theba.core.Stack Class Reference

List of all members.

Public Member Functions
VolumeReader	getWriter ()
void	flush ()
boolean	isWritable ()
	Stack (int w, int h, int d, String fileName)
	Stack (VolumeReader reader)
void	setVoxelUnchecked (int x, int y, int z, int val)
void	setVoxel (int x, int y, int z, int val)
short	getVoxelUnchecked (int x, int y, int z)
short	getVoxel (int x, int y, int z)
short	getVoxel (Point3D p)
short[]	getSlice (int z)
void	putSlice (short[] data, int z)
int	getDepth ()
void	setDepth (int depth)
int	getHeight ()
void	setHeight (int height)
int	getWidth ()
void	setWidth (int width)

Detailed Description

This class represents a three-dimensional volume, with short as its base datatype.

The volume is stored slice, by sice, line by line linearly in memory. Hence the orientation of the volume has a lot to say when it comes to cache efficiency. The current stack is optimized for viewing along the width/height axis.

For best efficiency the entire depth-range should be in cache at once.

Author:: jensbw

Definition at line 21 of file Stack.java.

Constructor & Destructor Documentation

theba.core.Stack.Stack	(	int	w,
		int	h,
		int	d,
		String	fileName
	)

Definition at line 44 of file Stack.java.

theba.core.Stack.Stack ( VolumeReader reader )

Definition at line 53 of file Stack.java.

References theba.core.io.VolumeReader.getDepth(), theba.core.io.VolumeReader.getHeight(), and theba.core.io.VolumeReader.getWidth().

Member Function Documentation

void theba.core.Stack.flush ( )

Definition at line 36 of file Stack.java.

References theba.core.io.VolumeReader.flush().

Referenced by theba.core.ImageFunctions.erode3d().

int theba.core.Stack.getDepth ( )

Definition at line 141 of file Stack.java.

Referenced by theba.trackers.FiberTracker.autoSegment(), theba.trackers.BackTracker.autoSegment(), theba.core.ImageFunctions.dilate3d(), theba.trackers.HHTracker.dilate3d_toWhite(), theba.trackers.FiberTracker.dilate3d_toWhite(), theba.trackers.BackTracker.dilate3d_toWhite(), theba.core.ImageFunctions.distance3d(), theba.core.ImageFunctions.erode3d(), theba.core.gui.ThebaGUI.fiberChordMeasurements(), theba.core.ImageFunctions.floodFill3D(), theba.core.ImageFunctions.floodFill3D26(), theba.core.ImageFunctions.median3d(), theba.plugins.WatershedPlugin.process(), theba.plugins.ErodePlugin.process(), theba.plugins.DistanceMap2DPlugin.process(), theba.plugins.DilatePlugin.process(), theba.trackers.BackTracker.removeCrack(), theba.trackers.BackTracker.traceWalls(), theba.trackers.HHTracker.track(), theba.trackers.FloodTracker3D.track(), theba.trackers.FiberTracker.track(), and theba.trackers.BackTracker.track().

int theba.core.Stack.getHeight ( )

Definition at line 149 of file Stack.java.

short [] theba.core.Stack.getSlice ( int z )

Definition at line 133 of file Stack.java.

References theba.core.io.VolumeReader.getSlice().

Referenced by theba.core.ImageFunctions.dilate3d(), theba.trackers.HHTracker.dilate3d_toWhite(), theba.trackers.FiberTracker.dilate3d_toWhite(), theba.trackers.BackTracker.dilate3d_toWhite(), theba.core.ImageFunctions.distance3d(), theba.core.ImageFunctions.erode3d(), theba.core.ImageFunctions.floodFill3D(), theba.core.ImageFunctions.median3d(), theba.plugins.WatershedPlugin.process(), theba.plugins.ErodePlugin.process(), theba.plugins.DistanceMap2DPlugin.process(), and theba.plugins.DilatePlugin.process().

short theba.core.Stack.getVoxel ( Point3D p )

Gets a voxel. Values outside of bounds are returned as 0

Parameters:

	xmin
	ymin
	ymax
	val

Definition at line 125 of file Stack.java.

References theba.core.io.VolumeReader.getSlice(), theba.core.math.Point3D.x, theba.core.math.Point3D.y, and theba.core.math.Point3D.z.

short theba.core.Stack.getVoxel	(	int	x,
		int	y,
		int	z
	)

Gets a voxel. Values outside of bounds are returned as 0

Parameters:

	x
	y
	z
	val

Definition at line 110 of file Stack.java.

References theba.core.io.VolumeReader.getSlice().

Referenced by theba.core.ImageFunctions.delete3D(), theba.core.gui.ThebaGUI.fiberChordMeasurements(), and theba.core.ImageFunctions.floodFill3D26().

short theba.core.Stack.getVoxelUnchecked	(	int	x,
		int	y,
		int	z
	)

Gets a voxel from the volume. Values outside of bounds may result in an Exception, or erroneous values (use this function with caution)

Parameters:

	x
	y
	z

Returns:

Definition at line 98 of file Stack.java.

References theba.core.io.VolumeReader.getSlice().

Referenced by theba.core.ImageFunctions.floodFill3D(), theba.core.ImageFunctions.floodFill3D26(), theba.core.RegionMask.getPixelAt(), theba.core.RegionMask.isSet(), and theba.trackers.FloodTracker3D.track().

int theba.core.Stack.getWidth ( )

Definition at line 157 of file Stack.java.

VolumeReader theba.core.Stack.getWriter ( )

Definition at line 32 of file Stack.java.

boolean theba.core.Stack.isWritable ( )

Definition at line 40 of file Stack.java.

void theba.core.Stack.putSlice	(	short[]	data,
		int	z
	)

Definition at line 137 of file Stack.java.

References theba.core.io.VolumeReader.putSlice().

Referenced by theba.plugins.ErodePlugin.process(), theba.plugins.DistanceMap2DPlugin.process(), and theba.plugins.DilatePlugin.process().

void theba.core.Stack.setDepth ( int depth )

Definition at line 145 of file Stack.java.

void theba.core.Stack.setHeight ( int height )

Definition at line 153 of file Stack.java.

void theba.core.Stack.setVoxel	(	int	x,
		int	y,
		int	z,
		int	val
	)

Set a voxel to the given value. Values outside of bounds are ignored

Parameters:

	x
	y
	z
	val

Definition at line 82 of file Stack.java.

References theba.core.io.VolumeReader.getSlice().

Referenced by theba.core.ImageFunctions.floodFill3D26().

void theba.core.Stack.setVoxelUnchecked	(	int	x,
		int	y,
		int	z,
		int	val
	)

Sets a voxel to the given value. Values outside of bounds may result in an Exception, or erroneous values (use this function with caution)

Parameters:

	x
	y
	z

Returns:

Definition at line 69 of file Stack.java.

References theba.core.io.VolumeReader.getSlice().

Referenced by theba.core.ImageFunctions.floodFill3D26().

void theba.core.Stack.setWidth ( int width )

Definition at line 161 of file Stack.java.

The documentation for this class was generated from the following file:

src/theba/core/Stack.java

theba.core.Stack Class Reference

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation