Thanks, Arjan, that solution was fantastic and simple! I can confirm
that converting to triangles eliminates the segfault on my dataset. I
really appreciate your help!
Ian
On 12/8/2011 12:12 PM, Arjan Geers wrote:
Hello Ian,
Your input file's cell type is 'quad' and it seems
that vmtkbifurcationsections requires it to be 'triangle'. Try running
the pype below, which has vmtksurfacetriangle added to it. It worked
for me with your data.
vmtkmeshreader -ifile input.vtu --pipe vmtkmeshtosurface --pipe
vmtksurfacetriangle --pipe vmtkcenterlines -seedselector openprofiles
-endpoints 1 --pipe vmtkbranchextractor --pipe vmtkbranchclipper
--pipe vmtkbifurcationsections -distancespheres 2 -ofile output.vtp
Hope this helps,
Arjan
On Thu, Dec 8, 2011 at 12:29 AM, Ian Campbell <[email protected]
<mailto:[email protected]>> wrote:
Hello Luca et al,
I'm trying to use vmtkbifurcationsections on a carotid bifurcation CFD
dataset in hopes of extracting just the carotid bulb.
Unfortunately, I'm
getting a Segfault when vmtkbifurcationsections runs in my pipe,
both on
a Fedora 14 system running the latest code from Git, as well as a
Windows 7 system running the 0.9.0 binaries. I see from the
mailing list
archives that people have used this script successfully in the
past and
from Github that it this hasn't been updated in that time, so perhaps
it's my dataset that is causing the issue?
In any case, this pype causes a segfault:
vmtkmeshreader -ifile /mnt/hgfs/tmp/041blunt_WSS_1_0.vtu --pipe
vmtkmeshtosurface --pipe vmtkcenterlines -seedselector openprofiles
-endpoints 1 --pipe vmtkbranchextractor --pipe vmtkbranchclipper
--pipe
vmtkbifurcationsections -distancespheres 2 -ofile test_bifsections.vtp
I have tried multiple files from my patient series and all give
the same
error. These are Fluent-exported Ensight Gold files that have been
converted to .vtm/.vtu format with Paraview, and I'm only loading the
.vtu containing wall surface data. Sample file that causes crash here:
http://dl.dropbox.com/u/2364470/041blunt_WSS_1_0.vtu
Backtrace of the segmentation fault is below (maybe too much
information
for the list...). Have others had any luck with
vmtkbifurcationsections?
Thanks!
Ian
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff5801876 in vtkDataArrayTemplate<float>::GetTuple
(this=0x12deb20, i=-4638906531247145681, tuple=0x7fffffffc320) at
/opt/vmtk_build/VTK/Common/vtkDataArrayTemplate.txx:615
(gdb) backtrace
#0 0x00007ffff5801876 in vtkDataArrayTemplate<float>::GetTuple
(this=0x12deb20, i=-4638906531247145681, tuple=0x7fffffffc320) at
/opt/vmtk_build/VTK/Common/vtkDataArrayTemplate.txx:615
#1 0x00007ffff40e8ddd in vtkPoints::GetPoint (this=0x1f240a0,
id=-4638906531247145681, x=0x7fffffffc320) at
/opt/vmtk_build/VTK/Common/vtkPoints.h:122
#2 0x00007ffff4292d36 in vtkPolyData::GetCell (this=0x214fd10,
cellId=3577, cell=0x14a3ce0) at
/opt/vmtk_build/VTK/Filtering/vtkPolyData.cxx:446
#3 0x00007fffef7ca508 in vtkCutter::DataSetCutter
(this=0x12dce40, input=0x214fd10, output=0x14ac7c0) at
/opt/vmtk_build/VTK/Graphics/vtkCutter.cxx:579
#4 0x00007fffef7c98e7 in vtkCutter::RequestData (this=0x12dce40,
request=0x14ad920, inputVector=0x1f266c0, outputVector=0x1f26760)
at /opt/vmtk_build/VTK/Graphics/vtkCutter.cxx:378
#5 0x00007ffff429124e in vtkPolyDataAlgorithm::ProcessRequest
(this=0x12dce40, request=0x14ad920, inputVector=0x1f266c0,
outputVector=0x1f26760) at
/opt/vmtk_build/VTK/Filtering/vtkPolyDataAlgorithm.cxx:91
#6 0x00007fffef7cc9e7 in vtkCutter::ProcessRequest
(this=0x12dce40, request=0x14ad920, inputVector=0x1f266c0,
outputVector=0x1f26760) at
/opt/vmtk_build/VTK/Graphics/vtkCutter.cxx:1122
#7 0x00007ffff4166cc1 in vtkExecutive::CallAlgorithm
(this=0x1f268d0, request=0x14ad920, direction=1, inInfo=0x1f266c0,
outInfo=0x1f26760) at
/opt/vmtk_build/VTK/Filtering/vtkExecutive.cxx:747
#8 0x00007ffff414f361 in vtkDemandDrivenPipeline::ExecuteData
(this=0x1f268d0, request=0x14ad920, inInfo=0x1f266c0,
outInfo=0x1f26760) at
/opt/vmtk_build/VTK/Filtering/vtkDemandDrivenPipeline.cxx:507
#9 0x00007ffff414ea1f in vtkDemandDrivenPipeline::ProcessRequest
(this=0x1f268d0, request=0x14ad920, inInfoVec=0x1f266c0,
outInfoVec=0x1f26760) at
/opt/vmtk_build/VTK/Filtering/vtkDemandDrivenPipeline.cxx:279
#10 0x00007ffff4314e75 in
vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x1f268d0,
request=0x14ad920, inInfoVec=0x1f266c0, outInfoVec=0x1f26760) at
/opt/vmtk_build/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:271
#11 0x00007ffff414f128 in vtkDemandDrivenPipeline::UpdateData
(this=0x1f268d0, outputPort=0) at
/opt/vmtk_build/VTK/Filtering/vtkDemandDrivenPipeline.cxx:449
#12 0x00007ffff4315092 in vtkStreamingDemandDrivenPipeline::Update
(this=0x1f268d0, port=0) at
/opt/vmtk_build/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:321
#13 0x00007ffff4164f65 in vtkExecutive::Update (this=0x1f268d0) at
/opt/vmtk_build/VTK/Filtering/vtkExecutive.cxx:315
#14 0x00007ffff414eaba in vtkDemandDrivenPipeline::Update
(this=0x1f268d0) at
/opt/vmtk_build/VTK/Filtering/vtkDemandDrivenPipeline.cxx:312
#15 0x00007ffff4314fba in vtkStreamingDemandDrivenPipeline::Update
(this=0x1f268d0) at
/opt/vmtk_build/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:301
#16 0x00007ffff40d9152 in vtkAlgorithm::Update (this=0x12dce40) at
/opt/vmtk_build/VTK/Filtering/vtkAlgorithm.cxx:1283
#17 0x00007fffe3a1921e in
vtkvmtkPolyDataBranchSections::ExtractCylinderSection
(cylinder=0x214fd10, origin=0x7fffffffcbd0, normal=0x7fffffffcbb0,
section=0x14a25b0, closed=@0x7fffffffcbaf) at
/opt/vmtk/vtkVmtk/ComputationalGeometry/vtkvmtkPolyDataBranchSections.cxx:514
#18 0x00007fffe3a099d9 in
vtkvmtkPolyDataBifurcationSections::ComputeBifurcationSections
(this=0x214af50, input=0x2033000, bifurcationGroupId=1,
upStreamGroupIds=0x202d910, downStreamGroupIds=0x123ef30,
output=0x214c6a0) at
/opt/vmtk/vtkVmtk/ComputationalGeometry/vtkvmtkPolyDataBifurcationSections.cxx:590
#19 0x00007fffe3a0887f in
vtkvmtkPolyDataBifurcationSections::RequestData (this=0x214af50,
inputVector=0x202cba0, outputVector=0x202df30) at
/opt/vmtk/vtkVmtk/ComputationalGeometry/vtkvmtkPolyDataBifurcationSections.cxx:416
#20 0x00007ffff429124e in vtkPolyDataAlgorithm::ProcessRequest
(this=0x214af50, request=0x17ae560, inputVector=0x202cba0,
outputVector=0x202df30) at
/opt/vmtk_build/VTK/Filtering/vtkPolyDataAlgorithm.cxx:91
#21 0x00007ffff4166cc1 in vtkExecutive::CallAlgorithm
(this=0x15d6860, request=0x17ae560, direction=1, inInfo=0x202cba0,
outInfo=0x202df30) at
/opt/vmtk_build/VTK/Filtering/vtkExecutive.cxx:747
#22 0x00007ffff414f361 in vtkDemandDrivenPipeline::ExecuteData
(this=0x15d6860, request=0x17ae560, inInfo=0x202cba0,
outInfo=0x202df30) at
/opt/vmtk_build/VTK/Filtering/vtkDemandDrivenPipeline.cxx:507
#23 0x00007ffff414ea1f in vtkDemandDrivenPipeline::ProcessRequest
(this=0x15d6860, request=0x17ae560, inInfoVec=0x202cba0,
outInfoVec=0x202df30) at
/opt/vmtk_build/VTK/Filtering/vtkDemandDrivenPipeline.cxx:279
#24 0x00007ffff4314e75 in
vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x15d6860,
request=0x17ae560, inInfoVec=0x202cba0, outInfoVec=0x202df30) at
/opt/vmtk_build/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:271
#25 0x00007ffff414f128 in vtkDemandDrivenPipeline::UpdateData
(this=0x15d6860, outputPort=0) at
/opt/vmtk_build/VTK/Filtering/vtkDemandDrivenPipeline.cxx:449
#26 0x00007ffff4315092 in vtkStreamingDemandDrivenPipeline::Update
(this=0x15d6860, port=0) at
/opt/vmtk_build/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:321
#27 0x00007ffff4164f65 in vtkExecutive::Update (this=0x15d6860) at
/opt/vmtk_build/VTK/Filtering/vtkExecutive.cxx:315
#28 0x00007ffff414eaba in vtkDemandDrivenPipeline::Update
(this=0x15d6860) at
/opt/vmtk_build/VTK/Filtering/vtkDemandDrivenPipeline.cxx:312
#29 0x00007ffff4314fba in vtkStreamingDemandDrivenPipeline::Update
(this=0x15d6860) at
/opt/vmtk_build/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:301
#30 0x00007ffff40d9152 in vtkAlgorithm::Update (this=0x214af50) at
/opt/vmtk_build/VTK/Filtering/vtkAlgorithm.cxx:1283
#31 0x00007ffff477f12e in PyvtkAlgorithm_Update (self=0xfb8aa0,
args=0x7ffff7f94050) at
/opt/vmtk_build/VTK-Build/Filtering/vtkAlgorithmPython.cxx:1747
#32 0x000000000049c32d in PyEval_EvalFrameEx ()
#33 0x000000000049d38a in PyEval_EvalFrameEx ()
#34 0x000000000049dfdf in PyEval_EvalCodeEx ()
#35 0x000000000049c74a in PyEval_EvalFrameEx ()
#36 0x000000000049d38a in PyEval_EvalFrameEx ()
#37 0x000000000049dfdf in PyEval_EvalCodeEx ()
#38 0x000000000049e0c2 in PyEval_EvalCode ()
#39 0x00000000004c0830 in PyRun_FileExFlags ()
#40 0x00000000004c1527 in PyRun_SimpleFileExFlags ()
#41 0x000000000041adfd in Py_Main ()
#42 0x00007ffff69a3ead in __libc_start_main () from
/lib/x86_64-linux-gnu/libc.so.6
#43 0x000000000041a081 in _start ()
------------------------------------------------------------------------------
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to serve as a reference, checklist
and point of
discussion for anyone considering optimizing the pricing and
packaging model
of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/
_______________________________________________
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------------------------------------------------------------------------------
Cloud Services Checklist: Pricing and Packaging Optimization
This white paper is intended to serve as a reference, checklist and point of
discussion for anyone considering optimizing the pricing and packaging model
of a cloud services business. Read Now!
http://www.accelacomm.com/jaw/sfnl/114/51491232/
_______________________________________________
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