Hi Arjan,
Thank you so much for your reply. I liked the idea of using centerline
attributes to use L and D.
Along the same lines, I was hoping I could also discuss the possiblility of
locating the same point on 2 different centerlines. For example, say I have CL1
which is a straight line and say CL2 which turns to 90 deg at some point. I
want to locate the point where the CL2 turns and find the same point on CL1.
Can I do this using D and L also?
To elaborate a little more, let us assume that both centerlines start at the
same point (x,y,z). Then, if I calculate L at one point (x2,y2,z2) in CL2 and
then find the same L and pick the corresponding point (x1,y1,z1) on CL1, will
(x1,y1,z1) and (x2,y2,z2) be approximately the same in physical space?
Thank you again for your time and support,
Manasi
________________________________
From: Arjan Geers [ajge...@gmail.com]
Sent: Thursday, April 26, 2012 5:46 PM
To: Ramachandran, Manasi
Cc: vmtk-users@lists.sourceforge.net
Subject: Re: [vmtk-users] Problem with VMTKcenterlinegeometry
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<mailto: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<mailto:ajge...@gmail.com>]
Sent: Thursday, April 26, 2012 11:44 AM
To: Ramachandran, Manasi
Cc: vmtk-users@lists.sourceforge.net<mailto: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<mailto: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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