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

Class MTBImageRGB

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDData

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

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

All Implemented Interfaces:

MTBImageManipulator, KeyListener, EventListener

public class MTBImageRGB
extends MTBImage

Class for easy access to RGB (hyper)stacks. This image consists of three separate byte images, thus the data is not a reference to ImagePlus data, but is allocated for this MTBImage object. Indices range is different from ImageJ Here, indices in each dimension range from 0 to (dimSize - 1), while ImageJ stack indices range from 1 to dimSize.

Author:

gress

Nested Class Summary

Nested classes/interfaces inherited from class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage

MTBImage.FactoryMethod, MTBImage.MTBImageFactory, MTBImage.MTBImageType

Field Summary

Fields

Modifier and Type	Field and Description
protected byte[][]	m_dataB reference to the ImagePlus pixel data (blue channel)
protected byte[][]	m_dataG reference to the ImagePlus pixel data (green channel)
protected byte[][]	m_dataR reference to the ImagePlus pixel data (red channel)
private MTBImageByte	m_imgB reference to the red channel MTBImage
private MTBImageByte	m_imgG reference to the red channel MTBImage
private MTBImageByte	m_imgR reference to the red channel MTBImage
protected String[]	m_sliceLabels slice labels

Fields inherited from class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage

calibration, m_currentC, m_currentSliceIdx, m_currentT, m_img, m_imgStack, m_sizeC, m_sizeStack, m_sizeT, m_sizeX, m_sizeY, m_sizeZ, m_type, UNTITLED, xml

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	MTBImageRGB(ij.ImagePlus img) Constructor
protected	MTBImageRGB(int sizeX, int sizeY, int sizeZ, int sizeT, int sizeC) Constructor

Method Summary

Modifier and Type	Method and Description
void	fillWhite() Set all pixels of the image to white, i.e. the maximal available value.
MTBImage	getChannelB() Get a reference to the blue channel image.
MTBImage	getChannelG() Get a reference to the green channel image.
MTBImage	getChannelR() Get a reference to the red channel image.
String	getCurrentSliceLabel() Get the slice label of the slice specified by the actual slice index
ij.ImagePlus	getImagePlus() Get an ImagePlus object.
double[]	getMinMaxDouble() Get minimum and maximum value of the image (all channels) as double
int[]	getMinMaxInt() Get minimum and maximum value of the image as int
int[]	getValue(int x, int y) Get RGB value from the specified position in the actual slice.
int[]	getValue(int x, int y, int z, int t, int c) Get RGB value from the specified position.
int	getValueB(int x, int y) Get blue value from the specified position in the actual slice.
int	getValueB(int x, int y, int z, int t, int c) Get blue value from the specified position.
double	getValueDouble(int x, int y) Get the value of the actual slice at coordinate (x,y) as a Double
double	getValueDouble(int x, int y, int z) Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
double	getValueDouble(int x, int y, int z, int t, int c) Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
int	getValueG(int x, int y) Get green value from the specified position in the actual slice.
int	getValueG(int x, int y, int z, int t, int c) Get green value from the specified position.
int	getValueInt(int x, int y) Get the value of the actual slice at coordinate (x,y) as an Integer
int	getValueInt(int x, int y, int z) Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
int	getValueInt(int x, int y, int z, int t, int c) Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
int	getValueR(int x, int y) Get red value from the specified position in the actual slice.
int	getValueR(int x, int y, int z, int t, int c) Get red value from the specified position.
void	putValue(int x, int y, int red, int green, int blue) Put a new RGB value at the specified position in the actual slice.
void	putValue(int x, int y, int z, int t, int c, int red, int green, int blue) Put a new RGB value at the specified position.
void	putValueB(int x, int y, int blue) Put a new blue value at the specified position in the actual slice.
void	putValueB(int x, int y, int z, int t, int c, int blue) Put a new blue value at the specified position.
void	putValueDouble(int x, int y, double value) Set the value of the actual slice at coordinate (x,y) using a Double
void	putValueDouble(int x, int y, int z, double value) Set the voxel value of the actual z-stack at coordinate (x,y,z)
void	putValueDouble(int x, int y, int z, int t, int c, double value) Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
void	putValueG(int x, int y, int green) Put a new green value at the specified position in the actual slice.
void	putValueG(int x, int y, int z, int t, int c, int green) Put a new green value at the specified position.
void	putValueInt(int x, int y, int value) Set the value of the actual slice at coordinate (x,y) using an Integer
void	putValueInt(int x, int y, int z, int value) Set the voxel value of the actual z-stack at coordinate (x,y,z)
void	putValueInt(int x, int y, int z, int t, int c, int value) Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
void	putValueR(int x, int y, int red) Put a new red value at the specified position in the actual slice.
void	putValueR(int x, int y, int z, int t, int c, int red) Put a new red value at the specified position.
void	setCurrentSliceLabel(String label) Set the slice label of the slice specified by the actual slice index
void	setStepsizeT(double stepsize) Set the stepsize in t-dimension (timestep).
void	setStepsizeX(double stepsize) Set the physical size of a voxel (stepsize) in x-dimension.
void	setStepsizeY(double stepsize) Set the physical size of a voxel (stepsize) in y-dimension.
void	setStepsizeZ(double stepsize) Set the physical size of a voxel (stepsize) in z-dimension.
void	setTitle(String title) Set the images title
void	setUnitT(String unit) Set the unit of the t-dimension.
void	setUnitX(String unit) Set the unit of the x-dimension.
void	setUnitY(String unit) Set the unit of the y-dimension.
void	setUnitZ(String unit) Set the unit of the z-dimension.
protected void	updateImagePlus() Creates or updates an ImagePlus of RGB type from the MTBImage RGB(3 byte-channels) data, can be returned by getImagePlus() or displayed by show()

Methods inherited from class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage

adoptSliceLabels, close, convertType, convertType, copyPhysicalProperties, createMTBImage, createMTBImage, createMTBImageByte, drawCircle2D, drawFilledCircle2D, drawLine2D, drawLine2D, drawPoint2D, duplicate, duplicate, duplicate, equals, equalSize, fillBlack, getCalibration, getCurrentSlice, getCurrentSlice, getCurrentSliceCoords, getCurrentSliceIndex, getCurrentZStackCoords, getImagePart, getImagePart, getSizeC, getSizeStack, getSizeT, getSizeX, getSizeY, getSizeZ, getSlice, getSlice, getSliceLabel, getStepsizeT, getStepsizeX, getStepsizeY, getStepsizeZ, getTitle, getTitleRunning, getType, getTypeMax, getTypeMin, getTypeName, getUnitT, getUnitX, getUnitY, getUnitZ, getXML, hasImagePlus, isValidType, keyPressed, keyReleased, keyTyped, ordinalToType, scaleValues, setCalibration, setCalibrationFromUnderlyingIJImage, setCurrentSlice, setCurrentSliceCoords, setCurrentSliceIndex, setCurrentZStackCoordinates, setImagePart, setSlice, setSliceLabel, setXML, show, stringToType, toString, updateAndRepaintWindow, updateImageSize_ImgToProp, updatePhysProperties_ImgToProp, updatePhysProperties_PropToImg

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDData

cloneProperties, getLocation, getProperty, getPropertyKeys, print, setLocation, setProperty

Methods inherited from class java.lang.Object

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

Field Detail

m_dataR

protected byte[][] m_dataR

reference to the ImagePlus pixel data (red channel)

m_dataG

protected byte[][] m_dataG

reference to the ImagePlus pixel data (green channel)

m_dataB

protected byte[][] m_dataB

reference to the ImagePlus pixel data (blue channel)

m_imgR

private MTBImageByte m_imgR

reference to the red channel MTBImage

m_imgG

private MTBImageByte m_imgG

reference to the red channel MTBImage

m_imgB

private MTBImageByte m_imgB

reference to the red channel MTBImage

m_sliceLabels

protected String[] m_sliceLabels

slice labels

Constructor Detail

MTBImageRGB

protected MTBImageRGB(ij.ImagePlus img)

Constructor

Parameters:

img -

MTBImageRGB

protected MTBImageRGB(int sizeX,
                      int sizeY,
                      int sizeZ,
                      int sizeT,
                      int sizeC)

Constructor

Parameters:

sizeX - size in x-dimension

sizeY - size in y-dimension

sizeZ - size in z-dimension

sizeT - size in t-dimension

sizeC - size in c-dimension

Method Detail

setTitle

public void setTitle(String title)

Set the images title

Overrides:

setTitle in class MTBImage

Parameters:

title -

getImagePlus

public ij.ImagePlus getImagePlus()

Get an ImagePlus object. An ImagePlus object of type ImagePlus.COLOR_RGB is created and returned. This ImagePlus does not share memory with this MTBImage.

Specified by:

getImagePlus in class MTBImage

Returns:

ImagePlus object

updateImagePlus

protected void updateImagePlus()

Creates or updates an ImagePlus of RGB type from the MTBImage RGB(3 byte-channels) data, can be returned by getImagePlus() or displayed by show()

Specified by:

updateImagePlus in class MTBImage

getCurrentSliceLabel

public String getCurrentSliceLabel()

Get the slice label of the slice specified by the actual slice index

Overrides:

getCurrentSliceLabel in class MTBImage

Returns:

setCurrentSliceLabel

public void setCurrentSliceLabel(String label)

Set the slice label of the slice specified by the actual slice index

Overrides:

setCurrentSliceLabel in class MTBImage

Parameters:

label -

setStepsizeX

public void setStepsizeX(double stepsize)

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

Overrides:

setStepsizeX in class MTBImage

Parameters:

stepsize - Stepsize in x-dimension.

setStepsizeY

public void setStepsizeY(double stepsize)

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

Overrides:

setStepsizeY in class MTBImage

Parameters:

stepsize - Stepsize in y-dimension.

setStepsizeZ

public void setStepsizeZ(double stepsize)

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

Overrides:

setStepsizeZ in class MTBImage

Parameters:

stepsize - Stepsize in z-dimension.

setStepsizeT

public void setStepsizeT(double stepsize)

Set the stepsize in t-dimension (timestep).

Overrides:

setStepsizeT in class MTBImage

Parameters:

stepsize - Stepsize in t-dimension.

setUnitX

public void setUnitX(String unit)

Set the unit of the x-dimension.

Overrides:

setUnitX in class MTBImage

Parameters:

unit - String of x-dimension unit.

setUnitY

public void setUnitY(String unit)

Set the unit of the y-dimension.

Overrides:

setUnitY in class MTBImage

Parameters:

unit - String of y-dimension unit.

setUnitZ

public void setUnitZ(String unit)

Set the unit of the z-dimension.

Overrides:

setUnitZ in class MTBImage

Parameters:

unit - String of z-dimension unit.

setUnitT

public void setUnitT(String unit)

Set the unit of the t-dimension.

Overrides:

setUnitT in class MTBImage

Parameters:

unit - String of t-dimension unit.

getMinMaxDouble

public double[] getMinMaxDouble()

Get minimum and maximum value of the image (all channels) as double

Specified by:

getMinMaxDouble in class MTBImage

Returns:

min at double[0], max at double[1]

getMinMaxInt

public int[] getMinMaxInt()

Get minimum and maximum value of the image as int

Specified by:

getMinMaxInt in class MTBImage

Returns:

min at int[0], max at int[1]

getValueDouble

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

Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity

Specified by:

getValueDouble in interface MTBImageManipulator

Specified by:

getValueDouble in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

z - z-coordinate ranging from 0 to (sizeZ - 1)

t - t-coordinate ranging from 0 to (sizeT - 1)

c - c-coordinate ranging from 0 to (sizeC - 1)

Returns:

RGB value (three byte-values) stored in an int (like ImageJ), then casted to double

getValueDouble

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

Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity

Specified by:

getValueDouble in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

z - z-coordinate ranging from 0 to (sizeZ - 1)

Returns:

value as int

getValueDouble

public double getValueDouble(int x,
                             int y)

Get the value of the actual slice at coordinate (x,y) as a Double

Specified by:

getValueDouble in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

Returns:

RGB value (three byte-values) stored in an int (like ImageJ), then casted to double

getValueInt

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

Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity

Specified by:

getValueInt in interface MTBImageManipulator

Specified by:

getValueInt in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

z - z-coordinate ranging from 0 to (sizeZ - 1)

t - t-coordinate ranging from 0 to (sizeT - 1)

c - c-coordinate ranging from 0 to (sizeC - 1)

Returns:

RGB value (three byte-values) stored in an int (like ImageJ)

getValueInt

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

Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity

Specified by:

getValueInt in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

z - z-coordinate ranging from 0 to (sizeZ - 1)

Returns:

value as int

getValueInt

public int getValueInt(int x,
                       int y)

Get the value of the actual slice at coordinate (x,y) as an Integer

Specified by:

getValueInt in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

Returns:

RGB value (three byte-values) stored in an int (like ImageJ)

putValueDouble

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

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

Specified by:

putValueDouble in interface MTBImageManipulator

Specified by:

putValueDouble in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

z - z-coordinate ranging from 0 to (sizeZ - 1)

t - t-coordinate ranging from 0 to (sizeT - 1)

c - c-coordinate ranging from 0 to (sizeC - 1)

RGB - value (three byte-values) stored in an int (like ImageJ), then casted to double

putValueDouble

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

Set the voxel value of the actual z-stack at coordinate (x,y,z)

Specified by:

putValueDouble in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

z - z-coordinate ranging from 0 to (sizeZ - 1)

value - to set the voxel to

putValueDouble

public void putValueDouble(int x,
                           int y,
                           double value)

Set the value of the actual slice at coordinate (x,y) using a Double

Specified by:

putValueDouble in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

RGB - value (three byte-values) stored in an int (like ImageJ), then casted to double

putValueInt

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

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

Specified by:

putValueInt in interface MTBImageManipulator

Specified by:

putValueInt in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

z - z-coordinate ranging from 0 to (sizeZ - 1)

t - t-coordinate ranging from 0 to (sizeT - 1)

c - c-coordinate ranging from 0 to (sizeC - 1)

RGB - value (three byte-values) stored in an int (like ImageJ)

putValueInt

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

Set the voxel value of the actual z-stack at coordinate (x,y,z)

Specified by:

putValueInt in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

z - z-coordinate ranging from 0 to (sizeZ - 1)

value - to set the voxel to

putValueInt

public void putValueInt(int x,
                        int y,
                        int value)

Set the value of the actual slice at coordinate (x,y) using an Integer

Specified by:

putValueInt in class MTBImage

Parameters:

x - x-coordinate ranging from 0 to (sizeX - 1)

y - y-coordinate ranging from 0 to (sizeY - 1)

RGB - value (three byte-values) stored in an int (like ImageJ)

getValue

public int[] getValue(int x,
                      int y,
                      int z,
                      int t,
                      int c)

Get RGB value from the specified position.

Parameters:

x -

y -

z -

t -

c -

Returns:

3-element array with red[0], green[1], blue[2] values

getValue

public int[] getValue(int x,
                      int y)

Get RGB value from the specified position in the actual slice.

Parameters:

x -

y -

Returns:

3-element array with red[0], green[1], blue[2] values

putValue

public void putValue(int x,
                     int y,
                     int z,
                     int t,
                     int c,
                     int red,
                     int green,
                     int blue)

Put a new RGB value at the specified position. RGB values must be in the range [0, 255]

Parameters:

x -

y -

z -

t -

c -

red -

green -

blue -

putValue

public void putValue(int x,
                     int y,
                     int red,
                     int green,
                     int blue)

Put a new RGB value at the specified position in the actual slice. RGB values must be in the range [0, 255]

Parameters:

x -

y -

red -

green -

blue -

getValueR

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

Get red value from the specified position.

Parameters:

x -

y -

z -

t -

c -

Returns:

red value

getValueR

public int getValueR(int x,
                     int y)

Get red value from the specified position in the actual slice.

Parameters:

x -

y -

Returns:

red value

getValueG

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

Get green value from the specified position.

Parameters:

x -

y -

z -

t -

c -

Returns:

green value

getValueG

public int getValueG(int x,
                     int y)

Get green value from the specified position in the actual slice.

Parameters:

x -

y -

Returns:

green value

getValueB

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

Get blue value from the specified position.

Parameters:

x -

y -

z -

t -

c -

Returns:

blue value

getValueB

public int getValueB(int x,
                     int y)

Get blue value from the specified position in the actual slice.

Parameters:

x -

y -

Returns:

blue value

putValueR

public void putValueR(int x,
                      int y,
                      int z,
                      int t,
                      int c,
                      int red)

Put a new red value at the specified position. Red values must be in the range [0, 255]

Parameters:

x -

y -

z -

t -

c -

red -

putValueR

public void putValueR(int x,
                      int y,
                      int red)

Put a new red value at the specified position in the actual slice. Red values must be in the range [0, 255]

Parameters:

x -

y -

red -

putValueG

public void putValueG(int x,
                      int y,
                      int z,
                      int t,
                      int c,
                      int green)

Put a new green value at the specified position. Green values must be in the range [0, 255]

Parameters:

x -

y -

z -

t -

c -

green -

putValueG

public void putValueG(int x,
                      int y,
                      int green)

Put a new green value at the specified position in the actual slice. Green values must be in the range [0, 255]

Parameters:

x -

y -

green -

putValueB

public void putValueB(int x,
                      int y,
                      int z,
                      int t,
                      int c,
                      int blue)

Put a new blue value at the specified position. Blue values must be in the range [0, 255]

Parameters:

x -

y -

z -

t -

c -

blue -

putValueB

public void putValueB(int x,
                      int y,
                      int blue)

Put a new blue value at the specified position in the actual slice. Blue values must be in the range [0, 255]

Parameters:

x -

y -

blue -

getChannelR

public MTBImage getChannelR()

Get a reference to the red channel image.

Returns:

MTBImage of type MTB_BYTE

getChannelG

public MTBImage getChannelG()

Get a reference to the green channel image.

Returns:

MTBImage of type MTB_BYTE

getChannelB

public MTBImage getChannelB()

Get a reference to the blue channel image.

Returns:

MTBImage of type MTB_BYTE

fillWhite

public void fillWhite()

Description copied from class: MTBImage

Set all pixels of the image to white, i.e. the maximal available value.

Overrides:

fillWhite in class MTBImage