[vtkusers] Strange rendering with 2-voxel thick volume
Elvis Stansvik
elvis.stansvik at orexplore.com
Thu Oct 5 10:48:33 EDT 2017
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
>> >>> >> >> )
>> >>> >> >> _______________________________________________
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>> >>> >> >>
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>> >>> >> >>
>> >>> >> >> 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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>> >>> >> >>
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