[vtkusers] [EXTERNAL] Efficiently visualizing duplicate data in biological model

[Gerrick Bivins]

Hi Paul,
I'm a little confused on what your data layout is and how you'd actually like it to be
but have you tried using either of these:
http://www.vtk.org/doc/nightly/html/classvtkCellDataToPointData.html
http://www.vtk.org/doc/nightly/html/classvtkPointDataToCellData.html

Gerrick


-----Original Message-----
From: vtkusers [mailto:vtkusers-bounces at vtk.org] On Behalf Of Paul Melis
Sent: Thursday, April 30, 2015 6:29 AM
To: vtkusers at vtk.org
Subject: [EXTERNAL] [vtkusers] Efficiently visualizing duplicate data in biological model

Hi,

(Sorry for the lengthy introduction below, I feel some detail is needed before framing my question :))

I'm working with output data from a simulation of certain biological cells, currently a few hundred of them. Each cell is modeled with a few hundred vertices and triangles and can deform and interact with other cells. There's both per-vertex data for each cell (like force), as well as per-biological-cell data for the whole cell (like volume, amount of deformation, etc). The two different sets of data are stored in separate
HDF5 files per timestep and we're using Xdmf to read the cell geometry + per-vertex data in as VTK polydata for visualization.

The per-biological-cell data is stored as arrays of scalars indexed by biological cell ID. The (biological) cell polydata has a per-vertex "cellId" scalar value referencing this cell ID. For visualizing the per-biological-cell values (coloring a whole biological cell with one color based on the "cell-global" value) I'm currently using a bit of Python to add extra point-data arrays to the polydata for each per-biological-cell value, thereby massively duplicating the per-biological-cell values to each point/vertex. This works, but it's a bit slow already (I'm processing on-the-fly during reading) and the datasets will need to scale up to much larger numbers of cells. 
Duplicating the per-biological-cell values to each point-data array and storing them in a preprocess is doable, but wastes a lot of disk space. 
And the current separation of files for per-vertex and per-biological-cell data seems natural (although obviously they could be datasets in the same HDF5 file, but that wouldn't solve the duplication issue I'm pondering on).

I've tried to find good ways to handle this case in VTK (or even on the level of Xdmf), but don't see filters or operations that handle this case out of the box. Is there a better approach than the "manual" data duplication that I'm using at the moment?

Thanks in advance for any reply,
Paul

-- 

Paul Melis
| Groepsleider & Adviseur Visualisatie | SURFsara | Science Park 140 | 
| 1098 XG Amsterdam | T 020 800 1312 | paul.melis at surfsara.nl | 
| www.surfsara.nl |
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