[ITK-dev] [ITK] problems itk resample filter

[Pfaehler, EAG (ngmb)]

Thanks, I did this. Now I get an image, with the desired size, but there all image values are 0. I get the same when I use linear interpolation…
Does someone know, what could be the reason?

Thanks in advance,

Regards

Elli

Van: Samuel Gerber [mailto:samuel.gerber at kitware.com]
Verzonden: vrijdag 8 september 2017 14:51
Aan: Pfaehler, EAG (ngmb)
CC: insight-developers at itk.org
Onderwerp: Re: [ITK] [ITK-dev] problems itk resample filter

I believe you might need to call resizeFilter2->Update()



On Fri, Sep 8, 2017 at 8:32 AM, Pfaehler, EAG (ngmb) <e.a.g.pfaehler at umcg.nl<mailto:e.a.g.pfaehler at umcg.nl>> wrote:
Dear all,

I would need some help to resample so that it has isotropic voxels in the end.
For this, I wanted to use the Nearest Neighbor Interpolator and the ResampleFilterType.
My code is running, but the output of the filter has always the dimensions [0 0 0], so is not existent.
What am I doing wrong? (see code below)

Thanks in advance!
Elli

typedef itk::NearestNeighborInterpolateImageFunction<ImageType, T> NearestNeighborInterpolatorType;
typedef itk::ResampleImageFilter<ImageType, ImageType>    ResampleFilterType;
typedef itk::AffineTransform <double, 3> TransformType;
//use nearest neighbor interpolation
typename NearestNeighborInterpolatorType::Pointer nearestNeighborInterpolator = NearestNeighborInterpolatorType::New();
typename ImageType::DirectionType direction;
typename TransformType::Pointer transform = TransformType::New();
    //transform->SetIdentity();
typedef itk::NearestNeighborInterpolateImageFunction<ImageType, double> InterpolatorType;
//typedef itk::LinearInterpolateImageFunction<ImageType, double >  InterpolatorType;
typename InterpolatorType::Pointer interpolator = InterpolatorType::New();

typename ResampleFilterType::Pointer resizeFilter2 = ResampleFilterType::New();
resizeFilter2->SetTransform(transform);

resizeFilter2->SetInterpolator( interpolator );
resizeFilter2->SetDefaultPixelValue(0);
    //resizeFilter2->SetInterpolator();

const typename ImageType::SpacingType& inputSpacing = image->GetSpacing();
//sampling
double outputSpacing[3];
    // Fetch original image size
   const typename ImageType::RegionType& inputRegion = image->GetLargestPossibleRegion();
   const typename ImageType::SizeType& inputSize = inputRegion.GetSize();
    unsigned int oldWidth = inputSize[0];
    unsigned int oldHeight = inputSize[1];
    unsigned int oldDepth = inputSize[2];
    unsigned int newWidth;
    unsigned int newHeight;
    unsigned int newDepth;
       //get the new height etc of image
       double minimum = inputSpacing[0];
       if (inputSpacing[1]<minimum){
           minimum = inputSpacing[1];
       }
       if (inputSpacing[2] < minimum){
           minimum = inputSpacing[2];
       }
       outputSpacing[0] = minimum;
       outputSpacing[1] = minimum;
       outputSpacing[2] = minimum;
       newWidth = (double) oldWidth * inputSpacing[0]/minimum;
       ewHeight = (double) oldHeight * inputSpacing[1]/minimum;
       newDepth = (double) oldDepth * inputSpacing[2]/minimum;
       // Set the output spacing as specified on the command line
      resizeFilter2->SetOutputSpacing(outputSpacing);
    // Set the computed size
    itk::Size<3> outputSize = { {newWidth, newHeight, newDepth} };
    resizeFilter2->SetSize(outputSize);
    // Specify the input for the resamplers
    resizeFilter2->SetInput(image);
    ImageType::Pointer imageNew = resizeFilter2->GetOutput();
   const typename ImageType::RegionType& outputRegion = imageNew->GetLargestPossibleRegion();
       const typename ImageType::SizeType& outputSize2 = outputRegion.GetSize();

________________________________
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

_______________________________________________
Powered by www.kitware.com<http://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://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-developers

_______________________________________________
Community mailing list
Community at itk.org<mailto:Community at itk.org>
http://public.kitware.com/mailman/listinfo/community



--
Samuel Gerber
R&D Engineer
Kitware, Inc.
________________________________
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.

The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-developers/attachments/20170908/96f64b2f/attachment-0001.html>