doc/examples/alphashape.rst
 author Dmitriy Morozov Sun, 20 Dec 2009 07:45:29 -0800 branch dev changeset 181 1ee6edc17cb6 parent 134 c270826fd4a8 permissions -rw-r--r--
Python bindings work again
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.. _alpha-shape-example:

Alpha shape example
===================

The example given in :sfile:`examples/alphashapes/alphashapes.py` takes a
filename containing points in 2D or 3D on the command line. It generates the
alpha shape filtration of those points, and computes its persistence. It then
outputs the persistence diagram in the format of a point (dimension, birth,
death) per line.

.. literalinclude:: ../../examples/alphashapes/alphashapes.py
:language: python

After the points are read into the list ``points``, the functions
:ref:`fill_alpha*_complex <alphashapes>` fill the :class:`Filtration` with the
simplices of the Delaunay triangulation. Each one has its :attr:`~Simplex.data`
attribute set to the tuple consisting of its alpha shape value (the minimum value of the squared
distance function on its dual Voronoi cell) and whether the simplex is regular
or critical.

The filtration then sorts the simplices with
respect to their data and dimension (via :func:`data_dim_cmp`)::

f = Filtration()
fill_alpha*_complex(points, f)
f.sort(data_dim_cmp)

We initialize :class:`StaticPersistence`, and pair the simplices::

p = StaticPersistence(f)
p.pair_simplices()

Iterating over the :class:`StaticPersistence`, we output the points of the
persistence diagram (dimension, birth, death) in the last for loop. If the
simplex is unpaired (``i.unpaired()``), the class it creates survives till infinity.
```