Hi Kevin,
I have new clipping code that solves this problem, I would like to include
it in the next upcoming release (VTK7, fixes for El Capitan, etc).
I have added an issue on Github.
Luca
On Thursday, December 10, 2015 at 11:14:38 PM UTC+1, Kevin Lau wrote:
>
> Dear all,
>
> I'm also encountering something similar to the problem described above,
> and was wondering if anyone has any suggestions.
>
> When I'm clipping the my model (see front.png), the proximity of daughter
> vessel to its parent causes the group ID to be assigned incorrectly (see
> side.png), which ultimately leaves a hole in the parent vessel.
>
> I tried playing with the -cutoffradiusfactor option (less than 1, greater
> than 1) to see if this would help, but it's too close to the parent -
> leaving either the hole or an empty geometry.
>
> Does anyone have any suggestions?
>
> Many thanks,
>
> Kevin
>
> On Monday, 4 February 2013 05:20:36 UTC-5, Luca Antiga wrote:
>>
>> Hi Patrick,
>> I see what the issue is. In fact, there currently is no check in the
>> clipping code that guarantees that this situation doesn't occur, and
>> I've been meaning to handle this in a better way for a long time.
>>
>> More than being wide, the vein is not convex. This means that
>> the centerline has to lay in one of the two "ears" of the cross-section,
>> and in this case it chose the outer ear.
>>
>> I included this into the fixes for the next release. In the meantime,
>> what
>> you could do is to smooth the model using vmtksurfacesmoothing to
>> make the cross section is less concave and compute the centerlines
>> from the smoothed model. Then, you can use that set of centerlines
>> to clip the original model.
>>
>> vmtksurfacesmoothing -ifile surface.vtp -passband 0.01 -iterations 30
>> -ofile surface_smooth.vtp
>>
>> It would be great if you could send me your surface (or a decimated
>> version of it) so that I can use it to test my future solution (I won't
>> use
>> it for anything else).
>>
>> Best,
>>
>>
>> Luca
>>
>>
>>
>> On Feb 1, 2013, at 2:48 AM, Patrick McGah wrote:
>>
>> > Hi all,
>> >
>> > I'm having a problem with clipping branches. I've been able to
>> > successfully calculated the center lines and extracted the branch
>> > groups (the geometry an AV fistula - a vein that's fully connected to
>> > an artery - with one inflow artery, an outflow vein, and an outflow
>> > artery). However, when I use vmtkbranchclipper, the outflow vein is
>> > being cut incorrectly. A small segment of the vein is being grouped
>> > with the inflow artery. Ultimately I want to map and patch the
>> > surfaces of each branch, but the artery can't be mapped correctly
>> > since it's topology is now no longer a cylinder shape. I think part of
>> > this problem is that the vein is very wide, and so the distance from
>> > the wall to the center line is very large. As a result, part of the
>> > vein wall is actually closer in distance to the artery centerline (I
>> > think). Any thought or ways to work around this?
>> >
>> > Thanks,
>> >
>> > Patrick
>> >
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