Dear Samuel,
so far, your image seems tob e correct.
You could also check m_Dimensions[3], it should be 12.
The Geometry3D vector is inherited from the Superclass, BaseData.
It has a member m_TimeSLicedGeometries, which then has a member m_Geometry3Ds,
which has to be a vector containing a Geometry3D for every image time step.
Hope this helps,
Tobias
------------------------------------------------------------
Tobias Schwarz
DKFZ
German Cancer Research Center (Deutsches Krebsforschungszentrum)
Member of the Helmholtz Association
Division of Medical & Biological Informatics E130
Im Neuenheimer Feld 280
D-69120 Heidelberg
Phone: 49-(0)6221-42-2353
Fax: 49-(0)6221-42-2345
E-Mail: [email protected]<mailto:[email protected]>
Web: www.dkfz.de<http://www.dkfz.de>
Confidentiality Note: This message is intended only for the use of the named
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Von: Samuel Silva [mailto:[email protected]]
Gesendet: Dienstag, 17. November 2009 10:25
An: Schwarz Tobias; mitk-users
Betreff: Re: AW: AW: [mitk-users] Creating 4D image from 3D images
Dear Tobias,
I am sorry to answer your query only now but other things got in the way in the
meantime.
I have checked the 4D image and I get:
==========================================
m_Channels = [1]({m_Pointer=0x00000000 })
m_Volumes = [12]({m_Pointer=0x13038d18 },{m_Pointer=0x119f0a60
},{m_Pointer=0x132aa8c0 },{m_Pointer=0x132b0ab8 },{m_Pointer=0x134ac3d8 },...)
m_Slices = [744]({m_Pointer=0x00000000 },{m_Pointer=0x00000000
},{m_Pointer=0x00000000 },{m_Pointer=0x00000000 },{m_Pointer=0x00000000 },...)
m_Dimension = 4
============================================
(do you need to see additional data? I put in only the ones that seemed
relevant.)
I find no geometries vector inside the image. Am I not looking at the proper
place? Should it be there?
The time stepper keeps giving me -1.
Well, from the above data you can see that the image contains 12 volumes. And,
if it can give you more information, I am able to use a timeSelector on it to
extract the different timepoints like this:
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput( image );
timeSelector->SetTimeNr( t );
timeSelector->Update();
auxImage = timeSelector->GetOutput();
Is there any place where I can look deeper? For example, where MITK looks into
the image geometry before rendering?
Thanks in advance for all the help you can give me.
Best regards,
Samuel
Schwarz Tobias wrote:
Dear Samuel,
the time stepper seems to be correctly created. It should only show -1 when the
image has only one timestep.
As far as I remember, it is checked if data is present in the image, and if a
valid geometry is present in the corresponding Timeslicedgeometry.
Can you check with a debugger if your 4D image has a valid vector of images and
geometries?
Best regards,
Tobias
------------------------------------------------------------
Tobias Schwarz
DKFZ
German Cancer Research Center (Deutsches Krebsforschungszentrum)
Member of the Helmholtz Association
Division of Medical & Biological Informatics E130
Im Neuenheimer Feld 280
D-69120 Heidelberg
Phone: 49-(0)6221-42-2353
Fax: 49-(0)6221-42-2345
E-Mail: [email protected]<mailto:[email protected]>
Web: www.dkfz.de<http://www.dkfz.de>
Confidentiality Note: This message is intended only for the use of the named
recipient(s) and may obtain confidential and/or privileged information. If you
are not the intended recipient, please contact the sender and delete the
message. Any unauthorized use of the information contained in this message is
prohibited.
Von: Samuel Silva [mailto:[email protected]]
Gesendet: Dienstag, 22. September 2009 18:27
An: Schwarz Tobias
Cc: [email protected]<mailto:[email protected]>;
Wegner Ingmar
Betreff: Re: AW: [mitk-users] Creating 4D image from 3D images
Dear Tobias,
Thanks *a lot* for your help. I had been around this problem for some time now
and I think I would always miss that detail. It now works well.
As far as I could tell, by what I have read, having a timeslidedgeometry MITK
would allow me to deal with the different timepoints in a flash by using the
SliceNavigationController present in the QmitkStdMultiWidget.
QmitkSliderNavigatorWidget *sliderNavigatorTime = new
QmitkSliderNavigatorWidget( this );
vlayout_sideWidget->addWidget(sliderNavigatorTime);
new QmitkStepperAdapter(
sliderNavigatorTime,
multiWidget->GetTimeNavigationController()->GetTime(),
"TimeStepperAdaptor"
);
Unfortunately, the above code keeps giving me a slider with a -1 (i.e., no
access to the multiple timepoints. I manage to have such a slider working for
the slices though.
It seems that when the SliceNavigatorController is initialized (when the image
is loaded) that the geometry it gets has only one timestep.
I am surely missing some simple detail. I'll keep on looking.
Thanks again for your help!
Best regards,
Samuel
Schwarz Tobias wrote:
Dear Samuel,
the code you sent us look almost correct. Only problem I see in the moment is
the import of the 3D images into the 4D image.
Instead of the line:
image4D->SetImportVolume(image, i, 0, mitk::Image::ReferenceMemory);
please try the following:
mitkIpPicDescriptor* currentVolume =
image->GetVolumeData(0)->GetPicDescriptor();
image4D->SetPicVolume( currentVolume , myTimeStep);
This is because the SetImportVolume function expects a void* of data, if you
give it a SmartPointer it will not work correctly.
I hope this can help you,
Best regards,
Tobias
------------------------------------------------------------
Tobias Schwarz
DKFZ
German Cancer Research Center (Deutsches Krebsforschungszentrum)
Member of the Helmholtz Association
Division of Medical & Biological Informatics E130
Im Neuenheimer Feld 280
D-69120 Heidelberg
Phone: 49-(0)6221-42-2353
Fax: 49-(0)6221-42-2345
E-Mail: [email protected]<mailto:[email protected]>
Web: www.dkfz.de<http://www.dkfz.de>
Confidentiality Note: This message is intended only for the use of the named
recipient(s) and may obtain confidential and/or privileged information. If you
are not the intended recipient, please contact the sender and delete the
message. Any unauthorized use of the information contained in this message is
prohibited.
Von: Samuel Silva [mailto:[email protected]]
Gesendet: Montag, 21. September 2009 13:35
An: [email protected]<mailto:[email protected]>
Betreff: [mitk-users] Creating 4D image from 3D images
Hello!
I posted a question regarding this subject a while ago and since I got no
answer I'll get back to it (as I still haven't solved the problem) with a
slightly different scenario.
Well, I have a 4D DICOM set which I successfully manage to load (separating the
different timepoints and creating a node for each) just by using MITK's code. I
can visualize all the loaded 3D images (timepoints) without any problem.
What I now wanted to do (for the sake of better data organization in my app, as
I want to load several 4D sets) is to build a 4D MITK image from the 3D images.
This way I would only have one item in the DataTree for each 4D set and manage
visualization setting the timepoint.
I did something like this:
===============================================================================
void MyApp::fileOpenGetFactoryOutput( mitk::DataTreeNodeFactory & factory,
mitk::DataTreeNode::Pointer parentNode)
{
mitk::DataTreePreOrderIterator it(m_Tree);
mitk::Image::Pointer image;
mitk::Image::Pointer firstImage;
bool dataFound = false;
mitk::DataTreeNode::Pointer newNode4D = mitk::DataTreeNode::New();
mitk::Image::Pointer image4D = mitk::Image::New();
mitk::TimeSlicedGeometry::Pointer geom = mitk::TimeSlicedGeometry::New();
for ( unsigned int i = 0 ; i < factory.GetNumberOfOutputs( ); ++i )
{
mitk::DataTreeNode::Pointer node = factory.GetOutput( i );
tmpNodeList.push_back(node); // this is just to get an alternative node
list...
if ( node.IsNotNull( ) )
{
image = dynamic_cast<mitk::Image*>(node->GetData());
if ( image.IsNotNull() && firstImage.IsNull() )
{
firstImage = image;
firstNode = newNode4D;
geom->InitializeEvenlyTimed(image->GetGeometry(),
factory.GetNumberOfOutputs( ));
image4D->Initialize ( image->GetPixelType(), *geom);
}
if ( node->GetData() != NULL )
{
dataFound = true;
image4D->SetImportVolume(image, i, 0, mitk::Image::ReferenceMemory);
}
}
}
newNode4D->SetData( image4D ); //crashes here!!!
mitk::DataStorage::GetInstance()->Add( newNode4D, parentNode );
m_ToolReferenceDataSelectionBox->UpdateDataDisplay();
m_ToolWorkingDataSelectionBox->UpdateDataDisplay();
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
standardViewsInitialized =
mitk::RenderingManager::GetInstance()->InitializeViews( &it );
}
==============================================================
Things work OK until newNode4D->SetData( image4D ) where it crashes.
By debugging "inside" the SetData I managed to know that the error occurs in
mitk::_ComputeExtremaInItkImage(..), more precisely when inside the while cycle
which computes max and min values for the image. At some early point the
itkdefaultpixelaccessorfunctor cannot retrieve a pixel value. What can be the
reason?
Does the code I present above have any error?
Has anyone tried to do something like this with success?
As far as I could tell, just before the SetData line, image4D has the pointers
for all the volumes in m_Volumes set correctly. All other pointer lists
(m_Slices, m_Channels) have no pointers in them. I suppose this is normal,
since I am setting volumes?
Any idea on what is happening? Things I can do to perform further debugging?
Thanks in advance for all the help!
Samuel
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