edu.washington.biostr.sig.brainj3d.volume
Class VolumeData

java.lang.Object
  java.util.Observable
      edu.washington.biostr.sig.brainj3d.data.Data
          edu.washington.biostr.sig.brainj3d.volume.VolumeData

All Implemented Interfaces:

Serializable

public class VolumeData
extends Data
implements Serializable

Default view parameters:
Structural:
nThreashold = 0
pThreashold = 0
pWindow = top .5%
nWindow = bottom .5%
pColor = "White"
nColor = "cyan"

alpha = .5
Function:
nThreashold = 0
pThreashold = 0
pWindow = max
nWindow = min
pColor = "warm"
nColor = "cold"
alpha = .5

Version:

1.0

Author:

Eider Moore

See Also:

Serialized Form

Field Summary

static String	ATLAS_COLOR
static String	PROP_ALPHA
static String	PROP_N_SCHEME
static String	PROP_N_THRESHOLD
static String	PROP_N_WINDOW
static String	PROP_P_SCHEME
static String	PROP_P_THRESHOLD
static String	PROP_P_WINDOW

Fields inherited from class edu.washington.biostr.sig.brainj3d.data.Data

file, SAVE_STATE_CHANGED, saved

Constructor Summary

VolumeData(VolumeArray data)
Create a volume 3d.

Method Summary

boolean	canDiskCache() Return true if we can cache this Data or part of it to disk.
VolumeArray	getArray()
double	getCutoff(double percent, boolean top) Get the cutoff between the top percent% and the bottom.
Map<String,Object>	getDefaultParameters(Set<Tag> metadata) Get the default parameters for this Data.
javax.vecmath.Vector3f	getDown(int slice)
javax.vecmath.Matrix4d	getIndex2Space()
int	getInterval()
javax.vecmath.Point3f	getLocation(float xPercent, float yPercent, float zPercent) Get a location from a percent.
Object	getLock() Get the lock that this data uses to synchronize itself.
int	getMaxTime()
double	getMaxValue()
float	getMaxX()
float	getMaxY()
float	getMaxZ()
int	getMinTime()
double	getMinValue()
float	getMinX()
float	getMinY()
float	getMinZ()
void	getPercent(javax.vecmath.Point3f p) Get the percent equivilant for the given point.
javax.vecmath.Vector3f	getRight(int slice)
javax.vecmath.Matrix4d	getSpace2Index()
FileType	getType() Every piece of data has a type.
javax.vecmath.Point3f	getUL(int slice, javax.vecmath.Point3f percent)
boolean	hasTime() return true if this data varies with time
protected void	initialize() Set up some of the variables that we need from the transform.
boolean	invertX()
boolean	invertY()
boolean	invertZ()
boolean	isImmutable() Find out if this data is immutable.
void	setInvertX(boolean invert)
void	setInvertY(boolean invert)
void	setInvertZ(boolean invert)
boolean	shareable()

Methods inherited from class edu.washington.biostr.sig.brainj3d.data.Data

cacheTo, finalize, getFile, isSaved, isSerialized, readFrom, setFile, setSaved, sharable, toString

Methods inherited from class java.util.Observable

addObserver, clearChanged, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers, setChanged

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

PROP_ALPHA

public static final String PROP_ALPHA

See Also:

Constant Field Values

PROP_P_SCHEME

public static final String PROP_P_SCHEME

See Also:

Constant Field Values

PROP_N_SCHEME

public static final String PROP_N_SCHEME

See Also:

Constant Field Values

PROP_P_WINDOW

public static final String PROP_P_WINDOW

See Also:

Constant Field Values

PROP_N_WINDOW

public static final String PROP_N_WINDOW

See Also:

Constant Field Values

PROP_P_THRESHOLD

public static final String PROP_P_THRESHOLD

See Also:

Constant Field Values

PROP_N_THRESHOLD

public static final String PROP_N_THRESHOLD

See Also:

Constant Field Values

ATLAS_COLOR

public static final String ATLAS_COLOR

See Also:

Constant Field Values

Constructor Detail

VolumeData

public VolumeData(VolumeArray data)

Create a volume 3d.

Parameters:

x - The maximum x index.

y - The maximum y index.

z - The maximum z index.

trans - The transform from indices to physical units (most likely mm).

Method Detail

invertX

public boolean invertX()

invertY

public boolean invertY()

invertZ

public boolean invertZ()

setInvertX

public void setInvertX(boolean invert)

setInvertY

public void setInvertY(boolean invert)

setInvertZ

public void setInvertZ(boolean invert)

getType

public FileType getType()

Description copied from class: Data

Every piece of data has a type. The type is used to filter out file names, get the decoders and the encoders.

Specified by:

getType in class Data

Returns:

getLock

public Object getLock()

Description copied from class: Data

Get the lock that this data uses to synchronize itself. It may return null if the data is immutable.

Overrides:

getLock in class Data

Returns:

by default this.

isImmutable

public boolean isImmutable()

Description copied from class: Data

Find out if this data is immutable.

Overrides:

isImmutable in class Data

Returns:

false by default

getMaxValue

public double getMaxValue()

getMinValue

public double getMinValue()

getArray

public VolumeArray getArray()

getMinX

public float getMinX()

getMaxX

public float getMaxX()

getMinY

public float getMinY()

getMaxY

public float getMaxY()

getMinZ

public float getMinZ()

getMaxZ

public float getMaxZ()

getMaxTime

public int getMaxTime()

getMinTime

public int getMinTime()

getInterval

public int getInterval()

getIndex2Space

public javax.vecmath.Matrix4d getIndex2Space()

getSpace2Index

public javax.vecmath.Matrix4d getSpace2Index()

initialize

protected final void initialize()

Set up some of the variables that we need from the transform.

getLocation

public javax.vecmath.Point3f getLocation(float xPercent,
                                         float yPercent,
                                         float zPercent)

Get a location from a percent.

Parameters:

xPercent -

yPercent -

zPercent -

Returns:

getPercent

public void getPercent(javax.vecmath.Point3f p)

Get the percent equivilant for the given point. The percent is the percent in each direction from the start of the bounding box for this object to the end of the bounding box. If there is no bounding box, leaving the point unedited is appropriate.

Parameters:

point -

getDown

public javax.vecmath.Vector3f getDown(int slice)

getRight

public javax.vecmath.Vector3f getRight(int slice)

getUL

public javax.vecmath.Point3f getUL(int slice,
                                   javax.vecmath.Point3f percent)

shareable

public boolean shareable()

canDiskCache

public boolean canDiskCache()

Description copied from class: Data

Return true if we can cache this Data or part of it to disk.

Specified by:

canDiskCache in class Data

Returns:

getCutoff

public double getCutoff(double percent,
                        boolean top)

Get the cutoff between the top percent% and the bottom.

Parameters:

percent -

whether - to get the top or bottom percent.

Returns:

getDefaultParameters

public Map<String,Object> getDefaultParameters(Set<Tag> metadata)

Description copied from class: Data

Get the default parameters for this Data.

Overrides:

getDefaultParameters in class Data

Returns:

hasTime

public boolean hasTime()

Description copied from class: Data

return true if this data varies with time

Overrides:

hasTime in class Data

Returns:

false by default