Tools21cm

Tools21cm: A python package to analyse the large-scale 21-cm signal from the Epoch of Reionization and Cosmic Dawn - Published in JOSS (2020)

https://github.com/sambit-giri/tools21cm

Science Score: 100.0%

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

✓
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 8 DOI reference(s) in README and JOSS metadata
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Academic publication links
Links to: arxiv.org, joss.theoj.org
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Committers with academic emails
2 of 12 committers (16.7%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

21-cm-cosmology 21-cm-powerspectrum cosmic-dawn epoch-of-reionization reionization

Scientific Fields

Artificial Intelligence and Machine Learning Computer Science - 62% confidence

Last synced: 6 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: sambit-giri
License: mit
Language: Jupyter Notebook
Default Branch: master
Homepage:
Size: 83.9 MB

Statistics

Stars: 23
Watchers: 4
Forks: 19
Open Issues: 7
Releases: 2

Topics

21-cm-cosmology 21-cm-powerspectrum cosmic-dawn epoch-of-reionization reionization

Created almost 9 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Citation

Tools21cm

A python package for analysing simulated 21-cm signal during the Epoch of Reionization (EoR) and Cosmic Dawn (CD). Full documentation (with examples, installation instructions and complete module description) can be found at readthedocs.

Package details

The package provides tools to analyse cosmological simulations of EoR and CD. It contains modules to create mock 21-cm observations for current and upcoming radio telescopes, such as LOFAR, MWA and SKA, and to construct statistical measures.

Input

Currently, Tools21cm supports the following simulation codes:

Outputs

There are various manipulation and analysis moduled in Tools21cm.

Angular coordinates: methods to convert data between physical (cMpc) coordinates and observational (angular-frequency) coordinates
Bubble Statistics: methods to calcluate the sizes of the regions of interest and estimate the size distributions
Cosmological calculators: various functions for calculating some cosmological stuff
Identifying regions: methods to identify regions of interest in images
Lightcone: methods to construct lightcones
Power spectrum: contains functions to estimate various two point statistics
Reading simuation outputs: methods to read simulations outputs
Smoothing: methods to smooth or reduce resolution of the data to reduce noise
Point statistics: contains various useful statistical methods
Temperature: methods to estimate the brightness temperature
Radio telescope noise:
- simulate the radio telescope observation strategy
- simulate telescope noise
Topology: methods to estimate the topology of the region of interest
Foreground model: methods to simulate and analyse the foreground signal for 21 cm signal

For detail documentation and how to use them, see here.

Under Developement

Radio telescope beam:
- simulate the sensitivity and evolution of the primary beam
- simulate the impact of side-lobes

INSTALLATION

Before installing this package, please make sure that cython and numpy are installed. One can install a stable version of this package using pip by running the following command::

pip install tools21cm

This package is being actively under-development, which involves addition of new modules and bug fixes. In order to use the latest version, one can clone this package.

To install the package from source, one should clone this package running the following::

git clone https://github.com/sambit-giri/tools21cm.git

To install the package in the standard location, run the following in the root directory::

python setup.py install

In order to install it in a separate directory::

python setup.py install --home=directory

One can also install the latest version using pip by running the following command::

pip install git+https://github.com/sambit-giri/tools21cm.git

The dependencies should be installed automatically during the installation process. If they fail for some reason, you can install them manually before installing tools21cm. The list of required packages can be found in the requirements.txt file present in the root directory.

Tests

For testing, one can use pytest or nosetests. Both packages can be installed using pip. To run all the test script, run the either of the following::

python -m pytest tests

nosetests -v

📖 Citation

If you use tools21cm in your work, please cite the following paper:

Giri, S., Mellema, G., & Jensen, H. (2020). Tools21cm: A python package to analyse the large-scale 21-cm signal from the Epoch of Reionization and Cosmic Dawn. Journal of Open Source Software, 5(52), 2363.
https://doi.org/10.21105/joss.02363

BibTeX: bibtex @article{giri2020tools21cm, title={Tools21cm: A python package to analyse the large-scale 21-cm signal from the Epoch of Reionization and Cosmic Dawn}, author={Giri, Sambit and Mellema, Garrelt and Jensen, Hannes}, journal={Journal of Open Source Software}, volume={5}, number={52}, pages={2363}, year={2020}, publisher={Open Journals} }

CONTRIBUTING

If you find any bugs or unexpected behavior in the code, please feel free to open a Github issue. The issue page is also good if you seek help or have suggestions for us. For more details, please see here.

Owner

Name: Sambit Kumar Giri
Login: sambit-giri
Kind: user
Location: Zurich
Company: University of Zurich

Website: https://sambit-giri.github.io/
Twitter: sam_giri
Repositories: 10
Profile: https://github.com/sambit-giri

JOSS Publication

Tools21cm: A python package to analyse the large-scale 21-cm signal from the Epoch of Reionization and Cosmic Dawn

Published

August 10, 2020

DOI

10.21105/joss.02363

Volume 5, Issue 52, Page 2363

Authors

Sambit K. Giri

Department of Astronomy and Oskar Klein Centre, Stockholm University, AlbaNova, SE-106 91 Stockholm, Sweden, Institute for Computational Science, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland

Garrelt Mellema

Department of Astronomy and Oskar Klein Centre, Stockholm University, AlbaNova, SE-106 91 Stockholm, Sweden

Hannes Jensen
Self

Editor

Amy Roberts

Citation (CITATION.md)

If you use this package to model the impact of baryonic effects on the matter power spectrum, you should cite:

    Giri S. K., Schneider A., 2021, JCAP, 2021, 046. doi:10.1088/1475-7516/2021/12/046

@ARTICLE{2021JCAP...12..046G,
       author = {Giri, Sambit K. and Schneider, Aurel},
        title = "{Emulation of baryonic effects on the matter power spectrum and constraints from galaxy cluster data}",
      journal = {\jcap},
     keywords = {cosmological simulations, galaxy clusters, power spectrum, weak gravitational lensing, Astrophysics - Cosmology and Nongalactic Astrophysics},
         year = 2021,
        month = dec,
       volume = {2021},
       number = {12},
          eid = {046},
        pages = {046},
          doi = {10.1088/1475-7516/2021/12/046},
archivePrefix = {arXiv},
       eprint = {2108.08863},
 primaryClass = {astro-ph.CO},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2021JCAP...12..046G},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

GitHub Events

Total

Issues event: 24
Watch event: 4
Issue comment event: 20
Push event: 107
Pull request review event: 1
Pull request event: 9
Fork event: 1
Create event: 3

Last Year

Issues event: 24
Watch event: 4
Issue comment event: 20
Push event: 107
Pull request review event: 1
Pull request event: 9
Fork event: 1
Create event: 3

Committers

Last synced: 7 months ago

All Time

Total Commits: 763
Total Committers: 12
Avg Commits per committer: 63.583
Development Distribution Score (DDS): 0.641

Past Year

Commits: 193
Committers: 2
Avg Commits per committer: 96.5
Development Distribution Score (DDS): 0.005

Top Committers

Name	Email	Commits
sambit-giri	s**i@g**m	274
sambit-giri	s**i@o**m	265
Sambit Giri	s**i@S**l	100
Sambit Kumar Giri	s**i@a**e	79
Garrelt Mellema	g**t@a**e	16
Michele Bianco	M**o@s**k	14
Michele Bianco	m**o@p**m	9
David Prelogovic	d**c@g**m	2
Andrés Felipe Gómez	A**0@g**m	1
sambit-giri	s**t@n**e	1
Michele Bianco	m**e@m**e	1
Garrelt Mellema	g**l@a**e	1

Committer Domains (Top 20 + Academic)

astro.su.se: 2 as-4648.astro.su.se: 1 michele-thinkpad-p14s.home: 1 n157-p44.eduroam.kth.se: 1 sussex.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 36
Total pull requests: 44
Average time to close issues: 2 months
Average time to close pull requests: 17 days
Total issue authors: 17
Total pull request authors: 5
Average comments per issue: 1.53
Average comments per pull request: 0.11
Merged pull requests: 34
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 18
Pull requests: 10
Average time to close issues: 10 days
Average time to close pull requests: 4 minutes
Issue authors: 8
Pull request authors: 2
Average comments per issue: 1.06
Average comments per pull request: 0.0
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

sambit-giri (10)
garrelt (5)
FurenDeng (3)
micbia (3)
Guo-Jian-Wang (2)
dpiras (2)
Luzexuan (2)
dbsi-pinkman (1)
iliantiliev (1)
astrophys (1)
abonaldi (1)
NGillet (1)
dprelogo (1)
Aritra-Kundu (1)
moll-re (1)

Pull Request Authors

micbia (16)
garrelt (13)
sambit-giri (10)
Andresfgomez970 (3)
dprelogo (1)

Top Labels

Issue Labels

bug (2) help wanted (1)

Pull Request Labels

enhancement (3)

Packages

Total packages: 1
Total downloads:
- pypi 508 last-month

Total dependent packages: 1
Total dependent repositories: 1
Total versions: 32
Total maintainers: 1

pypi.org: tools21cm

Documentation: https://tools21cm.readthedocs.io/
License: mit
Latest release: 2.3.8
published 7 months ago

Versions: 32
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 508 Last month

Rankings

Dependent packages count: 10.0%

Average: 20.2%

Dependent repos count: 21.7%

Downloads: 28.9%

Maintainers (1)

sam_giri

Last synced: 7 months ago

Dependencies

docs/requirements_doc.txt pypi

ipython *
nbsphinx *
numpydoc *
sphinx >=2.3
sphinx-rtd-theme *
sphinx_readable_theme *

requirements.txt pypi

astropy *
joblib *
matplotlib *
numpy *
pyfftw *
pytest *
scikit-image *
scikit-learn *
scipy *
tqdm *

setup.py pypi

astropy *
cosmospectra *
joblib *
matplotlib *
numba *
numpy *
pyfftw *
pytest *
scikit-image *
scikit-learn *
scipy *
tqdm *

.github/workflows/build-and-deploy.yml actions

actions/checkout v3 composite
actions/upload-artifact v3 composite
ruby/setup-ruby v2 composite

.github/workflows/ci.yml actions

actions/checkout v3 composite
conda-incubator/setup-miniconda v2 composite

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

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

environment.yml pypi

pyproject.toml pypi

pytest ^6.2 develop
astropy ^4.0
cython ^0.29
joblib ^1.0
matplotlib ^3.4
numba ^0.57.1
numpy ^1.21
pandas ^1.3
pytest ^6.2
python >=3.8
scikit-image ^0.18
scikit-learn ^0.24
scipy ^1.7
torch ^2.1.0
tqdm ^4.60

Tools21cm

Science Score: 100.0%

Keywords

Scientific Fields

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Tools21cm

Package details

Input

Outputs

Under Developement

INSTALLATION

Tests

📖 Citation

CONTRIBUTING

Owner

JOSS Publication

Tools21cm: A python package to analyse the large-scale 21-cm signal from the Epoch of Reionization and Cosmic Dawn

Authors

Editor

Tags

Citation (CITATION.md)

GitHub Events

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pypi.org: tools21cm

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Maintainers (1)

Dependencies