artisynth.core.renderables

Class DicomViewer

java.lang.Object

artisynth.core.modelbase.ModelComponentBase

artisynth.core.modelbase.RenderableComponentBase

artisynth.core.renderables.DicomViewer

All Implemented Interfaces:

ModelComponent, RenderableComponent, TransformableGeometry, java.lang.Cloneable, HasProperties, HierarchyNode, HasRenderProps, IsRenderable, IsSelectable, Renderable, Scannable

public class DicomViewer
extends RenderableComponentBase
implements TransformableGeometry

Nested Class Summary

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.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

Constructor Summary

Constructors

Constructor and Description
DicomViewer(DicomImage image) Creates a new viewer widget, with supplied DICOM image.
DicomViewer(java.lang.String name, DicomImage image) Creates a new viewer widget, with supplied name and DICOM image
DicomViewer(java.lang.String name, java.io.File imagePath) Reads DICOM files into a 3D (+time) image
DicomViewer(java.lang.String name, java.io.File imagePath, java.util.regex.Pattern filePattern) Reads DICOM files into a 3D (+time) image
DicomViewer(java.lang.String name, java.io.File imagePath, java.util.regex.Pattern filePattern, boolean checkSubdirs) Reads DICOM files into a 3D (+time) image
DicomViewer(java.lang.String name, java.util.List<java.io.File> files) Reads DICOM files into a 3D (+time) image
DicomViewer(java.lang.String name, java.lang.String imagePath) Reads DICOM files into a 3D (+time) image
DicomViewer(java.lang.String name, java.lang.String imagePath, java.util.regex.Pattern filePattern) Reads DICOM files into a 3D (+time) image
DicomViewer(java.lang.String name, java.lang.String imagePath, java.util.regex.Pattern filePattern, boolean checkSubdirs) Reads DICOM files into a 3D (+time) image

Method Summary

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.
static RenderProps	createDefaultRenderProps()
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()
DicomImage	getImage()
DicomPixelInterpolator	getPixelInterpolator()
int	getTimeIndex()
IntegerInterval	getTimeIndexRange()
AffineTransform3d	getTransform()
java.lang.String[]	getWindowNames()
StringRange	getWindowRange()
double	getX()
double	getY()
double	getZ()
boolean	isSelectable() Returns true if this object is in fact selectable.
int	numWindows()
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 enable) Sets whether or not to draw the 3D bounding box outline
void	setDrawXY(boolean enable) Sets whether or not to draw the XY plane (at the current 'z' coordinate)
void	setDrawXZ(boolean enable) Sets whether or not to draw the XZ plane (at the current 'y' coordinate)
void	setDrawYZ(boolean enable) Sets whether or not to draw the YZ plane (at the current 'x' coordinate
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	setWindow(java.lang.String presetName) Sets the current interpolation window to use, based on a preset name
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.modelbase.RenderableComponentBase

copy, getRenderHints, getRenderProps, getSelection, numSelectionQueriesNeeded, setRenderProps, updateRenderProps

Methods inherited from class artisynth.core.modelbase.ModelComponentBase

checkFlag, checkName, checkNameUniqueness, clearFlag, clone, connectToHierarchy, createTempFlag, disconnectFromHierarchy, getChildren, getGrandParent, getHardReferences, getName, getNameRange, getNavpanelVisibility, getNavpanelVisibility, getNumber, getParent, getProperty, getSoftReferences, hasChildren, hasState, isConnectedToHierarchy, isFixed, isMarked, isSelected, isWritable, makeValidName, makeValidName, notifyParentOfChange, postscan, printReferences, recursivelyContained, recursivelyContains, removeTempFlag, scan, setFixed, setFlag, setMarked, setName, setNavpanelVisibility, setNavpanelVisibility, setNumber, setParent, setSelected, 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, hasState, isFixed, isMarked, isSelected, notifyParentOfChange, postscan, scan, setFixed, setMarked, setName, setNumber, setParent, setSelected, updateReferences

Methods inherited from interface maspack.properties.HasProperties

getProperty

Methods inherited from interface maspack.properties.HierarchyNode

getChildren, hasChildren

Methods inherited from interface maspack.util.Scannable

isWritable, write

Field Detail

myProps

public static PropertyList myProps

Constructor Detail

DicomViewer

public DicomViewer(java.lang.String name,
                   DicomImage image)

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

Parameters:

name - widget name

image - DICOM image data

DicomViewer

public DicomViewer(DicomImage image)

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

Parameters:

image - DICOM image data

DicomViewer

public DicomViewer(java.lang.String name,
                   java.lang.String imagePath,
                   java.util.regex.Pattern filePattern,
                   boolean checkSubdirs)

Reads DICOM files into a 3D (+time) image

Parameters:

name - name of the viewer component

imagePath - directory containing DICOM files

filePattern - pattern for accepting/rejecting contained files. The pattern is applied to the absolute file names of all files contained in the imagePath

checkSubdirs - recursively check sub-folders for further DICOM files

DicomViewer

public DicomViewer(java.lang.String name,
                   java.util.List<java.io.File> files)

Reads DICOM files into a 3D (+time) image

Parameters:

name - name of the viewer component

files - list of DICOM files to load

DicomViewer

public DicomViewer(java.lang.String name,
                   java.lang.String imagePath,
                   java.util.regex.Pattern filePattern)

Reads DICOM files into a 3D (+time) image

Parameters:

name - name of the viewer component

imagePath - directory containing DICOM files

filePattern - pattern for accepting/rejecting contained files. The pattern is applied to the absolute file names of all files contained in the imagePath

DicomViewer

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

Reads DICOM files into a 3D (+time) image

Parameters:

name - name of the viewer component

imagePath - directory containing DICOM files

DicomViewer

public DicomViewer(java.lang.String name,
                   java.io.File imagePath,
                   java.util.regex.Pattern filePattern,
                   boolean checkSubdirs)

Reads DICOM files into a 3D (+time) image

Parameters:

name - name of the viewer component

imagePath - directory containing DICOM files

filePattern - pattern for accepting/rejecting contained files. The pattern is applied to the absolute file names of all files contained in the imagePath

checkSubdirs - recursively check sub-folders for further DICOM files

DicomViewer

public DicomViewer(java.lang.String name,
                   java.io.File imagePath,
                   java.util.regex.Pattern filePattern)

Reads DICOM files into a 3D (+time) image

Parameters:

name - name of the viewer component

imagePath - directory containing DICOM files

filePattern - pattern for accepting/rejecting contained files. The pattern is applied to the absolute file names of all files contained in the imagePath

DicomViewer

public DicomViewer(java.lang.String name,
                   java.io.File imagePath)

Reads DICOM files into a 3D (+time) image

Parameters:

name - name of the viewer component

imagePath - directory containing DICOM files

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 ModelComponentBase

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 RenderableComponentBase

Returns:

new render properties for this object

getImage

public DicomImage getImage()

Returns:

the DICOM image being displayed

numWindows

public int numWindows()

Returns:

the number of interpolation windows available in the DICOM image

getWindowNames

public java.lang.String[] getWindowNames()

Returns:

the names of all possible interpolation windows available in the DICOM image

setWindow

public void setWindow(java.lang.String presetName)

Sets the current interpolation window to use, based on a preset name

Parameters:

presetName - name of the interpolation window

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 - normalized slice coordinates

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 RenderableComponentBase

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 - 3D 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

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

Specified by:

render in class RenderableComponentBase

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.

getPixelInterpolator

public DicomPixelInterpolator getPixelInterpolator()

Returns:

the current pixel interpolator

getWindowRange

public StringRange getWindowRange()

Returns:

range of valid window names

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 RenderableComponentBase

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 - normalized 'x' coordinate

getY

public double getY()

Returns:

the current normalized 'y' coordinate

setY

public void setY(double y)

Sets the current normalized 'y' coordinate

Parameters:

y - normalized 'y' coordinate

getZ

public double getZ()

Returns:

the current normalized 'z' coordinate

setZ

public void setZ(double z)

Sets the current normalized 'z' coordinate

Parameters:

z - normalized 'z' coordinate

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 DICOM image

getDrawYZ

public boolean getDrawYZ()

Returns:

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

setDrawYZ

public void setDrawYZ(boolean enable)

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

Parameters:

enable - if true, enables drawing of 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 enable)

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

Parameters:

enable - if true, enables drawing of 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 enable)

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

Parameters:

enable - if true, enables drawing of XY plane

getDrawBox

public boolean getDrawBox()

Returns:

whether or not to draw the 3D bounding box outline

setDrawBox

public void setDrawBox(boolean enable)

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

Parameters:

enable - if true, enables drawing of the 3D 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

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

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

Parameters:

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

flags - specifies conditions associated with the transformation