Hi,
thanks for the hint about the iterator. Indeed that was missing in my
snippet. However the cast of the images in the scene files to mitk::image*
fails. I did some further research about the scene files. They were created
using MITK workbench 2012-06. When loading the scene files into MITK
workbench 2012-09 and saved again, the errors at casting to mitk::image*
disappear.
Here is the mitk log when loading the files acquired with MITK 2012-06:
tisch@tisch-Precision-M6500:~/lib/MITK/bin/MITK-build/bin$ ./mitkWorkbench
[Fri Oct 5 18:36:51 2012
0.350] Registering PicFileIOFactory
Fri Oct 5 18:36:51 2012 Debug: org.commontk.eventadmin.LogLevel=2
in startOrUpdate,
/home/tisch/lib/MITK/bin/CTK-src/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215
Fri Oct 5 18:36:51 2012 Debug: org.commontk.eventadmin.CacheSize=30
in startOrUpdate,
/home/tisch/lib/MITK/bin/CTK-src/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217
Fri Oct 5 18:36:51 2012 Debug: org.commontk.eventadmin.ThreadPoolSize=20
in startOrUpdate,
/home/tisch/lib/MITK/bin/CTK-src/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219
Fri Oct 5 18:36:51 2012 Debug: org.commontk.eventadmin.Timeout=5000
in startOrUpdate,
/home/tisch/lib/MITK/bin/CTK-src/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221
Fri Oct 5 18:36:51 2012 Debug: org.commontk.eventadmin.RequireTopic=true
in startOrUpdate,
/home/tisch/lib/MITK/bin/CTK-src/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223
Fri Oct 5 18:36:51 2012 Debug: org.commontk.eventadmin.LogLevel=2
in startOrUpdate,
/home/tisch/lib/MITK/bin/CTK-src/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:215
Fri Oct 5 18:36:51 2012 Debug: org.commontk.eventadmin.CacheSize=30
in startOrUpdate,
/home/tisch/lib/MITK/bin/CTK-src/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:217
Fri Oct 5 18:36:51 2012 Debug: org.commontk.eventadmin.ThreadPoolSize=20
in startOrUpdate,
/home/tisch/lib/MITK/bin/CTK-src/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:219
Fri Oct 5 18:36:51 2012 Debug: org.commontk.eventadmin.Timeout=5000
in startOrUpdate,
/home/tisch/lib/MITK/bin/CTK-src/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:221
Fri Oct 5 18:36:51 2012 Debug: org.commontk.eventadmin.RequireTopic=true
in startOrUpdate,
/home/tisch/lib/MITK/bin/CTK-src/Plugins/org.commontk.eventadmin/ctkEAConfiguration.cpp:223
[0.400] Logfile: /home/tisch/.local/share/data/DKFZ/MITK
Workbench_263351614/data/15/mitk.log
[0.770] [BlueBerry] BlueBerry Workbench ready
#2.360# ERROR: No property reader found for SmartPointerProperty
#2.370# ERROR: There were errors while loding property list file
/home/tisch/.mitk/SceneIOTempDirectory1572/naaaaa. Your data may be
corrupted
#2.370# ERROR: Could not load properties for node.
#2.490# ERROR: No property reader found for SmartPointerProperty
#2.490# ERROR: There were errors while loding property list file
/home/tisch/.mitk/SceneIOTempDirectory1572/oaaaaa. Your data may be
corrupted
#2.490# ERROR: Could not load properties for node.
#2.620# ERROR: No property reader found for SmartPointerProperty
#2.620# ERROR: There were errors while loding property list file
/home/tisch/.mitk/SceneIOTempDirectory1572/paaaaa. Your data may be
corrupted
#2.620# ERROR: Could not load properties for node.
[2.630] Loading /home/tisch/.mitk/SceneIOTempDirectory1572/paaaaa_c5.vtp as
vtk
[2.640] [shader.repository] found default mitk shader at
'/home/tisch/lib/MITK/Core/Code/Rendering'
[2.640] [shader.repository] found shader 'mitkShaderLighting'
[2.660] Loading /home/tisch/.mitk/SceneIOTempDirectory1572/qaaaaa_c4.vtp as
vtk
[2.680] Loading /home/tisch/.mitk/SceneIOTempDirectory1572/raaaaa_c3.vtp as
vtk
#2.780# ERROR: No property reader found for SmartPointerProperty
#2.780# ERROR: There were errors while loding property list file
/home/tisch/.mitk/SceneIOTempDirectory1572/taaaaa. Your data may be
corrupted
#2.780# ERROR: Could not load properties for node.
#2.880# ERROR: No property reader found for SmartPointerProperty
#2.880# ERROR: There were errors while loding property list file
/home/tisch/.mitk/SceneIOTempDirectory1572/uaaaaa. Your data may be
corrupted
#2.880# ERROR: Could not load properties for node.
[2.890] Loading /home/tisch/.mitk/SceneIOTempDirectory1572/uaaaaa_c7.vtp as
vtk
[2.900] Loading /home/tisch/.mitk/SceneIOTempDirectory1572/vaaaaa_c6.vtp as
vtk
#2.960# ERROR: There were errors while loding scene file
/home/tisch/.mitk/SceneIOTempDirectory1572/index.xml. Your data may be
corrupted
#2.960# ERROR: There were errors while loding scene file
/home/tisch/data/4Planitzer/Patient_ap.mitk. Your data may be corrupted
Thanks,
Stefan
On Fri, Oct 5, 2012 at 5:49 PM, Sascha Zelzer
<[email protected]>wrote:
> Maybe I just don't see it... where are you incrementing the "objIt"
> iterator?
>
> - Sascha
>
>
> On 10/05/2012 01:19 PM, Stefan Dänzer wrote:
>
> 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
>
>
>
--
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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