[Insight-users] [ITK Community] 3d SEGMENTATION OF .OBJ FILE

Tue Nov 19 02:48:37 EST 2013

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] <
ml-node+s2283740n7584406h17 at n2.nabble.com>

> 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?
> >>> >> > >
> >>> >> > >
> >>> >> > >
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