[Insight-developers] Removal of itkWarpJacobianDeterminantFilter.h

[Tom Vercauteren]

Hi Hans,

Thanks for the heads up!

I remember discussing the DeformationFieldJacobianDeterminantFilter
issue some time ago. See the following posts:
http://www.itk.org/pipermail/insight-users/2007-July/022858.html
http://www.itk.org/pipermail/insight-users/2007-July/022866.html

Adding a flag to DeformationFieldJacobianDeterminantFilter and
removing WarpJacobianDeterminantFilter is OK for me. The only thing
that bugs me is that the default behavior of
DeformationFieldJacobianDeterminantFilter (i.e. the current one) would
be to compute a somewhat "meaningless" quantity. And as far as I
understand it, it might not be possible to set
m_GenerateEffectiveJacobianDeterminant to true by default since this
would break backwards compatibility.

However, if we consider the current behavior of
DeformationFieldJacobianDeterminantFilter to be a bug (which I do),
changing the default behavior should IMHO not be considered as
breaking backwards compatibility. Other people might have a different
feeling about that though:
http://www.vtk.org/Wiki/ITK_Backward_Compatibility_Open_Discussion

Another option might be to;
1) Allow both behaviors in WarpJacobianDeterminantFilter
2) Set the default behavior of WarpJacobianDeterminantFilter to be
m_GenerateEffectiveJacobianDeterminant=true
3) Put WarpJacobianDeterminantFilter in the main ITK tree (not in Review)
4) Deprecate DeformationFieldJacobianDeterminantFilter

The advantage of this would also be that the name of the filter
WarpJacobianDeterminantFilter would better represent the default
behavior.

Regards,

Tom

On Fri, Jul 11, 2008 at 3:29 AM, Johnson, Hans <hans-johnson at uiowa.edu> wrote:
> Luis,
>
> I see that you are adding the Diffeomorphic Demons to ITK Review.  GREAT!
>  I've been working with that code for a few months now, and it really is a
> nice addition to ITK.
>
> I was reviewing the code in itkWarpJacobianDeterminantFilter.h, and
> comparing it against itkDeformationFieldJacobianDeterminantFilter.h  It
> seems that all the functionality of the WarpJacobianDeterminant can be added
> to the DeformationFieldJacobianDeterminant with little effort.  I've
> attached my local copies that have the necessary changes (it passes
> regression test for being backwards compatible, and it address the comment
> in itkDeformationFieldJacobianDeterminantFilter.
>
> NOTE 1:  itkWarpJacobianDeterminant and
> itkDeformationFieldJacobianDeterminant have different template
> parameterization, but this seems to be a style choice.
> NOTE 2: I've added another private member variable to precompute the
> 0.5*weightings.  This is not a necessary change for getting the new
> functionality.
>
> I'd like to know your thoughts if this seems like a reasonable change.  If
> you agree, I will work through committing the enhanced version of
> itkDeformationFieldJacobianDeterminant, and removing the
> itkWarpJacobianDeterminantFilter from itk Review.
>
> Thanks,
> Hans
>
> ===== Patch ===
> Index: itkDeformationFieldJacobianDeterminantFilter.h
> ===================================================================
> RCS file:
> /cvsroot/Insight/Insight/Code/BasicFilters/itkDeformationFieldJacobianDeterminantFilter.h,v
> retrieving revision 1.3
> diff -b -r1.3 itkDeformationFieldJacobianDeterminantFilter.h
> 6c6
> <   Date:      $Date: 2005-08-24 18:00:04 $
> ---
>>   Date:      $Date: 2005/08/24 18:00:04 $
> 42,44c42,44
> <  * should be 1.0. In general, in order to obtain the effective deformation
> <  * Jacobian determinant, 1.0 must be added to each Jacobian value in the
> <  * output.
> ---
>>  * is 1.0.  In order to compute the effective deformation Jacobian
>> determinant
>>  * 1.0 must be added to the diagonal elements of Jacobian prior to taking
>> the derivative.
>>  * i.e. det([ (1.0+dx/dx)  dx/dy dx/dz ; dy/dx (1.0+dy/dy) dy/dz; dz/dx
>> dz/dy (1.0+dz/dz) ])
> 240d239
> <     unsigned i, j;
> 243c242
> <     for (i = 0; i < ImageDimension; ++i)
> ---
>>     for (unsigned int i = 0; i < ImageDimension; ++i)
> 245c244
> <       for (j = 0; j < VectorDimension; ++j)
> ---
>>       for (unsigned int j = 0; j < VectorDimension; ++j)
> 247,248c246
> <         J[i][j] = m_DerivativeWeights[i]
> <                   * 0.5 * (it.GetNext(i)[j] - it.GetPrevious(i)[j]);
> ---
>>         J[i][j] = m_HalfDerivativeWeights[i] * (it.GetNext(i)[j] -
>> it.GetPrevious(i)[j]);
> 249a248,251
>>       if(m_GenerateEffectiveJacobianDeterminant)
>>         {
>>         // add one on the diagonal to consider the warping and not only
>> the deformation field
>>         J[i][i] += 1.0;
> 251,252c253,255
> <
> <     return vnl_det(J);
> ---
>>       }
>>     const TRealType value=vnl_det(J);
>>     return value;
> 256a260,261
>>   /** Pre-compute 0.5*m_DerivativeWeights since that is the only thing
>> used in the computations. */
>>   TRealType
>> m_HalfDerivativeWeights[itk::GetImageDimension<TInputImage>::ImageDimension];
> 267a273
>>   bool m_GenerateEffectiveJacobianDeterminant;
> Index: itkDeformationFieldJacobianDeterminantFilter.txx
> ===================================================================
> RCS file:
> /cvsroot/Insight/Insight/Code/BasicFilters/itkDeformationFieldJacobianDeterminantFilter.txx,v
> retrieving revision 1.3
> diff -b -r1.3 itkDeformationFieldJacobianDeterminantFilter.txx
> 6c6
> <   Date:      $Date: 2006-01-11 19:43:31 $
> ---
>>   Date:      $Date: 2006/01/11 19:43:31 $
> 37d36
> <   unsigned int i;
> 40c39
> <   for (i = 0; i < ImageDimension; i++)
> ---
>>   for (unsigned int i = 0; i < ImageDimension; i++)
> 43a43
>>     m_HalfDerivativeWeights[i] = static_cast<TRealType>(0.5);
> 44a45
>>   m_GenerateEffectiveJacobianDeterminant=false;//Needs to be false for
>> backwards compatibility;
> 58a60
>>       m_HalfDerivativeWeights[i] = 0.5*data[i];
> 79a82
>>       m_HalfDerivativeWeights[i] = static_cast<TRealType>(0.5);
> 156a160
>>       m_HalfDerivativeWeights[i]=0.5*m_DerivativeWeights[i];
> 240a245,248
>>   os << indent << "m_HalfDerivativeWeights = ";
>>   for (i = 0; i < ImageDimension; i++)
>>     { os << m_HalfDerivativeWeights[i] << " "; }
>>   os << std::endl;
> 244a253,254
>>   os << indent << "m_GenerateEffectiveJacobianDeterminant = " <<
>> m_GenerateEffectiveJacobianDeterminant
>>      << std::endl;
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