[Insight-users] Get and Set itk Origin

[jef vdmb]

I included some code (used in a templated function) to clarify my question:

    // ImageTypes
    typedef itk::Image<PixelType, Dimension> InputImageType;
        
    // Read
    typedef itk::ImageFileReader<InputImageType> InputReaderType;
    typename InputReaderType::Pointer reader = InputReaderType::New();
    reader->SetFileName( m_InputFileName);
    reader->Update();
    typename InputImageType::Pointer input= reader->GetOutput();
    std::cout<<"Input Origin is "<<input->GetOrigin()<<std::endl;
    
    // Filter
    typedef   itk::MirrorPadImageFilter<InputImageType, InputImageType> MirrorPadImageFilterType;
    typename  MirrorPadImageFilterType::Pointer mirrorFilter=MirrorPadImageFilterType::New();
    mirrorFilter->SetInput(input);
    typename InputImageType::SizeType size;
    size.Fill(10);
    mirrorFilter->SetPadLowerBound(size);
    mirrorFilter->Update();

    // Output
    typename InputImageType::Pointer output=mirrorFilter->GetOutput();
    std::cout<<"Output Origin is "<<output->GetOrigin()<<std::endl;
    output->Update();
    std::cout<<"Output Origin is "<<output->GetOrigin()<<std::endl;

    // Write
    typedef itk::ImageFileWriter<InputImageType> WriterType;
    typename WriterType::Pointer writer = WriterType::New();
    writer->SetFileName(m_ArgsInfo.output_arg);
    writer->SetInput(output);
    writer->Update();

Output of this piece of code is 

Input Origin is [0, 0, -282]
Output Origin is [0, 0, -282]
Output Origin is [0, 0, -282]


However the written output has header file:

ObjectType = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 1 0 0 0 1 0 0 0 1
Offset = -20 -20 -302
CenterOfRotation = 0 0 0
AnatomicalOrientation = RAI
ElementSpacing = 2 2 2
DimSize = 245 186 292
ElementType = MET_FLOAT
ElementDataFile = air_padded.raw

In this header, the origin HAS changed according to the padding size at the lower end?

Thank you in advance for your help,
Jef



> Date: Tue, 15 Sep 2009 08:22:50 -0400
> Subject: Re: [Insight-users] Get and Set itk Origin
> From: bill.lorensen at gmail.com
    Send
> To: jvdmb at hotmail.com
> CC: insight-users at itk.org
> 
> Maybe you should post some code. What you describe should work.
> 
> Bill
> 
> On Tue, Sep 15, 2009 at 5:32 AM, jef vdmb <jvdmb at hotmail.com> wrote:
> > Hi,
> >
> > I am having a hard time understanding the way meta data like the image
> > origin is updated after a pipeline execution.
> >
> > My situation is the following:
> >
> > * an image is read
> > * next passed as input to a filter (in this case MirrorPadImageFilter, but I
> > have seen it for others as well)
> > * the filter is updated (->Update());
> > * the output retrieved using ->GetOutput()
> >
> > The initial input had origin (0,0,0). The output however should have an
> > origin different from zero (with the parameters I used for the
> > MirrorPadImageFilter). When the output is interrogated for its origin
> > (->GetOrigin() ), it (wrongly) shows all zeros. When writing the image
> > afterwards, it was written with the correct origin ( offset field of the
> > .mhd image format).
> >
> > It would seem my output image is not yet updated at the time I performed the
> > ->GetOrigin(). The last filter was however explicitly updated just before
> > and even an "->Update()" on the output image itself doesn't modify this
> > behaviour.
> >
> > I would like to retrieve the origin for further processing but seem to end
> > up with the uninitialized (0,0,0).  I would appreciate any suggestions on
> > how to assure the meta information is fully updated.
> >
> > Regards,
> > Jef
> >
> >
> >
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