[Insight-users] Question on itk::ResampleImageFilter for up and downsampling images

[Bill Lorensen]

You can do all of that using similar logic that is in the shrink filter.

On Thu, Dec 3, 2009 at 11:41 AM, Lodron, Gerald
<Gerald.Lodron at joanneum.at> wrote:
>
> I already saw that but i want to allow upscaling as well as downscaling (and i think the shrink filter is only for one direction). The other thing is that i want also to specify the up/downscaling per direction (anisotropic, the shrink filter makes it isotropic). I read DICOM images so i should not change the position of the image at all (the images which should be down/upscaled are registered and should also be registered after  up/downscaling).
>
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: Bill Lorensen [mailto:bill.lorensen at gmail.com]
> Gesendet: Donnerstag, 03. Dezember 2009 17:36
> An: Lodron, Gerald
> Cc: insight-users at itk.org
> Betreff: Re: [Insight-users] Question on itk::ResampleImageFilter for up and downsampling images
>
> Gerald,
>
> Another approach we used in itkShrinkImageFIlter modifies the origin of the output so that the center's of the input and output align. I think this is what you want. Here is a snippet from Code/BasicFilters/itkShrinkImageFilter.txx. In your case, the input and output start index should be 0.
>
>  // Compute origin offset
>  // The physical center's of the input and output should be the same
>  ContinuousIndex<double, TOutputImage::ImageDimension> inputCenterIndex;
>  ContinuousIndex<double, TOutputImage::ImageDimension> outputCenterIndex;
>  for (i = 0; i < TOutputImage::ImageDimension; i++)
>    {
>    inputCenterIndex[i] = inputStartIndex[i] + (inputSize[i] - 1) / 2.0;
>    outputCenterIndex[i] = outputStartIndex[i] + (outputSize[i] - 1) / 2.0;
>    }
>
>  typename TOutputImage::PointType inputCenterPoint;
>  typename TOutputImage::PointType outputCenterPoint;
>  inputPtr->TransformContinuousIndexToPhysicalPoint(inputCenterIndex,
> inputCenterPoint);
>  outputPtr->TransformContinuousIndexToPhysicalPoint(outputCenterIndex,
> outputCenterPoint);
>
>  typename TOutputImage::PointType outputOrigin = outputPtr->GetOrigin();
>  outputOrigin = outputOrigin + (inputCenterPoint - outputCenterPoint);
>  outputPtr->SetOrigin(outputOrigin);
>
>
>
> On Thu, Dec 3, 2009 at 11:07 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>> Sorry I read your e-mail too quickly.
>> Attached is code I wrote a while back. It keep the same origin, but
>> adjusts the spacing.
>>
>> Bill
>>
>> On Thu, Dec 3, 2009 at 10:37 AM, Lodron, Gerald
>> <Gerald.Lodron at joanneum.at> wrote:
>>> No, i am already using 3.16 and i did not changed such a flag.
>>>
>>> Best regards
>>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: Bill Lorensen [mailto:bill.lorensen at gmail.com]
>>> Gesendet: Donnerstag, 03. Dezember 2009 16:35
>>> An: Lodron, Gerald
>>> Cc: insight-users at itk.org
>>> Betreff: Re: [Insight-users] Question on itk::ResampleImageFilter for
>>> up and downsampling images
>>>
>>> What version of itk are you using? Prior to itk 3.16 there was an issue with the location of sample points. IN 3.16 we changed the default for ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY to be ON.
>>> This made itk consistent with the behavior described in the software guide. It also corrected the 1/2 pixel offset you are seeing when down/up sampling.
>>>
>>> If you are using 3.14, you can set
>>> ITK_USE_CENTERED_PIXEL_COORDINATES_CONSISTENTLY ON when you run cmake.
>>>
>>> Bill
>>>
>>> On Thu, Dec 3, 2009 at 9:49 AM, Lodron, Gerald <Gerald.Lodron at joanneum.at> wrote:
>>>>
>>>>
>>>> Hello,
>>>>
>>>> I want to write a code to reduce/increase the resolution of an image and i am using the itk::ResampleImageFilter. The code works fine but there is one small problem: When i compare the original and the resampled image with a checkerboard i see that the images are not registered any more (so there must be a problem with the origin). How should i set the origin? Here my code:
>>>>
>>>> Input:
>>>>
>>>> Int *iDownsampleFactor;                                 // = e.g.
>>>> {2,0.5,4}; Itk::OrientedImage<PixelType ,3>::Pointer image;
>>>>
>>>> Code:
>>>>
>>>> Typedef itk::ResampleImageFilter<InputImageType, OutputImageType,
>>>> InterpolationPrecisionType> ResampleType;
>>>>
>>>> ResampleType::Pointer  resampler = ResampleType::New();
>>>>
>>>> OutputImageType::SpacingType                    Spacing;
>>>> OutputImageType::PointType                      Origin;
>>>> OutputImageType::DirectionType          Direction =
>>>> image->GetDirection(); OutputImageType::SizeType
>>>> Size; OutputImageType::RegionType::IndexType  Index =
>>>> image->getLargestPossibleRegion().GetIndex();
>>>>
>>>> For (int i=0; i<3; i++)
>>>> {
>>>>        Spacing[i] = image->GetSpacing()[i] * iDownsampleFactor[i] ;
>>>>        Origin[i] = image->GetOrigin()[i];//????????????????????
>>>>        Size[i] =
>>>> image->GetLargestPossibleRegion().GetSize()[i]/iDownsampleFactor[i]
>>>> image->;
>>>> }
>>>>
>>>> Resampler->SetInput(image);
>>>> resampler->SetOutputSpacing( Spacing ); SetOutputOrigin(  Origin  );
>>>> resampler->SetOutputDirection(  Direction  ); SetSize( Size );
>>>> resampler->SetOutputStartIndex(  Index );
>>>>
>>>> Output = resampler->GetOutput();        //Wrong
>>>> alignment/registration to input
>>>>
>>>> Best regards
>>>>
>>>>
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>>
>