scikit-surgerycalibration
===============================
.. image:: https://github.com/SciKit-Surgery/scikit-surgerycalibration /raw/master/weiss_logo.png
:height: 128px
:width: 128px
:target: https://github.com/SciKit-Surgery/scikit-surgerycalibration
:alt: Logo
|
.. image:: https://github.com/SciKit-Surgery/scikit-surgerycalibration/workflows/.github/workflows/ci.yml/badge.svg
:target: https://github.com/SciKit-Surgery/scikit-surgerycalibration/actions
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.. image:: https://coveralls.io/repos/github/SciKit-Surgery/scikit-surgerycalibration/badge.svg?branch=master&service=github
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.. image:: https://readthedocs.org/projects/scikit-surgerycalibration /badge/?version=latest
:target: http://scikit-surgerycalibration .readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://img.shields.io/badge/Cite-SciKit--Surgery-informational
:target: https://doi.org/10.1007/s11548-020-02180-5
:alt: The SciKit-Surgery paper
.. image:: https://img.shields.io/twitter/follow/scikit_surgery?style=social
:target: https://twitter.com/scikit_surgery?ref_src=twsrc%5Etfw
:alt: Follow scikit_surgery on twitter
Author(s): Stephen Thompson; Contributor(s): Matt Clarkson, Thomas Dowrick and Miguel Xochicale
scikit-surgerycalibration is part of the `SciKit-Surgery`_ software project, developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.
scikit-surgerycalibration is tested on Python 3.7.
scikit-surgerycalibration contains algorithms to perform calibrations useful during surgery, for example pointer calibration, ultrasound calibration, and camera calibration.
Please explore the project structure, and request or implement your desired functionality.
.. features-start
Features
--------
* `Pivot Calibration <https://scikit-surgerycalibration.readthedocs.io/en/latest/module_ref.html#pivot-calibration>`_ for pivot calibration.
* `Calibration <https://scikit-surgerycalibration.readthedocs.io/en/latest/module_ref.html#video-calibration>`_ of mono or stereo tracked video data, calculating camera intrinsics and handeye transformation.
.. features-end
Cloning
-------
You can clone the repository using the following command:
::
git clone https://github.com/SciKit-Surgery/scikit-surgerycalibration
git clone git@github.com:SciKit-Surgery/scikit-surgerycalibration.git # Alternatively, use password-protected SSH key.
Developing
----------
We recommend using `anaconda`_ or `miniconda`_ to create a python 3.7 environment,
then using `tox`_ to install all dependencies inside a dedicated `venv`_. We then use
github `actions`_ to run a matrix of builds for Windows, Linux and Mac and various python versions.
All library dependencies are specified via ``requirements-dev.txt`` which refers to ``requirements.txt``.
So, assuming either `anaconda`_ or `miniconda`_ is installed, and your current working directory is the root directory of this project:
::
conda create --name scikit-surgery python=3.7
conda activate scikit-surgery
pip install tox
tox
As the `tox`_ command runs, it will install all dependencies in a sub-directory ``.tox/py37`` (Linux/Mac) or ``.tox\py37`` (Windows).
`tox`_ will also run pytest and linting for you.
To run commands inside the same environment as `tox`_, you should:
::
source .tox/py37/bin/activate
on Linux/Mac, or if you are Windows user:
::
.tox\py37\Scripts\activate
Then you can run pytest, linting, or directly run python scripts, and
know that the environment was created correctly by `tox`_.
Generating documentation
^^^^^^^^^^^^^^^^^^^^^^^^
The simplest way is again using `tox`_.
::
tox -e docs
then open ``docs/build/html/index.html`` in your browser.
Running tests
^^^^^^^^^^^^^
Pytest is used for running unit tests:
::
python -m pytest
pytest -v -s tests/algorithms/test_triangulate.py #example for individual tests
Linting
^^^^^^^
This code conforms to the PEP8 standard. Pylint can be used to analyse the code:
::
pylint --rcfile=tests/pylintrc sksurgerycalibration
Installing
----------
You can pip install directly from the repository as follows:
::
pip install git+https://github.com/SciKit-Surgery/scikit-surgerycalibration
Contributing
------------
Please see the `contributing guidelines`_.
Useful links
------------
* `Source code repository`_
* `Documentation`_
Licensing and copyright
-----------------------
Copyright 2020 University College London.
scikit-surgerycalibration is released under the BSD-3 license. Please see the `license file`_ for details.
Acknowledgements
----------------
Supported by `Wellcome`_ and `EPSRC`_.
.. _`Wellcome EPSRC Centre for Interventional and Surgical Sciences`: http://www.ucl.ac.uk/weiss
.. _`source code repository`: https://github.com/SciKit-Surgery/scikit-surgerycalibration
.. _`Documentation`: https://scikit-surgerycalibration.readthedocs.io
.. _`SciKit-Surgery`: https://github.com/SciKit-Surgery/scikit-surgery/wiki/home
.. _`University College London (UCL)`: http://www.ucl.ac.uk/
.. _`Wellcome`: https://wellcome.ac.uk/
.. _`EPSRC`: https://www.epsrc.ac.uk/
.. _`anaconda`: https://www.anaconda.com/
.. _`miniconda`: https://docs.conda.io/en/latest/miniconda.html
.. _`tox`: https://tox.wiki/en/latest/
.. _`venv`: https://docs.python.org/3/library/venv.html
.. _`actions`: https://github.com/SciKit-Surgery/scikit-surgerycalibration/actions
.. _`contributing guidelines`: https://github.com/SciKit-Surgery/scikit-surgerycalibration /blob/master/CONTRIBUTING.rst
.. _`license file`: https://github.com/SciKit-Surgery/scikit-surgerycalibration /blob/master/LICENSE
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We then use\ngithub `actions`_ to run a matrix of builds for Windows, Linux and Mac and various python versions.\n\nAll library dependencies are specified via ``requirements-dev.txt`` which refers to ``requirements.txt``.\n\nSo, assuming either `anaconda`_ or `miniconda`_ is installed, and your current working directory is the root directory of this project:\n::\n\n conda create --name scikit-surgery python=3.7\n conda activate scikit-surgery\n pip install tox\n tox\n\nAs the `tox`_ command runs, it will install all dependencies in a sub-directory ``.tox/py37`` (Linux/Mac) or ``.tox\\py37`` (Windows).\n`tox`_ will also run pytest and linting for you.\n\nTo run commands inside the same environment as `tox`_, you should:\n::\n\n source .tox/py37/bin/activate\n\non Linux/Mac, or if you are Windows user:\n::\n\n .tox\\py37\\Scripts\\activate\n\nThen you can run pytest, linting, or directly run python scripts, and\nknow that the environment was created correctly by `tox`_.\n\n\nGenerating documentation\n^^^^^^^^^^^^^^^^^^^^^^^^\n\nThe simplest way is again using `tox`_.\n::\n\n tox -e docs\n\nthen open ``docs/build/html/index.html`` in your browser.\n\n\nRunning tests\n^^^^^^^^^^^^^\n\nPytest is used for running unit tests:\n::\n\n python -m pytest\n pytest -v -s tests/algorithms/test_triangulate.py #example for individual tests\n\n\nLinting\n^^^^^^^\nThis code conforms to the PEP8 standard. Pylint can be used to analyse the code:\n::\n\n pylint --rcfile=tests/pylintrc sksurgerycalibration\n\n\nInstalling\n----------\n\nYou can pip install directly from the repository as follows:\n::\n\n pip install git+https://github.com/SciKit-Surgery/scikit-surgerycalibration \n\n\n\nContributing\n------------\n\nPlease see the `contributing guidelines`_.\n\n\nUseful links\n------------\n\n* `Source code repository`_\n* `Documentation`_\n\n\nLicensing and copyright\n-----------------------\nCopyright 2020 University College London.\nscikit-surgerycalibration is released under the BSD-3 license. 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