<div dir="ltr">Hi Imre, Happy New Year!<div><br></div><div>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.</div><div><br></div><div>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?</div><div><br></div><div> - David</div><div><br><div class="gmail_extra"><br><div class="gmail_quote">On Sat, Jan 2, 2016 at 9:00 AM, Imre Goretzki <span dir="ltr"><<a href="mailto:goretzki.imre@gmail.com" target="_blank">goretzki.imre@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hey David,<br>
<br>
first of all: Happy new year :)<br>
<br>
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.<br>
<br>
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.<br>
<br>
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"?<span class=""><font color="#888888"><br>
<br>
- Imre</font></span><div><div class="h5"><br>
<br>
<div>Am 29.12.2015 um 13:27 schrieb Imre
Goretzki:<br>
</div>
<blockquote type="cite">
Hi David,<br>
<br>
thank you. I'll take a look at your class.<br>
<br>
Regards<br>
Imre<br>
<br>
<div>Am 29.12.2015 um 13:07 schrieb David
Gobbi:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Imre,
<div><br>
</div>
<div>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:</div>
<div><a href="https://github.com/dgobbi/AIRS/blob/master/ImageSegmentation/vtkImageConnectivityFilter.h" target="_blank">https://github.com/dgobbi/AIRS/blob/master/ImageSegmentation/vtkImageConnectivityFilter.h</a></div>
<div>I'll probably be contributing this filter to VTK sometime
in the near future.</div>
<div><br>
</div>
<div> - David</div>
<div><br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Dec 29, 2015 at 4:02 AM,
Imre Goretzki <span dir="ltr"><<a href="mailto:goretzki.imre@gmail.com" target="_blank"></a><a href="mailto:goretzki.imre@gmail.com" target="_blank">goretzki.imre@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Is there an
easier way in ITK?<br>
<br>
Thanks<span><font color="#888888"><br>
Imre</font></span>
<div>
<div><br>
<br>
<div>Am 28.12.2015 um 23:38 schrieb Imre
Goretzki:<br>
</div>
<blockquote type="cite"> Hey guys,<br>
<br>
I use the vtkPolyDataConnectivityFilter from
polydata to extract several different and more
or less unknown regions. <br>
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:<br>
<br>
filter->SetExtractionModeToAllRegions();<br>
filter->Update();<br>
...<br>
<br>
for (int i = 0; i <
filter->GetNumberOfExtractedRegions(); i++)<br>
{<br>
extractFilter->InitializeSpecifiedRegionList();<br>
extractFilter->AddSpecifiedRegion(i);<br>
extractFilter->Modified();<br>
extractFilter->Update();<br>
extractRegionData->DeepCopy(extractFilter->GetOutput());<br>
}<br>
extractFilter->InitializeSpecifiedRegionList();<br>
<br>
Background for this: I want to use the points
of each region to check whether they lie
within an object in my binary<br>
mask image. So the pipeline would be like
this:<br>
<br>
1) Get all Regions <br>
2) get region <i>i</i><br>
3) get points of region <i>i</i><br>
4) check if point <i>j</i> lies
within the binary mask <i>B</i> (<i>B</i>_<i>j</i>
== 255)<br>
4a) if true then add region
to the extractFilter and break (-> next
region <i>i</i>)<br>
4b) if false then continue
with next point <i>j</i><br>
5) Mark all regions red (done easily)<br>
6) Mark some regions green that are above a
specific size (can be accessed with
filter->GetRegionSizes() )<br>
7) Mark some regions yellow (the regions that
are extracted during step 1-4a) <br>
<br>
I do not know if the
PolyDataConnectivityFilter is the right class
for this, I think it is. <br>
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).<br>
<br>
I would now try to get the points from the
cells and check the binary mask, because the <br>
<br>
vtkPolyData->GetNumberOfPoints()<br>
<br>
and<br>
<br>
vtkPolyData->GetPoint(pointCounter, point);
<br>
<br>
are not working correctly in this scenario
(all regions are extracted because every
single region has every point?<br>
i did not verify my guess but I think there
would be the problem)<br>
<br>
The binary mask is a vtkImageData, that could
be transformed to vtkPolyData.<br>
The input image (already filtered with
vtkMarchingCubes) and the binary mask have the
same dimensions (x,y,z).<br>
<br>
I hope you can imagine what I'm trying to do
and have some tips for me, if my approach is
correct.<br>
<br>
Regards<br>
Imre</blockquote></div></div></div></blockquote></div></div></div></div></blockquote></blockquote>
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