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QSOnic

QSOnic: fast quasar continuum fitting - Published in JOSS (2024)

https://github.com/p-slash/qsonic

Science Score: 100.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README and JOSS metadata
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    Academic publication links
    Links to: joss.theoj.org
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    1 of 5 committers (20.0%) from academic institutions
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    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords from Contributors

exoplanets
Last synced: 6 months ago · JSON representation ·

Repository

Continuum fitting for DESI

Basic Info
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 2
  • Open Issues: 3
  • Releases: 27
Created over 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License Citation

README.rst 

======
QSOnic
======

*Lightining-fast continuum fitting*

.. image:: https://joss.theoj.org/papers/10.21105/joss.06373/status.svg
   :target: https://doi.org/10.21105/joss.06373

.. image:: https://img.shields.io/pypi/v/qsonic?color=blue
    :target: https://pypi.org/project/qsonic

.. image:: https://img.shields.io/badge/Source-qsonic-red
    :target: https://github.com/p-slash/qsonic

.. image:: https://github.com/p-slash/qsonic/actions/workflows/testing.yml/badge.svg
    :target: https://github.com/p-slash/qsonic/actions/workflows/testing.yml
    :alt: Tests Status

.. image:: https://readthedocs.org/projects/qsonic/badge/?version=latest
    :target: https://qsonic.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

**QSOnic** is an MPI-parallelized, highly optimized quasar continuum fitting package for DESI built on the same algorithm as `picca `_, but *faster*. It also provides an efficient API to read DESI quasar spectra. If you use this software, please cite the article in the Journal of Open Source Software (JOSS).

The key differences
-------------------
- You can use any desired input continuum from another continuum prediction method as input continuum model.
- Coadding of spectrograph arms can be performed after continuum fitting or disabled entirely.
- Continuum is multiplied by a fiducial mean flux when provided.
- You can pass fiducial var_lss (column **VAR_LSS**) and mean flux (column **MEANFLUX**) for observed wavelength **LAMBDA** in **STATS** extention of a FITS file. Wavelength should be linearly and equally spaced. This is the same format as rawio output from picca, except **VAR** column in picca is the variance on flux not deltas. We break away from that convention by explicitly requiring variance on deltas in a new column.
- If no fiducial is passed, we fit only for var_lss (no eta fitting by default). Eta fitting can be enabled by passing ``--var-fit-eta``. A covariance matrix is calculated based on delete-one Jackknife over subsamples between var_pipe and var_obs data points, and used in var_lss, eta fitting if ``--var-use-cov`` passed (soft recommendation to always enable this).
- Internal weights for continuum fitting and coadding are based on smoothed ``IVAR``, and output ``WEIGHT`` is based on this smoothed ivar. This smoothing can be turned off.
- Chi2 information as well as best fits are saved in continuum_chi2_catalog.fits. Chi2 is calculated using smooth ivar and var_lss, and does not subtract sum of ln(weights).

Similarities
------------
+ Delta files are the same. ``CONT`` column is mean flux times continuum even when fiducial mean flux is passed.
+ ``MEANSNR`` in header file and chi2 catalog is average of flux times square root of positive ivar values. Header values are per arm, but catalog values are the average over all arms.
+ Eta fitting does not rescale ``IVAR`` output. Pipeline noise will be modified with explicit calibration option.

Owner

  • Name: Naim Goksel Karacayli
  • Login: p-slash
  • Kind: user
  • Location: The Ohio State University

JOSS Publication

QSOnic: fast quasar continuum fitting
Published
May 08, 2024
DOI
Volume 9, Issue 97, Page 6373
Authors
Naim Göksel Karaçaylı ORCID
Center for Cosmology and AstroParticle Physics, The Ohio State University, 191 West Woodruff Avenue, Columbus, OH 43210, USA, Department of Astronomy, The Ohio State University, 4055 McPherson Laboratory, 140 W 18th Avenue, Columbus, OH 43210, USA, Department of Physics, The Ohio State University, 191 West Woodruff Avenue, Columbus, OH 43210, USA
Editor
Ivelina Momcheva ORCID
Tags
Cosmology Quasars Lyman-alpha forest
View PDF Review Thread Software Archive

Citation (CITATION.cff) 

cff-version: "1.2.0"
authors:
- family-names: Karaçaylı
  given-names: Naim Göksel
  orcid: "https://orcid.org/0000-0001-7336-8912"
doi: 10.5281/zenodo.11105006
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Karaçaylı
    given-names: Naim Göksel
    orcid: "https://orcid.org/0000-0001-7336-8912"
  date-published: 2024-05-08
  doi: 10.21105/joss.06373
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6373
  title: "QSOnic: fast quasar continuum fitting"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06373"
  volume: 9
title: "QSOnic: fast quasar continuum fitting"

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 628
  • Total Committers: 5
  • Avg Commits per committer: 125.6
  • Development Distribution Score (DDS): 0.228
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Naim Goksel Karacayli n****k@g****m 485
Naim Goksel Karacayli n****i@y****u 139
Andrei Cuceu a****u@g****m 2
Ivelina Momcheva i****a@g****m 1
Dan F-M f****y@g****m 1
Committer Domains (Top 20 + Academic)
yale.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 7
  • Total pull requests: 110
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 1 day
  • Total issue authors: 3
  • Total pull request authors: 4
  • Average comments per issue: 1.29
  • Average comments per pull request: 0.03
  • Merged pull requests: 109
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • p-slash (5)
  • gcalderone (1)
  • corentinravoux (1)
Pull Request Authors
  • p-slash (129)
  • ivastar (2)
  • dfm (2)
  • andreicuceu (1)
Top Labels
Issue Labels
enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 25 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 28
  • Total maintainers: 1
pypi.org: qsonic

Quasar continuum fitter for DESI

  • Versions: 28
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 25 Last month
Rankings
Dependent packages count: 6.6%
Downloads: 17.8%
Average: 24.9%
Forks count: 30.5%
Dependent repos count: 30.6%
Stargazers count: 39.1%
Maintainers (1)
ngkaracayli
Last synced: 6 months ago