Hi all,
Arjan is right, if the common tract is the same, working with abscissas is the
most robust solution. Unfortunately
I don't think there is a solution out of the box for what you want to do,
although there are several scripts and
classes that use the abscissa to split, measure and do all sorts of operations.
For instance, vmtkpointsplitextractor will split centerlines based on the
proximity to a physical point in space, which
is not what you need but it uses the same ingredients.
So, instead of Paraview you could also use Python directly, it depends on how
appealing this possibility looks to you
and whether this is a one-shot need for you or not.
To add a bit of answer to Arjan's answer on output formats, you could use
vmtksurfacewriter -ofile foo.dat -celldata 1
which, instead of one line per point containing coordinates and point data
arrays, will print one line per cell containing
the cellId and cell data arrays (including curvature, torsion and tortuosity).
Hope this helps
Luca
On May 3, 2012, at 4:18 PM, Arjan Geers wrote:
> Hi Manasi,
>
> To answer your second question:
>
> Let's assume a vessel with a single bifurcation. Before the bifurcation, the
> two centerlines will indeed follow approximately the same path. In other
> words, nearby points on CL1 and CL2 should have approximately the same
> abscissa. 'Approximately', because the exact path depends on the sampling of
> the centerline.
>
> To answer your first question:
>
> Let's assume the sampling of the two centerlines is exactly the same (it
> seems that the standard output of vmtkcenterlines is such). Sort the points
> by abscissa in ascending order (for example in Paraview's Spreadsheet View).
> You'll see that at first the points on row 2n and 2n+1 are the same (n =
> 0,1,2,...). Once CL1 and CL2 start to deviate, the points will be different.
>
> But... this approach is pretty ugly. Not knowing your goal I can't be sure,
> but I actually doubt the point you'll find is very meaningful (correct me if
> I'm wrong :-) ). It's not unlikely that there is a more appropriate solution
> readily available in VMTK. To familiarize yourself with the possibilities, I
> would recommend you to go through the tutorials "Computing Centerlines",
> "Branch Splitting", and "Geometric Analysis".
>
> Hope this helps,
>
> Arjan
>
> On Wed, May 2, 2012 at 11:55 PM, Ramachandran, Manasi
> <manasi-ramachand...@uiowa.edu> wrote:
> 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> 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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