vmtk-users

Re: [vmtk-users] pype error

[Simone M. <sim...@or...>]

Dear Adrian,
could you please add more information regarding your installation?
Did you compile it from source or you used a binary version of vmtk?

It seems to me a problem with python related to an import error of vmtk python scripts.

Kind Regards
Simone

--
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Orobix Srl
via L.A. Muratori 3, 24123 Bergamo, Italy

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On May 2, 2013, at 1:44 PM, adrianrh <adr...@st...> wrote:

> Hi!
> 
> I have tried reinstalling vmtk several times, but I keep getting this 
> error when running any command. Is there something wrong with my 
> installation? or maybe the python installation?
> 
> $ vmtklevelsetsegmentation -ifile image_volume.vti
> 
> Error from pype: cannot concatenate 'str' and 'exceptions.ImportError' 
> objects
> 
> Best Adrian Hope
> 
> 
> ------------------------------------------------------------------------------
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[vmtk-users] pype error

[adrianrh <adr...@st...>]

Hi!

I have tried reinstalling vmtk several times, but I keep getting this 
error when running any command. Is there something wrong with my 
installation? or maybe the python installation?

$ vmtklevelsetsegmentation -ifile image_volume.vti

Error from pype: cannot concatenate 'str' and 'exceptions.ImportError' 
objects

Best Adrian Hope

Re: [vmtk-users] mesh conversion to lifev

[Simone M. <sim...@or...>]

Dear Lucia,

your pipe seems to be ok. I tried to use it to convert a simple mesh.vtu file into .lifev and it worked.

In order to better understand the problem I suggest to try:

vmtkmeshwriter -ifile mesh.vtu -f lifev  -entityidsarray CellEntityIds -ofile mesh.lifev

entityidsarray it is usually CellEntityIds but you can check it by using vmtkmeshreader -ifile mesh.vtu

Kind Regards
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."

On May 2, 2013, at 1:51 AM, Lucia Mirabella <lmi...@ma...> wrote:

> Hi Luca,
> 
> I'm trying to save a vtu mesh in lifev format:
> 
> vmtkmeshreader -ifile mesh.vtu --pipe vmtkmeshwriter -f lifev -ofile mesh.lifev
> 
> but I get an error when I try:
> 
> Writing LifeV file.
> Error from pype: ambiguous call, multiple overloaded methods match the arguments
> 
> This doesn't happen if I save it in a different format. 
> 
> Do you have any idea on what I'm doing wrong? 
> 
> In case it helps understanding the problem, the vtu mesh was saved from Paraview originally, but I also "re-saved" it using vmtk before attempting the conversion to lifev.
> 
> Thanks!
> 
> Lucia
> 
> ------------------------------------------------------------------------------
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Re: [vmtk-users] 2 questions on segmentation

[Arjan G. <aj...@gm...>]

Hi Vikram,

To smooth out bumps, you could also look into ReMESH (
http://remesh.sourceforge.net/index.html). It allows you to select
triangles of the surface mesh and smooth or remove only those. It also has
a smooth hole filling algorithm.

Arjan


On Thu, May 2, 2013 at 11:00 AM, Vikram Mehta <vv...@gm...> wrote:

> Thanks Luca, will look into your suggestions.
>
> While waiting for your replies, I found another way outside of VMTK to
> align my stl but the smoothing issue is still to be resolved.
>
> Thanks again,
> Vikram.
>
>
>
> On Wed, May 1, 2013 at 1:13 PM, Luca Antiga <luc...@gm...> wrote:
>
>> Hello Vikram,
>>  thanks for your patience. Pretty busy couple of weeks.
>>
>> On Apr 23, 2013, at 2:51 PM, Vikram Mehta wrote:
>>
>> > Dear users,
>> >
>> > I have a couple of questions and I was hoping to get some advice on
>> this.
>> >
>> > 1) Is there a way of aligning one of the ends of the reconstructed
>> geometry with any of the axes?
>> >     I use the geometries as a model for CFD simulations and some other
>> processing methods in matlab. I need the vessel to be aligned with the x
>> axis (for example) with the center of the inlet at the origin so that my
>> boundary conditions are prescribed accurately.. I usually do it in other
>> meshing softwares and I was wondering if this could be done in VMTK prior
>> to exporting it as an STL file.
>>
>> There isn't a way to directly do this in vmtk using a script, but you can
>> extract the origin and normal of a boundary using vmtkmeshboundaryinspector
>> (you'll need to generate a mesh with vmtkmeshgenerator first, just use a
>> fixed -edgelength - any mesh size will do if you just need to inspect the
>> boundaries for the origin and normal), compute the transformation yourself
>> and apply it with vmtkmeshtransform (by specifying the coefficients of the
>> 4x4 transform matrix in lexicographic order with the -matrix option).
>>
>> > 2) Sometimes during the segmentation process, I end up with
>> reconstructions with artificial bumps on them. Is there a way to
>> INDIVIDUALLY smooth these bumps out ? Are there ways to avoid this ?  I do
>> not want to over smooth the entire vessel and hence a way of smoothing just
>> the rough/bumpy bits would be great !    Any suggestions would help !
>>
>> Yes, it happens sometimes, probably depending on the image features. A
>> localized smoothing filter is something I thought about and wouldn't be
>> hard to implement, but it isn't in vmtk right now.
>> The way to get around this is to use vmtksurfaceclipper (preferably using
>> -type sphere), clip a bump and then cap it using vmtksurfacecapper -method
>> smooth.
>>
>> Best,
>>
>> Luca
>>
>> > Any help is greatly appreciated !
>> >
>> > Many thanks in advance
>> > Vikram.
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Try New Relic Now & We'll Send You this Cool Shirt
>> > New Relic is the only SaaS-based application performance monitoring
>> service
>> > that delivers powerful full stack analytics. Optimize and monitor your
>> > browser, app, & servers with just a few lines of code. Try New Relic
>> > and get this awesome Nerd Life shirt!
>> http://p.sf.net/sfu/newrelic_d2d_apr_______________________________________________
>> > vmtk-users mailing list
>> > vmt...@li...
>> > https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>>
>
>
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>

Re: [vmtk-users] 2 questions on segmentation

[Vikram M. <vv...@gm...>]

Thanks Luca, will look into your suggestions.

While waiting for your replies, I found another way outside of VMTK to
align my stl but the smoothing issue is still to be resolved.

Thanks again,
Vikram.



On Wed, May 1, 2013 at 1:13 PM, Luca Antiga <luc...@gm...> wrote:

> Hello Vikram,
>  thanks for your patience. Pretty busy couple of weeks.
>
> On Apr 23, 2013, at 2:51 PM, Vikram Mehta wrote:
>
> > Dear users,
> >
> > I have a couple of questions and I was hoping to get some advice on this.
> >
> > 1) Is there a way of aligning one of the ends of the reconstructed
> geometry with any of the axes?
> >     I use the geometries as a model for CFD simulations and some other
> processing methods in matlab. I need the vessel to be aligned with the x
> axis (for example) with the center of the inlet at the origin so that my
> boundary conditions are prescribed accurately.. I usually do it in other
> meshing softwares and I was wondering if this could be done in VMTK prior
> to exporting it as an STL file.
>
> There isn't a way to directly do this in vmtk using a script, but you can
> extract the origin and normal of a boundary using vmtkmeshboundaryinspector
> (you'll need to generate a mesh with vmtkmeshgenerator first, just use a
> fixed -edgelength - any mesh size will do if you just need to inspect the
> boundaries for the origin and normal), compute the transformation yourself
> and apply it with vmtkmeshtransform (by specifying the coefficients of the
> 4x4 transform matrix in lexicographic order with the -matrix option).
>
> > 2) Sometimes during the segmentation process, I end up with
> reconstructions with artificial bumps on them. Is there a way to
> INDIVIDUALLY smooth these bumps out ? Are there ways to avoid this ?  I do
> not want to over smooth the entire vessel and hence a way of smoothing just
> the rough/bumpy bits would be great !    Any suggestions would help !
>
> Yes, it happens sometimes, probably depending on the image features. A
> localized smoothing filter is something I thought about and wouldn't be
> hard to implement, but it isn't in vmtk right now.
> The way to get around this is to use vmtksurfaceclipper (preferably using
> -type sphere), clip a bump and then cap it using vmtksurfacecapper -method
> smooth.
>
> Best,
>
> Luca
>
> > Any help is greatly appreciated !
> >
> > Many thanks in advance
> > Vikram.
> >
> >
> ------------------------------------------------------------------------------
> > Try New Relic Now & We'll Send You this Cool Shirt
> > New Relic is the only SaaS-based application performance monitoring
> service
> > that delivers powerful full stack analytics. Optimize and monitor your
> > browser, app, & servers with just a few lines of code. Try New Relic
> > and get this awesome Nerd Life shirt!
> http://p.sf.net/sfu/newrelic_d2d_apr_______________________________________________
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> > https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>

[vmtk-users] mesh conversion to lifev

[Lucia M. <lmi...@ma...>]

Hi Luca,

I'm trying to save a vtu mesh in lifev format:

vmtkmeshreader -ifile mesh.vtu --pipe vmtkmeshwriter -f lifev -ofile mesh.lifev

but I get an error when I try:

Writing LifeV file.
Error from pype: ambiguous call, multiple overloaded methods match the arguments

This doesn't happen if I save it in a different format. 

Do you have any idea on what I'm doing wrong? 

In case it helps understanding the problem, the vtu mesh was saved from Paraview originally, but I also "re-saved" it using vmtk before attempting the conversion to lifev.

Thanks!

Lucia

[vmtk-users] RE : VMTK Mesh Problem

[Joly F. <flo...@um...>]

Hi,
In ICEM look at the aorta tutorial, there is the whole explanation on how to split the surface by angle to get the inlet/outlets (same process on StarCCM+ or OpenFOAM by the way. ICEM can also generate boundary layer cells.

Regards,


Florian 

-------- Message d'origine--------
De: Luca Antiga [mailto:luc...@or...]
Date: mer. 5/1/2013 08:36
À: Vincent Ip
Cc: vmt...@li...
Objet : Re: [vmtk-users] VMTK Mesh Problem
 
Hi Vincent,

On May 1, 2013, at 6:49 AM, Vincent Ip wrote:

> Dear VMTK users,
> 
> I encounter a situation that when I export the surface to STL format and trying to mesh it with ANSYS ICEM.
> I cannot define the inlet and outlet as they are incorporated into the wall (the whole thing).
> Is there anything I should do besides clipping and capping before exporting the surface to STL format?

I don't use ICEM so I'm not sure of what's the best way to go here. Unfortunately STL doesn't support the definition of 
surface region indicators associated to either points or cells, so I guess there should be a way to do something like
this within ICEM.

Any ICEM users out there that can help out?

> The second problem is that I had repeated crashing when I try to mesh it with VMTK and this happen whenever I add the boundary layer.
> The vessel geometry I got is a segment from ICA siphon segment to M2 and it is extracted from Time-of-flight MRA. It does appear to be a bit bumpy in appearance, probably due to its low resolution, so I'm not sure if this could be the problem. Or if I need a very powerful computer to run the VMTK??

FYI, there's new robust boundary layer code coming up in vmtk in the near future.

Having said that, the old code shouldn't crash (in the worst case it generates elements with negative Jacobian here and there).
Are you sure you are generating a mesh with a good density? If you generate very coarse meshes the mesh itself could degenerate 
during the remeshing phase. Just a thought.

In any case, feel free to send your model over and I'll take a look as soon as I can.

Best,

Luca


> Please kindly comment.
> 
> Thanks,
> Vincent
> 
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
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------------------------------------------------------------------------------
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Code-level diagnostics for performance bottlenecks with <2% overhead
Download for free and get started troubleshooting in minutes.
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Re: [vmtk-users] VMTK

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

Hello Hamed,
 it looks like you don't have write permissions at the path where you are trying to write the files and read them afterwards.
Try to specify a full path at all -ifile and -ofile options, like -ofile C:\Users\Hamed\image_volume_voi.vti
Best,

Luca

On 30/apr/2013, at 13:43, Hamed Rezaie <ham...@ya...> wrote:

> hello to every body
> I need your favor
> when I want to extract surface from DICOM images by the  below command
> "vmtkimagereader -f dicom -d  C:/Users/Hamed/Downloads/Compressed/br1 --pipe vmtkmarchingcubes -ifile image_volume_voi.vti -l 300.0 -ofile mc_surface.vtp --pipe vmtksurfaceviewer"
> an empty rendering windows and an error windows like the picture which is attached  is appeared.
> I need to extract the geometry of COW but I could not progress is there any one who can help me.
> <error VMTK.png>
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
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Re: [vmtk-users] RE : VMTK Mesh Problem

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

Great. Thanks a lot, Florian.

Luca

On 01/mag/2013, at 14:39, "Joly Florian" <flo...@um...> wrote:

> Hi,
> In ICEM look at the aorta tutorial, there is the whole explanation on how to split the surface by angle to get the inlet/outlets (same process on StarCCM+ or OpenFOAM by the way. ICEM can also generate boundary layer cells.
> 
> Regards,
> 
> 
> Florian 
> 
> -------- Message d'origine--------
> De: Luca Antiga [mailto:luc...@or...]
> Date: mer. 5/1/2013 08:36
> À: Vincent Ip
> Cc: vmt...@li...
> Objet : Re: [vmtk-users] VMTK Mesh Problem
> 
> Hi Vincent,
> 
> On May 1, 2013, at 6:49 AM, Vincent Ip wrote:
> 
>> Dear VMTK users,
>> 
>> I encounter a situation that when I export the surface to STL format and trying to mesh it with ANSYS ICEM.
>> I cannot define the inlet and outlet as they are incorporated into the wall (the whole thing).
>> Is there anything I should do besides clipping and capping before exporting the surface to STL format?
> 
> I don't use ICEM so I'm not sure of what's the best way to go here. Unfortunately STL doesn't support the definition of 
> surface region indicators associated to either points or cells, so I guess there should be a way to do something like
> this within ICEM.
> 
> Any ICEM users out there that can help out?
> 
>> The second problem is that I had repeated crashing when I try to mesh it with VMTK and this happen whenever I add the boundary layer.
>> The vessel geometry I got is a segment from ICA siphon segment to M2 and it is extracted from Time-of-flight MRA. It does appear to be a bit bumpy in appearance, probably due to its low resolution, so I'm not sure if this could be the problem. Or if I need a very powerful computer to run the VMTK??
> 
> FYI, there's new robust boundary layer code coming up in vmtk in the near future.
> 
> Having said that, the old code shouldn't crash (in the worst case it generates elements with negative Jacobian here and there).
> Are you sure you are generating a mesh with a good density? If you generate very coarse meshes the mesh itself could degenerate 
> during the remeshing phase. Just a thought.
> 
> In any case, feel free to send your model over and I'll take a look as soon as I can.
> 
> Best,
> 
> Luca
> 
> 
>> Please kindly comment.
>> 
>> Thanks,
>> Vincent
>> 
>> ------------------------------------------------------------------------------
>> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
>> Get 100% visibility into your production application - at no cost.
>> Code-level diagnostics for performance bottlenecks with <2% overhead
>> Download for free and get started troubleshooting in minutes.
>> http://p.sf.net/sfu/appdyn_d2d_ap1
>> _______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> 
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
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> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 

Re: [vmtk-users] VMTK Mesh Problem

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

Hi Vincent,

On May 1, 2013, at 6:49 AM, Vincent Ip wrote:

> Dear VMTK users,
> 
> I encounter a situation that when I export the surface to STL format and trying to mesh it with ANSYS ICEM.
> I cannot define the inlet and outlet as they are incorporated into the wall (the whole thing).
> Is there anything I should do besides clipping and capping before exporting the surface to STL format?

I don't use ICEM so I'm not sure of what's the best way to go here. Unfortunately STL doesn't support the definition of 
surface region indicators associated to either points or cells, so I guess there should be a way to do something like
this within ICEM.

Any ICEM users out there that can help out?

> The second problem is that I had repeated crashing when I try to mesh it with VMTK and this happen whenever I add the boundary layer.
> The vessel geometry I got is a segment from ICA siphon segment to M2 and it is extracted from Time-of-flight MRA. It does appear to be a bit bumpy in appearance, probably due to its low resolution, so I'm not sure if this could be the problem. Or if I need a very powerful computer to run the VMTK??

FYI, there's new robust boundary layer code coming up in vmtk in the near future.

Having said that, the old code shouldn't crash (in the worst case it generates elements with negative Jacobian here and there).
Are you sure you are generating a mesh with a good density? If you generate very coarse meshes the mesh itself could degenerate 
during the remeshing phase. Just a thought.

In any case, feel free to send your model over and I'll take a look as soon as I can.

Best,

Luca


> Please kindly comment.
> 
> Thanks,
> Vincent
> 
> ------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
> Get 100% visibility into your production application - at no cost.
> Code-level diagnostics for performance bottlenecks with <2% overhead
> Download for free and get started troubleshooting in minutes.
> http://p.sf.net/sfu/appdyn_d2d_ap1
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] vmtkApps?

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

Hi Evan,

On Apr 26, 2013, at 8:39 AM, Evan Kao wrote:

> Hi Luca,
> 
> I had some questions on using the Python scripts (having little Python experience):
> 
> 1.  Into which directory should I move the files (in Windows; files obtained from the source file zip)?

You can move the files (you just need the files in vmtkApps/CerebralAneurysms/ParentVesselReconstruction) into any directory. 
The you should invoke the scripts at the command line, but in order to do this you need Windows to "see" python and the vmtk modules.
What are the directories where Python and vmtk are installed on our machine?

> 2.  I was confused by the form of the command "python patchandinterpolatecenterline.py directoryPath id1 lateral" from the tutorial.  Are we supposed to call these functions from the command line/Python shell or can we still do it inside vmtk?

They are meant to be run outside of vmtk, at the command line.

Luca

> Thanks for the help,
> Evan Kao
> 
> 
> 
> On Mon, Apr 22, 2013 at 11:03 AM, Evan Kao <to...@gm...> wrote:
> Hi Luca,
> 
> Thanks for the info.
> 
> 
> On Mon, Apr 22, 2013 at 7:01 AM, Luca Antiga <luc...@or...> wrote:
> Hello Evan,
>  at the present stage you can download them from github.com/vmtk/vmtk
> 
> If you don't use git, just get the source code zip at
> 
> https://github.com/vmtk/vmtk/archive/master.zip
> 
> and unpack. vmtkApps contains the Python scripts you're looking for.
> 
> Best,
> 
> Luca
> 
> 
> On Apr 20, 2013, at 12:09 AM, Evan Kao wrote:
> 
> > Hello vmtk-users,
> >
> > I'm interested in going through the parent vessel reconstruction tutorial but I don't think I have the relevant Python scripts.  The tutorial says the files are in the vmtkApps folder, but I couldn't find anything like that.  Are they usually included in the installation?  Where could I find these scripts (and possibly other vmtkApps)?
> >
> > Thank you,
> > Evan Kao
> > ------------------------------------------------------------------------------
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> > analytics on semi-structured data. The platform includes APIs for building
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> 
> 
> 

Re: [vmtk-users] vmtkimagevoiselector -boxbounds : what's wrong?

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

Hi Giuseppe,

On Apr 25, 2013, at 5:52 PM, Giuseppe Isu wrote:

> Hi everebody,
> 
> I'm facing a geometry reconstruction task on vmtk. I need to reconstruct a carotid bifurcation, but I'm experiencing some difficulties at the bulb region. Generally I have an amazing image quality, I can easily segment level sets for all branches (high meta levels within the lumen over  1000 and low levels otherwise), but due to blood recirculation  I have low levels and kind of disturbed uneven image at the bulb. I tried to initialize the segmentation in different ways but the result is always a staired surface which follows the pixel level fluctuations in that region. 

I have seen similar issues in the presence of complex flow patterns in the past.

> I thought to use vmtkimagevoiselector to divide my voi in three domains in order to isolate the bulb volume, and then smooth the image only in the bifurcation region. 
> 
> The idea is to perform level set segmentation separately for the three domains and then use vmtkimagecompose to reassemble my segmented volume. 
> 
> A problem occurs when I pipe vmtkimagevoiselector. To obtain a precise subdivision of the original volume I want to use -boxbounds insead of interactive voi selection. I pipe this code:
> 
> vmtkimagevoiselector -ifile myname.vti -interactive 0 -boundbox xmin xmax ymin ymax zmin zmax -ofile myoutput.vti --pipe vmtkimageviewer 
> 
> but the output image results empty. what's wrong?  it seems to me to have used the right pipe synthax. 
> 
> Then if I omit the part "-interactive 0" I get the interactive option to be enabled typing "i" and, again, empty image. 

Setting aside the issue with vmtkimagevoiselector for a second, I suggest you don't split the image in three domains, but just keep your
original image around, generate a (full-sized) smooth version and create three (or two, as a matter of facts) different segmentations for the
different regions, using the original or smoothed images as you see fit.

Then you can compose the resulting level set images using vmtkimagecompose, which will effectively merge the shapes you segmented
in a single shape.

Now, on to the vmtkimagevoiselector. BoxBounds are specified in physical units (mm?), not in indices - this might be the problem. 
To have vmtkimageviewer show physical units, specify the -continuouscursor 1 option at the command line for vmtkimageviewer itself.
By clicking on the image planes you'll see the position in physical units appearing on screen.

Hope this helps.

Luca


> 
> Can you give me any tip? 
> 
> Thank you all  
> 
> -- 
> Giuseppe 
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
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> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
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Re: [vmtk-users] problem with python wrappings: vtkvmtkSegmentationPython, vtkvmtkITKPython import

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

Hi Greg,
 sorry for the wait. 
Thanks for the report, it looks like there are missing symbols in the dll that is
loaded by the pyd, although it's hard to understand what's going on in the absence 
of more information.
If you don't need functionality in Segmentation, commenting out the incriminated lines
in vtkvmtk.py will do for now.
We'll investigate further, just let me know if you find something out yourself.
Best,

Luca


On Apr 25, 2013, at 3:37 AM, Greg Fokum wrote:

> hi all, 
> I have compiles vmtk master from git , my paths and python paths are set properly ( I can load all vtk, itk, vmtk except the last two lines below:
> ...
> if os.name == 'posix':
>     from libvtkvmtkCommonPython import *
>     from libvtkvmtkComputationalGeometryPython import *
>     from libvtkvmtkDifferentialGeometryPython import *
>     from libvtkvmtkIOPython import *
>     from libvtkvmtkMiscPython import *
>     from libvtkvmtkRenderingPython import *
>     from libvtkvmtkSegmentationPython import *
>     from libvtkvmtkITKPython import *
> else:
>     from vtkvmtkCommonPython import *
>     from vtkvmtkComputationalGeometryPython import *
>     from vtkvmtkDifferentialGeometryPython import *
>     from vtkvmtkIOPython import *
>     from vtkvmtkMiscPython import *
>     from vtkvmtkRenderingPython import *
>     ==> from vtkvmtkSegmentationPython import *
>     ==> from vtkvmtkITKPython import *
> 
> When loading vtkvmtkSegmentationPython,  I get error
> 
>     from vmtk import vmtkscripts
>   File "C:\Development\install\VMTK\lib\vmtk\vmtk\vmtkscripts.py", line 118, in <module>
>     exec('from '+item+' import *')
>   File "<string>", line 1, in <module>
>   File "C:\Development\install\VMTK\lib\vmtk\vmtk\vmtkactivetubes.py", line 21, in <module>
>     import vtkvmtk
>   File "C:\Development\install\VMTK\lib\vmtk\vmtk\vtkvmtk.py", line 23, in <module>
>     from vtkvmtkSegmentationPython import *
> ImportError: DLL load failed: The specified procedure cou:ld not be found.
> 
> 
> Does anyone know how to fix this ?
> 
> Thank you.
> 
> GT
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service 
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr_______________________________________________
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Re: [vmtk-users] 2 questions on segmentation

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

Hello Vikram,
 thanks for your patience. Pretty busy couple of weeks.

On Apr 23, 2013, at 2:51 PM, Vikram Mehta wrote:

> Dear users,
> 
> I have a couple of questions and I was hoping to get some advice on this.
> 
> 1) Is there a way of aligning one of the ends of the reconstructed geometry with any of the axes?
>     I use the geometries as a model for CFD simulations and some other processing methods in matlab. I need the vessel to be aligned with the x axis (for example) with the center of the inlet at the origin so that my boundary conditions are prescribed accurately.. I usually do it in other meshing softwares and I was wondering if this could be done in VMTK prior to exporting it as an STL file.

There isn't a way to directly do this in vmtk using a script, but you can extract the origin and normal of a boundary using vmtkmeshboundaryinspector (you'll need to generate a mesh with vmtkmeshgenerator first, just use a fixed -edgelength - any mesh size will do if you just need to inspect the boundaries for the origin and normal), compute the transformation yourself and apply it with vmtkmeshtransform (by specifying the coefficients of the 4x4 transform matrix in lexicographic order with the -matrix option).

> 2) Sometimes during the segmentation process, I end up with reconstructions with artificial bumps on them. Is there a way to INDIVIDUALLY smooth these bumps out ? Are there ways to avoid this ?  I do not want to over smooth the entire vessel and hence a way of smoothing just the rough/bumpy bits would be great !    Any suggestions would help !

Yes, it happens sometimes, probably depending on the image features. A localized smoothing filter is something I thought about and wouldn't be hard to implement, but it isn't in vmtk right now.
The way to get around this is to use vmtksurfaceclipper (preferably using -type sphere), clip a bump and then cap it using vmtksurfacecapper -method smooth.

Best,

Luca

> Any help is greatly appreciated !
> 
> Many thanks in advance
> Vikram.
> 
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service 
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] VMTK Mesh Problem

[Vincent Ip <drv...@gm...>]

Dear VMTK users,

I encounter a situation that when I export the surface to STL format and trying to mesh it with ANSYS ICEM.
I cannot define the inlet and outlet as they are incorporated into the wall (the whole thing).
Is there anything I should do besides clipping and capping before exporting the surface to STL format?

The second problem is that I had repeated crashing when I try to mesh it with VMTK and this happen whenever I add the boundary layer.
The vessel geometry I got is a segment from ICA siphon segment to M2 and it is extracted from Time-of-flight MRA. It does appear to be a bit bumpy in appearance, probably due to its low resolution, so I'm not sure if this could be the problem. Or if I need a very powerful computer to run the VMTK??

Please kindly comment.

Thanks,
Vincent

Re: [vmtk-users] help vmtk

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

Hello Hamed,

Did you already try each of those commands individually, without piping?
That might help pinpoint where the problem is.  You should also probably
post whatever error vmtk gives you.

- Evan Kao


On Mon, Apr 29, 2013 at 2:03 PM, Hamed Rezaie <ham...@ya...>wrote:

> I can not produce a surface I use the below commands . I need help. please
> guide me .
> vmtkimagereader -f dicom -d  C:/Users/Hamed/Downloads/Compressed/br1
> --pipe vmtkimagevoiselector -ofile image_volume_voi.vti --pipe
> vmtkimagereader -ifile image_volume_voi.vti --pipe vmtkmarchingcubes -l
> 300.0 -ofile mc_surface.vtp --pipe vmtkrenderer  --pipe vmtksurfaceviewer
>
>
> ------------------------------------------------------------------------------
> Try New Relic Now & We'll Send You this Cool Shirt
> New Relic is the only SaaS-based application performance monitoring service
> that delivers powerful full stack analytics. Optimize and monitor your
> browser, app, & servers with just a few lines of code. Try New Relic
> and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>

[vmtk-users] help vmtk

[Hamed R. <ham...@ya...>]

I can not produce a surface I use the below commands . I need help. please guide me .

vmtkimagereader -f dicom -d  C:/Users/Hamed/Downloads/Compressed/br1 --pipe vmtkimagevoiselector -ofile image_volume_voi.vti --pipe vmtkimagereader -ifile image_volume_voi.vti --pipe vmtkmarchingcubes -l 300.0 -ofile mc_surface.vtp --pipe vmtkrenderer  --pipe vmtksurfaceviewer

Re: [vmtk-users] (no subject)

[Hamed R. <ham...@ya...>]

I can not generate a surface from my DICOM image the command which I use is based on tutorial and is mentioned below is there any one who can 
help me ?
vmtkimagereader -f dicom -d  
C:/Users/Hamed/Downloads/Compressed/br1 --pipe vmtkimageviewer --pipe 
vmtkimagevoiselector -ofile image_volume_voi.vti --pipe 
vmtkmarchingcubes -ifile image_volume_voi.vti -l 300.0 -ofile 
mc_surface.vtp --pipe vmtksurfaceviewer

[vmtk-users] (no subject)

[Hamed R. <ham...@ya...>]

I can not generate a surface from my DICOM image the command which I use is based on tutorial and is mentioned below is there any one who can 
help me ?
vmtkimagereader -f dicom -d  
C:/Users/Hamed/Downloads/Compressed/br1 --pipe vmtkimageviewer --pipe 
vmtkimagevoiselector -ofile image_volume_voi.vti --pipe 
vmtkmarchingcubes -ifile image_volume_voi.vti -l 300.0 -ofile 
mc_surface.vtp --pipe vmtksurfaceviewer

[vmtk-users] (no subject)

[Hamed R. <ham...@ya...>]

ham...@ya...

Re: [vmtk-users] vmtkApps?

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

Hi Luca,

I had some questions on using the Python scripts (having little Python
experience):

1.  Into which directory should I move the files (in Windows; files
obtained from the source file zip)?
2.  I was confused by the form of the command "python
patchandinterpolatecenterline.py directoryPath id1 lateral" from the
tutorial.  Are we supposed to call these functions from the command
line/Python shell or can we still do it inside vmtk?

Thanks for the help,
Evan Kao



On Mon, Apr 22, 2013 at 11:03 AM, Evan Kao <to...@gm...> wrote:

> Hi Luca,
>
> Thanks for the info.
>
>
> On Mon, Apr 22, 2013 at 7:01 AM, Luca Antiga <luc...@or...>wrote:
>
>> Hello Evan,
>>  at the present stage you can download them from github.com/vmtk/vmtk
>>
>> If you don't use git, just get the source code zip at
>>
>> https://github.com/vmtk/vmtk/archive/master.zip
>>
>> and unpack. vmtkApps contains the Python scripts you're looking for.
>>
>> Best,
>>
>> Luca
>>
>>
>> On Apr 20, 2013, at 12:09 AM, Evan Kao wrote:
>>
>> > Hello vmtk-users,
>> >
>> > I'm interested in going through the parent vessel reconstruction
>> tutorial but I don't think I have the relevant Python scripts.  The
>> tutorial says the files are in the vmtkApps folder, but I couldn't find
>> anything like that.  Are they usually included in the installation?  Where
>> could I find these scripts (and possibly other vmtkApps)?
>> >
>> > Thank you,
>> > Evan Kao
>> >
>> ------------------------------------------------------------------------------
>> > Precog is a next-generation analytics platform capable of advanced
>> > analytics on semi-structured data. The platform includes APIs for
>> building
>> > apps and a phenomenal toolset for data science. Developers can use
>> > our toolset for easy data analysis & visualization. Get a free account!
>> >
>> http://www2.precog.com/precogplatform/slashdotnewsletter_______________________________________________
>> > vmtk-users mailing list
>> > vmt...@li...
>> > https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>>
>

[vmtk-users] vmtkimagevoiselector -boxbounds : what's wrong?

[Giuseppe I. <giu...@gm...>]

Hi everebody,

I'm facing a geometry reconstruction task on vmtk. I need to reconstruct a
carotid bifurcation, but I'm experiencing some difficulties at the bulb
region. Generally I have an amazing image quality, I can easily segment
level sets for all branches (high meta levels within the lumen over  1000
and low levels otherwise), but due to blood recirculation  I have low
levels and kind of disturbed uneven image at the bulb. I tried to
initialize the segmentation in different ways but the result is always a
staired surface which follows the pixel level fluctuations in that region.

I thought to use vmtkimagevoiselector to divide my voi in three domains in
order to isolate the bulb volume, and then smooth the image only in the
bifurcation region.

The idea is to perform level set segmentation separately for the three
domains and then use vmtkimagecompose to reassemble my segmented volume.

A problem occurs when I pipe vmtkimagevoiselector. To obtain a precise
subdivision of the original volume I want to use -boxbounds insead of
interactive voi selection. I pipe this code:

vmtkimagevoiselector -ifile myname.vti -interactive 0 -boundbox xmin xmax
ymin ymax zmin zmax -ofile myoutput.vti --pipe vmtkimageviewer

but the output image results empty. what's wrong?  it seems to me to have
used the right pipe synthax.

Then if I omit the part "-interactive 0" I get the interactive option to be
enabled typing "i" and, again, empty image.


Can you give me any tip?

Thank you all

-- 
Giuseppe

[vmtk-users] problem with python wrappings: vtkvmtkSegmentationPython, vtkvmtkITKPython import

[Greg F. <gre...@gm...>]

hi all,
I have compiles vmtk master from git , my paths and python paths are set
properly ( I can load all vtk, itk, vmtk except the last two lines below:
...
if os.name == 'posix':
    from libvtkvmtkCommonPython import *
    from libvtkvmtkComputationalGeometryPython import *
    from libvtkvmtkDifferentialGeometryPython import *
    from libvtkvmtkIOPython import *
    from libvtkvmtkMiscPython import *
    from libvtkvmtkRenderingPython import *
    from libvtkvmtkSegmentationPython import *
    from libvtkvmtkITKPython import *
else:
    from vtkvmtkCommonPython import *
    from vtkvmtkComputationalGeometryPython import *
    from vtkvmtkDifferentialGeometryPython import *
    from vtkvmtkIOPython import *
    from vtkvmtkMiscPython import *
    from vtkvmtkRenderingPython import *
    ==> from vtkvmtkSegmentationPython import *
    ==> from vtkvmtkITKPython import *

When loading vtkvmtkSegmentationPython,  I get error

    from vmtk import vmtkscripts
  File "C:\Development\install\VMTK\lib\vmtk\vmtk\vmtkscripts.py", line
118, in <module>
    exec('from '+item+' import *')
  File "<string>", line 1, in <module>
  File "C:\Development\install\VMTK\lib\vmtk\vmtk\vmtkactivetubes.py", line
21, in <module>
    import vtkvmtk
  File "C:\Development\install\VMTK\lib\vmtk\vmtk\vtkvmtk.py", line 23, in
<module>
    from vtkvmtkSegmentationPython import *
ImportError: DLL load failed: The specified procedure could not be found.


Does anyone know how to fix this ?

Thank you.

GT

[vmtk-users] 2 questions on segmentation

[Vikram M. <vv...@gm...>]

Dear users,

I have a couple of questions and I was hoping to get some advice on this.

1) Is there a way of aligning one of the ends of the reconstructed geometry
with any of the axes?
    I use the geometries as a model for CFD simulations and some other
processing methods in matlab. I need the vessel to be aligned with the x
axis (for example) with the center of the inlet at the origin so that my
boundary conditions are prescribed accurately.. I usually do it in other
meshing softwares and I was wondering if this could be done in VMTK prior
to exporting it as an STL file.


2) Sometimes during the segmentation process, I end up with reconstructions
with artificial bumps on them. Is there a way to INDIVIDUALLY smooth these
bumps out ? Are there ways to avoid this ?  I do not want to over smooth
the entire vessel and hence a way of smoothing just the rough/bumpy bits
would be great !    Any suggestions would help !

Any help is greatly appreciated !

Many thanks in advance
Vikram.

Re: [vmtk-users] vmtkApps?

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

Hi Luca,

Thanks for the info.


On Mon, Apr 22, 2013 at 7:01 AM, Luca Antiga <luc...@or...> wrote:

> Hello Evan,
>  at the present stage you can download them from github.com/vmtk/vmtk
>
> If you don't use git, just get the source code zip at
>
> https://github.com/vmtk/vmtk/archive/master.zip
>
> and unpack. vmtkApps contains the Python scripts you're looking for.
>
> Best,
>
> Luca
>
>
> On Apr 20, 2013, at 12:09 AM, Evan Kao wrote:
>
> > Hello vmtk-users,
> >
> > I'm interested in going through the parent vessel reconstruction
> tutorial but I don't think I have the relevant Python scripts.  The
> tutorial says the files are in the vmtkApps folder, but I couldn't find
> anything like that.  Are they usually included in the installation?  Where
> could I find these scripts (and possibly other vmtkApps)?
> >
> > Thank you,
> > Evan Kao
> >
> ------------------------------------------------------------------------------
> > Precog is a next-generation analytics platform capable of advanced
> > analytics on semi-structured data. The platform includes APIs for
> building
> > apps and a phenomenal toolset for data science. Developers can use
> > our toolset for easy data analysis & visualization. Get a free account!
> >
> http://www2.precog.com/precogplatform/slashdotnewsletter_______________________________________________
> > vmtk-users mailing list
> > vmt...@li...
> > https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>