vmtk-users

Re: [vmtk-users] vmtknetworkextraction won't work

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

Dear Chih-Yang,
 I've tried out vmtknetworkextraction on your model and it works for me.

Here's the pipe I'm using to produce the image:

vmtknetworkextraction -ifile DSA-crop.vtp --pipe vmtkrenderer --pipe vmtksurfaceviewer -ifile DSA-crop.vtp -opacity 0.3 --pipe vmtksurfaceviewer -i @vmtknetworkextraction.o

Hope this helps


Luca






On Jul 22, 2013, at 5:06 PM, Chih-Yang Hsu wrote:

> 
> Dear Dr. Antiga,
> 
> Hi, my name is Chih-yang Hsu, I am involved in a research project regarding
> developing cerebral vascular network.
> I have problems working with vmtknetworkextraction.
> I can extract the centerlines of the network by using vmtkcenterlines but
> not vmtknetworkextraction. Can you please help me on this issue?
> Whenever I uses vmtknetworkextraction, the Pypepad would stop working after
> displaying Executing vmtknetworkextraction.
> I've attached a surface file in this e-mail that I've tried to extract the
> centerlines.
> The version I use is vmtk 1.0 in Win7 64 bit.
> Your help is appreciated.
> 
> Best regards,
> Chih-Yang Hsu
> 
> 
> -- 
> Chih-Yang Hsu
> Research Assistant, Office: (312) 355-2520
> Laboratory for Product and Process Design, Prof. Andreas Linninger
> Department of Bioengineering, College of Engineering
> University of Illinois at Chicago
> <DSA-crop.vtp>------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
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Re: [vmtk-users] vesselness filtering parameters

[ddwilde <dav...@ug...>]

Hi Luca,

Thanks for your help and the work you've put into it.

best,

david

On 19-07-13 16:59, Luca Antiga wrote:
> Hello David,
>  the difference originates from the fact that vesselness was not scaled:
>
> "Toggle scaling the objectness measure with the magnitude of the 
> largest absolute eigenvalue"
> itkHessianToObjectnessMeasureImageFilter::ScaleObjectnessMeasure
>
> I now added a flag in vmtkimagevesselenhancement
> -scaled 0
> or
> -scaled 1
> to toggle scaling off (the default) or on.
>
> If you set it to 1 the output image will look a lot like Slicer's.
>
> Note that you'll have to recompile vmtk from github.com/vmtk/vmtk 
> <http://github.com/vmtk/vmtk> to have this additional option available.
>
> Best,
>
>
> Luca
>
>
>
> On Jul 16, 2013, at 10:37 AM, ddwilde wrote:
>
>> The imagecast gives the same result.
>> In the attachment is a (smaller) image dataset.
>>
>> David
>>
>> On 16-07-13 10:14, Luca Antiga wrote:
>>> Yes, that's a marked difference indeed.
>>>
>>> Have you tried casting the image to float?
>>>
>>> vmtkimagecast -ifile CT.nii -type float --pipe 
>>> vmtkimagevesselenhancement  -ofile vessel.nii -method frangi 
>>> -sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha 0.3 -beta 500 
>>> -gamma 150
>>>
>>> Let me know, feel free to share your volume of interest (better 
>>> small than large).
>>>
>>> Luca
>>>
>>>
>>> On Jul 16, 2013, at 9:33 AM, ddwilde wrote:
>>>
>>>> Hi Luca,
>>>>
>>>> Thanks for the reply.
>>>> However, the -stepmethod doesn't seem to be the problem. I've also 
>>>> inspected the source code from the plugin and I still think that 
>>>> all the parameters are the same. Is it maybe possible that the 
>>>> difference occurs in the loading of the dataset (datatype=int16)? 
>>>> To be more specific about the problem I've attached a screenshot of 
>>>> the vmtk-slicer plugin and the vmtk results.
>>>>
>>>> kind regards,
>>>> david
>>>>
>>>> On 15-07-13 16:13, Luca Antiga wrote:
>>>>> Hello David,
>>>>>
>>>>>  you can find the source code for the vesselness Slicer plugin here
>>>>>
>>>>> https://github.com/haehn/VMTKSlicerExtension/blob/master/PythonModules/SlicerVmtkCommonLib/VesselnessFilteringLogic.py
>>>>>
>>>>> I see that method for generating the steps is kept as the default 
>>>>> (for the C++ class), which is "logarithmic", while vmtk default is 
>>>>> "equispaced".
>>>>>
>>>>> Try to specify
>>>>> -stepmethod logarithmic
>>>>>
>>>>> in the vmtk command line and see what happens.
>>>>>
>>>>> Best,
>>>>>
>>>>>
>>>>> Luca
>>>>>
>>>>>
>>>>>
>>>>> On Jul 15, 2013, at 1:53 PM, ddwilde wrote:
>>>>>
>>>>>> Hi VMTK users,
>>>>>>
>>>>>> I used the VMTK-plugin in Slicer4 to get a frangi vesselness 
>>>>>> filtered
>>>>>> image of an angiografic CT image of a mouse dataset (with good 
>>>>>> results).
>>>>>> However when I try to apply the same filter in VMTK directly 
>>>>>> (with the
>>>>>> same parameters), I get different results. There appears to be a lot
>>>>>> more background noise. Is the definition of the parameters different
>>>>>> between both methods or am I doing something wrong?
>>>>>>
>>>>>> Thanks,
>>>>>> David
>>>>>>
>>>>>> Used parameters:
>>>>>> Slicer: Tube<-> Plates: 0.3 // Blobs <-> Tubes: 500 // Contrast: 
>>>>>> 150 //
>>>>>> minimum Diameter: 1[vx] // maximum Diameter: 5[vx]
>>>>>> VMTK: alpha: 0.3                //          beta: 500           //
>>>>>> gamma: 150  //  sigmamin: 0.05 [mm]      //  sigmamax : 0.25 [mm] //
>>>>>> sigmasteps: 5
>>>>>> VMTKcommand: vmtkimagevesselenhancement  -ifile CT.nii -ofile 
>>>>>> vessel.nii
>>>>>> -method frangi -sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha 
>>>>>> 0.3
>>>>>> -beta 500 -gamma 150
>>>>>>
>>>>>> the image resolution is 0.05 mm
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> See everything from the browser to the database with AppDynamics
>>>>>> Get end-to-end visibility with application monitoring from 
>>>>>> AppDynamics
>>>>>> Isolate bottlenecks and diagnose root cause in seconds.
>>>>>> Start your free trial of AppDynamics Pro today!
>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>>>>> _______________________________________________
>>>>>> vmtk-users mailing list
>>>>>> vmt...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>>>
>>>>
>>>> <slicer_plugin.png><vmtk.png>
>>>
>>
>> <CT_voi.nii>------------------------------------------------------------------------------
>> See everything from the browser to the database with AppDynamics
>> Get end-to-end visibility with application monitoring from AppDynamics
>> Isolate bottlenecks and diagnose root cause in seconds.
>> Start your free trial of AppDynamics Pro today!
>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>

Re: [vmtk-users] vesselness filtering parameters

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

Hello David,
 the difference originates from the fact that vesselness was not scaled:

"Toggle scaling the objectness measure with the magnitude of the largest absolute eigenvalue"
itkHessianToObjectnessMeasureImageFilter::ScaleObjectnessMeasure

I now added a flag in vmtkimagevesselenhancement 
-scaled 0
or
-scaled 1
to toggle scaling off (the default) or on.

If you set it to 1 the output image will look a lot like Slicer's.

Note that you'll have to recompile vmtk from github.com/vmtk/vmtk to have this additional option available.

Best,


Luca



On Jul 16, 2013, at 10:37 AM, ddwilde wrote:

> The imagecast gives the same result.
> In the attachment is a (smaller) image dataset.
> 
> David
> 
> On 16-07-13 10:14, Luca Antiga wrote:
>> Yes, that's a marked difference indeed.
>> 
>> Have you tried casting the image to float?
>> 
>> vmtkimagecast -ifile CT.nii -type float --pipe vmtkimagevesselenhancement  -ofile vessel.nii -method frangi -sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha 0.3 -beta 500 -gamma 150
>> 
>> Let me know, feel free to share your volume of interest (better small than large).
>> 
>> Luca
>> 
>> 
>> On Jul 16, 2013, at 9:33 AM, ddwilde wrote:
>> 
>>> Hi Luca,
>>> 
>>> Thanks for the reply. 
>>> However, the -stepmethod doesn't seem to be the problem. I've also inspected the source code from the plugin and I still think that all the parameters are the same. Is it maybe possible that the difference occurs in the loading of the dataset (datatype=int16)? To be more specific about the problem I've attached a screenshot of the vmtk-slicer plugin and the vmtk results.
>>> 
>>> kind regards,
>>> david
>>> 
>>> On 15-07-13 16:13, Luca Antiga wrote:
>>>> Hello David,
>>>> 
>>>>  you can find the source code for the vesselness Slicer plugin here
>>>> 
>>>> https://github.com/haehn/VMTKSlicerExtension/blob/master/PythonModules/SlicerVmtkCommonLib/VesselnessFilteringLogic.py
>>>> 
>>>> I see that method for generating the steps is kept as the default (for the C++ class), which is "logarithmic", while vmtk default is "equispaced".
>>>> 
>>>> Try to specify 
>>>> -stepmethod logarithmic
>>>> 
>>>> in the vmtk command line and see what happens.
>>>> 
>>>> Best,
>>>> 
>>>> 
>>>> Luca
>>>> 
>>>> 
>>>> 
>>>> On Jul 15, 2013, at 1:53 PM, ddwilde wrote:
>>>> 
>>>>> Hi VMTK users,
>>>>> 
>>>>> I used the VMTK-plugin in Slicer4 to get a frangi vesselness filtered 
>>>>> image of an angiografic CT image of a mouse dataset (with good results). 
>>>>> However when I try to apply the same filter in VMTK directly (with the 
>>>>> same parameters), I get different results. There appears to be a lot 
>>>>> more background noise. Is the definition of the parameters different 
>>>>> between both methods or am I doing something wrong?
>>>>> 
>>>>> Thanks,
>>>>> David
>>>>> 
>>>>> Used parameters:
>>>>> Slicer: Tube<-> Plates: 0.3 // Blobs <-> Tubes: 500 // Contrast: 150 // 
>>>>> minimum Diameter: 1[vx] // maximum Diameter: 5[vx]
>>>>> VMTK: alpha: 0.3                //          beta: 500           // 
>>>>> gamma: 150  //  sigmamin: 0.05 [mm]      //  sigmamax : 0.25 [mm] // 
>>>>> sigmasteps: 5
>>>>> VMTKcommand: vmtkimagevesselenhancement  -ifile CT.nii -ofile vessel.nii 
>>>>> -method frangi -sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha 0.3 
>>>>> -beta 500 -gamma 150
>>>>> 
>>>>> the image resolution is 0.05 mm
>>>>> 
>>>>> ------------------------------------------------------------------------------
>>>>> See everything from the browser to the database with AppDynamics
>>>>> Get end-to-end visibility with application monitoring from AppDynamics
>>>>> Isolate bottlenecks and diagnose root cause in seconds.
>>>>> Start your free trial of AppDynamics Pro today!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> vmtk-users mailing list
>>>>> vmt...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>> 
>>> 
>>> <slicer_plugin.png><vmtk.png>
>> 
> 
> <CT_voi.nii>------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] Permission to post to vmtk-users

[Chih-Yang H. <ch...@ui...>]

-- 
Chih-Yang Hsu
Research Assistant, Office: (312) 355-2520
Laboratory for Product and Process Design, Prof. Andreas Linninger
Department of Bioengineering, College of Engineering
University of Illinois at Chicago

Re: [vmtk-users] Parallel Circuit

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

Hi Chanel,
 the centerline algorithm will generate the shortest (in some "special" metric) path from 
a source to a target, so one path per source/target pair. This is why one only the most 
"direct" path is traced and not the other (and not both).
In this sense, the algorithm is limited to an acyclic graph.
At the current state, generating both paths would require either "breaking" the cycles
or placing more seed/target pairs.
I'm very open to suggestions.

Best,

Luca


On Jul 17, 2013, at 5:09 PM, Chanel Johnson wrote:

> I have this surface and it generates a centerline but im trying to understand why it did not go through the first 90 degree turn. Is it possible that it can generate a centerline through the whole surface?
>  
> If not why not?
>  
> Thank you,
>  
> Chanel
> <design1.png>------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________
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> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] Another method?

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

Hi Chanel,
 I'm assuming this is the result of surface remeshing, right?
Can you post a screenshot of the original surface before remeshing?
Thanks

Luca


On Jul 16, 2013, at 8:48 PM, Chanel Johnson wrote:

> Is there a way I can make the surface more solid (more clear to see) and it can still generate a centerline?
>  
> Thanks,
>  
> Chanel
> <cavity001.png>------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] vesselness filtering parameters

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

Hi David,
 thanks for the data, I'll take a look.

Luca


On Jul 16, 2013, at 10:37 AM, ddwilde wrote:

> The imagecast gives the same result.
> In the attachment is a (smaller) image dataset.
> 
> David
> 
> On 16-07-13 10:14, Luca Antiga wrote:
>> Yes, that's a marked difference indeed.
>> 
>> Have you tried casting the image to float?
>> 
>> vmtkimagecast -ifile CT.nii -type float --pipe vmtkimagevesselenhancement  -ofile vessel.nii -method frangi -sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha 0.3 -beta 500 -gamma 150
>> 
>> Let me know, feel free to share your volume of interest (better small than large).
>> 
>> Luca
>> 
>> 
>> On Jul 16, 2013, at 9:33 AM, ddwilde wrote:
>> 
>>> Hi Luca,
>>> 
>>> Thanks for the reply. 
>>> However, the -stepmethod doesn't seem to be the problem. I've also inspected the source code from the plugin and I still think that all the parameters are the same. Is it maybe possible that the difference occurs in the loading of the dataset (datatype=int16)? To be more specific about the problem I've attached a screenshot of the vmtk-slicer plugin and the vmtk results.
>>> 
>>> kind regards,
>>> david
>>> 
>>> On 15-07-13 16:13, Luca Antiga wrote:
>>>> Hello David,
>>>> 
>>>>  you can find the source code for the vesselness Slicer plugin here
>>>> 
>>>> https://github.com/haehn/VMTKSlicerExtension/blob/master/PythonModules/SlicerVmtkCommonLib/VesselnessFilteringLogic.py
>>>> 
>>>> I see that method for generating the steps is kept as the default (for the C++ class), which is "logarithmic", while vmtk default is "equispaced".
>>>> 
>>>> Try to specify 
>>>> -stepmethod logarithmic
>>>> 
>>>> in the vmtk command line and see what happens.
>>>> 
>>>> Best,
>>>> 
>>>> 
>>>> Luca
>>>> 
>>>> 
>>>> 
>>>> On Jul 15, 2013, at 1:53 PM, ddwilde wrote:
>>>> 
>>>>> Hi VMTK users,
>>>>> 
>>>>> I used the VMTK-plugin in Slicer4 to get a frangi vesselness filtered 
>>>>> image of an angiografic CT image of a mouse dataset (with good results). 
>>>>> However when I try to apply the same filter in VMTK directly (with the 
>>>>> same parameters), I get different results. There appears to be a lot 
>>>>> more background noise. Is the definition of the parameters different 
>>>>> between both methods or am I doing something wrong?
>>>>> 
>>>>> Thanks,
>>>>> David
>>>>> 
>>>>> Used parameters:
>>>>> Slicer: Tube<-> Plates: 0.3 // Blobs <-> Tubes: 500 // Contrast: 150 // 
>>>>> minimum Diameter: 1[vx] // maximum Diameter: 5[vx]
>>>>> VMTK: alpha: 0.3                //          beta: 500           // 
>>>>> gamma: 150  //  sigmamin: 0.05 [mm]      //  sigmamax : 0.25 [mm] // 
>>>>> sigmasteps: 5
>>>>> VMTKcommand: vmtkimagevesselenhancement  -ifile CT.nii -ofile vessel.nii 
>>>>> -method frangi -sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha 0.3 
>>>>> -beta 500 -gamma 150
>>>>> 
>>>>> the image resolution is 0.05 mm
>>>>> 
>>>>> ------------------------------------------------------------------------------
>>>>> See everything from the browser to the database with AppDynamics
>>>>> Get end-to-end visibility with application monitoring from AppDynamics
>>>>> Isolate bottlenecks and diagnose root cause in seconds.
>>>>> Start your free trial of AppDynamics Pro today!
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> vmtk-users mailing list
>>>>> vmt...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>> 
>>> 
>>> <slicer_plugin.png><vmtk.png>
>> 
> 
> <CT_voi.nii>

Re: [vmtk-users] vesselness filtering parameters

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

Yes, that's a marked difference indeed.

Have you tried casting the image to float?

vmtkimagecast -ifile CT.nii -type float --pipe vmtkimagevesselenhancement  -ofile vessel.nii -method frangi -sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha 0.3 -beta 500 -gamma 150

Let me know, feel free to share your volume of interest (better small than large).

Luca


On Jul 16, 2013, at 9:33 AM, ddwilde wrote:

> Hi Luca,
> 
> Thanks for the reply. 
> However, the -stepmethod doesn't seem to be the problem. I've also inspected the source code from the plugin and I still think that all the parameters are the same. Is it maybe possible that the difference occurs in the loading of the dataset (datatype=int16)? To be more specific about the problem I've attached a screenshot of the vmtk-slicer plugin and the vmtk results.
> 
> kind regards,
> david
> 
> On 15-07-13 16:13, Luca Antiga wrote:
>> Hello David,
>> 
>>  you can find the source code for the vesselness Slicer plugin here
>> 
>> https://github.com/haehn/VMTKSlicerExtension/blob/master/PythonModules/SlicerVmtkCommonLib/VesselnessFilteringLogic.py
>> 
>> I see that method for generating the steps is kept as the default (for the C++ class), which is "logarithmic", while vmtk default is "equispaced".
>> 
>> Try to specify 
>> -stepmethod logarithmic
>> 
>> in the vmtk command line and see what happens.
>> 
>> Best,
>> 
>> 
>> Luca
>> 
>> 
>> 
>> On Jul 15, 2013, at 1:53 PM, ddwilde wrote:
>> 
>>> Hi VMTK users,
>>> 
>>> I used the VMTK-plugin in Slicer4 to get a frangi vesselness filtered 
>>> image of an angiografic CT image of a mouse dataset (with good results). 
>>> However when I try to apply the same filter in VMTK directly (with the 
>>> same parameters), I get different results. There appears to be a lot 
>>> more background noise. Is the definition of the parameters different 
>>> between both methods or am I doing something wrong?
>>> 
>>> Thanks,
>>> David
>>> 
>>> Used parameters:
>>> Slicer: Tube<-> Plates: 0.3 // Blobs <-> Tubes: 500 // Contrast: 150 // 
>>> minimum Diameter: 1[vx] // maximum Diameter: 5[vx]
>>> VMTK: alpha: 0.3                //          beta: 500           // 
>>> gamma: 150  //  sigmamin: 0.05 [mm]      //  sigmamax : 0.25 [mm] // 
>>> sigmasteps: 5
>>> VMTKcommand: vmtkimagevesselenhancement  -ifile CT.nii -ofile vessel.nii 
>>> -method frangi -sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha 0.3 
>>> -beta 500 -gamma 150
>>> 
>>> the image resolution is 0.05 mm
>>> 
>>> ------------------------------------------------------------------------------
>>> See everything from the browser to the database with AppDynamics
>>> Get end-to-end visibility with application monitoring from AppDynamics
>>> Isolate bottlenecks and diagnose root cause in seconds.
>>> Start your free trial of AppDynamics Pro today!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> vmtk-users mailing list
>>> vmt...@li...
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>> 
> 
> <slicer_plugin.png><vmtk.png>

Re: [vmtk-users] Computing centerline

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

Hello Chanel,
 in your pipe

vmtksurfaceremeshing -ifile D:/Users/210079074/CAD/skin.stl  -area 0.005 --pipe vmtkcenterlines --pipe vmtkrenderer --pipe vmtksurfaceviewer -opacity 0.25 --pipe vmtksurfaceviewer -i @vmtkcenterlines.o -array MaximumInscribedSphereRadius

try changing -area 0.005 to -area 0.0005 and see what happens

Best


Luca

On Jul 15, 2013, at 9:17 PM, Chanel Johnson wrote:

> Now i tried to run the same input on this stil file. and it should up like this.
> Im trying to do the same thing I was doing for the other surfaces. How do I lower the area argument?
>  
> Thanks,
>  
> Chanel
> <cavity01.png>------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

Re: [vmtk-users] vesselness filtering parameters

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

Hello David,

 you can find the source code for the vesselness Slicer plugin here

https://github.com/haehn/VMTKSlicerExtension/blob/master/PythonModules/SlicerVmtkCommonLib/VesselnessFilteringLogic.py

I see that method for generating the steps is kept as the default (for the C++ class), which is "logarithmic", while vmtk default is "equispaced".

Try to specify 
-stepmethod logarithmic

in the vmtk command line and see what happens.

Best,


Luca



On Jul 15, 2013, at 1:53 PM, ddwilde wrote:

> Hi VMTK users,
> 
> I used the VMTK-plugin in Slicer4 to get a frangi vesselness filtered 
> image of an angiografic CT image of a mouse dataset (with good results). 
> However when I try to apply the same filter in VMTK directly (with the 
> same parameters), I get different results. There appears to be a lot 
> more background noise. Is the definition of the parameters different 
> between both methods or am I doing something wrong?
> 
> Thanks,
> David
> 
> Used parameters:
> Slicer: Tube<-> Plates: 0.3 // Blobs <-> Tubes: 500 // Contrast: 150 // 
> minimum Diameter: 1[vx] // maximum Diameter: 5[vx]
> VMTK: alpha: 0.3                //          beta: 500           // 
> gamma: 150  //  sigmamin: 0.05 [mm]      //  sigmamax : 0.25 [mm] // 
> sigmasteps: 5
> VMTKcommand: vmtkimagevesselenhancement  -ifile CT.nii -ofile vessel.nii 
> -method frangi -sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha 0.3 
> -beta 500 -gamma 150
> 
> the image resolution is 0.05 mm
> 
> ------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
> _______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

[vmtk-users] vesselness filtering parameters

[ddwilde <dav...@ug...>]

Hi VMTK users,

I used the VMTK-plugin in Slicer4 to get a frangi vesselness filtered 
image of an angiografic CT image of a mouse dataset (with good results). 
However when I try to apply the same filter in VMTK directly (with the 
same parameters), I get different results. There appears to be a lot 
more background noise. Is the definition of the parameters different 
between both methods or am I doing something wrong?

Thanks,
David

Used parameters:
Slicer: Tube<-> Plates: 0.3 // Blobs <-> Tubes: 500 // Contrast: 150 // 
minimum Diameter: 1[vx] // maximum Diameter: 5[vx]
VMTK: alpha: 0.3                //          beta: 500           // 
gamma: 150  //  sigmamin: 0.05 [mm]      //  sigmamax : 0.25 [mm] // 
sigmasteps: 5
VMTKcommand: vmtkimagevesselenhancement  -ifile CT.nii -ofile vessel.nii 
-method frangi -sigmamin 0.05 -sigmamax 0.25 -sigmasteps 5 -alpha 0.3 
-beta 500 -gamma 150

the image resolution is 0.05 mm

[vmtk-users] New contributions

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

Many thanks to Martin Sandve Alnæs (https://github.com/martinal) and his fellow folks at Simula(http://simula.no/) for their recent contributions:

https://github.com/vmtk/vmtk/pull/71
https://github.com/vmtk/vmtk/pull/70
https://github.com/vmtk/vmtk/pull/69
https://github.com/vmtk/vmtk/pull/68
https://github.com/vmtk/vmtk/pull/67
https://github.com/vmtk/vmtk/pull/66 

Keep them coming!

Luca

Re: [vmtk-users] convert .DAT file to a .VTP file

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

Hello Haim,
 as you know the dat format throws away the cell connectivity information (it only retains the point coordinates), 
so there's not generic way of recreating a vtp from it.
However, as in your case, we can probably infer the connectivity by the fact that lines are written as a sequential
list of points.

One question before I can suggest you a solution: how many lines are there per file (i.e. do your dat files contain
once centerline per file or do you have more?)

Best,


Luca


On Jul 4, 2013, at 1:40 PM, Haim Ezer wrote:

> Hello, Luca, everybody.
> 
> I wonder if there is a simple way, to convert many files, saved by VMTK in dat format, to the vtp format.
> 
> I saved about a 100 centerlines, in the dat format, for the use in matlab, and now I want to use it in VMTK.
> 
> VMTK doesn't seem to read this file format, although it saves in this format.
> 
> Thanks
> 
> Haim
>  
> --
> Haim Ezer, MD
> Department of Neurosurgery,
> The western Galilee hospital in Nahariya
> Israel
> 
> E mail: hai...@gm... ,hai...@ya...
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
> 
> Build for Windows Store.
> 
> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users

--
Luca Antiga, PhD
Cofounder and Principal Scientist, Orobix Srl
via L.A. Muratori 3, 24123 Bergamo, Italy

orobix: www.orobix.com
home: lantiga.github.com
twitter: twitter.com/lantiga

[vmtk-users] convert .DAT file to a .VTP file

[Haim E. <hai...@ya...>]

Hello, Luca, everybody.

I wonder if there is a simple way, to convert many files, saved by VMTK in dat format, to the vtp format.

I saved about a 100 centerlines, in the dat format, for the use in matlab, and now I want to use it in VMTK.

VMTK doesn't seem to read this file format, although it saves in this format.

Thanks

Haim
 
-- Haim Ezer, MD
Department of Neurosurgery, 
The western Galilee hospital in Nahariya
Israel

E mail: hai...@gm... ,hai...@ya...

Re: [vmtk-users] vmtk distance to centerlines

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

Hello Vikram,
 it should work the following way:

vmtksurfaceviewer -ifile surface.vtp -array DistanceToCenterlines

The colormap is not currently very flexible (you just have red to blue and grayscale,
the latter with -grayscale 1). 
However, you can change the scalar range using -scalarrange 0.1 1.0 (where the numbers 
are the bottom and the top of the color range, respectively).

When I'm looking for something more flexible in terms of visualization, I usually resort 
to Paraview.

Cheers.


Luca


On Jul 2, 2013, at 1:24 PM, Vikram Mehta wrote:

> 
> Hi guys,
> 
> Maybe I am missing it but I want to know how I can visualize the results of running the vmtkdistancetocenterline command, in the form of a colored surface ? eg. blue to red indicating low to higher distances respectively.  Also, would it be possible to adjust the colormap ?
> 
> Many thanks in advance
> Vikram.
> 
> 

Re: [vmtk-users] Command line parameters for vmtkLevelSetSegmentation

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

Hi Richard,

On Jul 1, 2013, at 6:21 PM, Richard Abrich wrote:

> Hi Luca,
> 
> I managed to compile the latest source from the github repo on Windows 7 64-bit. However, I was getting the following error in vmtkLevelSetSegmentation.py on line 314:
> 
>         "AttributeError: 'module' object has no attribute 'vmtkImageInitialization'"
> 
> For whatever reason, "import vmtkscripts" at line 22 wasn't pulling in vmtkImageInitialization. I verified this by dumping the object's properties right before line 314:
> 
>         import vmtkimageinitialization
>         l = dir(vmtkscripts)
>         self.PrintLog('\n'.join(l))
> 
> The only module missing is vmtkImageInitialization.
> 
> I got around this by replacing line 314:
> 
>         self.vmtkImageInitialization = vmtkscripts.vmtkImageInitialization()
> 
> with this:
> 
>         import vmtkimageinitialization
>         self.vmtkImageInitialization = vmtkimageinitialization.vmtkImageInitialization()

Thanks for looking into this, I'll look into why vmtkscripts does not include vmtkimageinitialization, from a first check it's not clear to me.

> I then call the script as follows:
> 
>         vmtkimagereader  -f dicom  -d C:/DICOM/ --pipe  vmtkimageinitialization -interactive 0 -method collidingfronts -sourcepoints 210  214  208 196  196  200 -targetpoints 204  204  204 188  190  193  --pipe vmtklevelsetsegmentation -iterations 100  -advection 1.0  -curvature 0.1  -propagation 0.0  --pipe vmtkimageviewer -i @.LevelSets
> 
> I currently have two questions:
> 
> 1) vmtkLevelSetSegmentation does not seem to have a non-interactive mode, as the above call brings up the VTK window and asks for the level set segmentation parameters. This is also apparent in the source code. Luca, do you have an uncommitted version of this file that supports non-interactive mode?

It should work, though. At line 286, if NumberOfIterations is set the script just runs level sets starting from InitialLevelSets, merges the result on the output and exits. Maybe send me the text output that gets printed while the pipe runs, it will help me understand what's going on.

> 2) The pipe to vmtkImageViewer at the end of the command does not display the segmentation, but the DICOM volume. How can I pipe the segmentation instead?

This way:

... --pipe vmtkimageviewer -i @.o

in this case you need to pipe the level sets explicitly because the associated variable name is LevelSet, while image viewer expects Image. The first upstream variable with that name is the output of the reader, which is what gets matched in your case (but probably the explanation is superfluous because I saw you were already doing an explicit piping there). The problem is that pipe syntax refers to the option name (o in this case) while you are using the variable name (this is how it works, although the variable name would make sense too).

Best,

Luca

> 
> Thanks,
> Richard
> 
> 
> 
> 
> On Wed, Jun 26, 2013 at 5:53 PM, Richard Abrich <ab...@gm...> wrote:
> Answering my own question again:
> 
> It turns out that the Colliding Fronts initialization code didn't support multiple start and end points. Lines 295-296:
> 
>             seedIds1.InsertNextId(self.Image.ComputePointId([self.SourcePoints[0],self.SourcePoints[1],self.SourcePoints[2]]))
>             seedIds2.InsertNextId(self.Image.ComputePointId([self.TargetPoints[0],self.TargetPoints[1],self.TargetPoints[2]]))
> 
> Need to be replaced with:
> 
>             for i in range(len(self.SourcePoints)/3):
>                 seedIds1.InsertNextId(self.Image.ComputePointId([self.SourcePoints[3*i+0],self.SourcePoints[3*i+1],self.SourcePoints[3*i+2]]))            
>             for i in range(len(self.TargetPoints)/3):
>                 seedIds2.InsertNextId(self.Image.ComputePointId([self.TargetPoints[3*i+0],self.TargetPoints[3*i+1],self.TargetPoints[3*i+2]]))  
> 
> Now it works.
> 
> 
> 
> On Wed, Jun 26, 2013 at 5:12 PM, Richard Abrich <ab...@gm...> wrote:
> Sorry for the deluge of emails. I wasn't able to successfully get the latest version of the VMTK source to run properly, so instead I just downloaded the latest version of vmtkImageInitialization.py, which accepts the parameters you specified.
> 
> My question is this: the description for the SourcePoints parameter is "list of source point IJK coordinates". Am I able to specify more than one SourcePoint and TargetPoint, and have it iterate over them? The alternative would be to save the results to disk after each call and then merge them all at the end before performing the LevelSetSegmentation, which seems pretty hacky.
> 
> 
> 
> On Wed, Jun 26, 2013 at 11:07 AM, Richard Abrich <ab...@gm...> wrote:
> Hi again,
> 
> I noticed that the latest version of VMTK in the Github repo has those parameters you specified. I'm currently compiling it, and will let you know how it goes.
> 
> Thanks,
> Richard
> 
> 
> 
> On Tue, Jun 25, 2013 at 5:37 PM, Richard Abrich <ab...@gm...> wrote:
> Hi Luca,
> 
> Sorry I forgot to CC my last email to the mailing list.
> 
> A couple of addendums to my previous email (below):
> 
> 1) I converted my data to the .mha format and am using the exact command you suggested.
> 
> 2) I used vmtk-exe.pyc instead of vmtk-exe.pyw in order to view the output. The relevant lines seem to be:
> 
> Parsing options vmtkimageinitialization 
> vmtkimageinitialization error: unknown option -interactive 
> 
> Just FYI, here is the revision information in the vmtkimageinitialization.py script:
> 
> ## Date:      $Date: 2006/05/31 10:51:21 $
> ## Version:   $Revision: 1.19 $
> 
> Is there a newer version I can grab from somewhere?
> 
> 
> On Tue, Jun 25, 2013 at 5:13 PM, Richard Abrich <ab...@gm...> wrote:
> Hi Luca,
> 
> Thanks so much for your help. I have a couple of questions:
> 
> 1) My data isn't .mha format, but rather stored as a dicom set. I tried to do something like this instead:
> 
> vmtkimagereader -f dicom -d C:/DICOM --pipe vmtkimageinitialization -interactive 0 -method collidingfronts -lowerthreshold 200.0 -sourcepoints 54 25 12 -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -iterations 200  -advection 1.0  -curvature 0.1  -propagation 0.0  -ofile C:/out.vtk
> 
> However, the output file wasn't written, and I'm not sure how to check whether anything happened.
> 
> 2) On a related note, I notice that in your example, you specify the ifile parameter for vmtklevelsetsegmentation again, even though you are piping the results from vmtkimageinitialization. Is this necessary? How can I do this using dicom sets instead?
> 
> 3) A few of the parameters you specify for vmtkimagereader (e.g. interactive, method, lowerthreshold, sourcepoints, targetpoints) aren't listed in the documentation at http://www.vmtk.org/VmtkScripts/vmtkimageinitialization/ . I can see that LowerThreshold and UpperThreshold are properties of the vmtkImageInitialization object in vmtkImageInitialization.py, but the other parameters are a mystery. Where can I read more about them?
> 
> Thanks again,
> Richard
> 
> 
> On Thu, Jun 20, 2013 at 4:41 PM, Luca Antiga <luc...@or...> wrote:
> Hi Richard,
>  indeed there is a way. The initialization phase in vmtklevelsetsegmentation is performed by vmtkimageinitialization,
> which accepts parameters at the command line and whose output can be piped to vmtklevelsetsegmentation (in which
> case the latter will use the initialized level sets generated by the former). vmtklevelsetsegmentation can also run
> non-interactively by specifying iterations and evolution parameters at the command line. Here's a sample pipe:
> 
> vmtkimageinitialization -ifile your_image_file.mha -interactive 0 -method collidingfronts -lowerthreshold 200.0 -sourcepoints 54 25 12 -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -ifile you_image_file.mha -iterations 500 -advection 1.0 -curvature 0.1 -propagation 0.0 -ofile level_set_file.mha
> 
> One caveat: sourcepoints and targetpoints are in IJK coordinates (i.e. voxel indices), not physical coordinates.
> 
> Hope this helps,
> 
> 
> Luca
> 
> 
> On Jun 18, 2013, at 10:51 PM, Richard Abrich wrote:
> 
>> Hello,
>> 
>> I'm interested in calling vmtkLevelSetSegmentation from a script. I want to run colliding fronts with arbitrary thresholds and start/end position vectors for the initial segmentation, and then run the level set segmentation with arbitrary parameters.
>> 
>> Unfortunately, there doesn't seem to be any way to specify these parameters from the command line. What might be the easiest way to accomplish this?
>> 
>> Thanks,
>> Richard
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Windows:
>> 
>> Build for Windows Store.
>> 
>> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> 
> 
> 
> 
> 
> 

[vmtk-users] vmtk distance to centerlines

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

Hi guys,

Maybe I am missing it but I want to know how I can visualize the results of
running the *vmtkdistancetocenterline *command, in the form of a colored
surface ? eg. blue to red indicating low to higher distances respectively.
Also, would it be possible to adjust the colormap ?

Many thanks in advance
Vikram.

Re: [vmtk-users] Command line parameters for vmtkLevelSetSegmentation

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

Hi Luca,

I managed to compile the latest source from the github repo on Windows 7
64-bit. However, I was getting the following error in
vmtkLevelSetSegmentation.py on line 314:

        "AttributeError: 'module' object has no attribute
'vmtkImageInitialization'"

For whatever reason, "import vmtkscripts" at line 22 wasn't pulling in
vmtkImageInitialization. I verified this by dumping the object's properties
right before line 314:

        import vmtkimageinitialization
        l = dir(vmtkscripts)
        self.PrintLog('\n'.join(l))

The only module missing is vmtkImageInitialization.

I got around this by replacing line 314:

        self.vmtkImageInitialization = vmtkscripts.vmtkImageInitialization()

with this:

        import vmtkimageinitialization
        self.vmtkImageInitialization =
vmtkimageinitialization.vmtkImageInitialization()

I then call the script as follows:

        vmtkimagereader  -f dicom  -d C:/DICOM/ --pipe
 vmtkimageinitialization -interactive 0 -method collidingfronts
-sourcepoints 210  214  208 196  196  200 -targetpoints 204  204  204 188
 190  193  --pipe vmtklevelsetsegmentation -iterations 100  -advection 1.0
 -curvature 0.1  -propagation 0.0  --pipe vmtkimageviewer -i @.LevelSets

I currently have two questions:

1) vmtkLevelSetSegmentation does not seem to have a non-interactive mode,
as the above call brings up the VTK window and asks for the level set
segmentation parameters. This is also apparent in the source code. Luca, do
you have an uncommitted version of this file that supports non-interactive
mode?

2) The pipe to vmtkImageViewer at the end of the command does not display
the segmentation, but the DICOM volume. How can I pipe the segmentation
instead?

Thanks,
Richard




On Wed, Jun 26, 2013 at 5:53 PM, Richard Abrich <ab...@gm...> wrote:

> Answering my own question again:
>
> It turns out that the Colliding Fronts initialization code didn't support
> multiple start and end points. Lines 295-296:
>
>
> seedIds1.InsertNextId(self.Image.ComputePointId([self.SourcePoints[0],self.SourcePoints[1],self.SourcePoints[2]]))
>
> seedIds2.InsertNextId(self.Image.ComputePointId([self.TargetPoints[0],self.TargetPoints[1],self.TargetPoints[2]]))
>
> Need to be replaced with:
>
>             for i in range(len(self.SourcePoints)/3):
>
> seedIds1.InsertNextId(self.Image.ComputePointId([self.SourcePoints[3*i+0],self.SourcePoints[3*i+1],self.SourcePoints[3*i+2]]))
>
>             for i in range(len(self.TargetPoints)/3):
>
> seedIds2.InsertNextId(self.Image.ComputePointId([self.TargetPoints[3*i+0],self.TargetPoints[3*i+1],self.TargetPoints[3*i+2]]))
>
>
> Now it works.
>
>
>
> On Wed, Jun 26, 2013 at 5:12 PM, Richard Abrich <ab...@gm...> wrote:
>
>> Sorry for the deluge of emails. I wasn't able to successfully get the
>> latest version of the VMTK source to run properly, so instead I just
>> downloaded the latest version of vmtkImageInitialization.py, which accepts
>> the parameters you specified.
>>
>> My question is this: the description for the SourcePoints parameter is
>> "list of source point IJK coordinates". Am I able to specify more than one
>> SourcePoint and TargetPoint, and have it iterate over them? The alternative
>> would be to save the results to disk after each call and then merge them
>> all at the end before performing the LevelSetSegmentation, which seems
>> pretty hacky.
>>
>>
>>
>> On Wed, Jun 26, 2013 at 11:07 AM, Richard Abrich <ab...@gm...>wrote:
>>
>>> Hi again,
>>>
>>> I noticed that the latest version of VMTK in the Github repo has those
>>> parameters you specified. I'm currently compiling it, and will let you know
>>> how it goes.
>>>
>>> Thanks,
>>> Richard
>>>
>>>
>>>
>>> On Tue, Jun 25, 2013 at 5:37 PM, Richard Abrich <ab...@gm...>wrote:
>>>
>>>> Hi Luca,
>>>>
>>>> Sorry I forgot to CC my last email to the mailing list.
>>>>
>>>> A couple of addendums to my previous email (below):
>>>>
>>>> 1) I converted my data to the .mha format and am using the exact
>>>> command you suggested.
>>>>
>>>> 2) I used vmtk-exe.pyc instead of vmtk-exe.pyw in order to view the
>>>> output. The relevant lines seem to be:
>>>>
>>>> Parsing options vmtkimageinitialization
>>>> vmtkimageinitialization error: unknown option -interactive
>>>>
>>>> Just FYI, here is the revision information in the
>>>> vmtkimageinitialization.py script:
>>>>
>>>> ## Date:      $Date: 2006/05/31 10:51:21 $
>>>> ## Version:   $Revision: 1.19 $
>>>>
>>>> Is there a newer version I can grab from somewhere?
>>>>
>>>>
>>>> On Tue, Jun 25, 2013 at 5:13 PM, Richard Abrich <ab...@gm...>wrote:
>>>>
>>>>> Hi Luca,
>>>>>
>>>>> Thanks so much for your help. I have a couple of questions:
>>>>>
>>>>> 1) My data isn't .mha format, but rather stored as a dicom set. I
>>>>> tried to do something like this instead:
>>>>>
>>>>> vmtkimagereader -f dicom -d C:/DICOM --pipe vmtkimageinitialization
>>>>> -interactive 0 -method collidingfronts -lowerthreshold 200.0 -sourcepoints
>>>>> 54 25 12 -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -iterations
>>>>> 200  -advection 1.0  -curvature 0.1  -propagation 0.0  -ofile C:/out.vtk
>>>>>
>>>>> However, the output file wasn't written, and I'm not sure how to check
>>>>> whether anything happened.
>>>>>
>>>>> 2) On a related note, I notice that in your example, you specify the
>>>>> ifile parameter for vmtklevelsetsegmentation again, even though you are
>>>>> piping the results from vmtkimageinitialization. Is this necessary? How can
>>>>> I do this using dicom sets instead?
>>>>>
>>>>> 3) A few of the parameters you specify for vmtkimagereader (e.g.
>>>>> interactive, method, lowerthreshold, sourcepoints, targetpoints) aren't
>>>>> listed in the documentation at
>>>>> http://www.vmtk.org/VmtkScripts/vmtkimageinitialization/ . I can see
>>>>> that LowerThreshold and UpperThreshold are properties of the
>>>>> vmtkImageInitialization object in vmtkImageInitialization.py, but the other
>>>>> parameters are a mystery. Where can I read more about them?
>>>>>
>>>>> Thanks again,
>>>>> Richard
>>>>>
>>>>>
>>>>> On Thu, Jun 20, 2013 at 4:41 PM, Luca Antiga <luc...@or...>wrote:
>>>>>
>>>>>> Hi Richard,
>>>>>>   indeed there is a way. The initialization phase in
>>>>>> vmtklevelsetsegmentation is performed by vmtkimageinitialization,
>>>>>> which accepts parameters at the command line and whose output can be
>>>>>> piped to vmtklevelsetsegmentation (in which
>>>>>> case the latter will use the initialized level sets generated by the
>>>>>> former). vmtklevelsetsegmentation can also run
>>>>>> non-interactively by specifying iterations and evolution parameters
>>>>>> at the command line. Here's a sample pipe:
>>>>>>
>>>>>> vmtkimageinitialization -ifile your_image_file.mha -interactive 0
>>>>>> -method collidingfronts -lowerthreshold 200.0 -sourcepoints 54 25 12
>>>>>> -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -ifile
>>>>>> you_image_file.mha -iterations 500 -advection 1.0 -curvature 0.1
>>>>>> -propagation 0.0 -ofile level_set_file.mha
>>>>>>
>>>>>> One caveat: sourcepoints and targetpoints are in IJK coordinates
>>>>>> (i.e. voxel indices), not physical coordinates.
>>>>>>
>>>>>> Hope this helps,
>>>>>>
>>>>>>
>>>>>> Luca
>>>>>>
>>>>>>
>>>>>> On Jun 18, 2013, at 10:51 PM, Richard Abrich wrote:
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> I'm interested in calling vmtkLevelSetSegmentation from a script. I
>>>>>> want to run colliding fronts with arbitrary thresholds and start/end
>>>>>> position vectors for the initial segmentation, and then run the level set
>>>>>> segmentation with arbitrary parameters.
>>>>>>
>>>>>> Unfortunately, there doesn't seem to be any way to specify these
>>>>>> parameters from the command line. What might be the easiest way to
>>>>>> accomplish this?
>>>>>>
>>>>>> Thanks,
>>>>>> Richard
>>>>>> ------------------------------------------------------------------------------
>>>>>> This SF.net email is sponsored by Windows:
>>>>>>
>>>>>> Build for Windows Store.
>>>>>>
>>>>>>
>>>>>> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
>>>>>> vmtk-users mailing list
>>>>>> vmt...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [vmtk-users] Command line parameters for vmtkLevelSetSegmentation

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

Answering my own question again:

It turns out that the Colliding Fronts initialization code didn't support
multiple start and end points. Lines 295-296:


seedIds1.InsertNextId(self.Image.ComputePointId([self.SourcePoints[0],self.SourcePoints[1],self.SourcePoints[2]]))

seedIds2.InsertNextId(self.Image.ComputePointId([self.TargetPoints[0],self.TargetPoints[1],self.TargetPoints[2]]))

Need to be replaced with:

            for i in range(len(self.SourcePoints)/3):

seedIds1.InsertNextId(self.Image.ComputePointId([self.SourcePoints[3*i+0],self.SourcePoints[3*i+1],self.SourcePoints[3*i+2]]))

            for i in range(len(self.TargetPoints)/3):

seedIds2.InsertNextId(self.Image.ComputePointId([self.TargetPoints[3*i+0],self.TargetPoints[3*i+1],self.TargetPoints[3*i+2]]))


Now it works.



On Wed, Jun 26, 2013 at 5:12 PM, Richard Abrich <ab...@gm...> wrote:

> Sorry for the deluge of emails. I wasn't able to successfully get the
> latest version of the VMTK source to run properly, so instead I just
> downloaded the latest version of vmtkImageInitialization.py, which accepts
> the parameters you specified.
>
> My question is this: the description for the SourcePoints parameter is
> "list of source point IJK coordinates". Am I able to specify more than one
> SourcePoint and TargetPoint, and have it iterate over them? The alternative
> would be to save the results to disk after each call and then merge them
> all at the end before performing the LevelSetSegmentation, which seems
> pretty hacky.
>
>
>
> On Wed, Jun 26, 2013 at 11:07 AM, Richard Abrich <ab...@gm...>wrote:
>
>> Hi again,
>>
>> I noticed that the latest version of VMTK in the Github repo has those
>> parameters you specified. I'm currently compiling it, and will let you know
>> how it goes.
>>
>> Thanks,
>> Richard
>>
>>
>>
>> On Tue, Jun 25, 2013 at 5:37 PM, Richard Abrich <ab...@gm...>wrote:
>>
>>> Hi Luca,
>>>
>>> Sorry I forgot to CC my last email to the mailing list.
>>>
>>> A couple of addendums to my previous email (below):
>>>
>>> 1) I converted my data to the .mha format and am using the exact command
>>> you suggested.
>>>
>>> 2) I used vmtk-exe.pyc instead of vmtk-exe.pyw in order to view the
>>> output. The relevant lines seem to be:
>>>
>>> Parsing options vmtkimageinitialization
>>> vmtkimageinitialization error: unknown option -interactive
>>>
>>> Just FYI, here is the revision information in the
>>> vmtkimageinitialization.py script:
>>>
>>> ## Date:      $Date: 2006/05/31 10:51:21 $
>>> ## Version:   $Revision: 1.19 $
>>>
>>> Is there a newer version I can grab from somewhere?
>>>
>>>
>>> On Tue, Jun 25, 2013 at 5:13 PM, Richard Abrich <ab...@gm...>wrote:
>>>
>>>> Hi Luca,
>>>>
>>>> Thanks so much for your help. I have a couple of questions:
>>>>
>>>> 1) My data isn't .mha format, but rather stored as a dicom set. I tried
>>>> to do something like this instead:
>>>>
>>>> vmtkimagereader -f dicom -d C:/DICOM --pipe vmtkimageinitialization
>>>> -interactive 0 -method collidingfronts -lowerthreshold 200.0 -sourcepoints
>>>> 54 25 12 -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -iterations
>>>> 200  -advection 1.0  -curvature 0.1  -propagation 0.0  -ofile C:/out.vtk
>>>>
>>>> However, the output file wasn't written, and I'm not sure how to check
>>>> whether anything happened.
>>>>
>>>> 2) On a related note, I notice that in your example, you specify the
>>>> ifile parameter for vmtklevelsetsegmentation again, even though you are
>>>> piping the results from vmtkimageinitialization. Is this necessary? How can
>>>> I do this using dicom sets instead?
>>>>
>>>> 3) A few of the parameters you specify for vmtkimagereader (e.g.
>>>> interactive, method, lowerthreshold, sourcepoints, targetpoints) aren't
>>>> listed in the documentation at
>>>> http://www.vmtk.org/VmtkScripts/vmtkimageinitialization/ . I can see
>>>> that LowerThreshold and UpperThreshold are properties of the
>>>> vmtkImageInitialization object in vmtkImageInitialization.py, but the other
>>>> parameters are a mystery. Where can I read more about them?
>>>>
>>>> Thanks again,
>>>> Richard
>>>>
>>>>
>>>> On Thu, Jun 20, 2013 at 4:41 PM, Luca Antiga <luc...@or...>wrote:
>>>>
>>>>> Hi Richard,
>>>>>   indeed there is a way. The initialization phase in
>>>>> vmtklevelsetsegmentation is performed by vmtkimageinitialization,
>>>>> which accepts parameters at the command line and whose output can be
>>>>> piped to vmtklevelsetsegmentation (in which
>>>>> case the latter will use the initialized level sets generated by the
>>>>> former). vmtklevelsetsegmentation can also run
>>>>> non-interactively by specifying iterations and evolution parameters at
>>>>> the command line. Here's a sample pipe:
>>>>>
>>>>> vmtkimageinitialization -ifile your_image_file.mha -interactive 0
>>>>> -method collidingfronts -lowerthreshold 200.0 -sourcepoints 54 25 12
>>>>> -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -ifile
>>>>> you_image_file.mha -iterations 500 -advection 1.0 -curvature 0.1
>>>>> -propagation 0.0 -ofile level_set_file.mha
>>>>>
>>>>> One caveat: sourcepoints and targetpoints are in IJK coordinates (i.e.
>>>>> voxel indices), not physical coordinates.
>>>>>
>>>>> Hope this helps,
>>>>>
>>>>>
>>>>> Luca
>>>>>
>>>>>
>>>>> On Jun 18, 2013, at 10:51 PM, Richard Abrich wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> I'm interested in calling vmtkLevelSetSegmentation from a script. I
>>>>> want to run colliding fronts with arbitrary thresholds and start/end
>>>>> position vectors for the initial segmentation, and then run the level set
>>>>> segmentation with arbitrary parameters.
>>>>>
>>>>> Unfortunately, there doesn't seem to be any way to specify these
>>>>> parameters from the command line. What might be the easiest way to
>>>>> accomplish this?
>>>>>
>>>>> Thanks,
>>>>> Richard
>>>>> ------------------------------------------------------------------------------
>>>>> This SF.net email is sponsored by Windows:
>>>>>
>>>>> Build for Windows Store.
>>>>>
>>>>>
>>>>> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
>>>>> vmtk-users mailing list
>>>>> vmt...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [vmtk-users] Command line parameters for vmtkLevelSetSegmentation

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

Sorry for the deluge of emails. I wasn't able to successfully get the
latest version of the VMTK source to run properly, so instead I just
downloaded the latest version of vmtkImageInitialization.py, which accepts
the parameters you specified.

My question is this: the description for the SourcePoints parameter is
"list of source point IJK coordinates". Am I able to specify more than one
SourcePoint and TargetPoint, and have it iterate over them? The alternative
would be to save the results to disk after each call and then merge them
all at the end before performing the LevelSetSegmentation, which seems
pretty hacky.



On Wed, Jun 26, 2013 at 11:07 AM, Richard Abrich <ab...@gm...> wrote:

> Hi again,
>
> I noticed that the latest version of VMTK in the Github repo has those
> parameters you specified. I'm currently compiling it, and will let you know
> how it goes.
>
> Thanks,
> Richard
>
>
>
> On Tue, Jun 25, 2013 at 5:37 PM, Richard Abrich <ab...@gm...> wrote:
>
>> Hi Luca,
>>
>> Sorry I forgot to CC my last email to the mailing list.
>>
>> A couple of addendums to my previous email (below):
>>
>> 1) I converted my data to the .mha format and am using the exact command
>> you suggested.
>>
>> 2) I used vmtk-exe.pyc instead of vmtk-exe.pyw in order to view the
>> output. The relevant lines seem to be:
>>
>> Parsing options vmtkimageinitialization
>> vmtkimageinitialization error: unknown option -interactive
>>
>> Just FYI, here is the revision information in the
>> vmtkimageinitialization.py script:
>>
>> ## Date:      $Date: 2006/05/31 10:51:21 $
>> ## Version:   $Revision: 1.19 $
>>
>> Is there a newer version I can grab from somewhere?
>>
>>
>> On Tue, Jun 25, 2013 at 5:13 PM, Richard Abrich <ab...@gm...>wrote:
>>
>>> Hi Luca,
>>>
>>> Thanks so much for your help. I have a couple of questions:
>>>
>>> 1) My data isn't .mha format, but rather stored as a dicom set. I tried
>>> to do something like this instead:
>>>
>>> vmtkimagereader -f dicom -d C:/DICOM --pipe vmtkimageinitialization
>>> -interactive 0 -method collidingfronts -lowerthreshold 200.0 -sourcepoints
>>> 54 25 12 -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -iterations
>>> 200  -advection 1.0  -curvature 0.1  -propagation 0.0  -ofile C:/out.vtk
>>>
>>> However, the output file wasn't written, and I'm not sure how to check
>>> whether anything happened.
>>>
>>> 2) On a related note, I notice that in your example, you specify the
>>> ifile parameter for vmtklevelsetsegmentation again, even though you are
>>> piping the results from vmtkimageinitialization. Is this necessary? How can
>>> I do this using dicom sets instead?
>>>
>>> 3) A few of the parameters you specify for vmtkimagereader (e.g.
>>> interactive, method, lowerthreshold, sourcepoints, targetpoints) aren't
>>> listed in the documentation at
>>> http://www.vmtk.org/VmtkScripts/vmtkimageinitialization/ . I can see
>>> that LowerThreshold and UpperThreshold are properties of the
>>> vmtkImageInitialization object in vmtkImageInitialization.py, but the other
>>> parameters are a mystery. Where can I read more about them?
>>>
>>> Thanks again,
>>> Richard
>>>
>>>
>>> On Thu, Jun 20, 2013 at 4:41 PM, Luca Antiga <luc...@or...>wrote:
>>>
>>>> Hi Richard,
>>>>   indeed there is a way. The initialization phase in
>>>> vmtklevelsetsegmentation is performed by vmtkimageinitialization,
>>>> which accepts parameters at the command line and whose output can be
>>>> piped to vmtklevelsetsegmentation (in which
>>>> case the latter will use the initialized level sets generated by the
>>>> former). vmtklevelsetsegmentation can also run
>>>> non-interactively by specifying iterations and evolution parameters at
>>>> the command line. Here's a sample pipe:
>>>>
>>>> vmtkimageinitialization -ifile your_image_file.mha -interactive 0
>>>> -method collidingfronts -lowerthreshold 200.0 -sourcepoints 54 25 12
>>>> -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -ifile
>>>> you_image_file.mha -iterations 500 -advection 1.0 -curvature 0.1
>>>> -propagation 0.0 -ofile level_set_file.mha
>>>>
>>>> One caveat: sourcepoints and targetpoints are in IJK coordinates (i.e.
>>>> voxel indices), not physical coordinates.
>>>>
>>>> Hope this helps,
>>>>
>>>>
>>>> Luca
>>>>
>>>>
>>>> On Jun 18, 2013, at 10:51 PM, Richard Abrich wrote:
>>>>
>>>> Hello,
>>>>
>>>> I'm interested in calling vmtkLevelSetSegmentation from a script. I
>>>> want to run colliding fronts with arbitrary thresholds and start/end
>>>> position vectors for the initial segmentation, and then run the level set
>>>> segmentation with arbitrary parameters.
>>>>
>>>> Unfortunately, there doesn't seem to be any way to specify these
>>>> parameters from the command line. What might be the easiest way to
>>>> accomplish this?
>>>>
>>>> Thanks,
>>>> Richard
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by Windows:
>>>>
>>>> Build for Windows Store.
>>>>
>>>>
>>>> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
>>>> vmtk-users mailing list
>>>> vmt...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>>
>>>>
>>>>
>>>
>>
>

Re: [vmtk-users] Command line parameters for vmtkLevelSetSegmentation

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

Hi again,

I noticed that the latest version of VMTK in the Github repo has those
parameters you specified. I'm currently compiling it, and will let you know
how it goes.

Thanks,
Richard



On Tue, Jun 25, 2013 at 5:37 PM, Richard Abrich <ab...@gm...> wrote:

> Hi Luca,
>
> Sorry I forgot to CC my last email to the mailing list.
>
> A couple of addendums to my previous email (below):
>
> 1) I converted my data to the .mha format and am using the exact command
> you suggested.
>
> 2) I used vmtk-exe.pyc instead of vmtk-exe.pyw in order to view the
> output. The relevant lines seem to be:
>
> Parsing options vmtkimageinitialization
> vmtkimageinitialization error: unknown option -interactive
>
> Just FYI, here is the revision information in the
> vmtkimageinitialization.py script:
>
> ## Date:      $Date: 2006/05/31 10:51:21 $
> ## Version:   $Revision: 1.19 $
>
> Is there a newer version I can grab from somewhere?
>
>
> On Tue, Jun 25, 2013 at 5:13 PM, Richard Abrich <ab...@gm...> wrote:
>
>> Hi Luca,
>>
>> Thanks so much for your help. I have a couple of questions:
>>
>> 1) My data isn't .mha format, but rather stored as a dicom set. I tried
>> to do something like this instead:
>>
>> vmtkimagereader -f dicom -d C:/DICOM --pipe vmtkimageinitialization
>> -interactive 0 -method collidingfronts -lowerthreshold 200.0 -sourcepoints
>> 54 25 12 -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -iterations
>> 200  -advection 1.0  -curvature 0.1  -propagation 0.0  -ofile C:/out.vtk
>>
>> However, the output file wasn't written, and I'm not sure how to check
>> whether anything happened.
>>
>> 2) On a related note, I notice that in your example, you specify the
>> ifile parameter for vmtklevelsetsegmentation again, even though you are
>> piping the results from vmtkimageinitialization. Is this necessary? How can
>> I do this using dicom sets instead?
>>
>> 3) A few of the parameters you specify for vmtkimagereader (e.g.
>> interactive, method, lowerthreshold, sourcepoints, targetpoints) aren't
>> listed in the documentation at
>> http://www.vmtk.org/VmtkScripts/vmtkimageinitialization/ . I can see
>> that LowerThreshold and UpperThreshold are properties of the
>> vmtkImageInitialization object in vmtkImageInitialization.py, but the other
>> parameters are a mystery. Where can I read more about them?
>>
>> Thanks again,
>> Richard
>>
>>
>> On Thu, Jun 20, 2013 at 4:41 PM, Luca Antiga <luc...@or...>wrote:
>>
>>> Hi Richard,
>>>   indeed there is a way. The initialization phase in
>>> vmtklevelsetsegmentation is performed by vmtkimageinitialization,
>>> which accepts parameters at the command line and whose output can be
>>> piped to vmtklevelsetsegmentation (in which
>>> case the latter will use the initialized level sets generated by the
>>> former). vmtklevelsetsegmentation can also run
>>> non-interactively by specifying iterations and evolution parameters at
>>> the command line. Here's a sample pipe:
>>>
>>> vmtkimageinitialization -ifile your_image_file.mha -interactive 0
>>> -method collidingfronts -lowerthreshold 200.0 -sourcepoints 54 25 12
>>> -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -ifile
>>> you_image_file.mha -iterations 500 -advection 1.0 -curvature 0.1
>>> -propagation 0.0 -ofile level_set_file.mha
>>>
>>> One caveat: sourcepoints and targetpoints are in IJK coordinates (i.e.
>>> voxel indices), not physical coordinates.
>>>
>>> Hope this helps,
>>>
>>>
>>> Luca
>>>
>>>
>>> On Jun 18, 2013, at 10:51 PM, Richard Abrich wrote:
>>>
>>> Hello,
>>>
>>> I'm interested in calling vmtkLevelSetSegmentation from a script. I want
>>> to run colliding fronts with arbitrary thresholds and start/end position
>>> vectors for the initial segmentation, and then run the level set
>>> segmentation with arbitrary parameters.
>>>
>>> Unfortunately, there doesn't seem to be any way to specify these
>>> parameters from the command line. What might be the easiest way to
>>> accomplish this?
>>>
>>> Thanks,
>>> Richard
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by Windows:
>>>
>>> Build for Windows Store.
>>>
>>>
>>> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
>>> vmtk-users mailing list
>>> vmt...@li...
>>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>>
>>>
>>>
>>
>

Re: [vmtk-users] Command line parameters for vmtkLevelSetSegmentation

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

Hi Luca,

Sorry I forgot to CC my last email to the mailing list.

A couple of addendums to my previous email (below):

1) I converted my data to the .mha format and am using the exact command
you suggested.

2) I used vmtk-exe.pyc instead of vmtk-exe.pyw in order to view the output.
The relevant lines seem to be:

Parsing options vmtkimageinitialization
vmtkimageinitialization error: unknown option -interactive

Just FYI, here is the revision information in the
vmtkimageinitialization.py script:

## Date:      $Date: 2006/05/31 10:51:21 $
## Version:   $Revision: 1.19 $

Is there a newer version I can grab from somewhere?


On Tue, Jun 25, 2013 at 5:13 PM, Richard Abrich <ab...@gm...> wrote:

> Hi Luca,
>
> Thanks so much for your help. I have a couple of questions:
>
> 1) My data isn't .mha format, but rather stored as a dicom set. I tried to
> do something like this instead:
>
> vmtkimagereader -f dicom -d C:/DICOM --pipe vmtkimageinitialization
> -interactive 0 -method collidingfronts -lowerthreshold 200.0 -sourcepoints
> 54 25 12 -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -iterations
> 200  -advection 1.0  -curvature 0.1  -propagation 0.0  -ofile C:/out.vtk
>
> However, the output file wasn't written, and I'm not sure how to check
> whether anything happened.
>
> 2) On a related note, I notice that in your example, you specify the ifile
> parameter for vmtklevelsetsegmentation again, even though you are piping
> the results from vmtkimageinitialization. Is this necessary? How can I do
> this using dicom sets instead?
>
> 3) A few of the parameters you specify for vmtkimagereader (e.g.
> interactive, method, lowerthreshold, sourcepoints, targetpoints) aren't
> listed in the documentation at
> http://www.vmtk.org/VmtkScripts/vmtkimageinitialization/ . I can see that
> LowerThreshold and UpperThreshold are properties of the
> vmtkImageInitialization object in vmtkImageInitialization.py, but the other
> parameters are a mystery. Where can I read more about them?
>
> Thanks again,
> Richard
>
>
> On Thu, Jun 20, 2013 at 4:41 PM, Luca Antiga <luc...@or...>wrote:
>
>> Hi Richard,
>>   indeed there is a way. The initialization phase in
>> vmtklevelsetsegmentation is performed by vmtkimageinitialization,
>> which accepts parameters at the command line and whose output can be
>> piped to vmtklevelsetsegmentation (in which
>> case the latter will use the initialized level sets generated by the
>> former). vmtklevelsetsegmentation can also run
>> non-interactively by specifying iterations and evolution parameters at
>> the command line. Here's a sample pipe:
>>
>> vmtkimageinitialization -ifile your_image_file.mha -interactive 0 -method
>> collidingfronts -lowerthreshold 200.0 -sourcepoints 54 25 12 -targetpoints
>> 89 60 24 --pipe vmtklevelsetsegmentation -ifile you_image_file.mha
>> -iterations 500 -advection 1.0 -curvature 0.1 -propagation 0.0 -ofile
>> level_set_file.mha
>>
>> One caveat: sourcepoints and targetpoints are in IJK coordinates (i.e.
>> voxel indices), not physical coordinates.
>>
>> Hope this helps,
>>
>>
>> Luca
>>
>>
>> On Jun 18, 2013, at 10:51 PM, Richard Abrich wrote:
>>
>> Hello,
>>
>> I'm interested in calling vmtkLevelSetSegmentation from a script. I want
>> to run colliding fronts with arbitrary thresholds and start/end position
>> vectors for the initial segmentation, and then run the level set
>> segmentation with arbitrary parameters.
>>
>> Unfortunately, there doesn't seem to be any way to specify these
>> parameters from the command line. What might be the easiest way to
>> accomplish this?
>>
>> Thanks,
>> Richard
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>>
>> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
>> vmtk-users mailing list
>> vmt...@li...
>> https://lists.sourceforge.net/lists/listinfo/vmtk-users
>>
>>
>>
>

Re: [vmtk-users] FDNEUT meshing using vmtk

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

Hi Elaine,
 ok, got it.

I don't remember the specs for entities in FDNEUT format exactly, 
but I don't think it's going to be too complicated to extend vtkvmtkFDNEUTWriter
to support entities.

If you can dig the FDNEUT spec out some wayback machine then I can point
you to the relevant portions of the code. In any case, the writer class should be 
pretty straightforward to read.

Best,

Luca


On Jun 20, 2013, at 11:18 PM, Elaine Tang wrote:

> Hey Luca,
> 
> Thanks for your reply. Yes I understand we are dealing with an antique here.. :)
> We are not using FIDAP solver, but we have an in-house code that specifically handle .FDNEUT mesh. Especially it reads the mesh based on the entity groups as sorted out in FDNEUT.(e.g. inlet/outlet boundary). Of course one possible long-term solution is to change our source code to accommodate more popular mesh type nowadays. But we have already been working with .FDNEUT for quite a number of cases. So we want to see if vmtk can help us with that, without the use of GAMBIT (since it is also quite old too). 
> 
> And I am guessing to extend that, rewriting some part of "vtkvmtkFDNEUTWriter" will do?
> 
> Thanks!
> 
> 
> 
> On 20 June 2013 16:35, Luca Antiga <luc...@or...> wrote:
> Hello Elaine,
>  your message made me realize I haven't dealt with the FIDAP format
> in a long time! FIDAP was the first CFD solver I've ever used...
> 
> Which brings me to the unfortunate consequence: the FDNEUT writer was
> written in the early days when there was no concept of CellEntityIds array in
> vmtkmeshwriter. So, while the writer produces a valid FDNEUT mesh, it doesn't
> take into account the entity information.
> 
> It shouldn't be hard to extend the writer with the FDNEUT specs at hand.
> 
> May I ask why you need the mesh in FDNEUT format? If it's not for using
> the FIDAP solver (which must have been abandoned for about ten years
> now) but for importing into, say, Gambit, then there might be other ways
> of getting there, through other formats that VTK supports.
> 
> Best,
> 
> Luca
> 
> 
> 
> 
> On Jun 18, 2013, at 10:37 PM, Elaine Tang wrote:
> 
> > Hi,
> >
> > I am trying to create FDNEUT mesh using vmtk, and using .stl as input. I want to specify each inlet/outlet as separate entity in the FDNEUT. I first created an stl with open caps.Then I import the stl and mesh it to vtu. From vmtkmeshboundaryinspector, it seems that my vtu mesh contains the surface and each inlet/outlet cap as separate entities, which is great. However, when I try to output the mesh in FDNEUT, the CellEntityIfd cannot be stored in the FDNEUT mesh. And in the FDNEUT, the mesh is one entity as a whole.  Any insight on this?
> >
> > Thanks!
> > --
> > Elaine Tang
> >
> > PhD Candidate
> > Cardiovascular Fluid Mechanics Laboratory
> > Chemical & Biomolecular Engineering
> > Georgia Institute of Technology
> > ------------------------------------------------------------------------------
> > This SF.net email is sponsored by Windows:
> >
> > Build for Windows Store.
> >
> > http://p.sf.net/sfu/windows-dev2dev_______________________________________________
> > vmtk-users mailing list
> > vmt...@li...
> > https://lists.sourceforge.net/lists/listinfo/vmtk-users
> 
> 
> 
> 
> -- 
> Elaine Tang
> 
> PhD Candidate
> Cardiovascular Fluid Mechanics Laboratory
> Chemical & Biomolecular Engineering
> Georgia Institute of Technology

Re: [vmtk-users] FDNEUT meshing using vmtk

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

Hey Luca,

Thanks for your reply. Yes I understand we are dealing with an antique
here.. :)
We are not using FIDAP solver, but we have an in-house code that
specifically handle .FDNEUT mesh. Especially it reads the mesh based on the
entity groups as sorted out in FDNEUT.(e.g. inlet/outlet boundary). Of
course one possible long-term solution is to change our source code to
accommodate more popular mesh type nowadays. But we have already been
working with .FDNEUT for quite a number of cases. So we want to see if vmtk
can help us with that, without the use of GAMBIT (since it is also quite
old too).

And I am guessing to extend that, rewriting some part of
"vtkvmtkFDNEUTWriter" will do?

Thanks!



On 20 June 2013 16:35, Luca Antiga <luc...@or...> wrote:

> Hello Elaine,
>  your message made me realize I haven't dealt with the FIDAP format
> in a long time! FIDAP was the first CFD solver I've ever used...
>
> Which brings me to the unfortunate consequence: the FDNEUT writer was
> written in the early days when there was no concept of CellEntityIds array
> in
> vmtkmeshwriter. So, while the writer produces a valid FDNEUT mesh, it
> doesn't
> take into account the entity information.
>
> It shouldn't be hard to extend the writer with the FDNEUT specs at hand.
>
> May I ask why you need the mesh in FDNEUT format? If it's not for using
> the FIDAP solver (which must have been abandoned for about ten years
> now) but for importing into, say, Gambit, then there might be other ways
> of getting there, through other formats that VTK supports.
>
> Best,
>
> Luca
>
>
>
>
> On Jun 18, 2013, at 10:37 PM, Elaine Tang wrote:
>
> > Hi,
> >
> > I am trying to create FDNEUT mesh using vmtk, and using .stl as input. I
> want to specify each inlet/outlet as separate entity in the FDNEUT. I first
> created an stl with open caps.Then I import the stl and mesh it to vtu.
> From vmtkmeshboundaryinspector, it seems that my vtu mesh contains the
> surface and each inlet/outlet cap as separate entities, which is great.
> However, when I try to output the mesh in FDNEUT, the CellEntityIfd cannot
> be stored in the FDNEUT mesh. And in the FDNEUT, the mesh is one entity as
> a whole.  Any insight on this?
> >
> > Thanks!
> > --
> > Elaine Tang
> >
> > PhD Candidate
> > Cardiovascular Fluid Mechanics Laboratory
> > Chemical & Biomolecular Engineering
> > Georgia Institute of Technology
> >
> ------------------------------------------------------------------------------
> > This SF.net email is sponsored by Windows:
> >
> > Build for Windows Store.
> >
> >
> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
> > vmtk-users mailing list
> > vmt...@li...
> > https://lists.sourceforge.net/lists/listinfo/vmtk-users
>
>


-- 
Elaine Tang

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

Re: [vmtk-users] Command line parameters for vmtkLevelSetSegmentation

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

Hi Richard,
 indeed there is a way. The initialization phase in vmtklevelsetsegmentation is performed by vmtkimageinitialization,
which accepts parameters at the command line and whose output can be piped to vmtklevelsetsegmentation (in which
case the latter will use the initialized level sets generated by the former). vmtklevelsetsegmentation can also run
non-interactively by specifying iterations and evolution parameters at the command line. Here's a sample pipe:

vmtkimageinitialization -ifile your_image_file.mha -interactive 0 -method collidingfronts -lowerthreshold 200.0 -sourcepoints 54 25 12 -targetpoints 89 60 24 --pipe vmtklevelsetsegmentation -ifile you_image_file.mha -iterations 500 -advection 1.0 -curvature 0.1 -propagation 0.0 -ofile level_set_file.mha

One caveat: sourcepoints and targetpoints are in IJK coordinates (i.e. voxel indices), not physical coordinates.

Hope this helps,


Luca


On Jun 18, 2013, at 10:51 PM, Richard Abrich wrote:

> Hello,
> 
> I'm interested in calling vmtkLevelSetSegmentation from a script. I want to run colliding fronts with arbitrary thresholds and start/end position vectors for the initial segmentation, and then run the level set segmentation with arbitrary parameters.
> 
> Unfortunately, there doesn't seem to be any way to specify these parameters from the command line. What might be the easiest way to accomplish this?
> 
> Thanks,
> Richard
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
> 
> Build for Windows Store.
> 
> http://p.sf.net/sfu/windows-dev2dev_______________________________________________
> vmtk-users mailing list
> vmt...@li...
> https://lists.sourceforge.net/lists/listinfo/vmtk-users