NiftiViewer (Artisynth API documentation)

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, HasPoseComponent, HasPosition, IndexedComponentList, ModelComponent, PostScannable, RenderableComponent, Traceable, TransformableGeometry, ScalableUnits, java.lang.Cloneable, HasProperties, HierarchyNode, HasRenderProps, IsRenderable, IsSelectable, Renderable, Scannable
```
public class NiftiViewer
extends Frame
implements RenderableComponent, TransformableGeometry, HasSurfaceMesh
```

Nested Class Summary
- Nested classes/interfaces inherited from interface artisynth.core.modelbase.ModelComponent
  ModelComponent.FilePathSaveType, ModelComponent.NavpanelVisibility
- Nested classes/interfaces inherited from interface artisynth.core.modelbase.CompositeComponent
  CompositeComponent.NavpanelDisplay

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 artisynth.core.modelbase.TransformableGeometry
  TG_ARTICULATED, TG_DRAGGER, TG_PRESERVE_ORIENTATION, TG_SIMULATING
- Fields inherited from interface maspack.render.IsRenderable
  TRANSPARENT, TWO_DIMENSIONAL
- Fields inherited from interface artisynth.core.modelbase.CopyableComponent
  COPY_REFERENCES, REST_POSITION

Fields
Modifier and Type	Field and Description
`static PropertyList`	`myProps`

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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addTransformableDependencies(TransformGeometryContext context, int flags)` Adds to `context` any transformable components which should be transformed as the same time as this component.
`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 FrameMarker attached to this frame and adds it to the frame's `markers` list.
`RenderProps`	`createRenderProps()` Factory method to create render properties appropriate to this object.
`PropertyList`	`getAllPropertyInfo()` Returns a list giving static information about all properties exported by this object.
`boolean`	`getDrawBox()`
`boolean`	`getDrawXY()`
`boolean`	`getDrawXZ()`
`boolean`	`getDrawYZ()`
`NiftiImage`	`getImage()`
`NiftiImage.ImageSpace`	`getImageSpace()`
`NiftiHeader.XFormCode`	`getImageSpaceDesc()`
`PointList<FrameMarker>`	`getMarkers()` Returns the list of FrameMarkers associated with this frame.
`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`	`hasState()` Queries if this component has state.
`boolean`	`isDuplicatable()` Returns true if this component can be duplicated.
`boolean`	`isSelectable()` Returns true if this object is in fact selectable.
`java.util.Iterator<ModelComponent>`	`iterator()`
`int`	`numSurfaceMeshes()` Returns the number of surfaces meshes associated with this component, or 0 if no meshes exist.
`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`	`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.

Methods inherited from class artisynth.core.mechmodels.Frame
add, add1DConstraintBlocks, add2DConstraintBlocks, addAttachedFrame, addAttachedFrame, addAttachedFrameWorld, addEffectiveFrameMass, addEffectivePointMass, addExternalForce, addForce, addForce, addFrameForce, addMarker, addMarker, addMarker, addMarkerWorld, addPointForce, addPointForce, addPosImpulse, addPosJacobian, addRelativeVelocity, addScaledExternalForce, addSolveBlock, addSolveBlocks, addTargetJacobian, addToPointVelocity, addVelJacobian, applyExternalForces, applyForces, applyGravity, canAddMarker, clearAttachedFrames, clearMarkers, collectMasterComponents, componentChanged, computeAppliedWrench, computeForceOnMasters, computeFrameLocation, computeFramePosition, computeFramePosVel, computeFrameVelocity, computePointCoriolis, computePointLocation, computePointPosition, computePointPosVel, computePointVelocity, createFrameAttachment, createMarker, createMassBlock, createPointAttachment, findComponent, get, get, getAttachedFrames, getAxisDrawStyle, getAxisLength, getBodyForce, getBodyVelocity, getBodyVelState, getByNumber, getChildren, getCopyReferences, getEffectiveMass, getEffectiveMass, getEffectiveMassForces, getExternalForce, getForce, getForce, getForce, getFrameDamping, getFrameDampingMode, getFrameMarkers, getJacobianType, getMass, getMass, getMoment, getNavpanelDisplay, getNumberLimit, 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, hasChildren, hasForce, hierarchyContainsReferences, indexOf, isMassConstant, mulInverseEffectiveMass, numComponents, postscan, remove, removeAttachedFrame, removeMarker, resetEffectiveMass, resetTargets, scaleDistance, scaleMass, scan, setAxisDrawStyle, setAxisLength, setBodyVelocity, setContactConstraint, setExternalForce, setForce, setForce, setFrameDamping, setFrameDampingMode, setNavpanelDisplay, setOrientation, setPose, setPosition, setPosState, setRandomForce, setRandomPosState, setRandomVelState, setRotaryDamping, setRotaryDampingMode, setRotation, setState, setState, setTargetActivity, setTargetOrientation, setTargetPos, setTargetPose, setTargetPosition, setTargetVel, setTargetVelocity, setVelocity, setVelocity, setVelState, transformPose, updateAttachmentPosStates, updateNameMap, 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.TransformableGeometry
transformPriority

Methods inherited from interface artisynth.core.mechmodels.HasSurfaceMesh
computeRayIntersection

Methods inherited from interface artisynth.core.modelbase.ModelComponent
connectToHierarchy, disconnectFromHierarchy, getHardReferences, getName, getNavpanelVisibility, getNumber, getParent, getSoftReferences, isFixed, isMarked, isSelected, notifyParentOfChange, scan, setFixed, setMarked, setName, setNumber, setParent, setSelected, setWritable, updateReferences

Methods inherited from interface maspack.properties.HasProperties
getProperty

Methods inherited from interface maspack.properties.HierarchyNode
getChildren, hasChildren

Methods inherited from interface artisynth.core.modelbase.PostScannable
postscan

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.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

Methods inherited from interface artisynth.core.modelbase.CompositeComponent
recursivelyFind

- 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()
```
    Description copied from class: Frame
    
    Returns the list of FrameMarkers associated with this frame.
    
    Overrides:
    
    getMarkers in class Frame
    
    Returns:
    
    frame marker list
  - createMarker
```
public FrameMarker createMarker(Line ray)
```
    Description copied from class: Frame
    
    Creates a FrameMarker attached to this frame and adds it to the frame's markers list. If the frame is an instance of HasSurfaceMesh, the marker's position is determined the nearest intersection of the specified ray and the mesh, with null being returned if there is no intersection. Otherwise, the marker's position is set to the frame's origin.
    
    Specified by:
    
    createMarker in interface IsMarkable
    
    Overrides:
    
    createMarker in class Frame
    
    Parameters:
    
    ray - to line intersect with the frame's surface mesh to determine the marker location
    
    Returns:
    
    created marker, or null if there is no mesh-ray intersection
  - 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
  - iterator
```
public java.util.Iterator<ModelComponent> iterator()
```
  - 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
  - isDuplicatable
```
public boolean isDuplicatable()
```
    Description copied from interface: CopyableComponent
    
    Returns true if this component can be duplicated. Duplication means that we can expect to be able to make a complete copy of the component along with all it's external references. This method should return true if and only if CopyableComponent.getCopyReferences(java.util.List<artisynth.core.modelbase.ModelComponent>, artisynth.core.modelbase.ModelComponent) returns true.
    This method is not currently used. It is intended to provide a faster way of determining if a component can be duplicated, without having to use CopyableComponent.getCopyReferences(java.util.List<artisynth.core.modelbase.ModelComponent>, artisynth.core.modelbase.ModelComponent) to build the list of copy references.
    
    Specified by:
    
    isDuplicatable in interface CopyableComponent
    
    Overrides:
    
    isDuplicatable in class Frame
    
    Returns:
    
    true if this component can be duplicated.
  - 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

Class NiftiViewer

Nested Class Summary

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

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

Field Summary

Fields inherited from class artisynth.core.mechmodels.Frame

Fields inherited from class artisynth.core.modelbase.ModelComponentBase

Fields inherited from interface artisynth.core.modelbase.TransformableGeometry

Fields inherited from interface maspack.render.IsRenderable

Fields inherited from interface artisynth.core.modelbase.CopyableComponent

Constructor Summary

Method Summary

Methods inherited from class artisynth.core.mechmodels.Frame

Methods inherited from class artisynth.core.mechmodels.DynamicComponentBase

Methods inherited from class artisynth.core.modelbase.RenderableComponentBase

Methods inherited from class artisynth.core.modelbase.ModelComponentBase

Methods inherited from class java.lang.Object

Methods inherited from interface artisynth.core.modelbase.TransformableGeometry

Methods inherited from interface artisynth.core.mechmodels.HasSurfaceMesh

Methods inherited from interface artisynth.core.modelbase.ModelComponent

Methods inherited from interface maspack.properties.HasProperties

Methods inherited from interface maspack.properties.HierarchyNode

Methods inherited from interface artisynth.core.modelbase.PostScannable

Methods inherited from interface maspack.util.Scannable

Methods inherited from interface maspack.render.IsSelectable

Methods inherited from interface maspack.render.IsRenderable

Methods inherited from interface maspack.render.HasRenderProps

Methods inherited from interface artisynth.core.mechmodels.DynamicComponent

Methods inherited from interface artisynth.core.mechmodels.DynamicAgent

Methods inherited from interface artisynth.core.modelbase.HasNumericState

Methods inherited from interface artisynth.core.mechmodels.ContactMaster

Methods inherited from interface artisynth.core.modelbase.CompositeComponent

Field Detail

myProps

Constructor Detail

NiftiViewer

NiftiViewer

NiftiViewer

Method Detail

getAllPropertyInfo

createDefaultRenderProps

createRenderProps

getImage

setSliceCoordinates

setSliceCoordinates

prerender

setTransform

setTransform

getTransform

getImageSpace

getImageSpaceDesc

setImageSpace

render

getPixelGenerator

setPixelGenerator

updateBounds

isSelectable

getX

setX

getY

setY

getZ

setZ

getTimeIndex

setTimeIndex

getTimeIndexRange

getDrawYZ

setDrawYZ

getDrawXZ

setDrawXZ

getDrawXY

setDrawXY

getDrawBox

setDrawBox

transformGeometry

transformGeometry

addTransformableDependencies

getMarkers

createMarker

getSurfaceMesh