Hi Yari, great. In that case I will point Matthias to your test file so he can take a look at it. https://www.dropbox.com/s/sl4x4jlch3pp5gp/test_dicom_anon.dcm?dl=0
Best, Caspar -----Ursprüngliche Nachricht----- Von: yari mattei [mailto:yari.mat...@student.supsi.ch] Gesendet: Dienstag, 23. Juni 2015 13:51 An: mitk-users@lists.sourceforge.net Betreff: Re: [mitk-users] Read different volume Hi Caspar, this is a test case for both the issue. For the timesteps, with the binary release is working fine also to me (all the timesteps are there, no crash), but I cannot manage to open it with the code I wrote following the tutorial (with timestep 0 is okay, but any other is crashing). I also tried with the code from Matthias, but is not working. Do you have any suggestion? I will answer about the mirroring issue in the other thread so I won't mix up the two topic :) Cheers, Yari Il 23.06.2015 13:17, Goch, Caspar Jonas ha scritto: > Hi Yari, > > this was a test case for the mirroring issue or the dicom loading issue? > > Either way, I tested it in the 2015.05 binary release on Windows and just > dragging and dropping it works fine (all timesteps are there, no crash). I am > then able to segment and the surface fits the image for me. > > Can you confirm this using the binary release? > > Best, > Caspar > > -----Ursprüngliche Nachricht----- > Von: yari mattei [mailto:yari.mat...@student.supsi.ch] > Gesendet: Dienstag, 23. Juni 2015 10:13 > An: mitk-users@lists.sourceforge.net > Betreff: Re: [mitk-users] Read different volume > > Hi guys, > > I finally obtained a sharable example of a DICOM file which cause the problem. > > I put it on dropbox this is the link to download it : > > https://www.dropbox.com/s/sl4x4jlch3pp5gp/test_dicom_anon.dcm?dl=0 > > I hope you find it helpful to find out what's going on :) > > Best, > > Yari > > Il 15.06.2015 10:44, Eisenmann, Matthias ha scritto: >> Hi Yari, >> >> now I attached the file mentioned in our last mail, sorry! >> >> Maybe I can investigate your other questions during our next bug squashing >> session on Wednesday. >> It would be great if you could double-check it with the provided code >> example. >> >> Best, >> Matthias >> >> -----Ursprüngliche Nachricht----- >> Von: yari mattei [mailto:yari.mat...@student.supsi.ch] >> Gesendet: Donnerstag, 11. Juni 2015 09:11 >> An: mitk-users@lists.sourceforge.net >> Betreff: Re: [mitk-users] Read different volume >> >> Hi guys, >> >> Sorry for the late answer. I am using the 2014.10.0 release of MITK do you >> think the bug is present in this version? Do you think is better to work >> directly on the master branch? >> >> I unfortunately didn't recieve any attachment, is it possible for you to >> send it to me? >> >> The code of my reader is the following (sorry if I didn't share it before): >> >> mitk::DataNode::Pointer MyMITKDICOMReader::readPhilips3D(const char >> *filename){ >> //intance of the DICOM reader >> mitk::DicomSeriesReader reader = mitk::DicomSeriesReader(); >> //check if the file is a Philips 3D DICOM >> if (!reader.IsPhilips3DDicom(filename)){ >> MITK_DEBUG << "THE FILE : " << filename << "IS NOT A PHILIPS 3D >> DICOM ! "; >> return NULL; >> } >> >> mitk::StringList files = mitk::StringList(); >> files.push_back(filename); >> >> UpdateCallBackMethod callback = false; >> >> mitk::Image::Pointer preLoadedImageBlock; >> >> return reader.LoadDicomSeries(files, true, true, false, >> callback, preLoadedImageBlock); } >> >> Thanks for whole the help. >> >> Best, >> >> Yari >> >> >> Il 03.06.2015 14:55, Eisenmann, Matthias ha scritto: >>> Hi Yari, >>> >>> we had a further look at it. Since you did not provide the complete code >>> (your own DICOM reader is missing), we adapted the MITK Tutorial Step 3 >>> Application (see attachment). We added the ImageTimeSelector to be >>> compatible with your code snippet. We could not reproduce the crash. >>> >>> Are you working with the current master branch? >>> There were some problems reading 4D-DICOM data in MITK due to an ITK update >>> some months ago (http://bugs.mitk.org/show_bug.cgi?id=18887). But that >>> seems to be fixed. >>> >>> Can you provide your complete cpp file and your data set if updating your >>> code base does not help? >>> >>> Best, >>> Matthias and Thomas >>> >>> -----Ursprüngliche Nachricht----- >>> Von: yari mattei [mailto:yari.mat...@student.supsi.ch] >>> Gesendet: Donnerstag, 28. Mai 2015 15:38 >>> An: mitk-users@lists.sourceforge.net >>> Betreff: Re: [mitk-users] Read different volume >>> >>> Hi guys, >>> >>> thanks a lot, what are you saying i totally right, after the update the >>> data are loaded. But when I am trinyg to display the image the application >>> crash. >>> >>> The code I wrote is the following : >>> >>> // Create a QApplication instance first >>> QApplication eco3DApp(argc, argv); >>> eco3DApp.setApplicationName("Eco 3D"); >>> >>> QmitkRegisterClasses(); >>> >>> mitk::StandaloneDataStorage::Pointer ds = >>> mitk::StandaloneDataStorage::New(); >>> >>> MyMITKDICOMReader myReader = MyMITKDICOMReader(); >>> >>> mitk::DataNode::Pointer node = >>> myReader.readPhilips3D("filePath"); >>> >>> //ds->Add(node); >>> mitk::Image::Pointer image = >>> dynamic_cast<mitk::Image*>(node->GetData()); >>> >>> //take a time >>> mitk::ImageTimeSelector::Pointer timeSelector = >>> mitk::ImageTimeSelector::New(); >>> >>> int timeStep = 1; >>> >>> timeSelector->SetInput( image ); >>> timeSelector->SetTimeNr( timeStep ); >>> timeSelector->Update(); >>> //timeSelector->UpdateLargestPossibleRegion(); >>> >>> >>> mitk::Image::Pointer timeStepImage = >>> timeSelector->GetOutput(); >>> >>> mitk::DataNode::Pointer stepImageNode = >>> mitk::DataNode::New(); >>> >>> stepImageNode->SetData(timeStepImage); >>> stepImageNode->Update(); >>> ds->Add(stepImageNode); >>> >>> QmitkRenderWindow renderWindow; >>> >>> // Tell the RenderWindow which (part of) the datastorage to render >>> renderWindow.GetRenderer()->SetDataStorage(ds); >>> >>> // Initialize the RenderWindow >>> mitk::TimeGeometry::Pointer geo = >>> ds->ComputeBoundingGeometry3D(ds->GetAll()); >>> mitk::RenderingManager::GetInstance()->InitializeViews(geo); >>> >>> renderWindow.show(); >>> renderWindow.resize(400, 400); //256, 256 original >>> renderWindow.move(QPoint(500, 100)); >>> >>> return eco3DApp.exec(); >>> >>> When I launch it, it crash after the eco3DApp.exec() call, with this >>> error >>> >>> Unhandled exception at 0x020B55DA (MitkCore.dll) in AwesomeApp.exe: >>> 0xC0000005: Access violation reading location 0x00000000. >>> >>> exactely in : >>> >>> > >>> MitkCore.dll!mitk::ImageDataItem::ConstructVtkImageData(itk::SmartPointer<mitk::Image >>> const > iP) Line 234 C++ >>> >>> line 254 is : >>> >>> const mitk::Vector3D vspacing = geom3d->GetSpacing(); >>> >>> Thanks for the help. >>> >>> Cheers >>> Yari >>> >>> >>> Il 28.05.2015 10:12, Eisenmann, Matthias ha scritto: >>>> Hi Yari, >>>> >>>> we had a look at your problem during our bug squashing session. We can >>>> reproduce the situation you described: After loading a 3D+t image only the >>>> first volume is initialized. >>>> >>>> Are you just wondering why this is the case or does your application crash? >>>> >>>> In our cases this is not a problem. The other volumes are initialized 'on >>>> demand' after calling the Update() method of ImageTimeSelector for a >>>> specific time step. >>>> >>>> Let us give you a pointer to a working example: The binary threshold tool >>>> of the segmentation plugin. >>>> In method >>>> mitk::BinaryThresholdTool::CreateNewSegmentationFromThreshold(...) each >>>> volume of a time series is processed. >>>> >>>> Best, >>>> Matthias and Thomas >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: yari mattei [mailto:yari.mat...@student.supsi.ch] >>>> Gesendet: Montag, 18. Mai 2015 14:32 >>>> An: mitk-users@lists.sourceforge.net >>>> Betreff: [mitk-users] Read different volume >>>> >>>> Hi everybody, >>>> >>>> I manage to open a Philips3D DICOM (with mithDicomSeriesReader) and I get >>>> a DataNode. >>>> >>>> I would like to show the 9 different time step contained in the DICOM file >>>> so I tried to get an image from the node with: >>>> >>>> mitk::Image::Pointer image = >>>> dynamic_cast<mitk::Image*>(node->GetData()); >>>> >>>> And to select the volume with: >>>> >>>> mitk::ImageTimeSelector::Pointer time = >>>> mitk::ImageTimeSelector::New(); >>>> >>>> time->SetInput(image); >>>> time->SetTimeNr(1); >>>> time->Update(); >>>> >>>> mitk::Image::Pointer image4 = time->GetOutput(); >>>> >>>> >>>> mitk::StandaloneDataStorage::Pointer ds4 = >>>> mitk::StandaloneDataStorage::New(); >>>> mitk::DataNode::Pointer node4 = mitk::DataNode::New(); >>>> >>>> node4->SetData(image4); >>>> >>>> ds4->Add(node4); >>>> >>>> This works only if I set the TimeNr to 0. I check with the debugger the >>>> value of the image and I see that there are 9 different volume but only >>>> the first one has values inside (the others are NULL). >>>> This is part of the dump of the debugger : >>>> - image {m_Pointer=0x164978e0 {m_Channels={ size=1 } >>>> m_Volumes={ size=9 } m_Slices={ size=1872 } ...} } >>>> itk::SmartPointer<mitk::Image> >>>> - m_Pointer 0x164978e0 {m_Channels={ size=1 } >>>> m_Volumes={ >>>> size=9 } m_Slices={ size=1872 } ...} mitk::Image * >>>> + [mitk::Image] {m_Channels={ size=1 } m_Volumes={ >>>> size=9 } m_Slices={ size=1872 } ...} MitkCore.dll!mitk::Image >>>> + mitk::SlicedData >>>> {m_LargestPossibleRegion={m_Index={m_Index=0x16497984 {0, 0, 0, 0, >>>> 0} } >>>> m_Size={m_Size=0x16497998 {224, ...} } } ...} mitk::SlicedData >>>> + m_Channels { size=1 } >>>> std::vector<itk::SmartPointer<mitk::ImageDataItem>,std::allocator<itk::SmartPointer<mitk::ImageDataItem> >>>> > > >>>> - m_Volumes { size=9 } >>>> std::vector<itk::SmartPointer<mitk::ImageDataItem>,std::allocator<itk::SmartPointer<mitk::ImageDataItem> >>>> > > >>>> [size] 9 int >>>> [capacity] 9 int >>>> + [0] {m_Pointer=0x1641ba88 {m_Data=0x235b0040 >>>> "" m_PixelType=0x164af8a8 {m_ComponentType=1 m_PixelType=SCALAR (1) ...} >>>> ...} } itk::SmartPointer<mitk::ImageDataItem> >>>> + [1] {m_Pointer=0x00000000 <NULL> } >>>> itk::SmartPointer<mitk::ImageDataItem> >>>> + [2] {m_Pointer=0x00000000 <NULL> } >>>> itk::SmartPointer<mitk::ImageDataItem> >>>> + [3] {m_Pointer=0x00000000 <NULL> } >>>> itk::SmartPointer<mitk::ImageDataItem> >>>> ....... >>>> >>>> >>>> Does anyone have any idea of what cause di problem? >>>> >>>> Thanks in advance >>>> >>>> Yari >>>> >>>> ------------------------------------------------------------------- >>>> - >>>> - >>>> - >>>> -------- One dashboard for servers and applications across >>>> Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ >>>> applications Performance metrics, stats and reports that give you >>>> Actionable Insights Deep dive visibility with transaction tracing using >>>> APM Insight. >>>> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y >>>> _______________________________________________ >>>> mitk-users mailing list >>>> mitk-users@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/mitk-users >>> -------------------------------------------------------------------- >>> - >>> - >>> -------- _______________________________________________ >>> mitk-users mailing list >>> mitk-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/mitk-users >> --------------------------------------------------------------------- >> - >> -------- _______________________________________________ >> mitk-users mailing list >> mitk-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/mitk-users > > ---------------------------------------------------------------------- > -------- Monitor 25 network devices or servers for free with > OpManager! > OpManager is web-based network management software that monitors > network devices and physical & virtual servers, alerts via email & sms > for fault. Monitor 25 devices for free with no restriction. Download > now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o > _______________________________________________ > mitk-users mailing list > mitk-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mitk-users ------------------------------------------------------------------------------ Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical & virtual servers, alerts via email & sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o _______________________________________________ mitk-users mailing list mitk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mitk-users ------------------------------------------------------------------------------ Monitor 25 network devices or servers for free with OpManager! OpManager is web-based network management software that monitors network devices and physical & virtual servers, alerts via email & sms for fault. Monitor 25 devices for free with no restriction. Download now http://ad.doubleclick.net/ddm/clk/292181274;119417398;o _______________________________________________ mitk-users mailing list mitk-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mitk-users
