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 <ajge...@gmail.com> 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 <vvme...@gmail.com> 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 <luca.ant...@gmail.com> 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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