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

Matt McCormick matt.mccormick at kitware.com
Fri Sep 8 09:32:13 EDT 2017 

Hi Elli,

The OutputOrigin and OutputDirection may need to be set so the
sampling grids overlap.

HTH,
Matt

On Fri, Sep 8, 2017 at 9:13 AM, Pfaehler, EAG (ngmb)
<e.a.g.pfaehler at umcg.nl> wrote:
> 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> 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();
>
>
>
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> _______________________________________________
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> --
>
> 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.
>
> _______________________________________________
> 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://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:
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