Hi Stefan,
at first glance I can't see any big mistake. Can you please describe in what
"trouble" you are? Are there runtime errors/crashes? Are the files incomplete
or something? Or is there any compilation error in your pasted code?
Regards
Thomas
From: Stefan Dänzer [mailto:[email protected]]
Sent: Freitag, 5. Oktober 2012 13:19
To: [email protected]
Subject: [mitk-users] Extract single files from Serialized MITK Scene
Hi all,
I've been trying to write a console application to extract all images (as .mhd)
and surfaces (as plain text .vtk) contained in a .mitk scene file. However I
have trouble to extract the corresponding files.
I have linked my application against MITK 2012-09 compiled from source. I can
open the scene in the mitkWorkbench, so I guess I must be missing something.
The scene layout is as follows:
someImage
|-someSegmentation1
|-someSurface1
|-someSegmentation2
|-someSurface2
|-someSegmentation3
|-someSurface3
where someSurface1 is the child of someSegmentation1 and someSegmentation1 is
the child of someSegmentation
Here is the snippet from the console app to extract the nodes as vtk-surface or
mhd-image:
// check if output folder exists, if not create the folder.
boost::filesystem::path dir( outputFolder);
if (boost::filesystem::create_directory(dir))
std::cout << "Created " << outputFolder << "\n";
else
std::cout << "Warning could not create " << outputFolder << "\n";
mitk::SceneIO::Pointer sceneIO = mitk::SceneIO::New();
mitk::DataStorage::Pointer dataStorage = sceneIO->LoadScene( inputFilename);
mitk::DataStorage::SetOfObjects::ConstPointer sceneObjs =
dataStorage->GetAll();
mitk::DataStorage::SetOfObjects::ConstIterator objIt = sceneObjs->Begin();
while(objIt != sceneObjs->End())
{
mitk::DataNode::Pointer node = objIt->Value();
std::cout << node->GetName() << std::endl;
std::string name = node->GetName();
std::string path;
path.append( outputFolder);
path.append( name);
// test dynamic_cast to image and to surface.
if( dynamic_cast<mitk::Image*>( node->GetData()))
{
mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData());
mitk::ImageWriter::Pointer imWriter = mitk::ImageWriter::New();
path.append( ".mhd");
imWriter->SetInput( image);
imWriter->SetFileName( path);
imWriter->Write();
}
else if( dynamic_cast<mitk::Surface*>( node->GetData()))
{
mitk::Surface::Pointer surface = dynamic_cast<mitk::Surface*>(
node->GetData());
mitk::SurfaceVtkWriter<vtkPolyDataWriter>::Pointer surfWriter =
mitk::SurfaceVtkWriter<vtkPolyDataWriter>::New();
path.append( ".vtk");
surfWriter->SetInput( surface);
surfWriter->SetFileName( path);
surfWriter->Write();
}
}
Thanks for any advice in advance,
Stefan
--
Stefan Daenzer
Körnerplatz 8
04107 Leipzig
Tel.: +49-157-84993879
"Work like you don't need the money, love like you've never been hurt and dance
like no one is watching." - Randall G Leighton
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