Re: [vmtk-users] 2 questions on segmentation

[Arjan G. <aj...@gm...>]

Hi Vikram,

To smooth out bumps, you could also look into ReMESH (
http://remesh.sourceforge.net/index.html). It allows you to select
triangles of the surface mesh and smooth or remove only those. It also has
a smooth hole filling algorithm.

Arjan


On Thu, May 2, 2013 at 11:00 AM, Vikram Mehta <vv...@gm...> wrote:

> Thanks Luca, will look into your suggestions.
>
> While waiting for your replies, I found another way outside of VMTK to
> align my stl but the smoothing issue is still to be resolved.
>
> Thanks again,
> Vikram.
>
>
>
> On Wed, May 1, 2013 at 1:13 PM, Luca Antiga <luc...@gm...> wrote:
>
>> Hello Vikram,
>>  thanks for your patience. Pretty busy couple of weeks.
>>
>> On Apr 23, 2013, at 2:51 PM, Vikram Mehta wrote:
>>
>> > Dear users,
>> >
>> > I have a couple of questions and I was hoping to get some advice on
>> this.
>> >
>> > 1) Is there a way of aligning one of the ends of the reconstructed
>> geometry with any of the axes?
>> >     I use the geometries as a model for CFD simulations and some other
>> processing methods in matlab. I need the vessel to be aligned with the x
>> axis (for example) with the center of the inlet at the origin so that my
>> boundary conditions are prescribed accurately.. I usually do it in other
>> meshing softwares and I was wondering if this could be done in VMTK prior
>> to exporting it as an STL file.
>>
>> There isn't a way to directly do this in vmtk using a script, but you can
>> extract the origin and normal of a boundary using vmtkmeshboundaryinspector
>> (you'll need to generate a mesh with vmtkmeshgenerator first, just use a
>> fixed -edgelength - any mesh size will do if you just need to inspect the
>> boundaries for the origin and normal), compute the transformation yourself
>> and apply it with vmtkmeshtransform (by specifying the coefficients of the
>> 4x4 transform matrix in lexicographic order with the -matrix option).
>>
>> > 2) Sometimes during the segmentation process, I end up with
>> reconstructions with artificial bumps on them. Is there a way to
>> INDIVIDUALLY smooth these bumps out ? Are there ways to avoid this ?  I do
>> not want to over smooth the entire vessel and hence a way of smoothing just
>> the rough/bumpy bits would be great !    Any suggestions would help !
>>
>> Yes, it happens sometimes, probably depending on the image features. A
>> localized smoothing filter is something I thought about and wouldn't be
>> hard to implement, but it isn't in vmtk right now.
>> The way to get around this is to use vmtksurfaceclipper (preferably using
>> -type sphere), clip a bump and then cap it using vmtksurfacecapper -method
>> smooth.
>>
>> Best,
>>
>> Luca
>>
>> > Any help is greatly appreciated !
>> >
>> > Many thanks in advance
>> > Vikram.
>> >
>> >
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