[Insight-users] Question regarding BSplineScatteredDataPointSetToImageFilter

[Kerstin Müller]

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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