grizli

Grizli: The "Grism redshift and line" analysis software

https://github.com/gbrammer/grizli

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
3 of 13 committers (23.1%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (13.1%) to scientific vocabulary

Keywords from Contributors

closember astronomy astropy astropy-affiliated astrophysics

Last synced: 6 months ago · JSON representation ·

Repository

Grizli: The "Grism redshift and line" analysis software

Basic Info

Host: GitHub
Owner: gbrammer
License: mit
Language: Python
Default Branch: master
Homepage:
Size: 14.7 MB

Statistics

Stars: 81
Watchers: 12
Forks: 58
Open Issues: 49
Releases: 0

Created almost 10 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation

README.rst

.. image:: examples/grizli_logo.png

.. image:: https://github.com/gbrammer/grizli/actions/workflows/python-package.yml/badge.svg
    :target: https://github.com/gbrammer/grizli/actions

.. image:: https://badge.fury.io/py/grizli.svg
    :target: https://badge.fury.io/py/grizli
    
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1146904.svg
   :target: https://doi.org/10.5281/zenodo.1146904

.. image:: https://readthedocs.org/projects/grizli/badge/?version=latest
   :target: https://grizli.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status
   
*Grism redshift & line* analysis software for space-based slitless spectroscopy
========================================================================================

What is ``grizli``?
~~~~~~~~~~~~~~~~~~~

This early release of `grizli` is intended to demonstrate and
demystify some general techniques for manipulating *HST* slitless
spectroscopic observations, providing software kernels to address
questions such as

    "How does the WFC3/IR G141 grism disperse the spectrum of a
    star/galaxy at pixel position `(x,y)` in my F140W direct image?".

Much of the background related to this question in the context of the
currently available software tools was discussed in a document by
`Brammer, Pirzkal and Ryan
(2014) `__. Along with a
detailed description of the format of the configuration files originally
developed for the aXe software, we provided a compact `Python
script `__
to address exactly the question above and strip away all of the many
layers of bookkeeping, file-IO, etc. in existing analysis pipelines such
as aXe (`Kummel et al.
2009 `__) and
"THREEDHST" (`Brammer et al.
2012 `__, `Momcheva
et al. 2015 `__). In
fact, that relatively simple script serves as the low-level kernel for
the way `grizli` computes the grism dispersion.

Eventually, `grizli` is intended to encourage and enable general users to move
away from simple "data reduction" (e.g., extracting a 1D spectrum of a
single object akin to standard slit spectroscopy) and toward
more quantitative and comprehensive **modeling** and fitting of slitless
spectroscopic observations, which typically involve overlapping spectra
of hundreds or thousands of objects in exposures taken with one or more
separate grisms and at multiple dispersion position angles. The products
of this type of analysis will be complete and uniform characterization
of the spectral properties (e.g., continuum shape, redshifts, line
fluxes) of all objects in a given exposure taken in the slitless
spectroscopic mode.

Installation & Documentation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Installation instructions and documentation (in progress) can be found at http://grizli.readthedocs.io.

Working Examples
~~~~~~~~~~~~~~~~~~~~~~

The following are IPython/jupyter notebooks demonstrating various aspects of the code functionality.  They render statically in the GitHub pages or can be run locally after cloning and installing the software repository.

- `Grizli-Pipeline `__ : End-to-end processing of WFC3/IR data.

  1. Query the MAST archive and automatically download files
  2. Image pre-processing  (astrometric alignment & background subtraction)
  3. Field contamination modeling
  4. Spectral extractions
  5. Redshift & emission line fits (multiple grisms)

- `Fit-with-Photometry `__ : Demonstrate simultaneous fitting with grism spectra + ancillary photometry

- `NewSpectrumFits `__: Demonstration of the lower-level fitting tools

  1. Unify the fitting tools between the stacked and exposure-level 2D cutouts ("beams").
 
- `Fit-Optimization `__ **(09.14.17)**: Custom fitting (hasn't been tested recently)

  1. Demonstrate some of the workings behind the fitting wrapper scripts by defining custom model functions with parameters to optimize.

The notebooks below are deprecated and haven't been tested against the master branch since perhaps late 2017.

- `Grizli Demo `__: Simple interaction with WFC3/IR spectra

- `Basic-Sim `__ **(5.5.16)**: Basic simulations based on single WFC3/IR grism and direct exposures

- `multimission-simulation `__ **(5.11.16)**: 
  
  1. Demonstration of more advanced simulation techniques using deep image mosaics and external catalogs/segmentation images as reference.
  2. Provide a comparison between dispersed spectra from WFC3/G141, *JWST*/NIRISS and *WFIRST*.

- `WFC3IR_Reduction `__ **(9.6.16)**: End-to-end processing of WFC3/IR data.

  1. Pre-processing of files downloaded from MAST (astrometric alignment & background subtraction)
  2. Field contamination modeling
  3. Spectral extractions
  4. Redshift & emission line fits (multiple grisms)
  
- `NIRISS-simulation `__ **(11.11.16)**: Simulation and analysis of JWST/NIRISS observations

  1. Simulate NIRISS spectra in three blocking filters and two orients offset by 90 degrees.
  2. Simulation field taken from the Hubble WFC3/IR Ultra-Deep Field, with the WFC3 F140W image as the morphological reference and photo-z templates taken as the spectral models. 
  3. Extract spectra and fit redshifts and emission lines from the combined six exposures.

Owner

Name: Gabe Brammer
Login: gbrammer
Kind: user
Company: University of Copenhagen

Website: http://gbrammer.github.io/
Repositories: 81
Profile: https://github.com/gbrammer

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: grizli
abstract: >-
  Grizli is a grism redshift and line analysis
  software. Grizli produces quantitative and comprehensive 
  modeling and fitting of slitless spectroscopic observations, 
  which typically involve overlapping spectra of hundreds or 
  thousands of objects in exposures taken with one or more separate 
  grisms and at multiple dispersion position angles. This type of 
  analysis provides complete and uniform characterization of the spectral 
  properties (e.g., continuum shape, redshifts, line fluxes) of all objects 
  in a given exposure taken in the slitless spectroscopic mode.
message: Please cite this software using these metadata.
doi: 10.5281/zenodo.1146904
url: https://github.com/gbrammer/grizli
publisher: GitHub
keywords: 
  - Astronomy software (1855)
type: software
authors:
  - given-names: Gabriel
    family-names: Brammer
    email: gbrammer@gmail.com
    affiliation: >-
      Cosmic Dawn Center, Niels Bohr Institute,
      University of Copenhagen
    orcid: 'https://orcid.org/0000-0003-2680-0055'

GitHub Events

Total

Create event: 10
Release event: 3
Issues event: 6
Watch event: 11
Delete event: 1
Issue comment event: 24
Push event: 56
Pull request review event: 1
Pull request event: 15
Fork event: 7

Last Year

Create event: 10
Release event: 3
Issues event: 6
Watch event: 11
Delete event: 1
Issue comment event: 24
Push event: 56
Pull request review event: 1
Pull request event: 15
Fork event: 7

Committers

Last synced: almost 3 years ago

All Time

Total Commits: 2,588
Total Committers: 13
Avg Commits per committer: 199.077
Development Distribution Score (DDS): 0.329

Top Committers

Name	Email	Commits
Gabriel Brammer	g**r@g**m	1,737
Gabriel Brammer	b**r@s**u	560
Jasleen Matharu	5**u@u**m	102
Victoria Strait	v**t@g**m	88
James Davies	j**s@m**e	40
Ivelina Momcheva	i**a@g**m	34
Victoria Strait	v**t@u**u	13
pascaloesch	p**h@g**m	4
Larry Bradley	l**y@g**m	3
Bharath Saiguhan	b**n@g**m	2
B.S. Bharath Saiguhan	b**g@p**n	2
Jasleen Matharu	j**u@t**u	2
JacobKosowski	9**i@u**m	1

Committer Domains (Top 20 + Academic)

tamu.edu: 1 prl.res.in: 1 ucdavis.edu: 1 mpia.de: 1 stsci.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 58
Total pull requests: 156
Average time to close issues: about 1 month
Average time to close pull requests: 18 days
Total issue authors: 25
Total pull request authors: 16
Average comments per issue: 1.83
Average comments per pull request: 1.11
Merged pull requests: 140
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 4
Pull requests: 27
Average time to close issues: N/A
Average time to close pull requests: 15 days
Issue authors: 4
Pull request authors: 5
Average comments per issue: 0.5
Average comments per pull request: 0.67
Merged pull requests: 18
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

gbrammer (11)
TheSkyentist (10)
victoriastrait (9)
chriswillott (3)
jkmatharu (2)
x12red (2)
njcleri (2)
Zhiyuan-G (2)
jensmelinder (2)
flairue (1)
YoRHazero (1)
DazhiDTU (1)
LalitwadeeKawinwanichakij (1)
Rimi98 (1)
paolasantini (1)

Pull Request Authors

gbrammer (113)
TheSkyentist (55)
KostasValeckas (7)
victoriastrait (5)
ivastar (4)
lizihao1008 (2)
pascaloesch (2)
keithbuckholz (2)
kmlgould (2)
Yunjingwu (1)
jdavies-st (1)
cgosmeyer (1)
PJ-Watson (1)
JacobKosowski (1)
lboogaard (1)

Top Labels

Issue Labels

bug (3) enhancement (2)

Pull Request Labels

enhancement (3)

Packages

Total packages: 1
Total downloads:
- pypi 1,091 last-month

Total dependent packages: 1
Total dependent repositories: 3
Total versions: 97
Total maintainers: 1

pypi.org: grizli

Grism redshift and line analysis software

Homepage: https://github.com/gbrammer/grizli
Documentation: https://grizli.readthedocs.io/
License: MIT
Latest release: 1.13.1
published 7 months ago

Versions: 97
Dependent Packages: 1
Dependent Repositories: 3
Downloads: 1,091 Last month

Rankings

Forks count: 6.3%

Downloads: 6.8%

Average: 8.2%

Stargazers count: 8.9%

Dependent repos count: 9.0%

Dependent packages count: 10.0%

Maintainers (1)

gbrammer

Last synced: 6 months ago

Dependencies

setup.py pypi

astropy *
cython *
numpy *

pyproject.toml pypi

.github/workflows/publish-to-pypi.yml actions

actions/checkout v3 composite
actions/download-artifact v3 composite
actions/upload-artifact v3 composite
pypa/gh-action-pypi-publish v1.5.1 composite

.github/workflows/python-package-ero.yml actions

actions/checkout v3 composite
actions/setup-python v3 composite

.github/workflows/python-package-with-jwst.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

.github/workflows/python-package.yml actions

actions/checkout v3 composite
actions/setup-python v4 composite

docs/requirements.txt pypi

Cython *
astropy *
docutils <0.18
matplotlib *
numpy *
pyyaml *
scikit-image *
scipy *
sphinx_astropy *
sregion *

environment.yml conda

hstcal

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

grizli

Science Score: 77.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.rst

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: grizli

Rankings

Maintainers (1)

Dependencies