Hello Joe,
I see you already solved the problem. Probably the data you wanted to access
was attached to cells, rather than to points.
Just so you know, the pointdata format (.dat) by default outputs data attached
to points, but you can switch to cell-attached
data using the -celldata 1 flag on the writer
vmtkcenterlinesections
-ifile neurosurgery/RICA_Pt001_1010rev.vtp
-centerlinesfile neurosurgery/RICA_Pt001_centerline_smooth.vtp
--pipe vmtksurfacewriter -i @.ocenterlines -celldata 1 -ofile
neurosurgery/sectiondata.dat
Best regards
Luca
On Jan 18, 2012, at 6:29 PM, Joe Santore wrote:
> Luca,
> I just realized that I was able to access the data by changing the output
> file from a .dat file to a .vtp file. I'm not sure why this is the case, but
> it works.
>
> Joe
>
> On Tue, Jan 17, 2012 at 6:39 PM, Joe Santore <joesant...@gmail.com> wrote:
> Hi Luca,
> Branchclipper fixed the error, but I'm only getting X,Y, and Z coordinates in
> the output file; there is no other data. I was able to run
> centerlinesections without a problem:
> vmtkcenterlinesections
> -ifile neurosurgery/RICA_Pt001_1010rev.vtp
> -centerlinesfile neurosurgery/RICA_Pt001_centerline_smooth.vtp
> -ocenterlinesfile neurosurgery/sectiondata.dat
>
> Thanks for the quick response,
> Joe
>
>
> On Fri, Jan 13, 2012 at 8:43 AM, Luca Antiga <luca.ant...@orobix.com> wrote:
> Hi Joe,
> I can't test it right away, but it looks to me like you're missing a step in
> which you clip the surface into branches according to the extracted
> centerline branches:
>
> vmtksurfacereader
> -ifile neurosurgery/RICA_Pt001_1010rev.vtp
> --pipe vmtkbranchextractor
> -ifile neurosurgery/RICA_Pt001_centerline_smooth.vtp
> -radiusarray@ MaximumInscribedSphereRadius
> --pipe vmtkbranchclipper
> --pipe vmtkbifurcationsections
> -distancespheres 5
> -ofile neurosurgery/bifurcationsections.dat
> --pipe vmtkbranchsections
> -ofile neurosurgery/branchsections.dat
>
> Note that using
>
> -radiusarray@ MaximumInscribedSphereRadius
>
> I'm forcing radiusarray to be pushed through the pipe, so you don't need to
> specify it for the subsequent scripts.
>
> Hope I nailed it.
>
> Best regards
>
>
> Luca
>
>
> On Jan 12, 2012, at 7:42 PM, Joe Santore wrote:
>
> > Hi,
> > I'm getting an error that says "GroupIdsArray with name specified does not
> > exist." It occurs for both of these functions, and I have them piped so
> > that they directly receive the data from branchextractor:
> > vmtksurfacereader
> > -ifile neurosurgery/RICA_Pt001_1010rev.vtp
> > --pipe vmtkbranchextractor
> > -ifile neurosurgery/RICA_Pt001_centerline_smooth.vtp
> > -radiusarray MaximumInscribedSphereRadius
> > --pipe vmtkbifurcationsections
> > -distancespheres 5
> > -radiusarray MaximumInscribedSphereRadius
> > -groupidsarray GroupIds
> > -ofile neurosurgery/bifurcationsections.dat
> > --pipe vmtkbranchsections
> > -radiusarray MaximumInscribedSphereRadius
> > -groupidsarray GroupIds
> > -ofile neurosurgery/branchsections.dat
> >
> > I've been trying to get this to work for some time, but everything I've
> > tried has failed. I know that branchextractor is passing GroupIds because
> > branchgeometry and bifurcationvectors work well when I pipe them.
> >
> > I would appreciate any advice you can give me,
> > Joe
> >
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