Just to add a comment on top of my last email: since the mesh is not
*that* coarse, it could be that there are issues with the mapping. In
case, to speed things up, just send over the model_clipped_mapping.vtp
file and I'll take a look.
Luca
On Oct 22, 2012, at 3:26 PM, Luca Antiga wrote:
> 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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