Click'n'Join-Mode extension to ITK-SNAP incuding global, dynamic watershed segmentation

CMakeLists.txt

@@ -55,12 +55,12 @@ endforeach()
 # These four fields should be modified when versions change
 SET(SNAP_VERSION_MAJOR 3)
 SET(SNAP_VERSION_MINOR 4)
-SET(SNAP_VERSION_PATCH 1)
-SET(SNAP_VERSION_QUALIFIER "-alpha")
+SET(SNAP_VERSION_PATCH 0)
+SET(SNAP_VERSION_QUALIFIER "")
 
 # These fields should also be modified each time
-SET(SNAP_VERSION_RELEASE_DATE "20151017")
-SET(SNAP_VERSION_RELEASE_DATE_FORMATTED "Oct 17, 2015")
+SET(SNAP_VERSION_RELEASE_DATE "20151130")
+SET(SNAP_VERSION_RELEASE_DATE_FORMATTED "Nov 30, 2015")
 
 # This field should only change when the format of the settings files changes
 # in a non backwards-compatible way
@@ -209,6 +209,7 @@ SET(LOGIC_CXX
   Logic/Framework/IRISImageData.cxx
   Logic/Framework/LayerIterator.cxx
   Logic/Framework/SNAPImageData.cxx
+  Logic/Framework/JOINImageData.cxx
   Logic/Framework/UndoDataManager_LabelType.cxx
   Logic/ImageWrapper/CommonRepresentationPolicy.cxx
   Logic/ImageWrapper/DisplayMappingPolicy.cxx
@@ -308,6 +309,7 @@ SET(LOGIC_HEADERS
   Logic/Framework/LayerAssociation.txx
   Logic/Framework/LayerIterator.h
   Logic/Framework/SNAPImageData.h
+  Logic/Framework/JOINImageData.h
   Logic/Framework/UndoDataManager.h
   Logic/Framework/UndoDataManager.txx
   Logic/ImageWrapper/CommonRepresentationPolicy.h
@@ -409,6 +411,8 @@ SET(UI_GENERIC_CXX
   GUI/Model/SnakeROIModel.cxx
   GUI/Model/SnakeROIResampleModel.cxx
   GUI/Model/SnakeWizardModel.cxx
+  GUI/Model/JoinModel.cxx
+  GUI/Model/GlobalWSWizardModel.cxx
   GUI/Model/StateManagement.cxx
   GUI/Model/SynchronizationModel.cxx
   GUI/Model/UIAction.cxx
@@ -481,6 +485,8 @@ SET(UI_GENERIC_HEADERS
   GUI/Model/SnakeROIModel.h
   GUI/Model/SnakeROIResampleModel.h
   GUI/Model/SnakeWizardModel.h
+  GUI/Model/JoinModel.h
+  GUI/Model/GlobalWSWizardModel.h
   GUI/Model/StateManagement.h
   GUI/Model/SynchronizationModel.h
   GUI/Model/UIAction.h
@@ -552,6 +558,8 @@ SET(UI_QT_CXX
   GUI/Qt/Components/RecentHistoryItemsView.cxx
   GUI/Qt/Components/SnakeToolROIPanel.cxx
   GUI/Qt/Components/SnakeWizardPanel.cxx
+  GUI/Qt/Components/JoinDataPanel.cxx
+  GUI/Qt/Components/GlobalWSWizardPanel.cxx
   GUI/Qt/Components/SNAPComponent.cxx
   GUI/Qt/Components/SNAPQtCommon.cxx
   GUI/Qt/Components/SliceViewPanel.cxx
@@ -576,6 +584,7 @@ SET(UI_QT_CXX
   GUI/Qt/View/PolygonDrawingInteractionMode.cxx
   GUI/Qt/View/SliceWindowInteractionDelegateWidget.cxx
   GUI/Qt/View/SnakeROIInteractionMode.cxx
+  GUI/Qt/View/JoinInteractionMode.cxx
   GUI/Qt/View/ThumbnailInteractionMode.cxx
   GUI/Qt/Windows/AboutDialog.cxx
   GUI/Qt/Windows/DropActionDialog.cxx
@@ -636,6 +645,8 @@ SET(UI_MOC_HEADERS
   GUI/Qt/Components/RecentHistoryItemsView.h
   GUI/Qt/Components/SnakeToolROIPanel.h
   GUI/Qt/Components/SnakeWizardPanel.h
+  GUI/Qt/Components/JoinDataPanel.h
+  GUI/Qt/Components/GlobalWSWizardPanel.h
   GUI/Qt/Components/SNAPComponent.h
   GUI/Qt/Components/SliceViewPanel.h
   GUI/Qt/Components/SynchronizationInspector.h
@@ -659,6 +670,7 @@ SET(UI_MOC_HEADERS
   GUI/Qt/View/PolygonDrawingInteractionMode.h
   GUI/Qt/View/SliceWindowInteractionDelegateWidget.h
   GUI/Qt/View/SnakeROIInteractionMode.h
+  GUI/Qt/View/JoinInteractionMode.h
   GUI/Qt/View/ThumbnailInteractionMode.h
   GUI/Qt/Windows/AboutDialog.h
   GUI/Qt/Windows/DropActionDialog.h
@@ -734,6 +746,8 @@ SET(UI_FORMS
   GUI/Qt/Components/SliceViewPanel.ui
   GUI/Qt/Components/SnakeToolROIPanel.ui
   GUI/Qt/Components/SnakeWizardPanel.ui
+  GUI/Qt/Components/JoinDataPanel.ui
+  GUI/Qt/Components/GlobalWSWizardPanel.ui
   GUI/Qt/Components/SynchronizationInspector.ui
   GUI/Qt/Components/ViewPanel3D.ui
   GUI/Qt/Components/ZoomInspector.ui

CTestConfig.cmake

@@ -6,10 +6,10 @@
 ##   ENABLE_TESTING()
 ##   INCLUDE(CTest)
 
-set(CTEST_PROJECT_NAME "ITK-SNAP master")
-set(CTEST_NIGHTLY_START_TIME "01:00:00 UTC")
+set(CTEST_PROJECT_NAME "ITK-SNAP 3.4")
+set(CTEST_NIGHTLY_START_TIME "00:00:00 UTC")
 
 set(CTEST_DROP_METHOD "http")
 set(CTEST_DROP_SITE "itksnap.org")
-set(CTEST_DROP_LOCATION "/cdash/submit.php?project=ITK-SNAP+master")
+set(CTEST_DROP_LOCATION "/cdash/submit.php?project=ITK-SNAP+3.4")
 set(CTEST_DROP_SITE_CDASH TRUE)

Common/SNAPCommon.h

@@ -92,6 +92,9 @@ extern const char SNAPBuildInfo[];
 // UnaryFunctorCache in the GreyImageWrapper type.  Greyscale instensities
 // 0 to MAXGREYVAL are used in a cache table, which would be too big with int
 typedef unsigned short LabelType;
+typedef itk::IdentifierType GWSType;
+typedef GWSType JSRType;
+typedef float WSRType;
 typedef short GreyType;
 extern const GreyType MAXGREYVAL;
 extern const GreyType MINGREYVAL;
@@ -117,6 +120,7 @@ enum LayerRole
   SNAP_ROLE = 0x0004,
   LABEL_ROLE = 0x0008,
   NO_ROLE = 0x0010,
+  JOIN_ROLE = 0x0020,
   ALL_ROLES = 0xffffffff
 };
 

GUI/Model/CursorInspectionModel.cxx

@@ -108,6 +108,7 @@ void CursorInspectionModel::SetParentModel(GlobalUIModel *parent)
   int role =
       MAIN_ROLE |
       OVERLAY_ROLE |
+      JOIN_ROLE |
       SNAP_ROLE;
 
   CurrentVoxelInfoItemSetDomain dom(parent, role);

GUI/Model/GlobalUIModel.cxx

@@ -34,6 +34,7 @@
 #include <PolygonDrawingModel.h>
 #include <AnnotationModel.h>
 #include <SnakeROIModel.h>
+#include <JoinModel.h>
 #include <SliceWindowCoordinator.h>
 #include <GenericImageData.h>
 #include <GuidedNativeImageIO.h>
@@ -47,6 +48,7 @@
 #include <LabelEditorModel.h>
 #include <CursorInspectionModel.h>
 #include <SnakeWizardModel.h>
+#include <GlobalWSWizardModel.h>
 #include <RandomAccessCollectionModel.h>
 #include <UIReporterDelegates.h>
 #include <ReorientImageModel.h>
@@ -112,6 +114,9 @@ GlobalUIModel::GlobalUIModel()
     m_SnakeROIModel[i] = SnakeROIModel::New();
     m_SnakeROIModel[i]->SetParent(m_SliceModel[i]);
 
+    m_JoinModel[i] = JoinModel::New();
+    m_JoinModel[i]->SetParent(m_SliceModel[i]);
+
     m_PaintbrushModel[i] = PaintbrushModel::New();
     m_PaintbrushModel[i]->SetParent(m_SliceModel[i]);
 
@@ -149,7 +154,7 @@ GlobalUIModel::GlobalUIModel()
   m_LoadedLayersSelectionModel->SetParentModel(this);
   m_LoadedLayersSelectionModel->SetRoleFilter(
         MAIN_ROLE | OVERLAY_ROLE |
-        SNAP_ROLE);
+        SNAP_ROLE | JOIN_ROLE);
 
   // 3D model
   m_Model3D = Generic3DModel::New();
@@ -175,6 +180,10 @@ GlobalUIModel::GlobalUIModel()
   m_SnakeROIResampleModel = SnakeROIResampleModel::New();
   m_SnakeROIResampleModel->SetParentModel(this);
 
+  // GlobalWS model
+  m_GlobalWSWizardModel = GlobalWSWizardModel::New();
+  m_GlobalWSWizardModel->SetParentModel(this);
+
   // Synchronization model
   m_SynchronizationModel = SynchronizationModel::New();
   m_SynchronizationModel->SetParentModel(this);
@@ -311,11 +320,12 @@ bool GlobalUIModel::CheckState(UIState state)
     case UIF_BASEIMG_LOADED:
       return m_Driver->IsMainImageLoaded();
     case UIF_IRIS_WITH_BASEIMG_LOADED:
-      return m_Driver->IsMainImageLoaded() && !m_Driver->IsSnakeModeActive();
+	return m_Driver->IsMainImageLoaded() && !m_Driver->IsSnakeModeActive();// && !m_Driver->IsJoinModeActive(); ///adding this will disable lablel change in Join mode, use UIF_NOT_SNAKE_OR_JOIN_MODE if needed.
     case UIF_IRIS_MODE:
-      return !m_Driver->IsSnakeModeActive();
+	return !m_Driver->IsSnakeModeActive() && !m_Driver->IsJoinModeActive();//not sure if Join extension here has any effect
     case UIF_IRIS_WITH_OVERLAY_LOADED:
       return m_Driver->IsMainImageLoaded() && !m_Driver->IsSnakeModeActive()
+	  && !m_Driver->IsJoinModeActive()
           && m_Driver->GetCurrentImageData()->GetNumberOfOverlays() > 0;
     case UIF_ROI_VALID:
       break;
@@ -333,6 +343,10 @@ bool GlobalUIModel::CheckState(UIState state)
       return m_Driver->GetCurrentImageData()->IsOverlayLoaded();
     case UIF_SNAKE_MODE:
       return m_Driver->IsSnakeModeActive();
+    case UIF_JOIN_MODE:
+      return m_Driver->IsJoinModeActive();
+    case UIF_NOT_SNAKE_OR_JOIN_MODE:
+	return m_Driver->IsMainImageLoaded() && !m_Driver->IsSnakeModeActive() && !m_Driver->IsJoinModeActive();
     case UIF_LEVEL_SET_ACTIVE:
       return m_Driver->IsSnakeModeLevelSetActive();
     case UIF_MULTIPLE_BASE_LAYERS:
@@ -402,6 +416,99 @@ void GlobalUIModel::ToggleOverlayVisibility()
   m_LayerGeneralPropertiesModel->SetLayer(curr_layer);
 }
 
+void GlobalUIModel::ToggleJsrcVisibility()
+{
+  // Are we in JOIN mode?
+  if(CheckState(UIF_JOIN_MODE)){
+      GenericImageData *id = m_Driver->GetCurrentImageData();
+
+      // Remember what layer is current in the general properties model
+      ImageWrapperBase *curr_layer = m_LayerGeneralPropertiesModel->GetLayer();
+
+      // Apply the toggle for all overlays
+      for(LayerIterator it = id->GetLayers(JOIN_ROLE); !it.IsAtEnd(); ++it){
+	  //if(dynamic_cast<JsrcImageWrapper *>(it.GetLayer())){//not tested
+	  if(strcmp(it.GetLayer()->GetNickname().c_str(), "Join Source Image") == 0){
+	      m_LayerGeneralPropertiesModel->SetLayer(it.GetLayer());
+	      m_LayerGeneralPropertiesModel->GetLayerVisibilityModel()->SetValue(
+		  !m_LayerGeneralPropertiesModel->GetLayerVisibilityModel()->GetValue());
+	      }
+	  }
+
+      // Restore the active layer
+      m_LayerGeneralPropertiesModel->SetLayer(curr_layer);
+  }
+}
+
+void GlobalUIModel::SetJsrcVisibility(bool set)
+{
+  // Are we in JOIN mode?
+  if(CheckState(UIF_JOIN_MODE)){
+      GenericImageData *id = m_Driver->GetCurrentImageData();
+
+      // Remember what layer is current in the general properties model
+      ImageWrapperBase *curr_layer = m_LayerGeneralPropertiesModel->GetLayer();
+
+      // Apply the toggle for all overlays
+      for(LayerIterator it = id->GetLayers(JOIN_ROLE); !it.IsAtEnd(); ++it){
+	  //if(dynamic_cast<JsrcImageWrapper *>(it.GetLayer())){//not tested
+	  if(strcmp(it.GetLayer()->GetNickname().c_str(), "Join Source Image") == 0){
+	      m_LayerGeneralPropertiesModel->SetLayer(it.GetLayer());
+	      m_LayerGeneralPropertiesModel->GetLayerVisibilityModel()->SetValue(set);
+	      }
+	  }
+
+      // Restore the active layer
+      m_LayerGeneralPropertiesModel->SetLayer(curr_layer);
+  }
+}
+
+void GlobalUIModel::SetJdstVisibility(bool set)
+{
+  // Are we in JOIN mode?
+  if(CheckState(UIF_JOIN_MODE)){
+      GenericImageData *id = m_Driver->GetCurrentImageData();
+
+      // Remember what layer is current in the general properties model
+      ImageWrapperBase *curr_layer = m_LayerGeneralPropertiesModel->GetLayer();
+
+      // Apply the toggle for all overlays
+      for(LayerIterator it = id->GetLayers(JOIN_ROLE); !it.IsAtEnd(); ++it){
+	  //if(dynamic_cast<JdstImageWrapper *>(it.GetLayer())){//not tested
+	  if(strcmp(it.GetLayer()->GetNickname().c_str(), "Join Destination Image") == 0){
+	      m_LayerGeneralPropertiesModel->SetLayer(it.GetLayer());
+	      m_LayerGeneralPropertiesModel->GetLayerVisibilityModel()->SetValue(set);
+	      }
+	  }
+
+      // Restore the active layer
+      m_LayerGeneralPropertiesModel->SetLayer(curr_layer);
+  }
+}
+
+void GlobalUIModel::SetWsrcVisibility(bool set)
+{
+  // Are we in JOIN mode?
+  if(CheckState(UIF_JOIN_MODE)){
+      GenericImageData *id = m_Driver->GetCurrentImageData();
+
+      // Remember what layer is current in the general properties model
+      ImageWrapperBase *curr_layer = m_LayerGeneralPropertiesModel->GetLayer();
+
+      // Apply the toggle for all overlays
+      for(LayerIterator it = id->GetLayers(JOIN_ROLE); !it.IsAtEnd(); ++it){
+	  //if(dynamic_cast<WsrcImageWrapper *>(it.GetLayer())){//not tested
+	  if(strcmp(it.GetLayer()->GetNickname().c_str(), "GWS Source Image") == 0){
+	      m_LayerGeneralPropertiesModel->SetLayer(it.GetLayer());
+	      m_LayerGeneralPropertiesModel->GetLayerVisibilityModel()->SetValue(set);
+	      }
+	  }
+
+      // Restore the active layer
+      m_LayerGeneralPropertiesModel->SetLayer(curr_layer);
+  }
+}
+
 void GlobalUIModel::AdjustOverlayOpacity(int delta)
 {
   // Are we in tiled mode or in stack mode?
@@ -789,6 +896,38 @@ GlobalUIModel::CreateIOWizardModelForSave(ImageWrapperBase *layer, LayerRole rol
   SmartPtr<AbstractSaveImageDelegate> delegate =
       m_Driver->CreateSaveDelegateForLayer(layer, role);
 
+  // Figure out the category name
+  std::string category;
+  switch(role)
+    {
+    case MAIN_ROLE:
+      category = "Main Image";
+      break;
+    case OVERLAY_ROLE:
+      category = "Overlay Image";
+      break;
+    case SNAP_ROLE:
+      if(dynamic_cast<SpeedImageWrapper *>(layer))
+        category = "Speed Image";
+      else if(dynamic_cast<LevelSetImageWrapper *>(layer))
+        category = "Level Set Image";
+      break;
+    case JOIN_ROLE:
+      if(dynamic_cast<JsrcImageWrapper *>(layer))
+        category = "Join Source Image";
+      else if(dynamic_cast<JdstImageWrapper *>(layer))
+        category = "Join Destination Image";
+      else if(dynamic_cast<WsrcImageWrapper *>(layer))
+        category = "GWS Source Image";
+      break;
+    case LABEL_ROLE:
+      category = "Segmentation Image";
+      break;
+    case NO_ROLE:
+    case ALL_ROLES:
+      break;
+    }
+
   // Create a model for IO
   SmartPtr<ImageIOWizardModel> modelIO = ImageIOWizardModel::New();
   modelIO->InitializeForSave(this, delegate, delegate->GetCategory().c_str());