Hi Luca,
Thanks for the additional suggestion.
You are right, there's lots of room for improvement regarding visualization
> in patching (and in general). Thanks for the suggestion!
>
Just to clarify further, I wasn't trying to suggest it needed any
improvement, just that one little feature didn't seem to be working
properly for me, which I suspect has more to do with Windows or myself than
vmtk.
Thanks,
Evan Kao
On Mon, Mar 4, 2013 at 4:31 AM, Luca Antiga <luca.ant...@gmail.com> wrote:
> Hi Evan,
>
> On Mar 1, 2013, at 7:51 PM, Evan Kao wrote:
>
> Hello Luca,
>
> Thanks for the quick response and help. Using subdivisions seemed to have
> fixed the problem of missing patches (I did end up having to use the
> AbscissaMetric array as the longitudinal axis in vmtkbranchpatching as
> opposed to StretchedMapping due to issues with Python crashing when trying
> to compute the bifurcation reference systems from the subdivided surface,
> but this is probably more of an issue with the system I'm using than one
> with vmtk).
>
>
> It's possible, but try to use subdivision after the mapping and prior to
> patching. You'll still see the little hole at the bifurcation center, which
> shouldn't be that big of a deal (although I don't know your exact
> application), but you'll be able to use StretchedMapping for the patching,
> which results in a more regular coverage of the surface.
>
> Why nonsense? The data is all there.
>>
>
> To clarify, I don't think the data is nonsense, but when I provide the
> flag -patcheddatafile xxx.vti/png for vmtkbranchpatching, it doesn't seems
> to visualize the data correctly, as seen in the image files I attached in
> the previous e-mail (I just see a gray rectangle). But it's probably not a
> big deal, since I can just export the raw data and visualize it however I
> want, as you suggested.
>
>
> You are right, there's lots of room for improvement regarding
> visualization in patching (and in general). Thanks for the suggestion!
>
> Luca
>
> Thanks,
> Evan Kao
>
> On Fri, Mar 1, 2013 at 4:01 AM, Luca Antiga <luca.ant...@gmail.com> wrote:
>
>> Hi Evan,
>>
>> On Mar 1, 2013, at 1:59 AM, Evan Kao wrote:
>>
>> Hello group,
>>
>> I am still having some trouble with mapping and patching data. When I
>> created the patched surface and viewed it, I noticed that some patches of
>> the surface were missing (see: missingpatches.png,
>> any011_wss_clipped_patching.vtp). Inspecting the surfaces generated from
>> the previous steps, it seems small pieces of the surface is cut out at the
>> bifurcation (surface after splitting.png, any011_wss_clipped.vtp), although
>> I don't know if that is related to the problem in the surface patching
>> step, or simply a result of the way the centerlines were formed
>> (centerlines,png, any011_wss_cl.vtp).
>>
>>
>> Both issues are related to the fact that the surface is probably too
>> coarse in some regions relative to the size of the patch. Also, due to the
>> way clipping is performed, you can have a small missing triangle at the
>> bifurcation, whose size decreases with the increase in the surface density.
>> This is due to the linear interpolation of the cuts on top of the
>> triangulation.
>> A workaround in these cases is to pass the surface through
>> vmtksurfacesubdivision -method butterfly -subdivisions 1
>> prior to patching.
>>
>> The image files generated with the patched data (both .vti and .png) were
>> nonsense (vmtkimageviewer of patcheddata.png,
>> any011_wss_clipped_patching.png, any011_wss_clipped_patching.vti).
>>
>>
>> Why nonsense? The data is all there. It's one image in which all three
>> branches are stored contiguously, this way:
>>
>> SECTORS x (SLAB_A + SLAB_B + SLAB_C)
>>
>> I attach a couple of screenshots that demonstrate it, obtained using
>> Paraview.
>>
>> It's probably not the most practical way to plot the data, though. I
>> suggest you export the vtp patched data this way:
>>
>> vmtksurfacewriter -ifile any011_wss_clipped_patching.vtp -ofile foo.dat
>> -celldata
>>
>> which will generate a csv-like file in which lines are individual
>> patches, each with its wss value, groupid, slab and sector.
>> This will allow you to generate plots of the unwrapped surface for your
>> needs using any general purpose plotting software by plotting sector on x,
>> slab on y and wss as the color.
>>
>> Hope this helps
>>
>> Luca
>>
>> To simplify the issue, I also tried mapping and patching only one branch
>> segment (the aneurysm) by cutting out the other branches with
>> vmtksurfaceclipper before any sort of branch extraction and splitting.
>> There didn't seem to be any issues with missing patches this time around,
>> but the .png file also failed to provide the expected results (the patched
>> 3D surface, and the "unwrapped" 2D surface).
>>
>> Any idea on what's going wrong?
>>
>> Thanks,
>> Evan Kao
>>
>>
>>
>>
>>
>> On Fri, Feb 22, 2013 at 3:54 PM, Evan Kao <tos...@gmail.com> wrote:
>>
>>> Thanks, Arjan. That was an extremely helpful explanation.
>>>
>>>
>>> On Wed, Feb 20, 2013 at 4:40 PM, Arjan Geers <ajge...@gmail.com> wrote:
>>>
>>>> Hi Evan,
>>>>
>>>> VTK polydata files store the location of points and information on how
>>>> these points are connected to form cells. Additionally, they can store
>>>> scalars and vectors at each point or cell. So, indeed, you want the WSS
>>>> field already included in the surface file before performing any
>>>> vmtkbranch* operations.
>>>>
>>>> Hopefully, you can export from your CFD solver an ASCII file similar to
>>>> surface.tec (attached). It contains x,y,z-coordinates of each point, the
>>>> wss magnitude at each point, and connectivity information. When opening
>>>> this surface with vmtksurfacereader, VMTK converts it into a VTK polydata,
>>>> which can then be written with vmtksurfacewriter (see surface.vtp
>>>> attached). To check what VMTK actually does when converting the ASCII file,
>>>> go to the function 'ReadTecplotSurfaceFile' in vmtksurfacereader.py. This
>>>> should provide you with some hints on how to convert your own format to
>>>> VTP.
>>>>
>>>> Hope this helps,
>>>>
>>>> Arjan
>>>>
>>>> PS: Since the commercial CFD solver Ansys-CFX is quite widely used, the
>>>> attached script cfx2vtp.py (variation on above-mentioned
>>>> 'ReadTecplotSurfaceFile') might be useful to some reading this email.
>>>> Converting surface.csv (attached) should give surface.vtp again.
>>>>
>>>>
>>>> On Wed, Feb 20, 2013 at 9:40 PM, Evan Kao <tos...@gmail.com> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I am confused about some of the details regarding the matching and
>>>>> patching of data in the tutorial. Specifically, at what stage in the
>>>>> process are we supposed to import the simulation data into vmtk, and how?
>>>>> For instance, in the tutorial, are the WSS and OSI distributions already
>>>>> part of the surface file ("aorta.vtp") before any processing occurs? It
>>>>> doesn't seem like there are any ways to import data in any of the
>>>>> vmtkbranchmetrics, vmtkbranchmapping, or vmtkbranchpatching functions.
>>>>> And
>>>>> what form does the data have to be in? It should be pretty easy to export
>>>>> nodal or cell CFD data as an array, but how would we incorporate that into
>>>>> vmtk?
>>>>>
>>>>> Thanks for your time,
>>>>> Evan Kao
>>>>>
>>>>>
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>>>>>
>>>>>
>>>>
>>>
>> <any011_wss_clipped_patching.png><centerlines.png><missing
>> patches.png><surface
>> after splitting.png><vmtkimageviewer of patched data.png>
>> <any011_wss_clipped_patching.vtp><any011_wss_clipped_patching.vti>
>> <any011_wss_cl.vtp><any011_wss_clipped.vtp>
>> ------------------------------------------------------------------------------
>>
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>>
>>
>
>
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