Data Analysis Plugins

To enable quick analysis of astronomical spectra, Specviz ships with a number of plugins that let you do various standard spectral analysis tasks. Note that these plugins all depend on specutils to do the actual analysis work - when doing these operations in the Notebook you are often better off using the specutils or astropy APIs directly instead of using the plugins. But for quick-look or interaction heavy workflows, the plugins provide a UI-based alternative.

Data analysis plugins are found in the plugin tray, accessed via the plugin icon in the upper right corner of the Specviz application window. Each plugin may be used to perform data analysis tasks on selected datasets.

Input/Output

Data to be operated on are selected in each plugin via a Data pulldown menu.

Metadata Viewer

This plugin allows viewing of any metadata associated with the selected data.

Export Plot

This plugin allows exporting the plot in a given viewer to various image formats.

Plot Options

This plugin gives access to per-viewer and per-layer plotting options.

Included in this plugin is a toggle called Plot Uncertainty, which will show uncertainty values as a shaded area above and below the spectrum. With this option toggled on, all spectra added to Specviz will have their uncertainty values displayed as well.

Gaussian Smooth

Gaussian Smooth is performed on a Spectrum1D data object. The spectrum is convolved with a Gaussian function. The Gaussian standard deviation in pixels must be entered into the Standard deviation field in the plugin.

A new Spectrum1D object is generated and is added to the spectrum viewer. It can be selected and shown in the viewer via the Data icon in the viewer toolbar.

Model Fitting

Astropy models can be fit to a spectrum via the Model Fitting plugin. Model components are selected via the Model pulldown menu. Each component should be given a Model ID. The Add Model button adds a Model Parameters block.

Model Parameters are automatically initialized with a guess. These starting values can be edited by the user. They may also be fixed by selecting the Fixed? checkbox, so that they are not fit or changed by the model fitting.

A mathematical expression must be entered into the Model Equation Editor to specify the mathematical combination of models. This is also necessary even if there is only one model component. The model components are specified by their Model ID. For example, add together Constant and Gaussian models with model IDs ‘C’ and ‘G1’ by entering the Model Equation ‘C+G1’.

Fitted models can be extracted from the app into notebook cells by using the get_models() method of the configuration helper class, e.g.:

specviz.get_models(model_label="Model")

The get_models() method returns the fitted astropy model objects. If only the parameters of the model are needed, those can be extracted using the following code:

specviz.get_model_parameters(model_label="Model")

If nothing is specified for the model_label keyword, information for all models will be returned.

Unit Conversion

The spectral flux density and spectral axis units can be converted using the Unit Conversion plugin. The Spectrum1D object to be converted is the currently selected spectrum in the spectrum viewer Data icon in the viewer toolbar.

Select the frequency, wavelength, or energy unit in the New Spectral Axis Unit pulldown (e.g. Angstrom, Hertz, erg).

Select the flux density unit in the New Flux Unit pulldown (e.g. Jansky, W/(Hz/m2), ph/(Angstrom cm2 s)).

The Apply button will convert the flux density and/or spectral axis units and create a new Spectrum1D object that is automatically switched to in the spectrum viewer. The name of the new Spectrum1D object is “_units_copy_” plus the flux and spectral units of the spectrum.

Line Lists

Line wavelengths can be plotted in the spectrum viewer using the Line Lists plugin.

Line lists (e.g. Common Stellar, SDSS, CO) can be selected from Preset Line Lists via the Available Line Lists pulldown. They are loaded and displayed by pressing Load List. Each loaded list is shown under Loaded Lines. Loaded line lists may be removed by pressing the circled-x button.

The Loaded Lines include a Custom line list which is automatically created, but populated with no lines. Lines may be added to the Custom line list by entering Line Name, Rest Value, and Unit for the spectral axis and pressing Add Line. Selected lines may be hidden by deselecting the associated check box.

The color of each line list may be adjusted with the color and saturation sliders. Entire line lists may be hidden in the display via Show All and Hide All, located at the bottom of each list. Similarly, all of the line lists may be shown or hidden via Plot All and Erase All, located at the bottom of the plugin.

Redshift Slider

Warning

Using the redshift slider with many active spectral lines causes performance issues. If the shifting of spectral lines lag behind the slider, try plotting less lines. You can deselect lines using, e.g., the “Erase All” button in the line lists UI.

The plugin also contains a redshift slider which shifts all of the plotted lines according to the provided redshift/RV. The slider applies a delta-redshift, snaps back to the center when releasing, and has limits that default based on the x-limits of the spectrum viewer. This provides a convenient method to fine-tune the position of the redshifted lines to the observed lines in the spectrum.

Line Analysis

The Line Analysis plugin returns statistics for a single spectral line. The line is selected via the region tool in the spectrum viewer to select a spectral subset. Note that you can have multiple subsets in Specviz, but the plugin will only show statistics for the selected subset.

A linear continuum is fitted and subtracted (divided for the case of equivalenth width) before computing the line statistics. By default, the continuum is fitted to a region surrounding the select line. The width of this region can be adjusted, with a visual indicator shown in the spectrum plot while the plugin is open. The thick line shows the linear fit which is then interpolated into the line region as shown by a thin line. Alternatively, a custom secondary region can be created and selected as the region to fit the linear continuum.

The statistics returned include the line centroid, gaussian sigma width, gaussian FWHM, total flux, and equivalent width.

Redshift from Centroid

Following the table of statistics, the centroid can be used to set the redshift by assigning the centroid value to a line added in the Line List Plugin. Select the corresponding line from the dropdown, or by locking the selection to the identified line and using the (line selector) tool in the spectrum viewer.