<p align="center">
<img src="https://raw.githubusercontent.com/andizq/andizq.github.io/master/discminer/discminer_logo.jpeg" width="500" height="" ></p>
<h2 align="center">The Channel Map Modelling Code</h2>
<div align="center">
<a href="https://github.com/andizq/discminer/blob/main/LICENSE"><img alt="License" src="https://img.shields.io/badge/license-MIT-FEE440.svg?style=for-the-badge"></a>
<a href="https://github.com/andizq/discminer/pulls"><img alt="Pull request?" src="https://img.shields.io/badge/Become%20a-miner%20%e2%9a%92-00BBF9.svg?style=for-the-badge"></a>
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<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg?style=for-the-badge"></a>
</div>
<div align="center">
Welcome to the discminer repository! Looking for quick examples and tutorials? Check out the docs.
<br />
<a href="https://github.com/andizq/discminer/issues/new?assignees=&labels=bug&title=bug%3A+">Report a Bug</a>
·
<a href="https://github.com/andizq/discminer/issues/new?assignees=&labels=enhancement&title=feature%3A+">Request a Feature</a>
·
<a href="https://github.com/andizq/discminer/issues/new?assignees=&labels=question&title=question%3A+">Ask a Question</a>
</div>
- Model channel maps from molecular line emission of discs by fitting intensity **and** rotation velocity
- Study the disc vertical structure by modelling front and back side emission surfaces
- Compute moment maps that accurately capture complex line profile morphologies
- Extract rotation curves, radial and meridional velocities, intensity and line width profiles
- Analyse the disc dynamical structure by modelling Keplerian motion + pressure support + self-gravity at once
- Identify velocity and intensity substructures; study their coherence and degree of localisation
- Non-axisymmetric models are possible; all attributes can be described as a function of $R,\phi,z$ disc coords
<img
src="images/discminer_outline.png"
alt="Discminer workflow and capabilities"
style="display: inline-block; margin: 0 auto; max-width: 500px">
## Mining tools
Discminer offers a wide range of analysis and visualisation tools to fully explore the physical and dynamical structure of your disc.
### cube
- Compute moment maps that accurately capture complex line profile morphologies.
- Output moment maps include **peak intensity**, **line width**, **line slope**, and **centroid velocity**.
- Easily clip, downsample, and convert to brightness temperature units.
- Quickly visualise model versus data channels and interactively extract spectra.
### rail
- Extract azimuthal and radial profiles of intensity, line width and velocity from moment maps.
- Compute rotation curves and decompose disc velocity into its three-dimensional components.
- Reveal large-scale signatures and quantify their pitch angle, width, extent, and coherence degree.
### pick
- Identify small-scale velocity and intensity perturbations, and estimate their localisation degree.
### plottools
- Customise intensity channels and residual maps, and highlight coherent and localised perturbations.
- Use sky or disc projections interchangeably for easier visualisation of features.
- Easily overlay the disc geometry (orientation and vertical structure) on any observable product.
- Overlay 1D profiles or 2D maps from external data to e.g. highlight the presence of dust substructures.
## Installation
```bash
pip install discminer
```
To upgrade the code,
```bash
pip install -U discminer
```
#### Optional dependencies
- [termtables](https://pypi.org/project/termtables)
- [termplotlib](https://pypi.org/project/termplotlib)
- [FilFinder](https://pypi.org/project/fil-finder)
- [schwimmbad](https://pypi.org/project/schwimmbad)
- [ipython](https://ipython.readthedocs.io/en/stable)
## How to use
The package documentation is still under construction, but you can find practical examples demonstrating the main
functionality of the code in the `./template` folder of this repository.
To run the examples on your local machine you can clone this repository and follow the instructions provided in the readme file,
```bash
git clone https://github.com/andizq/discminer.git
cd discminer/template
less README.rst
```
## Citation
If you find `discminer` useful for your research please cite the work of [Izquierdo et al. 2021](https://ui.adsabs.harvard.edu/abs/2021A%26A...650A.179I/abstract),
```latex
@ARTICLE{2021A&A...650A.179I,
author = {{Izquierdo}, A.~F. and {Testi}, L. and {Facchini}, S. and {Rosotti}, G.~P. and {van Dishoeck}, E.~F.},
title = "{The Disc Miner. I. A statistical framework to detect and quantify kinematical perturbations driven by young planets in discs}",
journal = {\aap},
keywords = {planet-disk interactions, planets and satellites: detection, protoplanetary disks, radiative transfer, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics},
year = 2021,
month = jun,
volume = {650},
eid = {A179},
pages = {A179},
doi = {10.1051/0004-6361/202140779},
archivePrefix = {arXiv},
eprint = {2104.09596},
primaryClass = {astro-ph.EP},
adsurl = {https://ui.adsabs.harvard.edu/abs/2021A&A...650A.179I},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
```
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Looking for quick examples and tutorials? Check out the docs.\n <br />\n <a href=\"https://github.com/andizq/discminer/issues/new?assignees=&labels=bug&title=bug%3A+\">Report a Bug</a>\n \u00b7\n <a href=\"https://github.com/andizq/discminer/issues/new?assignees=&labels=enhancement&title=feature%3A+\">Request a Feature</a>\n \u00b7\n <a href=\"https://github.com/andizq/discminer/issues/new?assignees=&labels=question&title=question%3A+\">Ask a Question</a>\n</div>\n\n- Model channel maps from molecular line emission of discs by fitting intensity **and** rotation velocity\n- Study the disc vertical structure by modelling front and back side emission surfaces\n- Compute moment maps that accurately capture complex line profile morphologies\n- Extract rotation curves, radial and meridional velocities, intensity and line width profiles\n- Analyse the disc dynamical structure by modelling Keplerian motion + pressure support + self-gravity at once\n- Identify velocity and intensity substructures; study their coherence and degree of localisation\n- Non-axisymmetric models are possible; all attributes can be described as a function of $R,\\phi,z$ disc coords\n\n\n<img\n src=\"images/discminer_outline.png\"\n alt=\"Discminer workflow and capabilities\"\n style=\"display: inline-block; margin: 0 auto; max-width: 500px\">\n\n## Mining tools\n\nDiscminer offers a wide range of analysis and visualisation tools to fully explore the physical and dynamical structure of your disc.\n\n\n### cube\n\n- Compute moment maps that accurately capture complex line profile morphologies.\n- Output moment maps include **peak intensity**, **line width**, **line slope**, and **centroid velocity**.\n- Easily clip, downsample, and convert to brightness temperature units.\n- Quickly visualise model versus data channels and interactively extract spectra.\n\n### rail\n\n- Extract azimuthal and radial profiles of intensity, line width and velocity from moment maps.\n- Compute rotation curves and decompose disc velocity into its three-dimensional components.\n- Reveal large-scale signatures and quantify their pitch angle, width, extent, and coherence degree.\n\n### pick\n\n- Identify small-scale velocity and intensity perturbations, and estimate their localisation degree.\n\n### plottools\n\n- Customise intensity channels and residual maps, and highlight coherent and localised perturbations.\n- Use sky or disc projections interchangeably for easier visualisation of features.\n- Easily overlay the disc geometry (orientation and vertical structure) on any observable product.\n- Overlay 1D profiles or 2D maps from external data to e.g. highlight the presence of dust substructures.\n\n\n## Installation\n\n```bash\npip install discminer\n```\n\nTo upgrade the code,\n\n```bash\npip install -U discminer\n```\n\n#### Optional dependencies\n\n- [termtables](https://pypi.org/project/termtables)\n- [termplotlib](https://pypi.org/project/termplotlib)\n- [FilFinder](https://pypi.org/project/fil-finder)\n- [schwimmbad](https://pypi.org/project/schwimmbad)\n- [ipython](https://ipython.readthedocs.io/en/stable)\n\n## How to use\n\nThe package documentation is still under construction, but you can find practical examples demonstrating the main\nfunctionality of the code in the `./template` folder of this repository.\n\nTo run the examples on your local machine you can clone this repository and follow the instructions provided in the readme file,\n\n```bash\ngit clone https://github.com/andizq/discminer.git\ncd discminer/template\nless README.rst\n```\n\n## Citation\n\nIf you find `discminer` useful for your research please cite the work of [Izquierdo et al. 2021](https://ui.adsabs.harvard.edu/abs/2021A%26A...650A.179I/abstract),\n\n```latex\n@ARTICLE{2021A&A...650A.179I,\n author = {{Izquierdo}, A.~F. and {Testi}, L. and {Facchini}, S. and {Rosotti}, G.~P. and {van Dishoeck}, E.~F.},\n title = \"{The Disc Miner. 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