https://github.com/ywx649999311/eztao

A Python Toolkit for AGN Time Series Analysis using CARMA models

Science Score: 36.0%

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1 of 7 committers (14.3%) from academic institutions
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Low similarity (14.5%) to scientific vocabulary

Keywords

agn astronomy carma drw gaussian-processes time-series

Keywords from Contributors

sequences projection interactive serializer measurement cycles packaging charts network-simulation modular

Last synced: 9 months ago · JSON representation

Repository

A Python Toolkit for AGN Time Series Analysis using CARMA models

Basic Info

Host: GitHub
Owner: ywx649999311
License: mit
Language: Python
Default Branch: master
Homepage:
Size: 11.8 MB

Statistics

Stars: 23
Watchers: 2
Forks: 9
Open Issues: 7
Releases: 13

Topics

agn astronomy carma drw gaussian-processes time-series

Created about 6 years ago · Last pushed 12 months ago

Metadata Files

Readme Changelog License

EzTao (易道)

EzTao is a toolkit for conducting AGN time-series/variability analysis, mainly utilizing the continuous-time auto-regressive moving average model (CARMA)

Installation

pip install git+https://github.com/ywx649999311/EzTao.git

Dependencies

python = ">=3.9,<3.13" celerite = ">= 0.3.0" scipy = "> 1.5.0" numba = ">= 0.57.0" matplotlib = ">=3.3.3" emcee = ">=0.3.0"

Quick Examples

Let's first simulate a DRW/CARMA(1,0) process with a variance of 0.3^2 and a relaxation timescale of 100 days. This time series will have a total of 200 data points and span 10 years. ```python import numpy as np import matplotlib.pyplot as plt from eztao.carma import DRW_term from eztao.ts import gpSimRand

define a DRW kernel & and simulate a process

amp = 0.2 tau = 100 DRWkernel = DRWterm(np.log(amp), np.log(tau)) t, y, yerr = gpSimRand(DRW_kernel, 10, 365*10, 200)

now, plot it

fig, ax = plt.subplots(1,1, dpi=150, figsize=(8,3)) ax.errorbar(t, y, yerr, fmt='.') ... ``` drw_sim

We can fit the simulated time series to the DRW model and see how well we can recover the input parameters. ```python from eztao.ts import drw_fit

bestfit = drwfit(t, y, yerr) print(f'Best-fit DRW parameters: {best_fit}') shell Best-fit DRW parameters: [0.17356983 88.36262467] ```

How does the power spectrum density (PSD) compare? ```python from eztao.carma import gp_psd

get psd functions

truepsd = gppsd(DRWkernel) bestpsd = gppsd(DRWterm(*np.log(best_fit)))

plot

fig, ax = plt.subplots(1,1, dpi=150, figsize=(6,3)) freq = np.logspace(-5, 2) ax.plot(freq, truepsd(freq), label='Input PSD') ax.plot(freq, bestpsd(freq), label='Best-fit PSD') ... ``` drw_psd

Note: How well the input and best-fit PSD match is up to how good the best-fit parameters are, which is highly influenced by the quality of the input time series.

For more examples, please check out the online documentation or run the tutorial notebooks at -> .

Development

poetry is used to solve dependencies and to build/publish this package. Below shows how setup the environment for development (assuming you already have poetry installed on your machine).  1. Clone this repository, and enter the repository folder. 2. Create a python virtual environment and activate it (the virtual environment name must be '.venv'). python -m venv .venv source .venv/bin/activate 3. Install dependencies and EzTao in editable mode. poetry install

Now you should be ready to start adding new features. Be sure to checkout the normal practice regarding how to use poetry on its website. When you are ready to push, also make sure the poetry.lock file is checked-in if any dependency has changed.

Citation

We are working on a paper to describe the full implementation of EzTao. In the meantime, if you find EzTao useful for your research, please consider acknowledging EzTao using the following:

@MISC{Yu2022, author = {{Yu}, Weixiang and {Richards}, Gordon T.}, title = "{EzTao: Easier CARMA Modeling}", keywords = {Software}, howpublished = {Astrophysics Source Code Library, record ascl:2201.001}, year = 2022, month = jan, eid = {ascl:2201.001}, pages = {ascl:2201.001}, archivePrefix = {ascl}, eprint = {2201.001}, adsurl = {https://ui.adsabs.harvard.edu/abs/2022ascl.soft01001Y}, adsnote = {Provided by the SAO/NASA Astrophysics Data System} }

Owner

Name: Weixiang Yu
Login: ywx649999311
Kind: user

Website: wx-yu.com
Twitter: astro_flyfish
Repositories: 5
Profile: https://github.com/ywx649999311

Physics PhD Candidate at Drexel University

GitHub Events

Total

Create event: 4
Release event: 1
Issues event: 7
Watch event: 3
Issue comment event: 5
Push event: 6
Pull request event: 5

Last Year

Create event: 4
Release event: 1
Issues event: 7
Watch event: 3
Issue comment event: 5
Push event: 6
Pull request event: 5

Committers

Last synced: over 1 year ago

All Time

Total Commits: 249
Total Committers: 7
Avg Commits per committer: 35.571
Development Distribution Score (DDS): 0.04

Past Year

Commits: 12
Committers: 3
Avg Commits per committer: 4.0
Development Distribution Score (DDS): 0.333

Top Committers

Name	Email	Commits
Weixiang Yu	w**3@d**u	239
dependabot[bot]	4****]	3
Weixiang Yu	y**9@g**m	3
LSSTAGNSC	1****s	1
Drew Oldag	4****g	1
David Wright	d**v@g**m	1
Matt Lowery	m**y@M**n	1

Committer Domains (Top 20 + Academic)

matts-mbp.lan: 1 drexel.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 63
Total pull requests: 34
Average time to close issues: 5 months
Average time to close pull requests: 18 days
Total issue authors: 6
Total pull request authors: 6
Average comments per issue: 0.4
Average comments per pull request: 0.5
Merged pull requests: 22
Bot issues: 0
Bot pull requests: 15

Past Year

Issues: 2
Pull requests: 8
Average time to close issues: 6 months
Average time to close pull requests: 13 minutes
Issue authors: 2
Pull request authors: 2
Average comments per issue: 0.0
Average comments per pull request: 0.25
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 6

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Top Authors

Issue Authors

ywx649999311 (58)
karandogra987 (2)
nevencaplar (1)
mwl10 (1)
drewoldag (1)

Pull Request Authors

dependabot[bot] (18)
ywx649999311 (16)
davecwright3 (2)
mwl10 (1)
drewoldag (1)
gtrichards (1)

Top Labels

Issue Labels

enhancement (12) feature (11) bug (6) documentation (3) celerite2 (3)

Pull Request Labels

dependencies (18) python (6)

Packages

Total packages: 1
Total downloads:
- pypi 116 last-month

Total dependent packages: 1
Total dependent repositories: 2
Total versions: 13
Total maintainers: 1

pypi.org: eztao

A toolkit for Active Galactic Nuclei (AGN) time-series analysis.

Homepage: https://github.com/ywx649999311/EzTao
Documentation: https://eztao.readthedocs.io/
License: MIT
Latest release: 0.4.4
published 12 months ago

Versions: 13
Dependent Packages: 1
Dependent Repositories: 2
Downloads: 116 Last month

Rankings

Dependent packages count: 4.8%

Downloads: 9.1%

Average: 10.4%

Dependent repos count: 11.5%

Forks count: 11.9%

Stargazers count: 14.6%

Maintainers (1)

weixiang_yu

Last synced: 9 months ago

Dependencies

docs/requirements.txt pypi

celerite ==0.4.0
emcee ==3.0.0
ipykernel *
jinja2 <3.1
matplotlib ==3.3.3
nbsphinx >=0.8.6
numba ==0.51.0
scipy ==1.5.0
sphinx ==3.4.1
sphinx-copybutton ==0.3.1
sphinx_rtd_theme ==0.5.0
toml ==0.10.2

environment.yml pypi

corner *
eztao ==0.4.0
importlib-metadata *

poetry.lock pypi

alabaster 0.7.12 develop
atomicwrites 1.4.0 develop
attrs 21.4.0 develop
babel 2.9.1 develop
beautifulsoup4 4.10.0 develop
black 21.12b0 develop
bleach 4.1.0 develop
certifi 2021.10.8 develop
cffi 1.15.0 develop
charset-normalizer 2.0.12 develop
click 8.1.2 develop
colorama 0.4.4 develop
coverage 6.3.2 develop
defusedxml 0.7.1 develop
docutils 0.16 develop
entrypoints 0.4 develop
fastjsonschema 2.15.3 develop
idna 3.3 develop
imagesize 1.3.0 develop
importlib-resources 5.6.0 develop
iniconfig 1.1.1 develop
jinja2 3.1.1 develop
joblib 0.17.0 develop
jsonschema 4.4.0 develop
jupyter-client 7.2.1 develop
jupyter-core 4.9.2 develop
jupyterlab-pygments 0.1.2 develop
markupsafe 2.1.1 develop
mistune 0.8.4 develop
mypy-extensions 0.4.3 develop
nbclient 0.5.13 develop
nbconvert 6.4.5 develop
nbformat 5.3.0 develop
nbsphinx 0.8.8 develop
nest-asyncio 1.5.5 develop
pandas 1.1.5 develop
pandocfilters 1.5.0 develop
pathspec 0.9.0 develop
platformdirs 2.5.1 develop
pluggy 1.0.0 develop
py 1.11.0 develop
pycparser 2.21 develop
pygments 2.11.2 develop
pyrsistent 0.18.1 develop
pytest 6.2.5 develop
pytest-cov 2.12.1 develop
pytz 2022.1 develop
pywin32 303 develop
pyzmq 22.3.0 develop
requests 2.27.1 develop
snowballstemmer 2.2.0 develop
soupsieve 2.3.1 develop
sphinx 3.5.4 develop
sphinx-copybutton 0.3.3 develop
sphinx-rtd-theme 0.5.2 develop
sphinxcontrib-applehelp 1.0.2 develop
sphinxcontrib-devhelp 1.0.2 develop
sphinxcontrib-htmlhelp 2.0.0 develop
sphinxcontrib-jsmath 1.0.1 develop
sphinxcontrib-qthelp 1.0.3 develop
sphinxcontrib-serializinghtml 1.1.5 develop
testpath 0.6.0 develop
toml 0.10.2 develop
tornado 6.1 develop
traitlets 5.1.1 develop
typed-ast 1.5.2 develop
urllib3 1.26.9 develop
webencodings 0.5.1 develop
celerite 0.4.2
cycler 0.11.0
emcee 3.1.1
fonttools 4.31.2
importlib-metadata 4.11.3
kiwisolver 1.4.2
llvmlite 0.34.0
matplotlib 3.5.1
numba 0.51.2
numpy 1.21.1
packaging 21.3
pillow 9.1.0
pyparsing 3.0.7
python-dateutil 2.8.2
scipy 1.6.1
setuptools-scm 6.4.2
six 1.16.0
tomli 1.2.3
typing-extensions 4.1.1
zipp 3.8.0

pyproject.toml pypi

Sphinx ^3.4.1 develop
black ^21.7b0 develop
joblib ^0.17.0 develop
nbsphinx >=0.8.6 develop
pandas ^1.1.4 develop
pytest ^6.0.1 develop
pytest-cov ^2.10.1 develop
sphinx-copybutton ^0.3.1 develop
sphinx-rtd-theme ^0.5.0 develop
toml ^0.10.1 develop
celerite >= 0.3.0
emcee >=3.0.0
importlib-metadata >= 2.0.0
matplotlib ^3.3.0
numba >= 0.51.0
python ^3.7
scipy > 1.5.0

https://github.com/ywx649999311/eztao

Science Score: 36.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

EzTao (易道)

Installation

Dependencies

Quick Examples

define a DRW kernel & and simulate a process

now, plot it

get psd functions

plot

Development

Citation

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

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: eztao

Rankings

Maintainers (1)

Dependencies