[vtkusers] method to extract regions

Imre Goretzki goretzki.imre at gmail.com
Sat Jan 2 17:14:51 EST 2016


Yes I would like to ignore the entire region.

No there will be no user interaction. This is completely unwanted - 
unfortunately.

Your last point could be helpful. Thanks David. I guess, I try that 
tomorrow.

- Imre


Am 02.01.2016 um 21:45 schrieb David Gobbi:
> On Sat, Jan 2, 2016 at 1:06 PM, Imre Goretzki <goretzki.imre at gmail.com 
> <mailto:goretzki.imre at gmail.com>> wrote:
>
>
>     Yes they can be partially outside the mask because I neither know
>     the sizes and locations of the regions I want to keep nor the
>     sizes and locations of the regions I want to discard for both
>     input image and mask image (the mask changes dynamically)
>
>     Ok so in later progress I could use the mask as the second input
>     (the stencil) and this removes the regions?
>
>
> The vtkImageConnectivityFilter ignores any pixels that are outside the 
> stencil (so that might be the reverse of what you want, since you want 
> to ignore the regions that are inside your mask).
>
> If a region is partly outside the stencil, then only the part that is 
> outside will be ignored.  The rest would be counted.  As far as I 
> understand, that is not what you want.  You would want the entire 
> region to be ignored, right?
>
> Is there any reason that you even need a "mask"?  Would it be just as 
> good if you could specify the unwanted regions by giving just one 
> point in each unwanted region, i.e. the user would use the mouse to 
> click on the unwanted regions?
>
> Actually, instead of using an input mask, it seems that it would be 
> best to allow vtkImageConnectivityFilter to assign a different label 
> value to each region.  Then, once you know which labels correspond to 
> which regions, you could pass this label image through a lookup table 
> that colors all of the unwanted regions black.
>
>  - David
>
>
>     My current code lets me get the regions I want to discard by
>     storing the polydata output of vtkPolyDataConnectivityFilter and
>     then iterate over the cells and their points
>
>     for (int i = 0; i < filter->GetNumberOfExtractedRegions(); i++)
>     {
>         vtkSmartPointer<vtkPolyData> extractRegionData =
>     vtkSmartPointer<vtkPolyData>::New(); //fast
>         extractFilter->InitializeSpecifiedRegionList(); //fast
>         extractFilter->AddSpecifiedRegion(i); //fast
>         extractFilter->Modified(); //fast
>         extractFilter->Update(); //very long
>     extractRegionData->DeepCopy(extractFilter->GetOutput()); //fast
>         regionList.push_back(extractRegionData); //fast
>     }
>     for (int i = 0; i < filter->GetNumberOfExtractedRegions(); i++)
>     {
>         // some other operations
>     }
>
>     The update() process takes a very long time. As an example, if I
>     have about 200 regions, this would take about 10 minutes. All
>     other following operations on the data and/or a
>     vtkPolyDataConnectivityFilter do not take so long.
>
>     - Imre
>
>
>     Am 02.01.2016 um 20:48 schrieb David Gobbi:
>>     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 <mailto: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 <mailto: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
>>>>             <mailto: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
>>>>>>                 <mailto: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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