Re: [vmtk-users] Beginner question
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Re: [vmtk-users] Beginner question
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From: Luca A. <luc...@gm...> - 2013-04-16 14:49:36
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Hi Vincent, what I would do to try to understand what goes wrong is to try simplifying the process: in the second pipe, set -boundarylayer 0, then just write out as msh directly after scaling: vmtksurfacereader -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkdistancetocenterlines -useradius 1 --pipe vmtkmeshgenerator -elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines -edgelengthfactor 0.3 -boundarylayer 0 -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu --pipe vmtkmeshscaling -scale 0.1 --pipe vmtkmeshwriter -entityidsarray CellEntityIds -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.msh Let's see what this produces. Luca -- Luca Antiga, PhD Cofounder and Principal Scientist, Orobix Srl via L.A. Muratori 3, 24123 Bergamo, Italy orobix: www.orobix.com home: lantiga.github.com twitter: twitter.com/lantiga On Apr 12, 2013, at 7:56 PM, Vincent Ip wrote: > And when I tried to open it with Fluent, it shows the following error messages: > > > Reading "\psf\Home\Desktop\CFD\Temp\level_sets_sm_ct_ex_2_q_scaled_t_l.msh"... > 563043 nodes. > 94612 mixed wall faces, zone 3. > 476 mixed wall faces, zone 4. > 456 mixed wall faces, zone 5. > 464 mixed wall faces, zone 6. > Error: read: face 5234350, zone 7. > Reading Faces: failed while reading section 13. > > Clearing partially read grid. > > Error: Read_Grid_Section: Aborted due to critical error. > Error Object: #f > > Error: Error reading "\psf\Home\Desktop\CFD\Temp\level_sets_sm_ct_ex_2_q_scaled_t_l.msh". > Error Object: #f > > Interrupting... > Done. > > Vincent > > On Apr 12, 2013, at 10:01 AM, Vincent Ip <drv...@gm...> wrote: > >> Thanks Luca for your prompt response! >> >> Here are the command lines I used: >> >> vmtksurfacereader -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct.vtp --pipe vmtkcenterlines -seedselector openprofiles --pipe vmtkflowextensions -adaptivelength 1 -extensionratio 20 -normalestimationratio 1 -interactive 0 -extensionmode boundarynormal --pipe vmtksurfacewriter -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp >> >> vmtksurfacereader -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp --pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles --pipe vmtkdistancetocenterlines -useradius 1 --pipe vmtkmeshgenerator -elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines -edgelengthfactor 0.3 -boundarylayer 1 -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu >> >> vmtklineartoquadratic -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q.vtu -rfile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2.vtp -entityidsarray CellEntityIds >> >> vmtkmeshscaling -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q.vtu -scale 0.1 -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu >> >> vmtkmeshboundaryinspector -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu -entityidsarray CellEntityIds >> >> vmtkmeshtetrahedralize -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t.vtu >> >> vmtkmeshlinearize -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t.vtu -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.vtu >> >> vmtkmeshwriter -ifile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.vtu -entityidsarray CellEntityIds -ofile /Users/Vincent/Desktop/CFD/Temp/level_sets_sm_ct_ex_2_q_scaled_t_l.msh >> >> And I am currently using MacOS 10.8.3 and my laptop is a 2.7GHz quad-core with 16GB ram. And I am using ANSYS 14.0. >> >> Please kindly advise on what steps should I follow for subsequent processing. >> Many many thanks indeed. >> >> Vincent >> >> On Apr 12, 2013, at 3:56 AM, Luca Antiga <luc...@gm...> wrote: >> >>> Hi Vincent, >>> for the future please keep messages on the list. I'm not the only >>> one that can solve your problem, by posting on the list you have >>> better chances to get useful feedback in shorter times. >>> >>> Hey, relax! No need to be desperate. Things can be tricky at the >>> beginning as there is a learning curve, but you'll be ok soon. >>> >>> I personally don't think the model is odd. The orientation of >>> the flow extensions is debatable (vmtk tries to take a representative >>> direction of the vessel upstream the end section, but it can generate >>> non particularly representative extensions in the case there are >>> high curvatures near the end section, as in your case). You can >>> try with >>> -extensionmode boundarynormal >>> for extensions that have the direction of the normal to the boundary, >>> and see what happens. >>> >>> In any case, I don't think the direction is odd enough to cause troubles, >>> so let's see the mesh. Can you send me the exact command line you >>> used to generate the mesh all the way to the generation of the msh >>> file? >>> >>> >>> Luca >>> >>> >>> On Apr 12, 2013, at 8:45 AM, Vincent Ip wrote: >>> >>>> Thanks Luca, >>>> >>>> I almost cried when I saw your email. You have no idea how desperate I am right now. >>>> Alright, I've attached a picture of what did I mean the model is odd after adding the flow extension. >>>> Please kindly comment. >>>> Many thanks!!! >>>> >>>> Vincent >>>> >>>> <PastedGraphic-1.tiff> >>>> On Apr 11, 2013, at 11:36 PM, Luca Antiga <luc...@gm...> wrote: >>>> >>>>> Hi Vincent, >>>>> welcome to vmtk. >>>>> In order to help you we need some more information about what's the actual issue you're coming across. Let's start with your first question: can you post a screenshot? >>>>> Cheers >>>>> >>>>> Luca >>>>> >>>>> On 12/apr/2013, at 08:15, Vincent Ip <drv...@gm...> wrote: >>>>> >>>>>> I am a new beginner in learning how to reconstruct blood vessel from MR angiogram source image for CFD analysis. >>>>>> >>>>>> I followed the VMTK tutorial step by step to reconstruct the middle cerebral artery and then export it to mesh for FLUENT. But it just doesn't work! >>>>>> >>>>>> I have a few questions that I don't understand and I really hope someone could show me some guidances (I'm really desperate!!) >>>>>> - After adding the flow extension, the mesh seems a bit odd and it doesn't look like the one which is depicted as an example on the page of 'generating a mesh'. Is it really necessary to make it or anything I missed to do during the meshing >>>>>> - And the *.msh file generated (for Fluent) is not readable by Fluent >>>>>> - I tried the netgen way but I don't know how to use it >>>>>> >>>>>> I am not sure what did I do wrong but I would appreciate if anyone could advise me on how to generate a proper CFD model from MRA. >>>>>> Many thanks in advance. >>>>>> >>>>>> Vincent >>>>>> ------------------------------------------------------------------------------ >>>>>> Precog is a next-generation analytics platform capable of advanced >>>>>> analytics on semi-structured data. The platform includes APIs for building >>>>>> apps and a phenomenal toolset for data science. Developers can use >>>>>> our toolset for easy data analysis & visualization. Get a free account! >>>>>> http://www2.precog.com/precogplatform/slashdotnewsletter >>>>>> _______________________________________________ >>>>>> vmtk-users mailing list >>>>>> vmt...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >>>> >>> >> > > ------------------------------------------------------------------------------ > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter_______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
