Dear Ido,
one missing piece of information is that vmtknetworkextraction works on
surfaces that have an opening (all openings are used as starting profiles) and
yours apparently doesn't have any.
Do the following
vmtksurfaceclipper -ifile yourfile.vtp --pipe vmtknetworkextraction -ofile
net.vtp -ographfile graph.vtp
When you see the rendering window, press 'i' to activate the clipping cube and
'space' to clip. Once you're done, press 'q' to proceed.
Hope this helps
Luca
On Dec 14, 2011, at 12:04 PM, ido yerushalmy wrote:
> Hi Luca,
> Thanks for the script.
> For some reason, when I run the line you sent me, the PypePad crashes and
> shuts down immediately.
> When I run it without the 'ographfile' option (vmtknetworkextraction -ifile
> C:\Temp\CleanedVol.vtp -ofile C:\Temp\output_network.vtp),
> I get a network file created but when opened there is nothing displayed
> (please see attached).
>
> One thing I find strange, is that the script did not ask me to define a
> starting point for the network (as opposed to the work flow via 3D Slicer).
> Is this normal?
>
> Thanks,
> Ido
>
> The PypePad output is pasted below:
> Creating vmtkNetworkExtraction instance.
> Automatic piping vmtknetworkextraction
> Parsing options vmtknetworkextraction
> SurfaceInputFileName = C:\Temp\CleanedVol.vtp
> NetworkOutputFileName = C:\Temp\output_network.vtp
> Explicit piping vmtknetworkextraction
> Input vmtknetworkextraction members:
> Id = 0
> Disabled = 0
> Surface = None
> SurfaceInputFileName = C:\Temp\CleanedVol.vtp
> AdvancementRatio = 1.05
> RadiusArrayName = Radius
> TopologyArrayName = Topology
> MarksArrayName = Marks
> NetworkOutputFileName = C:\Temp\output_network.vtp
> GraphLayoutOutputFileName =
> Reading VTK XML surface file.
> Executing vmtknetworkextraction ...
> Progress: 100%
> Done executing vmtknetworkextraction.
> Writing VTK XML network file.
> Output vmtknetworkextraction members:
> Id = 0
> Network = vtkPolyData
> GraphLayout = vtkPolyData
>
>
>
> On Mon, Dec 12, 2011 at 5:43 PM, Luca Antiga <luca.ant...@orobix.com> wrote:
> Hi Ido,
> it should be
>
> vmtknetworkextraction -ifile input_surface.vtp -ofile output_network.vtp
> -ographfile output_graph.vtp
>
> Let me know if you can run it successfully.
>
> Best regards
>
> Luca
>
>
> On Dec 11, 2011, at 1:28 PM, ido yerushalmy wrote:
>
>> Hi Luca,
>> I got the network by running the VMTKNetworkExtraction script via 3D-Slicer.
>> So, regarding your first question, I guess the rename of the radius array is
>> performed within that script (I didn't run centerlines algorithm).
>>
>> Regarding your request; Since I used the Slicer's GUI to extract the
>> network, I didn't have to use the Pype commands. Is there a chance you could
>> send me an example of such a command with the -ographfile option you
>> mentioned?
>>
>> Thanks again,
>> Ido
>>
>> On Wed, Dec 7, 2011 at 6:47 PM, Luca Antiga <luca.ant...@orobix.com> wrote:
>> Hi Ido,
>> I'm not sure what's going on here.
>> One thing I notice is that you have both a Topology array and a
>> MaximumInscribedSphereArray.
>> Did you rename the Radius array to MaximumInscribedSphereArray or is this
>> network a result of
>> vmtkcenterlines somehow? Just to know.
>>
>> Can you post the file written when you use -ographfile on
>> vmtknetworkextraction?
>>
>> Thanks
>>
>>
>> Luca
>>
>>
>> On Dec 1, 2011, at 1:57 PM, ido yerushalmy wrote:
>>
>> > Hi Luca,
>> > First of all, thanks for the explanation.
>> > However, there is still something I don't understand:
>> > In the attached vtk file, which is a result of network extraction,
>> > there are 4 appearances of (-1). Thus, I conclude there are 4
>> > endpoints for the network.
>> > However, when you visually look at the network you can notice that
>> > while the (-1) indeed depicts endpoints, there are additional
>> > endpoints as well.
>> >
>> > Am I missing something? How can I get ALL the endpoints?
>> >
>> > Thanks in advance,
>> > Ido Yerushalmy
>> >
>> > p.s. - I'm attaching an fcsv file as well which includes the edge
>> > points I extracted based on the (-1) locations. Can be opened in
>> > Slicer, or just by any text editor.
>> > <CleanedModelNet_3.vtk><netTargets.fcsv>
>>
>>
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>
>
> <output_network.vtp><CleanedVol.vtp>
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