogram

Plot a histogram of the signal. See get_histogram() for details. The method for determining the number of bins can be set in the Settings.

Mirror navigation

Mirror navigation axes of selected signals, i.e. they will always navigate together.

Share navigation

Mirror navigation axes of selected signals, and keep only one navigator plot.

Rebin

Opens a dialog to rebin the signal. See rebin() for details.

Model

Create Model

Add and plot a default model for the selected signal. Note that the Signal type is important in order to create the correct model type.

The newly created model is accessible through the Data view.

Add component

Add a component to the currently selected model.

The newly created component is accessible through the Data view.

Plot components

Toggle the plotting of each component together with the model, as performed by enable_plot_components().

Adjust component positions

Add/remove widgets to adjust the position of the components in the model, as performed by enable_adjust_position().

Decomposition

PCA

Performs decomposition if neccessary, then plots the scree for selecting the number of components to use for a decomposition model. The selection is made by clicking on the in the scree plot on the first component to not be included in the decomposition. The scree plot will then automatically close and the decomposition model plotted (see decomposition() and get_decomposition_model()).

BSS

Performs decomposition if neccessary, then plots the scree for selecting the number of components to use for a blind source separation. The selection is made by clicking in the scree plot on the first component to not be included in the decomposition. The scree plot will then automatically close and the BSS algortihm run (see blind_source_separation() and plot_bss_results()).

Decomposition results

Performs decomposition if necessary, then plots the decomposition results according to the hyperspy’s plot_decomposition_results().

Spectrum

Smooth Savitzky-Golay

Apply a Savitzky-Golay filter. See smooth_savitzky_golay() for details.

Smooth Lowess

Apply a Lowess smoothing filter. See smooth_lowess() for details.

Smooth Total variation

Total variation data smoothing. See smooth_tv() for details.

Butterworth filter

Apply a Butterworth filter. See filter_butterworth() for details.

Hanning taper

Apply a Hanning taper to both ends of the data. See hanning_taper() for details.

EELS

Remove Background

Interactively define the background, and remove it. See remove_background() for details.

Fourier Ratio Deconvoloution

Use the Fourier-Ratio method to deconvolve one signal from another.

Note

The background should be removed with e.g. Remove Background before running Fourier ratio deconvolution.

See fourier_ratio_deconvolution() for details.

Estimate thickness

Estimates the thickness (relative to the mean free path) of a sample using the log-ratio method. See hyperspy._signals.eels.EELSSpectrum.estimate_thickness() for details.

Browse EELSDB

Browse the EELSDB online database of standard EEL spectra.

Image

Gaussian Filter

Opens a dialog to interactively apply a gaussian smoothing filter.

Rotate

Opens a dialog to interactively rotate an image. Works on images in both navigation and signal space.

Diffraction

Virtual aperture

Add a virtual aperture to the diffraction image. The aperture can be moved around and resized, allowing for an interactive creation of virtual BF/DF images.

Virtual navigator

Set the navigator intensity by a virtual aperture.

Note

Setting a virtual navigator will replot the signal, so any existing apertures will be lost. Therefore always add the virtual navigator first if you want to use one.

_images/virtual_apertures.png

Example of a signal with a virtual navigator and three virtual apertures. The navigator (orange circle) selects the direct beam, giving a virtual bright-field image, while the other apertures select diffraction spots unique to three different grains/phases.

Virtual annulus

Add a virtual annulus to the diffraction image. An annulus is simply a hollow disc, and it can be moved around and resized, allowing for an interactive creation of virtual annular dark field images.

Math

Mean

Plot the mean of the current signal across all navigation axes.

Sum

Plot the sum of the current signal across all navigation axes.

Maximum

Plot the maximum of the current signal across all navigation axes.

Minimum

Plot the sum of the current signal across all navigation axes.

Std.dev.

Plot the standard deviation of the current signal across all navigation axes.

Variance

Plot the variances of the current signal. across all navigation axes

FFT

Perform a fast fourier transform on the active part of the signal.

Live FFT

Perform a fast fourier transform on the active part of the signal. The live FFT updates the FFT as the signal is navigated.

Signal FFT

Perform a fast fourier transform on the entire signal, not just the active part.

Inverse FFT

Perform an inverse fast fourier transform on the active part of the signal.

Inverse Signal FFT

Perform an inverse fast fourier transform on the entire signal.

Plot

Tight layout

Apply a tight layout to the selected plot. This is basically a workaround for the not so ideal basic layout for matplotlib figures, especially if they have been resized.

Settings

Version selector

Open dialog to select branch/version of HyperSpy/HyperSpyUI.

Warning

This can invalidate your installation of HyperSpyUI and/or HyperSpy. Use with caution!

Opens up a dialogbox that enables you to install a specific GitHub branch for HyperSpy and HyperSpyUI. This will basically download and install the selected branch using pip, whether or not that version works or if the HyperSpy and HyperSpyUI verions are internally compatible, or even compatible with your version of Python. As this can prevent you from starting the application afterwards, you might end up having to reinstall it.

Note

If your current installation is a git repository, this will check out the selected branch instead of doing a pip install.

Check for updates

Checks for updates to HyperSpy and HyperSpyUI. If the packages are not source installs, it checks for a new version on PyPI.

Plugin manager

Show the plugin manager dialog (see Plugin manager widget and PluginManager).

Reset layout

Resets layout of toolbars and widgets.

HyperSpy settings

Edit the HyperSpy package settings.

Edit settings

Shows a dialog for editing the application and plugins settings. See

Windows

Tile

Arranges all figures in a tile pattern.

Cascade

Arranges all figures in a cascade pattern.

Close all (windows)

Closes all matplotlib figures.