vmtk-users

Re: [vmtk-users] FDNEUT meshing using vmtk

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

Hello Elaine,
 your message made me realize I haven't dealt with the FIDAP format 
in a long time! FIDAP was the first CFD solver I've ever used...

Which brings me to the unfortunate consequence: the FDNEUT writer was 
written in the early days when there was no concept of CellEntityIds array in 
vmtkmeshwriter. So, while the writer produces a valid FDNEUT mesh, it doesn't 
take into account the entity information.

It shouldn't be hard to extend the writer with the FDNEUT specs at hand.

May I ask why you need the mesh in FDNEUT format? If it's not for using
the FIDAP solver (which must have been abandoned for about ten years 
now) but for importing into, say, Gambit, then there might be other ways
of getting there, through other formats that VTK supports.

Best,

Luca




On Jun 18, 2013, at 10:37 PM, Elaine Tang wrote:

> Hi,
> 
> I am trying to create FDNEUT mesh using vmtk, and using .stl as input. I want to specify each inlet/outlet as separate entity in the FDNEUT. I first created an stl with open caps.Then I import the stl and mesh it to vtu. From vmtkmeshboundaryinspector, it seems that my vtu mesh contains the surface and each inlet/outlet cap as separate entities, which is great. However, when I try to output the mesh in FDNEUT, the CellEntityIfd cannot be stored in the FDNEUT mesh. And in the FDNEUT, the mesh is one entity as a whole.  Any insight on this?
> 
> Thanks!
> -- 
> Elaine Tang
> 
> PhD Candidate
> Cardiovascular Fluid Mechanics Laboratory
> Chemical & Biomolecular Engineering
> Georgia Institute of Technology
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
> 
> Build for Windows Store.
> 
> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] Problems reading DICOM on Windows

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

Hi Ben,
 is this happening just for this DICOM set?

The fact that you get a crash both in the old VTK-based way (-f) and the ITK-based one (-ifile) 
could be symptomatic of the fact that there's something odd going on with the DICOMs, although
typically you shouldn't get a crash but an error message.

Are you sure you have enough memory to open the DICOM? I've experienced memory allocation 
limitations on older Windows systems in the past, so if your DICOM series is very large that might
be it (you should get an "Unable to allocate [something something]" as an error before the crash).

Hope this helps.


Luca


On Jun 18, 2013, at 5:05 PM, Berkowitz, Benjamin M wrote:

> I'm having problems reading in a DICOM set in the Windows binary.  I've tried importing using vmtkimagereader with the -f parameter as well as the -ifile parameter.  I've also just tried using vmtkimageviewer directly.  Each time, python crashes and it won't open the DICOMs.  Is it more likely a problem with the files themselves or a bug in VMTK?
> 
> Thanks,
> 
> Ben
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
> 
> Build for Windows Store.
> 
> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
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Re: [vmtk-users] using vmtk on windows7

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

Hello zj,

can you please open the Python shell and type

>> from vmtk import vtkvmtk

and

>> import vtk

and let me know what output you get?

Thanks


Luca


On Jun 18, 2013, at 9:48 AM, zj19872008 wrote:

>  
> Dear VMTK users,
> 
> I am a beginner in VMTK. I installed
> vmtk-1.0.1-win7-32bit.exe on my computer. 
> set the environment variable like this:
> PATH
>   C:\Program Files\vmtk\Install\bin;
>   C:\Program Files\vmtk\Install\lib;
>   C:\Program Files\vmtk\Install\lib\vtk-5.8;
>   C:\Program Files\vmtk\Install\lib\vmtk;
>   C:\Program Files\vmtk\Install\bin\Python;
> PYTHONPATH
>   C:\Program Files\vmtk\Install\lib\vmtk;
>   C:\Program Files\vmtk\Install\bin\Python;
>   C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;
>  
>  
> and type the command in Python(Command line)
> vmtkimagereader -ifile HL.dcm 
> But it showed up like this :"name vmtkimagereader is not defined"
> Thanks for your help!
> zj
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
> 
> Build for Windows Store.
> 
> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
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[vmtk-users] Command line parameters for vmtkLevelSetSegmentation

[Richard A. <ab...@gm...>]

Hello,

I'm interested in calling vmtkLevelSetSegmentation from a script. I want to
run colliding fronts with arbitrary thresholds and start/end position
vectors for the initial segmentation, and then run the level set
segmentation with arbitrary parameters.

Unfortunately, there doesn't seem to be any way to specify these parameters
from the command line. What might be the easiest way to accomplish this?

Thanks,
Richard

[vmtk-users] FDNEUT meshing using vmtk

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

Hi,

I am trying to create FDNEUT mesh using vmtk, and using .stl as input. I
want to specify each inlet/outlet as separate entity in the FDNEUT. I first
created an stl with open caps.Then I import the stl and mesh it to vtu.
>From vmtkmeshboundaryinspector, it seems that my vtu mesh contains the
surface and each inlet/outlet cap as separate entities, which is great.
However, when I try to output the mesh in FDNEUT, the CellEntityIfd cannot
be stored in the FDNEUT mesh. And in the FDNEUT, the mesh is one entity as
a whole.  Any insight on this?

Thanks!
-- 
Elaine Tang

PhD Candidate
Cardiovascular Fluid Mechanics Laboratory
Chemical & Biomolecular Engineering
Georgia Institute of Technology

Re: [vmtk-users] help vmtk

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

Hamed, make sure to specify a full path for your '-ofile' parameters, like '-ofile C:/Users/Hamed/Downloads/image_volume_voi.vti'.

Ben



________________________________
From: Hamed Rezaie [ham...@ya...]
Sent: Monday, April 29, 2013 4:03 PM
To: vmt...@li...
Subject: [vmtk-users] help vmtk

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

[vmtk-users] Problems reading DICOM on Windows

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

I'm having problems reading in a DICOM set in the Windows binary.  I've tried importing using vmtkimagereader with the -f parameter as well as the -ifile parameter.  I've also just tried using vmtkimageviewer directly.  Each time, python crashes and it won't open the DICOMs.  Is it more likely a problem with the files themselves or a bug in VMTK?

Thanks,

Ben

[vmtk-users] using vmtk on windows7

[zj19872008 <zj1...@si...>]

Dear VMTK users,

I am a beginner in VMTK. I installed
vmtk-1.0.1-win7-32bit.exe on my computer. 
set the environment variable like this:
PATH  C:\Program Files\vmtk\Install\bin;  C:\Program Files\vmtk\Install\lib;  C:\Program Files\vmtk\Install\lib\vtk-5.8;  C:\Program Files\vmtk\Install\lib\vmtk;  C:\Program Files\vmtk\Install\bin\Python;PYTHONPATH  C:\Program Files\vmtk\Install\lib\vmtk;  C:\Program Files\vmtk\Install\bin\Python;  C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;and type the command in Python(Command line)
vmtkimagereader -ifile HL.dcm 
But it showed up like this :"name vmtkimagereader is not defined"
Thanks for your help!



zj

Re: [vmtk-users] Wall shear stress computation with VMTK

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

Dear Emilie, Evan and Simone,
as Simone was pointing out, the vmtk script computes wall shear rate,
rather than WSS.

It actually does so through its definition (the contraction of the velocity 
gradient tensor with the surface normal), by *solely* by performing derivatives 
of the velocity field - so no pressure or viscosity involved, since we're
talking about derivatives of the velocity field, and the units for the WSR are 
consistent with whatever units your velocity is in. 

A caveat: the mesh units must be consistent with the velocity units (mesh
in mm, velocity in mm/s, mesh in cm, velocity in cm/s). If they aren't, you have
to account for the scaling factor.

Paraview computes gradients by taking partial derivatives using the shape
functions of each element (which is in general linear), computing a derivative 
value for each element and obtaining a nodal value by averaging over the 
cell neighborhood.

vmtk computes gradients by performing an L2 projection using a finite elements 
discretization. Intuitively the problem is: find the nodal values such that the integral 
over each element equals the integral obtained by evaluating derivatives within the
element at each nodal point. 

I hope this provides some clarification, in any case I'm here for further information.


Luca


On Jun 6, 2013, at 10:31 PM, Emilie Sauvage wrote:

> Hello Simone and Evan,
> 
> Thank you for your reply.
> I tried the function "vmtkmeshwallshearrate", and it seems to work fine. I
> get a nice picture, but unfortunately I don't know what am I looking at.
> With paraview filters, I tried to approximate the following formula:
> 
> The traction vector t is defined as
> 
> t = [-pI + mu*(nabla(v) + nabla(v)^T]*n   // n ... normal to surface
>                                         // I ... unit tensor
>                                         // mu ... viscosity
>                                         // v ... velocity vector field
> 
> and wall shear stress is given by
> 
> wss = mag( t - dot(t,n)n )
> 
> As you can see, it involves also pressure and viscosity of the fluid. I
> have several questions:
> 
> 1) The script does not ask for pressure field. Why?
> 2) The script does not ask for the viscosity of the fluid. Why?
> 3) What is the unit in which the WSS is written to the output file? My old
> file obtained with paraview and the WSS file obtained with VMTK show
> somewhat similar color maps, but the scale is completely different.
> 4) To join the request of Evan, could you please please be so kind and
> give some details about HOW are the velocity gradients computed? I need to
> have an idea about the accuracy of the algorithm.
> 
> Thank you again for your previous quick reply.
> 
> Best regards.
> 
> Emilie Sauvage.
> 
> 
> 
>> Hello vmtk users,
>> 
>> To piggyback on Emilie's query on computing velocity gradients, is
>> there documentation for either vmtk or Paraview on how they compute
>> gradients in general for unstructured meshes?  For instance, do they
>> use RBF-FD methods?  I couldn't seem to find anything about the
>> specifics.
>> 
>> Thanks,
>> Evan Kao
>> 
>> On 6/6/13, Simone Manini <sim...@or...> wrote:
>>> Dear Emily,
>>> I think you can use vmtkmeshwallshearrate which computes wsr from a
>>> velocity
>>> field.
>>> It supports any kind of mesh files supported by vmtk.
>>> You need to have the velocity array from components (u v w) so you can
>>> use
>>> vmtkmeshvectorfromcomponents:
>>> 
>>> vmtkmeshvectorfromcomponents -ifile input_file -vector Velocity
>>> -components
>>> u v w --pipe vmtkmeshwallshearrate -velocityarray Velocity -ofile
>>> output_file
>>> 
>>> Remember that the output file will be a surface file.
>>> 
>>> http://www.vmtk.org/VmtkScripts/vmtkmeshvectorfromcomponents
>>> http://www.vmtk.org/VmtkScripts/vmtkmeshwallshearrate
>>> 
>>> I hope it helps,
>>> Best 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 Jun 6, 2013, at 6:09 PM, "Emilie Sauvage"
>>> <emi...@uc...>
>>> wrote:
>>> 
>>>> Dear Luca,
>>>> 
>>>> I would like to ask you if there is a way of computing wall shear
>>>> stress
>>>> from nodal velocity and pressure values. In case this is possible,
>>>> could
>>>> you tell me what input file formats are supported?
>>>> I'm asking this because the flow solver that I use does not output wall
>>>> shear stress. I used ParaView to compute it, but my supervisor
>>>> expressed
>>>> some doubts about how accurate is vtk/ParaView when computing gradients
>>>> of velocity from Finite Element data on unstructured grid. I posted a
>>>> question on vtk mailing list, but did not get any reply. Then I thought
>>>> that maybe VMTK can actually do this ...
>>>> 
>>>> Thank you very much.
>>>> 
>>>> Best regards,
>>>> 
>>>> Emilie Sauvage
>>>> 
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> How ServiceNow helps IT people transform IT departments:
>>>> 1. A cloud service to automate IT design, transition and operations
>>>> 2. Dashboards that offer high-level views of enterprise services
>>>> 3. A single system of record for all IT processes
>>>> http://p.sf.net/sfu/servicenow-d2d-j
>>>> _______________________________________________
>>>> vmtk-users mailing list
>>>> vmt...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>> 
>>> 
>> 
> 
> 
> 
> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. A cloud service to automate IT design, transition and operations
> 2. Dashboards that offer high-level views of enterprise services
> 3. A single system of record for all IT processes
> http://p.sf.net/sfu/servicenow-d2d-j
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] Wall shear stress computation with VMTK

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

Dear Emilie,
1) The pressure field information is usually present in the mesh solution input file, the script uses it without asking for it.
2) The script computes wall shear rate, if you want wall shear stress you have to multiply wsr with the viscosity value.
3) The scale depends on the measurement units you used in your simulation (it does not make any conversion).
4) In my opinion if you build vector velocity from components using vmtk script or using Paraview (u*iHat + v*jHat + w*kHat) the final result is the same. I don't know which method vmtk/Paraview use, maybe Luca knows it.

Best 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 Jun 6, 2013, at 10:31 PM, "Emilie Sauvage" <emi...@uc...> wrote:

> Hello Simone and Evan,
> 
> Thank you for your reply.
> I tried the function "vmtkmeshwallshearrate", and it seems to work fine. I
> get a nice picture, but unfortunately I don't know what am I looking at.
> With paraview filters, I tried to approximate the following formula:
> 
> The traction vector t is defined as
> 
> t = [-pI + mu*(nabla(v) + nabla(v)^T]*n   // n ... normal to surface
>                                          // I ... unit tensor
>                                          // mu ... viscosity
>                                          // v ... velocity vector field
> 
> and wall shear stress is given by
> 
> wss = mag( t - dot(t,n)n )
> 
> As you can see, it involves also pressure and viscosity of the fluid. I
> have several questions:
> 
> 1) The script does not ask for pressure field. Why?
> 2) The script does not ask for the viscosity of the fluid. Why?
> 3) What is the unit in which the WSS is written to the output file? My old
> file obtained with paraview and the WSS file obtained with VMTK show
> somewhat similar color maps, but the scale is completely different.
> 4) To join the request of Evan, could you please please be so kind and
> give some details about HOW are the velocity gradients computed? I need to
> have an idea about the accuracy of the algorithm.
> 
> Thank you again for your previous quick reply.
> 
> Best regards.
> 
> Emilie Sauvage.
> 
> 
> 
>> Hello vmtk users,
>> 
>> To piggyback on Emilie's query on computing velocity gradients, is
>> there documentation for either vmtk or Paraview on how they compute
>> gradients in general for unstructured meshes?  For instance, do they
>> use RBF-FD methods?  I couldn't seem to find anything about the
>> specifics.
>> 
>> Thanks,
>> Evan Kao
>> 
>> On 6/6/13, Simone Manini <sim...@or...> wrote:
>>> Dear Emily,
>>> I think you can use vmtkmeshwallshearrate which computes wsr from a
>>> velocity
>>> field.
>>> It supports any kind of mesh files supported by vmtk.
>>> You need to have the velocity array from components (u v w) so you can
>>> use
>>> vmtkmeshvectorfromcomponents:
>>> 
>>> vmtkmeshvectorfromcomponents -ifile input_file -vector Velocity
>>> -components
>>> u v w --pipe vmtkmeshwallshearrate -velocityarray Velocity -ofile
>>> output_file
>>> 
>>> Remember that the output file will be a surface file.
>>> 
>>> http://www.vmtk.org/VmtkScripts/vmtkmeshvectorfromcomponents
>>> http://www.vmtk.org/VmtkScripts/vmtkmeshwallshearrate
>>> 
>>> I hope it helps,
>>> Best 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 Jun 6, 2013, at 6:09 PM, "Emilie Sauvage"
>>> <emi...@uc...>
>>> wrote:
>>> 
>>>> Dear Luca,
>>>> 
>>>> I would like to ask you if there is a way of computing wall shear
>>>> stress
>>>> from nodal velocity and pressure values. In case this is possible,
>>>> could
>>>> you tell me what input file formats are supported?
>>>> I'm asking this because the flow solver that I use does not output wall
>>>> shear stress. I used ParaView to compute it, but my supervisor
>>>> expressed
>>>> some doubts about how accurate is vtk/ParaView when computing gradients
>>>> of velocity from Finite Element data on unstructured grid. I posted a
>>>> question on vtk mailing list, but did not get any reply. Then I thought
>>>> that maybe VMTK can actually do this ...
>>>> 
>>>> Thank you very much.
>>>> 
>>>> Best regards,
>>>> 
>>>> Emilie Sauvage
>>>> 
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> How ServiceNow helps IT people transform IT departments:
>>>> 1. A cloud service to automate IT design, transition and operations
>>>> 2. Dashboards that offer high-level views of enterprise services
>>>> 3. A single system of record for all IT processes
>>>> http://p.sf.net/sfu/servicenow-d2d-j
>>>> _______________________________________________
>>>> vmtk-users mailing list
>>>> vmt...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>> 
>>> 
>> 
> 
> 
> 
> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. A cloud service to automate IT design, transition and operations
> 2. Dashboards that offer high-level views of enterprise services
> 3. A single system of record for all IT processes
> http://p.sf.net/sfu/servicenow-d2d-j
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] Wall shear stress computation with VMTK

[Emilie S. <emi...@uc...>]

Hello Simone and Evan,

Thank you for your reply.
I tried the function "vmtkmeshwallshearrate", and it seems to work fine. I
get a nice picture, but unfortunately I don't know what am I looking at.
With paraview filters, I tried to approximate the following formula:

The traction vector t is defined as

t = [-pI + mu*(nabla(v) + nabla(v)^T]*n   // n ... normal to surface
                                          // I ... unit tensor
                                          // mu ... viscosity
                                          // v ... velocity vector field

and wall shear stress is given by

wss = mag( t - dot(t,n)n )

As you can see, it involves also pressure and viscosity of the fluid. I
have several questions:

1) The script does not ask for pressure field. Why?
2) The script does not ask for the viscosity of the fluid. Why?
3) What is the unit in which the WSS is written to the output file? My old
file obtained with paraview and the WSS file obtained with VMTK show
somewhat similar color maps, but the scale is completely different.
4) To join the request of Evan, could you please please be so kind and
give some details about HOW are the velocity gradients computed? I need to
have an idea about the accuracy of the algorithm.

Thank you again for your previous quick reply.

Best regards.

Emilie Sauvage.



> Hello vmtk users,
>
> To piggyback on Emilie's query on computing velocity gradients, is
> there documentation for either vmtk or Paraview on how they compute
> gradients in general for unstructured meshes?  For instance, do they
> use RBF-FD methods?  I couldn't seem to find anything about the
> specifics.
>
> Thanks,
> Evan Kao
>
> On 6/6/13, Simone Manini <sim...@or...> wrote:
>> Dear Emily,
>> I think you can use vmtkmeshwallshearrate which computes wsr from a
>> velocity
>> field.
>> It supports any kind of mesh files supported by vmtk.
>> You need to have the velocity array from components (u v w) so you can
>> use
>> vmtkmeshvectorfromcomponents:
>>
>> vmtkmeshvectorfromcomponents -ifile input_file -vector Velocity
>> -components
>> u v w --pipe vmtkmeshwallshearrate -velocityarray Velocity -ofile
>> output_file
>>
>> Remember that the output file will be a surface file.
>>
>> http://www.vmtk.org/VmtkScripts/vmtkmeshvectorfromcomponents
>> http://www.vmtk.org/VmtkScripts/vmtkmeshwallshearrate
>>
>> I hope it helps,
>> Best 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 Jun 6, 2013, at 6:09 PM, "Emilie Sauvage"
>> <emi...@uc...>
>> wrote:
>>
>>> Dear Luca,
>>>
>>> I would like to ask you if there is a way of computing wall shear
>>> stress
>>> from nodal velocity and pressure values. In case this is possible,
>>> could
>>> you tell me what input file formats are supported?
>>> I'm asking this because the flow solver that I use does not output wall
>>> shear stress. I used ParaView to compute it, but my supervisor
>>> expressed
>>> some doubts about how accurate is vtk/ParaView when computing gradients
>>> of velocity from Finite Element data on unstructured grid. I posted a
>>> question on vtk mailing list, but did not get any reply. Then I thought
>>> that maybe VMTK can actually do this ...
>>>
>>> Thank you very much.
>>>
>>> Best regards,
>>>
>>>  Emilie Sauvage
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> How ServiceNow helps IT people transform IT departments:
>>> 1. A cloud service to automate IT design, transition and operations
>>> 2. Dashboards that offer high-level views of enterprise services
>>> 3. A single system of record for all IT processes
>>> http://p.sf.net/sfu/servicenow-d2d-j
>>> _______________________________________________
>>> vmtk-users mailing list
>>> vmt...@li...
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>>
>

Re: [vmtk-users] Wall shear stress computation with VMTK

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

Hello vmtk users,

To piggyback on Emilie's query on computing velocity gradients, is
there documentation for either vmtk or Paraview on how they compute
gradients in general for unstructured meshes?  For instance, do they
use RBF-FD methods?  I couldn't seem to find anything about the
specifics.

Thanks,
Evan Kao

On 6/6/13, Simone Manini <sim...@or...> wrote:
> Dear Emily,
> I think you can use vmtkmeshwallshearrate which computes wsr from a velocity
> field.
> It supports any kind of mesh files supported by vmtk.
> You need to have the velocity array from components (u v w) so you can use
> vmtkmeshvectorfromcomponents:
>
> vmtkmeshvectorfromcomponents -ifile input_file -vector Velocity -components
> u v w --pipe vmtkmeshwallshearrate -velocityarray Velocity -ofile
> output_file
>
> Remember that the output file will be a surface file.
>
> http://www.vmtk.org/VmtkScripts/vmtkmeshvectorfromcomponents
> http://www.vmtk.org/VmtkScripts/vmtkmeshwallshearrate
>
> I hope it helps,
> Best 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 Jun 6, 2013, at 6:09 PM, "Emilie Sauvage" <emi...@uc...>
> wrote:
>
>> Dear Luca,
>>
>> I would like to ask you if there is a way of computing wall shear stress
>> from nodal velocity and pressure values. In case this is possible, could
>> you tell me what input file formats are supported?
>> I'm asking this because the flow solver that I use does not output wall
>> shear stress. I used ParaView to compute it, but my supervisor expressed
>> some doubts about how accurate is vtk/ParaView when computing gradients
>> of velocity from Finite Element data on unstructured grid. I posted a
>> question on vtk mailing list, but did not get any reply. Then I thought
>> that maybe VMTK can actually do this ...
>>
>> Thank you very much.
>>
>> Best regards,
>>
>>  Emilie Sauvage
>>
>>
>> ------------------------------------------------------------------------------
>> How ServiceNow helps IT people transform IT departments:
>> 1. A cloud service to automate IT design, transition and operations
>> 2. Dashboards that offer high-level views of enterprise services
>> 3. A single system of record for all IT processes
>> http://p.sf.net/sfu/servicenow-d2d-j
>> _______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>

Re: [vmtk-users] Wall shear stress computation with VMTK

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

Dear Emily,
I think you can use vmtkmeshwallshearrate which computes wsr from a velocity field.
It supports any kind of mesh files supported by vmtk.
You need to have the velocity array from components (u v w) so you can use vmtkmeshvectorfromcomponents:

vmtkmeshvectorfromcomponents -ifile input_file -vector Velocity -components u v w --pipe vmtkmeshwallshearrate -velocityarray Velocity -ofile output_file

Remember that the output file will be a surface file.

http://www.vmtk.org/VmtkScripts/vmtkmeshvectorfromcomponents
http://www.vmtk.org/VmtkScripts/vmtkmeshwallshearrate

I hope it helps,
Best 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 Jun 6, 2013, at 6:09 PM, "Emilie Sauvage" <emi...@uc...> wrote:

> Dear Luca,
> 
> I would like to ask you if there is a way of computing wall shear stress
> from nodal velocity and pressure values. In case this is possible, could
> you tell me what input file formats are supported?
> I'm asking this because the flow solver that I use does not output wall
> shear stress. I used ParaView to compute it, but my supervisor expressed
> some doubts about how accurate is vtk/ParaView when computing gradients
> of velocity from Finite Element data on unstructured grid. I posted a
> question on vtk mailing list, but did not get any reply. Then I thought
> that maybe VMTK can actually do this ...
> 
> Thank you very much.
> 
> Best regards,
> 
>  Emilie Sauvage
> 
> 
> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. A cloud service to automate IT design, transition and operations
> 2. Dashboards that offer high-level views of enterprise services
> 3. A single system of record for all IT processes
> http://p.sf.net/sfu/servicenow-d2d-j
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] Wall shear stress computation with VMTK

[Emilie S. <emi...@uc...>]

Dear Luca,

 I would like to ask you if there is a way of computing wall shear stress
from nodal velocity and pressure values. In case this is possible, could
you tell me what input file formats are supported?
 I'm asking this because the flow solver that I use does not output wall
shear stress. I used ParaView to compute it, but my supervisor expressed
some doubts about how accurate is vtk/ParaView when computing gradients
of velocity from Finite Element data on unstructured grid. I posted a
question on vtk mailing list, but did not get any reply. Then I thought
that maybe VMTK can actually do this ...

Thank you very much.

Best regards,

  Emilie Sauvage

Re: [vmtk-users] Problems with sigmoid mask

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

Thank you so much!

Sent from my iPhone

On 27 May, 2013, at 8:08 AM, Luca Antiga <luc...@gm...> wrote:

> Hi Vincent,
> I'll find some time to give this a shot in the next few hours.
> I don't guarantee I'll succeed but stay tuned.
> 
> Luca
> 
> 
> On May 13, 2013, at 4:20 AM, Vincent Ip wrote:
> 
>> Dear VMTK users,
>> 
>> I followed the tutorial from VMTK website and tried to extract the geometry of right internal carotid artery from a CT DICOM images. As the right ICA is embedded in bone, I made the sigmoid mask followed by the usual steps in getting the surface (I used colliding fronts in this case). Despite repeated attempts with various threshold level, I still could not get the surface properly and here I come to seek the advice from you guys.
>> 
>> <Screen Shot 2013-05-12 at 7.10.05 PM.png>
>> 
>> This is the 'lump' I got when I tried to extract the C4 segment of the right ICA. I have already added the sigmoid function to this level set with isosurface for bone as 550 and -50 for air.
>> 
>> Here I attached the image_voi & the sigmoid feature files and I sincerely hope that someone could give me some hints on how to extract the surface without the bone in my way.
>> 
>> Many thanks in advance!
>> 
>> Vincent
>> 
>> <sigmoid_feature.vti><image_volume_voi.vti>------------------------------------------------------------------------------
>> Learn Graph Databases - Download FREE O'Reilly Book
>> "Graph Databases" is the definitive new guide to graph databases and 
>> their applications. This 200-page book is written by three acclaimed 
>> leaders in the field. The early access version is available now. 
>> Download your free book today! http://p.sf.net/sfu/neotech_d2d_may_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 

Re: [vmtk-users] change needed in VMTK CmakeLists.txt

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

Done.

Luca



On May 23, 2013, at 12:13 PM, Sebastian Ordas wrote:

> Hello Luca,
> 
> I would need the following lines in CmakeLists.txt uncommented in my 
> project:
> 
>     EXPORT_LIBRARY_DEPENDENCIES(
>       ${VMTK_BINARY_DIR}/VMTKLibraryDepends.cmake
>     )
> 
> what do you think?
> 
> thank you!
> sebastian
> 
> ------------------------------------------------------------------------------
> 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_may
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] VTK 5.10.0 compatibility

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

It's in, thanks

Luca

On May 23, 2013, at 12:51 PM, Sebastian Ordas wrote:

> One last for VTK 5.10.0 compatibility:
> 
> In vtkvmtkImageBoxPainter.cxx:
> 
> switch(output->GetScalarType())
>     {
>          #if (VTK_MAJOR_VERSION < 5)
>             // This is simple a #define for a big case list. It handles
>             // all data types vtk can handle.
>             vtkTemplateMacro6(vtkvmtkImageBoxPainterExecute, input, output,
>                               (VTK_TT *)(inPtr), (VTK_TT *)(outPtr), 
> relativeBoxExtent,
>                               (VTK_TT)this->PaintValue);
> 
>             #else
>              vtkTemplateMacro(
>              vtkvmtkImageBoxPainterExecute(input, output,
>                               (VTK_TT *)(inPtr), (VTK_TT *)(outPtr), 
> relativeBoxExtent,
>                               (VTK_TT)this->PaintValue));
>             #endif
>     default:
>       vtkGenericWarningMacro("Execute: Unknown input ScalarType");
>       return;
>     }
> 
> ------------------------------------------------------------------------------
> 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_may
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] missing include in vtkvmtkLevelSetSigmoidFilter.cxx

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

Hi Sebastian,
 good to hear from you. It's not needed on my build, but it's likely that it's needed
for other compilers / configurations. I added it now in the main repository.

Luca

On May 23, 2013, at 12:32 PM, Sebastian Ordas wrote:

> Hi Again,
> 
> Can you check if #include "vtkDataArray.h" is needed in 
> vtkvmtkLevelSetSigmoidFilter.cxx?
> It is so in my setting (VS2010, VTK  5.10)
> 
> thanks
> sebastian
> 
> ------------------------------------------------------------------------------
> 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_may
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] Problems with sigmoid mask

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

Hi Vincent,
 I'll find some time to give this a shot in the next few hours.
I don't guarantee I'll succeed but stay tuned.

Luca


On May 13, 2013, at 4:20 AM, Vincent Ip wrote:

> Dear VMTK users,
> 
> I followed the tutorial from VMTK website and tried to extract the geometry of right internal carotid artery from a CT DICOM images. As the right ICA is embedded in bone, I made the sigmoid mask followed by the usual steps in getting the surface (I used colliding fronts in this case). Despite repeated attempts with various threshold level, I still could not get the surface properly and here I come to seek the advice from you guys.
> 
> <Screen Shot 2013-05-12 at 7.10.05 PM.png>
> 
> This is the 'lump' I got when I tried to extract the C4 segment of the right ICA. I have already added the sigmoid function to this level set with isosurface for bone as 550 and -50 for air.
> 
> Here I attached the image_voi & the sigmoid feature files and I sincerely hope that someone could give me some hints on how to extract the surface without the bone in my way.
> 
> Many thanks in advance!
> 
> Vincent
> 
> <sigmoid_feature.vti><image_volume_voi.vti>------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and 
> their applications. This 200-page book is written by three acclaimed 
> leaders in the field. The early access version is available now. 
> Download your free book today! http://p.sf.net/sfu/neotech_d2d_may_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] VTK 5.10.0 compatibility

[Sebastian O. <seb...@gm...>]

One last for VTK 5.10.0 compatibility:

In vtkvmtkImageBoxPainter.cxx:

switch(output->GetScalarType())
     {
          #if (VTK_MAJOR_VERSION < 5)
             // This is simple a #define for a big case list. It handles
             // all data types vtk can handle.
             vtkTemplateMacro6(vtkvmtkImageBoxPainterExecute, input, output,
                               (VTK_TT *)(inPtr), (VTK_TT *)(outPtr), 
relativeBoxExtent,
                               (VTK_TT)this->PaintValue);

             #else
              vtkTemplateMacro(
              vtkvmtkImageBoxPainterExecute(input, output,
                               (VTK_TT *)(inPtr), (VTK_TT *)(outPtr), 
relativeBoxExtent,
                               (VTK_TT)this->PaintValue));
             #endif
     default:
       vtkGenericWarningMacro("Execute: Unknown input ScalarType");
       return;
     }

[vmtk-users] missing include in vtkvmtkLevelSetSigmoidFilter.cxx

[Sebastian O. <seb...@gm...>]

Hi Again,

Can you check if #include "vtkDataArray.h" is needed in 
vtkvmtkLevelSetSigmoidFilter.cxx?
It is so in my setting (VS2010, VTK  5.10)

thanks
sebastian

[vmtk-users] change needed in VMTK CmakeLists.txt

[Sebastian O. <seb...@gm...>]

Hello Luca,

I would need the following lines in CmakeLists.txt uncommented in my 
project:

     EXPORT_LIBRARY_DEPENDENCIES(
       ${VMTK_BINARY_DIR}/VMTKLibraryDepends.cmake
     )

what do you think?

thank you!
sebastian

Re: [vmtk-users] vmtkbranchextractor

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

Hello Helena,
 currently splitting and grouping is limited to a tree-like network. In order
to apply it to a non-tree topology you'll have to "break" the loop somewhere.
It's a limitation that should be removed at some point, we just don't have
the resources for making it top priority right now.
Thanks

Luca


On May 21, 2013, at 1:53 PM, Helena Molina Abril wrote:

> Hi,
> 
> I would like to know whether there is a way of automatically split and 
> group centerlines
> (like vmtkbranchextractor does) in a non tree-like network.
> 
> Thanks,
> Helena.
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> 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_may
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] vmtkbranchextractor

[Helena M. A. <h.m...@sh...>]

Hi,

I would like to know whether there is a way of automatically split and 
group centerlines
(like vmtkbranchextractor does) in a non tree-like network.

Thanks,
Helena.

Re: [vmtk-users] ReadTecplot surface data into VMTK

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

Tecplot provides, downloadable from their website, a library called tecio.
It's limited to a header and a .so (I think .dll is available on 
windows...), and it's very...fortranish...
But it can read and write the binary tecplot format, and is available 
for most platforms in common use today.  Once you have the tecplot 
format in memory (as a 2d array of doubles), you can write out any 
format you please, including any of those available in vmtk.

Alternately, you can use swig to wrap a small C program in a python 
module, and then write a pypes/vmtkScripts compatible python script that 
reads the tecplot binary file into memory, populates the appropriate VTK 
data structure (vtkPolyData most likely), and then passes it down into 
the next step in the vmtk pipeline.
-rd

On 05/14/2013 09:29 AM, Yong He wrote:
> Hi Luca,
>
> To test the methodology, by changing the header as
>
> VARIABLES = X,Y,Z,WSS
> ZONE T="ew", N=388, E=564, ZONETYPE=FETriangal
>
> I could read the dat file correctly for a triangular surface mesh and 
> write as a vtp file in VMTK. The contour plot of unwrapped vessel can 
> be created in Matlab.
>
> Tecplot does not have the functionality of converting a quadrilateral 
> surface mesh to a triangular mesh. Tecplot does not export ascii data 
> in earlier version; only binary files are supported. Paraview can read 
> the binary output file from Tecplot, but I did not find a way of 
> exporting a file that is readable by VMTK. Do you know if I can do 
> something in Paraview or any other software? I attached one example 
> Tecplot binary plt file in case you need it. Thank you very much.
>
> Yong
>
>
>
> ------------------------------------------------------------------------------
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> _______________________________________________
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