Dear Joe,
the figure was the result of David's mastery using Tecplot with data produced
by vmtk, but you can get pretty close with Paraview (www.paraview.org).
If you want to visualize the spheres, just use the Glyphs filter in Paraview.
Set the glyph radius to one and the glyph scale to one as well, set centerlines
as input and you'll get one sphere per centerline point. You can resample
centerlines using vmtkcenterlineresampling in order to reduce the number of
spheres, or you can use the Cut filter in Paraview to isolate a sphere of your
interest.
vmtk is quite limited with respect to pretty pictures, as of now. We were
thinking about adding a few scripts for visualization, this may actually happen
in
the near future.
Best regards
Luca
On Feb 3, 2012, at 11:32 PM, Joe Santore wrote:
> Hi Luca,
> Thanks for your help so far. I was looking at your journal article that was
> published in Stroke back in 2005, and I was wondering how you were able to
> visualize the inscribed spheres used to generate the centerline. Is there a
> function in vmtk that is able to do this? Please see photo below.
>
> Thanks,
> Joe
> <image.png>
>
>
>
> On Thu, Jan 19, 2012 at 5:09 AM, Luca Antiga <[email protected]> wrote:
> 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 <[email protected]> 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 <[email protected]> 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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