Add java visualization examples (#528)

* Create LineWidth.java

* Create LineWidth.md

* Add TestLineWidth.png - Test Image

* Create Legend.java

* Create Legend.md

* Add TestLegend.png - Test Image

* Create ProjectSphere.java

* Create ProjectSphere.md

* Add TestProjectSphere.png - Test Image

* Create ProteinRibbons.java

* Create ProteinRibbons.md

* Add TestProteinRibbons.png - Test Image

* Create ScalarVisibility.java

* Create ScalarVisibility.md

* Add TestScalarVisibility.png - Test Image

* Update Java.md

* Update ScalarVisibility.java

* Add TestScalarVisibility.png - Test Image

src/Java.md

@@ -224,6 +224,7 @@ It would be appreciated if there are any Java VTK experts who could convert any
 | Example Name | Classes Demonstrated | Description | Image |
 | -------------- | ---------------------- | ------------- | ------- |
 [Bottle](/Java/Modelling/Bottle) | vtkRotationalExtrusionFilter | Sweeps polygonal data creating "skirt" from free edges and lines, and lines from vertices
+[ProjectSphere](/Java/Visualization/ProjectSphere) | vtkProjectSphereFilter | Unroll a sphere or spherical-like model.
 [Spring](/Java/Modelling/Spring) | vtkRotationalExtrusionFilter | Rotation in combination with linear displacement and radius variation.
 
 ### Working with Structured 3D Data
@@ -385,10 +386,14 @@ This section includes vtkImageData, vtkStructuredGrid and vtkRectilinearGrid.
 [CursorShape](/Java/Visualization/CursorShape) | | Change the shape of the cursor. 
 [Cutter](/Java/VisualizationAlgorithms/Cutter) | vtkCutter | How to use vtkCutter by cutting through a cube.
 [Follower](/Java/Visualization/Follower) | vtkFollower | Draw text that stays right side up.
+[Legend](/java/Visualization/Legend) | vtkLegendBoxActor | Draw symbols with text
+[LineWidth](/Java/Visualization/LineWidth) | vtkActor vtkProperty | Change the width/thickness of lines in an actor.
 [Opacity](/Java/Visualization/Opacity) | vtkActor | Transparency, transparent.
 [OrientedGlyphs](/Java/Visualization/OrientedGlyphs) | vtkGlyph3D | Copies oriented and scaled glyph geometry to every input point
 [VectorFieldExample](/Java/Visualization/VectorFieldExample) | vtkXMLUnstructuredGridReader, vtkThresholdPoints, vtkGlyph3D | A vector field visualisation.
 [NoShading](/Java/Visualization/NoShading) | vtkActor | 
+[ProteinRibbons](/Java/Visualization/ProteinRibbons) | vtkProteinRibbonFilter | Display pdb ribbons.
+[ScalarVisibility](/Java/Visualization/ScalarVisibility) | vtkDataSetMapper | Switch between coloring the actor and coloring the data.
 [VisualizeImageData](/Java/Visualization/VisualizeImageData) | vtkDataSetMapper vtkImageData | Visualize the points of an ImageData.
 [VisualizeVTP](/Java/Visualization/VisualizeVTP) | vtkXMLPolyDataReader vtkPolyDataMapper | Visualize a VTP File.
 [WindowSize](/Java/Visualization/WindowSize) | vtkRenderWindow | Change the size of a window.

src/Java/Visualization/Legend.java

+import vtk.vtkActor;
+import vtk.vtkNamedColors;
+import vtk.vtkNativeLibrary;
+import vtk.vtkPolyDataMapper;
+import vtk.vtkRenderWindow;
+import vtk.vtkRenderWindowInteractor;
+import vtk.vtkRenderer;
+import vtk.vtkSphereSource;
+import vtk.vtkLegendBoxActor;
+import vtk.vtkCubeSource;
+import vtk.vtkPolyData;
+
+
+public class Legend 
+{
+  // -----------------------------------------------------------------
+  // Load VTK library and print which library was not properly loaded
+  static 
+  {
+    if (!vtkNativeLibrary.LoadAllNativeLibraries()) 
+    {
+      for (vtkNativeLibrary lib : vtkNativeLibrary.values()) 
+      {
+        if (!lib.IsLoaded()) 
+        {
+          System.out.println(lib.GetLibraryName() + " not loaded");
+        }
+      }
+    }
+    vtkNativeLibrary.DisableOutputWindow(null);
+  }
+  // -----------------------------------------------------------------
+
+  public static void main(String s[]) 
+  {
+    vtkNamedColors colors = new vtkNamedColors();
+
+    //For boxLegendColor
+    double boxLegendColor[] = new double[4];
+    //For ballLegendColor
+    double ballLegendColor[] = new double[4];
+    //Renderer Background Color
+    double Bgcolor[] = new double[4];
+    //Renderer legend Background Color
+    double legendBgcolor[] = new double[4];
+
+    colors.GetColor("Tomato", boxLegendColor);
+    colors.GetColor("banana", ballLegendColor);
+    colors.GetColor("cyan", Bgcolor);
+    colors.GetColor("warm_grey", legendBgcolor);
+    
+    vtkSphereSource sphereSource = new vtkSphereSource();
+    sphereSource.SetCenter(0.0, 0.0, 0.0);
+    sphereSource.SetRadius(5000.0);
+    sphereSource.Update();
+    
+    vtkPolyData polydata = sphereSource.GetOutput();
+    
+    // Create a mapper
+    vtkPolyDataMapper mapper = new vtkPolyDataMapper();
+    mapper.SetInputData(polydata);
+    
+    vtkActor actor = new vtkActor();
+    actor.SetMapper(mapper);
+    
+    vtkLegendBoxActor legend = new vtkLegendBoxActor();
+    legend.SetNumberOfEntries(2);
+    
+    vtkCubeSource legendBox = new vtkCubeSource();
+    legendBox.Update();
+    legend.SetEntry(0, legendBox.GetOutput(), "Box", boxLegendColor);
+    legend.SetEntry(1, sphereSource.GetOutput(), "Ball", ballLegendColor);
+    
+    // place legend in lower right
+    legend.GetPositionCoordinate().SetCoordinateSystemToView();
+    legend.GetPositionCoordinate().SetValue(.5, -1.0);
+    
+    legend.GetPosition2Coordinate().SetCoordinateSystemToView();
+    legend.GetPosition2Coordinate().SetValue(1.0, -0.5);
+    
+    legend.UseBackgroundOn();
+    legend.SetBackgroundColor(legendBgcolor);
+	   
+    // Create the renderer, render window and interactor.
+    vtkRenderer ren = new vtkRenderer();
+    vtkRenderWindow renWin = new vtkRenderWindow();
+    renWin.AddRenderer(ren);
+    vtkRenderWindowInteractor iren = new vtkRenderWindowInteractor();
+    iren.SetRenderWindow(renWin);
+    
+    // Visualise
+    ren.AddActor(actor);
+    ren.AddActor(legend);
+    ren.SetBackground(Bgcolor);
+    
+    renWin.SetSize(300, 300);
+    renWin.Render();
+
+    iren.Initialize();
+    iren.Start();
+  }
+}

src/Java/Visualization/Legend.md

+### Description
+
+vtkLegendBoxActor object is used to associate a symbol with a text string. 
+
+The user specifies a vtkPolyData to use as the symbol, and a string associated with the symbol. The actor can then be placed in the scene in the same way that any other vtkActor2D can be used.

src/Java/Visualization/LineWidth.java

+import vtk.vtkActor;
+import vtk.vtkNativeLibrary;
+import vtk.vtkPolyDataMapper;
+import vtk.vtkRenderWindow;
+import vtk.vtkRenderWindowInteractor;
+import vtk.vtkRenderer;
+import vtk.vtkLineSource;
+
+public class LineWidth 
+{
+  // -----------------------------------------------------------------
+  // Load VTK library and print which library was not properly loaded
+  static 
+  {
+    if (!vtkNativeLibrary.LoadAllNativeLibraries()) 
+    {
+      for (vtkNativeLibrary lib : vtkNativeLibrary.values()) 
+      {
+        if (!lib.IsLoaded()) 
+        {
+          System.out.println(lib.GetLibraryName() + " not loaded");
+        }
+      }
+    }
+    vtkNativeLibrary.DisableOutputWindow(null);
+  }
+  // -----------------------------------------------------------------
+
+  public static void main(String s[]) 
+  {
+        
+    vtkLineSource lineSource = new vtkLineSource();
+    
+    vtkPolyDataMapper mapper = new vtkPolyDataMapper();
+    mapper.SetInputConnection(lineSource.GetOutputPort());
+    
+    vtkActor actor = new vtkActor();
+    actor.SetMapper(mapper);
+    actor.GetProperty().SetLineWidth(5);
+    
+    // Create the renderer, render window and interactor.
+    vtkRenderer ren = new vtkRenderer();
+    vtkRenderWindow renWin = new vtkRenderWindow();
+    renWin.AddRenderer(ren);
+    vtkRenderWindowInteractor iren = new vtkRenderWindowInteractor();
+    iren.SetRenderWindow(renWin);
+    
+    ren.AddActor(actor);
+	  
+    renWin.SetSize(300, 300);
+    renWin.Render();
+
+    iren.Initialize();
+    iren.Start();
+  }
+}

src/Java/Visualization/LineWidth.md

+### Description
+
+vtkLineSource is a source object that creates a polyline defined by two endpoints. The number of segments composing the polyline is controlled by setting the object resolution.

src/Java/Visualization/ProjectSphere.java

+import vtk.vtkActor;
+import vtk.vtkNamedColors;
+import vtk.vtkNativeLibrary;
+import vtk.vtkRenderWindow;
+import vtk.vtkRenderWindowInteractor;
+import vtk.vtkRenderer;
+import vtk.vtkProjectSphereFilter;
+import vtk.vtkElevationFilter;
+import vtk.vtkParametricSuperEllipsoid;
+import vtk.vtkParametricFunctionSource;
+import vtk.vtkPolyData;
+import vtk.vtkPolyDataMapper;
+
+public class ProjectSphere
+{
+  // -----------------------------------------------------------------
+  // Load VTK library and print which library was not properly loaded
+  static 
+  {
+    if (!vtkNativeLibrary.LoadAllNativeLibraries()) 
+    {
+      for (vtkNativeLibrary lib : vtkNativeLibrary.values()) 
+      {
+        if (!lib.IsLoaded()) 
+        {
+          System.out.println(lib.GetLibraryName() + " not loaded");
+        }
+      }
+    }
+    vtkNativeLibrary.DisableOutputWindow(null);
+  }
+  // -----------------------------------------------------------------
+  
+  public static void main(String args[]) 
+  {
+    vtkNamedColors colors = new vtkNamedColors();
+
+    //Renderer Background Color
+    double leftRenderercolor[] = new double[4];
+    double rightRenderercolor[] = new double[4];
+
+    colors.GetColor("Tan", leftRenderercolor);
+    colors.GetColor("LightSlateGray", rightRenderercolor);
+    
+    vtkParametricSuperEllipsoid surface = new vtkParametricSuperEllipsoid();
+    surface.SetN1(2.0);
+    surface.SetN2(0.5);
+    
+    vtkParametricFunctionSource source = new vtkParametricFunctionSource();
+    source.SetParametricFunction(surface);
+    
+    vtkElevationFilter elevationFilter = new vtkElevationFilter();
+    elevationFilter.SetInputConnection(source.GetOutputPort());
+    elevationFilter.SetLowPoint(0.0, 0.0, -4.0);
+    elevationFilter.SetHighPoint(0.0, 0.0, 4.0);
+    elevationFilter.Update();
+    
+    // Deep copy the point data since in some versions of VTK, the ProjectSphereFilter modifies the input point data 
+    vtkPolyData pd1 = new vtkPolyData();
+    pd1.DeepCopy(elevationFilter.GetOutput());
+
+    vtkProjectSphereFilter sphereProject1 = new vtkProjectSphereFilter();
+    sphereProject1.SetInputConnection(elevationFilter.GetOutputPort());
+    sphereProject1.Update();
+
+    vtkPolyDataMapper mapper1 = new vtkPolyDataMapper();
+    mapper1.SetInputConnection(sphereProject1.GetOutputPort());
+    mapper1.SetScalarRange(sphereProject1.GetOutput().GetPointData().GetScalars().GetRange());
+    
+    vtkActor actor1 = new vtkActor();
+    actor1.SetMapper(mapper1);
+
+    vtkPolyDataMapper mapper2 = new vtkPolyDataMapper();
+    mapper2.SetInputData(pd1);
+    mapper2.SetScalarRange(pd1.GetPointData().GetScalars().GetRange());  
+    
+    vtkActor actor2 = new vtkActor();
+    actor2.SetMapper(mapper2);
+    	 
+    // A render window
+    vtkRenderWindow renderWindow = new vtkRenderWindow();
+
+    // Define viewport ranges
+    // (xmin, ymin, xmax, ymax)
+    double leftViewport[] = new double[] {0.0, 0.0, 0.5, 1.0};
+    double rightViewport[] = new double[] {0.5, 0.0, 1.0, 1.0};
+
+    // Setup both renderers
+    vtkRenderer leftRenderer = new vtkRenderer();
+    renderWindow.AddRenderer(leftRenderer);
+    leftRenderer.SetViewport(leftViewport);
+    leftRenderer.SetBackground(.6, .5, .4);
+
+    vtkRenderer rightRenderer = new vtkRenderer();
+    renderWindow.AddRenderer(rightRenderer);
+    rightRenderer.SetViewport(rightViewport);
+    rightRenderer.SetBackground(.4, .5, .6);
+
+    leftRenderer.AddActor(actor2);
+    rightRenderer.AddActor(actor1);
+
+    vtkRenderWindowInteractor iren = new vtkRenderWindowInteractor();
+    iren.SetRenderWindow(renderWindow);
+	
+    leftRenderer.GetActiveCamera().Azimuth(30);
+    leftRenderer.GetActiveCamera().Elevation(-30);
+    leftRenderer.ResetCamera();
+    
+    renderWindow.SetSize(640, 480);
+    renderWindow.Render();
+
+    iren.Initialize();
+    iren.Start();
+  }
+}

src/Java/Visualization/ProjectSphere.md

+### Description
+
+vtkProjectSphereFilter object is a  filter to 'unroll' a sphere. The unroll longitude is -180.

src/Java/Visualization/ProteinRibbons.java

+import vtk.vtkActor;
+import vtk.vtkNamedColors;
+import vtk.vtkNativeLibrary;
+import vtk.vtkRenderWindow;
+import vtk.vtkRenderWindowInteractor;
+import vtk.vtkRenderer;
+import vtk.vtkProteinRibbonFilter;
+import vtk.vtkPDBReader;
+import vtk.vtkInteractorStyleSwitch;
+import vtk.vtkPolyDataMapper;
+
+public class ProteinRibbons
+{
+  // -----------------------------------------------------------------
+  // Load VTK library and print which library was not properly loaded
+  static 
+  {
+    if (!vtkNativeLibrary.LoadAllNativeLibraries()) 
+    {
+      for (vtkNativeLibrary lib : vtkNativeLibrary.values()) 
+      {
+        if (!lib.IsLoaded()) 
+        {
+          System.out.println(lib.GetLibraryName() + " not loaded");
+        }
+      }
+    }
+    vtkNativeLibrary.DisableOutputWindow(null);
+  }
+  // -----------------------------------------------------------------
+  
+
+  public static void main(String args[]) 
+  {
+	  
+    //parse command line arguments
+    if (args.length != 1) 
+    {
+      System.err.println("Usage: java -classpath ... Filename(.pdb) e.g 2j6g.pdb");
+      return;
+    }
+    String Filename = args[0];
+  
+    vtkNamedColors colors = new vtkNamedColors();
+
+    //Renderer Background Color
+    double Bgcolor[] = new double[4];
+
+    colors.GetColor("Silver", Bgcolor);
+    
+    // read protein from pdb
+    vtkPDBReader reader = new vtkPDBReader();
+    reader.SetFileName(Filename);
+
+    // setup ribbon filter
+    vtkProteinRibbonFilter ribbonFilter = new vtkProteinRibbonFilter();
+    ribbonFilter.SetInputConnection(reader.GetOutputPort());
+
+    // setup poly data mapper
+    vtkPolyDataMapper polyDataMapper = new vtkPolyDataMapper();
+    polyDataMapper.SetInputConnection(ribbonFilter.GetOutputPort());
+
+    // setup actor
+    vtkActor actor = new vtkActor();
+    actor.SetMapper(polyDataMapper);
+    actor.GetProperty().SetDiffuse(.7);
+    actor.GetProperty().SetSpecular(.5);
+    actor.GetProperty().SetSpecularPower(80.0);
+
+    
+    // Create the renderer, render window and interactor.
+    vtkRenderer ren = new vtkRenderer();
+    vtkRenderWindow renWin = new vtkRenderWindow();
+    renWin.AddRenderer(ren);
+    vtkRenderWindowInteractor iren = new vtkRenderWindowInteractor();
+    iren.SetRenderWindow(renWin);
+    
+    vtkInteractorStyleSwitch style = new vtkInteractorStyleSwitch();
+    style.SetCurrentStyleToTrackballCamera();
+    
+    // Visualise
+    ren.AddActor(actor);
+    ren.ResetCameraClippingRange();
+    ren.SetBackground(Bgcolor);
+    
+    renWin.SetSize(300, 300);
+    renWin.SetMultiSamples(0);
+    renWin.Render();
+
+    iren.Initialize();
+    iren.Start();
+  }
+}

src/Java/Visualization/ProteinRibbons.md

+### Description
+
+vtkProteinRibbonFilter object is a polydata algorithm that generates protein ribbons.
+
+vtkPDBReader is a source object that reads Molecule files.

src/Java/Visualization/ScalarVisibility.java

+import vtk.vtkActor;
+import vtk.vtkNamedColors;
+import vtk.vtkNativeLibrary;
+import vtk.vtkPolyDataMapper;
+import vtk.vtkRenderWindow;
+import vtk.vtkRenderWindowInteractor;
+import vtk.vtkRenderer;
+import vtk.vtkPointSource;
+
+
+public class ScalarVisibility 
+{
+  // -----------------------------------------------------------------
+  // Load VTK library and print which library was not properly loaded
+  static 
+  {
+    if (!vtkNativeLibrary.LoadAllNativeLibraries()) 
+    {
+      for (vtkNativeLibrary lib : vtkNativeLibrary.values()) 
+      {
+        if (!lib.IsLoaded()) 
+        {
+          System.out.println(lib.GetLibraryName() + " not loaded");
+        }
+      }
+    }
+    vtkNativeLibrary.DisableOutputWindow(null);
+  }
+  // -----------------------------------------------------------------
+  
+  public static void main(String s[]) 
+  {
+    vtkNamedColors colors = new vtkNamedColors();
+
+    //For Actor Color
+    double actorColor[] = new double[4];
+    colors.GetColor("Red", actorColor);
+    
+    vtkPointSource pointSource = new vtkPointSource();
+    vtkPolyDataMapper mapper = new vtkPolyDataMapper();
+    mapper.SetInputConnection(pointSource.GetOutputPort());
+    mapper.ScalarVisibilityOff();
+    
+    vtkActor actor = new vtkActor();
+    actor.SetMapper( mapper );
+    actor.GetProperty().SetColor(actorColor);
+    actor.GetProperty().SetPointSize(8);
+	    
+    // Create the renderer, render window and interactor.
+    vtkRenderer ren = new vtkRenderer();
+    vtkRenderWindow renWin = new vtkRenderWindow();
+    renWin.AddRenderer(ren);
+    vtkRenderWindowInteractor iren = new vtkRenderWindowInteractor();
+    iren.SetRenderWindow(renWin);
+    
+    // Visualise
+    ren.AddActor(actor);
+	   
+    renWin.SetSize(300, 300);
+    renWin.Render();
+
+    iren.Initialize();
+    iren.Start();
+  }
+}

src/Java/Visualization/ScalarVisibility.md

+### Description
+
+vtkPointSource is a source object that creates a user-specified number of points within a specified radius about a specified center point.