Because of its use of glue as the underlying data-handling layer and its applicability in several different contexts, Specviz takes a modular approach to displaying data that has been loaded. This section describes how to affect how your spectra are being shown.
The first spectrum you load will be automatically displayed in the viewer with the view window set by the extent of the spectrum. Additional spectra loaded after the first may not be fully shown if they exceed the bounds of the plotted area, which are set based on the first displayed spectrum. The bounds can be changed via the :ref:`Pan/Zoom <pan-zoom>` tool or by deselecting the current spectra and selecting a different spectrum for display. Spectra generated by plugins (e.g., a spectrum generated by the Gaussian Smooth plugin) will generally be automatically displayed as well, and one can always see the spectra available and toggle their visibility in the data selection dropdown menu (see :ref:`Selecting Data Set <selecting-data-set>` for more detail). If you are working in the notebook, you can also enable more reproducible analysis by using the Python API. Both are detailed further below.
Data can be selected and de-selected under the "Data" tab. Here, you can click a checkbox next to the listed data to make the data visible (checked) or invisible (unchecked).
There are several ways to pan around a spectrum or zoom in on features of interest.
You can find the following Pan/Zoom tools available under the |icon-hammer-and-screwdriver| icon in the viewer toolbar:
The |icon-zoom-pan-2d| icon allows you to zoom using the scroll wheel. The window will zoom into the area around your cursor:
To pan, simply click and drag the window.
The |icon-zoom-pan-horiz| (horizontal) and |icon-zoom-pan-vert| (vertical) Zoom tools allow you to zoom along each axis, while locking the other. You can also zoom by scrolling.
The |icon-box-zoom| (box) and |icon-xrange-zoom| (x-range) zoom tools allow you to zoom by clicking and dragging with your mouse. The box zoom tool adjusts both the x and y range of the plot, whereas the x-range tool zooms only the x-axis to the selected region. While clicking and dragging you will see the selected region as a gray box, as below.
You can switch between the x-range zoom tool and the plot tool by right-clicking (or your trackpad equivalent) on the currently selected zoom icon on the viewer toolbar, which will open a menu of choices as in the screenshot below:
The Specviz helper contains a set of convenience methods to programmatically define the view of the spectrum viewer. You may instantiate a Specviz Helper via:
>>> from jdaviz import Specviz
>>> # Instantiate an instance of Specviz
>>> specviz = Specviz()
>>> # Display Specviz
>>> specviz.app # doctest: +SKIPYou can use the methods :meth:`jdaviz.configs.specviz.helper.Specviz.x_limits` and
:meth:`jdaviz.configs.specviz.helper.Specviz.y_limits` to modify the field of
view of Specviz. You can provide a scalar (which assumes the units of the loaded spectra),
a ~astropy.units.Quantity, or 'auto' to automatically scale:
>>> from astropy import units as u
>>> specviz.x_limits() #doctest: +SKIP
>>> specviz.x_limits(650*u.nm,750*u.nm) #doctest: +SKIP
>>> specviz.y_limits('auto', 110.0) #doctest: +SKIP
Additionally, you can provide the limit methods with a ~specutils.SpectralRegion. Specviz shall set the bounds the upper and lower bounds of the SpectralRegion
>>> from specutils import SpectralRegion
>>> bounds = SpectralRegion(0.45*u.nm, 0.6*u.nm)
>>> specviz.x_limits(bounds) #doctest: +SKIPYou can also quickly return to the default zoom using :meth:`jdaviz.configs.specviz.helper.Specviz.autoscale_x` and :meth:`jdaviz.configs.specviz.helper.Specviz.autoscale_y`.
To quickly flip an axis to change to and from ascending/descending, use :meth:`jdaviz.configs.specviz.helper.Specviz.flip_x` and :meth:`jdaviz.configs.specviz.helper.Specviz.flip_y`.
Spectral regions can be defined by clicking on the |icon-hammer-and-screwdriver| icon at the right of the viewer toolbar. Then, click the |icon-region-horiz| icon to set the cursor dragging function in "spectral region selection" mode.
Now, you can move the mouse to one of the end points (in wavelength) of the region you want to select, and drag it to the other end point. The selected region background will display in light gray color, and the spectral trace in color, coded to subset number.
You also see in the top tool bar that the region was added to the data hold, and is named "Subset 1".
Clicking on that selector, you can add more regions by selecting the "create new" entry:
Now just select the end points of the new region as before. It will be added to the data hold with name "Subset 2":
In a notebook cell, you can access the regions using the :meth:`~jdaviz.configs.specviz.helper.Specviz.get_spectral_regions` method:
To access plot settings for a particular viewer (including the spectrum viewer), click the |icon-settings-sliders| icon in the viewer toolbar or open the :ref:`Plot Options<specviz-plot-options>` plugin.
The top section of the :guilabel:`Layer` tab contains options to change the color of the spectrum (click the |icon-color-square| icon to see a color change menu), change visibility of the spectrum (|icon-eye| icon), and a drop-down box to select which layer will have its settings changed.
Width of the line for the spectrum in pixels. Larger values are thicker lines on the plot.
Minimum and maximum values of the y axis.
Sets the bounds of the plot (Vmin and Vmax) such that the selected percentage of the data is shown in the viewer. Editing either bound manually changes the "Percentile" selection to "Custom."