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

[Alberto Bert]

With the PasteImageFilter seems to be working.

Thank you all !

Alberto

> On 26 Jan 2016, at 16:57, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> 
> 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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