[vtkusers] Strange rendering with 2-voxel thick volume
Aashish Chaudhary
aashish.chaudhary at kitware.com
Thu Oct 5 11:48:29 EDT 2017
No worries...so we just checked the math the cell to point offset matrix
seems to be right but the delta seems wrong. Can you change this
> delta[0] = this->Extents[1] - this->Extents[0];
> delta[1] = this->Extents[3] - this->Extents[2];
> delta[2] = this->Extents[5] - this->Extents[4];
to this
delta[0] = this->Extents[1] - this->Extents[0] + 1;
delta[1] = this->Extents[3] - this->Extents[2] + 1;
delta[2] = this->Extents[5] - this->Extents[4] + 1;
Thanks,
On Thu, Oct 5, 2017 at 10:48 AM Elvis Stansvik <elvis.stansvik at orexplore.com>
wrote:
> 2017-10-05 16:34 GMT+02:00 Aashish Chaudhary <
> aashish.chaudhary at kitware.com>:
> > Thanks we are looking into it, earlier we moved the math from the shader
> to
> > a matrix that now we are forming in C++ so at this point we are looking
> at
> > the equation carefully. But yes, I thought you may have found a bug.
>
> Thanks for having a look. I suspect my std::max(..) is just a
> workaround and not a proper fix.
>
> Me and a colleague had another look, but I think we were both too
> tired to figure out if something was fundamentally wrong with the
> equations. Too late in the day :)
>
> Elvis
>
> >
> > - aashish
> >
> > On Thu, Oct 5, 2017 at 8:39 AM Elvis Stansvik <
> elvis.stansvik at orexplore.com>
> > wrote:
> >>
> >> 2017-10-05 10:38 GMT+02:00 Elvis Stansvik <elvis.stansvik at orexplore.com
> >:
> >> > 2017-10-04 18:12 GMT+02:00 Aashish Chaudhary
> >> > <aashish.chaudhary at kitware.com>:
> >> >> Got it, thanks!
> >> >
> >> > Although I'm not familiar at all with the code, I suspect this is what
> >> > happens with my 200x200x2 volume:
> >> >
> >> > In void
> >> >
> vtkOpenGLGPUVolumeRayCastMapper::vtkInternal::ComputeCellToPointMatrix()
> >> > {
> >> > this->CellToPointMatrix->Identity();
> >> > this->AdjustedTexMin[0] = this->AdjustedTexMin[1] =
> >> > this->AdjustedTexMin[2] = 0.0f;
> >> > this->AdjustedTexMin[3] = 1.0f;
> >> > this->AdjustedTexMax[0] = this->AdjustedTexMax[1] =
> >> > this->AdjustedTexMax[2] = 1.0f;
> >> > this->AdjustedTexMax[3] = 1.0f;
> >> >
> >> > if (!this->Parent->CellFlag) // point data
> >> > {
> >> > float delta[3];
> >> > delta[0] = this->Extents[1] - this->Extents[0];
> >> > delta[1] = this->Extents[3] - this->Extents[2];
> >> > delta[2] = this->Extents[5] - this->Extents[4];
> >> >
> >> > float min[3];
> >> > min[0] = 0.5f / delta[0];
> >> > min[1] = 0.5f / delta[1];
> >> > min[2] = 0.5f / delta[2];
> >> >
> >> > float range[3]; // max - min
> >> > range[0] = (delta[0] - 0.5f) / delta[0] - min[0];
> >> > range[1] = (delta[1] - 0.5f) / delta[1] - min[1];
> >> > range[2] = (delta[2] - 0.5f) / delta[2] - min[2];
> >> >
> >> > this->CellToPointMatrix->SetElement(0, 0, range[0]); // Scale diag
> >> > this->CellToPointMatrix->SetElement(1, 1, range[1]);
> >> > this->CellToPointMatrix->SetElement(2, 2, range[2]);
> >> > this->CellToPointMatrix->SetElement(0, 3, min[0]); // t vector
> >> > this->CellToPointMatrix->SetElement(1, 3, min[1]);
> >> > this->CellToPointMatrix->SetElement(2, 3, min[2]);
> >> >
> >> > // Adjust limit coordinates for texture access.
> >> > float const zeros[4] = {0.0f, 0.0f, 0.0f, 1.0f}; // GL tex min
> >> > float const ones[4] = {1.0f, 1.0f, 1.0f, 1.0f}; // GL tex max
> >> > this->CellToPointMatrix->MultiplyPoint(zeros,
> this->AdjustedTexMin);
> >> > this->CellToPointMatrix->MultiplyPoint(ones,
> this->AdjustedTexMax);
> >> > }
> >> > }
> >> >
> >> > delta[2] = 1 ==> min[2] = 0.5 ==> range[2] = 0
> >> >
> >> > So the scale factor in the third dimension will be 0 in
> >> > CellToPointMatrix, right? I guess this could be what accounts for the
> >> > strange rendering?
> >> >
> >> > Could/should this code be updated to take into account when the extent
> >> > delta is just 1, so that volumes 2 data points thick can be rendered?
> >>
> >> I've only tested it briefly, but this seems to give the correct
> >> rendering even with a 2 point thick input:
> >>
> >> diff --git a/Rendering/VolumeOpenGL2/vtkOpenGLGPUVolumeRayCastMapper.cxx
> >> b/Rendering/VolumeOpenGL2/vtkOpenGLGPUVolumeRayCastMapper.cxx
> >> index 8767bd0..88bbcba 100644
> >> --- a/Rendering/VolumeOpenGL2/vtkOpenGLGPUVolumeRayCastMapper.cxx
> >> +++ b/Rendering/VolumeOpenGL2/vtkOpenGLGPUVolumeRayCastMapper.cxx
> >> @@ -1495,9 +1495,9 @@ void
> >> vtkOpenGLGPUVolumeRayCastMapper::vtkInternal::ComputeCellToPointMatrix()
> >> if (!this->Parent->CellFlag) // point data
> >> {
> >> float delta[3];
> >> - delta[0] = this->Extents[1] - this->Extents[0];
> >> - delta[1] = this->Extents[3] - this->Extents[2];
> >> - delta[2] = this->Extents[5] - this->Extents[4];
> >> + delta[0] = std::max(2, this->Extents[1] - this->Extents[0]);
> >> + delta[1] = std::max(2, this->Extents[3] - this->Extents[2]);
> >> + delta[2] = std::max(2, this->Extents[5] - this->Extents[4]);
> >>
> >> float min[3];
> >> min[0] = 0.5f / delta[0];
> >>
> >> This ensures the texture does not collapse into 0 when the extent
> >> delta is 1. Would you consider this a correct fix?
> >>
> >> Elvis
> >>
> >> >
> >> > Elvis
> >> >
> >> >>
> >> >> On Wed, Oct 4, 2017 at 12:07 PM Elvis Stansvik
> >> >> <elvis.stansvik at orexplore.com> wrote:
> >> >>>
> >> >>> 2017-10-04 17:43 GMT+02:00 Aashish Chaudhary
> >> >>> <aashish.chaudhary at kitware.com>:
> >> >>> > thanks..I just wanted to make sure that we remove that as one of
> the
> >> >>> > culprit. I am wondering if it is something to do with the geometry
> >> >>> > (bbox) or
> >> >>> > something to do with some edge case (calculation that is going off
> >> >>> > because
> >> >>> > of very small delta). Although in the past we have tried very
> think
> >> >>> > volumes
> >> >>> >
> >> >>> > Is it possible for you to send a sample dataset to us?
> >> >>>
> >> >>> My test case includes the data used. It's simply a 200x200x2 volume
> >> >>> filled with all data points set to 0.01.
> >> >>>
> >> >>> Elvis
> >> >>>
> >> >>> >
> >> >>> > On Wed, Oct 4, 2017 at 10:09 AM Elvis Stansvik
> >> >>> > <elvis.stansvik at orexplore.com> wrote:
> >> >>> >>
> >> >>> >> Hi Aashish,
> >> >>> >>
> >> >>> >> 2017-10-04 15:47 GMT+02:00 Aashish Chaudhary
> >> >>> >> <aashish.chaudhary at kitware.com>:
> >> >>> >> > Please make sure that your sampling distance is less than < 2.
> >> >>> >> > You
> >> >>> >> > can
> >> >>> >> > set
> >> >>> >> > the sampling distance manually in the API.
> >> >>> >>
> >> >>> >> Hm. I don't think it's related to sampling distance. In the test
> >> >>> >> case
> >> >>> >> I'm not setting sampling distance at all, so I think it should
> >> >>> >> default
> >> >>> >> to 1, and then be automatically adjusted during interaction.
> >> >>> >>
> >> >>> >> In any case, even if I amend the test case with e.g.:
> >> >>> >>
> >> >>> >> volumeMapper->AutoAdjustSampleDistancesOff();
> >> >>> >> volumeMapper->SetSampleDistance(0.2);
> >> >>> >> ...
> >> >>> >> volumeMapper2->AutoAdjustSampleDistancesOff();
> >> >>> >> volumeMapper2->SetSampleDistance(0.2);
> >> >>> >>
> >> >>> >> The result is the same.
> >> >>> >>
> >> >>> >> Elvis
> >> >>> >>
> >> >>> >> >
> >> >>> >> > On Wed, Oct 4, 2017 at 8:23 AM Elvis Stansvik
> >> >>> >> > <elvis.stansvik at orexplore.com>
> >> >>> >> > wrote:
> >> >>> >> >>
> >> >>> >> >> Hi all,
> >> >>> >> >>
> >> >>> >> >> In the test case below, I render one 200x200x2 volume and one
> >> >>> >> >> 200x200x3 volume, both with the same settings.
> >> >>> >> >>
> >> >>> >> >> The 200x200x3 volume looks as expected (the light gray one in
> >> >>> >> >> the
> >> >>> >> >> attached screenshot), while the 200x200x2 one looks strange
> (too
> >> >>> >> >> dark,
> >> >>> >> >> and with some kind of gradient artifact).
> >> >>> >> >>
> >> >>> >> >> Is there some limitation on rendering a volume that is only 2
> >> >>> >> >> thick
> >> >>> >> >> in
> >> >>> >> >> one of the dimensions? I can understand why a volume of
> >> >>> >> >> thickness 1
> >> >>> >> >> can't be rendered properly, since VTK must have values to
> >> >>> >> >> interpolate
> >> >>> >> >> between, but 2 should be OK right?
> >> >>> >> >>
> >> >>> >> >> Thanks for any help.
> >> >>> >> >>
> >> >>> >> >> Elvis
> >> >>> >> >>
> >> >>> >> >>
> >> >>> >> >> main.cpp:
> >> >>> >> >>
> >> >>> >> >> #include <algorithm>
> >> >>> >> >>
> >> >>> >> >> #include <vtkColorTransferFunction.h>
> >> >>> >> >> #include <vtkGenericOpenGLRenderWindow.h>
> >> >>> >> >> #include <vtkGPUVolumeRayCastMapper.h>
> >> >>> >> >> #include <vtkImageData.h>
> >> >>> >> >> #include <vtkNew.h>
> >> >>> >> >> #include <vtkPiecewiseFunction.h>
> >> >>> >> >> #include <vtkProperty.h>
> >> >>> >> >> #include <vtkRenderer.h>
> >> >>> >> >> #include <vtkRenderWindow.h>
> >> >>> >> >> #include <vtkRenderWindowInteractor.h>
> >> >>> >> >> #include <vtkVolume.h>
> >> >>> >> >> #include <vtkVolumeProperty.h>
> >> >>> >> >>
> >> >>> >> >> int main(int argc, char *argv[])
> >> >>> >> >> {
> >> >>> >> >> vtkNew<vtkColorTransferFunction> colorFunction;
> >> >>> >> >> colorFunction->AddRGBPoint(0.0, 0.0, 0.0, 0.0);
> >> >>> >> >> colorFunction->AddRGBPoint(1.0, 0.0, 0.0, 0.0);
> >> >>> >> >>
> >> >>> >> >> vtkNew<vtkPiecewiseFunction> opacityFunction;
> >> >>> >> >> opacityFunction->AddPoint(0.0, 0.0);
> >> >>> >> >> opacityFunction->AddPoint(1.0, 1.0);
> >> >>> >> >>
> >> >>> >> >> // A 200x200x2 volume
> >> >>> >> >> vtkNew<vtkImageData> imageData;
> >> >>> >> >> imageData->SetExtent(0, 199, 0, 199, 0, 1);
> >> >>> >> >> imageData->AllocateScalars(VTK_FLOAT, 1);
> >> >>> >> >> std::fill_n(static_cast<float
> >> >>> >> >> *>(imageData->GetScalarPointer()),
> >> >>> >> >> 200 * 200 * 2, 0.01);
> >> >>> >> >>
> >> >>> >> >> vtkNew<vtkGPUVolumeRayCastMapper> volumeMapper;
> >> >>> >> >> volumeMapper->SetInputData(imageData.Get());
> >> >>> >> >>
> >> >>> >> >> vtkNew<vtkVolumeProperty> volumeProperty;
> >> >>> >> >> volumeProperty->SetScalarOpacity(opacityFunction.Get());
> >> >>> >> >> volumeProperty->SetColor(colorFunction.Get());
> >> >>> >> >> volumeProperty->ShadeOff();
> >> >>> >> >>
> >> >>> >> >> vtkNew<vtkVolume> volume;
> >> >>> >> >> volume->SetMapper(volumeMapper.Get());
> >> >>> >> >> volume->SetProperty(volumeProperty.Get());
> >> >>> >> >> volume->SetPosition(120, 0, 0);
> >> >>> >> >>
> >> >>> >> >> // A 200x200x3 volume
> >> >>> >> >> vtkNew<vtkImageData> imageData2;
> >> >>> >> >> imageData2->SetExtent(0, 199, 0, 199, 0, 2);
> >> >>> >> >> imageData2->AllocateScalars(VTK_FLOAT, 1);
> >> >>> >> >> std::fill_n(static_cast<float
> >> >>> >> >> *>(imageData2->GetScalarPointer()),
> >> >>> >> >> 200 * 200 * 3, 0.01);
> >> >>> >> >>
> >> >>> >> >> vtkNew<vtkGPUVolumeRayCastMapper> volumeMapper2;
> >> >>> >> >> volumeMapper2->SetInputData(imageData2.Get());
> >> >>> >> >>
> >> >>> >> >> vtkNew<vtkVolumeProperty> volumeProperty2;
> >> >>> >> >> volumeProperty2->SetScalarOpacity(opacityFunction.Get());
> >> >>> >> >> volumeProperty2->SetColor(colorFunction.Get());
> >> >>> >> >> volumeProperty2->ShadeOff();
> >> >>> >> >>
> >> >>> >> >> vtkNew<vtkVolume> volume2;
> >> >>> >> >> volume2->SetMapper(volumeMapper2.Get());
> >> >>> >> >> volume2->SetProperty(volumeProperty2.Get());
> >> >>> >> >> volume2->SetPosition(-120, 0, 0);
> >> >>> >> >>
> >> >>> >> >> vtkNew<vtkRenderer> renderer;
> >> >>> >> >> renderer->AddVolume(volume.Get());
> >> >>> >> >> renderer->AddVolume(volume2.Get());
> >> >>> >> >> renderer->SetBackground(1.0, 1.0, 1.0);
> >> >>> >> >>
> >> >>> >> >> // Render with "plain" render window / interactor
> >> >>> >> >> vtkNew<vtkRenderWindow> window;
> >> >>> >> >> window->SetMultiSamples(0);
> >> >>> >> >> window->AddRenderer(renderer.Get());
> >> >>> >> >>
> >> >>> >> >> vtkNew<vtkRenderWindowInteractor> interactor;
> >> >>> >> >> interactor->SetRenderWindow(window.Get());
> >> >>> >> >> interactor->Start();
> >> >>> >> >>
> >> >>> >> >> return 0;
> >> >>> >> >> }
> >> >>> >> >>
> >> >>> >> >>
> >> >>> >> >> CMakeLists.txt:
> >> >>> >> >>
> >> >>> >> >> cmake_minimum_required(VERSION 3.1)
> >> >>> >> >>
> >> >>> >> >> project(TestCase)
> >> >>> >> >>
> >> >>> >> >> find_package(VTK 8.0 COMPONENTS
> >> >>> >> >> vtkCommonCore
> >> >>> >> >> vtkCommonDataModel
> >> >>> >> >> vtkCommonExecutionModel
> >> >>> >> >> vtkCommonMath
> >> >>> >> >> vtkFiltersSources
> >> >>> >> >> vtkGUISupportQt
> >> >>> >> >> vtkInteractionStyle
> >> >>> >> >> vtkRenderingCore
> >> >>> >> >> vtkRenderingOpenGL2
> >> >>> >> >> vtkRenderingVolume
> >> >>> >> >> vtkRenderingVolumeOpenGL2
> >> >>> >> >> REQUIRED
> >> >>> >> >> )
> >> >>> >> >>
> >> >>> >> >> add_executable(TestCase main.cpp)
> >> >>> >> >>
> >> >>> >> >> target_link_libraries(TestCase PUBLIC
> >> >>> >> >> vtkCommonCore
> >> >>> >> >> vtkCommonDataModel
> >> >>> >> >> vtkCommonExecutionModel
> >> >>> >> >> vtkCommonMath
> >> >>> >> >> vtkFiltersSources
> >> >>> >> >> vtkInteractionStyle
> >> >>> >> >> vtkRenderingCore
> >> >>> >> >> vtkRenderingOpenGL2
> >> >>> >> >> vtkRenderingVolume
> >> >>> >> >> vtkRenderingVolumeOpenGL2
> >> >>> >> >> )
> >> >>> >> >>
> >> >>> >> >> target_include_directories(TestCase PUBLIC
> >> >>> >> >> ${VTK_INCLUDE_DIRS}
> >> >>> >> >> )
> >> >>> >> >>
> >> >>> >> >> target_compile_definitions(TestCase PUBLIC
> >> >>> >> >> ${VTK_DEFINITIONS}
> >> >>> >> >> )
> >> >>> >> >>
> >> >>> >> >> set_target_properties(TestCase PROPERTIES
> >> >>> >> >> CXX_STANDARD 14
> >> >>> >> >> CXX_STANDARD_REQUIRED ON
> >> >>> >> >> )
> >> >>> >> >> _______________________________________________
> >> >>> >> >> Powered by www.kitware.com
> >> >>> >> >>
> >> >>> >> >> Visit other Kitware open-source projects at
> >> >>> >> >> http://www.kitware.com/opensource/opensource.html
> >> >>> >> >>
> >> >>> >> >> Please keep messages on-topic and check the VTK FAQ at:
> >> >>> >> >> http://www.vtk.org/Wiki/VTK_FAQ
> >> >>> >> >>
> >> >>> >> >> Search the list archives at:
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> >> >>> >> >>
> >> >>> >> >> Follow this link to subscribe/unsubscribe:
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>
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