Merge pull request #22 from SciKit-Surgery/20-docs

20 docs

README.rst

@@ -7,6 +7,9 @@ glenoidplanefitting
    :target: https://github.com/SciKit-Surgery/glenoidplanefitting
    :alt: Logo
 
+
+|
+
 .. image:: https://github.com/SciKit-Surgery/glenoidplanefitting/workflows/.github/workflows/ci.yml/badge.svg
    :target: https://github.com/SciKit-Surgery/glenoidplanefitting/actions
    :alt: GitLab-CI test status
@@ -19,22 +22,49 @@ glenoidplanefitting
     :target: http://glenoidplanefitting.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/badge/-SciKit%20Surgery-blueviolet?style=flat&logo=youtube
+   :target: https://youtu.be/0z8eIjqAbzQ
+   :alt: SciKit-Surgery on YouTube
 
+.. image:: https://img.shields.io/twitter/url?style=social&url=http%3A%2F%2Fscikit-surgery.org
+   :target: https://twitter.com/intent/tweet?screen_name=scikit_surgery&ref_src=twsrc%5Etfw
+   :alt: Get in touch via twitter
 
-Author: Asta Olafsdottir
+.. 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
 
-glenoidplanefitting 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)`_.
+.. image:: https://img.shields.io/badge/-See%20us%20at%20SPIE%20202-yellow?style=flat
+   :target: https://spie.org/conferences-and-exhibitions/medical-imaging/program
+   :alt: SPIE Medical Imaging 2022
 
-glenoidplanefitting supports Python 2.7 and Python 3.6.
+Authors: Asta Olafsdottir, Stephen Thompson
 
-glenoidplanefitting is currently a demo project, which will add/multiply two numbers. Example usage:
+glenoidplanefitting provides tools for measuring the Glenoid version, useful when 
+planning reconstructive shoulder surgery.
+glenoidplanefitting 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)`_, in collaboration with surgeons at the 
+Royal National Orthopaedic Hospital 
+
+glenoidplanefitting is tested on Python 3.x, but may work with other versions of Python
+
+glenoidplanefitting currently requires the user to manually identify relevant anatomical 
+landmarks on the scapula and glenoid dish. These points can then be passed to 
+glenoidplanefitting to calculate the Glenoid version using multiple methods. Example usage:
 
 ::
 
-    python glenoidplanefitting.py 5 8
-    python glenoidplanefitting.py 3 6 --multiply
+    python glenoidplanefitting.py --fried_points landmark_friedman.fcsv --output friedman.vtp --visualise glenoid.vtp
 
-Please explore the project structure, and implement your own functionality.
+glenoidplanefitting is a work in progress with plans to automate the point picking to create
+software to enable a large scale comparison of different methods of Glenoid version 
+methods on a clinical data set. If you are interested in contributing to this work
+please get in touch or follow the guides below.
 
 Developing
 ----------
@@ -51,22 +81,11 @@ You can clone the repository using the following command:
 
 Running tests
 ^^^^^^^^^^^^^
-Pytest is used for running unit tests:
-::
-
-    pip install pytest
-    python -m pytest
-
-
-Linting
-^^^^^^^
-
-This code conforms to the PEP8 standard. Pylint can be used to analyse the code:
-
+We use tox to run tests and run static code analysis using Lint. 
 ::
 
-    pip install pylint
-    pylint --rcfile=tests/pylintrc glenoidplanefitting
+    pip install tox
+    python -m tox
 
 
 Installing
@@ -109,7 +128,7 @@ 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/glenoidplanefitting
 .. _`Documentation`: https://glenoidplanefitting.readthedocs.io
-.. _`scikit-surgery`: https://github.com/UCL/scikit-surgery/wiki
+.. _`scikit-surgery`: http://scikit-surgery.github.io/scikit-surgery/
 .. _`University College London (UCL)`: http://www.ucl.ac.uk/
 .. _`Wellcome`: https://wellcome.ac.uk/
 .. _`EPSRC`: https://www.epsrc.ac.uk/

docs/conf.py

@@ -30,7 +30,7 @@
 root_dir_abs = os.path.abspath(root_dir_rel)
 module_path = root_dir_abs
 sys.path.insert(0, module_path)
-logo_file = 'project-icon.png'
+logo_file = 'skglenoid_logo.png'
 logo_path = os.path.join('..', logo_file)
 
 # List of patterns, relative to source directory, that match files and
@@ -90,7 +90,7 @@ def setup(app):
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', 'sphinx.ext.imgmath', 'nbsphinx']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode', 'sphinx.ext.imgmath', 'nbsphinx', 'sphinx.ext.graphviz']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/dependency_graph.dot

@@ -0,0 +1,25 @@
+digraph prof {
+	ratio = fill;
+	node [style=filled];
+	"SciKit-SurgeryGlenoid" -> "NumPy";
+	"SciKit-SurgeryGlenoid" -> "SciKit-SurgeryVTK" [color="0.515 0.762 0.762"];
+	"SciKit-SurgeryGlenoid" -> "VTK";
+
+	"SciKit-SurgeryVTK" -> "NumPy";
+	"SciKit-SurgeryVTK" -> "VTk";
+	"SciKit-SurgeryVTK" -> "PySide2";
+	"SciKit-SurgeryVTK" -> "OpenCV-contrib-python";
+	"SciKit-SurgeryVTK" -> "SciKit-SurgeryCore" [color="0.515 0.762 0.762"];
+	"SciKit-SurgeryVTK" -> "SciKit-SurgeryImage" [color="0.515 0.762 0.762"];
+
+	"SciKit-SurgeryImage" -> "NumPy";
+	"SciKit-SurgeryImage" -> "OpenCV-contrib-python";
+	"SciKit-SurgeryImage" -> "SciKit-SurgeryCore" [color="0.515 0.762 0.762"];
+	"SciKit-SurgeryCore" -> "NumPy";
+
+"SciKit-SurgeryGlenoid" [color="0.515 0.762 0.762"];
+"SciKit-SurgeryVTK"[color="0.515 0.762 0.762"];
+"SciKit-SurgeryImage"[color="0.515 0.762 0.762"];
+"SciKit-SurgeryCore"[color="0.515 0.762 0.762"];
+} 
+

docs/dependency_graph.rst

@@ -0,0 +1,12 @@
+.. highlight:: shell
+
+.. _Dependency Graph:
+
+===============================================
+Dependency Graph
+===============================================
+
+.. graphviz:: dependency_graph.dot
+   :caption: glenoidplanefitting's Dependencies
+   :align: center
+

docs/index.rst

@@ -5,8 +5,8 @@ Contents
 .. toctree::
   :maxdepth: 1
 
+  dependency_graph
   Module Contents <modules>
-  notebooks/first_notebook
 
 * :ref:`modindex`
 * :ref:`genindex`

glenoidplanefitting/algorithms/friedman.py

@@ -2,8 +2,9 @@
 This is an implentation of Friedman's method, see
 
 Friedman RJ, Hawthorne KB and Genez BM.
-The use of computerized tomography in the measurement
-of glenoid version. J Bone and Joint Surg Am 1992; 74: 1032–7.
+`The use of computerized tomography in the measurement
+of glenoid version. <https://pubmed.ncbi.nlm.nih.gov/1522089/>`_
+J Bone and Joint Surg Am 1992; 74: 1032–7.
 
 """
 

glenoidplanefitting/algorithms/models.py

@@ -8,6 +8,7 @@ def make_plane_model(plane_centre, normal_vector, resolution = 10,
         plane_size = 200.0):
     """
     Makes a vtk plane source, with centre and normal vector
+
     :param plane_centre: a point on the plane
     :param normal_vector: the plane normal vector
 
@@ -26,7 +27,8 @@ def make_plane_model(plane_centre, normal_vector, resolution = 10,
 def make_friedman_model(point1, point2):
 
     """
-    Makese a vtk line source from two set points
+    Makes a vtk line source from two set points
+
     :param point1: one end of the line
     :param point2: other end of the line
 
@@ -42,7 +44,8 @@ def make_friedman_model(point1, point2):
 def make_vault_model(point1,point2):
 
     """
-    Makese a vtk line source from two set points
+    Makes a vtk line source from two set points
+
     :param point1: one end of the line
     :param point2: other end of the line
 

glenoidplanefitting/algorithms/plane_fitting.py

@@ -4,8 +4,9 @@
 This is an implementation of a two plane method, see
 
 A. Ganapathi, J. McCarron, Chen, J. Iannotti.
-Predicting normal glenoid version from the pathologic scapula:
+`Predicting normal glenoid version from the pathologic scapula:
 a comparison of 4 methods in 2- and 3-dimensional models
+<https://doi.org/10.1016/j.jse.2010.05.024>`_
 J Shoulder Elbow Surg (2011) 20, 234-244
 
 """

glenoidplanefitting/algorithms/vault.py

@@ -4,8 +4,9 @@
 This is an implentation of the vault method, see
 
 Matsumura N et al.
-Computed tomography measurement of glenoid vault version
+`Computed tomography measurement of glenoid vault version
 as an alternative measuring method for glenoid version.
+<https://doi.org/10.1186/1749-799x-9-17>`_
 Journal of Orthopaedic Surgery and Research 2014, 9:17
 
 """

glenoidplanefitting/widgets/visualisation.py

@@ -25,6 +25,7 @@ def renderer_common(bone):
 def render_window_common(renderer, window_name):
     """
     Creates and starts a render window and interactor.
+
     :param renderer: A vtk renderer to add to the render window
     :param window_name: A name for the window
     """
@@ -43,8 +44,9 @@ def render_window_common(renderer, window_name):
 def add_vtk_source(renderer, source):
     """
     simplifies adding a vtk geometry source to a renderer
-    :params renderer: a vtk renderer to add to
-    :params source: a vtk geometry source
+
+    :param renderer: a vtk renderer to add to
+    :param source: a vtk geometry source
     """
     mapper = vtk.vtkPolyDataMapper() #pylint:disable=no-member
     mapper.SetInputConnection(source.GetOutputPort())
@@ -55,6 +57,7 @@ def add_vtk_source(renderer, source):
 def vis_planes(bone, planes):
     """
     Visualisation for plane fitting methods
+
     :param bone: The model surface model
     :param planes: a list of planes, as returned by the
         plane fitting methods in algorithms.plane_fitting
@@ -71,8 +74,9 @@ def vis_fried(bone, cross1, cross2, glenoid1, result):
     """
     Visualise the lines resulting from the friedman
     method.
-    :params cross1, cross2: The end points of the line crossing the glenoid
-    :params glenoid1, result: The end points of the line defining the glenoid
+
+    :param cross1, cross2: The end points of the line crossing the glenoid
+    :param glenoid1, result: The end points of the line defining the glenoid
         version
     """
     renderer = renderer_common(bone)
@@ -90,8 +94,9 @@ def vis_vault(bone, cross1, cross2, glenoid1, result):
     """
     Visualise the lines resulting from the vault
     method.
-    :params cross1, cross2: The end points of the line crossing the glenoid
-    :params glenoid1, result: The end points of the line defining the glenoid
+
+    :param cross1, cross2: The end points of the line crossing the glenoid
+    :param glenoid1, result: The end points of the line defining the glenoid
         version
     """
     renderer = renderer_common(bone)

tox.ini

@@ -23,7 +23,7 @@ commands=pylint --rcfile=tests/pylintrc glenoidplanefitting tests
 
 [testenv:docs]
 basepython=python3.8
-changedir = doc
+changedir = docs
 commands = sphinx-build -M html . build
 
 [testenv:installer]