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Example: Setting landmarks in 3D using QT/ITK/VTK
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Example: Setting landmarks in 3D using QT/ITK/VTK
by Dirk Boye
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Dear listmembers,
I programmed an example in which itkImageFileReader is used to load a 3D image which is then viewed in a QVTKImage with the help of vtkImageViewer2. Points / landmarks can be set with the mouse and a vtkPointWidget and be saved as a vtkPolyData .vtk file afterwards. Everything in a nice QT GUI. I am new to VTK/ITK and it took some time to put everything together. Perhaps this will help anyone who is trying to achieve something similar. Check it out at http://github.com/dirkboye/myImageLandmarker or directly clone it with git clone git://github.com/dirkboye/myImageLandmarker.git Cheers, Dirk _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Example: Setting landmarks in 3D using QT/ITK/VTK
by Luis Ibanez
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Hi Dirk,
This is great ! Thanks for sharing with the community. We plan to reorganize the InsightApplications module this year. Would it be fine if we include your code as one of the new subdirectories ? Please let us know, Thanks Luis -------------------------------------------------------------- On Tue, Oct 20, 2009 at 9:15 AM, Dirk <body@...> wrote: > Dear listmembers, > > I programmed an example in which itkImageFileReader is used to load a > 3D image which is then viewed in a QVTKImage with the help of > vtkImageViewer2. > Points / landmarks can be set with the mouse and a vtkPointWidget > and be saved as a vtkPolyData .vtk file afterwards. > Everything in a nice QT GUI. > > I am new to VTK/ITK and it took some time to put everything together. > Perhaps this will help anyone who is trying to achieve something > similar. > > Check it out at http://github.com/dirkboye/myImageLandmarker > > or directly clone it with > git clone git://github.com/dirkboye/myImageLandmarker.git > > > Cheers, > Dirk > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://www.itk.org/mailman/listinfo/insight-users > Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Example: Setting landmarks in 3D using QT/ITK/VTK
by David Doria
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On Tue, Oct 20, 2009 at 9:15 AM, Dirk <body@...> wrote:
> Dear listmembers, > > I programmed an example in which itkImageFileReader is used to load a > 3D image which is then viewed in a QVTKImage with the help of > vtkImageViewer2. > Points / landmarks can be set with the mouse and a vtkPointWidget > and be saved as a vtkPolyData .vtk file afterwards. > Everything in a nice QT GUI. > > I am new to VTK/ITK and it took some time to put everything together. > Perhaps this will help anyone who is trying to achieve something > similar. > > Check it out at http://github.com/dirkboye/myImageLandmarker > > or directly clone it with > git clone git://github.com/dirkboye/myImageLandmarker.git > > > Cheers, > Dirk > __ Dirk, I just started looking into doing this from inside Paraview with polydata rather than imagedata. The idea was the to be able to apply the landmark filter to manually register two data sets without ever leaving paraview. Do you think there is anything that could be taken from this for my effort? Or should we leave this in a standalone QT app and I'll continue doing it for Paraview? Thanks, David _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Example: Setting landmarks in 3D using QT/ITK/VTK
by Dirk Boye
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Hi Luis,
Yes it would be fine and very cool :) I also created a new version which uses vtkSmartPointers! Cheers, Dirk On 10/22/2009 12:45:45 AM, Luis Ibanez wrote: > Hi Dirk, > > This is great ! > > Thanks for sharing with the community. > > We plan to reorganize the InsightApplications module this year. > > Would it be fine if we include your code as one of the new > subdirectories ? > > > Please let us know, > > > Thanks > > > Luis > > > -------------------------------------------------------------- > On Tue, Oct 20, 2009 at 9:15 AM, Dirk <body@...> wrote: > > Dear listmembers, > > > > I programmed an example in which itkImageFileReader is used to load > a > > 3D image which is then viewed in a QVTKImage with the help of > > vtkImageViewer2. > > Points / landmarks can be set with the mouse and a vtkPointWidget > > and be saved as a vtkPolyData .vtk file afterwards. > > Everything in a nice QT GUI. > > > > I am new to VTK/ITK and it took some time to put everything > together. > > Perhaps this will help anyone who is trying to achieve something > > similar. > > > > Check it out at http://github.com/dirkboye/myImageLandmarker > > > > or directly clone it with > > git clone git://github.com/dirkboye/myImageLandmarker.git > > > > > > Cheers, > > Dirk > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://www.itk.org/mailman/listinfo/insight-users > > > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: Example: Setting landmarks in 3D using QT/ITK/VTK
by Dirk Boye
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On 10/22/2009 12:55:28 AM, David Doria wrote:
> On Tue, Oct 20, 2009 at 9:15 AM, Dirk <body@...> wrote: > > Dear listmembers, > > > > I programmed an example in which itkImageFileReader is used to load > a > > 3D image which is then viewed in a QVTKImage with the help of > > vtkImageViewer2. > > Points / landmarks can be set with the mouse and a vtkPointWidget > > and be saved as a vtkPolyData .vtk file afterwards. > > Everything in a nice QT GUI. > > > > I am new to VTK/ITK and it took some time to put everything > together. > > Perhaps this will help anyone who is trying to achieve something > > similar. > > > > Check it out at http://github.com/dirkboye/myImageLandmarker > > > > or directly clone it with > > git clone git://github.com/dirkboye/myImageLandmarker.git > > > > > > Cheers, > > Dirk > > __ > > Dirk, > > I just started looking into doing this from inside Paraview with > polydata rather than imagedata. The idea was the to be able to apply > the landmark filter to manually register two data sets without ever > leaving paraview. Do you think there is anything that could be taken > from this for my effort? Or should we leave this in a standalone QT > app and I'll continue doing it for Paraview? > > Thanks, > > David > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://www.itk.org/mailman/listinfo/insight-users > > Hi David, I've never programmed something for Paraview (just using it to try out filters and view files) so I don't know if there's anything you could use but feel free to take any code you find useful for your project. Cheers, Dirk _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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ITK support for path generation
by Prashanth Ravindran-2
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Hi All-
I have set of 2-d points, and want to use these points to generate a curve that fits all these points, and lets me test if a given 2-d point lies on the curve (with some tolerance). Are there any classes that I can use to this end? Thanks, --Prashanth _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: ITK support for path generation
by Cory Quammen
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Prashanth,
Perhaps the NonUniformBSpline class will be useful to you? If you are using VTK in your project, you could have a look at the subclasses of vtkSpline. Cory On Wed, Nov 4, 2009 at 4:47 AM, Prashanth Ravindran <prashanth@...> wrote: > Hi All- > > I have set of 2-d points, and want to use these points to generate a curve that fits all these points, and lets me test if a given 2-d point lies on the curve (with some tolerance). Are there any classes that I can use to this end? > > Thanks, > --Prashanth > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.html > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://www.itk.org/mailman/listinfo/insight-users > -- Cory Quammen Center for Computer Integrated Systems for Microscopy and Manipulation (CISMM) Department of Computer Science University of North Carolina at Chapel Hill http://www.cs.unc.edu/~cquammen _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: ITK support for path generation
by Nicholas Tustison
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Hi Prashanth,
Take a look at the following which should help you with the first part. http://www.insight-journal.org/browse/publication/57 The relevant classes are currently in the Review directory. Good luck, Nick On Nov 4, 2009, at 4:47 AM, Prashanth Ravindran wrote: > Hi All- > > I have set of 2-d points, and want to use these points to generate > a curve that fits all these points, and lets me test if a given 2-d > point lies on the curve (with some tolerance). Are there any classes > that I can use to this end? > > Thanks, > --Prashanth > > _____________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://www.kitware.com/products/protraining.html > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://www.itk.org/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: ITK support for path generation
by Prashanth Ravindran-2
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Hi Nick-
These points are not ordered, i.e one does not know which point comes before the other, also the parametrization is not known a-priori. Ordering can be done via chain coding, and I know that there is ITK support for that, however is there a ITK way of calculating the parametrization? --Prashanth > From: Nicholas Tustison <ntustison@...> > To: Prashanth Ravindran <prashanth@...> > Cc: insight-users@... > Sent: Wed, November 4, 2009 6:49:09 PM > Subject: Re: [Insight-users] ITK support for path generation > > Hi Prashanth, > > Take a look at the following which should help you with the first part. > > http://www.insight-journal.org/browse/publication/57 > > The relevant classes are currently in the Review directory. > > Good luck, > Nick > > > On Nov 4, 2009, at 4:47 AM, Prashanth Ravindran wrote: > > > Hi All- > > > > I have set of 2-d points, and want to use these points to generate a curve > that fits all these points, and lets me test if a given 2-d point lies on the > curve (with some tolerance). Are there any classes that I can use to this end? > > > > Thanks, > > --Prashanth > > > > _____________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://www.kitware.com/products/protraining.html > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://www.itk.org/mailman/listinfo/insight-users _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: ITK support for path generation
by Nicholas Tustison
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Hi Prashanth,
Your email motivated me to complete an additional portion of my B- spline code which would answer the second component of your problem, i.e. determining whether or not a given point lies on the curve (with some tolerance). What the code actually does is, in the B-spline curve case, determine the parametric values of a point on the curve closest to a user-specified point. Are you still interested in this second part? Nick On Nov 4, 2009, at 8:43 AM, Prashanth Ravindran wrote: > Hi Nick- > > These points are not ordered, i.e one does not know which point > comes before the other, also the parametrization is not known a- > priori. Ordering can be done via chain coding, and I know that > there is ITK support for that, however is there a ITK way of > calculating the parametrization? > > --Prashanth > > >> From: Nicholas Tustison <ntustison@...> >> To: Prashanth Ravindran <prashanth@...> >> Cc: insight-users@... >> Sent: Wed, November 4, 2009 6:49:09 PM >> Subject: Re: [Insight-users] ITK support for path generation >> >> Hi Prashanth, >> >> Take a look at the following which should help you with the first >> part. >> >> http://www.insight-journal.org/browse/publication/57 >> >> The relevant classes are currently in the Review directory. >> >> Good luck, >> Nick >> >> >> On Nov 4, 2009, at 4:47 AM, Prashanth Ravindran wrote: >> >>> Hi All- >>> >>> I have set of 2-d points, and want to use these points to >>> generate a curve >> that fits all these points, and lets me test if a given 2-d point >> lies on the >> curve (with some tolerance). Are there any classes that I can use >> to this end? >>> >>> Thanks, >>> --Prashanth >>> >>> _____________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Kitware offers ITK Training Courses, for more information visit: >>> http://www.kitware.com/products/protraining.html >>> >>> Please keep messages on-topic and check the ITK FAQ at: >>> http://www.itk.org/Wiki/ITK_FAQ >>> >>> Follow this link to subscribe/unsubscribe: >>> http://www.itk.org/mailman/listinfo/insight-users > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: ITK support for path generation
by Prashanth Ravindran-2
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Hi Nick-
Of course I am interested. Thanks a lot for taking the effort. Thanks -- Prashanth ----- Original Message ---- > From: Nicholas Tustison <ntustison@...> > To: Prashanth Ravindran <prashanth@...> > Cc: insight-users@... > Sent: Fri, November 6, 2009 6:07:58 AM > Subject: Re: [Insight-users] ITK support for path generation > > Hi Prashanth, > > Your email motivated me to complete an additional portion of my B-spline code > which would answer the second component of your problem, i.e. determining > whether or not a given point lies on the curve (with some tolerance). What the > code actually does is, in the B-spline curve case, determine the parametric > values of a point on the curve closest to a user-specified point. Are you still > interested in this second part? > > Nick > > > On Nov 4, 2009, at 8:43 AM, Prashanth Ravindran wrote: > > > Hi Nick- > > > > These points are not ordered, i.e one does not know which point comes before > the other, also the parametrization is not known a-priori. Ordering can be done > via chain coding, and I know that there is ITK support for that, however is > there a ITK way of calculating the parametrization? > > > > --Prashanth > > > > > >> From: Nicholas Tustison > >> To: Prashanth Ravindran > >> Cc: insight-users@... > >> Sent: Wed, November 4, 2009 6:49:09 PM > >> Subject: Re: [Insight-users] ITK support for path generation > >> > >> Hi Prashanth, > >> > >> Take a look at the following which should help you with the first part. > >> > >> http://www.insight-journal.org/browse/publication/57 > >> > >> The relevant classes are currently in the Review directory. > >> > >> Good luck, > >> Nick > >> > >> > >> On Nov 4, 2009, at 4:47 AM, Prashanth Ravindran wrote: > >> > >>> Hi All- > >>> > >>> I have set of 2-d points, and want to use these points to generate a curve > >> that fits all these points, and lets me test if a given 2-d point lies on the > >> curve (with some tolerance). Are there any classes that I can use to this > end? > >>> > >>> Thanks, > >>> --Prashanth > >>> > >>> _____________________________________ > >>> Powered by www.kitware.com > >>> > >>> Visit other Kitware open-source projects at > >>> http://www.kitware.com/opensource/opensource.html > >>> > >>> Kitware offers ITK Training Courses, for more information visit: > >>> http://www.kitware.com/products/protraining.html > >>> > >>> Please keep messages on-topic and check the ITK FAQ at: > >>> http://www.itk.org/Wiki/ITK_FAQ > >>> > >>> Follow this link to subscribe/unsubscribe: > >>> http://www.itk.org/mailman/listinfo/insight-users > > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: ITK support for path generation
by Nicholas Tustison
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Were you able to get the first part working?
On Nov 5, 2009, at 11:25 PM, Prashanth Ravindran wrote: > Hi Nick- > > Of course I am interested. Thanks a lot for taking the effort. > > Thanks > -- Prashanth > > > > ----- Original Message ---- >> From: Nicholas Tustison <ntustison@...> >> To: Prashanth Ravindran <prashanth@...> >> Cc: insight-users@... >> Sent: Fri, November 6, 2009 6:07:58 AM >> Subject: Re: [Insight-users] ITK support for path generation >> >> Hi Prashanth, >> >> Your email motivated me to complete an additional portion of my B- >> spline code >> which would answer the second component of your problem, i.e. >> determining >> whether or not a given point lies on the curve (with some >> tolerance). What the >> code actually does is, in the B-spline curve case, determine the >> parametric >> values of a point on the curve closest to a user-specified point. >> Are you still >> interested in this second part? >> >> Nick >> >> >> On Nov 4, 2009, at 8:43 AM, Prashanth Ravindran wrote: >> >>> Hi Nick- >>> >>> These points are not ordered, i.e one does not know which point >>> comes before >> the other, also the parametrization is not known a-priori. Ordering >> can be done >> via chain coding, and I know that there is ITK support for that, >> however is >> there a ITK way of calculating the parametrization? >>> >>> --Prashanth >>> >>> >>>> From: Nicholas Tustison >>>> To: Prashanth Ravindran >>>> Cc: insight-users@... >>>> Sent: Wed, November 4, 2009 6:49:09 PM >>>> Subject: Re: [Insight-users] ITK support for path generation >>>> >>>> Hi Prashanth, >>>> >>>> Take a look at the following which should help you with the first >>>> part. >>>> >>>> http://www.insight-journal.org/browse/publication/57 >>>> >>>> The relevant classes are currently in the Review directory. >>>> >>>> Good luck, >>>> Nick >>>> >>>> >>>> On Nov 4, 2009, at 4:47 AM, Prashanth Ravindran wrote: >>>> >>>>> Hi All- >>>>> >>>>> I have set of 2-d points, and want to use these points to >>>>> generate a curve >>>> that fits all these points, and lets me test if a given 2-d point >>>> lies on the >>>> curve (with some tolerance). Are there any classes that I can use >>>> to this >> end? >>>>> >>>>> Thanks, >>>>> --Prashanth >>>>> >>>>> _____________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at >>>>> http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Kitware offers ITK Training Courses, for more information visit: >>>>> http://www.kitware.com/products/protraining.html >>>>> >>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://www.itk.org/mailman/listinfo/insight-users >>> > _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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Re: ITK support for path generation
by Nicholas Tustison
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Hi Prashanth, I recently updated my N3 bias correction filter which contains the relevant B-spline code to solve the second component of your problem. Specifically, you should look at the following function in the BSplineControlPointImageFilter class CalculateParametersClosestToDataPoint() which uses the LBFGSB optimizer to find the parametric values closest to a user-specified point. One can then calculate the actual point on the curve corresponding to the minimizing parametric values by calling the function EvaluateAtPoint() and determining the distance between the two points to determine whether it satisfies the specified threshold. Let me know if you have any questions. Nick On Nov 5, 2009, at 11:25 PM, Prashanth Ravindran wrote:
_____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.html Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users |
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