Hi Vikram,
I'm suggesting to pipe the vmtksurfacetriangle script right after
vmtkmarchingcubes
vmtkmarchingcubes -ifile some_file.vti --pipe vmtksurfacetriangle -ofile
thesurface.vtp
and see if this works.
Luca
On May 6, 2013, at 3:20 PM, Vikram Mehta wrote:
> 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 <luca.ant...@orobix.com> 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 <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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