Re: [vmtk-users] centerlines question

[Luca A. <an...@ma...>]

Hi Joong-Ho,
   for some reason the vtp file you attached was embedded in the  
message. I tried to delete the rest and keep the attached data, but  
it's invalid because there are spurious carriage returns around.
You could try to tar.gz the file and then attach it.

As to the pipe, just a quick suggestion (a feature of pypes you might  
have missed):
when you specify a variable that has to be repeated downstream the  
pipe, you can "push" it the first time you specify it, this way

> vmtkbranchextractor.py -ifile p001_part1_centerlines.vtp \
> -radiusarray@ MaximumInscribedSphereRadius \
> --pipe vmtkbranchclipper.py -ifile p001_part1_model.vtp \
> --pipe vmtksurfaceviewer -array GroupIds

In this pipe, -radiusarray@ will be pushed along the pipe and  
recognized by vmtkbranchclipper.

> But I failed to do this without vmtkbranchextractor in front of  
> vmtkbranchclipper, i.e. using the output file of vmtkbranchextractor.
Sorry, I don't understand what you mean :-) Could you be more specific?

I have to run now, I'll come back later to reply to your last question

Luca

--
Luca Antiga, PhD
Biomedical Technologies Laboratory,
Bioengineering Department,
Mario Negri Institute
email: an...@ma...
web: http://villacamozzi.marionegri.it/~luca
mail: Villa Camozzi, 24020, Ranica (BG), Italy
phone: +39 035 4535-381



On Jan 10, 2007, at 11:14 AM, Joong-Ho Won wrote:
> Hi Luca,
>
> I was just about to send you the files! Here I attach a segmented  
> image and a model obtained by running marching cubes on the image.
>
> As for branchclipper, I made something like the following work:
>
> vmtkbranchextractor.py -ifile p001_part1_centerlines.vtp \
> -radiusarray MaximumInscribedSphereRadius \
> --pipe vmtkbranchclipper.py -ifile p001_part1_model.vtp \
> -radiusarray MaximumInscribedSphereRadius \
> --pipe vmtksurfaceviewer -array GroupIds
>
> where p001_part1_centerlines.vtp is the centerlines obtained using  
> vmtkcenterlines. But I failed to do this without  
> vmtkbranchextractor in front of vmtkbranchclipper, i.e. using the  
> output file of vmtkbranchextractor.
>
> One more question:
>
> Given the (grouped) centerlines, I would like to read the  
> coordinates of the sample points and the radius of the max  
> inscribed sphere on each centerline, mostly having MATLAB in mind.  
> How can I do this?
>
> Thank you,
>
>    Joong-Ho.
>
>
>
> Luca Antiga wrote:
>> Hi Joong-Ho,
>>   good that it worked, but the issue is worth further  
>> investigation. Let me know when you can send the file over.
>> The branch clipper has to know what arrays to base the splitting on.
>> The quickest thing you can do in this case is pipe the clipper  
>> after the extractor
>> (in this case don't forget to remove the -ifile and - 
>> centerlinesfile options)
>> Ciao
>> Luca





--
Luca Antiga, PhD
Biomedical Technologies Laboratory,
Bioengineering Department,
Mario Negri Institute
email: an...@ma...
web: http://villacamozzi.marionegri.it/~luca
mail: Villa Camozzi, 24020, Ranica (BG), Italy
phone: +39 035 4535-381