[vtkusers] method to extract regions
David Gobbi
david.gobbi at gmail.com
Sat Jan 2 14:48:48 EST 2016
Thanks, that helps. Here is my understanding so far:
1) The mask is, originally, a polydata contour.
2) The mask indicates the regions you do not want.
3) The mask will be converted into a binary image before use.
What I still need to know is:
3) Will some regions be partially within and partially outside the mask?
Or will they always be entirely within or entirely outside?
The vtkImageConnectivityFilter takes two inputs: the first input is just an
image (of course) and the second input (which is optional) is an image
stencil (essentially a binary image). There is a filter called
vtkPolyDataToImageStencil which can be used create this second input from a
vtkPolyData object.
- David
On Sat, Jan 2, 2016 at 12:32 PM, Imre Goretzki <goretzki.imre at gmail.com>
wrote:
> I've drawn another image you could look at. The left image is the input
> data from which I would like to extract the regions. Here every region I
> would like to keep is painted green. The other two regions, that are
> painted red, have points that are located inside a region in the binary
> mask.
>
>
> For all points *P* in all regions *R* of image 1 with binary mask *B*
>
> If B_P == 255
> color region *R* red
> else
> color region *R* green
>
> - Imre
>
>
> Am 02.01.2016 um 20:16 schrieb David Gobbi:
>
> Sorry, but I still don't follow your explanation. I have some vague idea
> of what you are trying to do, but I don't understand well enough to give
> you any concrete advice. Can you try focussing on just one specific aspect
> of the problem, and then once I've understood that one aspect, we can move
> forward from there?
>
> - David
>
> On Sat, Jan 2, 2016 at 11:46 AM, Imre Goretzki <goretzki.imre at gmail.com>
> wrote:
>
>> Mh ok, I guess I did not explained my problem well enough.
>>
>> The vtkPolyDataConnectivityFilter returns regions, either the largest,
>> specified, seeded or all regions (your filter returns largest, seeded or
>> all). I'm interessted in the following:
>>
>> - all regions
>> - specified regions.
>>
>> The problem is not the filter, the performance or possible memory leaks,
>> I need the region's polydata representation because I have a second object
>> (vtkImageData or vtkPolyData, binary mask) that has some additional
>> information, that are not represented by the data (the input for the
>> vtkImageConnectivityFilter).
>>
>> Imagine the input for the filter as image 1 and the mask as image 2. Both
>> images have the same dimensions in all 3 directions (x, y, z) but contain
>> different information.
>>
>> image 2 will be transformed to a binary image mask
>>
>> from image 1 i need to extract regions, but if some (unknown) regions
>> have points that are located in the binary image mask, I do not want these
>> regions to be contained in the extracted region list.
>>
>> So it's not about your filter or the performance, but I have some
>> problems using this filter for my issue, because I cannot reach the
>> region's polydata.
>>
>> I hope this helps.
>>
>> - Imre
>>
>>
>> Am 02.01.2016 um 18:54 schrieb 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>
>> 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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