Merge branch 'JoinFilter' into master+gdWS

GUI/Model/JoinModel.cxx

@@ -94,75 +94,9 @@ bool
 JoinModel::processCnJ(bool reverse_mode){
     // Get the global objects
     IRISApplication *driver = m_Parent->GetDriver();
-    GlobalState *gs = driver->GetGlobalState();
-
-    // Get Join source image
-    JsrcImageWrapper *jsrc = driver->GetJOINImageData()->GetJsrc();
-
-    // Get Join destination image
-    JdstImageWrapper *jdst = driver->GetJOINImageData()->GetJdst();
-
-    // Get the segmentation image
-    //LabelImageWrapper *imgLabel = driver->GetCurrentImageData()->GetSegmentation();
-
-    // Get the paint properties
-    LabelType drawing_color = gs->GetDrawingColorLabel();
-    DrawOverFilter drawover = gs->GetDrawOverFilter();
-
-    // Define a region of interest
-    //LabelImageWrapper::ImageType::RegionType xTestRegion= jsrc->GetImage()->GetBufferedRegion();
-    JsrcImageWrapper::ImageType::RegionType xTestRegion= jsrc->GetImage()->GetLargestPossibleRegion();
 
     // Flag to see if anything was changed
-    bool flagUpdate = false;
-
-    JsrcImageWrapper::ImageType::ValueType JsrcClickPV= jsrc->GetImage()->GetPixel(to_itkIndex(m_MousePosition));
-    // JdstImageWrapper::ImageType::ValueType JdstClickPV= jdst->GetImage()->GetPixel(to_itkIndex(m_MousePosition));
-
-
-    // Iterate over the region
-    JsrcImageWrapper::Iterator  sit(jsrc->GetImage(), xTestRegion);
-    LabelImageWrapper::Iterator dit(jdst->GetImage(), xTestRegion);
-    for(; !sit.IsAtEnd(); ++sit, ++dit){
-
-	if(sit.Get() != JsrcClickPV)
-	    continue;
-
-	LabelType pxLabel = dit.Get();
-
-	// Standard paint mode
-	if(!reverse_mode)
-	    {
-	    if(drawover.CoverageMode == PAINT_OVER_ALL ||
-		(drawover.CoverageMode == PAINT_OVER_ONE && pxLabel == drawover.DrawOverLabel) ||
-		(drawover.CoverageMode == PAINT_OVER_VISIBLE && pxLabel != 0))
-		{
-		dit.Set(drawing_color);
-		if(pxLabel != drawing_color) flagUpdate = true;
-		}
-	    }
-	// Background paint mode (clear label over current label)
-	else
-	    {
-	    if(drawing_color != 0 && pxLabel == drawing_color)
-		{
-		dit.Set(0);
-		if(pxLabel != 0) flagUpdate = true;
-		}
-	    else if(drawing_color == 0 && drawover.CoverageMode == PAINT_OVER_ONE)
-		{
-		dit.Set(drawover.DrawOverLabel);
-		if(pxLabel != drawover.DrawOverLabel) flagUpdate = true;
-		}
-	    }
-	}
-
-    // Image has been updated
-    if(flagUpdate)
-	{
-	jdst->GetImage()->Modified();
-	//imgLabel->GetImage()->Modified();
-	}
+    bool flagUpdate= driver->ExecuteCnJCopy(to_itkIndex(m_MousePosition));
 
     return flagUpdate;
     }

Logic/Common/itkJoinCopyFilter.cxx

@@ -0,0 +1,76 @@
+////image filter to set DrawingColor in output image if input pixel equals SeedValue
+
+#ifndef __itkJoinCopyFilter_cxx
+#define __itkJoinCopyFilter_cxx
+
+#include "itkJoinCopyFilter.h"
+#include <itkImageRegionIterator.h>
+#include <itkImageRegionConstIterator.h>
+#include <itkProgressReporter.h>
+
+namespace itk{
+
+    template<typename TInputImage1, typename TInputImage2>
+    JoinCopyFilter<TInputImage1, TInputImage2>
+    ::JoinCopyFilter(){
+	m_SeedActive= false;
+	m_SeedIndex.Fill(0);
+	m_SeedValue= NumericTraits<typename TInputImage2::PixelType>::Zero;
+	}
+
+    template<typename TInputImage1, typename TInputImage2>
+    void JoinCopyFilter<TInputImage1, TInputImage2>
+    ::SetJsrc(const TInputImage1 *image1){
+	this->SetNthInput( 0, const_cast< TInputImage1 * >( image1 ) );
+	}
+
+    template<typename TInputImage1, typename TInputImage2>
+    void JoinCopyFilter<TInputImage1, TInputImage2>
+    ::SetJdst(const TInputImage2 *image2){
+	this->SetNthInput( 1, const_cast< TInputImage2 * >( image2 ) );
+	}
+
+
+    template<typename TInputImage1, typename TInputImage2>
+    void JoinCopyFilter<TInputImage1, TInputImage2>
+    ::BeforeThreadedGenerateData(){
+
+	if(m_SeedActive){
+	    typename TInputImage1::ConstPointer input = dynamic_cast<const TInputImage1 *>( ProcessObject::GetInput(0) );
+	    m_SeedValue= input->GetPixel(m_SeedIndex);
+	    }
+	m_UpdateFlag= false;
+	}
+
+
+    template<typename TInputImage1, typename TInputImage2>
+    void JoinCopyFilter<TInputImage1, TInputImage2>
+    ::ThreadedGenerateData(const typename Superclass::OutputImageRegionType& outputRegionForThread, ThreadIdType threadId){
+
+	if(m_SeedActive){
+	    typename TInputImage1::ConstPointer input = dynamic_cast<const TInputImage1 *>( ProcessObject::GetInput(0) );
+	    typename TInputImage2::Pointer output = this->GetOutput();
+
+	    itk::ImageRegionConstIterator<TInputImage1> iti(input, outputRegionForThread);
+	    itk::ImageRegionIterator<TInputImage2> ito(output, outputRegionForThread);
+
+	    // support progress methods/callbacks with 1000 updates
+	    ProgressReporter progress(this, threadId, outputRegionForThread.GetNumberOfPixels(), 1000);
+
+	    while(!iti.IsAtEnd()){
+		if(iti.Get() == m_SeedValue){
+		    ito.Set(m_DrawingColor);
+		    }
+		++iti;
+		++ito;
+		progress.CompletedPixel();
+		}
+
+	    m_UpdateFlag= true;
+	    m_SeedActive= false;
+	    //output->Modified();
+	    }
+	}
+    }// end namespace
+
+#endif //__itkJoinCopyFilter_cxx

Logic/Common/itkJoinCopyFilter.h

@@ -0,0 +1,73 @@
+#ifndef __itkJoinCopyFilter_h
+#define __itkJoinCopyFilter_h
+
+#include <itkInPlaceImageFilter.h>
+
+namespace itk{
+    /** \class JoinCopyFilter
+     * \brief: sets DrawingColor in output image if input pixel equals SeedValue
+     *
+     * \ingroup ImageFilters
+     */
+    template<typename TInputImage1, typename TInputImage2>
+	class JoinCopyFilter:
+    public InPlaceImageFilter<TInputImage2>{
+    public:
+	/** Standard class typedefs. */
+	typedef JoinCopyFilter                                Self;
+	typedef InPlaceImageFilter<TInputImage2>     Superclass;
+	typedef SmartPointer<Self>                                 Pointer;
+	typedef SmartPointer< const Self >                         ConstPointer;
+
+	/** Method for creation through the object factory. */
+	itkNewMacro(Self);
+
+	/** Run-time type information (and related methods). */
+	itkTypeMacro(JoinCopyFilter, InPlaceImageFilter);
+
+	void SetJsrc(const TInputImage1 *image1);
+	void SetJdst(const TInputImage2 *image2);
+
+	/** Set/Get SeedIndex value */
+	itkSetMacro(SeedIndex, typename TInputImage1::IndexType);
+	itkGetConstMacro(SeedIndex, typename TInputImage1::IndexType);
+
+	/** Set/Get DrawingColor value */
+	itkSetMacro(DrawingColor, typename TInputImage2::ValueType);
+	itkGetConstMacro(DrawingColor, typename TInputImage2::ValueType);
+
+	/** Get UpdateFlag value */
+	itkGetConstMacro(UpdateFlag, bool);
+
+	/** Get/Set SeedActive value */
+	itkSetMacro(SeedActive, bool);
+	itkGetConstMacro(SeedActive, bool);
+
+    protected:
+	JoinCopyFilter();
+	~JoinCopyFilter(){}
+
+	bool m_SeedActive;
+	typename TInputImage1::IndexType m_SeedIndex;
+	typename TInputImage1::ValueType m_SeedValue;
+	typename TInputImage2::ValueType m_DrawingColor;
+	bool m_UpdateFlag;
+
+
+	virtual void BeforeThreadedGenerateData();
+	virtual void ThreadedGenerateData(const typename Superclass::OutputImageRegionType& outputRegionForThread, ThreadIdType threadId);
+
+    private:
+	JoinCopyFilter(const Self &); //purposely not implemented
+	void operator=(const Self &);  //purposely not implemented
+
+	};
+    } //namespace ITK
+
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "itkJoinCopyFilter.cxx"
+#endif
+
+#endif // __itkJoinCopyFilter_h
+

Logic/Framework/IRISApplication.cxx

@@ -289,10 +289,35 @@ ::InitializeJOINImageData(const SNAPSegmentationROISettings &roi, int CnJMode, c
   // Remember the ROI object
   m_GlobalState->SetSegmentationROISettings(roi);
 
+  // Initialize JoinCopyFilter
+  m_JOINImageData->InitializeJoinCF();
+
   // The set of layers has changed
   InvokeEvent(LayerChangeEvent());
 }
 
+bool 
+IRISApplication
+::ExecuteCnJCopy(JsrcImageWrapper::ImageType::IndexType SeedIndex)
+{
+  assert(m_JOINImageData->IsJsrcLoaded());
+
+  GlobalState *gs = GetGlobalState();
+
+  // Get the paint properties
+  LabelType drawing_color = gs->GetDrawingColorLabel();
+  DrawOverFilter drawover = gs->GetDrawOverFilter();
+
+  m_JOINImageData->GetJoinCF()->SetSeedIndex(SeedIndex);
+  m_JOINImageData->GetJoinCF()->SetDrawingColor(drawing_color);
+  m_JOINImageData->GetJoinCF()->SetSeedActive(true);
+  m_JOINImageData->GetJoinCF()->Update();
+  m_JOINImageData->GetJdst()->SetImage(m_JOINImageData->GetJoinCF()->GetOutput()); //needed because output has stolen the input's buffer and the input has no image buffer.
+
+  InvokeEvent(LayerChangeEvent());
+  return m_JOINImageData->GetJoinCF()->GetUpdateFlag();
+}
+
 void 
 IRISApplication
 ::CopySegementationToJsrc(const SNAPSegmentationROISettings &roi,

Logic/Framework/IRISApplication.h

@@ -46,6 +46,7 @@
 #include "SystemInterface.h"
 #include "UndoDataManager.h"
 #include "SNAPEvents.h"
+#include "JOINImageData.h" //for JsrcImageWrapper::ImageType::IndexType
 
 // #include "itkImage.h"
 
@@ -320,6 +321,11 @@ class IRISApplication : public itk::Object
   void InitializeJOINImageData(const SNAPSegmentationROISettings &roi, int CnJMode, const char* FileName,
                                CommandType *progressCommand = NULL);
 
+  /**
+   * Execute CnJ CopyFilter
+   */
+  bool ExecuteCnJCopy(JsrcImageWrapper::ImageType::IndexType SeedIndex);
+
   /**
    * Copy Segmentation to Jsrc for JOIN-mode 0
    */

Logic/Framework/JOINImageData.cxx

@@ -35,6 +35,20 @@
 
 #include "IRISApplication.h"
 #include "JOINImageData.h"
+//#include "itkJCFilterWatcher.h"
+#include <itkCommand.h>
+
+
+void FilterEventHandlerITK2(itk::Object *caller, const itk::EventObject &event, void*){
+
+    const itk::ProcessObject* filter = static_cast<const itk::ProcessObject*>(caller);
+
+    if(itk::ProgressEvent().CheckEvent(&event))
+	fprintf(stderr, "\r%s progress: %5.1f%%", filter->GetNameOfClass(), 100.0 * filter->GetProgress());//stderr is flushed directly
+    else if(itk::EndEvent().CheckEvent(&event))
+	std::cerr << std::endl << std::flush;
+    }
+
 
 JOINImageData
 ::JOINImageData(){
@@ -301,4 +315,34 @@ void JOINImageData::UnloadAll(){
 
     InvokeEvent(LayerChangeEvent());
     }
+
+void 
+JOINImageData
+::InitializeJoinCF(){
+    ////make sure Jsrc and Jdst exist
+    assert(IsJsrcLoaded());
+    assert(IsJdstLoaded());
+
+    ////Initialize JoinCopyFilter
+    m_JoinCF= JoinCopyFilterType::New();
+
+    m_JoinCF->SetJsrc(m_JsrcWrapper->GetImage());
+    m_JoinCF->SetJdst(m_JdstWrapper->GetImage());
+    //m_JdstWrapper->SetImage(m_JoinCF->GetOutput()); //causes segfault due to missing transform of uninitialized output
+    m_JoinCF->InPlaceOn(); //makes 2nd input (SetJdst) be the output
+
+    itk::CStyleCommand::Pointer eventCallbackITK;
+    eventCallbackITK = itk::CStyleCommand::New();
+    eventCallbackITK->SetCallback(FilterEventHandlerITK2);
+
+    m_JoinCF->AddObserver(itk::ProgressEvent(), eventCallbackITK);
+    m_JoinCF->AddObserver(itk::EndEvent(), eventCallbackITK);
+
+    }
+
+JOINImageData::JoinCopyFilterPointer
+JOINImageData::GetJoinCF(){
+    ////todo: introduce check if m_JoinCF was initialized
+    return m_JoinCF;
+    }
 

Logic/Framework/JOINImageData.h

@@ -39,6 +39,7 @@
 
 #include "GenericImageData.h"
 #include "itkImageAdaptor.h"
+#include "itkJoinCopyFilter.h"
 
 /**
  * \class JOINImageData
@@ -57,6 +58,9 @@ class JOINImageData : public GenericImageData
   typedef JdstImageWrapper::ImageType                     JdstImageType;
   typedef WsrcImageWrapper::ImageType                     WsrcImageType;
 
+  typedef itk::JoinCopyFilter<JsrcImageType, JdstImageType> JoinCopyFilterType;
+  typedef JoinCopyFilterType::Pointer JoinCopyFilterPointer;
+
   /** Initialize to a ROI from another image data object */
   void InitializeToROI(GenericImageData *source,
                        const SNAPSegmentationROISettings &roi,
@@ -88,6 +92,8 @@ class JOINImageData : public GenericImageData
   bool IsWsrcLoaded();
   void SetWsrcSticky(bool sticky);
 
+  void InitializeJoinCF();
+  JoinCopyFilterType::Pointer GetJoinCF();
 
 protected:
 
@@ -102,6 +108,9 @@ class JOINImageData : public GenericImageData
 
   // GWS source image
   SmartPtr<WsrcImageWrapper> m_WsrcWrapper;
+
+  JoinCopyFilterPointer m_JoinCF;
+
 };
 
 

todo

@@ -1,5 +1,12 @@
 TODOs for GWS:
 
+- implement JoinCopyFilter (templated over dimension)
+-- multi-threaded ImageRegionIterator
+-- multi-threaded ImageScanlineIterator
+-- FloodFilledImageFunctionConditionalIterator (Modules/Segmentation/RegionGrowing/include/itkConnectedThresholdImageFilter.hxx)
+--- add 2D/3D option to GUI + implementation
+- optimize CopySegementationToJdst and CopySegementationToJsrc
+
 - combine mode 2 with mode 0 and add extra button for "LoadImageToJsrc"
 -- restructure JoinDataPanel to have two main buttons: CnJ from Seg. or File OR CnJ from gWS
 - add 'n' for next smallest unused label see eg m_Wrapper->GetHistogram(nBins) in ./Logic/ImageWrapper/DisplayMappingPolicy.cxx