[ITK Community] [Insight-users] 3d SEGMENTATION OF .OBJ FILE
Brian Helba
brian.helba at kitware.com
Tue Nov 19 10:04:12 EST 2013
Hi,
I assume that line 40 is "connector->SetInput(reader->GetOutput());".
vtkImageData is derived from vtkDataObject, but you may need to downcast.
Try calling vtkImageData::SafeDownCast [1] on the object returned by
"reader->GetOutput()", before passing it to "connector->SetInput(..)".
If that doesn't work, you can try using
"reader->GetOutput()->Print(std::cout);" to get some information on the
object, to help with debugging.
[1]
http://www.vtk.org/doc/nightly/html/classvtkImageData.html#ae4345f90722e82bec2f70f5d5a5b1f38
Enjoy,
Brian
On Tue, Nov 19, 2013 at 5:00 AM, azmagillian <
xrysafenia.malliastolidou at gmail.com> wrote:
> thanks for replying!
> i tried that but the below code gives me error: error C2664: ' cannot
> convert parameter 1 from 'vtkDataObject *' to 'vtkImageData *'
>
> d:\InsightToolkit-4.4.2\Modules\Bridge\VtkGlue\test\itkVTKImageToImageFilterTest.cxx
> 40
>
>
> int itkVTKImageToImageFilterTest(int, char*[])
> {
> typedef itk::Image<double, 2> ImageType;
>
> typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
>
> std::string inputFilename = "C:\\build_test2read\\test3vtk";
>
> // Get all data from the file
> vtkSmartPointer<vtkGenericDataObjectReader> reader =
> vtkSmartPointer<vtkGenericDataObjectReader>::New();
> reader->SetFileName(inputFilename.c_str());
> reader->Update();
>
>
> ConnectorType::Pointer connector = ConnectorType::New();
> connector->SetInput(reader->GetOutput());
> connector->Update();
>
> connector->GetOutput()->Print(std::cout);
> connector->GetImporter()->Print(std::cout);
> connector->GetExporter()->Print(std::cout);
>
> connector->Print(std::cout);
>
> return EXIT_SUCCESS;
> }
>
>
>
>
>
> 2013/11/19 Jon Haitz Legarreta Gorroño [via ITK Insight Users] <
> ml-node+s2283740n7584410h41 at n2.nabble.com>
>
> > Hi,
> > you should replace the vtkImageNoiseSource for a VTK file type reader.
> The
> > following [1] example ilustrates how to proceed.
> >
> > In the example Matt pointed, the VTK image source is vtkImageNoiseSource,
> > which creates an image filled with noise.
> >
> > So you would connect the output of your reader to the connector:
> >
> > std::string inputFilename = argv[1];
> > // Get all data from the file
> > vtkSmartPointer<vtkGenericDataObjectReader> reader =
> > vtkSmartPointer<vtkGenericDataObjectReader>::New();
> > reader->SetFileName(inputFilename.c_str());
> >
> > connector->SetInput(reader->GetOutput());
> >
> >
> > HTH,
> > JON HAITZ
> >
> >
> > [1] www.vtk.org/Wiki/VTK/Examples/Cxx/IO/GenericDataObjectReader
> >
> >
> >
> >
> > On 19 November 2013 08:48, azmagillian <[hidden email]<
> http://user/SendEmail.jtp?type=node&node=7584410&i=0>
> > > wrote:
> >
> >> Matt thank you so much! I think that's what i need but for 3 dimensions
> >>
> >> so below at the code i should change Image<double,2> to Image<double,3>?
> >> and where should i put my file .vtk input ??
> >>
> >>
> >> #include "itkVTKImageToImageFilter.h"
> >> 20
> >> 21 #include "vtkImageNoiseSource.h"
> >> 22 #include "vtkSmartPointer.h"
> >> 23
> >> 24 int itkVTKImageToImageFilterTest(int, char*[])
> >> 25 {
> >> 26 typedef itk::Image<double, 2> ImageType;
> >> 27 typedef vtkSmartPointer<vtkImageNoiseSource> VTKNoiseType;
> >> 28 typedef itk::VTKImageToImageFilter<ImageType> ConnectorType;
> >> 29
> >> 30 VTKNoiseType noise_source = VTKNoiseType::New();
> >> 31 noise_source->SetWholeExtent(0,20,0,20,0,0);
> >> 32 noise_source->SetMinimum(0.0);
> >> 33 noise_source->SetMaximum(1.0);
> >> 34 noise_source->Update();
> >> 35
> >> 36 ConnectorType::Pointer connector = ConnectorType::New();
> >> 37 connector->SetInput(noise_source->GetOutput());
> >> 38 connector->Update();
> >> 39
> >> 40 connector->GetOutput()->Print(std::cout);
> >> 41 connector->GetImporter()->Print(std::cout);
> >> 42 connector->GetExporter()->Print(std::cout);
> >> 43
> >> 44 connector->Print(std::cout);
> >> 45
> >> 46 return EXIT_SUCCESS;
> >> 47 }
> >>
> >>
> >> 2013/11/18 Matt McCormick-2 [via ITK Insight Users] <
> >> [hidden email] <http://user/SendEmail.jtp?type=node&node=7584410&i=1>>
> >>
> >>
> >> > Hi,
> >> >
> >> > Code to convert a VTK ImageData to an ITK Image can be found in the
> >> > ITKVtkGlue module [1].
> >> >
> >> > Hope this helps,
> >> > Matt
> >> >
> >> > [1]
> >> >
> >>
> http://itk.org/gitweb?p=ITK.git;a=blob;f=Modules/Bridge/VtkGlue/test/itkVTKImageToImageFilterTest.cxx;h=b22c9e8685cf26290249554d58232d3d14b24a97;hb=HEAD
> >> >
> >> > On Mon, Nov 18, 2013 at 5:14 AM, azmagillian
> >> > <[hidden email] <http://user/SendEmail.jtp?type=node&node=7584406&i=0
> >>
> >>
> >> > wrote:
> >> >
> >> > > Jon you said you made a filter to "transform your VTK data object
> to
> >> an
> >> > > ITK image so that you can use ITK's segmentation filter."
> >> > >
> >> > > Where can i find it?
> >> > >
> >> > > Thanks!!!
> >> > >
> >> > >
> >> > > 2013/11/15 Jon Haitz Legarreta Gorroño [via ITK Insight Users] <
> >> > > [hidden email] <
> http://user/SendEmail.jtp?type=node&node=7584406&i=1
> >> >>
> >>
> >> > >
> >> > >> You should either use the filter Hans mentioned or the one I did to
> >> > >> transform your VTK data object to an ITK image so that you can use
> >> > ITK's
> >> > >> segmentation filter.
> >> > >>
> >> > >> JON HAITZ
> >> > >>
> >> > >>
> >> > >>
> >> > >> On 15 November 2013 10:19, azmagillian <[hidden email]<
> >> > http://user/SendEmail.jtp?type=node&node=7584387&i=0>
> >> > >> > wrote:
> >> > >>
> >> > >>> Thank you all again !
> >> > >>>
> >> > >>> As i figured the first step would be to apply the Conncted
> Threshold
> >> > Image
> >> > >>> Filter to 3d input
> >> > >>>
> >> > >>> what changes should i make to the code?
> >> > >>> can i use as an input .vtk file (i converted .obj file to .vtk ) ?
> >> > >>>
> >> > >>>
> >> > >>> 2013/11/14 Jon Haitz Legarreta Gorroño [via ITK Insight Users] <
> >> > >>> [hidden email] <
> >> http://user/SendEmail.jtp?type=node&node=7584387&i=1>>
> >> >
> >> > >>>
> >> > >>>
> >> > >>> > Hi there,
> >> > >>> > you can find ITK's region growing segmentation filters here:
> >> > >>> >
> >> > http://www.itk.org/Doxygen/html/group__RegionGrowingSegmentation.html
> >> > >>> >
> >> > >>> > You will find some guidelines to use them in the ITK SW guide:
> >> > >>> > http://www.itk.org/ItkSoftwareGuide.pdf (not up-to-date, but
> >> there
> >> > is
> >> > >>> an
> >> > >>> > ongoing effort to make it again).
> >> > >>> >
> >> > >>> > HTH,
> >> > >>> > JON HAITZ
> >> > >>> >
> >> > >>> >
> >> > >>> > On 14 November 2013 15:09, azmagillian <[hidden email]<
> >> > >>> http://user/SendEmail.jtp?type=node&node=7584364&i=0>
> >> > >>>
> >> > >>> > > wrote:
> >> > >>> >
> >> > >>> >> Hans thanks for replying!
> >> > >>> >>
> >> > >>> >> right now i have successfully read and display my .obj with vtk
> >> > >>> >>
> >> > >>> >> for next step what should i do to use on this an itk filter ?
> >> > >>> >>
> >> > >>> >> also is there code for seeded 3D region growing segmentation ?
> >> > >>> >>
> >> > >>> >> i didn't get how to use this code
> >> > >>> >> http://insight-journal.org/browse/publication/178
> >> > >>> >>
> >> > >>> >>
> >> > >>> >> 2013/11/14 Johnson, Hans J [via ITK Insight Users] <
> >> > >>> >> [hidden email] <
> >> > http://user/SendEmail.jtp?type=node&node=7584364&i=1>>
> >> > >>>
> >> > >>> >>
> >> > >>> >>
> >> > >>> >> > There is some code that can allow conversion. It is not
> fully
> >> > >>> >> documented,
> >> > >>> >> > but last time I tried, it worked well.
> >> > >>> >> >
> >> > >>> >> > http://insight-journal.org/browse/publication/178
> >> > >>> >> >
> >> > >>> >> >
> >> > >>> >> > Hans
> >> > >>> >> >
> >> > >>> >> >
> >> > >>> >> >
> >> > >>> >> > On 11/14/13, 6:06 AM, "azmagillian" <[hidden email]<
> >> > >>> >> http://user/SendEmail.jtp?type=node&node=7584358&i=0>>
> >> > >>> >>
> >> > >>> >> >
> >> > >>> >> > wrote:
> >> > >>> >> >
> >> > >>> >> > >Dear, ITK users , thanks in advance for your help
> >> > >>> >> > >
> >> > >>> >> > >I want to perform 3d segmentation of a .obj file
> >> > >>> >> > >my thought was to use connectedthreshold but there is not an
> >> > example
> >> > >>> >> for
> >> > >>> >> > >3d
> >> > >>> >> > >then i tried to use confidenceconnected threshold but i
> can't
> >> > give
> >> > >>> a.
> >> > >>> >> obj
> >> > >>> >> > >as
> >> > >>> >> > >input
> >> > >>> >> > >
> >> > >>> >> > >any ideas ?
> >> > >>> >> > >is there a way to convert .obj to a format suitable for itk
> >> > filters?
> >> > >>> >> > >
> >> > >>> >> > >
> >> > >>> >> > >
> >> > >>> >> > >--
> >> > >>> >> > >View this message in context:
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> >> > >>> >> >
> >> > >>> >>
> >> > >>>
> >> >
> >>
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> >> > >>> >> > >-tp7584357.html
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Medical Imaging
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