Dear Emilie,
what could be happening is that the surface mesh is coarse and patches
are comparable in size to the underlying mesh, which might create issues
with the patch clipping.
I suggest you subdivide your surface prior to patching (or prior to mapping
altogether), using
vmtksurfacesubdivision -subdivisions 1 -method loop -ifile ... -ofile ...
You could also try with -subdivisions 2, if the surface mesh is very coarse.
Hope this helps
Luca
On Oct 15, 2012, at 7:24 PM, Emilie Sauvage wrote:
> Dear Luca,
>
> thank you very much for your help. Your advice about clipping the short
> branch indeed solved my problem. Unfortunately, I am stuck with the
> following step as well. I ran this command:
>
> vmtkbranchpatching -ifile model_clipped_mapping.vtp -groupidsarray
> GroupIds -longitudinalmappingarray StretchedMapping -circularmappingarray
> AngularMetric -longitudinalpatchsize 0.5 -circularpatches 12 -ofile
> model_clipped_patching.vtp
>
> The surface that I obtained has holes in it. I tried to change the
> longitudinal patch size and number of circular patches, but this does not
> remove the holes. Do you know what am I doing wrong? Vmtk does not issue
> any error message.
>
> Thank you very much.
>
> Emilie
>
>
>> Dear Emilie,
>> I'm finally getting back to you.
>> So, the splitting is very reasonable, it actually worked well. The small
>> gaps are
>> due to the finite resolution of the mesh, if you want to make them
>> smaller, you'll
>> have to subdivide the surface using vmtksurfacesubdivision.
>>
>> What was actually creating problems is the very short open branch in the
>> attached
>> figure: the branch was not long enough to represent a real branch on its
>> own, so
>> the parent vessel was not a topologically a tube, because it contained
>> that hole.
>>
>> The solution is easy: run vmtksurfacecapper and close off that small
>> branch. Then
>> run the mapping script. I did and it worked well.
>>
>> Best,
>>
>> Luca
>>
>>
>>
>>
>> On Sep 25, 2012, at 6:12 PM, Emilie Sauvage wrote:
>>
>>> Dear Luca,
>>>
>>> I'm sending you the file you requested and also the input file with
>>> which
>>> I started the whole tutorial (model.vtp.tar.gz). There are holes between
>>> the split branches (I attached two screenshots) and I don't know if this
>>> is normal or not. I'd be grateful for any hint for solution of this
>>> problem.
>>>
>>> Thank you very much.
>>>
>>> Emilie Sauvage
>>>
>>>> Dear Emilie,
>>>>
>>>> I currently don't have time to reproduce the pipe on the data (but
>>>> thanks
>>>> for
>>>> the pointers to the data so I can get to it as soon as I can).
>>>>
>>>> In the meantime, can you share your model_clipped_metrics.vtp file? In
>>>> that
>>>> model, the branches are already split, and the problem should manifest
>>>> itself
>>>> by looking at where the split lines are located. Probably
>>>> vmtkbranchclipper
>>>> has produced an invalid clipping of the surface, so I'd like to take a
>>>> look.
>>>>
>>>> Thank you and best regards
>>>>
>>>>
>>>> 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 Sep 20, 2012, at 4:34 PM, Emilie Sauvage wrote:
>>>>
>>>>> Dear VMTK users and developers,
>>>>>
>>>>> I'm trying to reproduce the tutorial "Mapping and Patching" on a
>>>>> vascular
>>>>> geometry. But I'm facing a problem during the process.
>>>>> Everything goes well until I reach to step where the code is
>>>>> "Executing
>>>>> vmtkbranchmapping".
>>>>> There I got a first a warning saying :"Input poly data is not
>>>>> topologically a cylinder" then an error saying: "Branch not
>>>>> topologically
>>>>> a cylinder".
>>>>>
>>>>> Here is the complete command line I used:
>>>>> vmtkbranchmapping -ifile model_clipped_metrics.vtp -centerlinesfile
>>>>> model_cl.vtp -referencesystemsfile model_cl_rs.vtp -normalsarray
>>>>> ParallelTransportNormals -abscissasarray Abscissas -groupidsarray
>>>>> GroupIds
>>>>> -centerlineidsarray CenterlineIds -tractidsarray TractIds
>>>>> -referencesystemsnormalarray Normal -radiusarray
>>>>> MaximumInscribedSphereRadius -blankingarray Blanking
>>>>> -angularmetricarray
>>>>> AngularMetric -abscissametricarray AbscissaMetric -ofile
>>>>> model_clipped_mapping.vtp
>>>>>
>>>>> In fact the geometry I use is globally a tortuous pipe with some
>>>>> outlets
>>>>> (to my opinion), and has the particularity to show an aneurysm. I took
>>>>> the
>>>>> geometry from the AneuriskWeb. The geometry is precisely called C0016.
>>>>>
>>>>> Has anyone experienced the same problem? Is there something wrong with
>>>>> this geometry? Is it the fact that there is an aneurysm on the way?
>>>>>
>>>>> Thanks in advance for your answer.
>>>>>
>>>>> Emilie Sauvage.
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
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>>>>
>>>>
>>> <model.vtp.tar.gz><model_clipped_metrics.vtp.tar.gz><clipped_metrics1.png><clipped_metrics2.png>------------------------------------------------------------------------------
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>>
>>
> <stretched_mapping.jpg>
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