MangoContext (Mango Plugin API)

```
public interface MangoContext
```
An application context. This is the most executive class in the application and maintains a list of open VolumeManagers.

Author:

michaelmartinez

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`TOOL_MODE_ADD_POINT`
`static int`	`TOOL_MODE_ADD_REGION`
`static int`	`TOOL_MODE_DRAW_ELLIPSE`
`static int`	`TOOL_MODE_DRAW_RECT`
`static int`	`TOOL_MODE_NAV`
`static int`	`TOOL_MODE_PAINT_ELLIPSE_EDIT`
`static int`	`TOOL_MODE_PAINT_ELLIPSE_ERASE`
`static int`	`TOOL_MODE_PAINT_ELLIPSE_PAINT`
`static int`	`TOOL_MODE_PAINT_RECT_EDIT`
`static int`	`TOOL_MODE_PAINT_RECT_ERASE`
`static int`	`TOOL_MODE_PAINT_RECT_PAINT`
`static int`	`TOOL_MODE_TRACE_LINE`
`static int`	`TOOL_MODE_TRACE_REGION`
`static int`	`TOOL_MODE_WAND_COPY`
`static int`	`TOOL_MODE_WAND_DILATE_ERODE`
`static int`	`TOOL_MODE_WAND_PRESERVE`
`static int`	`TOOL_MODE_WAND_REMOVE`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`capture()` Programmatically clicks the Toolbox camera button.
`JButton`	`createColorPickerButton(VolumeManager manager, MangoColorSelectedListener listener, boolean showUsedOnly)` Creates a ROI color picker widget.
`void`	`exit()` Exit the application and clear all resources.
`List<Analysis>`	`getAllAnalyses()` Returns a list of all analyses.
`List<AnalysisPoint>`	`getAllAnalysisPoints()` Returns a list of all analysis points.
`List<VolumeManager>`	`getAllVolumeManagers()` Returns a list of all the currently loaded VolumeManagers.
`List<VolumeManager>`	`getAllVolumeManagersFrom(VolumeManager manager)` Returns a list of all currently loaded VolumeManagers, starting with the specified manager.
`String`	`getBuildNumber()` Returns the Mango build number.
`Atlas`	`getCurrentAtlas()` Returns the current Atlas.
`VolumeManager`	`getCurrentVolumeManager()` Returns the currently selected VolumeManager.
`int`	`getCurrentVolumeManagerIndex()` Returns the index of the currently selected VolumeManager.
`File`	`getLibDir()` Returns the lib directory.
`List<VolumeManager>`	`getOtherVolumeManagers(VolumeManager manager)` Returns a list of all the currently loaded VolumeManagers, except the specified.
`int`	`getTool()` Returns the current ROI tool (see tool code constants).
`String`	`getVersion()` Returns the Mango version.
`boolean`	`isMultisliceMode()` Returns true if multislice mode is set, false otherwise
`boolean`	`isRadiologicalMode()` Returns true for radiological display, false for neurological display
`boolean`	`isWorldMode()` Returns true if world mode is set, false otherwise
`ImageVolume`	`makeNewVolume()` Creates a new ImageVolume.
`VolumeManager`	`makeNewVolumeManager(ImageDimensions imageDims, VoxelDimensions voxelDims, ImageType imageType, ByteBuffer[] buffers, boolean readOnly, String name)` Create a new VolumeManager with an empty image.
`VolumeManager`	`makeNewVolumeManager(String openLocation)` Creates a new VolumeManager by loading an ImageVolume from the specified location.
`VolumeManager`	`makeNewVolumeManagerURL(String url)` Creates a new VolumeManager by loading an ImageVolume from the specified URL.
`ProgressMeter`	`makeProgressMeter()` Creates a ProgressMeter.
`void`	`runScript(String scriptName)` Runs the specified script.
`void`	`setAtlas(String name)` Sets the current Atlas.
`void`	`setCurrentVolumeManager(VolumeManager manager)` Sets the specified VolumeManager to be currently selected.
`void`	`setCurrentVolumeManagerIndex(int index)` Sets the VolumeManager at the specified index to be currently selected.
`void`	`setMultisliceMode(boolean multislice)` Sets ROI "multislice" mode.
`void`	`setRadiologicalMode(boolean radiologicalMode)` Sets radiological display mode.
`void`	`setTool(int code)` Sets the current ROI tool (see tool code constants).
`void`	`setToolRange(boolean useRange, double min, double max, boolean onlyWhenShiftKeyPressed)` Sets the ROI tool intensity range.
`void`	`setToolRelativeRange(double range)` Sets the ROI tool relative range (only applies to "magic wand" Add tool).
`void`	`setWorldMode(boolean world)` Sets "world space" mode.
`void`	`updateViewers()` Redraws all the VolumeManagers.

- Field Detail
  - TOOL_MODE_ADD_POINT
```
static final int TOOL_MODE_ADD_POINT
```
    See Also:
    Constant Field Values
  - TOOL_MODE_ADD_REGION
```
static final int TOOL_MODE_ADD_REGION
```
    See Also:
    Constant Field Values
  - TOOL_MODE_DRAW_ELLIPSE
```
static final int TOOL_MODE_DRAW_ELLIPSE
```
    See Also:
    Constant Field Values
  - TOOL_MODE_DRAW_RECT
```
static final int TOOL_MODE_DRAW_RECT
```
    See Also:
    Constant Field Values
  - TOOL_MODE_NAV
```
static final int TOOL_MODE_NAV
```
    See Also:
    Constant Field Values
  - TOOL_MODE_PAINT_ELLIPSE_EDIT
```
static final int TOOL_MODE_PAINT_ELLIPSE_EDIT
```
    See Also:
    Constant Field Values
  - TOOL_MODE_PAINT_ELLIPSE_ERASE
```
static final int TOOL_MODE_PAINT_ELLIPSE_ERASE
```
    See Also:
    Constant Field Values
  - TOOL_MODE_PAINT_ELLIPSE_PAINT
```
static final int TOOL_MODE_PAINT_ELLIPSE_PAINT
```
    See Also:
    Constant Field Values
  - TOOL_MODE_PAINT_RECT_EDIT
```
static final int TOOL_MODE_PAINT_RECT_EDIT
```
    See Also:
    Constant Field Values
  - TOOL_MODE_PAINT_RECT_ERASE
```
static final int TOOL_MODE_PAINT_RECT_ERASE
```
    See Also:
    Constant Field Values
  - TOOL_MODE_PAINT_RECT_PAINT
```
static final int TOOL_MODE_PAINT_RECT_PAINT
```
    See Also:
    Constant Field Values
  - TOOL_MODE_TRACE_LINE
```
static final int TOOL_MODE_TRACE_LINE
```
    See Also:
    Constant Field Values
  - TOOL_MODE_TRACE_REGION
```
static final int TOOL_MODE_TRACE_REGION
```
    See Also:
    Constant Field Values
  - TOOL_MODE_WAND_COPY
```
static final int TOOL_MODE_WAND_COPY
```
    See Also:
    Constant Field Values
  - TOOL_MODE_WAND_DILATE_ERODE
```
static final int TOOL_MODE_WAND_DILATE_ERODE
```
    See Also:
    Constant Field Values
  - TOOL_MODE_WAND_PRESERVE
```
static final int TOOL_MODE_WAND_PRESERVE
```
    See Also:
    Constant Field Values
  - TOOL_MODE_WAND_REMOVE
```
static final int TOOL_MODE_WAND_REMOVE
```
    See Also:
    Constant Field Values
- Method Detail
  - getAllAnalyses
```
List<Analysis> getAllAnalyses()
```
    Returns a list of all analyses.
    
    Returns:
    a list of all analyses
  - getAllAnalysisPoints
```
List<AnalysisPoint> getAllAnalysisPoints()
```
    Returns a list of all analysis points.
    
    Returns:
    a list of all analysis points
  - capture
```
void capture()
```
    Programmatically clicks the Toolbox camera button.
  - createColorPickerButton
```
JButton createColorPickerButton(VolumeManager manager,
                              MangoColorSelectedListener listener,
                              boolean showUsedOnly)
```
    Creates a ROI color picker widget.
    
    Parameters:
    manager - the VolumeManager
    listener - the listener
    showUsedOnly - true to enable only used ROI colors, false otherwise
    
    Returns:
    the ROI color picker widget
  - getAllVolumeManagers
```
List<VolumeManager> getAllVolumeManagers()
```
    Returns a list of all the currently loaded VolumeManagers.
    
    Returns:
    a list of all the currently loaded VolumeManagers
  - getAllVolumeManagersFrom
```
List<VolumeManager> getAllVolumeManagersFrom(VolumeManager manager)
```
    Returns a list of all currently loaded VolumeManagers, starting with the specified manager.
    
    Parameters:
    manager - the starting VolumeManager
    
    Returns:
    a list of all currently loaded VolumeManagers
  - getBuildNumber
```
String getBuildNumber()
```
    Returns the Mango build number.
    
    Returns:
    the Mango build number
  - getCurrentVolumeManager
```
VolumeManager getCurrentVolumeManager()
```
    Returns the currently selected VolumeManager.
    
    Returns:
    the currently selected VolumeManager
  - getCurrentVolumeManagerIndex
```
int getCurrentVolumeManagerIndex()
```
    Returns the index of the currently selected VolumeManager.
    
    Returns:
    the index of the currently selected VolumeManager
  - getLibDir
```
File getLibDir()
```
    Returns the lib directory.
    
    Returns:
    the lib directory
  - getOtherVolumeManagers
```
List<VolumeManager> getOtherVolumeManagers(VolumeManager manager)
```
    Returns a list of all the currently loaded VolumeManagers, except the specified.
    
    Parameters:
    manager - the VolumeManager to ignore
    
    Returns:
    a list of all the currently loaded VolumeManagers, except the specified
  - getVersion
```
String getVersion()
```
    Returns the Mango version.
    
    Returns:
    the Mango version
  - makeNewVolume
```
ImageVolume makeNewVolume()
```
    Creates a new ImageVolume.
    
    Returns:
    a new ImageVolume
  - makeNewVolumeManager
```
VolumeManager makeNewVolumeManager(String openLocation)
                                   throws InvalidHeaderException,
                                          IOException
```
    Creates a new VolumeManager by loading an ImageVolume from the specified location.
    
    Parameters:
    openLocation - the location of a ImageVolume to load
    
    Returns:
    a new VolumeManager
    
    Throws:
    
    InvalidHeaderException
    
    IOException
  - makeNewVolumeManagerURL
```
VolumeManager makeNewVolumeManagerURL(String url)
                                      throws InvalidHeaderException,
                                             IOException
```
    Creates a new VolumeManager by loading an ImageVolume from the specified URL.
    
    Parameters:
    url - the location of the ImageVolume to load
    
    Returns:
    a new VolumeManager
    
    Throws:
    
    InvalidHeaderException
    
    IOException
  - makeNewVolumeManager
```
VolumeManager makeNewVolumeManager(ImageDimensions imageDims,
                                 VoxelDimensions voxelDims,
                                 ImageType imageType,
                                 ByteBuffer[] buffers,
                                 boolean readOnly,
                                 String name)
```
    Create a new VolumeManager with an empty image.
    
    Parameters:
    imageDims - the image dimensions
    voxelDims - the voxel dimensions
    imageType - the image type
    buffers - the buffer array (one per series point)
    readOnly - true if the image is read-only, false otherwise
    name - a name for the image
    
    Returns:
    a new VolumeManager
  - makeProgressMeter
```
ProgressMeter makeProgressMeter()
```
    Creates a ProgressMeter.
    
    Returns:
    a ProgressMeter
  - runScript
```
void runScript(String scriptName)
```
    Runs the specified script.
    
    Parameters:
    scriptName - the name of the script to run
  - setAtlas
```
void setAtlas(String name)
```
    Sets the current Atlas.
    
    Parameters:
    name - the name of the atlas to make current
  - getCurrentAtlas
```
Atlas getCurrentAtlas()
```
    Returns the current Atlas.
    
    Returns:
    the current Atlas
  - setCurrentVolumeManager
```
void setCurrentVolumeManager(VolumeManager manager)
```
    Sets the specified VolumeManager to be currently selected.
    
    Parameters:
    manager - the VolumeManager to set as current
  - setCurrentVolumeManagerIndex
```
void setCurrentVolumeManagerIndex(int index)
```
    Sets the VolumeManager at the specified index to be currently selected.
    
    Parameters:
    index - the index of the VolumeManager to set as current
  - setMultisliceMode
```
void setMultisliceMode(boolean multislice)
```
    Sets ROI "multislice" mode.
    
    Parameters:
    multislice - true for multislice mode, false otherwise
  - isMultisliceMode
```
boolean isMultisliceMode()
```
    Returns true if multislice mode is set, false otherwise
    
    Returns:
    true if multislice mode is set
  - isWorldMode
```
boolean isWorldMode()
```
    Returns true if world mode is set, false otherwise
    
    Returns:
    true if world mode is set, false otherwise
  - getTool
```
int getTool()
```
    Returns the current ROI tool (see tool code constants).
    
    Returns:
    the current ROI tool
  - setTool
```
void setTool(int code)
```
    Sets the current ROI tool (see tool code constants).
    
    Parameters:
    code - the ROI tool code
  - setToolRange
```
void setToolRange(boolean useRange,
                double min,
                double max,
                boolean onlyWhenShiftKeyPressed)
```
    Sets the ROI tool intensity range.
    
    Parameters:
    useRange - true to use range, false to not use range
    min - the tool range minimum
    max - the tool range maximum
    onlyWhenShiftKeyPressed - only enable the range when the Shift key is depressed
  - setToolRelativeRange
```
void setToolRelativeRange(double range)
```
    Sets the ROI tool relative range (only applies to "magic wand" Add tool).
    
    Parameters:
    range - the range, above and below, the selected voxel value
  - setWorldMode
```
void setWorldMode(boolean world)
```
    Sets "world space" mode.
    
    Parameters:
    world - true for "world space", false otherwise
  - updateViewers
```
void updateViewers()
```
    Redraws all the VolumeManagers.
  - exit
```
void exit()
```
    Exit the application and clear all resources.
  - isRadiologicalMode
```
boolean isRadiologicalMode()
```
    Returns true for radiological display, false for neurological display
    
    Returns:
    true for radiological display, false for neurological display
  - setRadiologicalMode
```
void setRadiologicalMode(boolean radiologicalMode)
```
    Sets radiological display mode.
    
    Parameters:
    radiologicalMode - true for radiological display, false for neurological display

Interface MangoContext

Field Summary

Method Summary

Field Detail

TOOL_MODE_ADD_POINT

TOOL_MODE_ADD_REGION

TOOL_MODE_DRAW_ELLIPSE

TOOL_MODE_DRAW_RECT

TOOL_MODE_NAV

TOOL_MODE_PAINT_ELLIPSE_EDIT

TOOL_MODE_PAINT_ELLIPSE_ERASE

TOOL_MODE_PAINT_ELLIPSE_PAINT

TOOL_MODE_PAINT_RECT_EDIT

TOOL_MODE_PAINT_RECT_ERASE

TOOL_MODE_PAINT_RECT_PAINT

TOOL_MODE_TRACE_LINE

TOOL_MODE_TRACE_REGION

TOOL_MODE_WAND_COPY

TOOL_MODE_WAND_DILATE_ERODE

TOOL_MODE_WAND_PRESERVE

TOOL_MODE_WAND_REMOVE

Method Detail

getAllAnalyses

getAllAnalysisPoints

capture

createColorPickerButton

getAllVolumeManagers

getAllVolumeManagersFrom

getBuildNumber

getCurrentVolumeManager

getCurrentVolumeManagerIndex

getLibDir

getOtherVolumeManagers

getVersion

makeNewVolume

makeNewVolumeManager

makeNewVolumeManagerURL

makeNewVolumeManager

makeProgressMeter

runScript

setAtlas

getCurrentAtlas

setCurrentVolumeManager

setCurrentVolumeManagerIndex

setMultisliceMode

isMultisliceMode

isWorldMode

getTool

setTool

setToolRange

setToolRelativeRange

setWorldMode

updateViewers

exit

isRadiologicalMode

setRadiologicalMode