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

Dženan Zukić dzenanz at gmail.com
Sat Apr 15 10:33:57 EDT 2017 

Hi Matias,

center of rotation should use physical units (millimeters).

Regards,
Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Sat, Apr 15, 2017 at 10:27 AM, Matias Montroull <matimontg at gmail.com>
wrote:

> Dzenan,
> The center of rotation is set to use milimeters or image coordinates?
> Thanks
>
> Matias
>
> On Apr 14, 2017 2:17 PM, "Dženan Zukić" <dzenanz at gmail.com> wrote:
>
>> 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->GetLargestPossible
>> Region().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>
>>>>> Sent from the ITK - Users mailing list archive
>>>>> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>>>>>
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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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>>
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