Re: [vmtk-users] 2 questions on segmentation
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Re: [vmtk-users] 2 questions on segmentation
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From: Luca A. <luc...@or...> - 2013-05-06 13:24:22
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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 <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. >> > >> > ------------------------------------------------------------------------------ >> > Try New Relic Now & We'll Send You this Cool Shirt >> > New Relic is the only SaaS-based application performance monitoring service >> > that delivers powerful full stack analytics. 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Try New Relic >> > and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr_______________________________________________ >> > vmtk-users mailing list >> > vmt...@li... >> > https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> >> >> ------------------------------------------------------------------------------ >> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET >> Get 100% visibility into your production application - at no cost. >> Code-level diagnostics for performance bottlenecks with <2% overhead >> Download for free and get started troubleshooting in minutes. >> http://p.sf.net/sfu/appdyn_d2d_ap1 >> >> _______________________________________________ >> vmtk-users mailing list >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> >> >> <Screen Shot 2013-05-06 at 14.06.02.png>------------------------------------------------------------------------------ >> >> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET >> Get 100% visibility into your production application - at no cost. >> Code-level diagnostics for performance bottlenecks with <2% overhead >> Download for free and get started troubleshooting in minutes. >> http://p.sf.net/sfu/appdyn_d2d_ap1_______________________________________________ >> vmtk-users mailing list >> vmt...@li... >> https://lists.sourceforge.net/lists/listinfo/vmtk-users > > |
