Merge pull request #18 from Yatoom/develop

Develop

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/api.rst

@@ -0,0 +1,9 @@
+==============
+Public classes
+==============
+
+.. toctree::
+  :maxdepth: 2
+  :glob:
+
+  public/*

docs/conf.py

@@ -0,0 +1,64 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+import sphinx_rtd_theme
+import numpydoc
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Foronoi'
+copyright = '2021, Jeroen van Hoof'
+author = 'Jeroen van Hoof'
+
+# The full version, including alpha/beta/rc tags
+release = '1.0.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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_rtd_theme',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.intersphinx',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+autoclass_content = 'both'

docs/index.rst

@@ -0,0 +1,48 @@
+.. Foronoi documentation master file, created by
+   sphinx-quickstart on Sun Apr  4 20:32:46 2021.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Foronoi's documentation!
+===================================
+
+Foronoi is a Python implementation of the Fortune's algorithm based on the description of "Computational Geometry:
+Algorithms and Applications" by de Berg et al.
+
+This algorithm is a sweep line algorithm that scans top down over the
+cell points and traces out the lines via breakpoints in between parabola's (arcs). Once a new point is inserted, a check
+is done to see if it will converge with the lines on the left or right. If that's the case, it will insert a so-called
+circle-event which causes a new vertex (i.e. a cross-way between edges) to be created in the middle of the circle.
+
+The algorithm keeps track of the status (everything above the line is handled) in a so-called status-structure. This
+status-structure is a balanced binary search tree that keeps track of the positions of the arcs (in its leaf nodes) and
+the breakpoints (in its internal nodes). This data structure allows for fast look-up times, so that the entire
+algorithm can run in `O(n log n)` time.
+
+This implementation includes some additional features to the standard algorithm. For example, this implementation is
+able to clip the diagram to a bounding box in different shapes. And it will clean up zero-length edges that occur in
+edge-cases where two events happen at the same time so that it is more practical to use.
+
+
+.. image:: ../voronoi.gif
+  :width: 800
+  :alt: Voronoi diagram under construction
+
+Table of contents
++++++++++++++++++
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   installation
+   api
+   private
+
+
+Indices and tables
+++++++++++++++++++
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/installation.rst

@@ -0,0 +1,12 @@
+Installation
+===================
+
+Manual
+++++++
+First, clone the repository and then install the package.
+
+.. code-block:: bash
+
+   git clone https://github.com/Yatoom/voronoi.git
+   cd voronoi
+   python setup.py install

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/private.rst

@@ -0,0 +1,9 @@
+==============
+Private classes
+==============
+
+.. toctree::
+  :maxdepth: 2
+  :glob:
+
+  private/*

docs/private/arc.rst

@@ -0,0 +1,6 @@
+.. _arc:
+
+Arc
+=========
+.. autoclass:: voronoi.nodes.Arc
+   :members:

docs/public/algorithm.rst

@@ -0,0 +1,7 @@
+.. _algorithm:
+
+Algorithm
+=========
+.. autoclass:: voronoi.algorithm.Algorithm
+   :members:
+

docs/public/coordinate.rst

@@ -0,0 +1,7 @@
+.. _coordinate:
+
+Coordinate
+==========
+.. autoclass:: voronoi.graph.Coordinate
+   :members:
+

docs/public/half_edge.rst

@@ -0,0 +1,6 @@
+.. _halfedge:
+
+HalfEdge
+=========
+.. autoclass:: voronoi.graph.HalfEdge
+   :members:

docs/public/point.rst

@@ -0,0 +1,6 @@
+.. _point:
+
+Point
+=========
+.. autoclass:: voronoi.graph.Point
+   :members:

docs/public/polygon.rst

@@ -0,0 +1,6 @@
+.. _polygon:
+
+Polygon
+=======
+.. autoclass:: voronoi.graph.Polygon
+   :members:

docs/public/vertex.rst

@@ -0,0 +1,6 @@
+.. _vertex:
+
+Vertex
+=========
+.. autoclass:: voronoi.graph.Vertex
+   :members:

docs/public/visualization.rst

@@ -0,0 +1,6 @@
+.. _visualization:
+
+Visualizer
+==========
+.. automodule:: voronoi.visualization.visualizer
+   :members:

docs/public/voronoi.rst

@@ -0,0 +1,6 @@
+.. _vertex:
+
+Voronoi
+=========
+.. autoclass:: voronoi.Voronoi
+   :members:

examples/bounding_polygon.py

@@ -67,5 +67,5 @@
 
 # Visualize the tree
 TreeVisualizer() \
-    .plot(v.beach_line) \
+    .plot(v.status_tree) \
     .render("output/tree.dot", view=True)

examples/observers.py

@@ -31,7 +31,8 @@
 
         # Callback that saves the figure every step
         # If no callback is provided, it will simply display the figure in a matplotlib window
-        callback=lambda observer, figure: figure.savefig(f"output/voronoi/{observer.n_messages:02d}.png")
+        callback=lambda observer, figure: figure.savefig(f"output/voronoi/{observer.n_messages:02d}.png"),
+        visualize_before_clipping=True
     )
 )
 

examples/profiling_performance.py

@@ -0,0 +1,41 @@
+from voronoi import Voronoi, Polygon
+import cProfile
+import pstats
+
+
+def profiler(command, filename="profile.stats", n_stats=20):
+    """Profiler for a python program
+
+    Runs cProfile and outputs ordered statistics that describe
+    how often and for how long various parts of the program are executed.
+
+    Parameters
+    ----------
+    command: str
+        Command string to be executed.
+    filename: str
+        Name under which to store the stats.
+    n_stats: int or None
+        Number of top stats to show.
+    """
+
+    cProfile.run(command, filename)
+    stats = pstats.Stats(filename).strip_dirs().sort_stats("cumtime")
+    return stats.print_stats(n_stats or {})
+
+
+# Define some points (a.k.a sites or cell points)
+points = [
+    (2.5, 2.5), (4, 7.5), (7.5, 2.5), (6, 7.5), (4, 4), (3, 3), (6, 3)
+]
+
+# Define a bounding box / polygon
+polygon = Polygon([
+    (2.5, 10), (5, 10), (10, 5), (10, 2.5), (5, 0), (2.5, 0), (0, 2.5), (0, 5)
+])
+
+# Initialize the algorithm
+v = Voronoi(polygon)
+
+# Profile the construction of the voronoi diagram
+profiler('v.create_diagram(points=points)')