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

Class MTBImageDouble

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDData

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

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

All Implemented Interfaces:

MTBImageManipulator, KeyListener, EventListener

public class MTBImageDouble
extends MTBImage

Class for easy access to Double (hyper)stacks. The Int type is a Non-ImageJ type, 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 double[][]	m_data image data
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	MTBImageDouble(int sizeX, int sizeY, int sizeZ, int sizeT, int sizeC) Constructor

Method Summary

Modifier and Type	Method and Description
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 as double
int[]	getMinMaxInt() Get minimum and maximum value of the image as int
double	getValueDouble(int x, int y) Get the value of the actual slice at coordinate (x,y) as an 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	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
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	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	setCurrentSliceLabel(String label) Set the slice label of the slice specified by the actual slice index
protected void	updateImagePlus() Creates or updates an ImagePlus of Float type from the MTBImage Double 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, fillWhite, 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, setStepsizeT, setStepsizeX, setStepsizeY, setStepsizeZ, setTitle, setUnitT, setUnitX, setUnitY, setUnitZ, 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_data

protected double[][] m_data

image data

m_sliceLabels

protected String[] m_sliceLabels

slice labels

Constructor Detail

MTBImageDouble

protected MTBImageDouble(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

getImagePlus

public ij.ImagePlus getImagePlus()

Get an ImagePlus object. An ImagePlus object of type ImagePlus.GRAY32 (FloatProcessor) is created and double values are casted to float. The ImagePlus diplay range is set to [min, max] of the MTBImage. 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 Float type from the MTBImage Double 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 -

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:

value as int

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:

value as int

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)

value - to set the voxel to

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)

value - to set the voxel to

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

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

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

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

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:

voxel value

getValueDouble

public double getValueDouble(int x,
                             int y)

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

voxel value

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)

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)

value - to set the voxel to

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]

getMinMaxDouble

public double[] getMinMaxDouble()

Get minimum and maximum value of the image as double

Specified by:

getMinMaxDouble in class MTBImage

Returns:

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