[Insight-users] Problems with fixedReader->Update();

[Bill Lorensen]

You should not store the deformation as unsigned char. unsigned char
can only represent integral values from 0 to 255. Use float and save
the data in meta format (.mhd). Paraview reads meta I believe.

Bill


2009/7/22 motes motes <mort.motes at gmail.com>:
> Your are correct:
>
>   typedef unsigned char
> PixelType;
>   typedef itk::Point<PixelType, ImageDimension>            PointType;
>   typedef itk::Vector<PixelType, ImageDimension>          VectorType;
>
> solved the problem. I looked at the examples in the itksoftwareguide and
> they used float for the point and vectortype so assumed incorrectly that
> this was unrelated.
>
> Another thing. The deformation field looks like this:
>
> http://img18.imageshack.us/img18/5054/deform.jpg
>
> and like this when I open it with paraview:
>
> http://img23.imageshack.us/img23/5054/deform.jpg
>
> If I use the calculator to change to vector nothing happens.
>
> In the itkSoftwareGuide it says:
>
> "It may be also desirable to write the deformation field as an image of
> vectors. This can be done
> with the following code."
>
>         typedef itk::ImageFileWriter< DeformationFieldType >
> FieldWriterType;
>         FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
>         fieldWriter->SetFileName( argv[4] );
>         fieldWriter->SetInput( filter->GetOutput() );
>         fieldWriter->Update();
>
> "Note that the file format used for writing the deformation field must be
> capable of representing
> multiple components per pixel. This is the case for the MetaImage and VTK
> file formats for
> example."
>
>
> As I understand I need to store the deformation field in another format than
> PNG (unless this format supports "multiple components per pixel") to make
> the conversion to vectors in paraview. Is that correct?
>
>
>
>
> 2009/7/22 Bill Lorensen <bill.lorensen at gmail.com>
>>
>> The source code he posted shows that he is trying to write the type:
>> typedef itk::Image<VectorType, ImageDimension>
>>                 DeformationFieldType;
>> where VectorType is float.
>>
>> 2009/7/21 Ramón Casero Cañas <ramon.casero at comlab.ox.ac.uk>:
>> > Bill Lorensen wrote:
>> >>
>> >> The thrown exception is very clear...
>> >> Exception thrown
>> >>
>> >> itk::ExceptionObject (00CAE438)
>> >> Location: "void __thiscall itk::PNGImageIO::WriteSlice(const class
>> >> std::basic_string<char,struct std::char_traits<c
>> >> har>,class std::allocator<char> > &,const void *)"
>> >> File: ..\..\..\Code\IO\itkPNGImageIO.cxx
>> >> Line: 473
>> >> Description: PNG supports unsigned char and unsigned short
>> >>
>> >> You must choose an output file type that supports the type you are
>> >> trying to write. I would suggest .mhd. If you can think of a better
>> >> exception message, please let us know.
>> >
>> >
>> > Hi Bill,
>> >
>> > Thaks for your reply. I don't think we have expressed any issues about
>> > the
>> > exception itself, but motes said that he's defining the PixelType as
>> > unsigned char/short, yet writing the data fails.
>> >
>> > Oh! Is this a problem with any of the intermediate steps changing the
>> > pixel
>> > type?
>> >
>> > On a related note: Where is the method GetComponentType() called by
>> > PNGImageIO::WriteSlice declared? I'm sure it's very obvious where it is,
>> > but
>> > I have been searching for it in the ITK code (grep and [1]), and I
>> > couldn't
>> > find it.
>> >
>> > [1] http://www.itk.org/Doxygen/html/functions.html
>> >
>> > Cheers,
>> >
>> > R.
>> >
>> > --
>> > Ramón Casero Cañas, DPhil
>> >
>> > Computational Biology, Computing Laboratory
>> > University of Oxford
>> > Wolfson Building, Parks Rd
>> > Oxford OX1 3QD
>> >
>> > tlf     +44 (0) 1865 610807
>> > web     http://web.comlab.ox.ac.uk/people/Ramon.CaseroCanas
>> > photos  http://www.flickr.com/photos/rcasero/
>> >
>
>