[vtk-developers] potential speedup for the vtkpolydatatoimagestencil

David Gobbi david.gobbi at gmail.com
Mon Jan 23 14:27:50 EST 2012

On Mon, Jan 23, 2012 at 12:09 PM, Mark Roden <mmroden at gmail.com> wrote:
> Hi David,
> Thanks for the response, I'll take a look at the clipclosedsurface
> class.  That may be what I want anyway (does it allow for any one
> plane to have a hollow interior?), but if you've already done the
> hashing there, then I'll take a look at porting it to this class as
> well.  Or should there be a shared routine that both classes use, if
> the work done is very similar?

A shared routine would be ideal, I had hoped to eventually write a
vtkCutClosedSurface filter for that purpose.

The vtkClipClosedSurface class does allow holes.  It is described
here: http://vtk.org/Wiki/VTK/Closed_Surface_Clipping

 - David

> On Mon, Jan 23, 2012 at 11:04 AM, David Gobbi <david.gobbi at gmail.com> wrote:
>> On Mon, Jan 23, 2012 at 11:19 AM, Mark Roden <mmroden at gmail.com> wrote:
>>> Hi David,
>>> I'm looking to make the vtkpolydatatoimagestencil class faster.  Right
>>> now, on a core i7 machine and in using release-compiled code,
>>> translating a body mask in an rtstruct to pixels using this filter is
>>> prohibitively expensive in time (upwards of a minute for the mask).
>>> There are three possible speedups to do here, in my mind.  I wanted to
>>> clear them by you, because I don't want to fork vtk to solve this
>>> problem, but the problem has become a serious problem for us.
>>> First, treat each plane independently of one another, and then have
>>> each plane processed by different threads.  This change is fairly
>>> straightforward theoretically, and something you mentioned you were
>>> looking into a while back
>>> (http://www.vtk.org/pipermail/vtkusers/2011-January/114538.html).  Is
>>> this something you're still investigating?
>> There were three things that I was considering:
>> 1) multi-threading so that each CPU gets N slices to work on
>> 2) increasing the efficiency of the polygon cutting code, I added some
>> nice cutting code to vtkClipClosedSurface and planned to eventually
>> also use it in vtkPolyDataToImageStencil
>> 3) improving the efficiency or extent insertion for the stencils
>> So far I've only done #3, which was the least important but was the
>> easiest.  Right now my own apps are bottlenecking on my segmentation
>> algorithms, rather than on vtkPolyDataToImageStencil, so improving
>> vtkPolyDataToImageStencil hasn't been a high priority.
>>> For my work on other projects, I've found that the intel tbb
>>> (http://threadingbuildingblocks.org/) makes multithreading this kind
>>> of work very easy; the library is free and works with any c++ project
>>> that uses the C++0x standard and can use lambda expressions.
>> VTK will have to continue to support pre-C++0x compilers for a long
>> time, several more years at least.  So if threading is to be done, it
>> should be done with VTK's threading classes.
>>> Second, change the interior while/for loop collision detection to be a
>>> hash table.  Right now, in the ThreadedExecute function, there is this
>>> code:
>>>    for (vtkIdType i = 0; i < numberOfPoints; ++i)
>>>      {
>>> ...
>>>      while( lines->GetNextCell(npts, pointIds) )
>>>        {
>>>        for (vtkIdType j = 0; j < npts; ++j)
>>>          if ( pointIds[j] == i )
>>>            {
>>> But what if collision detection was changed to uses a hash table where
>>> the hashing function automatically detected point collisions through a
>>> single pass through the data?
>> I use a hash vtkClipClosedSurface to accelerate the clipping (i.e. #2
>> on my to-do list above).  Take a look at the vtkClipClosedSurface
>> code, specifically the vtkCCSEdgeLocator class.
>>> Third, there does not appear to be an iterator over the points vector,
>>> but a Get and Set function.  These functions appear to be pretty slow,
>>> and go through several thunking layers before data can actually be set
>>> or not.  Is there an iterator class for points as there is for lines?
>>> If not, how hard would it be to create such a class?
>> The vtkPoints::GetData() method returns an array (either a
>> vtkFloatArray or a vtkDoubleArray) that contains the points.  Once you
>> have this array, the GetTupleValue() method is a purely inlined method
>> that can be used to efficiently get the points.  If you know ahead of
>> time whether the points are double or float, then this is probably the
>> most efficient way of accessing them, apart from getting the raw
>> "float *" or "double *".
>>  - David

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