[Insight-users] Question regarding BSplineScatteredDataPointSetToImageFilter
Nicholas Tustison
ntustison at gmail.com
Tue Jan 10 07:02:19 EST 2012
Hi Kerstin,
Please keep the correspondence on the user's list.
Why are you setting your vector to all zeros?
> VectorType v;
> v[0] = 0.0;
> v[1] = 0.0;
> v[2] = 0.0;
and why are you setting the location of your points to
(idx,idx,idx,t)?
> point[0] = idx;
> point[1] = idx;
> point[2] = idx;
> point[3] = t;
That can't possibly be right. Did you look at the sample
code I gave you?
Nick
On Jan 9, 2012, at 2:04 AM, Kerstin Müller wrote:
> Hi,
>
> thank you very much!
> However I'm still struggeling with a heap corruption problem. I'm not sure if I set my parameters correct.
>
> typedef float RealType;
>
> typedef itk::Vector<RealType, 3> VectorType;
> typedef itk ::Image <VectorType , 4 > TimeVaryingDeformationFieldType;
> typedef itk :: PointSet <VectorType , 4 > TimeVaryingDeformationFieldPointSetType;
>
> TimeVaryingDeformationFieldPointSetType::Pointer fieldPoints = TimeVaryingDeformationFieldPointSetType:: New ();
> fieldPoints->Initialize();
>
> // Set the sample points just for testing 10 linear points no movement
> for ( int t = 0; t < m_configuration.num_projections ; t++ )
> {
> int num = 0;
> for( int idx = 0; idx <= 10; idx++ )
> {
>
> VectorType v;
> v[0] = 0.0;
> v[1] = 0.0;
> v[2] = 0.0;
>
>
> TimeVaryingDeformationFieldPointSetType::PointType point;
> point[0] = idx;
> point[1] = idx;
> point[2] = idx;
> point[3] = t;
>
> fieldPoints->SetPoint( num, point );
> fieldPoints->SetPointData(num, v);
> num++;
>
> }
> }
>
>
> TimeVaryingDeformationFieldType::PointType origin;
> TimeVaryingDeformationFieldType::SpacingType spacing;
> TimeVaryingDeformationFieldType::SizeType size;
>
> // Define the parametric domain
> spacing[0] = 1.0f;
> spacing[1] = 1.0f;
> spacing[2] = 1.0f;
> spacing[3] = 2.0f;
>
> size[0] = 128;
> size[1] = 128;
> size[2] = 128;
> size[3] = 66;
>
> origin[0] = 0.0f;
> origin[1] = 0.0f;
> origin[2] = 0.0f;
> origin[3] = 0.0f;
>
> // Define the filter and set the parameters
> typedef itk::myBSplineScatteredDataPointSetToImageFilter<TimeVaryingDeformationFieldPointSetType, TimeVaryingDeformationFieldType> BSplineFilterType;
> BSplineFilterType::Pointer filter = BSplineFilterType::New();
>
> filter ->SetSize( size );
> filter ->SetOrigin( origin );
> filter ->SetSpacing( spacing );
> filter -> SetGenerateOutputImage ( false );
> filter -> SetNumberOfLevels ( 2 );
> filter -> SetSplineOrder ( 3 );
>
>
> BSplineFilterType :: ArrayType ncps;
> ncps.SetElement(0,8);
> ncps.SetElement(1,8);
> ncps.SetElement(2,8);
> ncps.SetElement(3,34);
> filter -> SetNumberOfControlPoints ( ncps );
>
> filter ->SetInput( fieldPoints );
>
> filter->SetDebug(true);
>
> try
> {
> filter ->Update ();
> }
> catch ( itk::ExceptionObject & excp )
> {
> std :: cerr << "Test 2: itkBSplineScatteredDataImageFilter exception thrown" << std:: endl;
> std::cerr<< excp <<std::endl;
> }
>
> Thank you very much!
>
> Best,
>
> Kerstin
> 2012/1/4 Nicholas Tustison <ntustison at gmail.com>
> Okay, here's some pseudocode which hasn't been tested
> since you have to provide it the interface to your values
> but you should get the general idea.
>
> typedef float RealType;
> typedef itk::Image<RealType, ImageDimension> RealImageType;
>
> // Read in your reference image which will define the domain of
> // your B-spline displacement field. Assume, for simplicity, that it
> // has identity direction
>
> typedef itk::ImageFileReader<RealImageType> ImageReaderType;
> typename ImageReaderType::Pointer reader = ImageReaderType::New();
> reader->SetFileName( XXXX );
> reader->Update();
>
> typedef itk::Vector<RealType, ImageDimension> VectorType;
> typedef itk::Image<VectorType, ImageDimension+1> TimeVaryingDeformationFieldType;
>
> typedef itk::PointSet<VectorType, ImageDimension+1> TimeVaryingDeformationFieldPointSetType;
> typename TimeVaryingDeformationFieldPointSetType::Pointer fieldPoints =
> TimeVaryingDeformationFieldPointSetType::New();
> fieldPoints->Initialize();
> unsigned long count = 0;
>
> // Assume points are stored in a 2-D matrix called 'mySamplePoints' where the column
> // is the time point and the row is the point
>
> for( unsigned int t = 0; t < numberOfTimePoints; t++ )
> {
> for( unsigned int n = 0; n < numberOfPointsPerTimePoint; n++ )
> {
> VectorType displacement = mySamplePoints[n][t] - mySamplePoints[n][0];
>
> TimeVaryingDeformationFieldPointSetType::PointType parametric point;
> for( unsigned int d = 0; d < ImageDimension; d++ )
> {
> point[d] = ( mySamplePoints[n][0] )[d];
> }
> point[ImageDimension] = t;
>
> fieldPoints->SetPoint( count, point );
> fieldPoints->SetPointData( count, displacement );
> count++;
> }
> }
>
> TimeVaryingDeformationFieldType::PointType origin;
> TimeVaryingDeformationFieldType::SpacingType spacing;
> TimeVaryingDeformationFieldType::SizeType size;
>
> for( unsigned int d = 0; d < ImageDimension; d++ )
> {
> origin[d] = reader->GetOutput()->GetOrigin()[d];
> size[d] = reader->GetOutput()->GetLargestPossibleRegion().GetSize()[d];
> spacing[d] = reader->GetOutput()->GetSpacing()[d];
> }
> // Now include the temporal information. You can change this to whatever
> // resolution you like. You just need to make sure that
> // ( size[ImageDimension] - 1 ) * spacing[ImageDimension] = ( numberOfTimePoints - 1)
> //
> origin[ImageDimension] = 0;
> size[ImageDimension] = numberOfTimePoints - 1;
> spacing[ImageDimension] = 1;
>
> typedef itk::BSplineScatteredDataPointSetToImageFilter
> <TimeVaryingDeformationFieldPointSetType, TimeVaryingDeformationFieldType> BSplineFilterType;
> typename BSplineFilterType::Pointer bspliner = BSplineFilterType::New();
> bspliner->SetOrigin( origin );
> bspliner->SetSpacing( spacing );
> bspliner->SetSize( size );
> bspliner->SetGenerateOutputImage( XXXX );
> bspliner->SetNumberOfLevels( XXXX );
> bspliner->SetSplineOrder( XXXX );
> bspliner->SetNumberOfControlPoints( XXXX );
> bspliner->SetInput( fieldPoints );
> bspliner->Update();
>
>
>
>
> On Jan 4, 2012, at 2:52 AM, Kerstin Müller wrote:
>
>> Hi,
>>
>> yes correctly.
>>
>> 2012/1/3 Nicholas Tustison <ntustison at gmail.com>
>> Okay, I'm assuming that these points correspond in
>> time, correct? For example, point 937 in time point 0
>> corresponds to point 937 in time point 1, 2, 3, ...133,
>> right?
>>
>>
>>
>> On Jan 3, 2012, at 11:55 AM, Kerstin Müller wrote:
>>
>>> Hi,
>>>
>>> the basic problem I wanna solve:
>>>
>>> I'll have scattered points in 3D which vary over time, they describe a motion of a surface over time. They are not ordered in x-y-and z-dimension.
>>> Now I want to represent that motion by BSplines in order to generate a dense motion vector field defined on specific 3D voxel positions.
>>> I'll have 133 timesteps and ~960 sample points in each time step. Now I want to fit the BSpline to it and resample it.
>>>
>>> All the best,
>>>
>>> Kerstin
>>>
>>> 2012/1/3 Nicholas Tustison <ntustison at gmail.com>
>>> In that case, let's start with the basic problem set-up.
>>> Before, you described your problem as follows:
>>>
>>>
>>>>> I'm using the BSplineScatteredDataPointSetToImageFilter from the Insight Journal. However,
>>>>> I cannot find the correct parameter in order to make the filter work and does not crash during the evaluation.
>>>>> I'll have scattered 3-D points over time and I want to fit a 4-D Bspline field to that points. Afterwards I want to evaluate the Bspline on a dense volume grid to one time step.
>>>
>>>
>>> What do these scattered 3D+t points represent?
>>> Is it a curve, a time-varying scalar field, or something
>>> else?
>>>
>>>
>>
>>
>
>
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