Re: [vmtk-users] Fwd: Bifurcation reference systems

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Dear Sara,
  the splitting in your screenshot looks legal to me. I wonder what  
the problem is. I guess at this point the only chance is if you send  
me your vtp file.
In the meantime, I updated the bifurcation geometry tutorial section.  
I'll proceed with the other sections shortly.
Let me know if you still have problems after trying out the new  
command lines in the tutorial.
Regards

Luca

On Aug 6, 2009, at 7:04 PM, Sara Nomeland wrote:

> Hi Luca,
> Attached you will find a screenshot of my model and the split  
> cneterlines. I tried using the command you mentioned below, but it  
> would not work the PypePad got stuck on excuting  
> vmtkcenterlineviewer....
> So I used the following command: vmtkcenterlines -ifile foo.vtp -- 
> pipe vmtkbranchextractor -ofile foo_clsp.vtp --pipe  
> vmtkcenterlineviewer -cellarray CenterlineIds --pipe  
> vmtkcenterlineviewer -cellarray TractIds --pipe vmtkcenterlineviewer  
> -cellarray GroupIds --pipe vmtkcenterlineviewer -cellarray Blanking
> and I took a screen shot of the -cellarray GroupIds window.
>
> I hope this helps!
>
> Thanks for all you help!
> Sara
>
> On Thu, Aug 6, 2009 at 2:17 AM, Luca Antiga <luc...@gm...>  
> wrote:
> Hi Sara,
>  it's quite odd. Can you post a screenshot showing your model and  
> another one showing your split centerlines? (e.g. with
> vmtkcenterlineviewer -ifile foo_cl.vtp -cellarray GroupIds)
>
> As for your other message, the tutorial is really the next thing in  
> the pipeline. I can't reply right now due to time constraints, but  
> I'll post a reply ASAP.
>
> Luca
>
>
> On Aug 5, 2009, at 8:06 PM, Sara Nomeland wrote:
>
>> Hi Luca,
>>
>> Thank you for your suggestion, it did work, apparently I cannot  
>> have any spaces in the commands and they work correctly.
>>
>> I have one last question. When working with the vmtkbranchextractor  
>> -ifile foo_cl.vtp -radiusarray MaximumInscribedSphereRadius --pipe  
>> vmtkbifurcationreferencesystems -ofile foo_rs.dat command it makes  
>> a .dat file, but there is nothing in the file except X Y Z, with no  
>> points.
>>
>> I went through the computing centerlines tutorial and then I went  
>> through the branch splitting tutrorial. Then I get to the  
>> Bifurcation reference systems portion and what I need are those  
>> points which are the bifurcation orgin and the two point data  
>> arrays. There doesn't seem to be any problem in any of the command  
>> windows even the file is made, there just is nothing in the file.  
>> Any thoughts to what could be the problem, file location, etc..?
>>
>> Thanks,
>> Sara
>>
>> On Wed, Aug 5, 2009 at 2:48 AM, Luca Antiga <luc...@gm...>  
>> wrote:
>> Hi Sara,
>>  I guess it's the same problem with breaking the line here. Try  
>> keeping it all in one line.
>> Let us know
>>
>> Luca
>>
>>
>> On Aug 4, 2009, at 8:19 PM, Sara Nomeland wrote:
>>
>>> Hello VMTK users and Luca,
>>>
>>> Using the following command:  vmtkbranchextractor -ifile  
>>> foo_cl.vtp -radiusarray MaximumInscribedSphereRadius --pipe
>>> vmtkbifurcationreferencesystems -ofile foo_rs.vtp
>>> I am not able to output the rs.vtp file which has the information  
>>> I believe I need.
>>>
>>> I get the same error in the PypePad window outputs:
>>>
>>>    Creating vmtkBifurcationReferenceSystems instance.
>>>    Automatic piping vmtkbifurcationreferencesystems
>>> Parsing options vmtkbifurcationreferencesystems
>>>     ReferenceSystemsOutputFileName = 2.3_rs.dat
>>> Explicit piping vmtkbifurcationreferencesystems
>>> Input vmtkbifurcationreferencesystems members:
>>>     Id = 0
>>>     Disabled = 0
>>>     Centerlines = None
>>>     CenterlinesInputFileName =
>>>     RadiusArrayName =
>>>     BlankingArrayName =
>>>     GroupIdsArrayName =
>>>     ReferenceSystemsNormalArrayName = Normal
>>>     ReferenceSystemsUpNormalArrayName = UpNormal
>>>     ReferenceSystemsOutputFileName = 2.3_rs.dat
>>> Executing vmtkbifurcationreferencesystems ...
>>> Error: No input centerlines.
>>>
>>> Also an error in the Command window:
>>> Exception in Tkinter callback
>>> Traceback <mmost recent call last>:
>>>            File "C:\Packages\Python25\lib\lib-tk\Tkinter.py" ,  
>>> line 1414, in __call__
>>>                    return self.func(*args)
>>>            File "C:\Program Files\VMTK\lib\vmtk\vmtk\pypepad.py",  
>>> line 217, in RunAllCommand
>>>                     self.RunPype(line)
>>>            File "C:\Program Files\VMTK\lib\vmtk\vmtk\pypepad.py",  
>>> line 151, in RunPype
>>>                      pipe.ParseArguments()
>>>            File "C:\Program Files\VMTK\lib\vmtk\vmtk\pype.py",  
>>> line 94, in ParseArguments
>>>                      
>>> self 
>>> .ScriptList.append([os.path.splitext(os.path.split(scriptSlice[0]) 
>>> [1])[0],scriptSlice[1:]])
>>> IndexError: list index out of range
>>>
>>> Is there a location compatibilty problem wih the file location? Am  
>>> I using the command incorrectly? I hope this helps when solving  
>>> this problem, let me know.
>>>
>>> Thanks,
>>> Sara
>>>
>>>
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>>
>> --
>> Luca Antiga, PhD
>> Head, Medical Imaging Unit,
>> Biomedical Engineering Department,
>> Mario Negri Institute.
>> mail: Villa Camozzi, 24020, Ranica (BG), Italy
>> phone: +39 035 4535-381
>> email: an...@ma...
>> web: http://villacamozzi.marionegri.it/~luca
>>
>>
>
> --
> Luca Antiga, PhD
> Head, Medical Imaging Unit,
> Biomedical Engineering Department,
> Mario Negri Institute.
> mail: Villa Camozzi, 24020, Ranica (BG), Italy
> phone: +39 035 4535-381
> email: an...@ma...
> web: http://villacamozzi.marionegri.it/~luca
>
>
>
>
> -- 
> Sara Nomeland B.S.B.E
> Biomedical Engineering
> sar...@mu...
> (612)709-8762
> <surface&cl.doc>

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