[Insight-users] VectorImage Orientation from NRRD

[Gordon Kindlmann]

This patch confuses two independent issues:

1) turning on ITK_USE_ORIENTED_IMAGE_DIRECTION.  It sounds like  
you're happy with this, specifically the resulting enhancements in  
orientation behavior to itkVectorImage.  Great.

2) itkNrrdImageIO.cxx's conversion of explicitly RAS orientation to  
the implicit LPS orientation of ITK.  You're understandably not happy  
with this.

The patch you suggest confuses the issues by disabling (2) when (1)  
is off, but the two things are completely unrelated, so I'm not going  
to commit this.

The real solution is to enable explicit run-time control of whether  
the RAS -> LPS orientation conversion happens inside itkNrrdImageIO.   
This would replace how you used ITK_USE_ORIENTED_IMAGE_DIRECTION in  
your patch, with some new member variable (and would use "if ()"  
instead of "#ifndef").

Before I try anything like that, though, I need others to comment on

1) Whether there are any existing examples of state variables in file  
input, so that at run-time users can vary the handling of data after  
its read from disk, and before its returned to ITK.

2) Documentation of ITK's use of LPS for 3-D orientation  
specification.  Is it really the policy, or not?

Gordon

On Oct 19, 2008, at 9:31 PM, Daniel Betz wrote:

> Hello Gordon,
>
> as far as I can see are the following files affected
>
> itkNrrdImageIO.cxx
> itkNiftiImageIO.cxx
> itkAnalyzeImageIO.cxx
> itkGE4ImageIO.cxx
> itkGE5ImageIO.cxx
> itkGEAdwImageIO.cxx
> itkPolygonGroupSpatialObjectXMLFile.cxx
> itkSiemensVisionImageIO.cxx
>
>
> With the new oriented itk::Image it is actually very easy to get
> a file correctly loaded. With the commit to itkVectorImage.txx a
> few ours ago I need only three "#ifndef" in itkNrrdImageIO.cxx and
> my test program from the beginning of this thread passed.
>
> <diff>
> Index: Code/IO/itkNrrdImageIO.cxx
> ===================================================================
> RCS file: /cvsroot/Insight/Insight/Code/IO/itkNrrdImageIO.cxx,v
> retrieving revision 1.38
> diff -u -r1.38 itkNrrdImageIO.cxx
> --- Code/IO/itkNrrdImageIO.cxx  16 May 2007 19:44:55 -0000  1.38
> +++ Code/IO/itkNrrdImageIO.cxx  19 Oct 2008 23:48:47 -0000
> @@ -442,6 +442,7 @@
>        case nrrdSpacingStatusDirection:
>          if (AIR_EXISTS(spacing))
>            {
> +#ifndef ITK_USE_ORIENTED_IMAGE_DIRECTION
>            // only set info if we have something to set
>            switch (nrrd->space)
>              {
> @@ -464,6 +465,7 @@
>                // to LPS is well-defined
>                break;
>              }
> +#endif
>            this->SetSpacing(axii, spacing);
>
>            for (unsigned int saxi=0; saxi < nrrd->spaceDim; saxi++)
> @@ -496,6 +498,7 @@
>          {
>          spaceOrigin[saxi] = nrrd->spaceOrigin[saxi];
>          }
> +#ifndef ITK_USE_ORIENTED_IMAGE_DIRECTION
>        switch (nrrd->space)
>          {
>          // convert non-LPS coords into LPS coords, when we can
> @@ -514,6 +517,7 @@
>            // to LPS is well-defined
>            break;
>          }
> +#endif
>        for (unsigned int saxi=0; saxi < nrrd->spaceDim; saxi++)
>          {
>          this->SetOrigin(saxi, spaceOrigin[saxi]);
> @@ -641,13 +645,16 @@
>        case nrrdSpaceRightAnteriorSuperior:
>        case nrrdSpaceLeftAnteriorSuperior:
>        case nrrdSpaceLeftPosteriorSuperior:
> +#ifndef ITK_USE_ORIENTED_IMAGE_DIRECTION
>          // in all these cases we could convert
>          EncapsulateMetaData<std::string>(thisDic, std::string(key),
> -                                         std::string( airEnumStr 
> (nrrdSpace,
> nrrdSpaceLeftPosteriorSuperior )));
> +                                         std::string( airEnumStr 
> (nrrdSpace,
> +                                          
> nrrdSpaceLeftPosteriorSuperior )));
>          break;
>        default:
>          // we're not coming from a space for which the conversion
>          // to LPS is well-defined
> +#endif
>          EncapsulateMetaData<std::string>(thisDic, std::string(key),
>                                           std::string(val));
>          break;
> </diff>
>
> Regards
> Daniel Betz
>