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

Fri May 8 00:32:25 EDT 2015

Hi Paul,

You could create a three component point array of colors on the polydata.
The colors can be mapped from a lookup table based on which biological cell
the pointId belongs to. You can alter the lookup table based on the
variable being color-mapped.

This example demonstrates coloring points by added a point array of colors:
http://www.vtk.org/Wiki/VTK/Examples/Cxx/PolyData/TriangleColoredPoints

Hope this helps.

Warm Regards,

Sankhesh Jhaveri
Research & Development Engineer
Kitware, Inc.
*Phone*: (518) 881 4417
*Fax*: (518) 371 4573

On Thu, Apr 30, 2015 at 10:51 AM, Paul Melis <paul.melis at surfsara.nl> wrote:

> Hi Gerrick,
>
> I tried to make the two different "cells" apparent: VTK cells and
> biological cells in the model (the latter being represented by a piece of
> polydata), but apparently failed :) The filters you suggest work on VTK
> points and cells only, not the higher level of biological cells in the
> model I'm looking for.
>
> I'll try to add more detail. I have several biological cells in my
> polydata object that are each represented by a few hundred points and
> triangles (basically a distorted sphere per biological cell). All cells in
> the simulation are represented by a single VTK polydata object (so not a
> polydata object per cell). There is a point-data array called "cellId" that
> holds the biological cell ID, so polydata points that form the same
> biological cell in the model will have the same cell ID value.
>
> For each of the biological cells there is a single value for a number of
> model output values, e.g. volume of the biological cell, total amount of
> distortion, etc. These values I'd like to visualize by coloring the whole
> cell (i.e. that cell's subset of the polydata) with a color-mapped value.
> It seems the only way to do that in VTK is to propagate the value to show
> for a cell (say volume) to all that cell's polydata points, for each of the
> biological cells, and then do color-mapped rendering as usual.
>
> However, this value propagation is not something VTK can do for me it
> seems, so I've written it manually in Python at the moment. The way this
> works is that I add a point-data array to the polydata object for each
> value, e.g. Volume. It then takes the values per biological cell from an
> HDF5 file and assigns those values to the polydata points, based on the
> biological cell ID of each point, thereby duplicating e.g. the volume value
> for cell 123 on all points having cellID value 123.
>
> This value propagation takes a bit of processing that I'd like to minimize
> while interactively visualizing and reading in new timesteps. Preprocessing
> all timestep files is possible, but will add a lot of duplicate data,
> something I'd like to avoid.
>
> Regards,
> Paul
>
> On 04/30/2015 04:27 PM, Gerrick Bivins wrote:
>
>> 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
>>
>>
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