Loading Data into Specviz

By design, Specviz only supports data that can be parsed as Spectrum1D objects, as that allows the Python-level interface and parsing tools to be defined in specutils instead of being duplicated in Jdaviz. Spectrum1D objects are very flexible in their capabilities, however, and hence should address most astronomical spectrum use cases.

See also

Reading from a File

Specutils documentation on loading data as Spectrum1D objects.

There are two primary ways in which a user can load their data into the Specviz application: through the UI, or via the Python API (for most user cases this means inside a notebook). These are separately detailed below.

Importing data through the GUI

The first way that users can load their data into the Specviz application is by using the Import Data button in the application’s user interface.

This process is fairly straightforward, users need only click on the Import Data button:

and choose a file that can be parsed as a Spectrum1D in the text field:

After clicking Import, the data file will be parsed and loaded into the application. A notification will appear to let users know if the data import was successful, and if possible the data will be immediately displayed. If an incompatible spectrum is already being displayed, the newly loaded data will be available in the Data menu but not immediately visible in the viewer. Afterward, the new dataset can be found in the Data tab of each viewer’s menu. Here, users can select which spectra that have be loaded to be visualized in the viewer.

Loading data via the API

Alternatively, if users are working in a coding environment like a Jupyter notebook, they have access to the Specviz helper class API. Using this API, users can load data into the application through code. Below is an example of importing the Specviz helper class, creating a Spectrum1D object from a data file via the specutils.Spectrum1D.read method:

>>> from specutils import Spectrum1D
>>> spec1d = Spectrum1D.read("/path/to/data/file") 
>>> specviz = Specviz()  
>>> specviz.load_spectrum(spec1d)  

You can also pass the path to a file that Spectrum1D understands directly to the jdaviz.configs.specviz.Specviz.load_spectrum method:

>>> specviz.load_spectrum("path/to/data/file") 

This method works well for data files that specutils understands. However, if you are using your own data file or in-memory data, you can instead create a Spectrum1D object directly. In this example that is done using randomly generated data, and then that Spectrum1D object is loaded into the Specviz application:

>>> from jdaviz import Specviz
>>> import numpy as np
>>> import astropy.units as u
>>> from specutils import Spectrum1D
>>> flux = np.random.randn(200)*u.Jy
>>> wavelength = np.arange(5100, 5300)*u.AA
>>> spec1d = Spectrum1D(spectral_axis=wavelength, flux=flux)
>>> specviz = Specviz()
>>> specviz.load_spectrum(spec1d)  

For more information about using the Specutils package, please see the Specutils documentation.

Loading multiple spectra via the API

In addition to loading single spectra as above, in some cases it may be useful to load multiple related spectra at once into the Jdaviz application. The most common such case is when you have spectra of the same object covering multiple wavelength ranges and want to look at and analyze the entire range of spectral coverage simultaneously. The jdaviz.configs.specviz.Specviz.load_spectrum accepts a SpectrumList object, in which case it will both load the individual Spectrum1D objects in the list and additionally attempt to stitch together the spectra into a single data object so that they can be manipulated and analyzed in the application as a single entity:

>>> from specutils import SpectrumList
>>> spec_list = SpectrumList([spec1d_1, spec1d_2]) 
>>> specviz.load_spectrum(spec_list) 

In the screenshot below, the combined spectrum is plotted in gray, and one of the single component spectra are also selected and plotted in red. Note that the “stitching” algorithm to combine the spectra is a simple concatenation of data, so in areas where the wavelength ranges of component spectra overlap you may see the line plot jumping between points of the two spectra, as at the beginning and end of the red region in the screenshot below:

This functionality is also available in limited instances by providing a directory path to the jdaviz.configs.specviz.Specviz.load_spectrum method. Note that the read method of SpectrumList is only set up to handle directory input in limited cases, for example JWST MIRI MRS data, and will throw an error in other cases. In cases that it does work, only files in the directory level specified will be read, with no recursion into deeper folders.