Tutorial Step9 is now based on compilable code.

Documentation/Doxygen/Tutorial/Step09.dox

@@ -2,212 +2,71 @@
 
 \page Step09Page MITK Tutorial - Step 9: A plug-in
 
-MITK uses a very modular concept to maximize reusability and portability. You start an application (for example mitkWorkbench, 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.
+MITK uses a very modular concept to maximize reusability and portability. A MITK application based on the BlueBerry
+application framework (for example the MITK Workbench) consists of several bundles (or plug-ins). A bundle can contain
+resources and program logic. It can also contribute so-called Views to the main application, which provide a specific
+user interface for controlling the bundles functions.
 
-The creation of a MITK plug-in is considerably facilitated by using the MITK BundleGenerator as described in \ref NewPluginPage .
+The creation of a MITK plug-in is considerably facilitated by using the MITK PluginGenerator as described in \ref NewPluginPage .
 
-The mentioned tool was used to create a plug-in QmitkRegionGrowing.
-Let's first look at what files the BundleGenerator created:
+The mentioned tool was used to create a plug-in called org.mitk.example.gui.regiongrowing.
+Let's first look at what files the PluginGenerator created:
 
 \verbatim
 documentation\doxygen\
-  modules.dox............................. Doxygen file for documenting your plug-in
+  modules.dox......................... Doxygen file for documenting 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
+  icon.xpm............................ The icon of your plug-in. GIMP or other programs (including your text editor)
+                                       can be used to change this
 
 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
+  QmitkRegionGrowingView.cpp.......... The most important file, implementing behaviour
+  QmitkRegionGrowingView.h............ Header file of the functionality
+  QmitkRegionGrowingViewControls.ui... XML file of the Qt Designer, describes buttons, combo boxes, etc. of your controls
 
-CMakeLists.txt \.......................... Build system related files for CMake
+CMakeLists.txt \...................... Build system related files for CMake
 files.cmake    /
-manifest_headers.cmake.................... Information about your plug-in
-plugin.xml ............................... BlueBerry integration
+manifest_headers.cmake................ Information about your plug-in
+plugin.xml ........................... BlueBerry integration
 \endverbatim
 
 If you are not familiar with Qt development, please look into
-<a href="http://doc.trolltech.com/4.6/designer-manual.html">this Trolltech page describing .ui files</a> (no, forget about the please, DO it!)
+<a href="http://doc.qt.digia.com/4.7/designer-manual.html">this Digia page describing .ui files</a> (no, forget about the please, DO it!)
 
 The C++ files implement a subclass of QmitkAbstractView. In this special case of QmitkRegionGrowing, we added the ability to set some seed points and run a region grower. If you are interested in the concrete changes necessary to turn a freshly generated QmitkRegionGrowing into an integrated one:
 
-Since an access to the StdMultiWidget is needed, manifest_headers.cmake has to be edited:
-\verbatim
-set(Require-Plugin org.mitk.gui.qt.common org.mitk.gui.qt.stdmultiwidgeteditor)
-\endverbatim
-
-To add a PointSet for the seed points:
+To add a mitk::PointSet for the seed points:
 QmitkRegionGrowingView.h
 
-Add includes:
-\verbatim
-#include "QmitkPointListWidget.h"
-#include "QmitkStdMultiWidget.h"
-#include "QmitkStdMultiWidgetEditor.h"
-\endverbatim
+Add includes and forward declarations:
+\snippet QmitkRegionGrowingView.h includes
 
-Add the point set as protected object and add Pointers for a QmitkPointListWidget and a QmitkStdMultiWidget:
-\verbatim
-/// \brief This is the actual seed point data object
-mitk::PointSet::Pointer m_PointSet;
-
-QmitkPointListWidget* lstPoints;
-QmitkStdMultiWidget* m_MultiWidget;
-\endverbatim
+Add the point set and a pointer to a QmitkPointListWidget as a private member:
+\snippet QmitkRegionGrowingView.h members
 
 QmitkRegionGrowingView.cpp
 
 CreateQtPartControl():
-\verbatim
-// create a QmitkPointListWidget and add it to the widget created from .ui file
-lstPoints = new QmitkPointListWidget();
-m_Controls.verticalLayout->addWidget(lstPoints);
-
-// get access to StdMultiWidget by using RenderWindowPart
-QmitkStdMultiWidgetEditor* qSMWE = dynamic_cast<QmitkStdMultiWidgetEditor*>(GetRenderWindowPart());
-m_MultiWidget = qSMWE->GetStdMultiWidget();
-
-// let the point set widget know about the multi widget (crosshair updates)
-lstPoints->SetMultiWidget( m_MultiWidget );
-
-// create a new DataTreeNode containing a PointSet with some interaction
-m_PointSet = mitk::PointSet::New();
-
-mitk::DataNode::Pointer pointSetNode = mitk::DataNode::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)
-GetDataStorage()->Add( pointSetNode );
-
-// tell the GUI widget about out point set
-lstPoints->SetPointSetNode( pointSetNode );
-\endverbatim
+\snippet QmitkRegionGrowingView.cpp cpp-createqtpartcontrol
 
 To use the ITK region grower:
 
 QmitkRegionGrowingView.h
 
-Add protected method:
-\verbatim
-/*!
-\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 );
-\endverbatim
+Add the private method:
+\snippet QmitkRegionGrowingView.h itkimageprocessing
 
 QmitkRegionGrowingView.cpp
 
 Add includes:
-\verbatim
-// MITK
-#include "mitkImageAccessByItk.h"
-#include "mitkITKImageImport.h"
-#include "mitkProperties.h"
-#include "mitkColorProperty.h"
-
-// ITK
-#include <itkConnectedThresholdImageFilter.h>
+\snippet QmitkRegionGrowingView.cpp cpp-includes
 
-\endverbatim
-
-DoImageProcessing();
-\verbatim
-// 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
-\endverbatim
+DoImageProcessing():
+\snippet QmitkRegionGrowingView.cpp cpp-doimageprocessing
 
 And add the new method:
-\verbatim
-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 );
-  }
-
-  MITK_INFO << "Values between " << min << " and " << max;
-
-  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::DataNode::Pointer newNode = mitk::DataNode::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->GetDataStorage()->Add( newNode );
-  mitk::RenderingManager::GetInstance()->RequestUpdateAll();
-}
-
-\endverbatim
+\snippet QmitkRegionGrowingView.cpp cpp-itkimageaccess
 
 Have fun using MITK!
 

Examples/Plugins/PluginList.cmake

@@ -11,4 +11,5 @@ set(MITK_EXAMPLE_PLUGINS
   org.mitk.example.gui.selectionservicemitk.views:ON
   org.mitk.example.gui.extensionpointdefinition:ON
   org.mitk.example.gui.extensionpointcontribution:ON
+  org.mitk.example.gui.regiongrowing:ON
 )

Examples/Plugins/org.mitk.example.gui.regiongrowing/CMakeLists.txt

@@ -0,0 +1,7 @@
+project(org_mitk_example_gui_regiongrowing)
+
+MACRO_CREATE_MITK_CTK_PLUGIN(
+  EXPORT_DIRECTIVE REGIONGROWING_EXPORT
+  EXPORTED_INCLUDE_SUFFIXES src
+  MODULE_DEPENDENCIES QmitkExt
+)

Examples/Plugins/org.mitk.example.gui.regiongrowing/documentation/UserManual/Manual.dox

@@ -0,0 +1,18 @@
+/**
+\page org_mitk_example_gui_regiongrowing Region Grower Example
+
+\image html icon.xpm "Icon of Region Grower Example"
+
+Available sections:
+  - \ref org_mitk_example_gui_regiongrowingOverview
+
+\section org_mitk_example_gui_regiongrowingOverview
+Describe the features of your awesome plugin here
+<ul>
+<li>Increases productivity
+<li>Creates beautiful images
+<li>Generates PhD thesis
+<li>Brings world peace
+</ul>
+
+*/

Examples/Plugins/org.mitk.example.gui.regiongrowing/documentation/UserManual/icon.xpm

@@ -0,0 +1,21 @@
+/* XPM */
+static const char * icon_xpm[] = {
+"16 16 2 1",
+" 	c #FF0000",
+".	c #000000",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                "};

Examples/Plugins/org.mitk.example.gui.regiongrowing/documentation/doxygen/modules.dox

@@ -0,0 +1,16 @@
+/**
+  \defgroup org_mitk_example_gui_regiongrowing org.mitk.example.gui.regiongrowing
+  \ingroup MITKPlugins
+
+  \brief Describe your plugin here.
+
+*/
+
+/**
+  \defgroup org_mitk_example_gui_regiongrowing_internal Internal
+  \ingroup org_mitk_example_gui_regiongrowing
+
+  \brief This subcategory includes the internal classes of the org.mitk.example.gui.regiongrowing plugin. Other
+  plugins must not rely on these classes. They contain implementation details and their interface
+  may change at any time. We mean it.
+*/

Examples/Plugins/org.mitk.example.gui.regiongrowing/files.cmake

@@ -0,0 +1,42 @@
+set(SRC_CPP_FILES
+
+)
+
+set(INTERNAL_CPP_FILES
+  org_mitk_example_gui_regiongrowing_Activator.cpp
+  QmitkRegionGrowingView.cpp
+)
+
+set(UI_FILES
+  src/internal/QmitkRegionGrowingViewControls.ui
+)
+
+set(MOC_H_FILES
+  src/internal/org_mitk_example_gui_regiongrowing_Activator.h
+  src/internal/QmitkRegionGrowingView.h
+)
+
+# list of resource files which can be used by the plug-in
+# system without loading the plug-ins shared library,
+# for example the icon used in the menu and tabs for the
+# plug-in views in the workbench
+set(CACHED_RESOURCE_FILES
+  resources/icon.xpm
+  plugin.xml
+)
+
+# list of Qt .qrc files which contain additional resources
+# specific to this plugin
+set(QRC_FILES
+
+)
+
+set(CPP_FILES )
+
+foreach(file ${SRC_CPP_FILES})
+  set(CPP_FILES ${CPP_FILES} src/${file})
+endforeach(file ${SRC_CPP_FILES})
+
+foreach(file ${INTERNAL_CPP_FILES})
+  set(CPP_FILES ${CPP_FILES} src/internal/${file})
+endforeach(file ${INTERNAL_CPP_FILES})

Examples/Plugins/org.mitk.example.gui.regiongrowing/manifest_headers.cmake

@@ -0,0 +1,5 @@
+set(Plugin-Name "Region Grower Example")
+set(Plugin-Version "0.1")
+set(Plugin-Vendor "DKFZ, Medical and Biological Informatics")
+set(Plugin-ContactAddress "")
+set(Require-Plugin org.mitk.gui.qt.common)

Examples/Plugins/org.mitk.example.gui.regiongrowing/plugin.xml

@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<plugin>
+
+  <extension point="org.blueberry.ui.views">
+    <view id="org.mitk.views.example.regiongrowing"
+          name="Region Growing"
+          class="QmitkRegionGrowingView"
+          icon="resources/icon.xpm" />
+  </extension>
+
+</plugin>

Examples/Plugins/org.mitk.example.gui.regiongrowing/resources/icon.xpm

@@ -0,0 +1,21 @@
+/* XPM */
+static const char * icon_xpm[] = {
+"16 16 2 1",
+" 	c #FF0000",
+".	c #000000",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                ",
+"                "};