MITK uses a very modular concept to maximize reusability and portability. You start an application (for example ExtApp, the sample application provided by MITK). An application has several bundles (or plug-ins). A bundle can be a functionality, which in turn can be a view, each of these terms specifying certain behaviour and attributes.
The creation of a MITK plug-in is considerably facilitated by using the MITK BundleGenerator as described in How to create a new MITK Plug-in .
The mentioned tool was used to create a plug-in QmitkRegionGrowing. Let's first look at what files the BundleGenerator created:
documentation\doxygen\
modules.dox............................. Doxygen file for documenting your plug-in
META-INF\
MANIFEST.MF............................. Information about your plug-in
resources\
icon.xpm................................ The icon of your plug-in. GIMP or other programs (including your text editor)
can be used to change this
QmitkMITKRegionGrowingView.qrc.......... QT file for managing resources
src\internal\
QmitkMITKRegionGrowingView.cpp.......... The most important file, implementing behaviour
QmitkMITKRegionGrowingView.h............ Header file of the functionality
QmitkMITKRegionGrowingViewControls.ui... XML file of the Qt Designer, describes buttons, combo boxes, etc. of your controls
src\
RegiongrowingDll.h...................... Manages the import/export of your plug-in dll
CMakeLists.txt \.......................... Build system related files for CMake
files.cmake /
manifest.cpp \............................ BlueBerry integration
plugin.xml /
If you are not familiar with Qt development, please look into this Trolltech page describing .ui files (no, forget about the please, DO it!)
The C++ files implement a subclass of QmitkFunctionality, so they ARE functionalities. In this special case of QmitkRegionGrowing, we added the ability to set some seed points and run a region grower. If your are interested in the concrete changes necessary to turn a freshly generated QmitkRegionGrowing into an integrated one:
To add a PointSet for the seed points: QmitkRegionGrowingView.h
Add includes:
#include "mitkPointSet.h" #include <itkImage.h>
Add the point set as protected object:
/// \brief This is the actual seed point data object mitk::PointSet::Pointer m_PointSet;
Add includes:
#include "QmitkPointListWidget.h"
CreateQtPartControl():
// let the point set widget know about the multi widget (crosshair updates)
m_Controls->lstPoints->SetMultiWidget( m_MultiWidget );
// create a new DataTreeNode containing a PointSet with some interaction
m_PointSet = mitk::PointSet::New();
mitk::DataTreeNode::Pointer pointSetNode = mitk::DataTreeNode::New();
pointSetNode->SetData( m_PointSet );
pointSetNode->SetName("seed points for region growing");
pointSetNode->SetProperty("helper object", mitk::BoolProperty::New(true) );
pointSetNode->SetProperty("layer", mitk::IntProperty::New(1024) );
// add the pointset to the data tree (for rendering and access by other modules)
GetDefaultDataStorage()->Add( pointSetNode );
// tell the GUI widget about out point set
m_Controls->lstPoints->SetPointSetNode( pointSetNode );
StdMultiWidgetAvailable():
m_Controls->lstPoints->SetMultiWidget( m_MultiWidget );
StdMultiWidgetNotAvailable():
m_Controls->lstPoints->SetMultiWidget( NULL );
To use the ITK region grower:
Add protected method:
/*! \brief ITK image processing function This function is templated like an ITK image. The MITK-Macro AccessByItk determines the actual pixel type and dimensionality of a given MITK image and calls this function for further processing (in our case region growing) */ template < typename TPixel, unsigned int VImageDimension > void ItkImageProcessing( itk::Image< TPixel, VImageDimension >* itkImage, mitk::Geometry3D* imageGeometry );
Add includes:
// MITK #include "mitkImageAccessByItk.h" #include "mitkITKImageImport.h" #include "mitkProperties.h" #include "mitkColorProperty.h" // ITK #include <itkConnectedThresholdImageFilter.h>
DoImageProcessing();
// So we have an image. Let's see if the user has set some seed points already
if ( m_PointSet->GetSize() == 0 )
{
// no points there. Not good for region growing
QMessageBox::information( NULL, "Region growing functionality",
"Please set some seed points inside the image first.\n"
"(hold Shift key and click left mouse button inside the image.)"
);
return;
}
// actually perform region growing. Here we have both an image and some seed points
AccessByItk_1( image, ItkImageProcessing, image->GetGeometry() ); // some magic to call the correctly templated function
And add the new method:
template < typename TPixel, unsigned int VImageDimension >
void QmitkRegionGrowingView::ItkImageProcessing( itk::Image< TPixel, VImageDimension >* itkImage, mitk::Geometry3D* imageGeometry )
{
typedef itk::Image< TPixel, VImageDimension > InputImageType;
typedef typename InputImageType::IndexType IndexType;
// instantiate an ITK region growing filter, set its parameters
typedef itk::ConnectedThresholdImageFilter<InputImageType, InputImageType> RegionGrowingFilterType;
typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
regionGrower->SetInput( itkImage ); // don't forget this
// determine a thresholding interval
IndexType seedIndex;
TPixel min( std::numeric_limits<TPixel>::max() );
TPixel max( std::numeric_limits<TPixel>::min() );
mitk::PointSet::PointsContainer* points = m_PointSet->GetPointSet()->GetPoints();
for ( mitk::PointSet::PointsConstIterator pointsIterator = points->Begin();
pointsIterator != points->End();
++pointsIterator )
{
// first test if this point is inside the image at all
if ( !imageGeometry->IsInside( pointsIterator.Value()) )
{
continue;
}
// convert world coordinates to image indices
imageGeometry->WorldToIndex( pointsIterator.Value(), seedIndex);
// get the pixel value at this point
TPixel currentPixelValue = itkImage->GetPixel( seedIndex );
// adjust minimum and maximum values
if (currentPixelValue > max)
max = currentPixelValue;
if (currentPixelValue < min)
min = currentPixelValue;
regionGrower->AddSeed( seedIndex );
}
std::cout << "Values between " << min << " and " << max << std::endl;
min -= 30;
max += 30;
// set thresholds and execute filter
regionGrower->SetLower( min );
regionGrower->SetUpper( max );
regionGrower->Update();
mitk::Image::Pointer resultImage = mitk::ImportItkImage( regionGrower->GetOutput() );
mitk::DataTreeNode::Pointer newNode = mitk::DataTreeNode::New();
newNode->SetData( resultImage );
// set some properties
newNode->SetProperty("binary", mitk::BoolProperty::New(true));
newNode->SetProperty("name", mitk::StringProperty::New("dumb segmentation"));
newNode->SetProperty("color", mitk::ColorProperty::New(1.0,0.0,0.0));
newNode->SetProperty("volumerendering", mitk::BoolProperty::New(true));
newNode->SetProperty("layer", mitk::IntProperty::New(1));
newNode->SetProperty("opacity", mitk::FloatProperty::New(0.5));
// add result to data tree
this->GetDefaultDataStorage()->Add( newNode );
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
Have fun using MITK!
If you meet any difficulties during your first steps, don't hesitate to ask on the MITK mailing list mitk-users@lists.sourceforge.net! People there are kind and will try to help you.
1.7.2