[vtk-developers] potential speedup for the vtkpolydatatoimagestencil

Karthik Krishnan karthik.krishnan at kitware.com
Fri Feb 24 22:24:52 EST 2012 

On Sat, Feb 25, 2012 at 3:13 AM, Mark Roden <mmroden at gmail.com> wrote:

> We need to display the contour itself, not voxels that are inside the
> contour.


Then why would you be generating the stencil ? Just cut the polydata with
the slice plane and display it.



>  It seems that Eclipse has trained everyone to expect this
> appearance, and the rtstruct itself is based around this premise.
>
> Unless we can get a contour through that approach?
>
> On Fri, Feb 24, 2012 at 1:40 PM, Karthik Krishnan
> <karthik.krishnan at kitware.com> wrote:
> > But isn't vtkPolyDataToImageStencil, extrusion etc overkill for your
> > specific problem. Why not compute the mask by looping over all voxels
> within
> > the bounds of the contour on a slice and using vtkPolygon::PointInPolygon
> > for every such voxel. It evaluates inside-outside by using rayfiring and
> > that should run much faster; in the order of milliseconds
> >
> > On Sat, Feb 25, 2012 at 2:21 AM, Mark Roden <mmroden at gmail.com> wrote:
> >>
> >> Hi David,
> >>
> >> Sorry for being extremely tardy on continuing this thread, but the
> >> issue took a back burner to more pressing problems that arose pretty
> >> suddenly.
> >>
> >> Anyway, I think I see what's going on here, and I have some hypotheses.
> >>
> >> We have a vtkPolyData read in by GDCM.  This structure is read in via
> >> double precision (a change I've made recently that may or may not have
> >> any bearing).
> >>
> >> If we use the following series of vtk classes, the data can be
> >> visualized on a CT Dicom image (whose z coordinates are in float
> >> space, as best as I can tell):
> >>
> >> vtkLinearExtrusionFilter
> >> vtkPolyDataToImageStencil
> >> vtkImageStencil
> >>
> >> This series of operations, on one test data set, requires 25 seconds
> >> on a fairly fast machine to produce contours for all the organs in the
> >> structure set.  On our testers' machines, that number is roughly
> >> triple, meaning that they are going nuts with waiting times.
> >>
> >> If we remove the extruder, then the time drops to 10 seconds, a pretty
> >> significant speedup (using vtk git source from 10 jan 2012).  Problem
> >> is, now the data are not visible on the CT image at all.  I suspect
> >> that they are not visible because the coordinates do not match
> >> _exactly_ in z, but I really have no way to back up that hypothesis.
> >>
> >> It seems that the extruder, in this case, is acting as an error range
> >> in z; ie, allowing the stencil a bit more leeway to finding the proper
> >> plane in Z.  Trouble is, that code path is triggering the slow path
> >> you talked about.
> >>
> >> Is there a way to set a kind of z tolerance to the stencil to achieve
> >> the same effect?  Or am I off-base as to why the contours would not
> >> appear on the data?
> >>
> >> Thanks,
> >> Mark
> >>
> >>
> >> On Wed, Jan 25, 2012 at 4:20 PM, David Gobbi <david.gobbi at gmail.com>
> >> wrote:
> >> > Hi Mark,
> >> >
> >> > In all my previous replies to your questions, I assumed that your data
> >> > consisted of a surface (i.e. with polygonal faces).  If your data is a
> >> > series of polylines, then that changes things... particularly with
> >> > respect to what version of VTK you are using.
> >> >
> >> > If your data consists of a series 2D polyline contours in 3D space,
> >> > prior to VTK 5.8, vtkPolyDataToImageStencil could not use this kind of
> >> > data, it required a 3D surface and it would cut that surface to
> >> > generate contours.  In VTK 5.8, the ability to directly process a
> >> > series of 2D contours was added, but very inefficiently.  In VTK git,
> >> > the code for handling a series of 2D contours was modified to become
> >> > much more efficient.
> >> >
> >> > For the vtkPolyDataToImageStencil in VTK 5.8, the PolyDataCutter
> >> > function does this: if the input contains any only polylines, then the
> >> > "if (cell->GetCellDimension() == 1)" branch is used.  If the input
> >> > contains any polygons, however, then the "if (cell->GetCellDimension()
> >> > == 2)" branch is used.  Only this latter branch actually does any
> >> > cutting/contouring of the data.
> >> >
> >> > In VTK git, the code for polylines uses its own efficient subroutine
> >> > called PolyDataSelector.  So for polyline contours, this is the best
> >> > version to use. Also, for polyline contours, the "loose end" code will
> >> > not find any loose ends (and therefore not eat up any CPU) if the
> >> > polylines that make up your contours are already closed.  You can
> >> > always run your contours through vtkCleanPolyData and vtkStripper to
> >> > ensure that this is the case.
> >> >
> >> >  - David
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > On Wed, Jan 25, 2012 at 4:08 PM, Mark Roden <mmroden at gmail.com>
> wrote:
> >> >> OK, so I've looked further into this problem, and it seems that I was
> >> >> optimizing the wrong thing.
> >> >>
> >> >> If I comment out everything other than the PolyDataCutter method
> >> >> (specifically, the call to 'contour' in there), then contours take
> the
> >> >> same amount of time to load as they do with everything turned on.
>  All
> >> >> of the time is being spent in the Contour routine.
> >> >>
> >> >> However, rtstructs are already organized into contours.  Each set of
> >> >> three numbers corresponds to a point in 3D space, and then each
> >> >> succeeding group corresponds to the next point in the contour.  From
> >> >> what I can determine, there is no need for this PolyDataCutter
> >> >> routine.
> >> >>
> >> >> How can I tell the vtkPolyDataToImageStencil class that the data are
> >> >> already properly organized, that each point that follows is connected
> >> >> to the one previous, and in the case of a CLOSED contour, the last
> >> >> connects to the first?
> >> >>
> >> >> On Mon, Jan 23, 2012 at 11:27 AM, David Gobbi <david.gobbi at gmail.com
> >
> >> >> wrote:
> >> >>> 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
> >> _______________________________________________
> >> Powered by www.kitware.com
> >>
> >> Visit other Kitware open-source projects at
> >> http://www.kitware.com/opensource/opensource.html
> >>
> >> Follow this link to subscribe/unsubscribe:
> >> http://www.vtk.org/mailman/listinfo/vtk-developers
> >>
> >
> >
> >
> > --
> > --
> > karthik
> >
>



-- 
--
karthik
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/vtk-developers/attachments/20120225/e3f82aee/attachment.html>

More information about the vtk-developers mailing list