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

Fri Apr 14 13:15:49 EDT 2017

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.
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
> ------------------------------
> If you reply to this email, your message will be added to the discussion
> below:
> http://itk-users.7.n7.nabble.com/Rotating-image-results-in-
> last-slices-being-half-empty-tp38081p38116.html
> To unsubscribe from Rotating image results in last slices being half
> empty, click here.
> NAML
> <http://itk-users.7.n7.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml>
> --
> Matias
>
> ------------------------------
> 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
> <http://itk-users.7.n7.nabble.com/> at Nabble.com.
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20170414/28966a68/attachment.html>