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

azmagillian xrysafenia.malliastolidou at gmail.com
Tue Nov 19 05:00:08 EST 2013 

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