Getting started

Getting started#

Installation#

Important

Python >=3.10 is required to run specvizitor. If you have an older version of Python installed in your system, you can use conda to create a virtual environment with Python version 3.10+ (if you are looking for a minimal conda installer, check out miniforge).

Install the latest version of specvizitor using pip:

>> pip install specvizitor

If you wish to install specvizitor from source, refer to the Installing from source section.

Basic usage#

Important

This tutorial shows how to do inspections of Grizli data products. Instructions on how to inspect other kinds of spectroscopic datasets in specvizitor can be found in the User Guide.

In this demo, we will be using data from the JWST Cycle 2 program “ALT”, reduced using the Grizli tool.

  1. Download the data as a ZIP file from here (total size: 25.5 MB).

  2. Unzip the archive and navigate to the directory where the files have been extracted to:

    >> unzip specvizitor_demo.zip
>> cd specvizitor_demo

  3. Start specvizitor:

    >> specvizitor

  4. Navigate to File ‣ New…. Optionally give a name to the project (we use demo.csv for this tutorial) and specify the path to the catalog (the catalog.fits file in the specvizitor_demo directory):

    _images/demo1.png

    Click OK. You should now see the Grizli data products created for the first of the three galaxies included in this demo:

    _images/demo2.png

    Below is the description of what is shown in the data viewer.

    • Top row, left to right: an image cutout in the F356W filter (the filter used in the NIRCam/grism observations), a series of emission line maps, and a redshift probability distribution function (z-PDF);

    • Middle row: a 2D spectrum stack of all exposures;

    • Bottom row: a 1D spectrum.

  5. This galaxy was correctly identified by Grizli as an OIII-emitter at z ≈ 5.76 (you can see this on the right under Object Information). Save the redshift by pressing Ctrl+S or by clicking Save! next to the redshift slider. The saved value will appear in Inspection Results:

    _images/demo3.png

  6. Go to the next object by pressing →:

    _images/demo4.png

  7. This object has an unphysical redshift value of -1.0 stored in the catalog (which means that spectrum fitting failed). Find the redshift that best describes the data by interacting with the slider at the bottom of the window:

    _images/demo5.gif

    This galaxy is likely to be an SIII-emitter at z ≈ 2.68!

  8. Save the redshift of the second object (see step 5).

  9. Go to the last object by pressing → one more time:

    _images/demo6.png

    The 2D spectrum shows only a single emission line which prevents us from unambiguously identifying the redshift of this object. However, we can see that Grizli suggests that this is an Halpha-emitter at z ≈ 4.31, which seems very plausible.

  10. Save the redshift of the last object and close the window.

  11. Finally, check the contents of the output file (also known as the inspection file) created by specvizitor:

    >> cat demo.csv
id,starred,z_sviz,comment
16605,False,5.760862,
26932,False,2.677225,
34927,False,4.307806,

    Here, id is the ID of the object, and z_sviz is the redshift saved in Inspection Results.

Congratulations on completing the tutorial! If you want to learn more about specvizitor, navigate to the User Guide section.

Updating specvizitor#

To update specvizitor to the latest version, run the following command:

>> pip install specvizitor -U

Tip

If you see error messages after installing the update, try to run specvizitor with the --purge option: specvizitor --purge. Note that this action will erase application settings, including custom widget configurations. If “purging” specvizitor does not help, refer to the Troubleshooting section.