Re: [vmtk-users] 2 questions on segmentation

[Vikram M. <vv...@gm...>]

Hi Luca,

Yes these bumps/holes occured when I tried a smoothing script straight
after marching cubes. It occurs at 3-4 spots on the reconstruction.

Are you suggesting increasing the number of surface triangles ?

Best
Vikram.



On Mon, May 6, 2013 at 2:13 PM, Luca Antiga <luc...@or...> wrote:

> Hi Virkam,
>  you haven't provided a lot of info on this, but this looks like a VTK
> Marching Cubes issue that arises sometimes.
> Try to use vmtksurfacetriangle right after vmtkmarchingcubes (and before
> any other smoothing or other scripts).
> Best,
>
> Luca
>
>
> On May 6, 2013, at 3:09 PM, Vikram Mehta wrote:
>
> Thank you for your suggestions.
>
> I came across a new problem today - would you happen to know what causes
> this ? And how I can repair my reconstruction ?
>
> Please find an image attached of the problem.
>
> Many thanks in advance
> Vikram.
>
>
>
> On Thu, May 2, 2013 at 10:18 AM, Arjan Geers <aj...@gm...> wrote:
>
>> 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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> <Screen Shot 2013-05-06 at 14.06.02.png>
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