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From: Devrim T. <dev...@ho...> - 2019-06-18 08:39:05
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Dear vmtk society, I have closely followed this mailing list and searched all over it and a lot of things were helpful but unfortunately not enough. I want to generate cross sections of a carotid artery in order to obtain the geometric info. I have .vtp files and 3 surfaces: lumen, tissue and calcium. My goal is to generate cross sections for each surface and i have generated this but the cross sections do not seem so right (some sharpness). I made sure my centerlines were also smoothed. The way i went around it to make it geometrically correct was by using one centerline in order to obtain the cross sections for each surface. The tissue and lumen are bifurcating surfaces but the calcium is not. I would really appreciate some guidance on this matter. Thank you, Dev |
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From: Carlos A. B. <car...@gm...> - 2016-03-23 14:24:00
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Hi everyone, I have an old instalation of vmtk, from 2014, and I want to know wich version it is, I am trying vmtk --version in the command line, but that does not work. Any clues on how to get my vmtk version. By the way the installation is from source. Thank yo in advance, Carlos |
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From: Arjan G. <aj...@gm...> - 2015-12-18 19:09:13
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Dear Dhananjay,
Glad you find it useful. I think the elements of your surface mesh can have
any number of nodes. Line 73 of the script extracts this information from
the csv-file. Try it out to see if it works.
If you have more questions, feel free to email me directly as this is no
longer a VMTK-related issue.
Arjan
On Thu, Dec 17, 2015 at 4:02 PM, <dha...@gm...> wrote:
> Dear Dr. Geers,
>
> I would like to thank you for sharing the cfx2vtp python script that
> converts .csv files created in ANSYS CFD-Post to .vtp format. I had a brief
> query concerning the mesh handling capabilities of the aforementioned
> script file. I would like to know whether quadrilateral and polyhedral
> surface meshes can be read into the script and converted to the
> corresponding .vtp file.
>
> Thanking You
>
> Dhananjay Subramaniam
>
> On Wednesday, February 20, 2013 at 3:40:21 PM UTC-5, tossin 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
>>
> --
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> For more options, visit https://groups.google.com/d/optout.
>
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From: Sammer Z. <sam...@fa...> - 2015-10-20 02:19:44
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Hello I have question to post I have segmented the right artery some how in vmtk by selecting VOI first but for viewing it in Matlab i have converted my levelsets.vti file into .nrrd format and then i read that .nrrd file in Matlab. This time the shape of artery was fine as it was in vmtk but i really dont understand about the dimensions.The dimensions which i got they are 346*374*172 although the dimension of original volumes are 512*512*304. I want to compare my segmented result (which i did in Matlab) with the one that i have got in vmtk but i am unable to do it because of dimensions. Please help me in this regard. Thanks in advance Waiting for your kind response |
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From: Simone M. <sim...@or...> - 2015-04-02 08:53:43
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Dear … -_-, first of all, the official vmtk-users list is here https://groups.google.com/forum/#!forum/vmtk-users This is deprecated: vmt...@li... I can understand that you have compiled it from source under Windows. Do you have python under PATH? Try to run the vmtk-exe.py from terminal and see if there are errors. In the future, I would suggest to install vmtk under windows using the installer or the python egg. Best Regards, Simone On Tuesday, Mar 31, 2015 at 6:39 am, -_- <554...@qq...>, wrote: Hi all, I have generated vmtk1.2 by vs2012. However,when i try to open "vmtk-exe.py", it just flash and automatically closed.Please give me some advice. best wishes! |
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From: -︿_︿- <554...@qq...> - 2015-03-31 04:39:35
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Hi all,
I have generated vmtk1.2 by vs2012. However,when i try to open "vmtk-exe.py", it just flash and automatically closed.Please give me some advice.
best wishes! |
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From: Chiara T. <chi...@iu...> - 2015-03-25 11:54:52
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Dear vmtk users, I am using vmtkimagevoiselector with the following line: vmtkimagevoiselector -ifile path-to-image-file.mhd -ofile path-to-voi-image-file.mhd -boxbounds 130.7949696779251 213.64265620708466 134.87211960554123 155.42095524072647 309.0 427.0 -interactive 0 Whilst executing I get the following error: itk::ERROR: ImageFileWriter(0x7fa6c3c8fc10): Largest possible region does not fully contain requested paste IO regionPaste IO region: ImageIORegion (0x7fff513ff278) and python just quit. Any idea why this happens? Am I doing someting wrong? The box bounds are inside the image, I just copy paste the box bounds of a previous vmtkimagevoiselector on a 4D CTA datasets. I first cut the first image and try to apply the same cut to the following images of the dataset. Thank you Chiara |
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From: pranathi v. <pra...@gm...> - 2015-01-19 16:43:55
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Hello all, I have tried installing VMTK by using precompiled version and source version too. I have errors both ways. I have installed all the required softwares like git, CMake and python 2.7 for windows 64 bit computer. Firstly when I run a command like vmtkimagereader -f dicom -d D:\ --pipe vmtkimageviewer in pypepad it says executing vmtkimageviewer but no window pops up. Similarly if I type vmtkimagereader -f dicom -d D:\ vmtkimagevoiselector -ofile image_volume_voi.vti there is no rendering window. Secondly, after I cloned vmtk using git anf build it using CMake configuring and generating are perfectly done but when I build the solution file using Microsoft visual studio 2012 there are 15 errors Error 102 error MSB6006: "cmd.exe" exited with code 1. C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets 170 5 ITK Error 102 error MSB6006: "cmd.exe" exited with code 1. C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V120\Microsoft.CppCommon.targets 170 5 ITK Error 136 error LNK1112: module machine type 'x64' conflicts with target machine type 'X86' [C:\Users\Kiranmayee Vemuri\Downloads\PRANU\pranu\vmtkbld\VTK-Build\Wrapping\Python\vtkPythonCore.vcxproj] C:\Users\Kiranmayee Vemuri\Downloads\PRANU\pranu\vmtkbld\python27.lib(python27.dll) VTK Please help me in installing correctly VMTK Regards, Pranathi |
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From: Simone M. <sim...@or...> - 2014-10-29 09:29:06
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Dear Teiv, try to use vmtksurfacewriter instead of vmtkmeshwriter. The output of vmtkcenterlines is a polydata object. Best Regards Simone — Simone Manini, Eng Project Manager, OROBIX Srl via Camozzi 144, 24121 Bergamo, Italy orobix: www.orobix.com web: daron1337.github.io twitter: @daron1337 phone: +39 035 0273786 +39 035 0170561 "This message originates from Orobix Srl and its contents and attachments are privileged and confidential and are intended only for the individual(s) or entity(ies) named above. This message should not be forwarded, distributed or disclosed. Any unauthorized use, dissemination and duplication is strictly prohibited and may be unlawful. All personal messages express views solely of the sender, which are not to be attributed to Orobix Srl, and may not be copied or distributed without this disclaimer. If you are not the intended recipient or received this message in error, please delete this message and notify the sender by reply e-mail. Opinions, conclusions and other information in this message that do not relate to the official business of Orobix Srl shall be understood as neither given nor endorsed by it." On Tuesday, Oct 28, 2014 at 8:01 am, Teiv <te...@gm...>, wrote: Hello Luca, Could you please show me a way to output the result of the vmtkcenterlines command in the Ascii format so as it can be read by Gmesh. I have used the following commands but it has not been successful: $ vmtkcenterlines -ifile aorta.vtk --pipe vmtkmeshwriter -ofile foo.vtk -mode ascii I really appreciate any help you can provide. Best, Teiv. On Friday, November 2, 2012 6:31:27 PM UTC+9, Luca Antiga wrote: Hi everyone, about the STL thing, the vtk writer used in vmtk supports ASCII files out of the box, only I haven't exposed that option at the script level until today. I just pushed a commit on the source code repository to allow this: ... --pipe vmtksurfacewriter -ofile foo.stl -mode ascii It works for stl, vtu, vtk, vtp, ply. If you're in a rush, get these two files https://raw.github.com/vmtk/vmtk/master/vmtkScripts/vmtksurfacewriter.py https://raw.github.com/vmtk/vmtk/master/vmtkScripts/vmtkmeshwriter.py and copy them over to your {installpath}/lib/vmtk/vmtk folder, replacing the old ones. Note, it's the lib folder, not the bin folder (you'll find two files called vmtksurfacewriter and vmtkmeshwriter, without the py extension: they're not the right ones to replace). Luca PS: Richard, thanks a lot for sharing the script, very much appreciated. On Nov 1, 2012, at 8:19 PM, Richard Downe wrote: Personally, I write my stl files myself, because I build my surfaces in another program. Attached is a perl script I've used for converting .off files to .stl -- should be trivial to adapt it to python/iterate over a vtkPolyData instead of .off input. -rd On 11/01/2012 01:40 PM, Vikram Mehta wrote: Hi Arjan, Thanks alot for your response. I seem to have got all the data I needed. On a separate note, Does anyone know how to save your surface file as an ASCII STL and not a binary one. Thanks alot ! Vikram. On Tue, Oct 16, 2012 at 9:47 PM, Arjan Geers <ajg...@gmail.com> wrote: Hi Vikram, You could try this: vmtksurfacereader -ifile /home/vm308/catheter.vtp --pipe vmtkcenterlines -seedselector openprofiles -ofile catheter_cl.dat It should give you the coordinates of the centerline points in a human-readable format. Good luck with it, Arjan On Tue, Oct 16, 2012 at 7:58 PM, Vikram Mehta <vvm...@gmail.com> wrote: Dear VMTK users, I have a surface reconstruction of a catheter within a coronary artery and have also generated the centerlines for it. However, for further processing, I need the coordinates of the catheter centerline and was wondering if you all had any idea to do this ? I tried using vmtkcenterlinegeometry but I might be doing something wrong, vmtksurfacereader -ifile /home/vm308/catheter.vtp --pipe vmtkcenterlines -seedselector openprofiles --pipe vmtkcenterlinegeometry -ofile catheter_clg.vtp Ideally I would like a .txt file (basically a point cloud) - is this achievable ? Please advise. Looking forward to your replies Thanks in advance, Vikram. ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. 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Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct_______________________________________________ vmtk-users mailing list vmtk-...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/vmtk-users -- You received this message because you are subscribed to the Google Groups "vmtk-users" group. To unsubscribe from this group and stop receiving emails from it, send an email to vmt...@go.... To post to this group, send email to vmt...@go.... For more options, visit https://groups.google.com/d/optout. |
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From: Dr. R. G. <gro...@mh...> - 2014-08-15 12:44:51
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Dear Michel, dear Luca, Coming back to Hessian-based measures of Yours, which I've tried out two years ago: Is my understanding correct that the response function V of [Descôteaux et. al.MICCAI 2006] and [Luca ITK-Journal 2007] differ for N=3 and M=2? i.e. for N=3, M=2: Rblob = vnl_math_abs( l3 + l3 - l2 - l1 ) / l3 in itkDescoteauxSheetnessImageFilter corresponding to Ra (NOT Rb) in itkHessianToObjectnessMeasureImageFilter, which is undefined for N=3, M=2. Rsheet = l2 / l3 in itkDescoteauxSheetnessImageFilter corresponds to Rb in itkHessianToObjectnessMeasureImageFilter, both equal for N=3, M=2. When has each definition its optimal use? Additionally, In Descôteaux2006 a zero level-set segmentation approach is described based on a vector field constructed from initial ellipsoids positioned at high sheetness measures. Are there ITK-Filters to achieve that same approach or something similar? Which would I need? Many thanks again for Your replies and help. Roman On 05/09/12 17:10, Audette, Michel A. wrote: > Do a google on sheetness. Maxime Descôteaux and I had modified this type of > operator a few years back to improve the detection of curviplanar bones (MICCAI > paper, republished in J. Computer Assisted Surgery), which was a tweak of his > and Frangi's work on vesselness operators. > > Michel > > Michel Audette, Ph.D. > Assistant Professor, > Department of Modeling, Simulation and Visualization Engineering, > Old Dominion University, > Norfolk, VA. > ________________________________________ > From: ins...@it... [ins...@it...] on behalf of > Ho Cheung [hoc...@gm...] > Sent: Wednesday, September 05, 2012 8:41 AM > To: Dr. Roman Grothausmann > Cc: ins...@it...; vmt...@li...; Luca Antiga > Subject: Re: [Insight-users] enhancing plate like structures (by modifying > itkHessianSmoothed3DToVesselnessMeasureImageFilter) > > Hi Dr. Grothausmann, > > The measure in ITK appears to be based on Sato > (http://www.spl.harvard.edu/archive/spl-pre2007/pages/papers/yoshi/node3.html#SECTION00021000000000000000) > and I don't see an easy way to modify it so that it detects plate like > structures instead of line like structures. > > If speed is not a major concern for you, may I suggest you implement a similar > measure? Frangi's original vesselness enhancement formula > (http://www.dtic.upf.edu/~afrangi/articles/miccai1998.pdf) can be easily > modified for what you need and is based on Eigenvalues like Sato. > > According to equations 10, 11, 12, 13 in Frangi's paper and my interpretation of > what the measures do, what you need is high Ra, Rb, and S values, so the formula > becomes: > > V = [1 - exp(-Ra^2/2a^2)][1 - exp(-Rb^2/2b^2)][1 - exp(-S^2/2c62)] > > Hope, this helps, > > Ho Cheung > Research Assistant > Bio-Image Analytics Laboratory - University of Houston > (832) 215-6347 > > > > On Sep 5, 2012, at 3:36 AM, Dr. Roman Grothausmann > <gro...@mh...> wrote: > > > Dear mailing list members, dear Luca, > > > > > > Recently I was trying to enhance vascular structures from airways with the > vessel enhancement filters from ITK (objectness and vessel enhancement). The > problem is that these vessels are not filled in the tomograms our imaging > technique yields. Only the airway walls are imaged, which corresponds to an > uneven 2D surface. Since it is only a 3D not an ND problem, I tried to modify > itkHessianSmoothed3DToVesselnessMeasureImageFilter to enhance not vessels (1D) > structures but plates/walls. Therefore I exchanged lambda 1 and 3 in the > weighting function. Sadly, I could not get the filter to enhance the airway walls. > > Have I missed anything or would enhancing plateness this way only work for > not-curved planes? > > > > > > Here the important part of the diff of my changes: > > > > diff -au > itk/IJ-Vessel_Enhancement_Diffusion.1/itkHessianSmoothed3DToVesselnessMeasureImageFilter.txx > itk/plateness3D_01/itkHessianSmoothed3DToPlatenessMeasureImageFilter.txx > > > > > > > > + ////swap Lambda1 and Lambda3 to enhance "plateness" > > + double swap_tmp= Lambda1; > > + Lambda3= Lambda1; > > + Lambda1= swap_tmp; > > + ///swapping done > > + > > double Lambda1Abs = vnl_math_abs( Lambda1 ); > > double Lambda2Abs = vnl_math_abs( Lambda2 ); > > double Lambda3Abs = vnl_math_abs( Lambda3 ); > > @@ -162,14 +168,13 @@ > > double vesMeasure_3 = > > ( 1 - vcl_exp( -1.0 * (( vnl_math_sqr( S )) / ( 2.0 * ( GammaSqr))))); > > > > - double vesMeasure_4 = > > - vcl_exp ( -1.0 * ( 2.0 * vnl_math_sqr( m_C )) / > > - ( Lambda2Abs * (Lambda3Sqr))); > > + double vesMeasure_4 = 1; ////plateness for now not smoothed > > + //double vesMeasure_4 = vcl_exp ( -1.0 * ( 2.0 * vnl_math_sqr( m_C )) > / ( Lambda2Abs * (Lambda3Sqr))); ////check if this makes sense for plateness > > > > > > Many thanks for any help or hints. > > 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 > > 30625 Hannover > > > > Tel. +49 511 532-9574 > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://www.itk.org/mailman/listinfo/insight-users > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://www.itk.org/mailman/listinfo/insight-users > > > -- > BEGIN-ANTISPAM-VOTING-LINKS > ------------------------------------------------------ > > Teach CanIt if this mail (ID 699566122) is spam: > Spam: https://www.spamtrap.odu.edu/b.php?i=699566122&m=6758d860fb26&t=20120905&c=s > Not spam: > https://www.spamtrap.odu.edu/b.php?i=699566122&m=6758d860fb26&t=20120905&c=n > Forget vote: > https://www.spamtrap.odu.edu/b.php?i=699566122&m=6758d860fb26&t=20120905&c=f > ------------------------------------------------------ > END-ANTISPAM-VOTING-LINKS > -- 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 |
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From: Lia S. <lia...@po...> - 2014-07-15 05:52:06
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new iphone5s is here BUEANP.COM very cheap |
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From: Carlos A. B. <car...@gm...> - 2014-06-05 21:33:19
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Hi vmtk community,
I'm trying to understand the output of the vmtkbifurcationvectors filter.
After following the tutorial I successfully compute the bifurcation
vectors, but I would like to know a litle more about the output,
Suppose I have an Y shaped tree, then the filter gives me a polydata with 3
points (P1,P2,P3), I understand each point is associated to an specific
artery (through the GroupId array), and all three belong to the same
bifurcation (BifurcationGroupId). I can also know the direction by querying
the BifurcationVectorsOrientation array, and angles with the corresponding
arrays. What I found difficult to understand is how this 3 points are
calculated, because all angles and in/out vectors depend on them, so I try
to read he source code first. Please, correct-me if i miss-understood
something:
First the bifurcation is identify,
Then, for each cell i (arterial segment) involved in the bifurcation
The orientation (in/out) is determined
The subset of cell points at the begin and end of the segment are
determined (by the radius)
A weighted averaged is used for computing two points (for the beginning
and end of the cell) which are called averageTouchingPoint and
averageLastPoint
Then, depending on the orientation, the bifurcation vector of the cell
is computed by subtracting this points, and one of them is used as the
bifurcation point Pi.
Then, if that is the way of computing P1, P2 and P3, that explains why they
usually don't touch the associated centerline, for example for a C shaped
branch, the bifurcation point will be inside the C, right?
I was thinking also that the bifurcation plane centroid is never used for
computing the bifurcation point nor the bifurcation vectors of each cell,
correct?
For example the bifurcation point could be set to the averageTouchingPoint
and the bifurcation vector computed as bifurcationCentroid -
averageTouchingPoint.
Well Thank you very match for developing VMTK, and i hope you can help me
find out the exact way the bifurcation points are computed.
Regards
Carlos
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From: Evan K. <to...@gm...> - 2014-05-08 19:20:42
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Sorry, we never actually got around to trying it out with VMTK. On Thu, May 8, 2014 at 11:48 AM, 余绍德 <nic...@gm...> wrote: > How is this work going ? > The dense microvascular network seems fantastic. > > > 在 2013年8月9日星期五UTC-7上午10时47分54秒，tossin写道： > >> Hello VMTK-users, >> >> A colleague has asked about skeletonizing a dense microvascular network >> (see image). Is it sensible to use VMTK (like vmtknetworkextraction?) for >> something this extensive? >> >> [image: Inline image 1] >> >> Thanks, >> Evan Kao >> > -- > You received this message because you are subscribed to the Google Groups > "vmtk-users" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to vmt...@go.... > To post to this group, send email to vmt...@go.... > For more options, visit https://groups.google.com/d/optout. > |
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From: Dr. R. G. <gro...@mh...> - 2014-02-25 14:56:40
|
Dear Luca,
I've some updates on this issue:
1. using -usetetgen 1 with vmtkcenterlines or vmtkdelaunayvoronoi seem to fail
because the import mechanism (from tetgenio to vmtk) in vtkvmtkTetGenWrapper.cxx
ll: 482 seems not to work for the cells, the output only contains points even if
I add
tetgen.OutputVolumeElements = 1
to vmtkdelaunayvoronoi.py or vmtkcenterlines.py
I guess the cells are important for voronoiCostFunctionCalculator in
vtkvmtkPolyDataCenterlines.cxx. At least it works if I run tetgen separately e.g.
tetgen -pq -k test03_mc127_cap.stl
and then using -delaunaytessellationfile with vmtkcenterlines having changed the
line:
['DelaunayTessellation','delaunaytessellation','vtkUnstructuredGrid',1,'','optional
input Delaunay tessellation'],
to (added vmtkmeshreader):
['DelaunayTessellation','delaunaytessellation','vtkUnstructuredGrid',1,'','optional
input Delaunay tessellation','vmtkmeshreader'],
vmtkcenterlines -delaunaytessellationfile test03_mc127_cap.1.vtk -ifile
test03_mc127_cap.vtp -ofile test03_mc127_cap_clip_lmp_cl-skel.vtp -seedselector
pointlist -sourcepoints $rootN -targetpoints `awk '!/^#/ {print $2, $3, $4}'
03_test_surf_nw-skel.ep | grep -v "$rootN" | xargs`
However there is some big discrepancy (see image) between the resulting
endpoints (03_test_surf_nw-skel.ep) from vmtknetworkextraction (black), used as
endpoints for vmtkcenterlines and the result from tetgen -p (red) and tetgen -pq
(blue). For both vmtkcenterlines results it seems as if there were multiple
target points, however only one was supplied. The red skeleton even reaches to
the ouside of the surface. Also both results do not track some branches (e.g.
1st and 3rd branch from bottom left).
Any ideas what else I could try to make vmtkcenterlines work for this case?
Many thanks for any help or hints.
Roman
On 04/03/13 13:54, 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
>
--
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
|
|
From: Elaine T. <ela...@ga...> - 2014-02-06 15:04:45
|
Hi,
I am wondering why the vmtk that I have (I think it's version 1.0.1) cannot
read stl in ascii format. It works for binary format.I know the fix for
surface writing is like that:
vmtksurfacewriter -i @.o -mode ascii -ofile foo.vtk
But for vmtksurfacereader/ surfaceviewer, I got the following error when I
am trying to read an ascii STL:
[etang@desktop Elaine_practice]$ vmtksurfacereader -ifile foo.stl
Creating vmtkSurfaceReader instance.
Automatic piping vmtksurfacereader
Parsing options vmtksurfacereader
InputFileName = foo.stl
Explicit piping vmtksurfacereader
Input vmtksurfacereader members:
Id = 0
Disabled = 0
Format =
GuessFormat = 1
Surface = 0
InputFileName = foo.stl
SurfaceOutputFileName =
Executing vmtksurfacereader ...
Reading STL surface file.
ERROR: In /home/etang/vmtk/vmtk-build/VTK/IO/vtkSTLReader.cxx, line 446
vtkSTLReader (0x18b281c0): STLReader error reading file: foo.stl Premature
EOF while reading end solid.
*** glibc detected *** python: double free or corruption (!prev):
0x0000000018b30710 ***
======= Backtrace: =========
/lib64/libc.so.6[0x352bc7166f]
/lib64/libc.so.6(cfree+0x4b)[0x352bc7589b]
/lib64/libc.so.6(fclose+0x14b)[0x352bc6001b]
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkIO.so.5.10(_ZN12vtkSTLReader11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x24c)[0x2b8c67cbbe4c]
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN12vtkExecutive13CallAlgorithmEP14vtkInformationiPP20vtkInformationVectorS3_+0x54)[0x2b8c66f386d4]
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN23vtkDemandDrivenPipeline11ExecuteDataEP14vtkInformationPP20vtkInformationVectorS3_+0x4c)[0x2b8c66f2c8bc]
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN23vtkDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x293)[0x2b8c66f2f653]
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN32vtkStreamingDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x2a9)[0x2b8c6709ee69]
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN23vtkDemandDrivenPipeline10UpdateDataEi+0x9e)[0x2b8c66f2eb9e]
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN32vtkStreamingDemandDrivenPipeline6UpdateEi+0x7b)[0x2b8c67099fdb]
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFilteringPythonD.so.5.10[0x2b8c6691efff]
python(PyEval_EvalFrameEx+0x68e2)[0x49c862]
python(PyEval_EvalFrameEx+0x6b2f)[0x49caaf]
python(PyEval_EvalFrameEx+0x6b2f)[0x49caaf]
python(PyEval_EvalCodeEx+0x89b)[0x49dd1b]
python(PyEval_EvalFrameEx+0x5712)[0x49b692]
python(PyEval_EvalCodeEx+0x89b)[0x49dd1b]
python(PyEval_EvalFrameEx+0x5712)[0x49b692]
python(PyEval_EvalCodeEx+0x89b)[0x49dd1b]
python[0x4fc9ff]
python(PyObject_Call+0x5d)[0x4189cd]
python(PyEval_EvalFrameEx+0x399d)[0x49991d]
python(PyEval_EvalFrameEx+0x6b2f)[0x49caaf]
python(PyEval_EvalFrameEx+0x6b2f)[0x49caaf]
python(PyEval_EvalCodeEx+0x89b)[0x49dd1b]
python[0x4fc9ff]
python(PyObject_Call+0x5d)[0x4189cd]
python[0x41fedf]
python(PyObject_Call+0x5d)[0x4189cd]
python[0x46cf78]
python[0x466292]
python(PyObject_Call+0x5d)[0x4189cd]
python(PyEval_EvalFrameEx+0x111a)[0x49709a]
python(PyEval_EvalFrameEx+0x6b2f)[0x49caaf]
python(PyEval_EvalCodeEx+0x89b)[0x49dd1b]
python(PyEval_EvalCode+0x32)[0x49dd92]
python(PyRun_FileExFlags+0xc1)[0x4bfe31]
python(PyRun_SimpleFileExFlags+0x1d8)[0x4c00e8]
python(Py_Main+0xa7d)[0x414bbd]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x352bc1d9c4]
python[0x413d69]
======= Memory map: ========
00400000-0055d000 r-xp 00000000 fd:03 49283158
/usr/local/bin/python2.7
0075d000-00799000 rw-p 0015d000 fd:03 49283158
/usr/local/bin/python2.7
00799000-007a8000 rw-p 00799000 00:00 0
1847f000-18b51000 rw-p 1847f000 00:00 0
[heap]
352b800000-352b81c000 r-xp 00000000 fd:03 141230281
/lib64/ld-2.5.so
352ba1c000-352ba1d000 r--p 0001c000 fd:03 141230281
/lib64/ld-2.5.so
352ba1d000-352ba1e000 rw-p 0001d000 fd:03 141230281
/lib64/ld-2.5.so
352bc00000-352bd4f000 r-xp 00000000 fd:03 141230442
/lib64/libc-2.5.so
352bd4f000-352bf4e000 ---p 0014f000 fd:03 141230442
/lib64/libc-2.5.so
352bf4e000-352bf52000 r--p 0014e000 fd:03 141230442
/lib64/libc-2.5.so
352bf52000-352bf53000 rw-p 00152000 fd:03 141230442
/lib64/libc-2.5.so
352bf53000-352bf58000 rw-p 352bf53000 00:00 0
352c000000-352c082000 r-xp 00000000 fd:03 141230452
/lib64/libm-2.5.so
352c082000-352c281000 ---p 00082000 fd:03 141230452
/lib64/libm-2.5.so
352c281000-352c282000 r--p 00081000 fd:03 141230452
/lib64/libm-2.5.so
352c282000-352c283000 rw-p 00082000 fd:03 141230452
/lib64/libm-2.5.so
352c400000-352c402000 r-xp 00000000 fd:03 141230450
/lib64/libdl-2.5.so
352c402000-352c602000 ---p 00002000 fd:03 141230450
/lib64/libdl-2.5.so
352c602000-352c603000 r--p 00002000 fd:03 141230450
/lib64/libdl-2.5.so
352c603000-352c604000 rw-p 00003000 fd:03 141230450
/lib64/libdl-2.5.so
352c800000-352c816000 r-xp 00000000 fd:03 141230445
/lib64/libpthread-2.5.so
352c816000-352ca16000 ---p 00016000 fd:03 141230445
/lib64/libpthread-2.5.so
352ca16000-352ca17000 r--p 00016000 fd:03 141230445
/lib64/libpthread-2.5.so
352ca17000-352ca18000 rw-p 00017000 fd:03 141230445
/lib64/libpthread-2.5.so
352ca18000-352ca1c000 rw-p 352ca18000 00:00 0
352cc00000-352cc14000 r-xp 00000000 fd:03 146729449
/usr/lib64/libz.so.1.2.3
352cc14000-352ce13000 ---p 00014000 fd:03 146729449
/usr/lib64/libz.so.1.2.3
352ce13000-352ce14000 rw-p 00013000 fd:03 146729449
/usr/lib64/libz.so.1.2.3
352d400000-352d402000 r-xp 00000000 fd:03 146709883
/usr/lib64/libXau.so.6.0.0
352d402000-352d601000 ---p 00002000 fd:03 146709883
/usr/lib64/libXau.so.6.0.0
352d601000-352d602000 rw-p 00001000 fd:03 146709883
/usr/lib64/libXau.so.6.0.0
352d800000-352d805000 r-xp 00000000 fd:03 146729413
/usr/lib64/libXdmcp.so.6.0.0
352d805000-352da04000 ---p 00005000 fd:03 146729413
/usr/lib64/libXdmcp.so.6.0.0
352da04000-352da05000 rw-p 00004000 fd:03 146729413
/usr/lib64/libXdmcp.so.6.0.0
352dc00000-352dd05000 r-xp 00000000 fd:03 146729418
/usr/lib64/libX11.so.6.2.0
352dd05000-352df05000 ---p 00105000 fd:03 146729418
/usr/lib64/libX11.so.6.2.0
352df05000-352df0c000 rw-p 00105000 fd:03 146729418
/usr/lib64/libX11.so.6.2.0
352e400000-352e410000 r-xp 00000000 fd:03 146729536
/usr/lib64/libXext.so.6.4.0
352e410000-352e610000 ---p 00010000 fd:03 146729536
/usr/lib64/libXext.so.6.4.0
352e610000-352e611000 rw-p 00010000 fd:03 146729536
/usr/lib64/libXext.so.6.4.0
3531400000-3531415000 r-xp 00000000 fd:03 141230456
/lib64/libselinux.so.1
3531415000-3531615000 ---p 00015000 fd:03 141230456
/lib64/libselinux.so.1
3531615000-3531617000 rw-p 00015000 fd:03 141230456
/lib64/libselinux.so.1
3531617000-3531618000 rw-p 3531617000 00:00 0
3531800000-353183b000 r-xp 00000000 fd:03 141230455
/lib64/libsepol.so.1
353183b000-3531a3b000 ---p 0003b000 fd:03 141230455
/lib64/libsepol.so.1
3531a3b000-3531a3c000 rw-p 0003b000 fd:03 141230455
/lib64/libsepol.so.1
3531a3c000-3531a46000 rw-p 3531a3c000 00:00 0
3534600000-353460d000 r-xp 00000000 fd:03 141230462
/lib64/libgcc_s-4.1.2-20080825.so.1
353460d000-353480d000 ---p 0000d000 fd:03 141230462
/lib64/libgcc_s-4.1.2-20080825.so.1
353480d000-353480e000 rw-p 0000d000 fd:03 141230462
/lib64/libgcc_s-4.1.2-20080825.so.1
3534e00000-3534e09000 r-xp 00000000 fd:03 146729711
/usr/lib64/libSM.so.6.0.0
3534e09000-3535009000 ---p 00009000 fd:03 146729711
/usr/lib64/libSM.so.6.0.0
3535009000-353500a000 rw-p 00009000 fd:03 146729711
/usr/lib64/libSM.so.6.0.0
3535200000-3535217000 r-xp 00000000 fd:03 146729698
/usr/lib64/libICE.so.6.3.0
3535217000-3535416000 ---p 00017000 fd:03 146729698
/usr/lib64/libICE.so.6.3.0
3535416000-3535418000 rw-p 00016000 fd:03 146729698
/usr/lib64/libICE.so.6.3.0
3535418000-353541b000 rw-p 3535418000 00:00 0
3535600000-353572d000 r-xp 00000000 fd:03 141230458
/lib64/libcrypto.so.0.9.8e
353572d000-353592c000 ---p 0012d000 fd:03 141230458
/lib64/libcrypto.so.0.9.8e
353592c000-353594d000 rw-p 0012c000 fd:03 141230458
/lib64/libcrypto.so.0.9.8e
353594d000-3535951000 rw-p 353594d000 00:00 0
3535a00000-3535a02000 r-xp 00000000 fd:03 141230457
/lib64/libcom_err.so.2.1
3535a02000-3535c01000 ---p 00002000 fd:03 141230457
/lib64/libcom_err.so.2.1
3535c01000-3535c02000 rw-p 00001000 fd:03 141230457
/lib64/libcom_err.so.2.1
3535e00000-3535e11000 r-xp 00000000 fd:03 141230454
/lib64/libresolv-2.5.so
3535e11000-3536011000 ---p 00011000 fd:03 141230454
/lib64/libresolv-2.5.so
3536011000-3536012000 r--p 00011000 fd:03 141230454
/lib64/libresolv-2.5.so
3536012000-3536013000 rw-p 00012000 fd:03 141230454
/lib64/libresolv-2.5.so
3536013000-3536015000 rw-p 3536013000 00:00 0
3536200000-353622c000 r-xp 00000000 fd:03 146729448
/usr/lib64/libgssapi_krb5.so.2.2
353622c000-353642c000 ---p 0002c000 fd:03 146729448
/usr/lib64/libgssapi_krb5.so.2.2
353642c000-353642e000 rw-p 0002c000 fd:03 146729448
/usr/lib64/libgssapi_krb5.so.2.2
3536a00000-3536a02000 r-xp 00000000 fd:03 141230453
/lib64/libkeyutils-1.2.so
3536a02000-3536c01000 ---p 00002000 fd:03 141230453
/lib64/libkeyutils-1.2.so
3536c01000-3536c02000 rw-p 00001000 fd:03 141230453
/lib64/libkeyutils-1.2.so
3536e00000-3536e91000 r-xp 00000000 fd:03 146729442
/usr/lib64/libkrb5.so.3.3
3536e91000-3537091000 ---p 00091000 fd:03 146729442
/usr/lib64/libkrb5.so.3.3
3537091000-3537095000 rw-p 00091000 fd:03 146729442
/usr/lib64/libkrb5.so.3.3
3537200000-3537208000 r-xp 00000000 fd:03 146713250
/usr/lib64/libkrb5support.so.0.1
3537208000-3537407000 ---p 00008000 fd:03 146713250
/usr/lib64/libkrb5support.so.0.1
3537407000-3537408000 rw-p 00007000 fd:03 146713250
/usr/lib64/libkrb5support.so.0.1
3537600000-3537624000 r-xp 00000000 fd:03 146729427
/usr/lib64/libk5crypto.so.3.1
3537624000-3537823000 ---p 00024000 fd:03 146729427
/usr/lib64/libk5crypto.so.3.1
3537823000-3537825000 rw-p 00023000 fd:03 146729427
/usr/lib64/libk5crypto.so.3.1
3537a00000-3537a46000 r-xp 00000000 fd:03 141230459
/lib64/libssl.so.0.9.8e
3537a46000-3537c46000 ---p 00046000 fd:03 141230459
/lib64/libssl.so.0.9.8e
3537c46000-3537c4c000 rw-p 00046000 fd:03 141230459
/lib64/libssl.so.0.9.8e
3538e00000-3538ee6000 r-xp 00000000 fd:03 146729720
/usr/lib64/libstdc++.so.6.0.8
3538ee6000-35390e5000 ---p 000e6000 fd:03 146729720
/usr/lib64/libstdc++.so.6.0.8
35390e5000-35390eb000 r--p 000e5000 fd:03 146729720
/usr/lib64/libstdc++.so.6.0.8
35390eb000-35390ee000 rw-p 000eb000 fd:03 146729720
/usr/lib64/libstdc++.so.6.0.8
35390ee000-3539100000 rw-p 35390ee000 00:00 0
3539e00000-3539e5b000 r-xp 00000000 fd:03 146729800
/usr/lib64/libXt.so.6.0.0
3539e5b000-353a05a000 ---p 0005b000 fd:03 146729800
/usr/lib64/libXt.so.6.0.0
353a05a000-353a060000 rw-p 0005a000 fd:03 146729800
/usr/lib64/libXt.so.6.0.0
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2b8c6fe8f000-2b8c70064000 rw-p 2b8c6fb58000 00:00 0
2b8c70064000-2b8c702d6000 rw-p 2b8c6fb09000 00:00 0
7fff7e116000-7fff7e132000 rw-p 7ffffffe2000 00:00 0
[stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0
[vdso]
And there is no 'mode' option for surfacereader. Was this because of my
installation? Is there any fix without re-installing?
Thanks a lot!
--
Elaine Tang
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From: Simone M. <sim...@or...> - 2014-01-28 21:44:23
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Can you check if you are running Python 2.7 32 or 64 bit? Simone -- Simone Manini, Eng Orobix Srl via L.A. Muratori 3, 24123 Bergamo, Italy orobix: www.orobix.com home: http://daron1337.github.com twitter: twitter.com/daron1337 mobile: +39.328.60.22.017 office: +39.035.0296480 +39.035.42131 "This message originates from Orobix Srl and its contents and attachments are privileged and confidential and are intended only for the individual(s) or entity(ies) named above. This message should not be forwarded, distributed or disclosed. Any unauthorized use, dissemination and duplication is strictly prohibited and may be unlawful. All personal messages express views solely of the sender, which are not to be attributed to Orobix Srl, and may not be copied or distributed without this disclaimer. If you are not the intended recipient or received this message in error, please delete this message and notify the sender by reply e-mail. Opinions, conclusions and other information in this message that do not relate to the official business of Orobix Srl shall be understood as neither given nor endorsed by it." > Il giorno 28/gen/2014, alle ore 21:27, Evan Kao <to...@gm...> ha scritto: > > Hi all, > > I've just installed VMTK 1.2 on Windows 7 using the installers. However, for some reason when I open the vmtk-exe.py file, I only get the Python console without the Pypepad interface. Also, if I try to run some vmtk commands using the console, I get the error "DLL load failed". The installation page suggests VMTK 1.2 should work straight out of installation, but is it possible I need to change something else as well? > > Thanks, > Evan > ------------------------------------------------------------------------------ > WatchGuard Dimension instantly turns raw network data into actionable > security intelligence. It gives you real-time visual feedback on key > security issues and trends. Skip the complicated setup - simply import > a virtual appliance and go from zero to informed in seconds. > http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk > _______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Evan K. <to...@gm...> - 2014-01-28 21:36:51
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Hello Simone, I'm currently running the 64-bit version. - Evan On Tue, Jan 28, 2014 at 12:40 PM, Simone Manini <sim...@or...>wrote: > Can you check if you are running Python 2.7 32 or 64 bit? > > Simone > -- > Simone Manini, Eng > Orobix Srl > via L.A. Muratori 3, 24123 Bergamo, Italy > > orobix: www.orobix.com > home: http://daron1337.github.com > twitter: twitter.com/daron1337 > mobile: +39.328.60.22.017 > office: +39.035.0296480 > +39.035.42131 > > "This message originates from Orobix Srl and its contents and attachments > are privileged and confidential and are intended only for the individual(s) > or entity(ies) named above. This message should not be forwarded, > distributed or disclosed. Any unauthorized use, dissemination and > duplication is strictly prohibited and may be unlawful. All personal > messages express views solely of the sender, which are not to be attributed > to Orobix Srl, and may not be copied or distributed without this > disclaimer. If you are not the intended recipient or received this message > in error, please delete this message and notify the sender by reply e-mail. > Opinions, conclusions and other information in this message that do not > relate to the official business of Orobix Srl shall be understood as > neither given nor endorsed by it." > > Il giorno 28/gen/2014, alle ore 21:27, Evan Kao <to...@gm...> ha > scritto: > > Hi all, > > I've just installed VMTK 1.2 on Windows 7 using the installers. However, > for some reason when I open the vmtk-exe.py file, I only get the Python > console without the Pypepad interface. Also, if I try to run some vmtk > commands using the console, I get the error "DLL load failed". The > installation page suggests VMTK 1.2 should work straight out of > installation, but is it possible I need to change something else as well? > > Thanks, > Evan > > > ------------------------------------------------------------------------------ > WatchGuard Dimension instantly turns raw network data into actionable > security intelligence. It gives you real-time visual feedback on key > security issues and trends. Skip the complicated setup - simply import > a virtual appliance and go from zero to informed in seconds. > > http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk > > _______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users > > |
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From: Evan K. <to...@gm...> - 2014-01-28 20:28:15
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Hi all, I've just installed VMTK 1.2 on Windows 7 using the installers. However, for some reason when I open the vmtk-exe.py file, I only get the Python console without the Pypepad interface. Also, if I try to run some vmtk commands using the console, I get the error "DLL load failed". The installation page suggests VMTK 1.2 should work straight out of installation, but is it possible I need to change something else as well? Thanks, Evan |
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From: Luca A. <luc...@or...> - 2013-09-04 10:26:15
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Dear vmtk user, starting Aug 27 the Sourceforge mailing list has migrated to Google Groups. It is a superior tool for managing discussions in an open source project compared to the mailing list, it allows to - access the list for reading and posting from a convenient web interface - subscribe to either individual emails, email digests or avoid receiving emails altogether - search past discussions The group is here: https://groups.google.com/forum/#!forum/vmtk-users It is publicly accessible (i.e. you don't need to subscribe to read/search), while you'll need to subscribe to the group in order to post. The mailing list on Sourceforge will be deactivated in the near future. For any doubts or need for directions, please contact me directly. Best, Luca |
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From: Luca A. <luc...@or...> - 2013-08-27 11:11:39
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Dear all, starting today we are migrating the mailing list to Google Groups. It is a superior tool for managing discussions in an open source project compared to the mailing list. This way you'll be able to: - access the list for reading and posting from a convenient web interface - subscribe to either individual emails, email digests or avoid receiving emails altogether - search past discussions The group is here: https://groups.google.com/forum/#!forum/vmtk-users It is publicly accessible (i.e. you don't need to subscribe to read/search), while you'll need to subscribe to the group in order to post. I'll be sending this message for some time, after which the mailing list on Sourceforge will be deactivated. For any doubts or need for directions, please contact me directly. Best, Luca |
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From: Luca A. <luc...@or...> - 2013-08-27 08:24:31
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Hi Eduardo, sorry for the wait. It's in our todo list to move to VTK 6 at some point, but we haven't done it yet. It will likely involve modifying both Python and C++ classes according to the migration guide (http://www.vtk.org/Wiki/VTK/VTK_6_Migration_Guide). You're more than welcome to contribute to the process, in case let me know if you have time for this and we'll kickstart it. Others on the list are also welcome to shoot me a message to volunteer. Thanks! Luca On Aug 22, 2013, at 6:50 PM, Eduardo - Yahoo wrote: > Hi! > > Anybody knows if is possible integrate VTK 6.x with VMTK? And how could I do that? > > Thank you! > > Atenciosamente, > > Eduardo Camargo, M.Sc. > > Analista de Sistemas > Instituto Nacional de Ciência e Tecnologia em > Medicina Assistida por Computação Científica > INCT-MACC http://macc.lncc.br > Laboratório Nacional de Computação Científica > LNCC - http://www.lncc.br > ------------------------------------------------------------------------------ > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk_______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Luca A. <luc...@or...> - 2013-08-27 08:20:56
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Hi Xiaoli, yes, there is a vmtk script for that contributed to vmtk by Hugo Gratama van Andel: vmtkimagecurvedmpr (mpr stands for multi-planar reformat) Make sure you first run your centerlines through vmtkcenterlinegeometry and vmtkcenterlineattributes, this way vmtkcenterlinegeometry -ifile your_centerlines.vtp --pipe vmtkcenterlineattributes --pipe vmtkimagecurvedmpr -ifile your_image.mha -ofile sliced_image.mha Cheers, Luca On Aug 21, 2013, at 6:44 PM, Xiaoli Zhang wrote: > Hi all, > > I am wondering if there is a way in vmtk to get the cross-sectional image (from 3D volumetric grayscale image: vti) following the centerline (.vtp) and alway perpendicular to the centerline. > > Thanks, > Xiaoli > ------------------------------------------------------------------------------ > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk_______________________________________________ > vmtk-users mailing list > vmt...@li... > https://lists.sourceforge.net/lists/listinfo/vmtk-users |
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From: Luca A. <luc...@or...> - 2013-08-27 08:12:39
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Hi Xiaoli, things got busy and this delayed my vmtk list time. vmtkcenterlines works on any surface obtained in any way, only it needs to be orientable (i.e. you must be able to define outwards normals, unlike, say, a Klein bottle, https://en.wikipedia.org/wiki/Klein_bottle - this can also happen due to small-scale degeneracies) and manifold (i.e. each triangle edge must be share by at most two triangles). In your case it was neither due to the segmentation artifacts inside the vessel. So, yes, you can export an STL file from Amira, read it with vmtk and generate centerlines. Luca On Aug 21, 2013, at 6:39 PM, Xiaoli Zhang wrote: > Hi Luca, > > Thanks for pointing this out. Indeed this is the problem (at least it worked on the problematic dataset). It turned out there is some region inside the lumen not segmented, and that caused the problem. A quick question through: does vmtkcenterlines only work on surface created by vmtklevelsetsegmentation? Will it work on a manually segmented surface from Amira? > > Just FYI, following are my steps for segmentation and centerline creation: > 1. segment vessel wall from CT image (different from typical cast CT, only vessel wall has hyperintensity) > 2. fill the lumen to include both vessel wall segmented above and its lumen > 3. use vmtklevelsetsegmentation to generate deformable model from step 2's label field (not sure if it is necessary) > 4. create centerline > > Xiaoli > > > > > On Fri, Aug 16, 2013 at 7:59 AM, Luca Antiga <luc...@or...> wrote: > Hi Xiaoli, > I took a look at your surface. It's not immediately obvious, but there is a whole extra portion of surface inside of it (see screenshot taken with some translucency). This causes the algorithm to basically not work. > I'm not sure how you got to this point, but I suggest you try to re-segment the surface making sure you obtain a single compact 3D model. > Best, > > Luca > > <Screen Shot 2013-08-16 at 1.55.20 PM.png> > > On Aug 16, 2013, at 3:55 AM, Xiaoli Zhang wrote: > >> Hi Luca, >> >> Attached is the surface file I am working on. The levelset segmentation wasn't working very well on the outer curvature of the arch, but that shouldn't be the problem. Even if I am only working on descending aorta, it still won't work. >> >> Thanks, >> Xiaoli >> >> >> On Thu, Aug 15, 2013 at 5:09 PM, Luca Antiga <luc...@gm...> wrote: >> Hi, I see that there is a jagged line on the surface indicating that the surface is apparently not orientable, so normals flip where you see the dark line (since the shader interpolates normals). You can verify this in Paraview by applying the Glyph filter to the normals. >> >> This would explain dificulties with the centerline algorithm, since normals are used when extracting the inner Delaunay diagram. >> >> Can you send the surface over? I can try to understand what's causing normals to flip. >> >> Thanks >> >> Luca >> >> >> On 12/ago/2013, at 17:09, Xiaoli Zhang <zha...@gm...> wrote: >> >>> Hi Luca, >>> >>> Attached is the screenshots of the surface for centerline extraction from two different views. I have tried not to include aortic arch, but it didn't work either. Any suggestions will be appreciated. >>> >>> Thanks, >>> Xiaoli >>> >>> On Sun, Aug 11, 2013 at 4:24 PM, Luca Antiga <luc...@or...> wrote: >>> Hi Xiaoli, >>> there must be a Voronoi diagram degeneracy somewhere. Feel free to post a screenshot of the model, I can try to point you to the candidate spots. >>> Best, >>> >>> Luca >>> >>> >>> On Aug 8, 2013, at 7:50 PM, Xiaoli Zhang wrote: >>> >>>> It seems someone has encountered the same problem before: http://www.mail-archive.com/vmt...@li.../msg00283.html >>>> >>>> I followed Luca's suggestions apply smoothing (tried passband of 0.01 and 0.1) and add a subdivision step before vmtkcenterlines. Still no luck, vmtkcenterlines script will never return. Any suggestions? >>>> >>>> On Tue, Aug 6, 2013 at 9:23 PM, Xiaoli Zhang <zha...@gm...> wrote: >>>> I am new to vmtk and I am trying to extract centerline from CT image of the aorta. I prepared the surface in Amira and save as stl (ASCII) format. Then I ran vmtkcenterlines script and place a source point at inlet and a target point at outlet. vmtk then show "computing centerline" and staying for a very long time (>12 hours). The surface I am working on is a small file (stl size <1MB). >>>> >>>> Anyone can help please? I can send the screenshot of the surface and stl file if needed. Thanks. >>>> >>>> Xiaoli >>>> >>>> ------------------------------------------------------------------------------ >>>> Get 100% visibility into Java/.NET code with AppDynamics Lite! >>>> It's a free troubleshooting tool designed for production. >>>> Get down to code-level detail for bottlenecks, with <2% overhead. >>>> Download for free and get started troubleshooting in minutes. >>>> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk_______________________________________________ >>>> vmtk-users mailing list >>>> vmt...@li... >>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >>> >>> >>> <C9N3_surface_centerline.jpg> >>> ------------------------------------------------------------------------------ >>> Get 100% visibility into Java/.NET code with AppDynamics Lite! >>> It's a free troubleshooting tool designed for production. >>> Get down to code-level detail for bottlenecks, with <2% overhead. >>> Download for free and get started troubleshooting in minutes. >>> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> vmtk-users mailing list >>> vmt...@li... >>> https://lists.sourceforge.net/lists/listinfo/vmtk-users >> >> <C9N3.ls.mc.sm.vtp> > > |
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From: Eduardo - Y. <cam...@ya...> - 2013-08-22 16:50:34
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Hi! Anybody knows if is possible integrate VTK 6.x with VMTK? And how could I do that? Thank you! Atenciosamente, Eduardo Camargo, M.Sc. Analista de Sistemas Instituto Nacional de Ciência e Tecnologia em Medicina Assistida por Computação Científica INCT-MACC http://macc.lncc.br Laboratório Nacional de Computação Científica LNCC - http://www.lncc.br |
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From: Xiaoli Z. <zha...@gm...> - 2013-08-21 16:45:00
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Hi all, I am wondering if there is a way in vmtk to get the cross-sectional image (from 3D volumetric grayscale image: vti) following the centerline (.vtp) and alway perpendicular to the centerline. Thanks, Xiaoli |
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