[ITK-users] Rotating image results in last slices being half empty

Dženan Zukić dzenanz at gmail.com
Fri Apr 14 13:16:53 EDT 2017 

Here is the code I used:

#include <itkImageFileReader.h>
#include <itkImageFileWriter.h>
#include <itkResampleImageFilter.h>
#include <itkEuler3DTransform.h>

template< typename TImage >
itk::SmartPointer<TImage> ReadImage(const char *filename)
{
    typedef itk::ImageFileReader<TImage> ReaderType;
    typename ReaderType::Pointer r = ReaderType::New();
    r->SetFileName(filename);
    r->Update();
    return r->GetOutput();
}

template< typename TImage >
void WriteImage(itk::SmartPointer<TImage> out, const char *filename)
{
    typedef itk::ImageFileWriter<TImage> WriterType;
    typename WriterType::Pointer w = WriterType::New();
    w->SetInput(out);
    w->SetFileName(filename);
    //w->SetUseCompression(true);
    w->Update();
}

int main(int argc, char *argv[])
{
    const unsigned int dimension = 3;
    typedef itk::Image<short, dimension> ImageType;
    ImageType::Pointer inputImage = ReadImage<ImageType>("C:/CBCT.nrrd");

    typedef itk::ResampleImageFilter<ImageType, ImageType> FilterType;
    FilterType::Pointer FiltroResample = FilterType::New();
    FiltroResample->SetInput(inputImage);
    typedef itk::LinearInterpolateImageFunction<ImageType, double>
InterpolatorType;
    InterpolatorType::Pointer interpolator = InterpolatorType::New();
    FiltroResample->SetInterpolator(interpolator);
    FiltroResample->SetOutputDirection(inputImage->GetDirection());
    FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
    ImageType::SizeType inputSize =
inputImage->GetLargestPossibleRegion().GetSize();
    FiltroResample->SetSize(inputSize);
    const ImageType::SpacingType& inputSpacing = inputImage->GetSpacing();
    FiltroResample->SetOutputSpacing(inputSpacing);
    FiltroResample->SetDefaultPixelValue(-1000);
    typedef itk::Euler3DTransform<double> TransformType;
    TransformType::Pointer transform = TransformType::New();
    transform->SetRotation(0.2, 0.3, 0.5);
    double centro[3] = { 10,20,30 };
    transform->SetCenter(centro);
    FiltroResample->SetTransform(transform);
    FiltroResample->Update();
    WriteImage<ImageType>(FiltroResample->GetOutput(),
"C:/cbctResampled.nrrd");
}

On Fri, Apr 14, 2017 at 1:15 PM, Dženan Zukić <dzenanz at gmail.com> wrote:

> Hi Matias,
>
> I didn't compile to use with Slicer. I only open the input and output
> image in Slicer to visualize them.
>
> But making a Slicer CLI module is fairly easy. You can take a look at one
> <https://github.com/Slicer/Slicer/tree/master/Modules/CLI/AddScalarVolumes/>
> of the existing modules, docs
> <https://www.slicer.org/wiki/Documentation/Nightly/Developers/Modules> including
> extension wizard
> <https://www.slicer.org/wiki/Documentation/Nightly/Developers/ExtensionWizard>
> .
>
> Regards,
> Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>
> On Fri, Apr 14, 2017 at 12:26 PM, Matias <matimontg at gmail.com> wrote:
>
>> Thanks Dzenan. I actually use OrigenX and OrigenY to assign it to the DCM
>> tags. Just curious, how did you compile to use with Slicer?
>>
>> El jue., 13 de abr. de 2017 a la(s) 12:14, Dženan Zukić [via ITK - Users]
>> <[hidden email] <http:///user/SendEmail.jtp?type=node&node=38121&i=0>>
>> escribió:
>>
>>> Hi Matias,
>>>
>>> you are not using origenX or origenY after they are defined. But your
>>> program (with modifications to make it compile) works for me:
>>> [image: Inline image 1]
>>>
>>> Regards,
>>> Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)
>>>
>>> On Sat, Apr 8, 2017 at 6:08 PM, Matias <[hidden email]
>>> <http:///user/SendEmail.jtp?type=node&node=38116&i=0>> wrote:
>>> Hi, I'm rotating a volume (Using the Euler3DTransform) and the final set
>>> of slices are half black or empty. here's an example when rotating a volume
>>> of 10 slices: Am I missing something such as changing the origin or maybe
>>> computing the center incorrectly? (The center is passed as parameter from
>>> another program) And here's the code I'm using: typedef
>>> itk::ResampleImageFilter<ImageType, ImageType> FilterType;
>>> FilterType::Pointer FiltroResample = FilterType::New();
>>> FiltroResample->SetInput(reader->GetOutput()); typedef
>>> itk::LinearInterpolateImageFunction<ImageType, double >
>>> InterpolatorType; InterpolatorType::Pointer interpolator =
>>> InterpolatorType::New(); FiltroResample->SetInterpolator(interpolator);
>>> FiltroResample->SetOutputDirection(inputImage->GetDirection());
>>> FiltroResample->SetOutputOrigin(inputImage->GetOrigin());
>>> ImageType::SizeType inputSize = inputImage->GetLargestPossibleRegion().GetSize();
>>> FiltroResample->SetSize(inputSize); const ImageType::SpacingType&
>>> inputSpacing = inputImage->GetSpacing(); FiltroResample->SetOutputSpacing(inputSpacing);
>>> FiltroResample->SetDefaultPixelValue(-1000); typedef
>>> itk::Euler3DTransform< double > TransformType; //Transform
>>> TransformType::Pointer transform = TransformType::New(); double alfa, beta,
>>> gamma, centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z,
>>> origenX,origenY; gamma = atof(argv[2]); beta = atof(argv[3]); alfa =
>>> atof(argv[4]); centro_rotacion_X = atof(argv[5]); centro_rotacion_Y =
>>> atof(argv[6]); centro_rotacion_Z = atof(argv[7]); origenX = atof(argv[8]);
>>> origenY = atof(argv[9]); transform->SetRotation(gamma, beta, alfa); double
>>> centro[3] = { centro_rotacion_X, centro_rotacion_Y, centro_rotacion_Z };
>>> transform->SetCenter(centro); FiltroResample->SetTransform(transform);
>>> FiltroResample->Update();
>>> ------------------------------
>>> View this message in context: Rotating image results in last slices
>>> being half empty
>>> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081.html>
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>>
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>> ------------------------------
>> View this message in context: Re: [ITK-users] Rotating image results in
>> last slices being half empty
>> <http://itk-users.7.n7.nabble.com/Rotating-image-results-in-last-slices-being-half-empty-tp38081p38121.html>
>>
>> Sent from the ITK - Users mailing list archive
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>>
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>>
>> Visit other Kitware open-source projects at
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>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
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