vmtk-users

[vmtk-users] Problems with sigmoid mask

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

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.

Re: [vmtk-users] bifurcation plane

[qiang z. <zen...@ya...>]

Dear Luca,
Yeah, you are right when i am checking for what you said.
thank you.
YiQiang

--- 13年5月8日，周三, Luca Antiga <luc...@gm...> 写道：


发件人: Luca Antiga <luc...@gm...>
主题: Re: [vmtk-users] bifurcation plane
收件人: "qiang zeng" <zen...@ya...>
抄送: vmt...@li...
日期: 2013年5月8日,周三,下午4:02




Hi YiQiang,
 I don't think this is what happens: you only get one value per GroupId with the vmtkbranchgeometry script,
while with vmtkcenterlinegeometry you get a curvature value for each point on each centerline.
vmtkbranchgeometry looks at all centerlines tracts in a group and averages their curvature value.


Luca





On May 8, 2013, at 4:48 AM, qiang zeng wrote:






bifurcation plane is work well.
 
another problem, when I caculate the curvature using the following script "vmtkcenterlinegeometry -ifile foo_cl.vtp -smoothing 1 -ofile foo_clgm.vtp", I just get the one curvature value for every GroupIds. but in generally, the curve for every GroupIds has different points (point1, point2,...) and every point in curve has a curvature value respectively.
So how to understand this approach considering one curvature value as curvature value of entire GroupIds?
 
YiQiang  

--- 13年5月7日，周二, Luca Antiga <luc...@gm...> 写道：


发件人: Luca Antiga <luc...@gm...>
主题: Re: [vmtk-users] bifurcation plane
收件人: "qiang zeng" <zen...@ya...>
抄送: vmt...@li...
日期: 2013年5月7日,周二,下午2:40




Hi YiQiang,
 point1 and point2 are any two points on the plane away from the origin.
You could do
point1 = origin + upnormal
point2 = origin + normal x upnormal
where x indicates the cross product.


Luca

On 07/mag/2013, at 07:39, qiang zeng <zen...@ya...> wrote:








Usig the command line:
 
vmtkbranchextractor -ifile foo_cl.vtp -radiusarray@ MaximumInscribedSphereRadius --pipe
vmtkbifurcationreferencesystems -ofile foo_rs.dat
 
I get the one point and two vectors, then I fill the coordinate into the Paraview (point -> Origin, Normal -> Point1 and Upnormal -> Point2) ?

Best
YiQiang

--- 13年5月6日，周一, Luca Antiga <luc...@gm...> 写道：


发件人: Luca Antiga <luc...@gm...>
主题: Re: [vmtk-users] bifurcation plane
收件人: "qiang zeng" <zen...@ya...>
抄送: vmt...@li...
日期: 2013年5月6日,周一,下午8:54



Hi YiQiang, 
 the figure you attached was created in Paraview using the origin and normal of the plane
as computed with vmtk (you can output them in plain text using a .dat file format) to specify the plane 
in Paraview (Sources->Plane). It works well if the number of figures you create is small.


If you need to create the visualization automatically you'll need to write VTK code and use the
vtkPlaneSource class to create the plane.
The class: http://www.vtk.org/doc/nightly/html/classvtkPlaneSource.html
Examples: 
http://www.vtk.org/doc/nightly/html/c2_vtk_e_5.html#c2_vtk_e_vtkPlaneSource
http://www.vtk.org/doc/nightly/html/c2_vtk_t_15.html#c2_vtk_t_vtkPlaneSource


Best,




Luca





On May 6, 2013, at 9:40 AM, qiang zeng wrote:






Hi all,
When I am using VMTK, I want to display the bifurcation plane (the view is like aneurysm bifurcation plane, as an attachment "bifurcation plane.jpg").
Does anyone know a way to do this?
Best,
YiQiang<bifurcation plane.jpg>------------------------------------------------------------------------------
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Re: [vmtk-users] bifurcation plane

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

Hi YiQiang,
 I don't think this is what happens: you only get one value per GroupId with the vmtkbranchgeometry script,
while with vmtkcenterlinegeometry you get a curvature value for each point on each centerline.
vmtkbranchgeometry looks at all centerlines tracts in a group and averages their curvature value.

Luca


On May 8, 2013, at 4:48 AM, qiang zeng wrote:

> bifurcation plane is work well.
>  
> another problem, when I caculate the curvature using the following script "vmtkcenterlinegeometry -ifile foo_cl.vtp -smoothing 1 -ofile foo_clgm.vtp", I just get the one curvature value for every GroupIds. but in generally, the curve for every GroupIds has different points (point1, point2,...) and every point in curve has a curvature value respectively.
> So how to understand this approach considering one curvature value as curvature value of entire GroupIds?
>  
> YiQiang  
> --- 13年5月7日，周二, Luca Antiga <luc...@gm...> 写道：
> 
> 发件人: Luca Antiga <luc...@gm...>
> 主题: Re: [vmtk-users] bifurcation plane
> 收件人: "qiang zeng" <zen...@ya...>
> 抄送: vmt...@li...
> 日期: 2013年5月7日,周二,下午2:40
> 
> Hi YiQiang,
>  point1 and point2 are any two points on the plane away from the origin.
> You could do
> point1 = origin + upnormal
> point2 = origin + normal x upnormal
> where x indicates the cross product.
> 
> Luca
> 
> On 07/mag/2013, at 07:39, qiang zeng <zen...@ya...> wrote:
> 
>> Usig the command line:
>>  
>> vmtkbranchextractor -ifile foo_cl.vtp -radiusarray@ MaximumInscribedSphereRadius --pipe
>> vmtkbifurcationreferencesystems -ofile foo_rs.dat
>>  
>> I get the one point and two vectors, then I fill the coordinate into the Paraview (point -> Origin, Normal -> Point1 and Upnormal -> Point2) ?
>> Best
>> YiQiang
>> 
>> --- 13年5月6日，周一, Luca Antiga <luc...@gm...> 写道：
>> 
>> 发件人: Luca Antiga <luc...@gm...>
>> 主题: Re: [vmtk-users] bifurcation plane
>> 收件人: "qiang zeng" <zen...@ya...>
>> 抄送: vmt...@li...
>> 日期: 2013年5月6日,周一,下午8:54
>> 
>> Hi YiQiang,
>>  the figure you attached was created in Paraview using the origin and normal of the plane
>> as computed with vmtk (you can output them in plain text using a .dat file format) to specify the plane 
>> in Paraview (Sources->Plane). It works well if the number of figures you create is small.
>> 
>> If you need to create the visualization automatically you'll need to write VTK code and use the
>> vtkPlaneSource class to create the plane.
>> The class: http://www.vtk.org/doc/nightly/html/classvtkPlaneSource.html
>> Examples: 
>> http://www.vtk.org/doc/nightly/html/c2_vtk_e_5.html#c2_vtk_e_vtkPlaneSource
>> http://www.vtk.org/doc/nightly/html/c2_vtk_t_15.html#c2_vtk_t_vtkPlaneSource
>> 
>> Best,
>> 
>> Luca
>> 
>> 
>> On May 6, 2013, at 9:40 AM, qiang zeng wrote:
>> 
>>> Hi all,
>>> When I am using VMTK, I want to display the bifurcation plane (the view is like aneurysm bifurcation plane, as an attachment "bifurcation plane.jpg").
>>> Does anyone know a way to do this?
>>> Best,
>>> YiQiang
>>> <bifurcation plane.jpg>------------------------------------------------------------------------------
>>> 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] Error with tetrahedralization

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

Hi Vincent,
 the boundary layer code in vmtk is being revamped as soon as we have it fully tested.
The code that is right now in vmtk suffers from self-intersections in a few regions, which 
prevents the tetrahedral mesh generator to succeed.
What you can do at the moment is:
a) avoid using boundary layers
b) specify a -thicknessfactor (in the vmtkmeshgenerator script) that is lower than the default (which is 0.25)
Hope this helps

Luca


On May 7, 2013, at 7:56 PM, Vincent Ip wrote:

> Dear VMTK users,
> 
> I encountered a problem when I'm trying to generate a mesh from VMTK and here I attached the screen capture of the response from VMTK:
> 
> <Screen Shot 2013-05-07 at 10.53.13 AM.png>
> 
> And I've attached the surface model for your reference.
> Any idea of what's going on?
> 
> Thanks,
> Vincent
> 
> <model_sm_cl_ct_sb.vtp>------------------------------------------------------------------------------
> 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_______________________________________________
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> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] bifurcation plane

[qiang z. <zen...@ya...>]

bifurcation plane is work well.
 
another problem, when I caculate the curvature using the following script "vmtkcenterlinegeometry -ifile foo_cl.vtp -smoothing 1 -ofile foo_clgm.vtp", I just get the one curvature value for every GroupIds. but in generally, the curve for every GroupIds has different points (point1, point2,...) and every point in curve has a curvature value respectively.
So how to understand this approach considering one curvature value as curvature value of entire GroupIds?
 
YiQiang  

--- 13年5月7日，周二, Luca Antiga <luc...@gm...> 写道：


发件人: Luca Antiga <luc...@gm...>
主题: Re: [vmtk-users] bifurcation plane
收件人: "qiang zeng" <zen...@ya...>
抄送: vmt...@li...
日期: 2013年5月7日,周二,下午2:40




Hi YiQiang,
 point1 and point2 are any two points on the plane away from the origin.
You could do
point1 = origin + upnormal
point2 = origin + normal x upnormal
where x indicates the cross product.


Luca

On 07/mag/2013, at 07:39, qiang zeng <zen...@ya...> wrote:








Usig the command line:
 
vmtkbranchextractor -ifile foo_cl.vtp -radiusarray@ MaximumInscribedSphereRadius --pipe
vmtkbifurcationreferencesystems -ofile foo_rs.dat
 
I get the one point and two vectors, then I fill the coordinate into the Paraview (point -> Origin, Normal -> Point1 and Upnormal -> Point2) ?

Best
YiQiang

--- 13年5月6日，周一, Luca Antiga <luc...@gm...> 写道：


发件人: Luca Antiga <luc...@gm...>
主题: Re: [vmtk-users] bifurcation plane
收件人: "qiang zeng" <zen...@ya...>
抄送: vmt...@li...
日期: 2013年5月6日,周一,下午8:54



Hi YiQiang, 
 the figure you attached was created in Paraview using the origin and normal of the plane
as computed with vmtk (you can output them in plain text using a .dat file format) to specify the plane 
in Paraview (Sources->Plane). It works well if the number of figures you create is small.


If you need to create the visualization automatically you'll need to write VTK code and use the
vtkPlaneSource class to create the plane.
The class: http://www.vtk.org/doc/nightly/html/classvtkPlaneSource.html
Examples: 
http://www.vtk.org/doc/nightly/html/c2_vtk_e_5.html#c2_vtk_e_vtkPlaneSource
http://www.vtk.org/doc/nightly/html/c2_vtk_t_15.html#c2_vtk_t_vtkPlaneSource


Best,




Luca





On May 6, 2013, at 9:40 AM, qiang zeng wrote:






Hi all,
When I am using VMTK, I want to display the bifurcation plane (the view is like aneurysm bifurcation plane, as an attachment "bifurcation plane.jpg").
Does anyone know a way to do this?
Best,
YiQiang<bifurcation plane.jpg>------------------------------------------------------------------------------
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

[vmtk-users] Error with tetrahedralization

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

Dear VMTK users,

I encountered a problem when I'm trying to generate a mesh from VMTK and here I attached the screen capture of the response from VMTK:

Re: [vmtk-users] vmtkApps?

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

Hi Luca,

Thanks for the suggestion.  By looking through the file, I realized what my
mistake was.  The script requires the centerline files to be in their own
folder in the specified directory path, which in this case is C:\Program
Files (x86)\vmtk\Install\bin\id1, but I had them in C:\Program Files
(x86)\vmtk\Install\bin.


On Mon, May 6, 2013 at 11:36 PM, Luca Antiga <luc...@gm...> wrote:

> Hi Evan,
>  really hard to infer anything. Do you have any indication of where it's
> crashing? Like after centerlines, or before...
> You could place a few print statements along the python file you're
> running, just to have an idea of where it's failing.
>
> Luca
>
> On 07/mag/2013, at 00:47, Evan Kao <to...@gm...> wrote:
>
> Hi Luca,
>
> The function seems to import the modules fine for now, but for whatever
> reason, it keeps crashing when I actually try to use it.  I am only
> following the tutorial (pretty much just copying and pasting commands), so
> this might just be a problem with using Win XP 64-bit.
>
> The command line interface output gives:
> USAGE:
>       ./patchandinterpolatecenterlines.py inputfilesDirectory caseID
> aneurysmType
>
> Inputfiles Directory    C:\Program Files (x86)\vmtk\Install\bin
> case ID            id1
> Aneurysm Type        lateral
>
> Then a vtkOutputWindow pops up with an error, which is shortly followed by
> a python crash message.  Unfortunately, I can't seem to scroll through the
> vtkOutputWindow because it freezes up, so the error information is limited
> only to the screenshot I took (attached).  Is there anything you can glean
> from this?
>
> Thanks,
> Evan Kao
>
>
> On Mon, May 6, 2013 at 2:02 PM, Evan Kao <to...@gm...> wrote:
>
>> Hi Luca,
>>
>> I added the environmental variables, and got the error:
>>
>> File "patandinterpcl.py", line 369, in <module>
>>    inputfiledirectory = sys.argv[1]
>> IndexError: list index out of range
>>
>> Since I didn't enter any input arguments, I'm guessing this is supposed
>> to happen.  I'll try to use it with some files now.
>>
>> Thanks,
>> Evan Kao
>>
>>
>> On Mon, May 6, 2013 at 1:36 PM, Luca Antiga <luc...@or...>wrote:
>>
>>> Hi Evan,
>>>  ok, I see. Try with the following and please report the eventual error
>>> you get.
>>>
>>> PATH
>>>   C:\"Program Files (x86)"\vmtk\Install\bin;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vmtk;
>>>   C:\"Program Files (x86)"\vmtk\Install\bin\Python;
>>> PYTHONPATH
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vmtk;
>>>   C:\"Program Files (x86)"\vmtk\Install\bin\Python;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;
>>>
>>> Luca
>>>
>>>
>>> On May 6, 2013, at 9:28 PM, Evan Kao wrote:
>>>
>>> Hello Luca,
>>>
>>> I tried the batch file, but it didn't work.  I think "set" in Win XP
>>> only allows temporary changes to environmental variables.  I can however
>>> use My Computer > System Properties > Advanced > Environmental Variables to
>>> modify PATH permanently and create a new variable PYTHONPATH.  But some of
>>> the directories you gave didn't match up to what was installed.  Here are
>>> the list of directories in vmtk on my machine:
>>>
>>> C:\Program Files (x86)\vmtk\icon
>>> C:\Program Files (x86)\vmtk\Install
>>> C:\Program Files (x86)\vmtk\Install\bin
>>> C:\Program Files (x86)\vmtk\Install\lib
>>> C:\Program Files (x86)\vmtk\Install\bin\Python
>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk
>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\gtk
>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt
>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt4
>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\test
>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\tk
>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\util
>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\wx
>>> C:\Program Files (x86)\vmtk\Install\lib\vmtk
>>> C:\Program Files (x86)\vmtk\Install\lib\vtk-5.8
>>> C:\Program Files (x86)\vmtk\Install\lib\vmtk\vmtk
>>>
>>> I can make guesses on a few, but not all (like site-packages or
>>> InsightToolkit).
>>>
>>> Thanks,
>>> Evan Kao
>>>
>>>
>>> On Mon, May 6, 2013 at 5:44 AM, Luca Antiga <luc...@or...>wrote:
>>>
>>>> Hi Evan,
>>>>  it's an environment variables issue and yes, it's currently not nice
>>>> to run vmtkApps in Windows, sorry about this.
>>>>
>>>> What you can do is create a patchanterinterpolatecenterlines.bat file
>>>> (the name is irrelevant, the important is the .bat extension) with the
>>>> following content:
>>>>
>>>> set VMTK_DIR=C:\"Program Files (x86)"\vmtk
>>>> set
>>>> PATH=%VMTK_DIR%bin;%VMTK_DIR%lib\InsightToolkit;%VMTK_DIR%lib\Python;%PATH%
>>>> set
>>>> PYTHONPATH=%VMTK_DIR%lib\site-packages;%VMTK_DIR%lib\vtk-5.6;%VMTK_DIR%lib\vmtk
>>>> cd %VMTK_DIR%
>>>> python patchanterinterpolatecenterlines.py
>>>>
>>>> Then double click on the .bat file. Let me know if this works or what
>>>> error messages it produces.
>>>>
>>>> We'll have to think about a nicer solution than this in the future.
>>>>
>>>>
>>>> Luca
>>>>
>>>>
>>>> On May 2, 2013, at 10:04 PM, Evan Kao wrote:
>>>>
>>>> Hi Luca,
>>>>
>>>> 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?
>>>>>
>>>>
>>>> Both vmtk and Python are in their default directories (Python was
>>>> installed through vmtk):
>>>>
>>>> C:\Program Files (x86)\vmtk
>>>> C:\Python27
>>>>
>>>> It seems I was able to open patchanterinterpolatecenterlin
>>>> es.py in the command line interface, but it doesn't see the vmtkmodules ("Import Error: no module named vtk").  How can I remedy this?
>>>>
>>>> Thanks,
>>>> Evan Kao
>>>>
>>>>
>>>> On Wed, May 1, 2013 at 5:30 AM, Luca Antiga <luc...@or...>wrote:
>>>>
>>>>> 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
>>>>>>> >
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> > 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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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://p.sf.net/sfu/appdyn_d2d_ap2_______________________________________________
>>>>
>>>> vmtk-users mailing list
>>>> vmt...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>>
>>>>
>>>>
>>>
>>>
>>
> <vtkoutputwindowerror.JPG>
>
>
> ------------------------------------------------------------------------------
> 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
>
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>

Re: [vmtk-users] bifurcation plane

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

Hi YiQiang,
 point1 and point2 are any two points on the plane away from the origin.
You could do
point1 = origin + upnormal
point2 = origin + normal x upnormal
where x indicates the cross product.

Luca

On 07/mag/2013, at 07:39, qiang zeng <zen...@ya...> wrote:

> 
> Usig the command line:
>  
> vmtkbranchextractor -ifile foo_cl.vtp -radiusarray@ MaximumInscribedSphereRadius --pipe
> vmtkbifurcationreferencesystems -ofile foo_rs.dat
>  
> I get the one point and two vectors, then I fill the coordinate into the Paraview (point -> Origin, Normal -> Point1 and Upnormal -> Point2) ?
> Best
> YiQiang
> 
> --- 13年5月6日，周一, Luca Antiga <luc...@gm...> 写道：
> 
> 发件人: Luca Antiga <luc...@gm...>
> 主题: Re: [vmtk-users] bifurcation plane
> 收件人: "qiang zeng" <zen...@ya...>
> 抄送: vmt...@li...
> 日期: 2013年5月6日,周一,下午8:54
> 
> Hi YiQiang,
>  the figure you attached was created in Paraview using the origin and normal of the plane
> as computed with vmtk (you can output them in plain text using a .dat file format) to specify the plane 
> in Paraview (Sources->Plane). It works well if the number of figures you create is small.
> 
> If you need to create the visualization automatically you'll need to write VTK code and use the
> vtkPlaneSource class to create the plane.
> The class: http://www.vtk.org/doc/nightly/html/classvtkPlaneSource.html
> Examples: 
> http://www.vtk.org/doc/nightly/html/c2_vtk_e_5.html#c2_vtk_e_vtkPlaneSource
> http://www.vtk.org/doc/nightly/html/c2_vtk_t_15.html#c2_vtk_t_vtkPlaneSource
> 
> Best,
> 
> Luca
> 
> 
> On May 6, 2013, at 9:40 AM, qiang zeng wrote:
> 
>> 
>> Hi all,
>> When I am using VMTK, I want to display the bifurcation plane (the view is like aneurysm bifurcation plane, as an attachment "bifurcation plane.jpg").
>> Does anyone know a way to do this?
>> Best,
>> YiQiang
>> <bifurcation plane.jpg>------------------------------------------------------------------------------
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> 

Re: [vmtk-users] vmtkApps?

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

Hi Evan,
 really hard to infer anything. Do you have any indication of where it's crashing? Like after centerlines, or before...
You could place a few print statements along the python file you're running, just to have an idea of where it's failing. 

Luca

On 07/mag/2013, at 00:47, Evan Kao <to...@gm...> wrote:

> Hi Luca,
> 
> The function seems to import the modules fine for now, but for whatever reason, it keeps crashing when I actually try to use it.  I am only following the tutorial (pretty much just copying and pasting commands), so this might just be a problem with using Win XP 64-bit.
> 
> The command line interface output gives:
> USAGE:
>       ./patchandinterpolatecenterlines.py inputfilesDirectory caseID aneurysmType
> 
> Inputfiles Directory    C:\Program Files (x86)\vmtk\Install\bin
> case ID            id1
> Aneurysm Type        lateral
> 
> Then a vtkOutputWindow pops up with an error, which is shortly followed by a python crash message.  Unfortunately, I can't seem to scroll through the vtkOutputWindow because it freezes up, so the error information is limited only to the screenshot I took (attached).  Is there anything you can glean from this?
> 
> Thanks,
> Evan Kao
> 
> 
> On Mon, May 6, 2013 at 2:02 PM, Evan Kao <to...@gm...> wrote:
>> Hi Luca,
>> 
>> I added the environmental variables, and got the error:
>> 
>> File "patandinterpcl.py", line 369, in <module>
>>    inputfiledirectory = sys.argv[1]
>> IndexError: list index out of range
>> 
>> Since I didn't enter any input arguments, I'm guessing this is supposed to happen.  I'll try to use it with some files now.
>> 
>> Thanks,
>> Evan Kao
>> 
>> 
>> On Mon, May 6, 2013 at 1:36 PM, Luca Antiga <luc...@or...> wrote:
>>> Hi Evan,
>>>  ok, I see. Try with the following and please report the eventual error you get.
>>> 
>>> PATH
>>>   C:\"Program Files (x86)"\vmtk\Install\bin;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vmtk;
>>>   C:\"Program Files (x86)"\vmtk\Install\bin\Python;
>>> PYTHONPATH
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vmtk;
>>>   C:\"Program Files (x86)"\vmtk\Install\bin\Python;
>>>   C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;
>>> 
>>> Luca
>>> 
>>> 
>>> On May 6, 2013, at 9:28 PM, Evan Kao wrote:
>>> 
>>>> Hello Luca, 
>>>> 
>>>> I tried the batch file, but it didn't work.  I think "set" in Win XP only allows temporary changes to environmental variables.  I can however use My Computer > System Properties > Advanced > Environmental Variables to modify PATH permanently and create a new variable PYTHONPATH.  But some of the directories you gave didn't match up to what was installed.  Here are the list of directories in vmtk on my machine:
>>>> 
>>>> C:\Program Files (x86)\vmtk\icon
>>>> C:\Program Files (x86)\vmtk\Install
>>>> C:\Program Files (x86)\vmtk\Install\bin
>>>> C:\Program Files (x86)\vmtk\Install\lib
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\gtk
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt4
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\test
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\tk
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\util
>>>> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\wx
>>>> C:\Program Files (x86)\vmtk\Install\lib\vmtk
>>>> C:\Program Files (x86)\vmtk\Install\lib\vtk-5.8
>>>> C:\Program Files (x86)\vmtk\Install\lib\vmtk\vmtk
>>>> 
>>>> I can make guesses on a few, but not all (like site-packages or InsightToolkit).
>>>> 
>>>> Thanks,
>>>> Evan Kao
>>>> 
>>>> 
>>>> On Mon, May 6, 2013 at 5:44 AM, Luca Antiga <luc...@or...> wrote:
>>>>> Hi Evan,
>>>>>  it's an environment variables issue and yes, it's currently not nice to run vmtkApps in Windows, sorry about this.
>>>>> 
>>>>> What you can do is create a patchanterinterpolatecenterlines.bat file (the name is irrelevant, the important is the .bat extension) with the following content:
>>>>> 
>>>>> set VMTK_DIR=C:\"Program Files (x86)"\vmtk
>>>>> set PATH=%VMTK_DIR%bin;%VMTK_DIR%lib\InsightToolkit;%VMTK_DIR%lib\Python;%PATH%
>>>>> set PYTHONPATH=%VMTK_DIR%lib\site-packages;%VMTK_DIR%lib\vtk-5.6;%VMTK_DIR%lib\vmtk
>>>>> cd %VMTK_DIR%
>>>>> python patchanterinterpolatecenterlines.py
>>>>> 
>>>>> Then double click on the .bat file. Let me know if this works or what error messages it produces.
>>>>> 
>>>>> We'll have to think about a nicer solution than this in the future.
>>>>> 
>>>>> 
>>>>> Luca
>>>>> 
>>>>> 
>>>>> On May 2, 2013, at 10:04 PM, Evan Kao wrote:
>>>>> 
>>>>>> Hi Luca, 
>>>>>> 
>>>>>>> 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?
>>>>>> 
>>>>>> Both vmtk and Python are in their default directories (Python was installed through vmtk):
>>>>>> 
>>>>>> C:\Program Files (x86)\vmtk
>>>>>> C:\Python27
>>>>>> 
>>>>>> It seems I was able to open patchanterinterpolatecenterlin
>>>>>> es.py in the command line interface, but it doesn't see the vmtk modules ("Import Error: no module named vtk").  How can I remedy this?
>>>>>> 
>>>>>> Thanks,
>>>>>> Evan Kao
>>>>>> 
>>>>>> 
>>>>>> On Wed, May 1, 2013 at 5:30 AM, Luca Antiga <luc...@or...> wrote:
>>>>>>> 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
>>>>>>>>>> > ------------------------------------------------------------------------------
>>>>>>>>>> > 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
>>>>>> 
>>>>>> ------------------------------------------------------------------------------
>>>>>> 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://p.sf.net/sfu/appdyn_d2d_ap2_______________________________________________
>>>>>> 
>>>>>> vmtk-users mailing list
>>>>>> vmt...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> <vtkoutputwindowerror.JPG>
> ------------------------------------------------------------------------------
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> leaders in the field. The early access version is available now. 
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> _______________________________________________
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Re: [vmtk-users] vmtkApps?

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

Hi Luca,

I added the environmental variables, and got the error:

File "patandinterpcl.py", line 369, in <module>
   inputfiledirectory = sys.argv[1]
IndexError: list index out of range

Since I didn't enter any input arguments, I'm guessing this is supposed to
happen.  I'll try to use it with some files now.

Thanks,
Evan Kao


On Mon, May 6, 2013 at 1:36 PM, Luca Antiga <luc...@or...> wrote:

> Hi Evan,
>  ok, I see. Try with the following and please report the eventual error
> you get.
>
> PATH
>   C:\"Program Files (x86)"\vmtk\Install\bin;
>   C:\"Program Files (x86)"\vmtk\Install\lib;
>   C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;
>   C:\"Program Files (x86)"\vmtk\Install\lib\vmtk;
>   C:\"Program Files (x86)"\vmtk\Install\bin\Python;
> PYTHONPATH
>   C:\"Program Files (x86)"\vmtk\Install\lib\vmtk;
>   C:\"Program Files (x86)"\vmtk\Install\bin\Python;
>   C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;
>
> Luca
>
>
> On May 6, 2013, at 9:28 PM, Evan Kao wrote:
>
> Hello Luca,
>
> I tried the batch file, but it didn't work.  I think "set" in Win XP only
> allows temporary changes to environmental variables.  I can however use My
> Computer > System Properties > Advanced > Environmental Variables to modify
> PATH permanently and create a new variable PYTHONPATH.  But some of the
> directories you gave didn't match up to what was installed.  Here are the
> list of directories in vmtk on my machine:
>
> C:\Program Files (x86)\vmtk\icon
> C:\Program Files (x86)\vmtk\Install
> C:\Program Files (x86)\vmtk\Install\bin
> C:\Program Files (x86)\vmtk\Install\lib
> C:\Program Files (x86)\vmtk\Install\bin\Python
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\gtk
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt4
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\test
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\tk
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\util
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\wx
> C:\Program Files (x86)\vmtk\Install\lib\vmtk
> C:\Program Files (x86)\vmtk\Install\lib\vtk-5.8
> C:\Program Files (x86)\vmtk\Install\lib\vmtk\vmtk
>
> I can make guesses on a few, but not all (like site-packages or
> InsightToolkit).
>
> Thanks,
> Evan Kao
>
>
> On Mon, May 6, 2013 at 5:44 AM, Luca Antiga <luc...@or...>wrote:
>
>> Hi Evan,
>>  it's an environment variables issue and yes, it's currently not nice to
>> run vmtkApps in Windows, sorry about this.
>>
>> What you can do is create a patchanterinterpolatecenterlines.bat file
>> (the name is irrelevant, the important is the .bat extension) with the
>> following content:
>>
>> set VMTK_DIR=C:\"Program Files (x86)"\vmtk
>> set
>> PATH=%VMTK_DIR%bin;%VMTK_DIR%lib\InsightToolkit;%VMTK_DIR%lib\Python;%PATH%
>> set
>> PYTHONPATH=%VMTK_DIR%lib\site-packages;%VMTK_DIR%lib\vtk-5.6;%VMTK_DIR%lib\vmtk
>> cd %VMTK_DIR%
>> python patchanterinterpolatecenterlines.py
>>
>> Then double click on the .bat file. Let me know if this works or what
>> error messages it produces.
>>
>> We'll have to think about a nicer solution than this in the future.
>>
>>
>> Luca
>>
>>
>> On May 2, 2013, at 10:04 PM, Evan Kao wrote:
>>
>> Hi Luca,
>>
>> 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?
>>>
>>
>> Both vmtk and Python are in their default directories (Python was
>> installed through vmtk):
>>
>> C:\Program Files (x86)\vmtk
>> C:\Python27
>>
>> It seems I was able to open patchanterinterpolatecenterlin
>> es.py in the command line interface, but it doesn't see the vmtk modules
>> ("Import Error: no module named vtk").  How can I remedy this?
>>
>> Thanks,
>> Evan Kao
>>
>>
>> On Wed, May 1, 2013 at 5:30 AM, Luca Antiga <luc...@or...>wrote:
>>
>>> 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
>>>>> >
>>>>> ------------------------------------------------------------------------------
>>>>> > 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
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>> ------------------------------------------------------------------------------
>> 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://p.sf.net/sfu/appdyn_d2d_ap2_______________________________________________
>>
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>>
>>
>
>

Re: [vmtk-users] vmtkApps?

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

Hi Evan,
 ok, I see. Try with the following and please report the eventual error you get.

PATH
  C:\"Program Files (x86)"\vmtk\Install\bin;
  C:\"Program Files (x86)"\vmtk\Install\lib;
  C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;
  C:\"Program Files (x86)"\vmtk\Install\lib\vmtk;
  C:\"Program Files (x86)"\vmtk\Install\bin\Python;
PYTHONPATH
  C:\"Program Files (x86)"\vmtk\Install\lib\vmtk;
  C:\"Program Files (x86)"\vmtk\Install\bin\Python;
  C:\"Program Files (x86)"\vmtk\Install\lib\vtk-5.8;

Luca


On May 6, 2013, at 9:28 PM, Evan Kao wrote:

> Hello Luca, 
> 
> I tried the batch file, but it didn't work.  I think "set" in Win XP only allows temporary changes to environmental variables.  I can however use My Computer > System Properties > Advanced > Environmental Variables to modify PATH permanently and create a new variable PYTHONPATH.  But some of the directories you gave didn't match up to what was installed.  Here are the list of directories in vmtk on my machine:
> 
> C:\Program Files (x86)\vmtk\icon
> C:\Program Files (x86)\vmtk\Install
> C:\Program Files (x86)\vmtk\Install\bin
> C:\Program Files (x86)\vmtk\Install\lib
> C:\Program Files (x86)\vmtk\Install\bin\Python
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\gtk
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt4
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\test
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\tk
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\util
> C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\wx
> C:\Program Files (x86)\vmtk\Install\lib\vmtk
> C:\Program Files (x86)\vmtk\Install\lib\vtk-5.8
> C:\Program Files (x86)\vmtk\Install\lib\vmtk\vmtk
> 
> I can make guesses on a few, but not all (like site-packages or InsightToolkit).
> 
> Thanks,
> Evan Kao
> 
> 
> On Mon, May 6, 2013 at 5:44 AM, Luca Antiga <luc...@or...> wrote:
> Hi Evan,
>  it's an environment variables issue and yes, it's currently not nice to run vmtkApps in Windows, sorry about this.
> 
> What you can do is create a patchanterinterpolatecenterlines.bat file (the name is irrelevant, the important is the .bat extension) with the following content:
> 
> set VMTK_DIR=C:\"Program Files (x86)"\vmtk
> set PATH=%VMTK_DIR%bin;%VMTK_DIR%lib\InsightToolkit;%VMTK_DIR%lib\Python;%PATH%
> set PYTHONPATH=%VMTK_DIR%lib\site-packages;%VMTK_DIR%lib\vtk-5.6;%VMTK_DIR%lib\vmtk
> cd %VMTK_DIR%
> python patchanterinterpolatecenterlines.py
> 
> Then double click on the .bat file. Let me know if this works or what error messages it produces.
> 
> We'll have to think about a nicer solution than this in the future.
> 
> 
> Luca
> 
> 
> On May 2, 2013, at 10:04 PM, Evan Kao wrote:
> 
>> Hi Luca, 
>> 
>> 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?
>> 
>> Both vmtk and Python are in their default directories (Python was installed through vmtk):
>> 
>> C:\Program Files (x86)\vmtk
>> C:\Python27
>> 
>> It seems I was able to open patchanterinterpolatecenterlin
>> es.py in the command line interface, but it doesn't see the vmtk modules ("Import Error: no module named vtk").  How can I remedy this?
>> 
>> Thanks,
>> Evan Kao
>> 
>> 
>> On Wed, May 1, 2013 at 5:30 AM, Luca Antiga <luc...@or...> wrote:
>> 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
>>> > ------------------------------------------------------------------------------
>>> > 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
>>> 
>>> 
>>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> 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://p.sf.net/sfu/appdyn_d2d_ap2_______________________________________________
>> 
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> 

Re: [vmtk-users] vmtkApps?

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

Hello Luca,

I tried the batch file, but it didn't work.  I think "set" in Win XP only
allows temporary changes to environmental variables.  I can however use My
Computer > System Properties > Advanced > Environmental Variables to modify
PATH permanently and create a new variable PYTHONPATH.  But some of the
directories you gave didn't match up to what was installed.  Here are the
list of directories in vmtk on my machine:

C:\Program Files (x86)\vmtk\icon
C:\Program Files (x86)\vmtk\Install
C:\Program Files (x86)\vmtk\Install\bin
C:\Program Files (x86)\vmtk\Install\lib
C:\Program Files (x86)\vmtk\Install\bin\Python
C:\Program Files (x86)\vmtk\Install\bin\Python\vtk
C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\gtk
C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt
C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\qt4
C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\test
C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\tk
C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\util
C:\Program Files (x86)\vmtk\Install\bin\Python\vtk\wx
C:\Program Files (x86)\vmtk\Install\lib\vmtk
C:\Program Files (x86)\vmtk\Install\lib\vtk-5.8
C:\Program Files (x86)\vmtk\Install\lib\vmtk\vmtk

I can make guesses on a few, but not all (like site-packages or
InsightToolkit).

Thanks,
Evan Kao


On Mon, May 6, 2013 at 5:44 AM, Luca Antiga <luc...@or...> wrote:

> Hi Evan,
>  it's an environment variables issue and yes, it's currently not nice to
> run vmtkApps in Windows, sorry about this.
>
> What you can do is create a patchanterinterpolatecenterlines.bat file (the
> name is irrelevant, the important is the .bat extension) with the following
> content:
>
> set VMTK_DIR=C:\"Program Files (x86)"\vmtk
> set
> PATH=%VMTK_DIR%bin;%VMTK_DIR%lib\InsightToolkit;%VMTK_DIR%lib\Python;%PATH%
> set
> PYTHONPATH=%VMTK_DIR%lib\site-packages;%VMTK_DIR%lib\vtk-5.6;%VMTK_DIR%lib\vmtk
> cd %VMTK_DIR%
> python patchanterinterpolatecenterlines.py
>
> Then double click on the .bat file. Let me know if this works or what
> error messages it produces.
>
> We'll have to think about a nicer solution than this in the future.
>
>
> Luca
>
>
> On May 2, 2013, at 10:04 PM, Evan Kao wrote:
>
> Hi Luca,
>
> 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?
>>
>
> Both vmtk and Python are in their default directories (Python was
> installed through vmtk):
>
> C:\Program Files (x86)\vmtk
> C:\Python27
>
> It seems I was able to open patchanterinterpolatecenterlin
> es.py in the command line interface, but it doesn't see the vmtk modules
> ("Import Error: no module named vtk").  How can I remedy this?
>
> Thanks,
> Evan Kao
>
>
> On Wed, May 1, 2013 at 5:30 AM, Luca Antiga <luc...@or...>wrote:
>
>> 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
>>>> >
>>>> ------------------------------------------------------------------------------
>>>> > 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
>>>>
>>>>
>>>
>>
>>
>
> ------------------------------------------------------------------------------
> 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://p.sf.net/sfu/appdyn_d2d_ap2_______________________________________________
>
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>
>

Re: [vmtk-users] 2 questions on segmentation

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

Hi Luca,

Thanks alot, that seemed to do the trick.

Cheers
Vikram.



On Mon, May 6, 2013 at 2:24 PM, Luca Antiga <luc...@or...> wrote:

> Hi Vikram,
>  I'm suggesting to pipe the vmtksurfacetriangle script right after
> vmtkmarchingcubes
>
> vmtkmarchingcubes -ifile some_file.vti --pipe vmtksurfacetriangle -ofile
> thesurface.vtp
>
> and see if this works.
>
> Luca
>
>
> On May 6, 2013, at 3:20 PM, Vikram Mehta wrote:
>
> Hi Luca,
>
> Yes these bumps/holes occured when I tried a smoothing script straight
> after marching cubes. It occurs at 3-4 spots on the reconstruction.
>
> Are you suggesting increasing the number of surface triangles ?
>
> Best
> Vikram.
>
>
>
> On Mon, May 6, 2013 at 2:13 PM, Luca Antiga <luc...@or...>wrote:
>
>> Hi Virkam,
>>  you haven't provided a lot of info on this, but this looks like a VTK
>> Marching Cubes issue that arises sometimes.
>> Try to use vmtksurfacetriangle right after vmtkmarchingcubes (and before
>> any other smoothing or other scripts).
>> Best,
>>
>> Luca
>>
>>
>> On May 6, 2013, at 3:09 PM, Vikram Mehta wrote:
>>
>> Thank you for your suggestions.
>>
>> I came across a new problem today - would you happen to know what causes
>> this ? And how I can repair my reconstruction ?
>>
>> Please find an image attached of the problem.
>>
>> Many thanks in advance
>> Vikram.
>>
>>
>>
>> On Thu, May 2, 2013 at 10:18 AM, Arjan Geers <aj...@gm...> wrote:
>>
>>> 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
>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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
>>>>
>>>>
>>>
>> <Screen Shot 2013-05-06 at 14.06.02.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_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>>
>>
>
>

Re: [vmtk-users] 2 questions on segmentation

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

Hi Vikram,
 I'm suggesting to pipe the vmtksurfacetriangle script right after vmtkmarchingcubes

vmtkmarchingcubes -ifile some_file.vti --pipe vmtksurfacetriangle -ofile thesurface.vtp

and see if this works.

Luca


On May 6, 2013, at 3:20 PM, Vikram Mehta wrote:

> Hi Luca,
> 
> Yes these bumps/holes occured when I tried a smoothing script straight after marching cubes. It occurs at 3-4 spots on the reconstruction.
> 
> Are you suggesting increasing the number of surface triangles ?
> 
> Best
> Vikram.
> 
> 
> 
> On Mon, May 6, 2013 at 2:13 PM, Luca Antiga <luc...@or...> wrote:
> Hi Virkam,
>  you haven't provided a lot of info on this, but this looks like a VTK Marching Cubes issue that arises sometimes.
> Try to use vmtksurfacetriangle right after vmtkmarchingcubes (and before any other smoothing or other scripts).
> Best,
> 
> Luca
> 
> 
> On May 6, 2013, at 3:09 PM, Vikram Mehta wrote:
> 
>> Thank you for your suggestions.
>> 
>> I came across a new problem today - would you happen to know what causes this ? And how I can repair my reconstruction ? 
>> 
>> Please find an image attached of the problem.
>> 
>> Many thanks in advance
>> Vikram.
>> 
>> 
>> 
>> On Thu, May 2, 2013 at 10:18 AM, Arjan Geers <aj...@gm...> wrote:
>> 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
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> 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
>> 
>> 
>> 
>> <Screen Shot 2013-05-06 at 14.06.02.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_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> 

Re: [vmtk-users] 2 questions on segmentation

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

Hi Luca,

Yes these bumps/holes occured when I tried a smoothing script straight
after marching cubes. It occurs at 3-4 spots on the reconstruction.

Are you suggesting increasing the number of surface triangles ?

Best
Vikram.



On Mon, May 6, 2013 at 2:13 PM, Luca Antiga <luc...@or...> wrote:

> Hi Virkam,
>  you haven't provided a lot of info on this, but this looks like a VTK
> Marching Cubes issue that arises sometimes.
> Try to use vmtksurfacetriangle right after vmtkmarchingcubes (and before
> any other smoothing or other scripts).
> Best,
>
> Luca
>
>
> On May 6, 2013, at 3:09 PM, Vikram Mehta wrote:
>
> Thank you for your suggestions.
>
> I came across a new problem today - would you happen to know what causes
> this ? And how I can repair my reconstruction ?
>
> Please find an image attached of the problem.
>
> Many thanks in advance
> Vikram.
>
>
>
> On Thu, May 2, 2013 at 10:18 AM, Arjan Geers <aj...@gm...> wrote:
>
>> 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
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>>
>>>
>>
> <Screen Shot 2013-05-06 at 14.06.02.png>
> ------------------------------------------------------------------------------
>
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
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Re: [vmtk-users] 2 questions on segmentation

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

Hi Virkam,
 you haven't provided a lot of info on this, but this looks like a VTK Marching Cubes issue that arises sometimes.
Try to use vmtksurfacetriangle right after vmtkmarchingcubes (and before any other smoothing or other scripts).
Best,

Luca


On May 6, 2013, at 3:09 PM, Vikram Mehta wrote:

> Thank you for your suggestions.
> 
> I came across a new problem today - would you happen to know what causes this ? And how I can repair my reconstruction ? 
> 
> Please find an image attached of the problem.
> 
> Many thanks in advance
> Vikram.
> 
> 
> 
> On Thu, May 2, 2013 at 10:18 AM, Arjan Geers <aj...@gm...> wrote:
> 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.
> >
> > ------------------------------------------------------------------------------
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Re: [vmtk-users] bifurcation plane

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

Hi YiQiang,
 the figure you attached was created in Paraview using the origin and normal of the plane
as computed with vmtk (you can output them in plain text using a .dat file format) to specify the plane 
in Paraview (Sources->Plane). It works well if the number of figures you create is small.

If you need to create the visualization automatically you'll need to write VTK code and use the
vtkPlaneSource class to create the plane.
The class: http://www.vtk.org/doc/nightly/html/classvtkPlaneSource.html
Examples: 
http://www.vtk.org/doc/nightly/html/c2_vtk_e_5.html#c2_vtk_e_vtkPlaneSource
http://www.vtk.org/doc/nightly/html/c2_vtk_t_15.html#c2_vtk_t_vtkPlaneSource

Best,

Luca


On May 6, 2013, at 9:40 AM, qiang zeng wrote:

> Hi all,
> When I am using VMTK, I want to display the bifurcation plane (the view is like aneurysm bifurcation plane, as an attachment "bifurcation plane.jpg").
> Does anyone know a way to do this?
> Best,
> YiQiang
> <bifurcation plane.jpg>------------------------------------------------------------------------------
> Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
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Re: [vmtk-users] vmtkApps?

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

Hi Evan,
 it's an environment variables issue and yes, it's currently not nice to run vmtkApps in Windows, sorry about this.

What you can do is create a patchanterinterpolatecenterlines.bat file (the name is irrelevant, the important is the .bat extension) with the following content:

set VMTK_DIR=C:\"Program Files (x86)"\vmtk
set PATH=%VMTK_DIR%bin;%VMTK_DIR%lib\InsightToolkit;%VMTK_DIR%lib\Python;%PATH%
set PYTHONPATH=%VMTK_DIR%lib\site-packages;%VMTK_DIR%lib\vtk-5.6;%VMTK_DIR%lib\vmtk
cd %VMTK_DIR%
python patchanterinterpolatecenterlines.py

Then double click on the .bat file. Let me know if this works or what error messages it produces.

We'll have to think about a nicer solution than this in the future.


Luca


On May 2, 2013, at 10:04 PM, Evan Kao wrote:

> Hi Luca, 
> 
> 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?
> 
> Both vmtk and Python are in their default directories (Python was installed through vmtk):
> 
> C:\Program Files (x86)\vmtk
> C:\Python27
> 
> It seems I was able to open patchanterinterpolatecenterlin
> es.py in the command line interface, but it doesn't see the vmtk modules ("Import Error: no module named vtk").  How can I remedy this?
> 
> Thanks,
> Evan Kao
> 
> 
> On Wed, May 1, 2013 at 5:30 AM, Luca Antiga <luc...@or...> wrote:
> 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
>> > ------------------------------------------------------------------------------
>> > 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!
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>> 
>> 
>> 
> 
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Re: [vmtk-users] VMTK

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

Hi Hamed,
 what I meant is that you should use the full path to every file you read or write:

vmtkimagereader -f dicom -d C:/Users/Hamed/Downloads/Compressed/br1 --pipe vmtkimagevoiselector -ofile C:/Users/Hamed/image_volume_voi.vti

Also, don't start a pipe with --pipe, like
--pipe vmtkmarchingcubes -ifile image_volume_voi.vti -l 300.0 -ofile mc_surface.vtp --pipe vmtksurfaceviewer

Omit the first --pipe, like :
vmtkmarchingcubes -ifile C:/Users/Hamed/image_volume_voi.vti -l 300.0 -ofile C:/Users/Hamed/mc_surface.vtp --pipe vmtksurfaceviewer

(note that I included the full paths to the files).

Hope this helps

Luca

PS: please keep all messages on the mailing list.


On May 4, 2013, at 7:42 PM, Hamed Rezaie wrote:

> dear Luca thanks for your advice but I should that I could not understand what you mean.
> I have no problem for reading my image and making VOI  by the below command
> "vmtkimagereader -f dicom -d C:/Users/Hamed/Downloads/Compressed/br1 --pipe vmtkimagevoiselector -ofile image_volume_voi.vti" (picture 1)
>  and pressing Run all and after that pressing i and select the VOI and pressing q  but after that when I use the below command 
> " --pipe vmtkmarchingcubes -ifile image_volume_voi.vti -l 300.0 -ofile mc_surface.vtp --pipe vmtksurfaceviewer" (picture 2)
> and Run selection nothing happen and when I use all command together and Run all 
> the result is like picture 1 and after pressing i and q and again q the result is like picture 3.
> I am confused and could not do anything please help me
> kind regards
> Hamed
> From: Luca Antiga <luc...@or...>
> To: Hamed Rezaie <ham...@ya...> 
> Cc: "vmt...@li..." <vmt...@li...> 
> Sent: Wednesday, May 1, 2013 6:10 AM
> Subject: Re: [vmtk-users] VMTK
> 
> 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.
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>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> 
> <1.png><2.png><3.png>

Re: [vmtk-users] Converting from .VTI to .VTP

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

Hi Richard,
 a vtp file should contain polygonal surfaces (the 'p' in vtp stands for 'poly data', while the 'i' for 'image data').

Your best bet to load a vti file in Matlab is to convert it to some other image format, like nrrd
http://www.mathworks.com/matlabcentral/fileexchange/34653-nrrd-format-file-reader/content/nrrdread.m

or mha
http://www.mathworks.com/matlabcentral/fileexchange/29344-read-medical-data-3d/content/mha/mha_read_volume.m

Hope this helps.

Luca


On May 2, 2013, at 6:53 PM, Richard Abrich wrote:

> Hello everyone,
> 
> I used vmtklevelsetsegmentation to segment the coronary arteries in a CT volume, and saved them to a VTI file, which defaulted to the XML format. I'd like to import the data into Matlab for processing, but I haven't found a good way to do it. Therefore, I'd like to convert the VTI XML file into a VTP format.
> 
> Here is the command I'm running:
> 
> vmtkimagereader -ifile C:/levelsets.vti --pipe vmtkimagewriter -ofile C:/levelsets.vtp
> 
> However, this command fails with the following popup error message:
> 
> "Microsoft Visual C++ Runtime Library"
> "Runtime error! Program: C:\Python27\pythonw.exe This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information."
> 
> If I run it from the command line, the same output:
> 
> "This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information."
> 
> I've also tried using the explicit syntax with the same results:
> 
> vmtkimagereader -ifile C:/levelsets.vti --pipe vmtkimagewriter -i @vmtkimagereader.o -ofile C:/levelsets.vtp
> 
> I've tried running as administrator, to no avail.
> 
> I've attached the log of the complete output. I tried adding a debug message to the very beginning of the __init__(self) function in vmtkimagewriter, but it seems to never reach it.
> 
> I'm on Windows 7 64-bit, with 32GB of RAM. Any ideas?
> <output.log>------------------------------------------------------------------------------
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Re: [vmtk-users] mesh conversion to lifev

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

Hi Lucia,
 the error doesn't occur on my hand. Just in order to understand what's going on, do you get 
partial results written out to the file at all?
What you could do is locate the vmtkmeshwriter.py file in [vmtk-install-location]/lib/vmtk/vmtk
and scatter a few prints here and there in the WriteLifeVMeshFile method. The writer is all there,
there's no C++ counterparts so it shouldn't be too messy to debug.
Keep us posted

Luca



On May 2, 2013, at 5:08 PM, Simone Manini wrote:

> Dear Lucia,
> it is an error which is generated in vtkPythonOverload.cxx file.
> I don't know why it happens, I never seen this before. 
> Did you already try to use another file?
> Regards
> Simone
> 
> 
> --
> Simone Manini, Eng
> Orobix Srl
> via L.A. Muratori 3, 24123 Bergamo, Italy
> 
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> 
> On May 2, 2013, at 3:42 PM, Lucia Mirabella <lmi...@ma...> wrote:
> 
>> vmtkmeshwriter  -ifile lego_mesh_tet.vtu -f lifev  -entityidsarray CellEntityIds -ofile lego_mesh_tet.lifev
> 
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> Code-level diagnostics for performance bottlenecks with <2% overhead
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Re: [vmtk-users] ReadTecplot surface data into VMTK

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

Hello Yong,
 I've seen the file, there are a couple of issues.

First, the current Tecplot reader in vmtk is quite basic. It expects the header to be similar to the following:

VARIABLES = X,Y,Z,Something,SomethingElse
ZONE N=388,E=564,F=FEPOINT,ET=TRIANGLE

You have a more elaborate header:

TITLE     = "fluent12.0.16"
VARIABLES = "X"
"Y"
"Z"
"WSS dyne/cm2"
DATASETAUXDATA Common.PressureVar="4"
DATASETAUXDATA Common.UVar="5"
DATASETAUXDATA Common.VectorVarsAreVelocity="TRUE"
DATASETAUXDATA Common.VVar="6"
DATASETAUXDATA Common.WVar="7"
ZONE T="ew"
 STRANDID=1, SOLUTIONTIME=0.47499998
 Nodes=5850, Elements=5750, ZONETYPE=FEQuadrilateral
 DATAPACKING=POINT
 AUXDATA Common.BoundaryCondition="Wall"
 AUXDATA Common.IsBoundaryZone="TRUE"
 DT=(DOUBLE DOUBLE DOUBLE DOUBLE )

I reduced it to
VARIABLES = "X", "Y", "Z", "WSS dyne/cm2"
ZONE T="ew", N=5850, E=5750, ZONETYPE=FEQuadrilateral, DATAPACKING=POINT, AUXDATA Common.BoundaryCondition="Wall", AUXDATA Common.IsBoundaryZone="TRUE", DT=(DOUBLE DOUBLE DOUBLE DOUBLE )
 1.200498104E-02 8.789545441E-02 5.132280884E-01 1.406299010E+01
...

just to make the reader happy and I got something (see screenshot), but the current reader only supports triangles, not quads, so the surface isn't correct. Probably if you convert the quads to triangles within Tecplot (I don't know Tecplot, so I can't tell you how) the process will work.

Just so you know, Paraview (www.paraview.org) reads tec files. So I tried that too, but there was an error message saying that STRANDID is not currently supported. Can you save the file with an earlier Tecplot format version?

Luca




On May 1, 2013, at 5:09 PM, Yong He wrote:

> Hi VMTK users,
> 
> I want to use the VMTK mapping and patching scripts based on the ascii data file that is output from Tecplot 360 2011 (file format version 2009). I tried to use vmtksurfacereader to read the Tecplot .dat file and vmtksurfacewriter to save as a .vtp file, but I got the following error,
> 
> File "/usr/local/lib/vmtk/vmtk/vmtksurfacereader.py", line 98, in ReadTecplotSurfaceFile
>     self.PrintLog("Reading " + str(numberOfNodes)+" nodes.") UnboundLocalError: local variable 'numberOfNodes' referenced before assignment.
> 
> I know similar issues about reading Tecplot surface data into VMTK have been discussed before, but I still don't know how to proceed due to my limited knowledge of VTK, Python and VMTK. I attached a sample Tecplot data file, which contains the X, Y, Z and WSS data. I also tried to use Paraview and VisIt to convert to a vtp file, but neither worked. Hope you could guide me. Thank you very much.
> 
> Yong
> <tryvmtkpt2009.dat>------------------------------------------------------------------------------
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Re: [vmtk-users] vmtkApps?

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

Hi Luca,

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?
>

Both vmtk and Python are in their default directories (Python was installed
through vmtk):

C:\Program Files (x86)\vmtk
C:\Python27

It seems I was able to open patchanterinterpolatecenterlin
es.py in the command line interface, but it doesn't see the vmtk modules
("Import Error: no module named vtk").  How can I remedy this?

Thanks,
Evan Kao


On Wed, May 1, 2013 at 5:30 AM, Luca Antiga <luc...@or...> wrote:

> 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
>>> >
>>> ------------------------------------------------------------------------------
>>> > 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
>>>
>>>
>>
>
>

Re: [vmtk-users] mesh conversion to lifev

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

Dear Lucia,
it is an error which is generated in vtkPythonOverload.cxx file.
I don't know why it happens, I never seen this before. 
Did you already try to use another file?
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
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		+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 3:42 PM, Lucia Mirabella <lmi...@ma...> wrote:

> vmtkmeshwriter  -ifile lego_mesh_tet.vtu -f lifev  -entityidsarray CellEntityIds -ofile lego_mesh_tet.lifev

Re: [vmtk-users] mesh conversion to lifev

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

Dear Simone, 


thanks for your reply! I tried your suggestion, but I get the same error. I paste here below the full output, in case it helps identifying the problem. 


Thanks! 


Lucia 





$ vmtkmeshwriter -ifile lego_mesh_tet.vtu -f lifev -entityidsarray CellEntityIds -ofile lego_mesh_tet.lifev 


Creating vmtkMeshWriter instance. 
Automatic piping vmtkmeshwriter 
Parsing options vmtkmeshwriter 
MeshInputFileName = lego_mesh_tet.vtu 
Format = lifev 
OutputFileName = lego_mesh_tet.lifev 
CellEntityIdsArrayName = CellEntityIds 
Explicit piping vmtkmeshwriter 
Input vmtkmeshwriter members: 
Id = 0 
Disabled = 0 
Mesh = None 
MeshInputFileName = lego_mesh_tet.vtu 
Format = lifev 
GuessFormat = 1 
Compressed = 1 
OutputFileName = lego_mesh_tet.lifev 
Mesh = None 
Mode = binary 
CellEntityIdsArrayName = CellEntityIds 
CellEntityIdsOffset = -1 
WriteRegionMarkers = 0 
Reading VTK XML mesh file. 
Executing vmtkmeshwriter ... 
Writing LifeV file. 
Error from pype: ambiguous call, multiple overloaded methods match the arguments 




----- Original Message -----

From: "Simone Manini" <sim...@or...> 
To: "Lucia Mirabella" <lmi...@ma...> 
Cc: vmt...@li... 
Sent: Thursday, May 2, 2013 5:37:26 AM 
Subject: Re: [vmtk-users] mesh conversion to lifev 

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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