de.unihalle.informatik.MiToBo.core.datatypes.images

Class MTBImageWindow

java.lang.Object

de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow

All Implemented Interfaces:

MTBImageManipulator

public class MTBImageWindow
extends Object
implements MTBImageManipulator

Class for windowing a MTBImage. Creates a hyperrectangle window over a MTBImage to access sectors of the image (volume) easily. Translation of the window is supported.

Author:

gress

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MTBImageWindow.BoundaryPadding Padding of image: Method of how to obtain pixel values outside the image domain

Field Summary

Fields

Modifier and Type	Field and Description
protected MTBImageManipulator	m_impulator source image on which the window is applied
protected MTBImageWindow.BoundaryPadding	m_padMode padding mode for nonexistent values (outside the underlying image), see static finals
protected int	m_posC current c-position of the window in the source image
protected int	m_posT current t-position of the window in the source image
protected int	m_posX current x-position of the window in the source image
protected int	m_posY current y-position of the window in the source image
protected int	m_posZ current z-position of the window in the source image
protected int	m_sizeC size of the window in c-dimension
protected int	m_sizeT size of the window in t-dimension
protected int	m_sizeX size of the window in x-dimension
protected int	m_sizeY size of the window in y-dimension
protected int	m_sizeZ size of the window in z-dimension

Constructor Summary

Constructors

Constructor and Description
MTBImageWindow(int sizeX, int sizeY, int sizeZ, int sizeT, int sizeC, MTBImageManipulator sourceImage, MTBImageWindow.BoundaryPadding paddingMode) Create a new window on a given source MTBImageManipulator (i.e.

Method Summary

Modifier and Type	Method and Description
MTBImage	createImageFromWindow()
int	getSizeC() Get window size in c-dimension
int	getSizeT() Get window size in t-dimension
int	getSizeX() Get window size in x-dimension
int	getSizeY() Get window size in y-dimension
int	getSizeZ() Get window size in z-dimension
double	getStepsizeT() Get the stepsize in t-dimension (timestep)
double	getStepsizeX() Get the physical size of a voxel (stepsize) in x-dimension
double	getStepsizeY() Get the physical size of a voxel (stepsize) in y-dimension
double	getStepsizeZ() Get the physical size of a voxel (stepsize) in z-dimension
String	getTitle() Get title of underlying image
MTBImage.MTBImageType	getType() Get underlying data type
String	getUnitT() Get the unit of the t-dimension
String	getUnitX() Get the unit of the x-dimension
String	getUnitY() Get the unit of the y-dimension
String	getUnitZ() Get the unit of the z-dimension
double	getValueDouble(int x, int y, int z, int t, int c) Get the value of the 5D image at coordinate (x,y,z,t,c) as a Double
int	getValueInt(int x, int y, int z, int t, int c) Get the value of the 5D image at coordinate (x,y,z,t,c) as an Integer
int[]	getWindowPosition() Get the current window position
void	incrPositionC() Increment the window's position by 1 in the c-dimension
void	incrPositionC(int increment) Increment the window's position by 'increment' in the c-dimension
void	incrPositionT() Increment the window's position by 1 in the t-dimension
void	incrPositionT(int increment) Increment the window's position by 'increment' in the t-dimension
void	incrPositionX() Increment the window's position by 1 in the x-dimension
void	incrPositionX(int increment) Increment the window's position by 'increment' in the x-dimension
void	incrPositionY() Increment the window's position by 1 in the y-dimension
void	incrPositionY(int increment) Increment the window's position by 'increment' in the y-dimension
void	incrPositionZ() Increment the window's position by 1 in the z-dimension
void	incrPositionZ(int increment) Increment the window's position by 'increment' in the z-dimension
void	putValueDouble(int x, int y, int z, int t, int c, double value) Set the value of the 5D image at coordinate (x,y,z,t,c) using a Double
void	putValueInt(int x, int y, int z, int t, int c, int value) Set the value of the 5D image at coordinate (x,y,z,t,c) using an Integer
void	setPositionC(int c) Set the window's position to 'c' in the c-dimension
void	setPositionT(int t) Set the window's position to 't' in the t-dimension
void	setPositionX(int x) Set the window's position to 'x' in the x-dimension
void	setPositionY(int y) Set the window's position to 'y' in the y-dimension
void	setPositionZ(int z) Set the window's position to 'z' in the z-dimension
void	setSource(MTBImageManipulator sourceImage) Set a new source for the window.
void	setWindowPosition(int x, int y, int z, int t, int c) Set the window's position in the source image.

Methods inherited from class java.lang.Object

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

Field Detail

m_sizeX

protected int m_sizeX

size of the window in x-dimension

m_sizeY

protected int m_sizeY

size of the window in y-dimension

m_sizeZ

protected int m_sizeZ

size of the window in z-dimension

m_sizeT

protected int m_sizeT

size of the window in t-dimension

m_sizeC

protected int m_sizeC

size of the window in c-dimension

m_impulator

protected MTBImageManipulator m_impulator

source image on which the window is applied

m_posX

protected int m_posX

current x-position of the window in the source image

m_posY

protected int m_posY

current y-position of the window in the source image

m_posZ

protected int m_posZ

current z-position of the window in the source image

m_posT

protected int m_posT

current t-position of the window in the source image

m_posC

protected int m_posC

current c-position of the window in the source image

m_padMode

protected MTBImageWindow.BoundaryPadding m_padMode

padding mode for nonexistent values (outside the underlying image), see static finals

Constructor Detail

MTBImageWindow

public MTBImageWindow(int sizeX,
                      int sizeY,
                      int sizeZ,
                      int sizeT,
                      int sizeC,
                      MTBImageManipulator sourceImage,
                      MTBImageWindow.BoundaryPadding paddingMode)

Create a new window on a given source MTBImageManipulator (i.e. MTBImage or MTBImageWindow).

Parameters:

sizeX - size of the window in x-dimension

sizeY - size of the window in y-dimension

sizeZ - size of the window in z-dimension

sizeT - size of the window in t-dimension

sizeC - size of the window in c-dimension

sourceImage - source image on which the window is applied

paddingMode -

Method Detail

setSource

public void setSource(MTBImageManipulator sourceImage)

Set a new source for the window. The window's position and size stay as they are.

Parameters:

sourceImage - source image on which the window is applied

createImageFromWindow

public MTBImage createImageFromWindow()

getTitle

public String getTitle()

Get title of underlying image

Specified by:

getTitle in interface MTBImageManipulator

Returns:

getType

public MTBImage.MTBImageType getType()

Get underlying data type

Specified by:

getType in interface MTBImageManipulator

Returns:

data type ID

getSizeX

public int getSizeX()

Get window size in x-dimension

Specified by:

getSizeX in interface MTBImageManipulator

Returns:

size of x-dimension

getSizeY

public int getSizeY()

Get window size in y-dimension

Specified by:

getSizeY in interface MTBImageManipulator

Returns:

size of y-dimension

getSizeZ

public int getSizeZ()

Get window size in z-dimension

Specified by:

getSizeZ in interface MTBImageManipulator

Returns:

size of z-dimension

getSizeT

public int getSizeT()

Get window size in t-dimension

Specified by:

getSizeT in interface MTBImageManipulator

Returns:

size of t(ime)-dimension

getSizeC

public int getSizeC()

Get window size in c-dimension

Specified by:

getSizeC in interface MTBImageManipulator

Returns:

size of c(hannel)-dimension

getValueDouble

public double getValueDouble(int x,
                             int y,
                             int z,
                             int t,
                             int c)

Get the value of the 5D image at coordinate (x,y,z,t,c) as a Double

Specified by:

getValueDouble in interface MTBImageManipulator

Parameters:

x - x-coordinate

y - y-coordinate

z - z-coordinate

t - t-coordinate

c - c-coordinate

Returns:

voxel value

getValueInt

public int getValueInt(int x,
                       int y,
                       int z,
                       int t,
                       int c)

Get the value of the 5D image at coordinate (x,y,z,t,c) as an Integer

Specified by:

getValueInt in interface MTBImageManipulator

Parameters:

x - x-coordinate

y - y-coordinate

z - z-coordinate

t - t-coordinate

c - c-coordinate

Returns:

voxel value

putValueDouble

public void putValueDouble(int x,
                           int y,
                           int z,
                           int t,
                           int c,
                           double value)

Set the value of the 5D image at coordinate (x,y,z,t,c) using a Double

Specified by:

putValueDouble in interface MTBImageManipulator

Parameters:

x - x-coordinate

y - y-coordinate

z - z-coordinate

t - t-coordinate

c - c-coordinate

value - to set the voxel to

putValueInt

public void putValueInt(int x,
                        int y,
                        int z,
                        int t,
                        int c,
                        int value)

Set the value of the 5D image at coordinate (x,y,z,t,c) using an Integer

Specified by:

putValueInt in interface MTBImageManipulator

Parameters:

x - x-coordinate

y - y-coordinate

z - z-coordinate

t - t-coordinate

c - c-coordinate

value - to set the voxel to

setWindowPosition

public void setWindowPosition(int x,
                              int y,
                              int z,
                              int t,
                              int c)

Set the window's position in the source image. Set the position of the (upper left) window coordinate (0,0,0,0,0) to the specified position in the source image.

Parameters:

x - x-coordinate in source image

y - y-coordinate in source image

z - z-coordinate in source image

t - t-coordinate in source image

c - c-coordinate in source image

getWindowPosition

public int[] getWindowPosition()

Get the current window position

Returns:

window position ([0]=x-position, [1]=y-position, [2]=z-position, [3]=t-position, [4]=c-position)

incrPositionX

public void incrPositionX()

Increment the window's position by 1 in the x-dimension

incrPositionX

public void incrPositionX(int increment)

Increment the window's position by 'increment' in the x-dimension

Parameters:

increment -

incrPositionY

public void incrPositionY()

Increment the window's position by 1 in the y-dimension

incrPositionY

public void incrPositionY(int increment)

Increment the window's position by 'increment' in the y-dimension

Parameters:

increment -

incrPositionZ

public void incrPositionZ()

Increment the window's position by 1 in the z-dimension

incrPositionZ

public void incrPositionZ(int increment)

Increment the window's position by 'increment' in the z-dimension

Parameters:

increment -

incrPositionT

public void incrPositionT()

Increment the window's position by 1 in the t-dimension

incrPositionT

public void incrPositionT(int increment)

Increment the window's position by 'increment' in the t-dimension

Parameters:

increment -

incrPositionC

public void incrPositionC()

Increment the window's position by 1 in the c-dimension

incrPositionC

public void incrPositionC(int increment)

Increment the window's position by 'increment' in the c-dimension

Parameters:

increment -

setPositionX

public void setPositionX(int x)

Set the window's position to 'x' in the x-dimension

Parameters:

x -

setPositionY

public void setPositionY(int y)

Set the window's position to 'y' in the y-dimension

Parameters:

y -

setPositionZ

public void setPositionZ(int z)

Set the window's position to 'z' in the z-dimension

Parameters:

z -

setPositionT

public void setPositionT(int t)

Set the window's position to 't' in the t-dimension

Parameters:

t -

setPositionC

public void setPositionC(int c)

Set the window's position to 'c' in the c-dimension

Parameters:

c -

getStepsizeX

public double getStepsizeX()

Get the physical size of a voxel (stepsize) in x-dimension

Specified by:

getStepsizeX in interface MTBImageManipulator

Returns:

physical voxel size in x-dimension

getStepsizeY

public double getStepsizeY()

Get the physical size of a voxel (stepsize) in y-dimension

Specified by:

getStepsizeY in interface MTBImageManipulator

Returns:

physical voxel size in y-dimension

getStepsizeZ

public double getStepsizeZ()

Get the physical size of a voxel (stepsize) in z-dimension

Specified by:

getStepsizeZ in interface MTBImageManipulator

Returns:

physical voxel size in z-dimension

getStepsizeT

public double getStepsizeT()

Get the stepsize in t-dimension (timestep)

Specified by:

getStepsizeT in interface MTBImageManipulator

Returns:

time stepsize

getUnitX

public String getUnitX()

Get the unit of the x-dimension

Specified by:

getUnitX in interface MTBImageManipulator

Returns:

String of x-dimension's unit

getUnitY

public String getUnitY()

Get the unit of the y-dimension

Specified by:

getUnitY in interface MTBImageManipulator

Returns:

String of y-dimension's unit

getUnitZ

public String getUnitZ()

Get the unit of the z-dimension

Specified by:

getUnitZ in interface MTBImageManipulator

Returns:

String of z-dimension's unit

getUnitT

public String getUnitT()

Get the unit of the t-dimension

Specified by:

getUnitT in interface MTBImageManipulator

Returns:

String of t-dimension's unit