Hello Andreas,
I can't confirm having mitkPlanarCircles in the mitk scene. The retrieval
of all images (image and segmentations) fails, while extracting the
surfaces works fine. the reason is that the cast to mitk::Image* fails.
However I have found a workaround by opening the corresponding 2012-06
scene file with mitk 2012-09 and saving it again. I'm then able to extract
the whole scene from the new file correctly with my application.
Stefan
On Mon, Oct 8, 2012 at 10:03 AM, Fetzer, Andreas <
[email protected]> wrote:
> Hi Stefan,
>
> in version 2012.06 we had some problems with corrupt scene files. The
> reason for that was an uninitialized planar figure which is used within the
> context of our 3D interpolation. However as you noticed this issue is
> resolved with version 2012.09. I guess the "someSurface" nodes of your
> scene file are actually mitkPlanarCircles. Their icon in the data manager
> should be a blue circle and they should be named "Position XYZ". In this
> case your dynamic cast for mitkSurfaces would always fail. Could you check
> that?
>
> Best regards
> Andreas
>
> On 05.10.2012, at 18:45, Stefan Dänzer wrote:
>
> 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]
> <mailto:[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<tel:%2B49-157-84993879>
>
> "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
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>
> http://p.sf.net/sfu/newrelic-dev2dev_______________________________________________
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>
>
--
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
------------------------------------------------------------------------------
Don't let slow site performance ruin your business. Deploy New Relic APM
Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
http://p.sf.net/sfu/newrelic-dev2dev
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