Re: [vmtk-users] bifurcation plane

[Luca A. <luc...@or...>]

Hello Laura,
 what happens in vmtkbranchgeometry regarding curvature is the following:
- the curvature of each centerline tract is computed (as a continuous quantity along the line segment - same as for vmtkcenterlinegeometry)
- the curvature of each tract is averaged over the tract
- the average curvature for all tracts belonging to the same group id is averaged to produce the branch curvature value you read in output
I hope this clarifies things, feel free to ask for more details.
Best regards

Luca


On Aug 8, 2013, at 6:05 PM, Laura Ellwein wrote:

> Hi Luca,
> 
> I have a question about the curvature calculation that was brought up by another user a few months ago, so I am appending his email.
> 
> I understand that using 'vmtkcenterlinegeometry' gives a curvature value calculated for each centerline point, and I believe 'vmtkbranchgeometry' gives an average for each branch. I am looking for the latter for a population of coronary bifurcations and I want to make sure I am using the scripts correctly. In theory, should the curvature values using 'vmtkcenterlinegeometry' average to equal those output with 'vmtkbranchgeometry' assuming I split the branches in the right place? I can very clearly parse out the 'side branch' because of the break in the XYZ coordinates so I compared the average curvature output from the branch script and what I computed from the centerline script... they were not at all the same. Can you clarify these scripts a bit more and/or point me to a reference if that is easier?
> 
> Thank you,
> Laura Ellwein
> VCU
> 
> 
> - Laura
> 
> 
> On Wed, May 8, 2013 at 4:37 AM, qiang zeng <zen...@ya...> wrote:
> Dear Luca,
> Yeah, you are right when i am checking for what you said.
> thank you.
> YiQiang
> 
> --- 13年5月8日，周三, Luca Antiga <luc...@gm...> 写道：
> 
> 发件人: Luca Antiga <luc...@gm...>
> 主题: Re: [vmtk-users] bifurcation plane
> 收件人: "qiang zeng" <zen...@ya...>
> 抄送: vmt...@li...
> 日期: 2013年5月8日,周三,下午4:02
> 
> 
> Hi YiQiang,
>  I don't think this is what happens: you only get one value per GroupId with the vmtkbranchgeometry script,
> while with vmtkcenterlinegeometry you get a curvature value for each point on each centerline.
> vmtkbranchgeometry looks at all centerlines tracts in a group and averages their curvature value.
> 
> Luca
> 
> 
> On May 8, 2013, at 4:48 AM, qiang zeng wrote:
> 
>> bifurcation plane is work well.
>>  
>> another problem, when I caculate the curvature using the following script "vmtkcenterlinegeometry -ifile foo_cl.vtp -smoothing 1 -ofile foo_clgm.vtp", I just get the one curvature value for every GroupIds. but in generally, the curve for every GroupIds has different points (point1, point2,...) and every point in curve has a curvature value respectively.
>> So how to understand this approach considering one curvature value as curvature value of entire GroupIds?
>>  
>> YiQiang  
>> --- 13年5月7日，周二, Luca Antiga <luc...@gm...> 写道：
>> 
>> 发件人: Luca Antiga <luc...@gm...>
>> 主题: Re: [vmtk-users] bifurcation plane
>> 收件人: "qiang zeng" <zen...@ya...>
>> 抄送: vmt...@li...
>> 日期: 2013年5月7日,周二,下午2:40
>> 
>> Hi YiQiang,
>>  point1 and point2 are any two points on the plane away from the origin.
>> You could do
>> point1 = origin + upnormal
>> point2 = origin + normal x upnormal
>> where x indicates the cross product.
>> 
>> Luca
>> 
>> On 07/mag/2013, at 07:39, qiang zeng <zen...@ya...> wrote:
>> 
>>> Usig the command line:
>>>  
>>> vmtkbranchextractor -ifile foo_cl.vtp -radiusarray@ MaximumInscribedSphereRadius --pipe
>>> vmtkbifurcationreferencesystems -ofile foo_rs.dat
>>>  
>>> I get the one point and two vectors, then I fill the coordinate into the Paraview (point -> Origin, Normal -> Point1 and Upnormal -> Point2) ?
>>> Best
>>> YiQiang
>>> 
>>> --- 13年5月6日，周一, Luca Antiga <luc...@gm...> 写道：
>>> 
>>> 发件人: Luca Antiga <luc...@gm...>
>>> 主题: Re: [vmtk-users] bifurcation plane
>>> 收件人: "qiang zeng" <zen...@ya...>
>>> 抄送: vmt...@li...
>>> 日期: 2013年5月6日,周一,下午8:54
>>> 
>>> Hi YiQiang,
>>>  the figure you attached was created in Paraview using the origin and normal of the plane
>>> as computed with vmtk (you can output them in plain text using a .dat file format) to specify the plane 
>>> in Paraview (Sources->Plane). It works well if the number of figures you create is small.
>>> 
>>> If you need to create the visualization automatically you'll need to write VTK code and use the
>>> vtkPlaneSource class to create the plane.
>>> The class: http://www.vtk.org/doc/nightly/html/classvtkPlaneSource.html
>>> Examples: 
>>> http://www.vtk.org/doc/nightly/html/c2_vtk_e_5.html#c2_vtk_e_vtkPlaneSource
>>> http://www.vtk.org/doc/nightly/html/c2_vtk_t_15.html#c2_vtk_t_vtkPlaneSource
>>> 
>>> Best,
>>> 
>>> Luca
>>> 
>>> 
>>> On May 6, 2013, at 9:40 AM, qiang zeng wrote:
>>> 
>>>> Hi all,
>>>> When I am using VMTK, I want to display the bifurcation plane (the view is like aneurysm bifurcation plane, as an attachment "bifurcation plane.jpg").
>>>> Does anyone know a way to do this?
>>>> Best,
>>>> YiQiang
>>>> <bifurcation plane.jpg>------------------------------------------------------------------------------
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>>> 
> 
>