[ITK] [ITK-users] Merging segmentation masks in different region of interests

[Bill Lorensen]

Try PasteImageFilter:
http://itk.org/Wiki/ITK/Examples/ImageProcessing/PasteImageFilter


On Tue, Jan 26, 2016 at 9:33 AM, Bradley Lowekamp <brad at lowekamp.net> wrote:
> Hello,
>
> In general You can not efficiently iterate on pixel on an Image in Python or
> another scripting language. There are however filters which can  efficiently
> accomplish similar things.
>
> You should look into the ResampleImageFilter[1], and the
> PasteImageFilter[2].
>
> The most logical way to is to use the ResampleImageFilters’s
> SetReferenceImage parameter. Use an image to represent the domain of the
> composite images you have ( or the original image). Then resample each
> segmentation on the reference image. Then you can use the AndImageFilter or
> overloaded operators to compose the images together.
>
> It’s also possible to convert your segmented images into LabelMaps, so that
> they are represented  as run-length-encoded elements. This can be more
> efficient for some operations, but it’s a bit more tricky.
>
> HTH,
> Brad
>
> [1]
> http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ResampleImageFilter.html
> [2]
> http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1PasteImageFilter.html
>
> On Jan 26, 2016, at 9:21 AM, Alberto Bert <bert.alberto at gmail.com> wrote:
>
> Thanks Tim,
>
> according to the documentation, RegionOfInterestImageFilter should do what
> you say, that is why I tried to used it. Unfortunately, it seems not to keep
> the original logical references...
>
> I am not sure I can efficiently do what you suggest with SimpleITK, but if
> it turns out to be the only way, I guess I will need to switch to the
> original ITK. I hoped there was a way to do it without a pixel by pixel
> copy…
>
> Any other suggestions?
>
> Thanks!
> Alberto
>
> On 26 Jan 2016, at 11:31, Timothee Evain <tevain at telecom-paristech.fr>
> wrote:
>
> Hello Alberto,
>
> If I remember well, the RegionOfInterestImageFilter keeps the subparts in
> the same physical space, i.e. a same index will get you the same pixel/voxel
> in the ROI as in the original. So I would use an iterator to create your
> full mask image. Something like :
>
> itk::Image<Type,Dim>::Pointer FullMask=itk::Image<Type,Dim>::New();
> FullMask->SetRegions(OriginalImage->GetLargestPossibleRegion());
> FullMask->Allocate();
>
> itk::ImageRegionIteratorWithIndex<itk::Image<Type,Dim>>
> Iter(FullMask,FullMask->GetLargestPossibleRegion());
> Iter.GoToBegin();
>
> while(!Iter.IsAtEnd())
> {
>  itk::Index<Dim> CurrentPoint=Iter.GetIndex();
>  if(//There you test the index to know from which subimage it belong//)
>  {
>    Iter.Set(SubImage->GetPixel(CurrentPoint));
>  }
>  ++Iter;
> }
>
> HTH,
>
> Tim
>
> ----- Mail original -----
> De: "Alberto Bert" <bert.alberto at gmail.com>
> À: "ITK Users" <insight-users at itk.org>
> Envoyé: Mardi 26 Janvier 2016 11:07:49
> Objet: [ITK] [ITK-users] Merging segmentation masks in different region of
> interests
>
> Hi,
>
> I have several rectangular regions of interest from a single image
> (extracted using RegionOfInterestImageFilter), and I am processing one at a
> time to extract from each of them a segmentation masks (image of labels with
> 0 or 1). Finally, I would need to “merge” (i.e. “combine” or “and”) the
> various ROI masks (different size and origin) in a single mask having the
> same size and origin of the original image. Let’s say I would need to “put
> back in the right place” the ROI masks.
>
> The AndImageFilter does not allow me to combine the various ROI masks
> ("Inputs do not occupy the same physical space!”). I browsed the
> documentation but I could not find a viable solution...
>
> I am currently using SimpleITK.
>
> Can you help me please?
>
> Thanks a lot!
> Best
> Alberto
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