[Paraview] Blood vessel network (spatial graph) visualisation

[Utkarsh Ayachit]

Simon,

> To start off with, I am trying to work out if it's possible to display this
> type of network in ParaView as connected tubes, with radii scaled by the
> size of the vessels. As I say, these datasets are large, typically with
> around 300k segments. If this kind of visualisation is available (or
> potentially could be developed), the next challenge would be to find a file
> format that could be use to import them.

The most obvious choice is to use the "Tube" filter for a dataset that
comprises of line segments with radii specified as point-data. The
tube filter can be told to scale the radius based on any variable in
the data. For 300K segments, it may be fine, but if things get too
large fret not. We are looking into ways of doing the "tubing" in GPU
itself, so that's coming in the next release or two.

> My data is currently in Amira mesh (spatial graph) format, which consists of
> multiple fields that define 1) the 3D coordinates of the nodes, 2)
> connections (segments) between the nodes, 3) 3D coordinates defining the
> path of the segments and 4) scalar fields defining atrributes of the
> segments (e.g. vessel radius, blood flow, pressure, etc.).

AFAIK, ParaView currently doesn't support Amira mesh format. You have
multiple options,
1. You could use an already supported file format instead e.g. Legacy
VTK, VTK-XML, Xdmf etc. Both Legacy VTK and VTK-XML are simple enough
formats that should be reasonable for the size you mention.
2. Write your own reader using the Programmable Source. The ParaView
Guide [1] has a few examples to get you started.

Hope that helps get you started. As always, feel free to ask if you
have more questions.

Utkarsh


[1] http://www.paraview.org/paraview-guide/