Hi Yari,
this is fixed on our current master, although not in our latest release. You
can switch to the current master (which could be instable somewhere else) or
just do the following quick fix:
in the file Modules/Core/src/Algorithms/mitkImageTimeSelector.cpp
@@ -73,8 +73,12 @@ void mitk::ImageTimeSelector::GenerateData()
const Image::RegionType& requestedRegion =
this->GetOutput()->GetRequestedRegion();
//do we really need a complete volume at a time?
- if(requestedRegion.GetSize(2)>1)
- this->SetVolumeItem( this->GetVolumeData(m_TimeNr, m_ChannelNr), 0 );
+ if (requestedRegion.GetSize(2) > 1)
+ {
+ mitk::ImageDataItem::Pointer im = this->GetVolumeData(m_TimeNr,
m_ChannelNr)->Clone();
+ im->SetTimestep(0);
+ this->SetVolumeItem(im, 0);
+ }
Have fun!
Matthias and Thomas
-----Ursprüngliche Nachricht-----
Von: Goch, Caspar Jonas
Gesendet: Dienstag, 23. Juni 2015 14:00
An: 'yari mattei'; 'mitk-users@lists.sourceforge.net'; Eisenmann, Matthias
Betreff: AW: [mitk-users] Read different volume
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
>>>>
>>>> -------------------------------------------------------------------
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>>> --------------------------------------------------------------------
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>
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------------------------------------------------------------------------------
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network devices and physical & virtual servers, alerts via email & sms
for fault. Monitor 25 devices for free with no restriction. Download now
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