Stage (#137)

* Feature/default directory (#119)

* Add count label

* Use single default directory

* Add count label (#121)

* Add check for done status when ovewriting (#122)

* Feature/feedback enhancements (#123)

* Work on updating feedback types

* Implement basic comment interface

* Display comment in 2D view

* Fix bug with setting done from region table

* Add verified column, auto stretch comment column

* Use delegate for line edit in feedback table

* Finish feedback table updates

* Add verified color, working on logic for done and verified

* Finish logic for done and verified

* Add done/verified logic to region table

* Add search box

* Disable changing done status via shortcut if verified, set verified color when loading

* Remove console on windows

* Bugfix/done sort (#126)

* Stage (#124)

* Feature/default directory (#119)

* Add count label

* Use single default directory

* Add count label (#121)

* Add check for done status when ovewriting (#122)

* Feature/feedback enhancements (#123)

* Work on updating feedback types

* Implement basic comment interface

* Display comment in 2D view

* Fix bug with setting done from region table

* Add verified column, auto stretch comment column

* Use delegate for line edit in feedback table

* Finish feedback table updates

* Add verified color, working on logic for done and verified

* Finish logic for done and verified

* Add done/verified logic to region table

* Add search box

* Disable changing done status via shortcut if verified, set verified color when loading

* Remove console on windows

* Set data in addCheckWidget

* Fix sorting issue with feedback table

* Fix issue with merge

* Bump version number

* Feature/dot annotation (#134)

* Stage (#127)

* Feature/default directory (#119)

* Add count label

* Use single default directory

* Add count label (#121)

* Add check for done status when ovewriting (#122)

* Feature/feedback enhancements (#123)

* Work on updating feedback types

* Implement basic comment interface

* Display comment in 2D view

* Fix bug with setting done from region table

* Add verified column, auto stretch comment column

* Use delegate for line edit in feedback table

* Finish feedback table updates

* Add verified color, working on logic for done and verified

* Finish logic for done and verified

* Add done/verified logic to region table

* Add search box

* Disable changing done status via shortcut if verified, set verified color when loading

* Remove console on windows

* Bugfix/done sort (#126)

* Stage (#124)

* Feature/default directory (#119)

* Add count label

* Use single default directory

* Add count label (#121)

* Add check for done status when ovewriting (#122)

* Feature/feedback enhancements (#123)

* Work on updating feedback types

* Implement basic comment interface

* Display comment in 2D view

* Fix bug with setting done from region table

* Add verified column, auto stretch comment column

* Use delegate for line edit in feedback table

* Finish feedback table updates

* Add verified color, working on logic for done and verified

* Finish logic for done and verified

* Add done/verified logic to region table

* Add search box

* Disable changing done status via shortcut if verified, set verified color when loading

* Remove console on windows

* Set data in addCheckWidget

* Fix sorting issue with feedback table

* Fix issue with merge

* Bump version number

* Add region center sphere visualization

* Add button for dot annotation mode

* Add dot annotation mode

* Add 2D dot visualization

* Work on applying dot annotation to current full annotations

* Fix issues with center at edges, automatically show/hide dots based on mode

* Use triangle for out of plane 2D centers

* Use cone for triangle

* Enable picking 3D dot annotations

* Change dot annotation icon

* Set default verified and comment in RegionInfo

* Add shortcut to open/close feedback dialog

* Apply dot annotation in extract regions

* Only apply dot annotation to regions when saving in dot annotation mode

* Add verified shortcut to feedback table

* Feature/dot mode guard (#135)

* Use period for verified shortcut

* Add enable dot annotation checkbox to settings

* Add warning when switching to dot annotation mode

* Push history for dot mode

* Add separate action to apply dot annotation

* Use WIN32

CMakeLists.txt

@@ -4,7 +4,7 @@ if(POLICY CMP0020)
   cmake_policy(SET CMP0020 NEW)
 endif()
 
-set(SEGMENTOR_VERSION 0.4.3)
+set(SEGMENTOR_VERSION 0.4.4)
 
 project(Segmentor VERSION ${SEGMENTOR_VERSION})
 

Segmentor.qrc

@@ -26,5 +26,6 @@
   <file>icons/icon_filter_regions.png</file>
   <file>icons/icon_reset_view.png</file>
   <file>icons/icon_volume_render.png</file>
+  <file>icons/icon_dot.png</file>
 </qresource>
 </RCC>

interaction/InteractionCallbacks.cxx

@@ -246,6 +246,21 @@ void InteractionCallbacks::Visible(vtkObject* caller, unsigned long eventId, voi
 	}
 }
 
+void InteractionCallbacks::Dot(vtkObject* caller, unsigned long eventId, void* clientData, void *callData) {
+	vtkRenderWindowInteractor* rwi = static_cast<vtkInteractorStyle*>(caller)->GetInteractor();
+	VisualizationContainer* vis = static_cast<VisualizationContainer*>(clientData);
+
+	// Pick at the mouse location provided by the interactor	
+	int pick = Pick(rwi);
+
+	if (pick) {
+		// Get the position for the pick event		
+		double p[3];
+		PickPosition(p);
+		vis->SetDotAnnotation(p);
+	}
+}
+
 void InteractionCallbacks::MouseMove(vtkObject* caller, unsigned long eventId, void* clientData, void *callData) {
 	vtkRenderWindowInteractor* rwi = static_cast<vtkRenderWindowInteractor*>(caller);
 	VisualizationContainer* vis = static_cast<VisualizationContainer*>(clientData);

interaction/InteractionCallbacks.h

@@ -30,6 +30,7 @@ class InteractionCallbacks {
 	static void Grow(vtkObject* caller, unsigned long eventId, void* clientData, void *callData);
 	static void Done(vtkObject* caller, unsigned long eventId, void* clientData, void *callData);
 	static void Visible(vtkObject* caller, unsigned long eventId, void* clientData, void *callData);
+	static void Dot(vtkObject* caller, unsigned long eventId, void* clientData, void *callData);
 
 	static void MouseMove(vtkObject* caller, unsigned long eventId, void* clientData, void *callData);
 

interaction/InteractionEnums.h

@@ -9,7 +9,8 @@ enum InteractionMode {
 	MergeMode,
 	SplitMode,
 	GrowMode,
-	VisibleMode
+	VisibleMode,
+	DotMode
 };
 
 enum FilterMode {

interaction/vtkInteractorStyleSlice.cxx

@@ -242,6 +242,30 @@ void vtkInteractorStyleSlice::EndVisible()
 	this->StopState();
 }
 
+//----------------------------------------------------------------------------
+void vtkInteractorStyleSlice::StartDot()
+{
+	if (this->State != VTKIS_NONE)
+	{
+		return;
+	}
+	this->StartState(VTKIS_DOT_SLICE);
+}
+
+//----------------------------------------------------------------------------
+void vtkInteractorStyleSlice::EndDot()
+{
+	if (this->State != VTKIS_DOT_SLICE)
+	{
+		return;
+	}
+	if (this->HandleObservers)
+	{
+		this->InvokeEvent(DotEvent, nullptr);
+	}
+	this->StopState();
+}
+
 //----------------------------------------------------------------------------
 void vtkInteractorStyleSlice::WindowLevel()
 {
@@ -414,6 +438,10 @@ void vtkInteractorStyleSlice::OnLeftButtonDown()
 		{
 			this->StartVisible();
 		}
+		else if (this->Mode == DotMode)
+		{
+			this->StartDot();
+		}
 		else
 		{
 			// Rotate
@@ -474,6 +502,10 @@ void vtkInteractorStyleSlice::OnLeftButtonUp() {
 	case VTKIS_VISIBLE_SLICE:
 		this->EndVisible();
 		break;
+
+	case VTKIS_DOT_SLICE:
+		this->EndDot();
+		break;
 	}
 
 	// Call parent to handle all other states and perform additional work

interaction/vtkInteractorStyleSlice.h

@@ -20,6 +20,7 @@ class vtkCellPicker;
 #define VTKIS_MERGE_SLICE 2053
 #define VTKIS_GROW_SLICE 2054
 #define VTKIS_VISIBLE_SLICE 2055
+#define VTKIS_DOT_SLICE 2056
 
 class vtkInteractorStyleSlice : public vtkInteractorStyleImage {
 public:
@@ -56,6 +57,8 @@ class vtkInteractorStyleSlice : public vtkInteractorStyleImage {
 	virtual void EndGrow();
 	virtual void StartVisible();
 	virtual void EndVisible();
+	virtual void StartDot();
+	virtual void EndDot();
 
 	virtual void WindowLevel() override;
 	double GetWindow();
@@ -79,7 +82,8 @@ class vtkInteractorStyleSlice : public vtkInteractorStyleImage {
 		AddEvent,
 		MergeEvent,
 		GrowEvent,
-		VisibleEvent
+		VisibleEvent,
+		DotEvent
 	};
 
 protected:

interaction/vtkInteractorStyleVolume.cxx

@@ -383,7 +383,7 @@ void vtkInteractorStyleVolume::OnLeftButtonDown()
 	else if (this->Mode == VisibleMode)
 	{
 		this->StartVisible();
-	}	
+	}
 	else
 	{
 		// If shift is held down, start window level

qt/FeedbackDialog.cxx

@@ -39,10 +39,13 @@ FeedbackDialog::FeedbackDialog(QWidget* parent, VisualizationContainer* visualiz
 	QObject::connect(table, &FeedbackTable::highlightRegion, this, &FeedbackDialog::on_highlightRegion);
 	QObject::connect(table, &FeedbackTable::countChanged, this, &FeedbackDialog::on_countChanged);
 
-	// Shortcut
-	QShortcut* shortcut = new QShortcut(QKeySequence(Qt::ALT + Qt::Key_V), this);
+	// Shortcuts
+	QShortcut* shortcut = new QShortcut(QKeySequence(Qt::Key_Period), this);
 	QObject::connect(shortcut, &QShortcut::activated, this, &FeedbackDialog::on_verifiedShortcut);
 
+	QShortcut* closeShortcut = new QShortcut(QKeySequence(Qt::CTRL + Qt::Key_F), this);
+	QObject::connect(closeShortcut, &QShortcut::activated, this, &FeedbackDialog::close);
+
 	updateRegions();
 }
 
@@ -110,5 +113,5 @@ void FeedbackDialog::on_countChanged(int count) {
 }
 
 void FeedbackDialog::on_verifiedShortcut() {
-	//printf("DLKJF");
+	visualizationContainer->ToggleCurrentRegionVerified();
 }

qt/MainWindow.cxx

@@ -88,6 +88,7 @@ MainWindow::MainWindow() {
 
 	// Settings dialog
 	settingsDialog = new SettingsDialog(this, visualizationContainer);
+	QObject::connect(settingsDialog, &SettingsDialog::enableDotAnnotationChanged, this, &MainWindow::on_enableDotAnnotationChanged);
 
 	// Feedback dialog
 	feedbackDialog = new FeedbackDialog(this, visualizationContainer);
@@ -588,6 +589,32 @@ void MainWindow::on_actionSegment_Volume_triggered() {
 	}
 }
 
+void MainWindow::on_actionApply_Dot_Annotation_triggered() {
+	QMessageBox message;
+	message.setIcon(QMessageBox::Warning);
+	message.setText("Apply dot annotation.");
+	message.setInformativeText(
+		"This operation will replace each region with a single voxel at the region center.\n\n"
+		"Do you wish to continue?"
+	);
+	message.setStandardButtons(QMessageBox::Yes | QMessageBox::No);
+	message.setDefaultButton(QMessageBox::Save);
+	int ret = message.exec();
+
+	switch (ret) {
+	case QMessageBox::Yes:
+		visualizationContainer->ApplyDotAnnotation();
+		break;
+
+	case QMessageBox::No:
+		break;
+
+	default:
+		// Should never be reached
+		break;
+	}
+}
+
 void MainWindow::on_actionExit_triggered() {
 	close();
 }
@@ -691,6 +718,10 @@ void MainWindow::on_actionVisible() {
 	visualizationContainer->SetInteractionMode(VisibleMode);
 }
 
+void MainWindow::on_actionDot() {
+	visualizationContainer->SetInteractionMode(DotMode);
+}
+
 void MainWindow::on_actionUpdate() {
 	visualizationContainer->RelabelCurrentRegion();
 }
@@ -807,6 +838,22 @@ void MainWindow::on_brushRadiusSpinBox_valueChanged(int value) {
 	visualizationContainer->SetBrushRadius(value);
 }
 
+void MainWindow::on_enableDotAnnotationChanged(bool enable) {
+	// Enable apply dot annotation
+	actionApply_Dot_Annotation->setEnabled(enable);
+
+	// Enable dot mode
+	QList<QAction*> actions = modeBarWidget->findChild<QToolBar*>()->actions();
+
+	for (int i = 0; i < actions.length(); i++) {
+		QAction* action = actions[i];
+		if (action->objectName() == "dotModeAction") {
+			action->setEnabled(enable);
+			break;
+		}
+	}
+}
+
 void MainWindow::on_toggleView() {
 	if (qvtkWidgetLeft->isVisible()) {
 		qvtkWidgetLeft->setVisible(false);
@@ -1059,6 +1106,11 @@ void MainWindow::createModeBar() {
 	toolBar->addAction(createActionIcon(":/icons/icon_merge.png", "Merge with current region (m)", "m", interactionModeGroup, currentMode == MergeMode, &MainWindow::on_actionMerge));
 	toolBar->addAction(createActionIcon(":/icons/icon_grow.png", "Grow / shrink region (g)", "g", interactionModeGroup, currentMode == GrowMode, &MainWindow::on_actionGrow));
 	toolBar->addAction(createActionIcon(":/icons/icon_visible.png", "Toggle region visibility (v)", "v", interactionModeGroup, currentMode == VisibleMode, &MainWindow::on_actionVisible));
+
+	QAction* dotAction = createActionIcon(":/icons/icon_dot.png", "Dot annotation mode (Ctrl + d)", QKeySequence(Qt::CTRL + Qt::Key_D), interactionModeGroup, currentMode == DotMode, &MainWindow::on_actionDot);
+	dotAction->setObjectName("dotModeAction");
+	dotAction->setEnabled(false);
+	toolBar->addAction(dotAction);
 
 	toolBar->addSeparator();
 	toolBar->addWidget(createLabel("Actions", 0, 0, 5, 5));
@@ -1163,6 +1215,17 @@ QAction* MainWindow::createActionIcon(const QString& fileName, const QString& te
 	return action;
 }
 
+QAction* MainWindow::createActionIcon(const QString& fileName, const QString& text, const QKeySequence& shortcut, QActionGroup* group, bool checked, void (MainWindow::*slot)()) {
+	QAction* action = new QAction(QIcon(fileName), text, group);
+	action->setShortcut(QKeySequence(shortcut));
+	action->setCheckable(true);
+	action->setChecked(checked);
+
+	QObject::connect(action, &QAction::triggered, this, slot);
+
+	return action;
+}
+
 QLabel* MainWindow::createLabel(const QString& text, int topMargin, int bottomMargin, int leftMargin, int rightMargin) {
 	QString style = QStringLiteral("color:#999;margin-top:%1px;margin-bottom:%2px;margin-left:%3px;margin-right:%4px")
 		.arg(topMargin).arg(bottomMargin).arg(leftMargin).arg(rightMargin);

qt/MainWindow.h

@@ -62,6 +62,7 @@ public slots:
 	virtual void on_actionRedo_triggered();
 
 	virtual void on_actionSegment_Volume_triggered();
+	virtual void on_actionApply_Dot_Annotation_triggered();
 
 	virtual void on_actionExit_triggered();
 
@@ -90,6 +91,7 @@ public slots:
 	virtual void on_actionGrow();
 	virtual void on_actionDone();
 	virtual void on_actionVisible();
+	virtual void on_actionDot();
 
 	// Action events
 	virtual void on_actionUpdate();
@@ -142,6 +144,8 @@ public slots:
 	virtual void on_brushRadiusDown();
 	virtual void on_brushRadiusUp();
 
+	virtual void on_enableDotAnnotationChanged(bool enable);
+
 signals:
 
 	void windowLevelChanged(double window, double value);
@@ -184,6 +188,7 @@ public slots:
 	QAction* createActionIcon(const QString& fileName, const QString& text, const QKeySequence& shortcut, void (MainWindow::*slot)());
 	QAction* createActionIcon(const QString& fileName, const QString& text, const QString& shortcut, bool checked, void (MainWindow::*slot)(bool));
 	QAction* createActionIcon(const QString& fileName, const QString& text, const QString& shortcut, QActionGroup* group, bool checked, void (MainWindow::*slot)());
+	QAction* createActionIcon(const QString& fileName, const QString& text, const QKeySequence& shortcut, QActionGroup* group, bool checked, void (MainWindow::*slot)());
 	QLabel* createLabel(const QString& text, int topMargin = 10, int bottomMargin = 5, int leftMargin = 0, int rightMargin = 0);
 
 	InteractionMode navEditMode;

qt/MainWindow.ui

@@ -398,6 +398,7 @@
      <string>Analyze</string>
     </property>
     <addaction name="actionSegment_Volume"/>
+    <addaction name="actionApply_Dot_Annotation"/>
    </widget>
    <widget class="QMenu" name="menuView">
     <property name="title">
@@ -611,6 +612,17 @@
    <property name="text">
     <string>Show Feedback</string>
    </property>
+   <property name="shortcut">
+    <string>Ctrl+F</string>
+   </property>
+  </action>
+  <action name="actionApply_Dot_Annotation">
+   <property name="enabled">
+    <bool>false</bool>
+   </property>
+   <property name="text">
+    <string>Apply Dot Annotation</string>
+   </property>
   </action>
  </widget>
  <customwidgets>

qt/SettingsDialog.cxx

@@ -114,4 +114,9 @@ void SettingsDialog::on_gradientOpacityCheckBox_stateChanged(int state) {
 
 void SettingsDialog::on_autoAdjustSamplingCheckBox_stateChanged(int state) {
 	visualizationContainer->GetVolumeView()->SetVolumeRenderingAutoAdjustSampling(state != 0);
+}
+
+
+void SettingsDialog::on_enableDotAnnotationCheckBox_stateChanged(int state) {
+	emit enableDotAnnotationChanged(state != 0);
 }

qt/SettingsDialog.h

@@ -40,6 +40,11 @@ public slots:
 	virtual void on_gradientOpacityCheckBox_stateChanged(int state);
 	virtual void on_autoAdjustSamplingCheckBox_stateChanged(int state);
 
+	virtual void on_enableDotAnnotationCheckBox_stateChanged(int state);
+
+signals:
+	void enableDotAnnotationChanged(bool enable);
+
 protected:
 	VisualizationContainer* visualizationContainer;
 };

qt/SettingsDialog.ui

@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>314</width>
-    <height>367</height>
+    <height>425</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -330,6 +330,26 @@
      </layout>
     </widget>
    </item>
+   <item>
+    <widget class="QGroupBox" name="groupBox_5">
+     <property name="title">
+      <string>Dot annotation</string>
+     </property>
+     <layout class="QVBoxLayout" name="verticalLayout_5">
+      <item>
+       <layout class="QHBoxLayout" name="horizontalLayout_8">
+        <item>
+         <widget class="QCheckBox" name="enableDotAnnotationCheckBox">
+          <property name="text">
+           <string>Enable dot annotation</string>
+          </property>
+         </widget>
+        </item>
+       </layout>
+      </item>
+     </layout>
+    </widget>
+   </item>
    <item>
     <spacer name="verticalSpacer">
      <property name="orientation">