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| Overview | ||
| ======== | ||
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| ``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. | ||
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| 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., | ||
| 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. | ||
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| A bounce of all this was previously in `cpctools`_. | ||
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Collaborator
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Should be "bunch", not "bounce"?
Author
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Some of this?
Collaborator
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Be specific? "SOAP and hdf5er tools were previously in |
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| .. _`cpctools`: https://github.com/GMPavanLab/cpctools | ||
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| Optional Dependancies | ||
| --------------------- | ||
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| 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 | ||
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| * 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 | ||
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| Acknowledgements | ||
| ================ | ||
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| 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. | ||
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| Much of the original code in ``cpctools`` was written by Daniele Rapetti (Iximiel). | ||
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| 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). | ||
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| .. figure:: docs/source/_static/EU_image.png | ||
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Remove one of the "for example" or "e.g."