artisynth.core.renderables

Class NiftiViewer

java.lang.Object

artisynth.core.modelbase.ModelComponentBase

artisynth.core.modelbase.RenderableComponentBase

artisynth.core.mechmodels.DynamicComponentBase

artisynth.core.mechmodels.Frame

artisynth.core.renderables.NiftiViewer

All Implemented Interfaces:

CollidableDynamicComponent, ContactMaster, DynamicAgent, DynamicComponent, ForceEffector, FrameAttachable, HasSurfaceMesh, IsMarkable, MotionTargetComponent, PointAttachable, ComponentChangeListener, CompositeComponent, CopyableComponent, HasCoordinateFrame, HasNumericState, IndexedComponentList, ModelComponent, PostScannable, RenderableComponent, Traceable, TransformableGeometry, ScalableUnits, java.lang.Cloneable, HasProperties, HierarchyNode, HasRenderProps, IsRenderable, IsSelectable, Renderable, Scannable

public class NiftiViewer
extends Frame
implements CompositeComponent, RenderableComponent, TransformableGeometry, IsMarkable, HasSurfaceMesh

Nested Class Summary

Nested classes/interfaces inherited from interface artisynth.core.modelbase.CompositeComponent

CompositeComponent.NavpanelDisplay

Nested classes/interfaces inherited from interface artisynth.core.modelbase.ModelComponent

ModelComponent.NavpanelVisibility

Field Summary

Fields

Modifier and Type	Field and Description
static PropertyList	myProps

Fields inherited from class artisynth.core.mechmodels.Frame

dynamicVelInWorldCoords, myRenderFrame

Fields inherited from class artisynth.core.modelbase.ModelComponentBase

enforceUniqueCompositeNames, enforceUniqueNames, myNumber, NULL_OBJ, useCompactPathNames

Fields inherited from interface maspack.render.IsRenderable

TRANSPARENT, TWO_DIMENSIONAL

Fields inherited from interface artisynth.core.modelbase.TransformableGeometry

TG_ARTICULATED, TG_DRAGGER, TG_PRESERVE_ORIENTATION, TG_SIMULATING

Fields inherited from interface artisynth.core.modelbase.CopyableComponent

COPY_REFERENCES, REST_POSITION

Constructor Summary

Constructors

Constructor and Description
NiftiViewer(NiftiImage image) Creates a new viewer widget, with supplied Nifti image.
NiftiViewer(java.lang.String name, NiftiImage image, NiftiPixelGenerator voxelator) Creates a new viewer widget, with supplied name and Nifti image
NiftiViewer(java.lang.String name, java.lang.String imagePath) Reads a Nifti file into a 3D (+time) image

Method Summary

Modifier and Type	Method and Description
boolean	addMarker(Marker mkr) Adds the marker to the component (or potentially somewhere within the component hierarchy)
void	addTransformableDependencies(TransformGeometryContext context, int flags) Adds to context any transformable components which should be transformed as the same time as this component.
boolean	canAddMarker(Marker mkr) Checks whether or not the marker can be added to the component (or potentially somewhere within the component hierarchy), without actually adding it.
void	componentChanged(ComponentChangeEvent e) Notifies this composite component that a change has occured within one or more of its descendants.
NiftiViewer	copy(int flags, java.util.Map<ModelComponent,ModelComponent> copyMap) Create a copy of this component.
static RenderProps	createDefaultRenderProps()
FrameMarker	createMarker(Line ray) Creates a marker along a ray of intersection
FrameMarker	createMarker(Point3d pnt) Creates a marker at a specific location
RenderProps	createRenderProps() Factory method to create render properties appropriate to this object.
ModelComponent	findComponent(java.lang.String path) Recursively searches for a subcomponent of this ModelComponent, identified by a path of component names.
ModelComponent	get(int idx) Returns a specific subcomponent of this ModelComponent, identified by index.
ModelComponent	get(java.lang.String nameOrNumber) Returns a specific subcomponent of this ModelComponent, identified by name or string representation of the subcomponent's number
PropertyList	getAllPropertyInfo() Returns a list giving static information about all properties exported by this object.
ModelComponent	getByNumber(int num) Returns a specific subcomponent of this ModelComponent, identified by number.
java.util.Iterator<? extends HierarchyNode>	getChildren()
boolean	getDrawBox()
boolean	getDrawXY()
boolean	getDrawXZ()
boolean	getDrawYZ()
NiftiImage	getImage()
NiftiImage.ImageSpace	getImageSpace()
NiftiHeader.XFormCode	getImageSpaceDesc()
PointList<FrameMarker>	getMarkers()
CompositeComponent.NavpanelDisplay	getNavpanelDisplay() Returns the DisplayMode for this component.
int	getNumberLimit() Returns the current upper limit for numbers among all subcomponents in this composite.
NiftiPixelGenerator	getPixelGenerator()
PolygonalMesh	getSurfaceMesh() Returns the surface mesh associated with this component, or null if no mesh exists.
PolygonalMesh[]	getSurfaceMeshes() Returns an array listing all the (non-null) surface meshes associated with this component, or a zero-length array if there are none.
int	getTimeIndex()
IntegerInterval	getTimeIndexRange()
AffineTransform3d	getTransform()
double	getX()
double	getY()
double	getZ()
boolean	hasChildren()
boolean	hasState() Queries if this component has state.
boolean	hierarchyContainsReferences() Returns true if the component hierarchy formed by this component and its descendents is closed with respect to references.
int	indexOf(ModelComponent comp) Returns the index of a specified subcomponent, or -1 if that the component is not present.
boolean	isSelectable() Returns true if this object is in fact selectable.
java.util.Iterator<ModelComponent>	iterator()
int	numComponents() Returns the number of components in this CompositeComponent.
int	numSurfaceMeshes() Returns the number of surfaces meshes associated with this component, or 0 if no meshes exist.
void	postscan(java.util.Deque<ScanToken> tokens, CompositeComponent ancestor) Performs any required post-scanning for this component.
void	prerender(RenderList list) Called prior to rendering to allow this object to update the internal state required for rendering (such as by caching rendering coordinates).
void	render(Renderer renderer, int flags) Render this object using the functionality of the supplied Renderer.
void	scan(ReaderTokenizer rtok, java.lang.Object ref) Scans this element from a ReaderTokenizer.
void	setDisplayMode(CompositeComponent.NavpanelDisplay mode) Sets the display mode for this component.
void	setDrawBox(boolean set) Sets whether or not to draw the 3D bounding box outline
void	setDrawXY(boolean set) Sets whether or not to draw the XY plane (at the current 'z' coordinate)
void	setDrawXZ(boolean set) Sets whether or not to draw the XZ plane (at the current 'y' coordinate)
void	setDrawYZ(boolean set) Sets whether or not to draw the YZ plane (at the current 'x' coordinate)
void	setImageSpace(NiftiImage.ImageSpace space)
void	setPixelGenerator(NiftiPixelGenerator voxelator)
void	setSliceCoordinates(double x, double y, double z) Sets the normalized slice coordinates to display
void	setSliceCoordinates(Vector3d coords) Sets the normalized slice coordinates to display
void	setTimeIndex(int idx) Sets the current time index
void	setTransform(AffineTransform3d trans) Sets a 3D transform to apply to the image.
void	setTransform(AffineTransform3dBase trans) Sets a 3D transform to apply to the image
void	setX(double x) Sets the current normalized 'x' coordinate
void	setY(double y) Sets the current normalized 'y' coordinate
void	setZ(double z) Sets the current normalized 'z' coordinate
void	transformGeometry(AffineTransform3dBase X) Applies an affine transformation to the geometry of this component.
void	transformGeometry(GeometryTransformer gtr, TransformGeometryContext context, int flags) Transforms the geometry of this component, using the geometry transformer gtr to transform its individual attributes.
void	updateBounds(Vector3d pmin, Vector3d pmax) Update the minimum and maximum points for this object.
void	updateNameMap(java.lang.String newName, java.lang.String oldName, ModelComponent comp)

Methods inherited from class artisynth.core.mechmodels.Frame

add1DConstraintBlocks, add2DConstraintBlocks, addEffectiveFrameMass, addEffectivePointMass, addExternalForce, addForce, addForce, addFrameForce, addPointForce, addPointForce, addPosImpulse, addPosJacobian, addRelativeVelocity, addScaledExternalForce, addSolveBlock, addSolveBlocks, addTargetJacobian, addToPointVelocity, addVelJacobian, applyExternalForces, applyForces, applyGravity, collectMasterComponents, computeAppliedWrench, computeForceOnMasters, computeFrameLocation, computeFramePosition, computeFramePosVel, computeFrameVelocity, computePointCoriolis, computePointLocation, computePointPosition, computePointPosVel, computePointVelocity, createFrameAttachment, createMassBlock, createPointAttachment, getAxisDrawStyle, getAxisLength, getBodyForce, getBodyVelocity, getBodyVelState, getCopyReferences, getEffectiveMass, getEffectiveMass, getEffectiveMassForces, getExternalForce, getForce, getForce, getForce, getFrameDamping, getFrameDampingMode, getJacobianType, getMass, getMass, getMoment, getOrientation, getOrientation, getPosDerivative, getPose, getPose, getPosition, getPosState, getPosStateSize, getRenderFrame, getRotaryDamping, getRotaryDampingMode, getRotation, getSelection, getState, getTargetActivity, getTargetOrientation, getTargetPos, getTargetPose, getTargetPosition, getTargetVel, getTargetVelocity, getTraceablePositionProperty, getTraceables, getTransForce, getVelocity, getVelocity, getVelState, getVelStateSize, getWorldVelState, hasForce, isDuplicatable, isMassConstant, mulInverseEffectiveMass, resetEffectiveMass, resetTargets, scaleDistance, scaleMass, setAxisDrawStyle, setAxisLength, setBodyVelocity, setContactConstraint, setExternalForce, setForce, setForce, setFrameDamping, setFrameDampingMode, setOrientation, setPose, setPosition, setPosState, setRandomForce, setRandomPosState, setRandomVelState, setRotaryDamping, setRotaryDampingMode, setRotation, setState, setState, setTargetActivity, setTargetOrientation, setTargetPos, setTargetPose, setTargetPosition, setTargetVel, setTargetVelocity, setVelocity, setVelocity, setVelState, transformPose, updateAttachmentPosStates, velocityLimitExceeded, zeroExternalForces, zeroForces

Methods inherited from class artisynth.core.mechmodels.DynamicComponentBase

addAttachmentRequest, addConstrainer, addMasterAttachment, connectToHierarchy, disconnectFromHierarchy, getAttachment, getConstrainers, getInverseMass, getMasterAttachments, getSolveIndex, isActive, isAttached, isControllable, isDynamic, isParametric, removeAttachmentRequest, removeConstrainer, removeMasterAttachment, setAttached, setSolveIndex

Methods inherited from class artisynth.core.modelbase.RenderableComponentBase

defaultRenderPropsAreNull, getRenderHints, getRenderProps, isVisible, numSelectionQueriesNeeded, setRenderProps, setVisible, updateRenderProps

Methods inherited from class artisynth.core.modelbase.ModelComponentBase

checkFlag, checkName, checkNameUniqueness, clearFlag, clone, createTempFlag, getGrandParent, getHardReferences, getName, getNameRange, getNavpanelVisibility, getNavpanelVisibility, getNumber, getParent, getProperty, getSoftReferences, isFixed, isMarked, isScanning, isSelected, isWritable, makeValidName, makeValidName, notifyParentOfChange, printReferences, recursivelyContained, recursivelyContains, removeTempFlag, setFixed, setFlag, setMarked, setName, setNavpanelVisibility, setNavpanelVisibility, setNumber, setParent, setScanning, setSelected, setWritable, updateReferences, write

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface artisynth.core.modelbase.ModelComponent

connectToHierarchy, disconnectFromHierarchy, getHardReferences, getName, getNavpanelVisibility, getNumber, getParent, getSoftReferences, isFixed, isMarked, isSelected, notifyParentOfChange, setFixed, setMarked, setName, setNumber, setParent, setSelected, setWritable, updateReferences

Methods inherited from interface maspack.properties.HasProperties

getProperty

Methods inherited from interface maspack.util.Scannable

isWritable, write

Methods inherited from interface maspack.render.IsSelectable

getSelection, numSelectionQueriesNeeded

Methods inherited from interface maspack.render.IsRenderable

getRenderHints

Methods inherited from interface maspack.render.HasRenderProps

getRenderProps, setRenderProps

Methods inherited from interface artisynth.core.modelbase.TransformableGeometry

transformPriority

Methods inherited from interface artisynth.core.mechmodels.DynamicComponent

addAttachmentRequest, removeAttachmentRequest

Methods inherited from interface artisynth.core.mechmodels.DynamicAgent

addConstrainer, addMasterAttachment, getAttachment, getConstrainers, getInverseMass, getMasterAttachments, getSolveIndex, isActive, isAttached, isControllable, isDynamic, isParametric, removeConstrainer, removeMasterAttachment, setAttached, setSolveIndex

Methods inherited from interface artisynth.core.modelbase.HasNumericState

advanceState, getAuxVarDerivative, getAuxVarState, getStateVersion, numAuxVars, requiresAdvance, setAuxVarState

Methods inherited from interface artisynth.core.mechmodels.ContactMaster

isControllable

Field Detail

myProps

public static PropertyList myProps

Constructor Detail

NiftiViewer

public NiftiViewer(java.lang.String name,
                   NiftiImage image,
                   NiftiPixelGenerator voxelator)

Creates a new viewer widget, with supplied name and Nifti image

Parameters:

name - name of viewer

image - image to display

NiftiViewer

public NiftiViewer(NiftiImage image)

Creates a new viewer widget, with supplied Nifti image. The name of the component becomes the image name

Parameters:

image - image to display

NiftiViewer

public NiftiViewer(java.lang.String name,
                   java.lang.String imagePath)

Reads a Nifti file into a 3D (+time) image

Parameters:

name - name of the viewer component

imagePath - Nifti file

Method Detail

getAllPropertyInfo

public PropertyList getAllPropertyInfo()

Description copied from interface: HasProperties

Returns a list giving static information about all properties exported by this object.

Specified by:

getAllPropertyInfo in interface HasProperties

Overrides:

getAllPropertyInfo in class Frame

Returns:

static information for all exported properties

createDefaultRenderProps

public static RenderProps createDefaultRenderProps()

createRenderProps

public RenderProps createRenderProps()

Description copied from interface: HasRenderProps

Factory method to create render properties appropriate to this object.

Specified by:

createRenderProps in interface HasRenderProps

Overrides:

createRenderProps in class Frame

Returns:

new render properties for this object

getImage

public NiftiImage getImage()

Returns:

the Nifti image being displayed

setSliceCoordinates

public void setSliceCoordinates(double x,
                                double y,
                                double z)

Sets the normalized slice coordinates to display

Parameters:

x - in [0,1], sets the 'x' slice

y - in [0,1], sets the 'y' slice

z - in [0,1], sets the 'z' slice

setSliceCoordinates

public void setSliceCoordinates(Vector3d coords)

Sets the normalized slice coordinates to display

Parameters:

coords - slice coordinate of image planes

See Also:

setSliceCoordinates(double, double, double)

prerender

public void prerender(RenderList list)

Description copied from interface: IsRenderable

Called prior to rendering to allow this object to update the internal state required for rendering (such as by caching rendering coordinates). The object may add internal objects to the list of objects being rendered, by calling

list.addIfVisible (obj);

for each of the objects in question.

Specified by:

prerender in interface IsRenderable

Overrides:

prerender in class Frame

Parameters:

list - list of objects to be rendered

setTransform

public void setTransform(AffineTransform3dBase trans)

Sets a 3D transform to apply to the image

Parameters:

trans - transform

setTransform

public void setTransform(AffineTransform3d trans)

Sets a 3D transform to apply to the image. Required for property.

Parameters:

trans - 3D transform

getTransform

public AffineTransform3d getTransform()

Returns:

the 3D transform applied to the image. By default, this is the voxel-to-world transform

getImageSpace

public NiftiImage.ImageSpace getImageSpace()

getImageSpaceDesc

public NiftiHeader.XFormCode getImageSpaceDesc()

setImageSpace

public void setImageSpace(NiftiImage.ImageSpace space)

render

public void render(Renderer renderer,
                   int flags)

Description copied from interface: IsRenderable

Render this object using the functionality of the supplied Renderer.

Specified by:

render in interface IsRenderable

Overrides:

render in class Frame

Parameters:

renderer - provides the functionality used to perform the rendering.

flags - flags that may be used to control different aspects of the rendering. Flags are defined in Renderer and currently include Renderer.HIGHLIGHT and Renderer.SORT_FACES.

getPixelGenerator

public NiftiPixelGenerator getPixelGenerator()

Returns:

the current voxel generator

setPixelGenerator

public void setPixelGenerator(NiftiPixelGenerator voxelator)

updateBounds

public void updateBounds(Vector3d pmin,
                         Vector3d pmax)

Description copied from interface: IsRenderable

Update the minimum and maximum points for this object. In an x-y-z coordinate system with x directed to the right and y directed upwards, the minimum and maximum points can be thought of as defining the left-lower-far and right-upper-near corners of a bounding cube. This method should only reduce the elements of the minimum point and increase the elements of the maximum point, since it may be used as part of an iteration to determine the bounding cube for several different objects.

Specified by:

updateBounds in interface IsRenderable

Overrides:

updateBounds in class Frame

Parameters:

pmin - minimum point

pmax - maximum point

isSelectable

public boolean isSelectable()

Description copied from class: RenderableComponentBase

Returns true if this object is in fact selectable.

Specified by:

isSelectable in interface IsSelectable

Overrides:

isSelectable in class RenderableComponentBase

Returns:

true if this object is selectable

getX

public double getX()

Returns:

the current normalized 'x' coordinate

setX

public void setX(double x)

Sets the current normalized 'x' coordinate

Parameters:

x - x-coordinate for yz=plane

getY

public double getY()

Returns:

the current normalized 'y' coordinate

setY

public void setY(double y)

Sets the current normalized 'y' coordinate

Parameters:

y - y-coordinate for xz-plane

getZ

public double getZ()

Returns:

the current normalized 'z' coordinate

setZ

public void setZ(double z)

Sets the current normalized 'z' coordinate

Parameters:

z - z-coordinate for xy-plane

getTimeIndex

public int getTimeIndex()

Returns:

the current time index

setTimeIndex

public void setTimeIndex(int idx)

Sets the current time index

Parameters:

idx - time index

getTimeIndexRange

public IntegerInterval getTimeIndexRange()

Returns:

the number of time indices available in the Nifti image

getDrawYZ

public boolean getDrawYZ()

Returns:

whether or not to draw the YZ plane (at the current 'x' coordinate)

setDrawYZ

public void setDrawYZ(boolean set)

Sets whether or not to draw the YZ plane (at the current 'x' coordinate)

Parameters:

set - enable yz-plane

getDrawXZ

public boolean getDrawXZ()

Returns:

whether or not to draw the XZ plane (at the current 'y' coordinate)

setDrawXZ

public void setDrawXZ(boolean set)

Sets whether or not to draw the XZ plane (at the current 'y' coordinate)

Parameters:

set - xz-plane

getDrawXY

public boolean getDrawXY()

Returns:

whether or not to draw the XY plane (at the current 'z' coordinate)

setDrawXY

public void setDrawXY(boolean set)

Sets whether or not to draw the XY plane (at the current 'z' coordinate)

Parameters:

set - enable xy-plane

getDrawBox

public boolean getDrawBox()

Returns:

whether or not to draw the 3D bounding box outline

setDrawBox

public void setDrawBox(boolean set)

Sets whether or not to draw the 3D bounding box outline

Parameters:

set - enable bounding box

transformGeometry

public void transformGeometry(AffineTransform3dBase X)

Description copied from interface: TransformableGeometry

Applies an affine transformation to the geometry of this component. This method should be equivalent to

 TransformGeometryContext.transform (this, X, 0);
 

Specified by:

transformGeometry in interface TransformableGeometry

Overrides:

transformGeometry in class DynamicComponentBase

Parameters:

X - affine transformation to apply to the component

transformGeometry

public void transformGeometry(GeometryTransformer gtr,
                              TransformGeometryContext context,
                              int flags)

Description copied from interface: TransformableGeometry

Transforms the geometry of this component, using the geometry transformer gtr to transform its individual attributes. The context argument supplies information about what other components are currently being transformed, and also allows the requesting of update actions to be performed after all transform called have completed. The context is also the usual entity that calls this method, from within its TransformGeometryContext.apply(maspack.geometry.GeometryTransformer, int) method. The argument flags provides flags to specify various conditions associated with the the transformation. At present, the available flags are TransformableGeometry.TG_SIMULATING and TransformableGeometry.TG_ARTICULATED.

This method is not usually called directly by applications. Instead, it is typically called from within the TransformGeometryContext.apply(maspack.geometry.GeometryTransformer, int) method of the context, which takes care of the various operations needed for a complete transform operation, including calling TransformableGeometry.addTransformableDependencies(artisynth.core.modelbase.TransformGeometryContext, int) to collect other components that should be transformed, calling TransformableGeometry.transformGeometry(maspack.matrix.AffineTransform3dBase) for each component, notifying component parents that the geometry has changed, and calling any requested TransformGeometryActions. More details are given in the documentation for TransformGeometryContext.apply(maspack.geometry.GeometryTransformer, int).

TransformGeometryContext provides a number of static convenience transform methods which take care of building the context and calling apply() for a specified set of components.

This method should not generally call transformGeometry() for its descendant components. Instead, descendants needing transformation should be specified by adding them to the context in the method TransformableGeometry.addTransformableDependencies(artisynth.core.modelbase.TransformGeometryContext, int).

Specified by:

transformGeometry in interface TransformableGeometry

Overrides:

transformGeometry in class Frame

Parameters:

gtr - transformer implementing the transform

context - context information, including what other components are being transformed

flags - specifies conditions associated with the transformation

addTransformableDependencies

public void addTransformableDependencies(TransformGeometryContext context,
                                         int flags)

Description copied from interface: TransformableGeometry

Adds to context any transformable components which should be transformed as the same time as this component. This will generally include descendant components, and may also include other components to which this component is connected in some way.

This method is generally called from with the TransformGeometryContext.apply(maspack.geometry.GeometryTransformer, int) method of a TransformGeometryContext.

Specified by:

addTransformableDependencies in interface TransformableGeometry

Overrides:

addTransformableDependencies in class Frame

Parameters:

context - context information, to which the dependent components are added.

flags - specifies conditions associated with the transformation

getMarkers

public PointList<FrameMarker> getMarkers()

createMarker

public FrameMarker createMarker(Line ray)

Description copied from interface: IsMarkable

Creates a marker along a ray of intersection

Specified by:

createMarker in interface IsMarkable

Parameters:

ray - ray to intersect with

Returns:

created marker, or null if no intersection or not supported

createMarker

public FrameMarker createMarker(Point3d pnt)

Description copied from interface: IsMarkable

Creates a marker at a specific location

Specified by:

createMarker in interface IsMarkable

Parameters:

pnt - world location for marker

Returns:

create marker, or null if no intersection or not supported

canAddMarker

public boolean canAddMarker(Marker mkr)

Description copied from interface: IsMarkable

Checks whether or not the marker can be added to the component (or potentially somewhere within the component hierarchy), without actually adding it.

Specified by:

canAddMarker in interface IsMarkable

Parameters:

mkr - marker to add

Returns:

true if add would be successful, false otherwise

See Also:

IsMarkable.addMarker(Marker)

addMarker

public boolean addMarker(Marker mkr)

Description copied from interface: IsMarkable

Adds the marker to the component (or potentially somewhere within the component hierarchy)

Specified by:

addMarker in interface IsMarkable

Parameters:

mkr - marker to add

Returns:

true if add is successful, false otherwise

getSurfaceMesh

public PolygonalMesh getSurfaceMesh()

Description copied from interface: HasSurfaceMesh

Returns the surface mesh associated with this component, or null if no mesh exists. If multiple surface meshes exist, this should be first one in the array returned by HasSurfaceMesh.getSurfaceMeshes().

Specified by:

getSurfaceMesh in interface HasSurfaceMesh

Returns:

component's (primary) surface mesh

numSurfaceMeshes

public int numSurfaceMeshes()

Description copied from interface: HasSurfaceMesh

Returns the number of surfaces meshes associated with this component, or 0 if no meshes exist. If HasSurfaceMesh.getSurfaceMesh() returns null, then this method should return 0.

Specified by:

numSurfaceMeshes in interface HasSurfaceMesh

Returns:

number of surface meshes associated with this component

getSurfaceMeshes

public PolygonalMesh[] getSurfaceMeshes()

Description copied from interface: HasSurfaceMesh

Returns an array listing all the (non-null) surface meshes associated with this component, or a zero-length array if there are none. If HasSurfaceMesh.getSurfaceMesh() returns null, then a zero-length array should be returned.

Specified by:

getSurfaceMeshes in interface HasSurfaceMesh

Returns:

surface meshes associated with this component

getChildren

public java.util.Iterator<? extends HierarchyNode> getChildren()

Specified by:

getChildren in interface HierarchyNode

Overrides:

getChildren in class ModelComponentBase

iterator

public java.util.Iterator<ModelComponent> iterator()

hasChildren

public boolean hasChildren()

Specified by:

hasChildren in interface HierarchyNode

Overrides:

hasChildren in class ModelComponentBase

hasState

public boolean hasState()

Description copied from class: DynamicComponentBase

Queries if this component has state. Structure change events involving components that have state will cause the current state history of of the system to be cleared.

Specified by:

hasState in interface HasNumericState

Specified by:

hasState in interface ModelComponent

Overrides:

hasState in class DynamicComponentBase

Returns:

true if this component has state

get

public ModelComponent get(java.lang.String nameOrNumber)

Returns a specific subcomponent of this ModelComponent, identified by name or string representation of the subcomponent's number

Specified by:

get in interface CompositeComponent

Parameters:

nameOrNumber - name or number of the subcomponent

Returns:

named subcomponent, or null if the component does not exist.

get

public ModelComponent get(int idx)

Returns a specific subcomponent of this ModelComponent, identified by index.

Specified by:

get in interface CompositeComponent

Specified by:

get in interface IndexedComponentList

Parameters:

idx - index of the subcomponent

Returns:

indexed subcomponent, or null if the component does not exist.

getByNumber

public ModelComponent getByNumber(int num)

Returns a specific subcomponent of this ModelComponent, identified by number.

Specified by:

getByNumber in interface CompositeComponent

Parameters:

num - number of the subcomponent

Returns:

specified subcomponent, or null if the component does not exist.

numComponents

public int numComponents()

Returns the number of components in this CompositeComponent.

Specified by:

numComponents in interface CompositeComponent

Specified by:

numComponents in interface IndexedComponentList

Returns:

number of subcomponents

indexOf

public int indexOf(ModelComponent comp)

Returns the index of a specified subcomponent, or -1 if that the component is not present.

Specified by:

indexOf in interface CompositeComponent

Parameters:

comp - component whose index is requested

Returns:

indexed subcomponent

findComponent

public ModelComponent findComponent(java.lang.String path)

Recursively searches for a subcomponent of this ModelComponent, identified by a path of component names.

Specified by:

findComponent in interface CompositeComponent

Parameters:

path - path leading to the subcomponent

Returns:

named subcomponent, or null if the component does not exist.

getNumberLimit

public int getNumberLimit()

Returns the current upper limit for numbers among all subcomponents in this composite. This is one greater than the maximum subcomponent number currently assigned. A value of 0 means that there are no subcomponents. This method is useful for creating and sizing arrays whose contents are indexed by component numbers.

Specified by:

getNumberLimit in interface CompositeComponent

Returns:

upper limit for numbers among all subcomponents

getNavpanelDisplay

public CompositeComponent.NavpanelDisplay getNavpanelDisplay()

Returns the DisplayMode for this component. This specifies how the component should be displayed in a navigation panel.

Specified by:

getNavpanelDisplay in interface CompositeComponent

Returns:

display mode for this component

setDisplayMode

public void setDisplayMode(CompositeComponent.NavpanelDisplay mode)

Sets the display mode for this component. This controls how the component is displayed in a navigation panel. The default setting is NORMAL.

Parameters:

mode - new display mode

componentChanged

public void componentChanged(ComponentChangeEvent e)

Notifies this composite component that a change has occured within one or more of its descendants. When this occurs, the composite may need to invalidate cached information that depends on the descendants.

This method should propagate the notification up the component hierarchy by calling notifyParentOfChange.

Specified by:

componentChanged in interface ComponentChangeListener

Specified by:

componentChanged in interface CompositeComponent

Parameters:

e - optional argument giving specific information about the change

updateNameMap

public void updateNameMap(java.lang.String newName,
                          java.lang.String oldName,
                          ModelComponent comp)

Specified by:

updateNameMap in interface CompositeComponent

hierarchyContainsReferences

public boolean hierarchyContainsReferences()

Returns true if the component hierarchy formed by this component and its descendents is closed with respect to references. In other words, all components referenced by components within the hierarchy are themselves components within the hierarchy.

In particular, this means that one does not need to search outside the hierarchy when looking for dependencies.

Specified by:

hierarchyContainsReferences in interface CompositeComponent

Returns:

true if this component's hierarchy is closed with respect to references.

scan

public void scan(ReaderTokenizer rtok,
                 java.lang.Object ref)
          throws java.io.IOException

Description copied from class: ModelComponentBase

Scans this element from a ReaderTokenizer. The expected text format is assumed to be compatible with that produced by write.

Specified by:

scan in interface ModelComponent

Specified by:

scan in interface Scannable

Overrides:

scan in class ModelComponentBase

Parameters:

rtok - Tokenizer from which to scan the element

ref - optional reference object which can be used for resolving references to other objects

Throws:

java.io.IOException - if an I/O or formatting error occured

postscan

public void postscan(java.util.Deque<ScanToken> tokens,
                     CompositeComponent ancestor)
              throws java.io.IOException

Description copied from interface: PostScannable

Performs any required post-scanning for this component. This involves handling any information whose processing was deferred during the scan() method and stored in the token queue. The most common use of this method is to resolve the paths of component references, which may not have been created at the time of the initial scan() call.

Specified by:

postscan in interface PostScannable

Overrides:

postscan in class ModelComponentBase

Parameters:

tokens - token information that was stored during scan().

ancestor - ancestor component with respect to which reference component paths are defined.

Throws:

java.io.IOException - if an error is encountered (such as a reference to a non-existent component)

copy

public NiftiViewer copy(int flags,
                        java.util.Map<ModelComponent,ModelComponent> copyMap)

Description copied from interface: CopyableComponent

Create a copy of this component. If COPY_REFERENCES is set in flags, then any component referenced by this component should itself be set to a copy. This should be done first checking copyMap for an existing copy of the referenced component. If there is no existing copy, then a copy should be created by calling copy recursively and adding the new copy to copyMap.

Specified by:

copy in interface CopyableComponent

Overrides:

copy in class Frame

Parameters:

flags - flags to control the copying

copyMap - map to possible existing instances of referenced components

Returns:

copy of this component