Hi Manasi,
If you save the output as *.vtp and open it in Paraview, you'll see that
both tortuosity and length are cell data. They only have one value per
cell, i.e. centerline. All other variables are point data, defined at each
point of the centerline.
>From the looks of it, cell data is not written to *.tec or *.dat. If your
goal is to obtain either the length or tortuosity of a centerline, I'd
recommend using *.vtp.
Alternatively, you could run vmtkcenterlineattributes and obtain the length
in Tecplot by picking the abscissa value at the outlet (L), assuming the
abscissa at the inlet is 0. From the start/end coordinates of the
centerline you could calculate the Euclidean distance between the in- and
outlet (D). The tortuosity (Chi) would then be Chi = L/D - 1 (Piccinelli
TMI 2009).
Hope this helps,
Arjan
On Thu, Apr 26, 2012 at 11:46 PM, Ramachandran, Manasi <
manasi-ramachand...@uiowa.edu> wrote:
> Hi Arjan,
>
>
>
> Thank you for the reply. I ran this command:
>
>
>
> *vmtkcenterlinegeometry -ifile
> C:/Users/manasi.ramachandran/Documents/30677/stented/Negative20/stented_Series5_Negative20_levelsets_cl_CL.vtp
> -smoothing 1 -iterations 10 -outputsmoothed 1 -ofile
> C:/Users/manasi.ramachandran/Documents/30677/stented/Negative20/stented_Series5_Negative20_levelsets_cl_CLGM.tec
> *
>
>
>
> I can now get data printed on the tec file. There is no length or
> Tortuosity information though. Here are first few lines of my tec file:
>
>
>
> *VARIABLES =
> X,Y,Z,MaximumInscribedSphereRadius,EdgeArray0,EdgeArray1,EdgePCoordArray,Curvature,Torsion,FrenetTangent0,FrenetTangent1,FrenetTangent2,FrenetNormal0,FrenetNormal1,FrenetNormal2,FrenetBinormal0,FrenetBinormal1,FrenetBinormal2
> *
>
> *ZONE N=805,E=0,F=FEPOINT,ET=TRIANGLE*
>
> *375.212860107 127.314727783 -840.130249023 4.43752339446 5774.0 5774.0
> 0.0 0.0 0.0 -0.794417157975 0.0212929549817 -0.606999167366 0.581361416428
> 0.315991613505 -0.749778769827 0.1758416407 -0.948523015147 -0.263408062013
> *
>
> *375.533172607 127.303581238 -839.876281738 4.56642718039 1163.0 1163.0
> 0.0 0.106633669157 0.0 -0.794417157975 0.0212929549817 -0.606999167366
> 0.581361416428 0.315991613505 -0.749778769827 0.1758416407 -0.948523015147
> -0.263408062013*
>
>
>
>
>
> What am I doing wrong? Why am I not getting Length and Tortuosity to
> print into the file.
>
>
>
> Thank you for your help,
>
> Manasi
>
>
>
>
> ------------------------------
> *From:* Arjan Geers [ajge...@gmail.com]
> *Sent:* Thursday, April 26, 2012 11:44 AM
> *To:* Ramachandran, Manasi
> *Cc:* vmtk-users@lists.sourceforge.net
> *Subject:* Re: [vmtk-users] Problem with VMTKcenterlinegeometry
>
> Hi Manasi,
>
> The not-so-elegant solution to your problem may be here:
> http://sourceforge.net/mailarchive/message.php?msg_id=28032510
>
> Open the file .\vmtk 0.9.0\lib\vmtk\vmtk\vmtkcenterlinegeometry.py in a
> text editor and add the following lines near the end of the file:
>
> centerlineGeometry.SetLengthArrayName('Length')
> centerlineGeometry.SetTortuosityArrayName('Tortuosity')
>
> Run the following in PypePad to get the desired output:
>
> vmtkcenterlinegeometry -ifile cl.vtp -smoothing 1 -iterations 10
> -outputsmoothed 1 -ofile clgm.tec
>
> Notice that you should leave out of your script "-lengtharray Length"
> and "-tortuosityarray Tortuosity",because those array names are now
> hard-coded. Otherwise, you will receive again the error message:
> "vmtkcenterlinegeometry
> error: unknown option -lengtharray"
>
> Optionally, you could leave out "-curvaturearray Curvature", because the
> default value is 'Curvature'.* *And you could leave out "-i Centerlines",
> because
> you already specify the centerline with "-ifile cl.vtp".
>
> Hope this helps,
>
> Arjan
>
> On Thu, Apr 26, 2012 at 3:04 PM, Ramachandran, Manasi <
> manasi-ramachand...@uiowa.edu> wrote:
>
>> Hi,
>>
>>
>>
>> I am using VMTK0.9 on windows 7 (64 bit). I have some problem using
>> vmtkcenterlinegeometry.
>>
>>
>> I ran this command:
>> *vmtkcenterlinegeometry -i Centerlines -ifile
>> stented_Series5_Negative20_levelsets_cl_CL.vtp -lengtharray Length
>> -curvaturearray Curvature -tortuosityarray Tortuosity -smoothing 1
>> -iterations 10 -outputsmoothed 1 -ofile
>> stented_Series5_Negative20_levelsets_cl_CLGM.tec*
>>
>> And it will not detect most parameters. Here is the message I get:
>>
>> *Creating vmtkCenterlineGeometry instance.**
>> Automatic piping vmtkcenterlinegeometry**
>> Parsing options vmtkcenterlinegeometry**
>> vmtkcenterlinegeometry error: unknown option -lengtharray**
>> vmtkcenterlinegeometry : compute the local geometry of centerlines in**
>> terms of curvature and torsion**
>> Input arguments:**
>> -id Id (str,1); default=0: script id**
>> -handle Self (self,1): handle to self**
>> -disabled Disabled (bool,1); default=0: disable execution and**
>> piping**
>> -i Centerlines (vtkPolyData,1): the input centerlines**
>> -ifile CenterlinesInputFileName (str,1): filename for the default**
>> Centerlines reader**
>> -curvaturearray CurvatureArrayName (str,1); default=Curvature: name**
>> of the array where curvature values have to be stored**
>> -torsionarray TorsionArrayName (str,1); default=Torsion: name of**
>> the array where torsion values have to be stored**
>> -frenettangentarray FrenetTangentArrayName (str,1);**
>> default=FrenetTangent: name of the array where tangent vectors of**
>> the Frenet reference system have to be stored**
>> -frenetnormalarray FrenetNormalArrayName (str,1);**
>> default=FrenetNormal: name of the array where normal vectors of**
>> the Frenet reference system have to be stored**
>> -frenetbinormalarray FrenetBinormalArrayName (str,1);**
>> default=FrenetBinormal: name of the array where binormal vectors**
>> of the Frenet reference system have to be stored**
>> -smoothing LineSmoothing (bool,1); default=0**
>> -outputsmoothed OutputSmoothedLines (bool,1); default=0**
>> -iterations NumberOfSmoothingIterations (int,1) >= 0; default=100**
>> -factor SmoothingFactor (float,1) >= 0.0; default=0.1**
>> -ofile CenterlinesOutputFileName (str,1): filename for the default**
>> Centerlines writer**
>> Output arguments:**
>> -id Id (str,1); default=0: script id**
>> -handle Self (self,1): handle to self**
>> -o Centerlines (vtkPolyData,1): the output centerlines**
>> -curvaturearray CurvatureArrayName (str,1); default=Curvature: name**
>> of the array where curvature values are stored**
>> -torsionarray TorsionArrayName (str,1); default=Torsion: name of**
>> the array where torsion values are stored.*
>>
>> And when I try running the basic command with only -ifile and -ofile, I
>> get an empty .tec file. I dont know if it has anything to do with running
>> VMTK on windows. I am able to run vmtkcenterlineattributes
>> successfully. Please let me know if anyone else has had the same problem
>> and how you tried to fix it.
>>
>> Thanks,
>> Manasi
>>
>>
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