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44 changes: 23 additions & 21 deletions README.rst
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Overview
========

``dynsight`` is structured to support a wide range of tasks commonly
encountered in the analysis of many-body dynamical systems. These tasks
include handling trajectory data, computing single-particle descriptors,
performing time-series clustering and conducting various auxiliary analyses.
To achieve this, dynsight is organized into specialized modules, each
addressing a specific aspect of this workflow.

Previously in `cpctools`_.
``dynsight`` is an open platform for supporting a wide range of tasks commonly
encountered in the trajectory and data analysis of complex dynamical systems, essentially related
to the extraction of relevant information from data obtained from trajectories.
To achieve this, ``dynsight`` is organized into specialized modules, each addressing a
specific aspect of this workflow. For example, ``dynsight`` includes modules for, e.g.,

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Remove one of the "for example" or "e.g."

resolving trajectory data from movies (experimental: e.g., object recognition and tracking),
handling trajectory data (from simulations and experiments), computing single-particle descriptors,
performing time-series clustering, maximum information extraction from data, and conducting
various auxiliary analyses.

A bounce of all this was previously in `cpctools`_.

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Should be "bunch", not "bounce"?

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Some of this?

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Be specific? "SOAP and hdf5er tools were previously in cpctools_ and still use that code internally."?


.. _`cpctools`: https://github.com/GMPavanLab/cpctools

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Optional Dependancies
---------------------

Old versions ``dynsight`` used ``cpctools`` for SOAP calculations, if
Old versions of ``dynsight`` used ``cpctools`` for SOAP calculations: if
you are using Python 3.10 and below, you can use ``cpctools`` to access
``SOAPify`` and ``hd5er`` using ::

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TBD

* Most modules also use MDAnalysis, https://www.mdanalysis.org/pages/citations/
* If you use SOAP, please cite https://doi.org/10.1103/PhysRevB.87.184115 and DScribe https://singroup.github.io/dscribe/latest/citing.html
* If you use timeSOAP, please cite https://doi.org/10.1063/5.0147025
* If you use LENS, please cite: https://doi.org/10.1073/pnas.2300565120
* If you use onion-clustering, please cite: https://doi.org/10.1073/pnas.2403771121
* If you use tICA, please cite ``deeptime`` https://deeptime-ml.github.io/latest/index.html
* If you use ``dynsight.vision``, please cite Ultralytics YOLO https://docs.ultralytics.com/it/models/yolo11/#usage-examples
* If you use ``dynsight.track``, please cite Trackpy https://soft-matter.github.io/trackpy/dev/introduction.html
* If you use SOAP, please cite also original references: https://doi.org/10.1103/PhysRevB.87.184115 and DScribe https://singroup.github.io/dscribe/latest/citing.html
* If you use TimeSOAP, please cite also original reference: https://doi.org/10.1063/5.0147025
* If you use LENS, please cite also original reference: https://doi.org/10.1073/pnas.2300565120
* If you use onion-clustering, please cite also original reference: https://doi.org/10.1073/pnas.2403771121
* If you use tools to calculate Information Gain and Maximum Information Extraction, please cite also original reference: https://doi.org/10.48550/arXiv.2504.12990
* If you use tICA, please cite also original ``deeptime`` reference: https://deeptime-ml.github.io/latest/index.html
* If you use ``dynsight.vision``, please cite also original ``Ultralytics YOLO`` reference: https://docs.ultralytics.com/it/models/yolo11/#usage-examples
* If you use ``dynsight.track``, please cite also original ``Trackpy`` reference: https://soft-matter.github.io/trackpy/dev/introduction.html


Acknowledgements
================

We developed this code when working in the Pavan group,
https://www.gmpavanlab.polito.it/, whose members often provide very valuable
feedback, which we gratefully acknowledge.
This code is developed by the G.M. Pavan group, https://www.gmpavanlab.polito.it/,
whose members often provide very valuable feedback, which we gratefully acknowledge.

Much of the original code in ``cpctools`` was written by Daniele Rapetti (Iximiel).

The work was funded by the European Union and ERC under projects DYNAPOL and the
NextGenerationEU project, CAGEX.
This work was primarily supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement no. 818776- DYNAPOL), and also partially by the European Union under the NextGenerationEU program (grant CAGEX, SOE_0000033).

.. figure:: docs/source/_static/EU_image.png