[vtkusers] method to extract regions

[David Gobbi]

Hi Imre, Happy New Year!

I've read your email few times, and I feel that I must be missing some
important because there are several things that I don't understand about it.

The vtkImageConnectivityFilter is essentially just a connected component
filter.  In the output of this filter, all pixels outside the mask will be
colored black (they will have a value of zero).  So what I don't understand
about your email is why you say that non-rectangular regions are a
problem.  Are you just worried about the wasted memory?

 - David


On Sat, Jan 2, 2016 at 9:00 AM, Imre Goretzki <goretzki.imre at gmail.com>
wrote:

> Hey David,
>
> first of all: Happy new year :)
>
> I have some questions about your filter. First of all in part A of the
> attached image, is my understanding of extents, so if you have a region,
> you will get the x_min/x_max, y_min/y_max (and z_min/z_max for 3D). If you
> do not have rectangular regions than you could have some problems (see part
> A and B). In part B you see my mask. The red rectangle shows the case that
> the 4 corners of a 2D region cannot be directly checked, because the region
> that lies within this rectangle has little matches with the mask (none of
> the 4 corners are within the mask). The green rectangle has 3 out of 4
> edges that lie within the mask.
>
> Part C shows one of the worst cases of this approach (using extents)
> because there is so much space that does not belong to the actual region.
>
> My question: Is it possible to extend your filter to directly store the
> region data (for each region, for example as vtkImageData) if the
> extraction mode is set to "All"?
>
> - Imre
>
>
> Am 29.12.2015 um 13:27 schrieb Imre Goretzki:
>
> Hi David,
>
> thank you. I'll take a look at your class.
>
> Regards
> Imre
>
> Am 29.12.2015 um 13:07 schrieb David Gobbi:
>
> Hi Imre,
>
> I have a connectivity filter that works directly on images, it can label
> connected regions according to size and it should be much faster (probably
> 1000x) than doing voxel checks via polydata:
>
> https://github.com/dgobbi/AIRS/blob/master/ImageSegmentation/vtkImageConnectivityFilter.h
> I'll probably be contributing this filter to VTK sometime in the near
> future.
>
>  - David
>
>
> On Tue, Dec 29, 2015 at 4:02 AM, Imre Goretzki < <goretzki.imre at gmail.com>
> goretzki.imre at gmail.com> wrote:
>
>> Is there an easier way in ITK?
>>
>> Thanks
>> Imre
>>
>>
>> Am 28.12.2015 um 23:38 schrieb Imre Goretzki:
>>
>> Hey guys,
>>
>> I use the vtkPolyDataConnectivityFilter from polydata to extract several
>> different and more or less unknown regions.
>> My problem is that I want to extract regions from this filter, but if I
>> do this, the update process for all regions takes up to 10minutes:
>>
>> filter->SetExtractionModeToAllRegions();
>> filter->Update();
>> ...
>>
>> for (int i = 0; i < filter->GetNumberOfExtractedRegions(); i++)
>> {
>>     extractFilter->InitializeSpecifiedRegionList();
>>     extractFilter->AddSpecifiedRegion(i);
>>     extractFilter->Modified();
>>     extractFilter->Update();
>>     extractRegionData->DeepCopy(extractFilter->GetOutput());
>> }
>> extractFilter->InitializeSpecifiedRegionList();
>>
>> Background for this: I want to use the points of each region to check
>> whether they lie within an object in my binary
>> mask image. So the pipeline would be like this:
>>
>> 1) Get all Regions
>>     2) get region *i*
>>          3) get points of region *i*
>>              4) check if point *j* lies within the binary mask *B*     (
>> *B*_*j* == 255)
>>                  4a) if true then add region to the extractFilter and
>> break (-> next region *i*)
>>                  4b) if false then continue with next point *j*
>> 5) Mark all regions red (done easily)
>> 6) Mark some regions green that are above a specific size (can be
>> accessed with filter->GetRegionSizes() )
>> 7) Mark some regions yellow (the regions that are extracted during step
>> 1-4a)
>>
>> I do not know if the PolyDataConnectivityFilter is the right class for
>> this, I think it is.
>> If I store the extractRegionData in a vector, all regions have the same
>> number of points (which is kind of strange) but different number of cells
>> (region size == number of cells is correct).
>>
>> I would now try to get the points from the cells and check the binary
>> mask, because the
>>
>> vtkPolyData->GetNumberOfPoints()
>>
>> and
>>
>> vtkPolyData->GetPoint(pointCounter, point);
>>
>> are not working correctly in this scenario (all regions are extracted
>> because every single region has every point?
>> i did not verify my guess but I think there would be the problem)
>>
>> The binary mask is a vtkImageData, that could be transformed to
>> vtkPolyData.
>> The input image (already filtered with vtkMarchingCubes) and the binary
>> mask have the same dimensions (x,y,z).
>>
>> I hope you can imagine what I'm trying to do and have some tips for me,
>> if my approach is correct.
>>
>> Regards
>> Imre
>>
>>
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