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>
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* *
*Von:* Samuel Silva [mailto:[email protected]]
*Gesendet:* Montag, 21. September 2009 13:35
*An:* [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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