Tree Reconstruction
===================

This document describes the PypeTree implementation of the Modified
Verroust & Lazarus algorithm that can be applied to a botanical tree
point cloud to reconstruct it.

Connectivity
------------

Both the number of neighbors (``k``) and the search radius (``r``) can
be specifed, as they are not mutually exclusive or conflicting.

Level Sets
----------

The *y* (or upward dimension) is the column in the input dataset
corresponding to the height of the tree (0, 1, or 2). This is
important because the geodesic space is defined in the elongated
dimension of the tree, which is usually mostly directed in the upward
direction. Although PypeTree tries to guess it for you, its heuristic
(i.e. simply looking for the dimension with the largest span) is not
perfect, and you should be careful that the value is the right one.

The search for the *N*-connected components of a given level set is
the way branch cut segmentation is performed. Since having too many
very small components adds unnecessary noise to the model, it's
possible to filter those whose size is below a threshold, by lumping
them to one of their neighboring level sets. However, you have to be
careful with this, because the underlying computation can be quite
expensive with degenerate cases where many filtered components are
shuffled around. For a value of 0, this filtering computation simply
isn't triggered, so it's the most efficient option, at the expense of
producing noisier results.

Reconstruction
--------------

Smoothing
---------