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https://github.com/mattpitkin/psrqpy
A python module to query the ATNF pulsar catalogue
https://github.com/mattpitkin/psrqpy
atnf catalogue pulsar python
Last synced: about 1 month ago
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A python module to query the ATNF pulsar catalogue
- Host: GitHub
- URL: https://github.com/mattpitkin/psrqpy
- Owner: mattpitkin
- License: mit
- Created: 2017-11-15T11:27:08.000Z (about 7 years ago)
- Default Branch: main
- Last Pushed: 2024-04-25T08:21:35.000Z (9 months ago)
- Last Synced: 2024-04-25T09:34:29.996Z (9 months ago)
- Topics: atnf, catalogue, pulsar, python
- Language: Python
- Size: 3.23 MB
- Stars: 39
- Watchers: 5
- Forks: 25
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
- Citation: CITATION.cff
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README
# PSRQpy
This module aims to provide a python interface for querying the [ATNF pulsar catalogue](http://www.atnf.csiro.au/people/pulsar/psrcat/). It is an unofficial
package and is not endorsed by or affiliated with the ATNF.
Full documentation of the module can be found [here](http://psrqpy.readthedocs.io/).
Any comments or suggestions are welcome.
## Installation
To install the code from source, clone the git repository and run either:
```
python setup.py install --user
```
to install as a user, or
```
sudo python setup.py install
```
to install as root.
The module can also be installed using `pip` with:
```
pip install psrqpy
```
or in a [Conda](https://docs.conda.io/en/latest/) environment using:
```
conda install -c conda-forge psrqpy
```
### Requirements
The [requirements](requirements.txt) for installing the code are:
* [`requests`](http://docs.python-requests.org/en/master/)
* [`beautifulsoup4`](https://www.crummy.com/software/BeautifulSoup/bs4/doc/)
* [`numpy`](http://www.numpy.org/)
* [`scipy`](https://www.scipy.org/)
* [`astropy`](http://www.astropy.org/)
* [`pandas`](https://pandas.pydata.org/)
* [`ads`](https://ads.readthedocs.io/en/latest/)
* [`matplotlib`](https://matplotlib.org/)
## Examples
A simple query of the catalogue to, e.g., just return all pulsar frequencies, would be:
```python
import psrqpy
q = psrqpy.QueryATNF(params='F0')
# get frequencies as an astropy table
t = q.table
print(t['F0'])
```
You can query multiple parameters, e.g.:
```python
import psrqpy
q = psrqpy.QueryATNF(params=['F0', 'F1', 'RAJ', 'DecJ'])
# get values as an astropy table
t = q.table
print(t['F0'])
```
You can query specific pulsars, e.g.:
```
import psrqpy
q = psrqpy.QueryATNF(params=['F0', 'F1', 'RAJ', 'DecJ'], psrs=['J0534+2200', 'J0537-6910'])
# get values as an astropy table
t = q.table
# print the table
print(t)
JNAME F0 F0_ERR F1 F1_ERR RAJ RAJ_ERR DECJ DECJ_ERR
Hz Hz 1 / s2 1 / s2
---------- ------------- ------- ------------- ------ ------------ ------- ------------ --------
J0534+2200 29.946923 1e-06 -3.77535e-10 2e-15 05:34:31.973 0.005 +22:00:52.06 0.06
J0537-6910 62.0261895958 1.3e-09 -1.992272e-10 4e-17 05:37:47.416 0.11 -69:10:19.88 0.6
```
You can set [conditions](http://www.atnf.csiro.au/research/pulsar/psrcat/psrcat_help.html?type=normal#condition) for the searches,
e.g.:
```python
import psrqpy
q = psrqpy.QueryATNF(params=['Jname', 'f0'], condition='f0 > 100 && f0 < 200', assoc='GC')
```
where `assoc=GC` looks for all pulsars in globular clusters.
When a query is generated the entire catalogue is downloaded and stored in the `QueryATNF` object as
a pandas [`DataFrame`](https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.html).
The query can therefore be re-used to access data on different parameters, different pulsars, or
using different conditions, without the need to re-download the catalogue. We may originally want
to query pulsar frequencies using only frequencies greater than 10 Hz, with
```python
import psrqpy
q = psrqpy.QueryATNF(params=['F0'], condition='F0 > 10')
freqs = q.table['F0']
```
Using the same `QueryATNF` object we could change to get frequency derivatives for pulsars
with frequencies less than 10 Hz, with
```python
q.condition = 'F0 < 10'
q.query_params = 'F1'
fdot = q.table['F1']
```
In these cases the whole catalogue (with no conditions applied and all available parameters) stored as a pandas [`DataFrame`](https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.html)
is accessible with
```python
catalogue = q.catalogue
```
You can also [generate](http://psrqpy.readthedocs.io/en/latest/query.html#psrqpy.search.QueryATNF.ppdot) a
_lovely_ period vs. period derivative plot based on the latest catalogue information, using
just three lines of code, e.g.:
```python
from psrqpy import QueryATNF
query = QueryATNF(params=['P0', 'P1', 'ASSOC', 'BINARY', 'TYPE', 'P1_I'])
query.ppdot(showSNRs=True, showtypes='all')
```
gives
## Development and Support
Code development is done via the package's [GitHib repository](https://github.com/mattpitkin/psrqpy).
Any contributions can be made via a [fork and pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) model
from that repository, and must adhere to the [MIT license](#License). Any problems with the code
or support requests can be submitted via the repository's [Issue tracker](https://github.com/mattpitkin/psrqpy/issues).
## Test suite
There are tests supplied that cover many of the functions within PSRQpy. These can be run from the
base directory of the repository (after installing the [`pytest`](https://docs.pytest.org/en/latest/) and
[`pytest-socket`](https://pypi.org/project/pytest-socket/) modules, e.g., with `pip`) by just calling:
```bash
pytest
```
These tests are not included in the `pip` installed version of the code.
## Copyright and referencing for the catalogue
Regarding the use of the catalogue and software behind it, the [following statements](http://www.atnf.csiro.au/research/pulsar/psrcat/download.html) apply:
> PSRCAT is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. PSRCAT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
>
> PSRCAT makes use of "evaluateExpression: A Simple Expression Evaluator". Copyright © 1996 - 1999 Parsifal Software, All Rights Reserved.
>
> The programs and databases remain the property of the Australia Telescope National Facility, CSIRO, and are covered by the [CSIRO Legal Notice and Disclaimer](http://www.csiro.au/en/About/Footer/Legal-notice).
>
> If you make use of information from the ATNF Pulsar Catalogue in a publication, we would appreciate acknowledgement by reference to the publication "[The ATNF Pulsar Catalogue](http://adsabs.harvard.edu/abs/2005AJ....129.1993M)", R. N. Manchester, G. B. Hobbs, A. Teoh & M. Hobbs, Astronomical Journal, 129, 1993-2006 (2005) and by quoting the web address http://www.atnf.csiro.au/research/pulsar/psrcat for updated versions.
If making use of this code to access the catalogue, or produce plots, I would be grateful if (as well as citing the ATNF pulsar catalogue [paper](http://adsabs.harvard.edu/abs/2005AJ....129.1993M) and [URL](http://www.atnf.csiro.au/research/pulsar/psrcat) given above) you consider citing the [JOSS](http://joss.theoj.org/) [paper](https://doi.org/10.21105/joss.00538) for this software:
```tex
@article{psrqpy,
author = {{Pitkin}, M.},
title = "{psrqpy: a python interface for querying the ATNF pulsar catalogue}",
volume = 3,
number = 22,
pages = 538,
month = feb,
year = 2018,
journal = "{Journal of Open Source Software}",
doi = {10.21105/joss.00538},
url = {https://doi.org/10.21105/joss.00538}
}
```
## License
This code is licensed under the [MIT License](http://opensource.org/licenses/MIT).
© Matt Pitkin, 2017
[](https://badge.fury.io/py/psrqpy)
[](https://anaconda.org/conda-forge/psrqpy)
[](https://pypi.org/project/psrqpy/)
[](https://github.com/mattpitkin/psrqpy/actions?query=workflow%3Abuild)
[](https://codecov.io/gh/mattpitkin/psrqpy)
[](http://psrqpy.readthedocs.io/en/latest/?badge=latest)
[](http://joss.theoj.org/papers/711dc5566159f6e9f8ea5d07dbfaf5d2)
[](https://doi.org/10.5281/zenodo.1489692)
[](http://ascl.net/1812.017)