[vtkusers] [vtk-developers] How to use color mapping for vtkPistonMapper?

Mon Dec 9 03:01:28 EST 2013

Jeff,

Thanks. Just FYI the animation was generated by

Computing the Dv/Dt of the voltages on each segment of the neuron
Passing the generated Dv/Dt through an exponential decay over time filter so that the excitation is visible for slightly longer rather than flickering on/off very fast,
creating an alpha channel based on the ExpDecay*thickness*fudgeFactorPerSegmentType (the fudge factor is used to make the some more visible than some of the dendrites/axons etc)

then the opacity/alpha was combined with the original voltage level to get  the RGBA value using the TwoColorsToScalars lookuptable.

This makes the final animation more 'illustrative' than real in one sense, though it help greatly to see where the activity is taking place.

JB

From: Jeff Lee [mailto:jlee1549 at gmail.com]
Sent: 04 December 2013 16:04
To: Biddiscombe, John A.
Cc: David E DeMarle; Enya Shen; vtkdev; vtkusers at vtk.org
Subject: Re: [vtkusers] [vtk-developers] How to use color mapping for vtkPistonMapper?

nice animation JB!

On Wed, Dec 4, 2013 at 7:38 AM, Biddiscombe, John A. <biddisco at cscs.ch<mailto:biddisco at cscs.ch>> wrote:
Just noticed a mistake in my text after clicking send ...

Erratum : "Decided on Depth Sorting" - instead of depth peeling.

> -----Original Message-----
> From: Biddiscombe, John A.
> Sent: 04 December 2013 13:35
> To: Biddiscombe, John A.; David E DeMarle; Enya Shen
> Cc: vtkdev; vtkusers at vtk.org<mailto:vtkusers at vtk.org>
> Subject: RE: [vtkusers] [vtk-developers] How to use color mapping for
> vtkPistonMapper?
>
> https://hpcforge.org/scm/browser.php?group_id=117
> is a project called pv-zoltan
>
> I needed to do transparent rendering of neuron circuits which are very large
> and complex, depth peeling is one option, but for some of these circuits I had
> to use a machine with no graphics capabilities, so I wanted a software render
> option and decided on depth peeling. see
> ftp://ftp.cscs.ch/out/biddisco/bbp/videos/5k-voltage-differentials.avi skip to
> about 45 seconds in for an example of the data that is interesting - it's just
> under 1 billion triangles, rendered in parallel. Some of the scenes are very
> complex, so for depth peeling, you really need hundreds of layers to be sure
> it's perfect (though nobody would be able to tell the difference).
>
> What is pv-zoltan : it's a set of classes to allow parallel mesh redistribution
> using the zoltan library from trilinos. Once the mesh is partitioned, I then
> depth sort the triangles and render in parallel with sort last compositing.
> 1) There is a custom depth sort class in the code which generates a depth
> sorted ID list and attaches it to the dataset, then a custom
> vtkPolyDataMapper/Painter which renders using the sorted order (this
> differs from the vtkDepthSortPolyData in vtk which actually sorts the
> polygons (and all cell/point arrays)  and effectively doubles the memory use,
> then renders with the normal polydatamapper/painter).  By generating an Id
> ordering and then painting in that order, we only add 1 int per cell.
> 2) mesh partitioning with zoltan - and some enhancements to the rendering
> front end to bypass the default compositing in paraview and use the KdTree
> from zoltan to do the ordered compositing.
> 3) Once that was working, I wanted to try to do the depth sort on the GPU,
> so I looked at piston and found it to be very easy to modify to suit my needs.
> I have changed the vtkDataSetToPiston class and the vtkPistonMapper
> slightly (and the code will only work with triangle based geometry unless you
> uncomment the triangulation routine somewhere). When the PISTON code
> is enabled, the CPU depth sort is disabled (point 1 above) and instead push
> the dataset to GPU, do depth sort on the fly (some thrust code thrown in
> using thrust::sort_by_key<> and a distance functor) and render in one pass
> effectively. (two loops, but only one render pass).
> 4) There is some code in the colorGPU branch which activates the colour
> table lookup and generation on the GPU as well, but I didn't get time to look
> at it this morning to remind myself of what happens where and when. I seem
> to recall I have a small bug in there which makes the table get regenerated
> more often than it needs to. And possibly more CPU-GPU traffic than strictly
> necessary, but nothing serious.
> 5) Because the transparent rendering uses per vertex opacity - instead of
> using a scalars to colours, we use a new two scalars to colours (originally
> written for the point sprite renderer), this takes one array for scalars and one
> for opacity, so the lookup stuff is a bit more versatile than the standard.
> 6) Everything is handled (rather smoothly I think, even if I do say so myself)
> by the DepthSortRepreseantation which connects everything together. It
> just needs a couple of small fixes for paraview to get working, but most of it
> should compile ok and work - except for the ordered compositing which
> requires some extra info passed via the vtkBoundsExtentTranslator in the
> plugin which holds the region assignments generated by Zoltan and is used to
> send the KdTree to the compositing code in the front end.
>
> .... currently my depth sort branch is out of date/order, so I won't paste a
> paraview patch. You'd need to just comment out a couple of lines of the
> plugin code. I'd suggest looking  at the piston stuff and having a play with it. I
> can't remember if I added an option to disable the depth sort and only do the
> render on the GPU, the interesting part is where the cuda array handles are
> passed from the dataset after sorting etc and given to OpenGL for rendering,
> most of the piston code itself is irrelevant and it's only the push to gpu and
> pass of handles to GL that is interesting. Many thanks to the original Piston
> developers for showing how to do it.
>
> NB. running on a single process ought to work, but there may be a gotcha I've
> forgotten about. when I have a few hours spare I'll apply my patches to my
> current paraview tree and see if everything is still working ok and post an
> update.
>
> JB
>
>
> > -----Original Message-----
> > From: vtkusers-bounces at vtk.org<mailto:vtkusers-bounces at vtk.org> [mailto:vtkusers-bounces at vtk.org<mailto:vtkusers-bounces at vtk.org>] On
> > Behalf Of Biddiscombe, John A.
> > Sent: 03 December 2013 15:44
> > To: David E DeMarle; Enya Shen
> > Cc: vtkdev; vtkusers at vtk.org<mailto:vtkusers at vtk.org>
> > Subject: Re: [vtkusers] [vtk-developers] How to use color mapping for
> > vtkPistonMapper?
> >
> > Yes. I've enhanced the piston mapper and done the lookuptable on the
> GPU.
> > I'm stuck in a terminally dull meeting right now, but once I escape,
> > I'll brush off the code and post a link.
> >
> > JB
> >
> > From: David DeMarle
> > <dave.demarle at kitware.com<mailto:dave.demarle at kitware.com><mailto:dave.demarle at kitware.com<mailto:dave.demarle at kitware.com>>>
> > Date: Tuesday 3 December 2013 14:47
> > To: Enya Shen
> > <enya.shen2010 at gmail.com<mailto:enya.shen2010 at gmail.com><mailto:enya.shen2010 at gmail.com<mailto:enya.shen2010 at gmail.com>>>
> > Cc: VTK Developers <vtk-developers at vtk.org<mailto:vtk-developers at vtk.org><mailto:vtk-<mailto:vtk->
> > developers at vtk.org<mailto:developers at vtk.org>>>, "vtkusers at vtk.org<mailto:vtkusers at vtk.org><mailto:vtkusers at vtk.org<mailto:vtkusers at vtk.org>>"
> > <vtkusers at vtk.org<mailto:vtkusers at vtk.org><mailto:vtkusers at vtk.org<mailto:vtkusers at vtk.org>>>
> > Subject: Re: [vtk-developers] How to use color mapping for
> > vtkPistonMapper?
> >
> > Unfortunately I ran out of time and didn't get around to moving VTK's
> > lookup table over when I originally implemented that class. So, the
> > randow color map you see now is the only option when doing direct GPU
> > to GPU rendering. Unless you hack the class yourself to make the
> > transfer function configurable of course.
> >
> > If anyone out there has an updated implementation (ahem John B.)
> > please direct us to it and we can see about folding your improvements in.
> >
> > thanks
> >
> >
> > David E DeMarle
> > Kitware, Inc.
> > R&D Engineer
> > 21 Corporate Drive
> > Clifton Park, NY 12065-8662
> > Phone: 518-881-4909<tel:518-881-4909>
> >
> >
> > On Tue, Dec 3, 2013 at 12:24 AM, Enya Shen
> > <enya.shen2010 at gmail.com<mailto:enya.shen2010 at gmail.com><mailto:enya.shen2010 at gmail.com<mailto:enya.shen2010 at gmail.com>>> wrote:
> > Dear all,
> >
> > I try to use vtkPistonMapper, but when I set the color with
> > setColor(double[3]), I got nothing changed.
> >
> > Thanks for any example or advice!
> >
> > Regards,
> > Enya
> >
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