[ITK Community] [Insight-users] 3d SEGMENTATION OF .OBJ FILE
azmagillian
xrysafenia.malliastolidou at gmail.com
Wed Nov 20 03:58:23 EST 2013
hi to all ! i tried vtkImageData::SafeDownCast as Brian said but now i get
the below errors
Error 1 error LNK2019: unresolved external symbol "public: void
__thiscall vtkImageAlgorithm::SetInput(class vtkDataObject *)"
(?SetInput at vtkImageAlgorithm@@QAEXPAVvtkDataObject@@@Z) referenced in
function "public: void __thiscall itk::VTKImageToImageFilter<class
itk::Image<double,3> >::SetInput(class vtkImageData *)" (?SetInput@
?$VTKImageToImageFilter at V?$Image at N$02 at itk@@@itk@@QAEXPAVvtkImageData@@@Z)
itkVTKImageToImageFilterTest.obj
Error 2 fatal error LNK1120: 1 unresolved externals
D:\build_itk_2\bin\Debug\ITKVtkGlueTestDriver.exe
2013/11/19 Brian Helba [via ITK Insight Users] <
ml-node+s2283740n7584412h3 at n2.nabble.com>
> 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 <[hidden email]<http://user/SendEmail.jtp?type=node&node=7584412&i=0>
> > 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] <
>> [hidden email] <http://user/SendEmail.jtp?type=node&node=7584412&i=1>>
>>
>>
>> > 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:
>> >> > >>> >> > >
>> >> > >>> >> >
>> >> > >>> >>
>> >> > >>>
>> >> >
>> >>
>> http://itk-insight-users.2283740.n2.nabble.com/3d-SEGMENTATION-OF-OBJ-FILE
>> >> > >>> >> > >-tp7584357.html
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> Brian Helba
> Medical Imaging
> Kitware, Inc.
>
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