vmtk-users

Re: [vmtk-users] Segmentation error reporting

[Luca A. <luc...@or...>]

Hi Ben,
 thanks for reporting this, it's a useful fix.

Luca

On 08/mar/2013, at 00:07, "Berkowitz, Benjamin M" <ben...@ui...> wrote:

> Luca, 
> 
> I was segmenting using vmtklevelsetsegmentation and I got the following error:
> 
> Traceback (most recent call last):
>  File "segmentation_protocol.py", line 374, in <module>
>    main(sys.argv[1], sys.argv[2], sys.argv[3])
>  File "segmentation_protocol.py", line 309, in main
>    arteriesLvl, isGood = CreateArteries(voiImage, correctionsImage, artery, side, path, caseNumber)
>  File "segmentation_protocol.py", line 149, in CreateArteries
>    arteryLvlSet.Execute()
>  File "/Users/benberkowitz/vmtk-build/Install/lib/vmtk/vmtk/vmtklevelsetsegmentation.py", line 327, in Execute
>    self.vmtkImageInitialization.Execute()
>  File "/Users/benberkowitz/vmtk-build/Install/lib/vmtk/vmtk/vmtkimageinitialization.py", line 446, in Execute
>    initializationMethods[initializationType]()
>  File "/Users/benberkowitz/vmtk-build/Install/lib/vmtk/vmtk/vmtkimageinitialization.py", line 292, in CollidingFrontsInitialize
>    shiftScale.SetScale(1/(scalarRange[1]-scalarRange[0]))
> ZeroDivisionError: float division by zero
> 
> 
> I think it happened because I didn't have voxels selected in the colliding fronts initialization I had just finished.  Not sure how often anyone runs into that, but I thought I would report the error.
> 
> Thanks,
> Ben
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
> endpoint security space. For insight on selecting the right partner to 
> tackle endpoint security challenges, access the full report. 
> http://p.sf.net/sfu/symantec-dev2dev
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] Segmentation error reporting

[Berkowitz, B. M <ben...@ui...>]

Luca, 

I was segmenting using vmtklevelsetsegmentation and I got the following error:

Traceback (most recent call last):
  File "segmentation_protocol.py", line 374, in <module>
    main(sys.argv[1], sys.argv[2], sys.argv[3])
  File "segmentation_protocol.py", line 309, in main
    arteriesLvl, isGood = CreateArteries(voiImage, correctionsImage, artery, side, path, caseNumber)
  File "segmentation_protocol.py", line 149, in CreateArteries
    arteryLvlSet.Execute()
  File "/Users/benberkowitz/vmtk-build/Install/lib/vmtk/vmtk/vmtklevelsetsegmentation.py", line 327, in Execute
    self.vmtkImageInitialization.Execute()
  File "/Users/benberkowitz/vmtk-build/Install/lib/vmtk/vmtk/vmtkimageinitialization.py", line 446, in Execute
    initializationMethods[initializationType]()
  File "/Users/benberkowitz/vmtk-build/Install/lib/vmtk/vmtk/vmtkimageinitialization.py", line 292, in CollidingFrontsInitialize
    shiftScale.SetScale(1/(scalarRange[1]-scalarRange[0]))
ZeroDivisionError: float division by zero


I think it happened because I didn't have voxels selected in the colliding fronts initialization I had just finished.  Not sure how often anyone runs into that, but I thought I would report the error.

Thanks,
Ben

Re: [vmtk-users] not all end-points tracked by vmtkcenterlines

[Richard D. <ric...@ui...>]

On 03/07/2013 04:26 PM, Luca Antiga wrote:
> On Mar 7, 2013, at 9:44 PM, Richard Downe wrote:
>
>> Well...I'm not using vmtkbranchextractor.
>>
>> My branches and vessel are defined separately, and I merge them in a
>> pre-vmtk process.  I have centerlines a priori, but it is not a unified
>> centerline tree.  (I have until now been using source and target
>> points.  This works well in most vessels, but heavily branched ones
>> frequently drop a branch, often the largest one, during the run of
>> vmtkcenterlines, so after reading this thread, I concluded I wasn't
>> alone, and set about trying to reengineer it.)
> I'm not sure I fully understand. A screenshot would help.
I mean that the branches and vessel are segmented separately in 
different tools, and then projected into 3-d space using a variation on 
Frenet-Serret analysis.  I build a triangulated surface using CGAL from 
this point set, and using a python module I wrote myself, slurp this, 
along with the centerlines of the individual surfaces, into vmtk.

The reason for this is that I work with coronary ultrasound.  The 
segmentation of both the vessel and the branches are each less 
straightforward than they are for, say, pulmonary CT.

vmtkmeshgenerator failed outright until I began using vmtkcenterlines to 
help it calibrate the triangle and tetrahedral density.  (The ultimate 
goal is CFD analysis using Ansys Fluent).

In some heavily branched vessels, the outflow surface of one the 
branches shows up as unconnected to the rest of the mesh when I load it 
into fluent.  These are also generally vessels where vmtkcenterlines has 
convergence issues.

So...I'm not sure how I would use vmtkbranchextractor here, unless I 
could feed my initial triangulation into it?
As such, I'm attempting what I realize is something of a hack, feeding 
centerlines and radius information that I have a priori into 
vtkvmtkMergeCenterlines in an attempt to get a proper vessel tree 
without having to rely upon vmtkcenterlines' procedure.

I don't have the "blanking regions" stored anywhere, because it's not 
part of the workflow that leads up to this, but would be fairly trivial 
to surmise, as I could simply test each branch centerline point to see 
if it lies closer than vesselRadius[i] to vesselCenterline[i], for all i.

Thus, my centerline *is* already broken into branches, but not using 
vmtkbranchextractor.
Attached is a screenshot of the result of running it with what were 
clearly mistaken group/tract ids.  It clearly tried to connect all 
segments, but with no knowledge of where bifurcations were, simply 
tacked them all end-to-end to form 1 centerline.

So really...I'm trying to figure out, if I must synthesize group and 
tract ids, how do I do so in a way that will correctly inform the 
merging of my branch centerline segments?
-rd
>
>> I just tried running it with groupID==centerlineID for all centerlines,
>> and tractID = uniformly 1, and blanking = uniformly 0.
>>
>> The result was an unruly knot that suggested that it didn't know what to
>> connect to what.
> Yes, the centerline has to be first split into branches using vmtkbranchextractor
> (which will identify bifurcations, split and group) and then vmtkcenterlinemerge
> will generate one centerline per group and create a proper network.
>
>> I suspect, after digging through the vtkVmtk source code and looking at
>> this http://www.vmtk.org/Tutorials/BranchSplitting/ example, I need to
>> actually annotate the bifurcation regions by setting group and tract id,
>> and blanking, correctly.
> Yes, but you also need to split centerline cells in chunks, as depicted in
> the branch splitting tutorial.
>
>> If I understand this correctly, I can create a bifurcation region by
>> identifying where the branch departs the vessel, and appending 1
>> location on the vessel centerline to the branch centerline at the
>> proximal-most location.  And then, groupID increments at and after each
>> bifurcation region, and blanking is set to 1 in each bifurcation region.
>>
>> I'm less clear on tract ID.  Is it always either 1 or 2, depending
>> whether before or after the bifurcation point?  Or does it get set to a
>> unique value for each chunk vis a vis group id?
> Consider the individual centerline cell originally running between
> inlet and outlet. Now that you have split it in chunks, number each
> chunk from 0 to n. That's the tract id.
>
>> I won't be able to get to it until this evening, but I believe that's
>> the next logical step.
> Keep us posted. However, I'd also like to understand more of your approach,
> so if you could clarify your first paragraph that would be great.
>
> Thanks
>
> Luca
>
>> -rd
>>
>> On 03/07/2013 10:35 AM, Luca Antiga wrote:
>>> Hi Richard,
>>>   just pipe vmtkcenterlinemerge after vmtkbranchextractor and use -ofile to write the file out, that's the quickest.
>>> What is your exact issue?
>>>
>>> Roman: I haven't got an answer for you yet - I've been taking care of the quick messages but yours requires a free slot of time. Thanks for your patience.
>>>
>>> Luca
>>>
>>> On 06/mar/2013, at 18:31, Richard Downe <ric...@ui...> wrote:
>>>
>>>> Luca--
>>>> I've been vexed by a similar situation for awhile that I'm just now getting around to tackling.
>>>> One thing I *do* have, however, is centerlines for my main vessel an all branches.
>>>> I've noticed a vmtkcenterlinemerge.py/vtkvmtkMergeCenterlines.h/cxx that don't appear to be used anywhere, so I can't find a usage example.
>>>>
>>>> What do I need to pass in for the tract ids and blanking ids to make this work, or do you have a usage example somewhere?
>>>> -rd
>>>>
>>>> On 03/04/2013 07:00 AM, Luca Antiga wrote:
>>>>> Hi Roman,
>>>>>   I'll really need to take a closer look to the data you sent, I'm planning to do it in the next few days.
>>>>> Thanks
>>>>>
>>>>> Luca
>>>>>
>>>>> On Mar 4, 2013, at 1:54 PM, Dr. Roman Grothausmann wrote:
>>>>>
>>>>>> On 23/02/13 13:56, Luca Antiga wrote:
>>>>>>> Possible workarounds:
>>>>>>>
>>>>>>> 1. Try to use Tetgen to generate the internal Delaunay tessellation, instead of the default algorithm. This can be easily
>>>>>>> done by specifying -usetetgen 1 in the vmtkcenterlines command line
>>>>>> Using tetgen I get an error and the resulting VTP-file is empty (second workaround is still running):
>>>>>>
>>>>>> Reading VTK XML surface file.
>>>>>> Executing vmtkcenterlines ...
>>>>>> Cleaning surface.
>>>>>> Triangulating surface.
>>>>>> Computing centerlines.
>>>>>> Computing centerlines...Running TetGen.
>>>>>> TetGen command line options: pT1.000000e-08dzQ
>>>>>> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkNonManifoldFastMarching.cxx, line 667
>>>>>> vtkvmtkNonManifoldFastMarching (0xe6fdac0): Cost function array with name specified does not exist!
>>>>>>
>>>>>> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkSteepestDescentLineTracer.cxx, line 318
>>>>>> vtkvmtkSteepestDescentLineTracer (0xe6f9210): Descent array with name specified does not exist!
>>>>>>
>>>>>> Done executing vmtkcenterlines.
>>>>>> Writing VTK XML surface file.
>>>>>> Output vmtkcenterlines members:
>>>>>>
>>>>>>> 2. Compute the Delaunay tessellation on the closed surface (prior to cutting the endcaps open) using vmtkdelaunayvoronoi
>>>>>>> and feed it to vmtkcenterlines, this way:
>>>>>>>
>>>>>>> vmtkdelaunayvoronoi -ifile unclipped.vtp --pipe vmtkcenterlines -ifile clipped.vtp ...
>>>>>> Using this command causes no errors but the resulting file is also empty.
>>>>>>
>>>>>> Any ideas what else I could try?
>>>>>>
>>>>>> Many thanks for any help or hints.
>>>>>> Roman
>>>>>>
>>>>>>
>>>>>>
>>>>>>> This will allow you to take advantage of the clipped endcaps for the seedselector (since you feed clipped.vtp as input to vmtkcenterlines)
>>>>>>> but use the Delaunay tessellation computed from the unclipped one, which shouldn't have the issue with the artifactual inner tets.
>>>>>>>
>>>>>>> In any case, it would be good for me to have the surface so I can use it to fix the internal delaunay tet selection issue.
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Luca
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Feb 22, 2013, at 9:32 AM, Dr. Roman Grothausmann wrote:
>>>>>>>
>>>>>>>> (now with images)
>>>>>>>>
>>>>>>>> Dear mailing list members,
>>>>>>>>
>>>>>>>>
>>>>>>>> Another problem I have is that not all end-points that I extract from the output of vmtknetwork (magenta lines in attached image) are tracked by vmtkcenterlines (grey/blue lines), most are but some are not. See the end points of the magenta lines of which a grey line stretches like a cobweb string. After removing these cobweb lines I end up with the blue lines which are OK except for the lacking branches.
>>>>>>>> What could be the reason for that and how could I avoid it?
>>>>>>>>
>>>>>>>> Any help or hints are very much appreciated
>>>>>>>> Roman
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Dr. Roman Grothausmann
>>>>>>>>
>>>>>>>> Tomographie und Digitale Bildverarbeitung
>>>>>>>> Tomography and Digital Image Analysis
>>>>>>>>
>>>>>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>>>>>> Medizinische Hochschule Hannover
>>>>>>>> Carl-Neuberg-Str. 1
>>>>>>>> D-30625 Hannover
>>>>>>>>
>>>>>>>> Tel. +49 511 532-9574
>>>>>>>>
>>>>>>>>
>>>>>>>> <KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_03.gif><KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_05.gif>------------------------------------------------------------------------------
>>>>>>>> Everyone hates slow websites. So do we.
>>>>>>>> Make your web apps faster with AppDynamics
>>>>>>>> Download AppDynamics Lite for free today:
>>>>>>>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>>>>>>>> vmtk-users mailing list
>>>>>>>> vmt...@li...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>>>> -- 
>>>>>> Dr. Roman Grothausmann
>>>>>>
>>>>>> Tomographie und Digitale Bildverarbeitung
>>>>>> Tomography and Digital Image Analysis
>>>>>>
>>>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>>>> Medizinische Hochschule Hannover
>>>>>> Carl-Neuberg-Str. 1
>>>>>> D-30625 Hannover
>>>>>>
>>>>>> Tel. +49 511 532-9574
>>>>> ------------------------------------------------------------------------------
>>>>> Everyone hates slow websites. So do we.
>>>>> Make your web apps faster with AppDynamics
>>>>> Download AppDynamics Lite for free today:
>>>>> http://p.sf.net/sfu/appdyn_d2d_feb
>>>>> _______________________________________________
>>>>> vmtk-users mailing list
>>>>> vmt...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>> ------------------------------------------------------------------------------
>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
>> endpoint security space. For insight on selecting the right partner to
>> tackle endpoint security challenges, access the full report.
>> http://p.sf.net/sfu/symantec-dev2dev
>> _______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] not all end-points tracked by vmtkcenterlines

[Luca A. <luc...@or...>]

On Mar 7, 2013, at 9:44 PM, Richard Downe wrote:

> Well...I'm not using vmtkbranchextractor.
> 
> My branches and vessel are defined separately, and I merge them in a 
> pre-vmtk process.  I have centerlines a priori, but it is not a unified 
> centerline tree.  (I have until now been using source and target 
> points.  This works well in most vessels, but heavily branched ones 
> frequently drop a branch, often the largest one, during the run of 
> vmtkcenterlines, so after reading this thread, I concluded I wasn't 
> alone, and set about trying to reengineer it.)

I'm not sure I fully understand. A screenshot would help.

> I just tried running it with groupID==centerlineID for all centerlines, 
> and tractID = uniformly 1, and blanking = uniformly 0.
> 
> The result was an unruly knot that suggested that it didn't know what to 
> connect to what.

Yes, the centerline has to be first split into branches using vmtkbranchextractor
(which will identify bifurcations, split and group) and then vmtkcenterlinemerge
will generate one centerline per group and create a proper network.

> I suspect, after digging through the vtkVmtk source code and looking at 
> this http://www.vmtk.org/Tutorials/BranchSplitting/ example, I need to 
> actually annotate the bifurcation regions by setting group and tract id, 
> and blanking, correctly.

Yes, but you also need to split centerline cells in chunks, as depicted in
the branch splitting tutorial.

> If I understand this correctly, I can create a bifurcation region by 
> identifying where the branch departs the vessel, and appending 1 
> location on the vessel centerline to the branch centerline at the 
> proximal-most location.  And then, groupID increments at and after each 
> bifurcation region, and blanking is set to 1 in each bifurcation region.
> 
> I'm less clear on tract ID.  Is it always either 1 or 2, depending 
> whether before or after the bifurcation point?  Or does it get set to a 
> unique value for each chunk vis a vis group id?

Consider the individual centerline cell originally running between
inlet and outlet. Now that you have split it in chunks, number each
chunk from 0 to n. That's the tract id.

> I won't be able to get to it until this evening, but I believe that's 
> the next logical step.

Keep us posted. However, I'd also like to understand more of your approach,
so if you could clarify your first paragraph that would be great.

Thanks

Luca

> -rd
> 
> On 03/07/2013 10:35 AM, Luca Antiga wrote:
>> Hi Richard,
>>  just pipe vmtkcenterlinemerge after vmtkbranchextractor and use -ofile to write the file out, that's the quickest.
>> What is your exact issue?
>> 
>> Roman: I haven't got an answer for you yet - I've been taking care of the quick messages but yours requires a free slot of time. Thanks for your patience.
>> 
>> Luca
>> 
>> On 06/mar/2013, at 18:31, Richard Downe <ric...@ui...> wrote:
>> 
>>> Luca--
>>> I've been vexed by a similar situation for awhile that I'm just now getting around to tackling.
>>> One thing I *do* have, however, is centerlines for my main vessel an all branches.
>>> I've noticed a vmtkcenterlinemerge.py/vtkvmtkMergeCenterlines.h/cxx that don't appear to be used anywhere, so I can't find a usage example.
>>> 
>>> What do I need to pass in for the tract ids and blanking ids to make this work, or do you have a usage example somewhere?
>>> -rd
>>> 
>>> On 03/04/2013 07:00 AM, Luca Antiga wrote:
>>>> Hi Roman,
>>>>  I'll really need to take a closer look to the data you sent, I'm planning to do it in the next few days.
>>>> Thanks
>>>> 
>>>> Luca
>>>> 
>>>> On Mar 4, 2013, at 1:54 PM, Dr. Roman Grothausmann wrote:
>>>> 
>>>>> On 23/02/13 13:56, Luca Antiga wrote:
>>>>>> Possible workarounds:
>>>>>> 
>>>>>> 1. Try to use Tetgen to generate the internal Delaunay tessellation, instead of the default algorithm. This can be easily
>>>>>> done by specifying -usetetgen 1 in the vmtkcenterlines command line
>>>>> Using tetgen I get an error and the resulting VTP-file is empty (second workaround is still running):
>>>>> 
>>>>> Reading VTK XML surface file.
>>>>> Executing vmtkcenterlines ...
>>>>> Cleaning surface.
>>>>> Triangulating surface.
>>>>> Computing centerlines.
>>>>> Computing centerlines...Running TetGen.
>>>>> TetGen command line options: pT1.000000e-08dzQ
>>>>> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkNonManifoldFastMarching.cxx, line 667
>>>>> vtkvmtkNonManifoldFastMarching (0xe6fdac0): Cost function array with name specified does not exist!
>>>>> 
>>>>> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkSteepestDescentLineTracer.cxx, line 318
>>>>> vtkvmtkSteepestDescentLineTracer (0xe6f9210): Descent array with name specified does not exist!
>>>>> 
>>>>> Done executing vmtkcenterlines.
>>>>> Writing VTK XML surface file.
>>>>> Output vmtkcenterlines members:
>>>>> 
>>>>>> 2. Compute the Delaunay tessellation on the closed surface (prior to cutting the endcaps open) using vmtkdelaunayvoronoi
>>>>>> and feed it to vmtkcenterlines, this way:
>>>>>> 
>>>>>> vmtkdelaunayvoronoi -ifile unclipped.vtp --pipe vmtkcenterlines -ifile clipped.vtp ...
>>>>> Using this command causes no errors but the resulting file is also empty.
>>>>> 
>>>>> Any ideas what else I could try?
>>>>> 
>>>>> Many thanks for any help or hints.
>>>>> Roman
>>>>> 
>>>>> 
>>>>> 
>>>>>> This will allow you to take advantage of the clipped endcaps for the seedselector (since you feed clipped.vtp as input to vmtkcenterlines)
>>>>>> but use the Delaunay tessellation computed from the unclipped one, which shouldn't have the issue with the artifactual inner tets.
>>>>>> 
>>>>>> In any case, it would be good for me to have the surface so I can use it to fix the internal delaunay tet selection issue.
>>>>>> 
>>>>>> Best,
>>>>>> 
>>>>>> Luca
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On Feb 22, 2013, at 9:32 AM, Dr. Roman Grothausmann wrote:
>>>>>> 
>>>>>>> (now with images)
>>>>>>> 
>>>>>>> Dear mailing list members,
>>>>>>> 
>>>>>>> 
>>>>>>> Another problem I have is that not all end-points that I extract from the output of vmtknetwork (magenta lines in attached image) are tracked by vmtkcenterlines (grey/blue lines), most are but some are not. See the end points of the magenta lines of which a grey line stretches like a cobweb string. After removing these cobweb lines I end up with the blue lines which are OK except for the lacking branches.
>>>>>>> What could be the reason for that and how could I avoid it?
>>>>>>> 
>>>>>>> Any help or hints are very much appreciated
>>>>>>> Roman
>>>>>>> 
>>>>>>> 
>>>>>>> --
>>>>>>> Dr. Roman Grothausmann
>>>>>>> 
>>>>>>> Tomographie und Digitale Bildverarbeitung
>>>>>>> Tomography and Digital Image Analysis
>>>>>>> 
>>>>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>>>>> Medizinische Hochschule Hannover
>>>>>>> Carl-Neuberg-Str. 1
>>>>>>> D-30625 Hannover
>>>>>>> 
>>>>>>> Tel. +49 511 532-9574
>>>>>>> 
>>>>>>> 
>>>>>>> <KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_03.gif><KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_05.gif>------------------------------------------------------------------------------
>>>>>>> Everyone hates slow websites. So do we.
>>>>>>> Make your web apps faster with AppDynamics
>>>>>>> Download AppDynamics Lite for free today:
>>>>>>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>>>>>>> vmtk-users mailing list
>>>>>>> vmt...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>>> -- 
>>>>> Dr. Roman Grothausmann
>>>>> 
>>>>> Tomographie und Digitale Bildverarbeitung
>>>>> Tomography and Digital Image Analysis
>>>>> 
>>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>>> Medizinische Hochschule Hannover
>>>>> Carl-Neuberg-Str. 1
>>>>> D-30625 Hannover
>>>>> 
>>>>> Tel. +49 511 532-9574
>>>> ------------------------------------------------------------------------------
>>>> Everyone hates slow websites. So do we.
>>>> Make your web apps faster with AppDynamics
>>>> Download AppDynamics Lite for free today:
>>>> http://p.sf.net/sfu/appdyn_d2d_feb
>>>> _______________________________________________
>>>> vmtk-users mailing list
>>>> vmt...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> 
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
> endpoint security space. For insight on selecting the right partner to 
> tackle endpoint security challenges, access the full report. 
> http://p.sf.net/sfu/symantec-dev2dev
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] not all end-points tracked by vmtkcenterlines

[Richard D. <ric...@ui...>]

Well...I'm not using vmtkbranchextractor.

My branches and vessel are defined separately, and I merge them in a 
pre-vmtk process.  I have centerlines a priori, but it is not a unified 
centerline tree.  (I have until now been using source and target 
points.  This works well in most vessels, but heavily branched ones 
frequently drop a branch, often the largest one, during the run of 
vmtkcenterlines, so after reading this thread, I concluded I wasn't 
alone, and set about trying to reengineer it.)

I just tried running it with groupID==centerlineID for all centerlines, 
and tractID = uniformly 1, and blanking = uniformly 0.

The result was an unruly knot that suggested that it didn't know what to 
connect to what.

I suspect, after digging through the vtkVmtk source code and looking at 
this http://www.vmtk.org/Tutorials/BranchSplitting/ example, I need to 
actually annotate the bifurcation regions by setting group and tract id, 
and blanking, correctly.

If I understand this correctly, I can create a bifurcation region by 
identifying where the branch departs the vessel, and appending 1 
location on the vessel centerline to the branch centerline at the 
proximal-most location.  And then, groupID increments at and after each 
bifurcation region, and blanking is set to 1 in each bifurcation region.

I'm less clear on tract ID.  Is it always either 1 or 2, depending 
whether before or after the bifurcation point?  Or does it get set to a 
unique value for each chunk vis a vis group id?

I won't be able to get to it until this evening, but I believe that's 
the next logical step.
-rd

On 03/07/2013 10:35 AM, Luca Antiga wrote:
> Hi Richard,
>   just pipe vmtkcenterlinemerge after vmtkbranchextractor and use -ofile to write the file out, that's the quickest.
> What is your exact issue?
>
> Roman: I haven't got an answer for you yet - I've been taking care of the quick messages but yours requires a free slot of time. Thanks for your patience.
>
> Luca
>
> On 06/mar/2013, at 18:31, Richard Downe <ric...@ui...> wrote:
>
>> Luca--
>> I've been vexed by a similar situation for awhile that I'm just now getting around to tackling.
>> One thing I *do* have, however, is centerlines for my main vessel an all branches.
>> I've noticed a vmtkcenterlinemerge.py/vtkvmtkMergeCenterlines.h/cxx that don't appear to be used anywhere, so I can't find a usage example.
>>
>> What do I need to pass in for the tract ids and blanking ids to make this work, or do you have a usage example somewhere?
>> -rd
>>
>> On 03/04/2013 07:00 AM, Luca Antiga wrote:
>>> Hi Roman,
>>>   I'll really need to take a closer look to the data you sent, I'm planning to do it in the next few days.
>>> Thanks
>>>
>>> Luca
>>>
>>> On Mar 4, 2013, at 1:54 PM, Dr. Roman Grothausmann wrote:
>>>
>>>> On 23/02/13 13:56, Luca Antiga wrote:
>>>>> Possible workarounds:
>>>>>
>>>>> 1. Try to use Tetgen to generate the internal Delaunay tessellation, instead of the default algorithm. This can be easily
>>>>> done by specifying -usetetgen 1 in the vmtkcenterlines command line
>>>> Using tetgen I get an error and the resulting VTP-file is empty (second workaround is still running):
>>>>
>>>> Reading VTK XML surface file.
>>>> Executing vmtkcenterlines ...
>>>> Cleaning surface.
>>>> Triangulating surface.
>>>> Computing centerlines.
>>>> Computing centerlines...Running TetGen.
>>>> TetGen command line options: pT1.000000e-08dzQ
>>>> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkNonManifoldFastMarching.cxx, line 667
>>>> vtkvmtkNonManifoldFastMarching (0xe6fdac0): Cost function array with name specified does not exist!
>>>>
>>>> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkSteepestDescentLineTracer.cxx, line 318
>>>> vtkvmtkSteepestDescentLineTracer (0xe6f9210): Descent array with name specified does not exist!
>>>>
>>>> Done executing vmtkcenterlines.
>>>> Writing VTK XML surface file.
>>>> Output vmtkcenterlines members:
>>>>
>>>>> 2. Compute the Delaunay tessellation on the closed surface (prior to cutting the endcaps open) using vmtkdelaunayvoronoi
>>>>> and feed it to vmtkcenterlines, this way:
>>>>>
>>>>> vmtkdelaunayvoronoi -ifile unclipped.vtp --pipe vmtkcenterlines -ifile clipped.vtp ...
>>>> Using this command causes no errors but the resulting file is also empty.
>>>>
>>>> Any ideas what else I could try?
>>>>
>>>> Many thanks for any help or hints.
>>>> Roman
>>>>
>>>>
>>>>
>>>>> This will allow you to take advantage of the clipped endcaps for the seedselector (since you feed clipped.vtp as input to vmtkcenterlines)
>>>>> but use the Delaunay tessellation computed from the unclipped one, which shouldn't have the issue with the artifactual inner tets.
>>>>>
>>>>> In any case, it would be good for me to have the surface so I can use it to fix the internal delaunay tet selection issue.
>>>>>
>>>>> Best,
>>>>>
>>>>> Luca
>>>>>
>>>>>
>>>>>
>>>>> On Feb 22, 2013, at 9:32 AM, Dr. Roman Grothausmann wrote:
>>>>>
>>>>>> (now with images)
>>>>>>
>>>>>> Dear mailing list members,
>>>>>>
>>>>>>
>>>>>> Another problem I have is that not all end-points that I extract from the output of vmtknetwork (magenta lines in attached image) are tracked by vmtkcenterlines (grey/blue lines), most are but some are not. See the end points of the magenta lines of which a grey line stretches like a cobweb string. After removing these cobweb lines I end up with the blue lines which are OK except for the lacking branches.
>>>>>> What could be the reason for that and how could I avoid it?
>>>>>>
>>>>>> Any help or hints are very much appreciated
>>>>>> Roman
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Dr. Roman Grothausmann
>>>>>>
>>>>>> Tomographie und Digitale Bildverarbeitung
>>>>>> Tomography and Digital Image Analysis
>>>>>>
>>>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>>>> Medizinische Hochschule Hannover
>>>>>> Carl-Neuberg-Str. 1
>>>>>> D-30625 Hannover
>>>>>>
>>>>>> Tel. +49 511 532-9574
>>>>>>
>>>>>>
>>>>>> <KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_03.gif><KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_05.gif>------------------------------------------------------------------------------
>>>>>> Everyone hates slow websites. So do we.
>>>>>> Make your web apps faster with AppDynamics
>>>>>> Download AppDynamics Lite for free today:
>>>>>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>>>>>> vmtk-users mailing list
>>>>>> vmt...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>> -- 
>>>> Dr. Roman Grothausmann
>>>>
>>>> Tomographie und Digitale Bildverarbeitung
>>>> Tomography and Digital Image Analysis
>>>>
>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>> Medizinische Hochschule Hannover
>>>> Carl-Neuberg-Str. 1
>>>> D-30625 Hannover
>>>>
>>>> Tel. +49 511 532-9574
>>> ------------------------------------------------------------------------------
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_feb
>>> _______________________________________________
>>> vmtk-users mailing list
>>> vmt...@li...
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] not all end-points tracked by vmtkcenterlines

[Luca A. <luc...@or...>]

Hi Richard,
 just pipe vmtkcenterlinemerge after vmtkbranchextractor and use -ofile to write the file out, that's the quickest.
What is your exact issue?

Roman: I haven't got an answer for you yet - I've been taking care of the quick messages but yours requires a free slot of time. Thanks for your patience.

Luca

On 06/mar/2013, at 18:31, Richard Downe <ric...@ui...> wrote:

> Luca--
> I've been vexed by a similar situation for awhile that I'm just now getting around to tackling.
> One thing I *do* have, however, is centerlines for my main vessel an all branches.
> I've noticed a vmtkcenterlinemerge.py/vtkvmtkMergeCenterlines.h/cxx that don't appear to be used anywhere, so I can't find a usage example.
> 
> What do I need to pass in for the tract ids and blanking ids to make this work, or do you have a usage example somewhere?
> -rd
> 
> On 03/04/2013 07:00 AM, Luca Antiga wrote:
>> Hi Roman,
>>  I'll really need to take a closer look to the data you sent, I'm planning to do it in the next few days.
>> Thanks
>> 
>> Luca
>> 
>> On Mar 4, 2013, at 1:54 PM, Dr. Roman Grothausmann wrote:
>> 
>>> On 23/02/13 13:56, Luca Antiga wrote:
>>>> Possible workarounds:
>>>> 
>>>> 1. Try to use Tetgen to generate the internal Delaunay tessellation, instead of the default algorithm. This can be easily
>>>> done by specifying -usetetgen 1 in the vmtkcenterlines command line
>>> Using tetgen I get an error and the resulting VTP-file is empty (second workaround is still running):
>>> 
>>> Reading VTK XML surface file.
>>> Executing vmtkcenterlines ...
>>> Cleaning surface.
>>> Triangulating surface.
>>> Computing centerlines.
>>> Computing centerlines...Running TetGen.
>>> TetGen command line options: pT1.000000e-08dzQ
>>> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkNonManifoldFastMarching.cxx, line 667
>>> vtkvmtkNonManifoldFastMarching (0xe6fdac0): Cost function array with name specified does not exist!
>>> 
>>> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkSteepestDescentLineTracer.cxx, line 318
>>> vtkvmtkSteepestDescentLineTracer (0xe6f9210): Descent array with name specified does not exist!
>>> 
>>> Done executing vmtkcenterlines.
>>> Writing VTK XML surface file.
>>> Output vmtkcenterlines members:
>>> 
>>>> 2. Compute the Delaunay tessellation on the closed surface (prior to cutting the endcaps open) using vmtkdelaunayvoronoi
>>>> and feed it to vmtkcenterlines, this way:
>>>> 
>>>> vmtkdelaunayvoronoi -ifile unclipped.vtp --pipe vmtkcenterlines -ifile clipped.vtp ...
>>> Using this command causes no errors but the resulting file is also empty.
>>> 
>>> Any ideas what else I could try?
>>> 
>>> Many thanks for any help or hints.
>>> Roman
>>> 
>>> 
>>> 
>>>> This will allow you to take advantage of the clipped endcaps for the seedselector (since you feed clipped.vtp as input to vmtkcenterlines)
>>>> but use the Delaunay tessellation computed from the unclipped one, which shouldn't have the issue with the artifactual inner tets.
>>>> 
>>>> In any case, it would be good for me to have the surface so I can use it to fix the internal delaunay tet selection issue.
>>>> 
>>>> Best,
>>>> 
>>>> Luca
>>>> 
>>>> 
>>>> 
>>>> On Feb 22, 2013, at 9:32 AM, Dr. Roman Grothausmann wrote:
>>>> 
>>>>> (now with images)
>>>>> 
>>>>> Dear mailing list members,
>>>>> 
>>>>> 
>>>>> Another problem I have is that not all end-points that I extract from the output of vmtknetwork (magenta lines in attached image) are tracked by vmtkcenterlines (grey/blue lines), most are but some are not. See the end points of the magenta lines of which a grey line stretches like a cobweb string. After removing these cobweb lines I end up with the blue lines which are OK except for the lacking branches.
>>>>> What could be the reason for that and how could I avoid it?
>>>>> 
>>>>> Any help or hints are very much appreciated
>>>>> Roman
>>>>> 
>>>>> 
>>>>> --
>>>>> Dr. Roman Grothausmann
>>>>> 
>>>>> Tomographie und Digitale Bildverarbeitung
>>>>> Tomography and Digital Image Analysis
>>>>> 
>>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>>> Medizinische Hochschule Hannover
>>>>> Carl-Neuberg-Str. 1
>>>>> D-30625 Hannover
>>>>> 
>>>>> Tel. +49 511 532-9574
>>>>> 
>>>>> 
>>>>> <KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_03.gif><KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_05.gif>------------------------------------------------------------------------------
>>>>> Everyone hates slow websites. So do we.
>>>>> Make your web apps faster with AppDynamics
>>>>> Download AppDynamics Lite for free today:
>>>>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>>>>> vmtk-users mailing list
>>>>> vmt...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>> -- 
>>> Dr. Roman Grothausmann
>>> 
>>> Tomographie und Digitale Bildverarbeitung
>>> Tomography and Digital Image Analysis
>>> 
>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>> Medizinische Hochschule Hannover
>>> Carl-Neuberg-Str. 1
>>> D-30625 Hannover
>>> 
>>> Tel. +49 511 532-9574
>> 
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb
>> _______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 

Re: [vmtk-users] how to set the environment variables in windows7

[Luca A. <luc...@or...>]

To looks to me like your Aorta_voi.vtp file is in the Aorta_voi folder,
so it would be  
vmtksurfaceviewer -ifile C:\\Aorta_voi\\Aorta_voi.vtp

Luca

On Mar 7, 2013, at 4:10 PM, Haibin Cai wrote:

> Hi Luca,
>    Oh my god, It works!!! Thank you very much! I type "vmtkmarchingcubes -ifile C:\\Aorta_voi\\Aorta_voi.mha -ofile C:\\Aorta_voi\\Aorta_voi.vtp" in the Pypepad,and then a voi.vtp comes out in my file.Then I try to open the file.I type "vmtksurfaceviewer -ifile C:\\Aorta_voi.vtp",an error comes up. It says "ERROR: In C:\Users\orobix\Documents\VMTK\vmtk-build\VTK\IO\vtkXMLReader.cxx, line 219
> vtkXMLPolyDataReader (01E260C0): Error opening file C:\Aorta_voi.vtp".What can I do?
> Thanks,
> haibin
> 
> 
> 2013/3/7 Luca Antiga <luc...@gm...>
> Hi Haibin,
>  try with 
> 
> vmtkmarchingcubes -ifile foo.mha -ofile foo.vtp
> 
> mha and vti are both image file formats, it will work both ways.
> 
> Luca
> 
> 
> On Mar 7, 2013, at 3:50 PM, Haibin Cai wrote:
> 
>> Hi Luca,
>>     Thank you for your help, I add the followwing to my path----"C:\build\vmtk-build\Install\bin;C:\build\vmtk-build\Install\lib\vtk-5.10;C:\build\vmtk-build\Install\lib\vmtk;C:\build\vmtk-build\Install\lib\InsightToolkit;C:\build\vmtk-build\Install\bin\Python"
>>     Then I double click vmtk-exe.pyw.It is in----C:\Program Files\vmtk\Install\bin, then the PypePad comes out.I type "vmtkmarchingcubes --help",and it comes out Creating vmtkMarchingCubes instance ....just as your  instructions. so I want to type "vmtkmarchingcubes -ifile foo.vti -ofile foo.vtp",but an error comes out that "error opening file foo.vti".I do not have a file who's Suffix is vti or vtp. I only get the "Aorta_voi.mha" in your website,where can I find or download the .vti,.vtp files? 
>> Thanks,
>> haibin
>> 
>> 
>> 2013/3/7 Luca Antiga <luc...@or...>
>> Hi Haibin,
>>  Windows doesn't have a LD_LIBRARY_PATH environment variable. Instead, set everything to PATH.
>> 
>> By the way, you should find a recently added file in the vmtk-build/VMTK-build directory called
>> vmtk_startup.bat. vmtk should start if you double click on that. This shouldn't require to set any
>> environment variables.
>> I'd be very interested to know if this works for you, in this case I'll change the instructions on the website.
>> 
>> Best,
>> 
>> Luca
>> 
>> 
>> On Mar 7, 2013, at 2:43 PM, Haibin Cai wrote:
>> 
>>> Dear Luca and VTK/VMTK Users,
>>>    I have successfully build vmtk/VTK/ITK using the instructions of the VMTK website.But a problem comes out at step 5! I am using the operating system of windows7. Could you please tell me how to set the environment in windows7.
>>>   I know there are environment variables in windows7. I can add the $VMTKHOME/bin to the path.And I can build a variable named PYTHONPATH and gave it the value of $VMTKHOME/bin/Python;$VMTKHOME/lib/vtk-5.10;$VMTKHOME/lib/vmtk if you want.And also LD_LIBRARY_PATH.But I think it's not right, please help me! 
>>> Thanks 
>>> haibin
>>> ------------------------------------------------------------------------------
>>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
>>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
>>> endpoint security space. For insight on selecting the right partner to 
>>> tackle endpoint security challenges, access the full report. 
>>> http://p.sf.net/sfu/symantec-dev2dev_______________________________________________
>>> vmtk-users mailing list
>>> vmt...@li...
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>> 
>> 
>> ------------------------------------------------------------------------------
>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
>> endpoint security space. For insight on selecting the right partner to 
>> tackle endpoint security challenges, access the full report. 
>> http://p.sf.net/sfu/symantec-dev2dev_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> 
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
> endpoint security space. For insight on selecting the right partner to 
> tackle endpoint security challenges, access the full report. 
> http://p.sf.net/sfu/symantec-dev2dev_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] how to set the environment variables in windows7

[Haibin C. <jlc...@gm...>]

Hi Luca,
   Oh my god, It works!!! Thank you very much! I type "vmtkmarchingcubes
-ifile C:\\Aorta_voi\\Aorta_voi.mha -ofile C:\\Aorta_voi\\Aorta_voi.vtp" in
the Pypepad,and then a voi.vtp comes out in my file.Then I try to open the
file.I type "vmtksurfaceviewer -ifile C:\\Aorta_voi.vtp",an error comes up.
It says "ERROR: In
C:\Users\orobix\Documents\VMTK\vmtk-build\VTK\IO\vtkXMLReader.cxx, line 219
vtkXMLPolyDataReader (01E260C0): Error opening file C:\Aorta_voi.vtp".What
can I do?
Thanks,
haibin


2013/3/7 Luca Antiga <luc...@gm...>

> Hi Haibin,
>  try with
>
> vmtkmarchingcubes -ifile foo.mha -ofile foo.vtp
>
> mha and vti are both image file formats, it will work both ways.
>
> Luca
>
>
> On Mar 7, 2013, at 3:50 PM, Haibin Cai wrote:
>
> Hi Luca,
>     Thank you for your help, I add the followwing to my
> path----"C:\build\vmtk-build\Install\bin;C:\build\vmtk-build\Install\lib\vtk-5.10;C:\build\vmtk-build\Install\lib\vmtk;C:\build\vmtk-build\Install\lib\InsightToolkit;C:\build\vmtk-build\Install\bin\Python"
>     Then I double click vmtk-exe.pyw.It is in----C:\Program
> Files\vmtk\Install\bin, then the PypePad comes out.I type
> "vmtkmarchingcubes --help",and it comes out Creating vmtkMarchingCubes
> instance ....just as your  instructions. so I want to type "vmtkmarchingcubes
> -ifile foo.vti -ofile foo.vtp",but an error comes out that "error opening
> file foo.vti".I do not have a file who's Suffix is vti or vtp. I only get
> the "Aorta_voi.mha" in your website,where can I find or download the
> .vti,.vtp files?
> Thanks,
> haibin
>
>
> 2013/3/7 Luca Antiga <luc...@or...>
>
>> Hi Haibin,
>>  Windows doesn't have a LD_LIBRARY_PATH environment variable. Instead,
>> set everything to PATH.
>>
>> By the way, you should find a recently added file in the
>> vmtk-build/VMTK-build directory called
>> vmtk_startup.bat. vmtk should start if you double click on that. This
>> shouldn't require to set any
>> environment variables.
>> I'd be very interested to know if this works for you, in this case I'll
>> change the instructions on the website.
>>
>> Best,
>>
>> Luca
>>
>>
>> On Mar 7, 2013, at 2:43 PM, Haibin Cai wrote:
>>
>> Dear Luca and VTK/VMTK Users,
>>    I have successfully build vmtk/VTK/ITK using the instructions of the
>> VMTK website.But a problem comes out at step 5! I am using the operating
>> system of windows7. Could you please tell me how to set the environment in
>> windows7.
>>   I know there are environment variables in windows7. I can add the $VMTKHOME/bin
>> to the path.And I can build a variable named PYTHONPATH and gave it the
>> value of $VMTKHOME/bin/Python;$VMTKHOME/lib/vtk-5.10;$VMTKHOME/lib/vmtk
>> if you want.And also LD_LIBRARY_PATH.But I think it's not right, please
>> help me!
>> Thanks
>> haibin
>> ------------------------------------------------------------------------------
>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
>> endpoint security space. For insight on selecting the right partner to
>> tackle endpoint security challenges, access the full report.
>>
>> http://p.sf.net/sfu/symantec-dev2dev_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>>
>>
>
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
> endpoint security space. For insight on selecting the right partner to
> tackle endpoint security challenges, access the full report.
>
> http://p.sf.net/sfu/symantec-dev2dev_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>
>

Re: [vmtk-users] how to set the environment variables in windows7

[Luca A. <luc...@gm...>]

Hi Haibin,
 try with 

vmtkmarchingcubes -ifile foo.mha -ofile foo.vtp

mha and vti are both image file formats, it will work both ways.

Luca


On Mar 7, 2013, at 3:50 PM, Haibin Cai wrote:

> Hi Luca,
>     Thank you for your help, I add the followwing to my path----"C:\build\vmtk-build\Install\bin;C:\build\vmtk-build\Install\lib\vtk-5.10;C:\build\vmtk-build\Install\lib\vmtk;C:\build\vmtk-build\Install\lib\InsightToolkit;C:\build\vmtk-build\Install\bin\Python"
>     Then I double click vmtk-exe.pyw.It is in----C:\Program Files\vmtk\Install\bin, then the PypePad comes out.I type "vmtkmarchingcubes --help",and it comes out Creating vmtkMarchingCubes instance ....just as your  instructions. so I want to type "vmtkmarchingcubes -ifile foo.vti -ofile foo.vtp",but an error comes out that "error opening file foo.vti".I do not have a file who's Suffix is vti or vtp. I only get the "Aorta_voi.mha" in your website,where can I find or download the .vti,.vtp files? 
> Thanks,
> haibin
> 
> 
> 2013/3/7 Luca Antiga <luc...@or...>
> Hi Haibin,
>  Windows doesn't have a LD_LIBRARY_PATH environment variable. Instead, set everything to PATH.
> 
> By the way, you should find a recently added file in the vmtk-build/VMTK-build directory called
> vmtk_startup.bat. vmtk should start if you double click on that. This shouldn't require to set any
> environment variables.
> I'd be very interested to know if this works for you, in this case I'll change the instructions on the website.
> 
> Best,
> 
> Luca
> 
> 
> On Mar 7, 2013, at 2:43 PM, Haibin Cai wrote:
> 
>> Dear Luca and VTK/VMTK Users,
>>    I have successfully build vmtk/VTK/ITK using the instructions of the VMTK website.But a problem comes out at step 5! I am using the operating system of windows7. Could you please tell me how to set the environment in windows7.
>>   I know there are environment variables in windows7. I can add the $VMTKHOME/bin to the path.And I can build a variable named PYTHONPATH and gave it the value of $VMTKHOME/bin/Python;$VMTKHOME/lib/vtk-5.10;$VMTKHOME/lib/vmtk if you want.And also LD_LIBRARY_PATH.But I think it's not right, please help me! 
>> Thanks 
>> haibin
>> ------------------------------------------------------------------------------
>> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
>> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
>> endpoint security space. For insight on selecting the right partner to 
>> tackle endpoint security challenges, access the full report. 
>> http://p.sf.net/sfu/symantec-dev2dev_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> 
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
> endpoint security space. For insight on selecting the right partner to 
> tackle endpoint security challenges, access the full report. 
> http://p.sf.net/sfu/symantec-dev2dev_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] how to set the environment variables in windows7

[Haibin C. <jlc...@gm...>]

Hi Luca,
    Thank you for your help, I add the followwing to my
path----"C:\build\vmtk-build\Install\bin;C:\build\vmtk-build\Install\lib\vtk-5.10;C:\build\vmtk-build\Install\lib\vmtk;C:\build\vmtk-build\Install\lib\InsightToolkit;C:\build\vmtk-build\Install\bin\Python"
    Then I double click vmtk-exe.pyw.It is in----C:\Program
Files\vmtk\Install\bin, then the PypePad comes out.I type
"vmtkmarchingcubes --help",and it comes out Creating vmtkMarchingCubes
instance ....just as your  instructions. so I want to type "vmtkmarchingcubes
-ifile foo.vti -ofile foo.vtp",but an error comes out that "error opening
file foo.vti".I do not have a file who's Suffix is vti or vtp. I only get
the "Aorta_voi.mha" in your website,where can I find or download the
.vti,.vtp files?
Thanks,
haibin


2013/3/7 Luca Antiga <luc...@or...>

> Hi Haibin,
>  Windows doesn't have a LD_LIBRARY_PATH environment variable. Instead, set
> everything to PATH.
>
> By the way, you should find a recently added file in the
> vmtk-build/VMTK-build directory called
> vmtk_startup.bat. vmtk should start if you double click on that. This
> shouldn't require to set any
> environment variables.
> I'd be very interested to know if this works for you, in this case I'll
> change the instructions on the website.
>
> Best,
>
> Luca
>
>
> On Mar 7, 2013, at 2:43 PM, Haibin Cai wrote:
>
> Dear Luca and VTK/VMTK Users,
>    I have successfully build vmtk/VTK/ITK using the instructions of the
> VMTK website.But a problem comes out at step 5! I am using the operating
> system of windows7. Could you please tell me how to set the environment in
> windows7.
>   I know there are environment variables in windows7. I can add the $VMTKHOME/bin
> to the path.And I can build a variable named PYTHONPATH and gave it the
> value of $VMTKHOME/bin/Python;$VMTKHOME/lib/vtk-5.10;$VMTKHOME/lib/vmtk
> if you want.And also LD_LIBRARY_PATH.But I think it's not right, please
> help me!
> Thanks
> haibin
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the
> endpoint security space. For insight on selecting the right partner to
> tackle endpoint security challenges, access the full report.
>
> http://p.sf.net/sfu/symantec-dev2dev_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>
>

Re: [vmtk-users] how to set the environment variables in windows7

[Luca A. <luc...@or...>]

Hi Haibin,
 Windows doesn't have a LD_LIBRARY_PATH environment variable. Instead, set everything to PATH.

By the way, you should find a recently added file in the vmtk-build/VMTK-build directory called
vmtk_startup.bat. vmtk should start if you double click on that. This shouldn't require to set any
environment variables.
I'd be very interested to know if this works for you, in this case I'll change the instructions on the website.

Best,

Luca


On Mar 7, 2013, at 2:43 PM, Haibin Cai wrote:

> Dear Luca and VTK/VMTK Users,
>    I have successfully build vmtk/VTK/ITK using the instructions of the VMTK website.But a problem comes out at step 5! I am using the operating system of windows7. Could you please tell me how to set the environment in windows7.
>   I know there are environment variables in windows7. I can add the $VMTKHOME/bin to the path.And I can build a variable named PYTHONPATH and gave it the value of $VMTKHOME/bin/Python;$VMTKHOME/lib/vtk-5.10;$VMTKHOME/lib/vmtk if you want.And also LD_LIBRARY_PATH.But I think it's not right, please help me! 
> Thanks 
> haibin
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
> endpoint security space. For insight on selecting the right partner to 
> tackle endpoint security challenges, access the full report. 
> http://p.sf.net/sfu/symantec-dev2dev_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] how to set the environment variables in windows7

[Haibin C. <jlc...@gm...>]

Dear Luca and VTK/VMTK Users,
   I have successfully build vmtk/VTK/ITK using the instructions of the
VMTK website.But a problem comes out at step 5! I am using the operating
system of windows7. Could you please tell me how to set the environment in
windows7.
  I know there are environment variables in windows7. I can add the
$VMTKHOME/bin
to the path.And I can build a variable named PYTHONPATH and gave it the
value of $VMTKHOME/bin/Python;$VMTKHOME/lib/vtk-5.10;$VMTKHOME/lib/vmtk if
you want.And also LD_LIBRARY_PATH.But I think it's not right, please help
me!
Thanks
haibin

Re: [vmtk-users] not all end-points tracked by vmtkcenterlines

[Richard D. <ric...@ui...>]

Luca--
I've been vexed by a similar situation for awhile that I'm just now 
getting around to tackling.
One thing I *do* have, however, is centerlines for my main vessel an all 
branches.
I've noticed a vmtkcenterlinemerge.py/vtkvmtkMergeCenterlines.h/cxx that 
don't appear to be used anywhere, so I can't find a usage example.

What do I need to pass in for the tract ids and blanking ids to make 
this work, or do you have a usage example somewhere?
-rd

On 03/04/2013 07:00 AM, Luca Antiga wrote:
> Hi Roman,
>   I'll really need to take a closer look to the data you sent, I'm planning to do it in the next few days.
> Thanks
>
> Luca
>
> On Mar 4, 2013, at 1:54 PM, Dr. Roman Grothausmann wrote:
>
>> On 23/02/13 13:56, Luca Antiga wrote:
>>> Possible workarounds:
>>>
>>> 1. Try to use Tetgen to generate the internal Delaunay tessellation, instead of the default algorithm. This can be easily
>>> done by specifying -usetetgen 1 in the vmtkcenterlines command line
>> Using tetgen I get an error and the resulting VTP-file is empty (second workaround is still running):
>>
>> Reading VTK XML surface file.
>> Executing vmtkcenterlines ...
>> Cleaning surface.
>> Triangulating surface.
>> Computing centerlines.
>> Computing centerlines...Running TetGen.
>> TetGen command line options: pT1.000000e-08dzQ
>> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkNonManifoldFastMarching.cxx, line 667
>> vtkvmtkNonManifoldFastMarching (0xe6fdac0): Cost function array with name specified does not exist!
>>
>> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkSteepestDescentLineTracer.cxx, line 318
>> vtkvmtkSteepestDescentLineTracer (0xe6f9210): Descent array with name specified does not exist!
>>
>> Done executing vmtkcenterlines.
>> Writing VTK XML surface file.
>> Output vmtkcenterlines members:
>>
>>> 2. Compute the Delaunay tessellation on the closed surface (prior to cutting the endcaps open) using vmtkdelaunayvoronoi
>>> and feed it to vmtkcenterlines, this way:
>>>
>>> vmtkdelaunayvoronoi -ifile unclipped.vtp --pipe vmtkcenterlines -ifile clipped.vtp ...
>> Using this command causes no errors but the resulting file is also empty.
>>
>> Any ideas what else I could try?
>>
>> Many thanks for any help or hints.
>> Roman
>>
>>
>>
>>> This will allow you to take advantage of the clipped endcaps for the seedselector (since you feed clipped.vtp as input to vmtkcenterlines)
>>> but use the Delaunay tessellation computed from the unclipped one, which shouldn't have the issue with the artifactual inner tets.
>>>
>>> In any case, it would be good for me to have the surface so I can use it to fix the internal delaunay tet selection issue.
>>>
>>> Best,
>>>
>>> Luca
>>>
>>>
>>>
>>> On Feb 22, 2013, at 9:32 AM, Dr. Roman Grothausmann wrote:
>>>
>>>> (now with images)
>>>>
>>>> Dear mailing list members,
>>>>
>>>>
>>>> Another problem I have is that not all end-points that I extract from the output of vmtknetwork (magenta lines in attached image) are tracked by vmtkcenterlines (grey/blue lines), most are but some are not. See the end points of the magenta lines of which a grey line stretches like a cobweb string. After removing these cobweb lines I end up with the blue lines which are OK except for the lacking branches.
>>>> What could be the reason for that and how could I avoid it?
>>>>
>>>> Any help or hints are very much appreciated
>>>> Roman
>>>>
>>>>
>>>> --
>>>> Dr. Roman Grothausmann
>>>>
>>>> Tomographie und Digitale Bildverarbeitung
>>>> Tomography and Digital Image Analysis
>>>>
>>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>>> Medizinische Hochschule Hannover
>>>> Carl-Neuberg-Str. 1
>>>> D-30625 Hannover
>>>>
>>>> Tel. +49 511 532-9574
>>>>
>>>>
>>>> <KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_03.gif><KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_05.gif>------------------------------------------------------------------------------
>>>> Everyone hates slow websites. So do we.
>>>> Make your web apps faster with AppDynamics
>>>> Download AppDynamics Lite for free today:
>>>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>>>> vmtk-users mailing list
>>>> vmt...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>> -- 
>> Dr. Roman Grothausmann
>>
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>>
>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>> Medizinische Hochschule Hannover
>> Carl-Neuberg-Str. 1
>> D-30625 Hannover
>>
>> Tel. +49 511 532-9574
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] what's the edition of ITK in VMTK?

[Luca A. <luc...@gm...>]

Hello Haibin,
  currently vmtk relies on ITK 3.18, but soon we'll move to ITK 4 (the port has already been done).

You can find the latest version of the ITK applications here:

http://www.itk.org/ITK/resources/applications.html

They most certainly rely on ITK 4.

Best,


Luca


On Mar 6, 2013, at 8:14 AM, Haibin Cai wrote:

> Dear vmtk-users,
>     I want to use the ITK of VMTK,but I found that the Insight/Application is not in vmtk-build/ITK/Applications,the readme.txt says that it has been moved to a separate CVS checkout. So I decide to download the Insight/Application from the website(I don't know how to use CVS yet...).Here comes the problem,what's the edition of ITK in VMTK? I know the VTK in VMTK is 5.10, I get this information from the vtk directory name.
> 
> 
>     Thanks,
>          haibin
> ------------------------------------------------------------------------------
> Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester  
> Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the  
> endpoint security space. For insight on selecting the right partner to 
> tackle endpoint security challenges, access the full report. 
> http://p.sf.net/sfu/symantec-dev2dev_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] what's the edition of ITK in VMTK?

[Haibin C. <jlc...@gm...>]

Dear vmtk-users,

    I want to use the ITK of VMTK,but I found that the
Insight/Application is not in vmtk-build/ITK/Applications,the
readme.txt says that it has been moved to a separate CVS checkout. So
I decide to download the Insight/Application from the website(I don't
know how to use CVS yet...).Here comes the problem,what's the edition
of ITK in VMTK? I know the VTK in VMTK is 5.10, I get this information
from the vtk directory name.

    Thanks,
         haibin

Re: [vmtk-users] [help!] glibc error

[Luca A. <luc...@or...>]

Hello Chiara,
 from the final error you get, apparently you got all the installation right.
I wonder why you have to explicitly source .profile (any Ubuntu users out
there?). Maybe you have a .bashrc in your home that takes over the .profile?
Give it a check, and if you have a .bashrc move the lines you added to .profile
to .bashrc, open a new terminal window (it has to be new) and try again.

Anyway, the final error means that your system loaded VTK ok, but you're
apparently trying to load a vtp file using the STL reader (in VTK you have to
use different classes for different formats).

Can you please post the exact lines you're using to read the file?

Cheers


Luca


On Mar 5, 2013, at 3:54 PM, Chiara Trentin wrote:

> Dear Luca and VTK/VMTK Users,
> 
> sorry for the delay in my answer.
> I installed again Ubuntu on my PC for being sure I canceled a bad vmtk/vtk
> installation done in the past.
> I followed the Install from source guide in vmtk.org/Main/Installation step by
> step verifying that git, python an cmake are of the required version.
> I installed also build-essential.
> Afterwards I followed the Installation list, first git repository then mkdir cd
> into it, run cmake create Unix Makefile and sun the compiler.
> 
> Finally I set the PATH.
> Restart the pc an tryed a python script.
> First I obtained an error:
> 
> 
> >>> import vtk
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/opt/vmtk-build/Install/bin/Python/vtk/__init__.py", line 41, in <module>
>     from vtkCommonPython import *
> ImportError: libvtkCommonPythonD.so.5.10: cannot open shared object file: No
> such file or directory
> 
> I went through it with source .profile.
> 
> But running a script in which I am reading an STL File I got:
> 
> ERROR: In /opt/vmtk-build/VTK/IO/vtkSTLReader.cxx, line 378
> vtkSTLReader (0xa2304b8): STLReader error reading file: PRE_INNER_WALL.vtp
> Premature EOF while reading point.
> 
> Do you have any suggestion?
> Thanks a lot
> 
> Chiara
> 
> 2012/12/4 Chiara Trentin <chi...@iu...>
> Dear all,
> I have successfully installed vmtk/VTK/ITK using the instructions of the VMTK website.
> Unfortunately, when I try to run some module (e.g., vmtksurfacereader) the following error message appears:
> 
> ERROR: In /opt/vmtk-build/VTK/IO/vtkSTLReader.cxx, line 446
> vtkSTLReader (0xa709548): STLReader error reading file: Gamba_Piegata_lumen.stl Premature EOF while reading end solid.
> 
> *** glibc detected *** python: double free or corruption (!prev): 0x0a70b030 ***
> ======= Backtrace: =========
> /lib/i386-linux-gnu/libc.so.6(+0x75ee2)[0xb737eee2]
> bla bla bla
> 
> I have a similar issue when using VTK python scripts...
> Is there anyone who can help me?
> 
> In the following some useful info about the software version.
> 
> Ubuntu 12.04.1 LTS (release 12.04, precise)
> git 1.7.9.5
> python 2.7.3
> cmake 2.8.7
> linux-libc-dev 3.2.0-34.53
> 
> 
> Thanks a lot
> 
> Chiara
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] [help!] glibc error

[Chiara T. <chi...@iu...>]

Dear Luca and VTK/VMTK Users,

sorry for the delay in my answer.
I installed again Ubuntu on my PC for being sure I canceled a bad vmtk/vtk
installation done in the past.
I followed the Install from source guide in vmtk.org/Main/Installation step
by
step verifying that git, python an cmake are of the required version.
I installed also build-essential.
Afterwards I followed the Installation list, first git repository then
mkdir cd
into it, run cmake create Unix Makefile and sun the compiler.

Finally I set the PATH.
Restart the pc an tryed a python script.
First I obtained an error:


>>> import vtk
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/vmtk-build/Install/bin/Python/vtk/__init__.py", line 41, in
<module>
    from vtkCommonPython import *
ImportError: libvtkCommonPythonD.so.5.10: cannot open shared object file: No
such file or directory

I went through it with source .profile.

But running a script in which I am reading an STL File I got:

ERROR: In /opt/vmtk-build/VTK/IO/vtkSTLReader.cxx, line 378
vtkSTLReader (0xa2304b8): STLReader error reading file: PRE_INNER_WALL.vtp
Premature EOF while reading point.

Do you have any suggestion?
Thanks a lot

Chiara

2012/12/4 Chiara Trentin <chi...@iu...>

> Dear all,
> I have successfully installed vmtk/VTK/ITK using the instructions of the
> VMTK website.
> Unfortunately, when I try to run some module (e.g., vmtksurfacereader) the
> following error message appears:
>
> ERROR: In /opt/vmtk-build/VTK/IO/vtkSTLReader.cxx, line 446
> vtkSTLReader (0xa709548): STLReader error reading file:
> Gamba_Piegata_lumen.stl Premature EOF while reading end solid.
>
> *** glibc detected *** python: double free or corruption (!prev):
> 0x0a70b030 ***
> ======= Backtrace: =========
> /lib/i386-linux-gnu/libc.so.6(+0x75ee2)[0xb737eee2]
> bla bla bla
>
> I have a similar issue when using VTK python scripts...
> Is there anyone who can help me?
>
> In the following some useful info about the software version.
>
> Ubuntu 12.04.1 LTS (release 12.04, precise)
> git 1.7.9.5
> python 2.7.3
> cmake 2.8.7
> linux-libc-dev 3.2.0-34.53
>
>
> Thanks a lot
>
> Chiara
>
>
>
>
>
>
>
>
>

Re: [vmtk-users] how to use ITK and VTK in vmtk-build

[Luca A. <luc...@gm...>]

Hello Haibin,
 the files are in 
ITK/Wrapping/WrapITK/ExternalProjects/ItkVtkGlue/src

You should copy both the .h and .txx files to the directory where your helloworld.cxx resides.

If it still can't locate the files, then add this line 

INCLUDE_DIRECTORIES(${HelloWorld_SOURCE_DIR})

to your CMakeLists.txt, say before ADD_EXECUTABLE

Hope this helps

Luca


On Mar 5, 2013, at 5:48 AM, Haibin Cai wrote:

> Dear vmtk-users,
>     I have a problem in using vmtk. In order to make sure I have install it well, I want to test the ITK and VTK in it. So I write a cmakelists.txt and helloworld.cxx. And then I use cmake 2.8.8 to generate.Everything works well,but if I try to #include "itkImageToVTKImageFilter.h", it comes out that it can't find this file.
>     Here is my cmakelists.txt and HelloWorld.cxx.
> cmakelists.txt:
> cmake_minimum_required(VERSION 2.8)
> PROJECT(HelloWorld)
> FIND_PACKAGE(ITK REQUIRED)
> find_package(VTK REQUIRED)
> INCLUDE(${ITK_USE_FILE})
> include(${VTK_USE_FILE})
> ADD_EXECUTABLE(HelloWorld HelloWorld.cxx )
> TARGET_LINK_LIBRARIES(HelloWorld ITKCommon vtkRendering vtkCommon)
> HelloWorld.cxx
> #include "itkImage.h"
> #include <iostream>
> #include "vtkSmartPointer.h"
> #include "vtkRenderWindow.h"
> #include "vtkRenderer.h"
> #include "vtkRenderWindowInteractor.h"
> #include "vtkInteractorStyleTrackballCamera.h"
> #include "vtkCylinderSource.h"
> #include "vtkPolyDataMapper.h"
> #include "vtkActor.h"
> 
> int main()
> {
>   typedef itk::Image< unsigned short, 3 > ImageType;
> 
>   ImageType::Pointer image = ImageType::New();
> 
>   std::cout << "ITK Hello World !" << std::endl;
> 
>    vtkSmartPointer<vtkCylinderSource> cylinder =
>    vtkSmartPointer<vtkCylinderSource>::New();
>    cylinder->SetHeight( 3.0 );
>    cylinder->SetRadius( 1.0 );
>    cylinder->SetResolution( 10 );
>    
>    vtkSmartPointer<vtkPolyDataMapper> cylinderMapper =
>    vtkSmartPointer<vtkPolyDataMapper>::New();
>    cylinderMapper->SetInputConnection( cylinder->GetOutputPort() );
>   
>    vtkSmartPointer<vtkActor> cylinderActor =
>    vtkSmartPointer<vtkActor>::New();
>    cylinderActor->SetMapper( cylinderMapper );
>  
>    vtkSmartPointer<vtkRenderer> renderer =
>    vtkSmartPointer<vtkRenderer>::New();
>    renderer->AddActor( cylinderActor );
>    renderer->SetBackground( 0.1, 0.2, 0.4 );
>   
>    vtkSmartPointer<vtkRenderWindow> renWin =
>    vtkSmartPointer<vtkRenderWindow>::New();
>    renWin->AddRenderer( renderer );
>    renWin->SetSize( 300, 300 );
>  
>    vtkSmartPointer<vtkRenderWindowInteractor> iren =
>    vtkSmartPointer<vtkRenderWindowInteractor>::New();
>    iren->SetRenderWindow(renWin);
>    
>    vtkSmartPointer<vtkInteractorStyleTrackballCamera> style =
>    vtkSmartPointer<vtkInteractorStyleTrackballCamera>::New();
>    iren->SetInteractorStyle(style);
>   
>    iren->Initialize();
>    iren->Start();
>   return 0;
> }
> I change the ITK_DIR to D:/build/vmtk-build/ITK-Build, and VTK_DIR to D:/build/vmtk-build/VTK-Build.It works well.But if I use the following HelloWorld.cxx, 
> HelloWorld.cxx：
> #include "itkImage.h"
> #include "itkImageToVTKImageFilter.h"
> #include "vtkImageViewer.h"
> #include "vtkRenderWindowInteractor.h"
> #include "itkImageFileReader.h"
> #include "itkGDCMImageIO.h"
> int _tmain(int argc, char* argv[])
> {
> 	typedef itk::Image< unsigned short, 2 > ImageType;
> 	typedef itk::ImageFileReader<ImageType> ReaderType;
> 	typedef itk::ImageToVTKImageFilter< ImageType>		FilterType;
> 	ReaderType::Pointer reader = ReaderType::New();
> 	typedef itk::GDCMImageIO       ImageIOType;
> 	ImageIOType::Pointer dicomIO = ImageIOType::New();
> 	reader->SetImageIO( dicomIO );
> 	FilterType::Pointer connector = FilterType::New();
> 	reader->SetFileName("...................");
> 	connector->SetInput( reader->GetOutput() );
> 	vtkImageViewer * viewer = vtkImageViewer::New();
> 	vtkRenderWindowInteractor * renderWindowInteractor = vtkRenderWindowInteractor::New();
> 	viewer->SetupInteractor( renderWindowInteractor );
> 	viewer->SetInput( connector->GetOutput() );
> 	viewer->Render();
> 	viewer->SetColorWindow( 255 );
> 	viewer->SetColorLevel( 255 );
> 	renderWindowInteractor->Start();
> 	return 0;
> }
> an error comes that it can't find "itkImageToVTKImageFilter.h",I have tried to copy this file alone to the project,it doesn't help. please help me.
> Thanks ,
> ben
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] Mapping and Patching Data

[Luca A. <luc...@gm...>]

Hi Evan,

On Mar 5, 2013, at 12:31 AM, Evan Kao wrote:

> Hi Luca,
> 
> Thanks for the additional suggestion.
> 
> You are right, there's lots of room for improvement regarding visualization in patching (and in general). Thanks for the suggestion!
> 
> Just to clarify further, I wasn't trying to suggest it needed any improvement, just that one little feature didn't seem to be working properly for me, which I suspect has more to do with Windows or myself than vmtk. 

I don't think it's you or (for once) Windows. This is a vmtk feature that hasn't received much attention - I basically implemented what I needed at the time, and I didn't need to visualize the image data results from within vmtk. This can be improved a lot with a relatively low effort, I pinned it to my todo list.

Luca


> Thanks,
> Evan Kao
> 
> On Mon, Mar 4, 2013 at 4:31 AM, Luca Antiga <luc...@gm...> wrote:
> Hi Evan,
> 
> On Mar 1, 2013, at 7:51 PM, Evan Kao wrote:
> 
>> Hello Luca,
>> 
>> Thanks for the quick response and help.  Using subdivisions seemed to have fixed the problem of missing patches (I did end up having to use the AbscissaMetric array as the longitudinal axis in vmtkbranchpatching as opposed to StretchedMapping due to issues with Python crashing when trying to compute the bifurcation reference systems from the subdivided surface, but this is probably more of an issue with the system I'm using than one with vmtk).
> 
> It's possible, but try to use subdivision after the mapping and prior to patching. You'll still see the little hole at the bifurcation center, which shouldn't be that big of a deal (although I don't know your exact application), but you'll be able to use StretchedMapping for the patching, which results in a more regular coverage of the surface.
> 
>> Why nonsense? The data is all there.
>> 
>> To clarify, I don't think the data is nonsense, but when I provide the flag -patcheddatafile xxx.vti/png for vmtkbranchpatching, it doesn't seems to visualize the data correctly, as seen in the image files I attached in the previous e-mail (I just see a gray rectangle).  But it's probably not a big deal, since I can just export the raw data and visualize it however I want, as you suggested.
> 
> You are right, there's lots of room for improvement regarding visualization in patching (and in general). Thanks for the suggestion!
> 
> Luca
> 
>> Thanks,
>> Evan Kao
>> 
>> On Fri, Mar 1, 2013 at 4:01 AM, Luca Antiga <luc...@gm...> wrote:
>> Hi Evan,
>> 
>> On Mar 1, 2013, at 1:59 AM, Evan Kao wrote:
>> 
>>> Hello group,
>>> 
>>> I am still having some trouble with mapping and patching data.  When I created the patched surface and viewed it, I noticed that some patches of the surface were missing (see: missingpatches.png, any011_wss_clipped_patching.vtp).  Inspecting the surfaces generated from the previous steps, it seems small pieces of the surface is cut out at the bifurcation (surface after splitting.png, any011_wss_clipped.vtp), although I don't know if that is related to the problem in the surface patching step, or simply a result of the way the centerlines were formed (centerlines,png, any011_wss_cl.vtp).
>> 
>> Both issues are related to the fact that the surface is probably too coarse in some regions relative to the size of the patch. Also, due to the way clipping is performed, you can have a small missing triangle at the bifurcation, whose size decreases with the increase in the surface density. This is due to the linear interpolation of the cuts on top of the triangulation.
>> A workaround in these cases is to pass the surface through 
>> vmtksurfacesubdivision -method butterfly -subdivisions 1 
>> prior to patching.
>> 
>>> The image files generated with the patched data (both .vti and .png) were nonsense (vmtkimageviewer of patcheddata.png, any011_wss_clipped_patching.png, any011_wss_clipped_patching.vti).
>> 
>> Why nonsense? The data is all there. It's one image in which all three branches are stored contiguously, this way:
>> 
>> SECTORS x (SLAB_A + SLAB_B + SLAB_C)
>> 
>> I attach a couple of screenshots that demonstrate it, obtained using Paraview.
>> 
>> It's probably not the most practical way to plot the data, though. I suggest you export the vtp patched data this way:
>> 
>> vmtksurfacewriter -ifile any011_wss_clipped_patching.vtp -ofile foo.dat -celldata 
>> 
>> which will generate a csv-like file in which lines are individual patches, each with its wss value, groupid, slab and sector. 
>> This will allow you to generate plots of the unwrapped surface for your needs using any general purpose plotting software by plotting sector on x, slab on y and wss as the color.
>> 
>> Hope this helps
>> 
>> Luca
>> 
>>> To simplify the issue, I also tried mapping and patching only one branch segment (the aneurysm) by cutting out the other branches with vmtksurfaceclipper before any sort of branch extraction and splitting.  There didn't seem to be any issues with missing patches this time around, but the .png file also failed to provide the expected results (the patched 3D surface, and the "unwrapped" 2D surface).
>>> 
>>> Any idea on what's going wrong?
>>> 
>>> Thanks,
>>> Evan Kao
>>> 
>> 
>> 
>> 
>> 
>> 
>>> On Fri, Feb 22, 2013 at 3:54 PM, Evan Kao <to...@gm...> wrote:
>>> Thanks, Arjan.  That was an extremely helpful explanation.
>>> 
>>> 
>>> On Wed, Feb 20, 2013 at 4:40 PM, Arjan Geers <aj...@gm...> wrote:
>>> Hi Evan, 
>>> 
>>> VTK polydata files store the location of points and information on how these points are connected to form cells. Additionally, they can store scalars and vectors at each point or cell. So, indeed, you want the WSS field already included in the surface file before performing any vmtkbranch* operations. 
>>> 
>>> Hopefully, you can export from your CFD solver an ASCII file similar to surface.tec (attached). It contains x,y,z-coordinates of each point, the wss magnitude at each point, and connectivity information. When opening this surface with vmtksurfacereader, VMTK converts it into a VTK polydata, which can then be written with vmtksurfacewriter (see surface.vtp attached). To check what VMTK actually does when converting the ASCII file, go to the function 'ReadTecplotSurfaceFile' in vmtksurfacereader.py. This should provide you with some hints on how to convert your own format to VTP. 
>>> 
>>> Hope this helps, 
>>> 
>>> Arjan
>>> 
>>> PS: Since the commercial CFD solver Ansys-CFX is quite widely used, the attached script cfx2vtp.py (variation on above-mentioned 'ReadTecplotSurfaceFile') might be useful to some reading this email. Converting surface.csv (attached) should give surface.vtp again.
>>> 
>>> 
>>> On Wed, Feb 20, 2013 at 9:40 PM, Evan Kao <to...@gm...> wrote:
>>> Hello,
>>> 
>>> I am confused about some of the details regarding the matching and patching of data in the tutorial.  Specifically, at what stage in the process are we supposed to import the simulation data into vmtk, and how?  For instance, in the tutorial, are the WSS and OSI distributions already part of the surface file ("aorta.vtp") before any processing occurs?  It doesn't seem like there are any ways to import data in any of the vmtkbranchmetrics, vmtkbranchmapping, or vmtkbranchpatching functions.  And what form does the data have to be in?  It should be pretty easy to export nodal or cell CFD data as an array, but how would we incorporate that into vmtk?
>>> 
>>> Thanks for your time,
>>> Evan Kao
>>> 
>>> ------------------------------------------------------------------------------
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_feb
>>> _______________________________________________
>>> vmtk-users mailing list
>>> vmt...@li...
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>> 
>>> 
>>> 
>>> 
>>> <any011_wss_clipped_patching.png><centerlines.png><missing patches.png><surface after splitting.png><vmtkimageviewer of patched data.png><any011_wss_clipped_patching.vtp><any011_wss_clipped_patching.vti><any011_wss_cl.vtp><any011_wss_clipped.vtp>------------------------------------------------------------------------------
>>> 
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>>> vmtk-users mailing list
>>> vmt...@li...
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>> 
>> 
> 
> 
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] how to use ITK and VTK in vmtk-build

[Haibin C. <jlc...@gm...>]

Dear vmtk-users,

    I have a problem in using vmtk. In order to make sure I have
install it well, I want to test the ITK and VTK in it. So I write a
cmakelists.txt and helloworld.cxx. And then I use cmake 2.8.8 to
generate.Everything works well,but if I try to #include
"itkImageToVTKImageFilter.h", it comes out that it can't find this
file.

    Here is my cmakelists.txt and HelloWorld.cxx.

cmakelists.txt:

cmake_minimum_required(VERSION 2.8)
PROJECT(HelloWorld)
FIND_PACKAGE(ITK REQUIRED)
find_package(VTK REQUIRED)
INCLUDE(${ITK_USE_FILE})
include(${VTK_USE_FILE})
ADD_EXECUTABLE(HelloWorld HelloWorld.cxx )
TARGET_LINK_LIBRARIES(HelloWorld ITKCommon vtkRendering vtkCommon)

HelloWorld.cxx

#include "itkImage.h"
#include <iostream>
#include "vtkSmartPointer.h"
#include "vtkRenderWindow.h"
#include "vtkRenderer.h"
#include "vtkRenderWindowInteractor.h"
#include "vtkInteractorStyleTrackballCamera.h"
#include "vtkCylinderSource.h"
#include "vtkPolyDataMapper.h"
#include "vtkActor.h"

int main()
{
  typedef itk::Image< unsigned short, 3 > ImageType;

  ImageType::Pointer image = ImageType::New();

  std::cout << "ITK Hello World !" << std::endl;

   vtkSmartPointer<vtkCylinderSource> cylinder =
   vtkSmartPointer<vtkCylinderSource>::New();
   cylinder->SetHeight( 3.0 );
   cylinder->SetRadius( 1.0 );
   cylinder->SetResolution( 10 );

   vtkSmartPointer<vtkPolyDataMapper> cylinderMapper =
   vtkSmartPointer<vtkPolyDataMapper>::New();
   cylinderMapper->SetInputConnection( cylinder->GetOutputPort() );

   vtkSmartPointer<vtkActor> cylinderActor =
   vtkSmartPointer<vtkActor>::New();
   cylinderActor->SetMapper( cylinderMapper );

   vtkSmartPointer<vtkRenderer> renderer =
   vtkSmartPointer<vtkRenderer>::New();
   renderer->AddActor( cylinderActor );
   renderer->SetBackground( 0.1, 0.2, 0.4 );

   vtkSmartPointer<vtkRenderWindow> renWin =
   vtkSmartPointer<vtkRenderWindow>::New();
   renWin->AddRenderer( renderer );
   renWin->SetSize( 300, 300 );

   vtkSmartPointer<vtkRenderWindowInteractor> iren =
   vtkSmartPointer<vtkRenderWindowInteractor>::New();
   iren->SetRenderWindow(renWin);

   vtkSmartPointer<vtkInteractorStyleTrackballCamera> style =
   vtkSmartPointer<vtkInteractorStyleTrackballCamera>::New();
   iren->SetInteractorStyle(style);

   iren->Initialize();
   iren->Start();
  return 0;
}

I change the ITK_DIR to D:/build/vmtk-build/ITK-Build, and VTK_DIR to
D:/build/vmtk-build/VTK-Build.It works well.But if I use the following
HelloWorld.cxx,

HelloWorld.cxx：

#include "itkImage.h"
#include "itkImageToVTKImageFilter.h"
#include "vtkImageViewer.h"
#include "vtkRenderWindowInteractor.h"
#include "itkImageFileReader.h"
#include "itkGDCMImageIO.h"
int _tmain(int argc, char* argv[])
{
	typedef itk::Image< unsigned short, 2 > ImageType;
	typedef itk::ImageFileReader<ImageType> ReaderType;
	typedef itk::ImageToVTKImageFilter< ImageType>		FilterType;
	ReaderType::Pointer reader = ReaderType::New();
	typedef itk::GDCMImageIO       ImageIOType;
	ImageIOType::Pointer dicomIO = ImageIOType::New();
	reader->SetImageIO( dicomIO );
	FilterType::Pointer connector = FilterType::New();
	reader->SetFileName("...................");
	connector->SetInput( reader->GetOutput() );
	vtkImageViewer * viewer = vtkImageViewer::New();
	vtkRenderWindowInteractor * renderWindowInteractor =
vtkRenderWindowInteractor::New();
	viewer->SetupInteractor( renderWindowInteractor );
	viewer->SetInput( connector->GetOutput() );
	viewer->Render();
	viewer->SetColorWindow( 255 );
	viewer->SetColorLevel( 255 );
	renderWindowInteractor->Start();
	return 0;
}

an error comes that it can't find "itkImageToVTKImageFilter.h",I have
tried to copy this file alone to the project,it doesn't help. please
help me.

Thanks ,

ben

Re: [vmtk-users] Mapping and Patching Data

[Evan K. <to...@gm...>]

Hi Luca,

Thanks for the additional suggestion.

You are right, there's lots of room for improvement regarding visualization
> in patching (and in general). Thanks for the suggestion!
>

Just to clarify further, I wasn't trying to suggest it needed any
improvement, just that one little feature didn't seem to be working
properly for me, which I suspect has more to do with Windows or myself than
vmtk.

Thanks,
Evan Kao

On Mon, Mar 4, 2013 at 4:31 AM, Luca Antiga <luc...@gm...> wrote:

> Hi Evan,
>
> On Mar 1, 2013, at 7:51 PM, Evan Kao wrote:
>
> Hello Luca,
>
> Thanks for the quick response and help.  Using subdivisions seemed to have
> fixed the problem of missing patches (I did end up having to use the
> AbscissaMetric array as the longitudinal axis in vmtkbranchpatching as
> opposed to StretchedMapping due to issues with Python crashing when trying
> to compute the bifurcation reference systems from the subdivided surface,
> but this is probably more of an issue with the system I'm using than one
> with vmtk).
>
>
> It's possible, but try to use subdivision after the mapping and prior to
> patching. You'll still see the little hole at the bifurcation center, which
> shouldn't be that big of a deal (although I don't know your exact
> application), but you'll be able to use StretchedMapping for the patching,
> which results in a more regular coverage of the surface.
>
> Why nonsense? The data is all there.
>>
>
> To clarify, I don't think the data is nonsense, but when I provide the
> flag -patcheddatafile xxx.vti/png for vmtkbranchpatching, it doesn't seems
> to visualize the data correctly, as seen in the image files I attached in
> the previous e-mail (I just see a gray rectangle).  But it's probably not a
> big deal, since I can just export the raw data and visualize it however I
> want, as you suggested.
>
>
> You are right, there's lots of room for improvement regarding
> visualization in patching (and in general). Thanks for the suggestion!
>
> Luca
>
> Thanks,
> Evan Kao
>
> On Fri, Mar 1, 2013 at 4:01 AM, Luca Antiga <luc...@gm...> wrote:
>
>> Hi Evan,
>>
>> On Mar 1, 2013, at 1:59 AM, Evan Kao wrote:
>>
>> Hello group,
>>
>> I am still having some trouble with mapping and patching data.  When I
>> created the patched surface and viewed it, I noticed that some patches of
>> the surface were missing (see: missingpatches.png,
>> any011_wss_clipped_patching.vtp).  Inspecting the surfaces generated from
>> the previous steps, it seems small pieces of the surface is cut out at the
>> bifurcation (surface after splitting.png, any011_wss_clipped.vtp), although
>> I don't know if that is related to the problem in the surface patching
>> step, or simply a result of the way the centerlines were formed
>> (centerlines,png, any011_wss_cl.vtp).
>>
>>
>> Both issues are related to the fact that the surface is probably too
>> coarse in some regions relative to the size of the patch. Also, due to the
>> way clipping is performed, you can have a small missing triangle at the
>> bifurcation, whose size decreases with the increase in the surface density.
>> This is due to the linear interpolation of the cuts on top of the
>> triangulation.
>> A workaround in these cases is to pass the surface through
>> vmtksurfacesubdivision -method butterfly -subdivisions 1
>> prior to patching.
>>
>> The image files generated with the patched data (both .vti and .png) were
>> nonsense (vmtkimageviewer of patcheddata.png,
>> any011_wss_clipped_patching.png, any011_wss_clipped_patching.vti).
>>
>>
>> Why nonsense? The data is all there. It's one image in which all three
>> branches are stored contiguously, this way:
>>
>> SECTORS x (SLAB_A + SLAB_B + SLAB_C)
>>
>> I attach a couple of screenshots that demonstrate it, obtained using
>> Paraview.
>>
>> It's probably not the most practical way to plot the data, though. I
>> suggest you export the vtp patched data this way:
>>
>> vmtksurfacewriter -ifile any011_wss_clipped_patching.vtp -ofile foo.dat
>> -celldata
>>
>> which will generate a csv-like file in which lines are individual
>> patches, each with its wss value, groupid, slab and sector.
>> This will allow you to generate plots of the unwrapped surface for your
>> needs using any general purpose plotting software by plotting sector on x,
>> slab on y and wss as the color.
>>
>> Hope this helps
>>
>> Luca
>>
>> To simplify the issue, I also tried mapping and patching only one branch
>> segment (the aneurysm) by cutting out the other branches with
>> vmtksurfaceclipper before any sort of branch extraction and splitting.
>> There didn't seem to be any issues with missing patches this time around,
>> but the .png file also failed to provide the expected results (the patched
>> 3D surface, and the "unwrapped" 2D surface).
>>
>> Any idea on what's going wrong?
>>
>> Thanks,
>> Evan Kao
>>
>>
>>
>>
>>
>> On Fri, Feb 22, 2013 at 3:54 PM, Evan Kao <to...@gm...> wrote:
>>
>>> Thanks, Arjan.  That was an extremely helpful explanation.
>>>
>>>
>>> On Wed, Feb 20, 2013 at 4:40 PM, Arjan Geers <aj...@gm...> wrote:
>>>
>>>> Hi Evan,
>>>>
>>>> VTK polydata files store the location of points and information on how
>>>> these points are connected to form cells. Additionally, they can store
>>>> scalars and vectors at each point or cell. So, indeed, you want the WSS
>>>> field already included in the surface file before performing any
>>>> vmtkbranch* operations.
>>>>
>>>> Hopefully, you can export from your CFD solver an ASCII file similar to
>>>> surface.tec (attached). It contains x,y,z-coordinates of each point, the
>>>> wss magnitude at each point, and connectivity information. When opening
>>>> this surface with vmtksurfacereader, VMTK converts it into a VTK polydata,
>>>> which can then be written with vmtksurfacewriter (see surface.vtp
>>>> attached). To check what VMTK actually does when converting the ASCII file,
>>>> go to the function 'ReadTecplotSurfaceFile' in vmtksurfacereader.py. This
>>>> should provide you with some hints on how to convert your own format to
>>>> VTP.
>>>>
>>>> Hope this helps,
>>>>
>>>> Arjan
>>>>
>>>> PS: Since the commercial CFD solver Ansys-CFX is quite widely used, the
>>>> attached script cfx2vtp.py (variation on above-mentioned
>>>> 'ReadTecplotSurfaceFile') might be useful to some reading this email.
>>>> Converting surface.csv (attached) should give surface.vtp again.
>>>>
>>>>
>>>> On Wed, Feb 20, 2013 at 9:40 PM, Evan Kao <to...@gm...> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I am confused about some of the details regarding the matching and
>>>>> patching of data in the tutorial.  Specifically, at what stage in the
>>>>> process are we supposed to import the simulation data into vmtk, and how?
>>>>> For instance, in the tutorial, are the WSS and OSI distributions already
>>>>> part of the surface file ("aorta.vtp") before any processing occurs?  It
>>>>> doesn't seem like there are any ways to import data in any of the
>>>>> vmtkbranchmetrics, vmtkbranchmapping, or vmtkbranchpatching functions.  And
>>>>> what form does the data have to be in?  It should be pretty easy to export
>>>>> nodal or cell CFD data as an array, but how would we incorporate that into
>>>>> vmtk?
>>>>>
>>>>> Thanks for your time,
>>>>> Evan Kao
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Everyone hates slow websites. So do we.
>>>>> Make your web apps faster with AppDynamics
>>>>> Download AppDynamics Lite for free today:
>>>>> http://p.sf.net/sfu/appdyn_d2d_feb
>>>>> _______________________________________________
>>>>> vmtk-users mailing list
>>>>> vmt...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>>>
>>>>>
>>>>
>>>
>> <any011_wss_clipped_patching.png><centerlines.png><missing patches.png><surface
>> after splitting.png><vmtkimageviewer of patched data.png>
>> <any011_wss_clipped_patching.vtp><any011_wss_clipped_patching.vti>
>> <any011_wss_cl.vtp><any011_wss_clipped.vtp>
>> ------------------------------------------------------------------------------
>>
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>>
>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>>
>>
>
>

Re: [vmtk-users] vtk ASCII output

[Luca A. <luc...@or...>]

Hi Elaine,
 centerlines work exactly like surfaces, in the sense that you can write 
them out using vmtksurfacewriter, with the extra-caveat that you have to pipe 
the output to the writer explicitly, this way:

vmtkcenterlines -ifile foo.vtp [...other options...] --pipe vmtksurfacewriter -i @.o -mode ascii -ofile foo.vtk

To learn more about piping, read the basic pypes tutorial on vmtk.org

Best,

Luca


On Mar 4, 2013, at 8:56 PM, Elaine Tang wrote:

> HI Luca,
> 
> Thank you for your reply. What if I am trying to write centerlines and bifurcation as .vtk (instead of surface)? Those functions (e.g. vmtkcenterlines) don't seem to have the 'mode' option.
> 
> Thanks!
> Elaine
> 
> On 4 March 2013 07:28, Luca Antiga <luc...@or...> wrote:
> Hi Elaine,
>  just use an explicit writer script and specify -mode ascii as an option, like
> 
> vmtksurfacesmoothing -ifle foo.vtp --pipe vmtksurfacewriter -ofile foo.vtk -mode ascii
> 
> Best,
> 
> Luca
> 
> 
> On Mar 3, 2013, at 11:41 PM, Elaine Tang wrote:
> 
> > Hi,
> >
> > I recently installed VMTK on my RHEL 5 linux OS. Everything seems to run smoothly. However, whenever I try to output as ".vtk", it defaults to output as binary files. Is there any way to make it output as ASCII file as default?
> >
> > Thanks!
> > --
> > Elaine Tang
> > ------------------------------------------------------------------------------
> > Everyone hates slow websites. So do we.
> > Make your web apps faster with AppDynamics
> > Download AppDynamics Lite for free today:
> > http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> > vmtk-users mailing list
> > vmt...@li...
> > https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> 
> 
> 

Re: [vmtk-users] vtk ASCII output

[Elaine T. <ela...@ga...>]

HI Luca,

Thank you for your reply. What if I am trying to write centerlines and
bifurcation as .vtk (instead of surface)? Those functions (e.g.
vmtkcenterlines) don't seem to have the 'mode' option.

Thanks!
Elaine

On 4 March 2013 07:28, Luca Antiga <luc...@or...> wrote:

> Hi Elaine,
>  just use an explicit writer script and specify -mode ascii as an option,
> like
>
> vmtksurfacesmoothing -ifle foo.vtp --pipe vmtksurfacewriter -ofile foo.vtk
> -mode ascii
>
> Best,
>
> Luca
>
>
> On Mar 3, 2013, at 11:41 PM, Elaine Tang wrote:
>
> > Hi,
> >
> > I recently installed VMTK on my RHEL 5 linux OS. Everything seems to run
> smoothly. However, whenever I try to output as ".vtk", it defaults to
> output as binary files. Is there any way to make it output as ASCII file as
> default?
> >
> > Thanks!
> > --
> > Elaine Tang
> >
> ------------------------------------------------------------------------------
> > Everyone hates slow websites. So do we.
> > Make your web apps faster with AppDynamics
> > Download AppDynamics Lite for free today:
> >
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> > vmtk-users mailing list
> > vmt...@li...
> > https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>

Re: [vmtk-users] not all end-points tracked by vmtkcenterlines

[Dr. R. G. <gro...@mh...>]

On 23/02/13 13:56, Luca Antiga wrote:
> Possible workarounds:
>
> 1. Try to use Tetgen to generate the internal Delaunay tessellation, instead of the default algorithm. This can be easily
> done by specifying -usetetgen 1 in the vmtkcenterlines command line

Using tetgen I get an error and the resulting VTP-file is empty (second 
workaround is still running):

Reading VTK XML surface file.
Executing vmtkcenterlines ...
Cleaning surface.
Triangulating surface.
Computing centerlines.
Computing centerlines...Running TetGen.
TetGen command line options: pT1.000000e-08dzQ
ERROR: In 
/home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkNonManifoldFastMarching.cxx, 
line 667
vtkvmtkNonManifoldFastMarching (0xe6fdac0): Cost function array with name 
specified does not exist!

ERROR: In 
/home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkSteepestDescentLineTracer.cxx, 
line 318
vtkvmtkSteepestDescentLineTracer (0xe6f9210): Descent array with name specified 
does not exist!

Done executing vmtkcenterlines.
Writing VTK XML surface file.
Output vmtkcenterlines members:

> 2. Compute the Delaunay tessellation on the closed surface (prior to cutting the endcaps open) using vmtkdelaunayvoronoi
> and feed it to vmtkcenterlines, this way:
>
> vmtkdelaunayvoronoi -ifile unclipped.vtp --pipe vmtkcenterlines -ifile clipped.vtp ...

Using this command causes no errors but the resulting file is also empty.

Any ideas what else I could try?

Many thanks for any help or hints.
Roman



>
> This will allow you to take advantage of the clipped endcaps for the seedselector (since you feed clipped.vtp as input to vmtkcenterlines)
> but use the Delaunay tessellation computed from the unclipped one, which shouldn't have the issue with the artifactual inner tets.
>
> In any case, it would be good for me to have the surface so I can use it to fix the internal delaunay tet selection issue.
>
> Best,
>
> Luca
>
>
>
> On Feb 22, 2013, at 9:32 AM, Dr. Roman Grothausmann wrote:
>
>> (now with images)
>>
>> Dear mailing list members,
>>
>>
>> Another problem I have is that not all end-points that I extract from the output of vmtknetwork (magenta lines in attached image) are tracked by vmtkcenterlines (grey/blue lines), most are but some are not. See the end points of the magenta lines of which a grey line stretches like a cobweb string. After removing these cobweb lines I end up with the blue lines which are OK except for the lacking branches.
>> What could be the reason for that and how could I avoid it?
>>
>> Any help or hints are very much appreciated
>> Roman
>>
>>
>> --
>> Dr. Roman Grothausmann
>>
>> Tomographie und Digitale Bildverarbeitung
>> Tomography and Digital Image Analysis
>>
>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>> Medizinische Hochschule Hannover
>> Carl-Neuberg-Str. 1
>> D-30625 Hannover
>>
>> Tel. +49 511 532-9574
>>
>>
>> <KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_03.gif><KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_05.gif>------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>

-- 
Dr. Roman Grothausmann

Tomographie und Digitale Bildverarbeitung
Tomography and Digital Image Analysis

Institut für Funktionelle und Angewandte Anatomie, OE 4120
Medizinische Hochschule Hannover
Carl-Neuberg-Str. 1
D-30625 Hannover

Tel. +49 511 532-9574

Re: [vmtk-users] not all end-points tracked by vmtkcenterlines

[Luca A. <luc...@or...>]

Hi Roman,
 I'll really need to take a closer look to the data you sent, I'm planning to do it in the next few days.
Thanks

Luca

On Mar 4, 2013, at 1:54 PM, Dr. Roman Grothausmann wrote:

> On 23/02/13 13:56, Luca Antiga wrote:
>> Possible workarounds:
>> 
>> 1. Try to use Tetgen to generate the internal Delaunay tessellation, instead of the default algorithm. This can be easily
>> done by specifying -usetetgen 1 in the vmtkcenterlines command line
> 
> Using tetgen I get an error and the resulting VTP-file is empty (second workaround is still running):
> 
> Reading VTK XML surface file.
> Executing vmtkcenterlines ...
> Cleaning surface.
> Triangulating surface.
> Computing centerlines.
> Computing centerlines...Running TetGen.
> TetGen command line options: pT1.000000e-08dzQ
> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkNonManifoldFastMarching.cxx, line 667
> vtkvmtkNonManifoldFastMarching (0xe6fdac0): Cost function array with name specified does not exist!
> 
> ERROR: In /home/grr/programme/vmtk-1.0.1/vtkVmtk/ComputationalGeometry/vtkvmtkSteepestDescentLineTracer.cxx, line 318
> vtkvmtkSteepestDescentLineTracer (0xe6f9210): Descent array with name specified does not exist!
> 
> Done executing vmtkcenterlines.
> Writing VTK XML surface file.
> Output vmtkcenterlines members:
> 
>> 2. Compute the Delaunay tessellation on the closed surface (prior to cutting the endcaps open) using vmtkdelaunayvoronoi
>> and feed it to vmtkcenterlines, this way:
>> 
>> vmtkdelaunayvoronoi -ifile unclipped.vtp --pipe vmtkcenterlines -ifile clipped.vtp ...
> 
> Using this command causes no errors but the resulting file is also empty.
> 
> Any ideas what else I could try?
> 
> Many thanks for any help or hints.
> Roman
> 
> 
> 
>> 
>> This will allow you to take advantage of the clipped endcaps for the seedselector (since you feed clipped.vtp as input to vmtkcenterlines)
>> but use the Delaunay tessellation computed from the unclipped one, which shouldn't have the issue with the artifactual inner tets.
>> 
>> In any case, it would be good for me to have the surface so I can use it to fix the internal delaunay tet selection issue.
>> 
>> Best,
>> 
>> Luca
>> 
>> 
>> 
>> On Feb 22, 2013, at 9:32 AM, Dr. Roman Grothausmann wrote:
>> 
>>> (now with images)
>>> 
>>> Dear mailing list members,
>>> 
>>> 
>>> Another problem I have is that not all end-points that I extract from the output of vmtknetwork (magenta lines in attached image) are tracked by vmtkcenterlines (grey/blue lines), most are but some are not. See the end points of the magenta lines of which a grey line stretches like a cobweb string. After removing these cobweb lines I end up with the blue lines which are OK except for the lacking branches.
>>> What could be the reason for that and how could I avoid it?
>>> 
>>> Any help or hints are very much appreciated
>>> Roman
>>> 
>>> 
>>> --
>>> Dr. Roman Grothausmann
>>> 
>>> Tomographie und Digitale Bildverarbeitung
>>> Tomography and Digital Image Analysis
>>> 
>>> Institut für Funktionelle und Angewandte Anatomie, OE 4120
>>> Medizinische Hochschule Hannover
>>> Carl-Neuberg-Str. 1
>>> D-30625 Hannover
>>> 
>>> Tel. +49 511 532-9574
>>> 
>>> 
>>> <KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_03.gif><KO4_01_08_12_002_PD PMT_seg-8bit_fh0_obs_d1 orig_fh0_obs_mc50_lmp_nw-skel1.05_ep_s2t0_mo004_ep_cl_01_05.gif>------------------------------------------------------------------------------
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>> 
> 
> -- 
> Dr. Roman Grothausmann
> 
> Tomographie und Digitale Bildverarbeitung
> Tomography and Digital Image Analysis
> 
> Institut für Funktionelle und Angewandte Anatomie, OE 4120
> Medizinische Hochschule Hannover
> Carl-Neuberg-Str. 1
> D-30625 Hannover
> 
> Tel. +49 511 532-9574