SurfaceManager (Mango Plugin API)

```
public interface SurfaceManager
```
Manages surface data.

Author:

michaelmartinez

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`RENDER_TYPE_POINTS`
`static int`	`RENDER_TYPE_TRIANGLES`
`static int`	`RENDER_TYPE_WIREFRAME`
`static int`	`VIDEO_FORMAT_AVI_DIB`
`static int`	`VIDEO_FORMAT_AVI_MJPG`
`static int`	`VIDEO_FORMAT_AVI_PNG`
`static int`	`VIDEO_FORMAT_QUICKTIME_ANIMATION`
`static int`	`VIDEO_FORMAT_QUICKTIME_JPEG`
`static int`	`VIDEO_FORMAT_QUICKTIME_PNG`
`static int`	`VIDEO_FORMAT_QUICKTIME_RAW`
`static int`	`VIDEO_QUALITY_BEST`
`static int`	`VIDEO_QUALITY_FASTEST`
`static int`	`VIDEO_QUALITY_GOOD`

Method Summary

Methods
Modifier and Type	Method and Description
`Surface`	`addShapeFromLogical(List<ImageVolume> overlays, String name, int rgb, double roiThreshold, boolean shrinkWrap, boolean maximum, boolean imageSmoothing, double width, int kernelSize, double resX, double resY, double resZ, boolean surfaceSmoothing, double pointError, double featureAngle, int iterations)` Adds a surface shape from a logical.
`Surface`	`addShapeFromOverlay(ImageVolume overlay, String name, int rgb, double threshold, boolean shrinkWrap, boolean maximum, boolean imageSmoothing, double width, int kernelSize, double resX, double resY, double resZ, boolean surfaceSmoothing, double pointError, double featureAngle, int iterations)` Adds a surface shape from an overlay.
`Surface`	`addShapeFromROI(int roiColorIndex, String name, int rgb, double roiThreshold, boolean shrinkWrap, boolean maximum, boolean imageSmoothing, double width, int kernelSize, double resX, double resY, double resZ, boolean surfaceSmoothing, double pointError, double featureAngle, int iterations)` Adds a surface shape from a ROI.
`List<Surface>`	`addShapesFromFile(String openLocation)` Adds a surface shape from file.
`void`	`captureSnapshot(String saveLocation)` Save a snapshot of the surface viewer to the specified location.
`void`	`captureVideoStart(String saveLocation, int videoFormat, int videoQuality, int fps, boolean animate)` Starts saving a captured video to the specified file location.
`void`	`captureVideoStop()` Stops the video capture.
`void`	`exportTo(String saveLocation, String surfaceFormat, Surface surfaces, String options)` Exports the surface data to the specified file location.
`List<Surface>`	`getAddedShapes()` Returns a list of surfaces added to the base surface.
`List<Shape>`	`getAllPointsAndLines()` Returns a list of all points and lines.
`Surface`	`getBaseSurface()` Returns the base surface
`JFrame`	`getFrame()` Returns the parent window of the surface view.
`List<Shape>`	`getLines()` Returns a list of lines.
`List<Shape>`	`getPoints()` Returns a list of points.
`Surface[]`	`getSurfaces()` Returns an array of loaded surfaces.
`float`	`getThreshold()` Returns the threshold used to build the base surface.
`double[]`	`getViewTransform()` Returns the view transform (4x4).
`void`	`goToShape(Shape shape)` Move the current coordinate to the specified line or point shape.
`void`	`hideAll(boolean hidden)` Hide/show all the added surface shapes, lines, and points.
`void`	`lineToShape(Shape fromShape, Shape toShape)` Adds a direct line between two shapes.
`List<Analysis>`	`measureAll()` Measure all added surface shapes, lines, and points.
`void`	`pauseScriptForUserInput()` Pauses execution of a running script.
`void`	`removeAll()` Remove all the added surface shapes, lines, and points.
`void`	`removeShape(Shape shape)` Remove a line or point shape.
`void`	`removeSurface(Surface surface)` Remove an added surface shape.
`Object`	`runPlugin(String pluginName, String[] args)` Runs a surface plugin.
`List<Analysis>`	`runSurfaceAreaStats(Surface surface)` Runs surface area stats on the specified surface.
`List<Analysis>`	`runSurfaceVolumeStats(Surface surface)` Runs surface volume stats on the specified surface.
`void`	`saveAs(String saveLocation, Surface surfaces, boolean includeLinesAndPoints)` Saves the surface data in the Mango surface format.
`void`	`selectMenuOption(String name)` Selects menu options.
`void`	`setBackground(int rgb)` Sets the surface background
`void`	`setLighting(double ambient, double diffuse, double specular, double horizontal, double vertical)` Sets the lighting parameters.
`void`	`setMaterial(Surface surface, int rgb, boolean showOverlayColors, boolean showOnlyThisOverlayColor, boolean flatShading, int renderType, double transparency, double emmisivity, double shininess, double searchDistance)` Sets the material parameters.
`void`	`setMenuOption(String name, boolean value)` Sets menu items (typically checkboxes).
`void`	`surfaceToShape(Shape fromPoint, Shape toPoint)` Adds a line along the surface bewteen two shapes.
`void`	`updateSurface()` Redraws the surface view.

- Field Detail
  - RENDER_TYPE_POINTS
```
static final int RENDER_TYPE_POINTS
```
    See Also:
    Constant Field Values
  - RENDER_TYPE_TRIANGLES
```
static final int RENDER_TYPE_TRIANGLES
```
    See Also:
    Constant Field Values
  - RENDER_TYPE_WIREFRAME
```
static final int RENDER_TYPE_WIREFRAME
```
    See Also:
    Constant Field Values
  - VIDEO_FORMAT_AVI_DIB
```
static final int VIDEO_FORMAT_AVI_DIB
```
    See Also:
    Constant Field Values
  - VIDEO_FORMAT_AVI_MJPG
```
static final int VIDEO_FORMAT_AVI_MJPG
```
    See Also:
    Constant Field Values
  - VIDEO_FORMAT_AVI_PNG
```
static final int VIDEO_FORMAT_AVI_PNG
```
    See Also:
    Constant Field Values
  - VIDEO_FORMAT_QUICKTIME_ANIMATION
```
static final int VIDEO_FORMAT_QUICKTIME_ANIMATION
```
    See Also:
    Constant Field Values
  - VIDEO_FORMAT_QUICKTIME_JPEG
```
static final int VIDEO_FORMAT_QUICKTIME_JPEG
```
    See Also:
    Constant Field Values
  - VIDEO_FORMAT_QUICKTIME_PNG
```
static final int VIDEO_FORMAT_QUICKTIME_PNG
```
    See Also:
    Constant Field Values
  - VIDEO_FORMAT_QUICKTIME_RAW
```
static final int VIDEO_FORMAT_QUICKTIME_RAW
```
    See Also:
    Constant Field Values
  - VIDEO_QUALITY_BEST
```
static final int VIDEO_QUALITY_BEST
```
    See Also:
    Constant Field Values
  - VIDEO_QUALITY_FASTEST
```
static final int VIDEO_QUALITY_FASTEST
```
    See Also:
    Constant Field Values
  - VIDEO_QUALITY_GOOD
```
static final int VIDEO_QUALITY_GOOD
```
    See Also:
    Constant Field Values
- Method Detail
  - addShapeFromLogical
```
Surface addShapeFromLogical(List<ImageVolume> overlays,
                          String name,
                          int rgb,
                          double roiThreshold,
                          boolean shrinkWrap,
                          boolean maximum,
                          boolean imageSmoothing,
                          double width,
                          int kernelSize,
                          double resX,
                          double resY,
                          double resZ,
                          boolean surfaceSmoothing,
                          double pointError,
                          double featureAngle,
                          int iterations)
```
    Adds a surface shape from a logical.
    
    Parameters:
    overlays - the logical
    name - the name of the surface
    rgb - the color of the surface as an RGB color int
    roiThreshold - the build threshold (0 to 1)
    shrinkWrap - true to use shrinkwrap, false otherwise
    maximum - true if the threshold represents a maximum, false otherwise
    imageSmoothing - true to use image smoothing, false otherwise
    width - FWHM of the image smoothing filter
    kernelSize - kernel size of the image smoothing filter
    resX - the output X resolution
    resY - the output Y resolution
    resZ - the output Z resolution
    surfaceSmoothing - true to use surface smoothing, false otherwise
    pointError - the point error threshold
    featureAngle - the feature angle threshold
    iterations - number of iterations of surface smoothing
    
    Returns:
    the new Surface
  - addShapeFromOverlay
```
Surface addShapeFromOverlay(ImageVolume overlay,
                          String name,
                          int rgb,
                          double threshold,
                          boolean shrinkWrap,
                          boolean maximum,
                          boolean imageSmoothing,
                          double width,
                          int kernelSize,
                          double resX,
                          double resY,
                          double resZ,
                          boolean surfaceSmoothing,
                          double pointError,
                          double featureAngle,
                          int iterations)
```
    Adds a surface shape from an overlay.
    
    Parameters:
    overlay - the overlay
    name - the name of the surface
    rgb - the color of the surface as an RGB color int
    threshold - the build threshold
    shrinkWrap - true to use shrinkwrap, false otherwise
    maximum - true if the threshold represents a maximum, false otherwise
    imageSmoothing - true to use image smoothing, false otherwise
    width - FWHM of the image smoothing filter
    kernelSize - kernel size of the image smoothing filter
    resX - the output X resolution
    resY - the output Y resolution
    resZ - the output Z resolution
    surfaceSmoothing - true to use surface smoothing, false otherwise
    pointError - the point error threshold
    featureAngle - the feature angle threshold
    iterations - number of iterations of surface smoothing
    
    Returns:
    the new Surface
  - addShapeFromROI
```
Surface addShapeFromROI(int roiColorIndex,
                      String name,
                      int rgb,
                      double roiThreshold,
                      boolean shrinkWrap,
                      boolean maximum,
                      boolean imageSmoothing,
                      double width,
                      int kernelSize,
                      double resX,
                      double resY,
                      double resZ,
                      boolean surfaceSmoothing,
                      double pointError,
                      double featureAngle,
                      int iterations)
```
    Adds a surface shape from a ROI.
    
    Parameters:
    roiColorIndex - the ROI color index
    name - the name of the surface
    rgb - the color of the surface as an RGB color int
    roiThreshold - the build threshold (0 to 1)
    shrinkWrap - true to use shrinkwrap, false otherwise
    maximum - true if the threshold represents a maximum, false otherwise
    imageSmoothing - true to use image smoothing, false otherwise
    width - FWHM of the image smoothing filter
    kernelSize - kernel size of the image smoothing filter
    resX - the output X resolution
    resY - the output Y resolution
    resZ - the output Z resolution
    surfaceSmoothing - true to use surface smoothing, false otherwise
    pointError - the point error threshold
    featureAngle - the feature angle threshold
    iterations - number of iterations of surface smoothing
    
    Returns:
    the new Surface
  - addShapesFromFile
```
List<Surface> addShapesFromFile(String openLocation)
```
    Adds a surface shape from file.
    
    Parameters:
    openLocation - the file to load
    
    Returns:
    a list of Surfaces found in the file
  - captureSnapshot
```
void captureSnapshot(String saveLocation)
```
    Save a snapshot of the surface viewer to the specified location.
    
    Parameters:
    saveLocation - the location to save the snapshot file
  - captureVideoStart
```
void captureVideoStart(String saveLocation,
                     int videoFormat,
                     int videoQuality,
                     int fps,
                     boolean animate)
```
    Starts saving a captured video to the specified file location.
    
    Parameters:
    saveLocation - the location to save the video file
    videoFormat - the video format code (see constants)
    videoQuality - the video quality code (see constants)
    fps - the frames per second
    animate - true to automatically animate the projection, false otherwise
  - captureVideoStop
```
void captureVideoStop()
```
    Stops the video capture.
  - exportTo
```
void exportTo(String saveLocation,
            String surfaceFormat,
            Surface surfaces,
            String options)
```
    Exports the surface data to the specified file location.
    
    Parameters:
    saveLocation - the location to save the surface file
    surfaceFormat - the name of the surface plugin format
    surfaces - specify a single surface to save or "null" to save all surfaces
    options - options specific to this surface format
  - getAddedShapes
```
List<Surface> getAddedShapes()
```
    Returns a list of surfaces added to the base surface.
    
    Returns:
    a list of surfaces added to the base surface
  - getAllPointsAndLines
```
List<Shape> getAllPointsAndLines()
```
    Returns a list of all points and lines.
    
    Returns:
    a list of all points and lines
  - getBaseSurface
```
Surface getBaseSurface()
```
    Returns the base surface
    
    Returns:
    the base surface
  - getFrame
```
JFrame getFrame()
```
    Returns the parent window of the surface view.
    
    Returns:
    the parent window of the surface view
  - getLines
```
List<Shape> getLines()
```
    Returns a list of lines.
    
    Returns:
    a list of lines
  - getPoints
```
List<Shape> getPoints()
```
    Returns a list of points.
    
    Returns:
    a list of points
  - getSurfaces
```
Surface[] getSurfaces()
```
    Returns an array of loaded surfaces.
    
    Returns:
    an array of loaded surfaces
  - getThreshold
```
float getThreshold()
```
    Returns the threshold used to build the base surface.
    
    Returns:
    the threshold used to build the base surface
  - getViewTransform
```
double[] getViewTransform()
```
    Returns the view transform (4x4).
    
    Returns:
    the view transform
  - goToShape
```
void goToShape(Shape shape)
```
    Move the current coordinate to the specified line or point shape.
    
    Parameters:
    shape - the line or point shape
  - hideAll
```
void hideAll(boolean hidden)
```
    Hide/show all the added surface shapes, lines, and points.
    
    Parameters:
    hidden - true to hide, false to show
  - lineToShape
```
void lineToShape(Shape fromShape,
               Shape toShape)
```
    Adds a direct line between two shapes.
    
    Parameters:
    fromShape - the first shape
    toShape - the second shape
  - measureAll
```
List<Analysis> measureAll()
```
    Measure all added surface shapes, lines, and points.
    
    Returns:
    a list of Analyses
  - pauseScriptForUserInput
```
void pauseScriptForUserInput()
```
    Pauses execution of a running script.
  - removeAll
```
void removeAll()
```
    Remove all the added surface shapes, lines, and points.
  - removeShape
```
void removeShape(Shape shape)
```
    Remove a line or point shape.
    
    Parameters:
    shape - the line or point to remove
  - removeSurface
```
void removeSurface(Surface surface)
```
    Remove an added surface shape.
    
    Parameters:
    surface - the surface to remove
  - runPlugin
```
Object runPlugin(String pluginName,
               String[] args)
```
    Runs a surface plugin.
    
    Parameters:
    pluginName - the plugin name
    args - plugin arguments
    
    Returns:
    an optional return object
  - runSurfaceAreaStats
```
List<Analysis> runSurfaceAreaStats(Surface surface)
```
    Runs surface area stats on the specified surface.
    
    Parameters:
    surface - the specified surface
    
    Returns:
    a list of two Analyses, the visible part of the surface and the cut-away part (if applicable)
  - runSurfaceVolumeStats
```
List<Analysis> runSurfaceVolumeStats(Surface surface)
```
    Runs surface volume stats on the specified surface.
    
    Parameters:
    surface - the specified surface
    
    Returns:
    a list of two Analysis, the visible part of the surface ant the cut-away part (if applicable)
  - saveAs
```
void saveAs(String saveLocation,
          Surface surfaces,
          boolean includeLinesAndPoints)
```
    Saves the surface data in the Mango surface format.
    
    Parameters:
    saveLocation - the location to save the surface file
    surfaces - specify a single surface to save or "null" to save all surfaces
    includeLinesAndPoints - true to save lines and points, false otherwise
  - selectMenuOption
```
void selectMenuOption(String name)
```
    Selects menu options.
    
    Parameters:
    name - the menu item name
  - setBackground
```
void setBackground(int rgb)
```
    Sets the surface background
    
    Parameters:
    rgb - an RGB color int
  - setLighting
```
void setLighting(double ambient,
               double diffuse,
               double specular,
               double horizontal,
               double vertical)
```
    Sets the lighting parameters.
    
    Parameters:
    ambient - the ambient light parameter (0 to 1)
    diffuse - the diffuse light parameter (0 to 1)
    specular - the specular light parameter (0 to 1)
    horizontal - the horizontal light position (-1 to 1)
    vertical - the vertical light position (-1 to 1)
  - setMaterial
```
void setMaterial(Surface surface,
               int rgb,
               boolean showOverlayColors,
               boolean showOnlyThisOverlayColor,
               boolean flatShading,
               int renderType,
               double transparency,
               double emmisivity,
               double shininess,
               double searchDistance)
```
    Sets the material parameters.
    
    Parameters:
    surface - the surface
    rgb - the surface color as an RGB color int
    showOverlayColors - true to show overlay colors on the surface, false otherwise
    showOnlyThisOverlayColor - true to show only the overlay associated with this surface, false otherwise
    flatShading - true to use flat shading, false otherwise
    renderType - the render type (see constants)
    transparency - the transparency parameter (0 to 1)
    emmisivity - the emmisivity parameter (0 to 1)
    shininess - the shininess parameter (0 to 1)
    searchDistance - the distance (mm) to search above and below the surface when building overlay colors
  - setMenuOption
```
void setMenuOption(String name,
                 boolean value)
```
    Sets menu items (typically checkboxes).
    
    Parameters:
    name - the menu item name
    value - the menu item value
  - surfaceToShape
```
void surfaceToShape(Shape fromPoint,
                  Shape toPoint)
```
    Adds a line along the surface bewteen two shapes.
    
    Parameters:
    fromPoint - the first point
    toPoint - the second point
  - updateSurface
```
void updateSurface()
```
    Redraws the surface view.

Interface SurfaceManager

Field Summary

Method Summary

Field Detail

RENDER_TYPE_POINTS

RENDER_TYPE_TRIANGLES

RENDER_TYPE_WIREFRAME

VIDEO_FORMAT_AVI_DIB

VIDEO_FORMAT_AVI_MJPG

VIDEO_FORMAT_AVI_PNG

VIDEO_FORMAT_QUICKTIME_ANIMATION

VIDEO_FORMAT_QUICKTIME_JPEG

VIDEO_FORMAT_QUICKTIME_PNG

VIDEO_FORMAT_QUICKTIME_RAW

VIDEO_QUALITY_BEST

VIDEO_QUALITY_FASTEST

VIDEO_QUALITY_GOOD

Method Detail

addShapeFromLogical

addShapeFromOverlay

addShapeFromROI

addShapesFromFile

captureSnapshot

captureVideoStart

captureVideoStop

exportTo

getAddedShapes

getAllPointsAndLines

getBaseSurface

getFrame

getLines

getPoints

getSurfaces

getThreshold

getViewTransform

goToShape

hideAll

lineToShape

measureAll

pauseScriptForUserInput

removeAll

removeShape

removeSurface

runPlugin

runSurfaceAreaStats

runSurfaceVolumeStats

saveAs

selectMenuOption

setBackground

setLighting

setMaterial

setMenuOption

surfaceToShape

updateSurface