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‎.gitignore‎

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sites
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*.d
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# Byte-compiled / optimized / DLL files
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__pycache__/
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# Compiled Object files
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*.slo
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*.lo
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*.o
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*.obj
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# Precompiled Headers
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*.gch
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*.pch
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# Compiled Dynamic libraries
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*.so
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*.dylib
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*.dll
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# Fortran module files
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*.mod
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*.smod
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# Compiled Static libraries
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*.lai
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*.la
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*.a
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*.lib
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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# Executables
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*.exe
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*.out
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*.app
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e

‎CODE_OF_CONDUCT.md‎

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# Contributor Covenant Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to making participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, sex characteristics, gender identity and expression,
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level of experience, education, socio-economic status, nationality, personal
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appearance, race, religion, or sexual identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces
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when an individual is representing the project or its community. Examples of
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representing a project or community include using an official project e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event. Representation of a project may be
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further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the project team at mathis@rowland.harvard.edu. All
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complaints will be reviewed and investigated and will result in a response that
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is deemed necessary and appropriate to the circumstances. The project team is
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obligated to maintain confidentiality with regard to the reporter of an incident.
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Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
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[homepage]: https://www.contributor-covenant.org
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For answers to common questions about this code of conduct, see
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https://www.contributor-covenant.org/faq

‎LICENSE‎

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KINEMATIK: ANAYSIS OF ANIMAL MOVEMENT
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SOFTWARE LICENSE AGREEMENT
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ACADEMIC OR NON-PROFIT ORGANIZATION NONCOMMERCIAL RESEARCH USE ONLY
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[adapted from https://github.com/CMU-Perceptual-Computing-Lab/openpose/blob/master/LICENSE]
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BY USING OR DOWNLOADING THE SOFTWARE, YOU ARE AGREEING TO THE TERMS OF THIS LICENSE AGREEMENT. IF YOU DO NOT AGREE WITH THESE TERMS, YOU MAY NOT USE OR DOWNLOAD THE SOFTWARE.
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This is a license agreement ("Agreement") between your academic institution or non-profit organization or self (called "Licensee" or "You" in this Agreement) and Harvard University (called "Licensor" in this Agreement). All rights not specifically granted to you in this Agreement are reserved for Licensor.
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RESERVATION OF OWNERSHIP AND GRANT OF LICENSE:
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Licensor retains exclusive ownership of any copy of the Software (as defined below) licensed under this Agreement and hereby grants to Licensee a personal, non-exclusive,
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non-transferable license to use the Software for noncommercial research purposes, without the right to sublicense, pursuant to the terms and conditions of this Agreement. As used in this Agreement, the term "Software" means (i) the actual copy of all or any portion of code for program routines made accessible to Licensee by Licensor pursuant to this Agreement, inclusive of backups, updates, and/or merged copies permitted hereunder or subsequently supplied by Licensor, including all or any file structures, programming instructions, user interfaces and screen formats and sequences as well as any and all documentation and instructions related to it, and (ii) all or any derivatives and/or modifications created or made by You to any of the items specified in (i).
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CONFIDENTIALITY: Licensee acknowledges that the Software is proprietary to Licensor, and as such, Licensee agrees to receive all such materials in confidence and use the Software only in accordance with the terms of this Agreement. Licensee agrees to use reasonable effort to protect the Software from unauthorized use, reproduction, distribution, or publication.
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COPYRIGHT: The Software is owned by Licensor and is protected by United
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States copyright laws and applicable international treaties and/or conventions.
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PERMITTED USES: The Software may be used for your own noncommercial internal research purposes. You understand and agree that Licensor is not obligated to implement any suggestions and/or feedback you might provide regarding the Software, but to the extent Licensor does so, you are not entitled to any compensation related thereto.
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DERIVATIVES: You may create derivatives of or make modifications to the Software, however, You agree that all and any such derivatives and modifications will be owned by Licensor and become a part of the Software licensed to You under this Agreement. You may only use such derivatives and modifications for your own noncommercial internal research purposes, and you may not otherwise use, distribute or copy such derivatives and modifications in violation of this Agreement.
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BACKUPS: If Licensee is an organization, it may make that number of copies of the Software necessary for internal noncommercial use at a single site within its organization provided that all information appearing in or on the original labels, including the copyright and trademark notices are copied onto the labels of the copies.
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USES NOT PERMITTED: You may not distribute, copy or use the Software except as explicitly permitted herein. Licensee has not been granted any trademark license as part of this Agreement and may not use the name or mark “Kimematik" or any renditions thereof without the prior written permission of Licensor.
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You may not sell, rent, lease, sublicense, lend, time-share or transfer, in whole or in part, or provide third parties access to prior or present versions (or any parts thereof) of the Software.
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ASSIGNMENT: You may not assign this Agreement or your rights hereunder without the prior written consent of Licensor. Any attempted assignment without such consent shall be null and void.
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TERM: The term of the license granted by this Agreement is from Licensee's acceptance of this Agreement by downloading the Software or by using the Software until terminated as provided below.
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The Agreement automatically terminates without notice if you fail to comply with any provision of this Agreement. Licensee may terminate this Agreement by ceasing using the Software. Upon any termination of this Agreement, Licensee will delete any and all copies of the Software. You agree that all provisions which operate to protect the proprietary rights of Licensor shall remain in force should breach occur and that the obligation of confidentiality described in this Agreement is binding in perpetuity and, as such, survives the term of the Agreement.
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FEE: Provided Licensee abides completely by the terms and conditions of this Agreement, there is no fee due to Licensor for Licensee's use of the Software in accordance with this Agreement.
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DISCLAIMER OF WARRANTIES: THE SOFTWARE IS PROVIDED "AS-IS" WITHOUT WARRANTY OF ANY KIND INCLUDING ANY WARRANTIES OF PERFORMANCE OR MERCHANTABILITY OR FITNESS FOR A PARTICULAR USE OR PURPOSE OR OF NON-INFRINGEMENT. LICENSEE BEARS ALL RISK RELATING TO QUALITY AND PERFORMANCE OF THE SOFTWARE AND RELATED MATERIALS.
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SUPPORT AND MAINTENANCE: No Software support or training by the Licensor is provided as part of this Agreement.
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EXCLUSIVE REMEDY AND LIMITATION OF LIABILITY: To the maximum extent permitted under applicable law, Licensor shall not be liable for direct, indirect, special, incidental, or consequential damages or lost profits related to Licensee's use of and/or inability to use the Software, even if Licensor is advised of the possibility of such damage.
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EXPORT REGULATION: Licensee agrees to comply with any and all applicable
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U.S. export control laws, regulations, and/or other laws related to embargoes and sanction programs administered by the Office of Foreign Assets Control.
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SEVERABILITY: If any provision(s) of this Agreement shall be held to be invalid, illegal, or unenforceable by a court or other tribunal of competent jurisdiction, the validity, legality and enforceability of the remaining provisions shall not in any way be affected or impaired thereby.
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NO IMPLIED WAIVERS: No failure or delay by Licensor in enforcing any right or remedy under this Agreement shall be construed as a waiver of any future or other exercise of such right or remedy by Licensor.
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GOVERNING LAW: This Agreement shall be construed and enforced in accordance with the laws of the Commonwealth of Massachusetts without reference to conflict of laws principles.
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ENTIRE AGREEMENT AND AMENDMENTS: This Agreement constitutes the sole and entire agreement between Licensee and Licensor as to the matter set forth herein and supersedes any previous agreements, understandings, and arrangements between the parties relating hereto.
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************************************************************************
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THIRD-PARTY SOFTWARE NOTICES AND INFORMATION
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This project incorporates material from the project(s) listed below (collectively, "Third Party Code"). This Third Party Code is licensed to you under their original license terms set forth below. We reserves all other rights not expressly granted, whether by implication, estoppel or otherwise.
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scikit-kinematics - https://pypi.org/project/scikit-kinematics/
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Author: Thomas Haslwanter
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Date: 08-02-2019
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Ver: 0.8.1
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Licence: BSD 2-Clause License (http://opensource.org/licenses/BSD-2-Clause)
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Copyright (c) 2018, Thomas Haslwanter
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https://github.com/skvark/opencv-python/blob/master/LICENSE.txt
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************END OF THIRD-PARTY SOFTWARE NOTICES AND INFORMATION**********

‎README.md‎

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<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/1564770305666-REUUID2FV6D7B361DZMP/ke17ZwdGBToddI8pDm48kPXc-1wTDUYu2KG1axT7Q_oUqsxRUqqbr1mOJYKfIPR7LoDQ9mXPOjoJoqy81S2I8N_N4V1vUb5AoIIIbLZhVYy7Mythp_T-mtop-vrsUOmeInPi9iDjx9w8K4ZfjXt2dhYH2CD2cFRECnu4OwLnVR-scfeCFITgXNUMaLL3uIzDCjLISwBs8eEdxAxTptZAUg/KINEMATIK-logo.png?format=1000w" width="350" title="camera control" alt="cam cntrl" align="center" vspace = "80">
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#### A post-deeplabcut module for kinematic analysis
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### under construction ...
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### currently this is not publicly available, but feel free to "watch" or "star" to be notified of updates.
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## License
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Kinematik is freely available for non-commercial use, and may be redistributed under these conditions.
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Please, see the license for further details.
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## Contact
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Mackenzie Mathis - mackenzie@post.harvard.edu

‎kinematik/__init__.py‎

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"""
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Kinematik
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© A. & M. Mathis Labs
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"""
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from kinematik.version import __version__

‎kinematik/version.py‎

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__version__='0.0b0'

‎reinstall.sh‎

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pip uninstall kinematik
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python3 setup.py sdist bdist_wheel
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pip install dist/kinematik-0.0b0-py3-none-any.whl
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‎setup.py‎

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"""
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Kinematik Package
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© A. & M. Mathis Labs
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https://github.com/MMathisLab/Kinematik/
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Please see AUTHORS for contributors.
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https://github.com/MMathisLab/Kinematik/blob/master/AUTHORS
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"""
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import setuptools
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with open("README.md", "r") as fh:
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long_description = fh.read()
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setuptools.setup(
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name="kinematik",
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version="0.0b",
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author="Tanmay Nath, Kai Sandbrink, Alexander Mathis, Mackenzie Mathis",
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author_email="mackenzie@post.harvard.edu",
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description="Library for kinematic analysis",
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long_description=long_description,
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long_description_content_type="text/markdown",
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url="https://github.com/MMathisLab/Kinematik/",
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install_requires=['h5py~=2.7','imageio==2.3.0','intel-openmp',
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'ipython~=6.0.0','ipython-genutils==0.2.0',
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'matplotlib==3.0.3','moviepy~=0.2.3.5','numpy==1.14.5','opencv-python~=3.4',
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'pandas==0.21.0','patsy','python-dateutil==2.7.3','pyyaml>=5.1','requests',
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'ruamel.yaml==0.15','setuptools','scikit-image~=0.14.0','scikit-learn~=0.19.2',
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'scikit-kinematics','scipy~=1.1.0','six==1.11.0','statsmodels==0.9.0','tables',
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'tqdm>4','wheel==0.31.1'],
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packages=setuptools.find_packages(),
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include_package_data=True,
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classifiers=(
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"Programming Language :: Python :: 3",
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"Operating System :: OS Independent",
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))

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