Add neighbor radius control, use more accurate neighbor method

Author: davidborland

CMakeLists.txt

@@ -67,8 +67,8 @@ set(UI_RESOURCES
 # Create executable
 qt5_wrap_ui(UISrcs ${UI_FILES} )
 # CMAKE_AUTOMOC is ON so the MOC headers will be automatically wrapped.
-add_executable(Segmentor MACOSX_BUNDLE WIN32 ${CXX_FILES} ${UISrcs} ${QT_WRAP} ${UI_RESOURCES})
-#add_executable(Segmentor MACOSX_BUNDLE ${CXX_FILES} ${UISrcs} ${QT_WRAP} ${UI_RESOURCES})
+#add_executable(Segmentor MACOSX_BUNDLE WIN32 ${CXX_FILES} ${UISrcs} ${QT_WRAP} ${UI_RESOURCES})
+add_executable(Segmentor MACOSX_BUNDLE ${CXX_FILES} ${UISrcs} ${QT_WRAP} ${UI_RESOURCES})
 qt5_use_modules(Segmentor Core Gui)
 target_link_libraries(Segmentor ${VTK_LIBRARIES})
 install(TARGETS Segmentor 

qt/SettingsDialog.cxx

@@ -53,6 +53,9 @@ void SettingsDialog::initializeSettings() {
 
 	// Surface opacity
 	surfaceOpacitySpinBox->setValue(volumeView->GetVisibleOpacity());
+
+	// Neighbor radius
+	neighborRadiusSpinBox->setValue(visualizationContainer->GetNeighborRadius());
 }
 
 void SettingsDialog::on_windowSpinBox_valueChanged(double value) {
@@ -87,6 +90,10 @@ void SettingsDialog::on_surfaceOpacityDown() {
 	surfaceOpacitySpinBox->stepDown();
 }
 
+void SettingsDialog::on_neighborRadiusSpinBox_valueChanged(double value) {
+	visualizationContainer->SetNeighborRadius(value);
+}
+
 void SettingsDialog::on_voxelSizeSpinBox() {
 	visualizationContainer->SetVoxelSize(
 		xSizeSpinBox->value(),

qt/SettingsDialog.h

@@ -31,6 +31,8 @@ public slots:
 	virtual void on_surfaceOpacityUp();
 	virtual void on_surfaceOpacityDown();
 
+	virtual void on_neighborRadiusSpinBox_valueChanged(double value);
+
 	virtual void on_voxelSizeSpinBox();
 
 	virtual void on_windowLevelChanged(double window, double level);

qt/SettingsDialog.ui

@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>314</width>
-    <height>425</height>
+    <height>486</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -299,6 +299,52 @@
      </layout>
     </widget>
    </item>
+   <item>
+    <widget class="QGroupBox" name="groupBox_6">
+     <property name="title">
+      <string>Neighbor visibility</string>
+     </property>
+     <layout class="QVBoxLayout" name="verticalLayout_6">
+      <item>
+       <layout class="QHBoxLayout" name="horizontalLayout_9">
+        <item>
+         <widget class="QLabel" name="label_5">
+          <property name="text">
+           <string>Radius</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <spacer name="horizontalSpacer_5">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>40</width>
+            <height>20</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+        <item>
+         <widget class="QDoubleSpinBox" name="neighborRadiusSpinBox">
+          <property name="minimum">
+           <double>0.000000000000000</double>
+          </property>
+          <property name="maximum">
+           <double>10.000000000000000</double>
+          </property>
+          <property name="singleStep">
+           <double>1.000000000000000</double>
+          </property>
+         </widget>
+        </item>
+       </layout>
+      </item>
+     </layout>
+    </widget>
+   </item>
    <item>
     <widget class="QGroupBox" name="groupBox_4">
      <property name="title">

visualization/VisualizationContainer.cxx

@@ -8,6 +8,7 @@
 #include <vtkCallbackCommand.h>
 #include <vtkCamera.h>
 #include <vtkExtractVOI.h>
+#include <vtkGeometryFilter.h>
 #include <vtkImageConnectivityFilter.h>
 #include <vtkImageDilateErode3D.h>
 #include <vtkImageGaussianSmooth.h>
@@ -65,6 +66,7 @@ VisualizationContainer::VisualizationContainer(vtkRenderWindowInteractor* volume
 	filterRegions = false;
 
 	brushRadius = 1;
+	neighborRadius = 0.0;
 
 	// Qt main window
 	qtWindow = mainWindow;
@@ -421,6 +423,7 @@ VisualizationContainer::FileErrorCode VisualizationContainer::SaveImageData(cons
 		shiftScale->SetInputDataObject(data);
 
 		vtkSmartPointer<vtkTIFFWriter> writer = vtkSmartPointer<vtkTIFFWriter>::New();
+		writer->SetCompressionToNoCompression();
 		writer->SetFileName(fileName.c_str());
 		writer->SetInputConnection(shiftScale->GetOutputPort());
 		writer->Update();
@@ -458,6 +461,7 @@ VisualizationContainer::FileErrorCode VisualizationContainer::SaveSegmentationDa
 	}
 	else if (extension == "tif" || extension == "tiff") {
 		vtkSmartPointer<vtkTIFFWriter> writer = vtkSmartPointer<vtkTIFFWriter>::New();
+		writer->SetCompressionToNoCompression();
 		writer->SetFileName(fileName.c_str());
 		writer->SetInputDataObject(labels);
 		writer->Update();
@@ -945,22 +949,70 @@ void VisualizationContainer::ShowPlaneRegions() {
 void VisualizationContainer::ShowNeighborRegions() {
 	if (!regions) return;
 
-	for (RegionCollection::Iterator it = regions->Begin(); it != regions->End(); it++) {
-		Region* region = regions->Get(it);
+	if (currentRegion) {
+		int extent[6];
+		currentRegion->GetExtent(extent);
+
+		double a[6];
+		a[0] = extent[0] - neighborRadius;
+		a[1] = extent[1] + neighborRadius;
+		a[2] = extent[2] - neighborRadius;
+		a[3] = extent[3] + neighborRadius;
+		a[4] = extent[4] - neighborRadius;
+		a[5] = extent[5] + neighborRadius;
+		
+		vtkSmartPointer<vtkGeometryFilter> aSurface = vtkSmartPointer<vtkGeometryFilter>::New();
+		aSurface->SetInputConnection(currentRegion->GetCells());
+		aSurface->Update();
+
+		for (RegionCollection::Iterator it = regions->Begin(); it != regions->End(); it++) {
+			Region* region = regions->Get(it);
 
-		if (currentRegion) {
-			double d = sqrt(vtkMath::Distance2BetweenPoints(currentRegion->GetCenter(), region->GetCenter()));
-			double r = (currentRegion->GetLength() + region->GetLength()) / 4;
+			int b[6];
+			region->GetExtent(b);
 
-			if (d <= r * 1.05) {
-				region->SetVisible(true);
-				//surface->GetActor()->GetProperty()->SetOpacity(neighborOpacity);
+			bool intersect = !(
+				b[0] > a[1] || b[1] < a[0] ||
+				b[2] > a[3] || b[3] < a[2] ||
+				b[4] > a[5] || b[5] < a[4]
+			);
+
+			if (intersect) {
+				vtkSmartPointer<vtkGeometryFilter> bSurface = vtkSmartPointer<vtkGeometryFilter>::New();
+				bSurface->SetInputConnection(region->GetCells());
+				bSurface->Update();
+
+				double min = VTK_DOUBLE_MAX;
+				for (int i = 0; i < aSurface->GetOutput()->GetNumberOfPoints(); i++) {
+					double a[3];
+					aSurface->GetOutput()->GetPoint(i, a);
+
+					for (int j = 0; j < bSurface->GetOutput()->GetNumberOfPoints(); j++) {
+						double b[3];
+						bSurface->GetOutput()->GetPoint(j, b);
+
+						double d = vtkMath::Distance2BetweenPoints(a, b);
+
+						if (d < min) min = d;
+					}
+				}
+
+				if (min <= neighborRadius) {
+					region->SetVisible(true);
+					//surface->GetActor()->GetProperty()->SetOpacity(neighborOpacity);
+				}
+				else {
+					region->SetVisible(false);
+				}
 			}
 			else {
 				region->SetVisible(false);
 			}
 		}
-		else {
+	}
+	else {
+		for (RegionCollection::Iterator it = regions->Begin(); it != regions->End(); it++) {
+			Region* region = regions->Get(it);
 			region->SetVisible(false);
 		}
 	}
@@ -2211,6 +2263,14 @@ void VisualizationContainer::SetBrushRadius(int radius) {
 	Render();
 }
 
+double VisualizationContainer::GetNeighborRadius() {
+	return neighborRadius;
+}
+
+void VisualizationContainer::SetNeighborRadius(double radius) {
+	neighborRadius = radius;
+}
+
 void VisualizationContainer::Render() {
 	volumeView->Render();
 	sliceView->Render();

visualization/VisualizationContainer.h

@@ -130,6 +130,9 @@ class VisualizationContainer {
 	int GetBrushRadius();
 	void SetBrushRadius(int radius);
 
+	double GetNeighborRadius();
+	void SetNeighborRadius(double radius);
+
 	void Render();
 
 	void Undo();
@@ -191,6 +194,9 @@ class VisualizationContainer {
 	// Brush radius
 	int brushRadius;
 
+	// Neighbor radius
+	double neighborRadius;
+
 	void SetImageData(vtkImageData* imageData);
 	bool SetLabelData(vtkImageData* labelData, const std::vector<RegionInfo>& metadata);