Initial Commit

CONTRIBUTING.rst

@@ -0,0 +1,55 @@
+.. highlight:: shell
+
+===============================================
+Contributing to Fiducial Registration Educational Demonstration
+===============================================
+
+We welcome contributions to Fiducial Registration Educational Demonstration.
+
+
+Reporting bugs and feature requests
+-----------------------------------
+
+Please create a new issue on https://github.com/UCL/scikit-surgeryfredwebapp/issues/new
+
+When reporting a bug, please include:
+* The version of Fiducial Registration Educational Demonstration you are using
+* Your OS version (for example Windows 10 64-bit, macOS High Sierra, Ubuntu 16.04)
+* Detailed steps to reproduce the bug.
+
+
+Fixing bugs or implement features
+---------------------------------
+
+The easiest way to contribute is to follow these guidelines:
+
+1. Look through the issues on https://github.com/UCL/scikit-surgeryfredwebapp/issues and assign the relevant issue to yourself. If there is not an existing issue that covers your work, please create one: https://github.com/UCL/scikit-surgeryfredwebapp/issues/new
+2. Read the design considerations below.
+3. Fork the repository: https://github.com/UCL/scikit-surgeryfredwebapp/forks/new
+4. Create a branch for your changes. The branch name should start with the issue number, followed by hyphen separated words describing the issue. For example: 1-update-contribution-guidelines
+5. Make your changes following the coding guidelines below.
+6. Commit and push your changes to your fork. The commit message should start with `Issue #<issue number>`, for example: "Issue #1: Fixed typo". Commit in small, related chunks. Review each commit and explain its purpose in the commit message.
+7. Submit a merge request: https://github.com/UCL/scikit-surgeryfredwebapp/merge_requests/new
+
+Design Considerations
+---------------------
+
+1. As few dependencies as possible. Try to stick to standard scipy packages like numpy and pandas.
+2. Discuss extra dependencies with the team and maybe the outcome will be to create a new separate package, where you can be more specific and more modular.
+3. Unit test well, using pytest, with good coverage.
+4. All errors as exceptions rather than return codes.
+
+
+Coding guidelines
+-----------------
+
+1. Please follow PEP8 guidelines https://www.python.org/dev/peps/pep-0008/
+2. Create a python virtual environment (virtualenv) for development
+3. Make sure that pylint passes. You may disable specific warnings within the code where it is reasonable to do so
+4. Add unit tests for new and modified code
+5. Make sure all existing and new tests pass
+6. Make sure all docstrings have been added
+7. Make sure all dependencies have been added to requirements
+8. Make sure your code works for all required versions of Python
+9. Make sure your code works for all required operating systems
+

LICENSE

@@ -0,0 +1,32 @@
+
+BSD License
+
+Copyright (c) 2020, University College London
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from this
+  software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+OF THE POSSIBILITY OF SUCH DAMAGE.
+
+

README.rst

@@ -0,0 +1,85 @@
+Fiducial Registration Educational Demonstration
+===============================================
+
+.. image:: https://github.com/UCL/scikit-surgeryfredwebapp/raw/master/project-icon.png
+   :height: 128px
+   :width: 128px
+   :target: https://github.com/UCL/scikit-surgeryfredwebapp
+   :alt: Logo
+
+.. image:: https://github.com/UCL/scikit-surgeryfredwebapp/workflows/.github/workflows/ci.yml/badge.svg
+   :target: https://github.com/UCL/scikit-surgeryfredwebapp/actions
+   :alt: GitHub Actions CI status
+
+.. image:: https://coveralls.io/repos/github/UCL/scikit-surgeryfredwebapp/badge.svg?branch=master&service=github
+    :target: https://coveralls.io/github/UCL/scikit-surgeryfredwebapp?branch=master
+    :alt: Test coverage
+
+.. 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://zenodo.org/badge/269602581.svg
+   :target: https://zenodo.org/badge/latestdoi/269602581
+   :alt: DOI - Zenodo
+
+Author: Stephen Thompson
+
+This is web app front end for the Fiducial Registration Educational Demonstration (SciKit-SurgeryFRED), part of the `SciKit-Surgery`_ software project, developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.
+
+Fiducial Registration Educational Demonstration is intended to be used as part of an online tutorial in using fiducial based registration. The tutorial covers the basic theory of fiducial based registration, which is used widely in image guided interventions. The tutorial aims to help the students develop an intuitive understanding of key concepts in fiducial based registration, including Fiducial Localisation Error, Fiducial Registration Error, and Target Registration Error. 
+
+Citing
+------
+If you use SciKit-SurgeryFRED in your research or teaching please cite it. Individual releases can be cited via the Zenodo tag. SciKit-Surgery should be cited as:
+
+Thompson S, Dowrick T, Ahmad M, et al. "SciKit-Surgery: compact libraries for surgical navigation." International Journal of Computer Assisted Radiology and Surgery. 2020 May. DOI: 10.1007/s11548-020-02180-5.
+
+Developing
+----------
+
+Cloning
+^^^^^^^
+
+You can clone the repository using the following command:
+
+::
+
+    git clone https://github.com/UCL/scikit-surgeryfredwebapp
+
+
+Contributing
+^^^^^^^^^^^^
+
+Please see the `contributing guidelines`_.
+
+
+Useful links
+^^^^^^^^^^^^
+
+* `Source code repository`_
+
+
+Licensing and copyright
+-----------------------
+
+Copyright 2020 University College London.
+Fiducial Registration Educational Demonstration 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/UCL/scikit-surgeryfredwebapp
+.. _`Documentation`: https://scikit-surgeryfred.readthedocs.io
+.. _`SciKit-Surgery`: https://github.com/UCL/scikit-surgery/wiki
+.. _`University College London (UCL)`: http://www.ucl.ac.uk/
+.. _`Wellcome`: https://wellcome.ac.uk/
+.. _`EPSRC`: https://www.epsrc.ac.uk/
+.. _`contributing guidelines`: https://github.com/UCL/scikit-surgeryfredwebapp/blob/master/CONTRIBUTING.rst
+.. _`license file`: https://github.com/UCL/scikit-surgeryfred/blob/master/LICENSE
+