[Insight-users] Question regarding BSplineScatteredDataPointSetToImageFilter
Nicholas Tustison
ntustison at gmail.com
Tue Jan 10 07:33:15 EST 2012
That's fine. I'm assuming, though, that they reside
in a bounding box of some sort, correct? Just
assign those points to their continuous coordinates
inside that bounding box.
On Jan 10, 2012, at 5:31 AM, Kerstin Müller wrote:
> But my sample points are on continous world coordinates between for example -70.0 and 70.0.
>
> Best,
>
> Kerstin
>
> 2012/1/10 Nicholas Tustison <ntustison at gmail.com>
> Since your points reside in an image, an easy
> parameterization is to assign their location to
> their x,y,z location in the image. Does that make
> sense?
>
>
> On Jan 10, 2012, at 5:19 AM, Kerstin Müller wrote:
>
>>
>> Hi,
>>
>> yes I also used your sample code, but still I got a heap corruption error. That's why I just wanted to try if my sample points are the problem.
>> Do I need to scale them to a range between [0 1]?
>>
>> Best Regards,
>>
>> Kerstin
>>
>> 2012/1/10 Nicholas Tustison <ntustison at gmail.com>
>> 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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