Displaying Spectra
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 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 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.
Selecting/Showing Data Sets
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).
Pan/Zoom
There are several ways to pan around a spectrum or zoom in on features of interest.
Interactive Pan/Zoom (Desktop or Notebook Interface)
You can find the following Pan/Zoom tools available under the icon in the viewer toolbar:
2D Bidirectional Pan/Zoom
The 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.
Horizontal/Vertical Zoom
The (horizontal) and (vertical) Zoom tools allow you to zoom along each axis, while locking the other. You can also zoom by scrolling.
API Pan/Zoom (Notebook Interface)
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
Limit methods
You can use the methods jdaviz.configs.specviz.Specviz.x_limits
and
jdaviz.configs.specviz.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 Quantity
, or 'auto'
to automatically scale:
>>> from astropy import units as u
>>> specviz.x_limits()
>>> specviz.x_limits(650*u.nm,750*u.nm)
>>> specviz.y_limits('auto', 110.0)
Additionally, you can provide the limit methods with a 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)
Autoscale methods
You can also quickly return to the default zoom using
jdaviz.configs.specviz.Specviz.autoscale_x
and
jdaviz.configs.specviz.Specviz.autoscale_y
.
Axis Orientation methods
To quickly flip an axis to change to and from ascending/descending, use
jdaviz.configs.specviz.Specviz.flip_x
and
jdaviz.configs.specviz.Specviz.flip_y
.
Defining Spectral Regions
Spectral regions can be defined by clicking on the icon at the right of the viewer toolbar. Then, click the 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
get_spectral_regions()
method:
Plot Settings
To access plot settings for a particular viewer (including the spectrum viewer), click the icon, followed by the Layer tab.
Layer
The top section of the Layer tab contains options to change the color of the spectrum (click the icon to see a color change menu), change visibility of the spectrum ( icon), and a drop-down box to select which layer will have its settings changed.
Line Width
Width of the line for the spectrum in pixels. Larger values are thicker lines on the plot.
Vmin and Vmax
Minimum and maximum values of the y axis.
Percentile
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.”