ViewDataBeads (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.spim.registration.ViewDataBeads

All Implemented Interfaces:: Comparable<ViewDataBeads>

public class ViewDataBeads
extends Object
implements Comparable<ViewDataBeads>

Field Summary

Fields
Modifier and Type	Field and Description
`protected int`	`angle` the acquisition angle
`protected BeadStructure`	`beads` The Object for storing the potential beads
`protected int`	`channel` the channel
`protected int`	`channelIndex` the channel
`protected int`	`currentDownSamplingFactor`
`protected Image<FloatType>`	`downSampledImage` The currently downsampled image cached
`protected int`	`id` the unique(!) identification of the view
`protected int`	`illumination` the index of the illumination direction
`protected int[]`	`imageSize` The size of the input stack
`protected int[]`	`imageSizeOffset` The offset of the input stack
`protected float`	`initialSigma`
`protected int`	`integralRadius1`
`protected int`	`integralRadius2`
`protected float`	`integralThreshold`
`protected float`	`minInitialPeakValue`
`static float[]`	`minmaxset` Can be used to manually set min (minmaxset[0]) and max (minmaxset[1]) value for all views that are opened.
`protected float`	`minPeakValue`
`protected boolean`	`mirrorHorizontally`
`protected boolean`	`mirrorVertically`
`protected NucleusStructure`	`nuclei` The Object for storing the potential nuclei
`protected int`	`timePoint` the timepoint of this view
`protected boolean`	`useForFusion`
`protected boolean`	`useForRegistration`
`protected ViewErrorStatistics`	`viewError` The object for storing View-related error statistics
`protected ViewStructure`	`viewStructure` The structure of the views that will be aligned
`protected double`	`zStretching` The z-stretching of the input stack

Constructor Summary

Constructors
Constructor and Description

ViewDataBeads(int id, M model, String fileName, double zStretching)

Constructors
Constructor and Description
`ViewDataBeads(int id, M model, String fileName, double zStretching)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`closeImage()` Closes the input image stack of this view
`int`	`compareTo(ViewDataBeads o)`
`int`	`getAcqusitionAngle()`
`BeadStructure`	`getBeadStructure()`
`int`	`getChannel()`
`int`	`getChannelIndex()`
`Image<FloatType>`	`getDownSampledImage(int downSamplingFactor)` Gets a downsampled and normalized [0...1] version of the input image
`Image<FloatType>`	`getDownSampledImage(int downSamplingFactor, boolean normalize)` Gets a downsampled version of the input image
`String`	`getFileName()`
`int`	`getID()`
`int`	`getIllumination()`
`Image<FloatType>`	`getImage()` The link to the input image of this view, normalized to [0...1]
`Image<FloatType>`	`getImage(boolean normalize)` The link to the input image of this view
`Image<FloatType>`	`getImage(ContainerFactory imageFactory)` The link to the input image of this view normalized to [0...1]
`Image<FloatType>`	`getImage(ContainerFactory imageFactory, boolean normalize)` The link to the input image of this view
`int[]`	`getImageSize()`
`int[]`	`getImageSizeOffset()`
`float`	`getInitialSigma()`
`int`	`getIntegralRadius1()`
`int`	`getIntegralRadius2()`
`float`	`getIntegralThreshold()`
`float`	`getMaxValue()`
`float`	`getMaxValueUnnormed()`
`float`	`getMinInitialPeakValue()`
`float`	`getMinPeakValue()`
`float`	`getMinValue()`
`boolean`	`getMirrorHorizontally()`
`boolean`	`getMirrorVertically()`
`String`	`getName()`
`NucleusStructure`	`getNucleiStructure()`
`int`	`getNumDimensions()` Gets the number of dimensions from view 1
`int`	`getNumViews()`
`TileSPIM`	`getTile()`
`int`	`getTimePoint()`
`Transform3D`	`getTransform3D()` Returns the affine transformation of this `ViewDataBeads` as Java3D `Transform3D`
`AbstractAffineModel3D<?>`	`getUninitializedModel()`
`boolean`	`getUseForFusion()`
`boolean`	`getUseForRegistration()`
`ViewErrorStatistics`	`getViewErrorStatistics()`
`ViewStructure`	`getViewStructure()`
`double`	`getZStretching()`
`void`	`initErrorStatistics()`
`boolean`	`isConnected()` if the view is connected to any other view or excluded from the registration because no true correspondences were found
`boolean`	`loadDimensions()` Loads the dimensions from the *.dim files in the registration file directory
`boolean`	`loadRegistration()` Loads the registration matrix and the errors from the *.registration files in the registration file directory
`boolean`	`loadRegistrationTimePoint(int referenceTimePoint)` Loads the registration matrix and the errors relative to a reference timepoint from the *.registration files in the registration file directory
`boolean`	`loadSegmentation()` Loads the bead detections and its correspondences candidates as well as true correspondences from the *.beads.txt files in the registration file directory
`void`	`normalizeImage()`
`static float[]`	`normalizeImage(Image<FloatType> image)` Normalizes the image to the range [0...1]
`static float[]`	`normalizeImage(Image<FloatType> image, float[] minmax)` Normalizes the image to the range [0...1]
`void`	`setAcqusitionAngle(int angle)`
`void`	`setBeadStructure(BeadStructure beads)`
`void`	`setChannel(int channel)`
`void`	`setChannelIndex(int channelIndex)`
`void`	`setFileName(String fileName)`
`void`	`setID(int id)`
`void`	`setIllumination(int illumination)`
`void`	`setImageSize(int[] size)`
`void`	`setImageSizeOffset(int[] imageSizeOffset)`
`void`	`setInitialSigma(float s)`
`void`	`setIntegralRadius1(int r1)`
`void`	`setIntegralRadius2(int r2)`
`void`	`setIntegralThreshold(float threshold)`
`void`	`setMinInitialPeakValue(float m)`
`void`	`setMinPeakValue(float m)`
`void`	`setMirrorHorizontally(boolean state)`
`void`	`setMirrorVertically(boolean state)`
`void`	`setName(String shortName)`
`void`	`setNucleiStructure(NucleusStructure nuclei)`
`void`	`setTimePoint(int timePoint)`
`void`	`setUseForFusion(boolean useForFusion)`
`void`	`setUseForRegistration(boolean useForRegistration)`
`protected void`	`setViewStructure(ViewStructure viewStructure)`
`void`	`setZStretching(double zStretching)`
`String`	`toString()`
`void`	`unnormalizeImage()`
`boolean`	`writeRegistration()` Writes the registration matrix and the errors into the *.registration files in the registration file directory
`boolean`	`writeRegistrationTimeLapse(int referenceTimePoint)` Writes the registration matrix and the errors into the *.registration files in the registration file directory
`boolean`	`writeSegmentation()` Writes the segmentated beads, correspondence candidates and ransac correspondences into the *.beads.txt files in the registration file directory

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - minmaxset
```
public static float[] minmaxset
```
    Can be used to manually set min (minmaxset[0]) and max (minmaxset[1]) value for all views that are opened. Otherwise min and max will be read from the images
  - viewStructure
```
protected ViewStructure viewStructure
```
    The structure of the views that will be aligned
  - beads
```
protected BeadStructure beads
```
    The Object for storing the potential beads
  - nuclei
```
protected NucleusStructure nuclei
```
    The Object for storing the potential nuclei
  - viewError
```
protected ViewErrorStatistics viewError
```
    The object for storing View-related error statistics
  - id
```
protected int id
```
    the unique(!) identification of the view
  - channel
```
protected int channel
```
    the channel
  - channelIndex
```
protected int channelIndex
```
    the channel
  - useForRegistration
```
protected boolean useForRegistration
```
  - useForFusion
```
protected boolean useForFusion
```
  - initialSigma
```
protected float initialSigma
```
  - minPeakValue
```
protected float minPeakValue
```
  - minInitialPeakValue
```
protected float minInitialPeakValue
```
  - integralRadius1
```
protected int integralRadius1
```
  - integralRadius2
```
protected int integralRadius2
```
  - integralThreshold
```
protected float integralThreshold
```
  - timePoint
```
protected int timePoint
```
    the timepoint of this view
  - angle
```
protected int angle
```
    the acquisition angle
  - illumination
```
protected int illumination
```
    the index of the illumination direction
  - zStretching
```
protected double zStretching
```
    The z-stretching of the input stack
  - imageSize
```
protected int[] imageSize
```
    The size of the input stack
  - imageSizeOffset
```
protected int[] imageSizeOffset
```
    The offset of the input stack
  - downSampledImage
```
protected Image<FloatType> downSampledImage
```
    The currently downsampled image cached
  - currentDownSamplingFactor
```
protected int currentDownSamplingFactor
```
  - mirrorVertically
```
protected boolean mirrorVertically
```
  - mirrorHorizontally
```
protected boolean mirrorHorizontally
```
- Constructor Detail
  - ViewDataBeads
```
public ViewDataBeads(int id,
                     M model,
                     String fileName,
                     double zStretching)
```
    Type Parameters:
    
    M - - an implementation of the AbstractAffineModel3D
    
    Parameters:
    
    id - - an unique id
    
    model - - the model instance, unintitialized
    
    fileName - - the filename (or directory with 2d planes) of the view
    
    zStretching - - the z/xy stretching
- Method Detail
  - getUninitializedModel
```
public AbstractAffineModel3D<?> getUninitializedModel()
```
  - isConnected
```
public boolean isConnected()
```
    if the view is connected to any other view or excluded from the registration because no true correspondences were found
    
    Returns:
    
    true if it is connected, otherwise false
  - setViewStructure
```
protected void setViewStructure(ViewStructure viewStructure)
```
  - getViewStructure
```
public ViewStructure getViewStructure()
```
  - getNumViews
```
public int getNumViews()
```
  - getBeadStructure
```
public BeadStructure getBeadStructure()
```
  - setBeadStructure
```
public void setBeadStructure(BeadStructure beads)
```
  - getNucleiStructure
```
public NucleusStructure getNucleiStructure()
```
  - setNucleiStructure
```
public void setNucleiStructure(NucleusStructure nuclei)
```
  - initErrorStatistics
```
public void initErrorStatistics()
```
  - getViewErrorStatistics
```
public ViewErrorStatistics getViewErrorStatistics()
```
  - getID
```
public int getID()
```
  - setID
```
public void setID(int id)
```
  - getChannel
```
public int getChannel()
```
  - setChannel
```
public void setChannel(int channel)
```
  - getChannelIndex
```
public int getChannelIndex()
```
  - setChannelIndex
```
public void setChannelIndex(int channelIndex)
```
  - getTimePoint
```
public int getTimePoint()
```
  - setTimePoint
```
public void setTimePoint(int timePoint)
```
  - getUseForRegistration
```
public boolean getUseForRegistration()
```
  - setUseForRegistration
```
public void setUseForRegistration(boolean useForRegistration)
```
  - getUseForFusion
```
public boolean getUseForFusion()
```
  - setUseForFusion
```
public void setUseForFusion(boolean useForFusion)
```
  - setIntegralRadius1
```
public void setIntegralRadius1(int r1)
```
  - setIntegralRadius2
```
public void setIntegralRadius2(int r2)
```
  - setIntegralThreshold
```
public void setIntegralThreshold(float threshold)
```
  - setInitialSigma
```
public void setInitialSigma(float s)
```
  - setMinPeakValue
```
public void setMinPeakValue(float m)
```
  - setMinInitialPeakValue
```
public void setMinInitialPeakValue(float m)
```
  - getInitialSigma
```
public float getInitialSigma()
```
  - getMinPeakValue
```
public float getMinPeakValue()
```
  - getMinInitialPeakValue
```
public float getMinInitialPeakValue()
```
  - getIntegralRadius1
```
public int getIntegralRadius1()
```
  - getIntegralRadius2
```
public int getIntegralRadius2()
```
  - getIntegralThreshold
```
public float getIntegralThreshold()
```
  - getAcqusitionAngle
```
public int getAcqusitionAngle()
```
  - setAcqusitionAngle
```
public void setAcqusitionAngle(int angle)
```
  - getIllumination
```
public int getIllumination()
```
  - setIllumination
```
public void setIllumination(int illumination)
```
  - getFileName
```
public String getFileName()
```
  - setFileName
```
public void setFileName(String fileName)
```
  - getName
```
public String getName()
```
  - setName
```
public void setName(String shortName)
```
  - getTile
```
public TileSPIM getTile()
```
  - getTransform3D
```
public Transform3D getTransform3D()
```
    Returns the affine transformation of this ViewDataBeads as Java3D Transform3D
    
    Returns:
    
    - the transform
  - getZStretching
```
public double getZStretching()
```
  - setZStretching
```
public void setZStretching(double zStretching)
```
  - getImageSize
```
public int[] getImageSize()
```
  - setImageSize
```
public void setImageSize(int[] size)
```
  - getImageSizeOffset
```
public int[] getImageSizeOffset()
```
  - setImageSizeOffset
```
public void setImageSizeOffset(int[] imageSizeOffset)
```
  - getMinValue
```
public float getMinValue()
```
  - getMaxValue
```
public float getMaxValue()
```
  - getNumDimensions
```
public int getNumDimensions()
```
    Gets the number of dimensions from view 1
    
    Returns:
    
    - the number of dimensions
  - getMaxValueUnnormed
```
public float getMaxValueUnnormed()
```
  - getImage
```
public Image<FloatType> getImage()
```
    The link to the input image of this view, normalized to [0...1]
    
    Returns:
    
    the link or null unable to open
  - getImage
```
public Image<FloatType> getImage(boolean normalize)
```
    The link to the input image of this view
    
    Returns:
    
    the link or null unable to open
  - getDownSampledImage
```
public Image<FloatType> getDownSampledImage(int downSamplingFactor)
```
    Gets a downsampled and normalized [0...1] version of the input image
    
    Parameters:
    
    downSamplingFactor - - the factor
  - getDownSampledImage
```
public Image<FloatType> getDownSampledImage(int downSamplingFactor,
                                            boolean normalize)
```
    Gets a downsampled version of the input image
    
    Parameters:
    
    downSamplingFactor - - the factor
    
    normalize - - if normalized to [0...1] or not
    
    Returns:
  - setMirrorHorizontally
```
public void setMirrorHorizontally(boolean state)
```
  - setMirrorVertically
```
public void setMirrorVertically(boolean state)
```
  - getMirrorHorizontally
```
public boolean getMirrorHorizontally()
```
  - getMirrorVertically
```
public boolean getMirrorVertically()
```
  - getImage
```
public Image<FloatType> getImage(ContainerFactory imageFactory)
```
    The link to the input image of this view normalized to [0...1]
    
    Returns:
    
    the link or null unable to open
  - getImage
```
public Image<FloatType> getImage(ContainerFactory imageFactory,
                                 boolean normalize)
```
    The link to the input image of this view
    
    Returns:
    
    the link or null unable to open
  - unnormalizeImage
```
public void unnormalizeImage()
```
  - normalizeImage
```
public void normalizeImage()
```
  - normalizeImage
```
public static float[] normalizeImage(Image<FloatType> image)
```
    Normalizes the image to the range [0...1]
    
    Parameters:
    
    image - - the image to normalize
    
    Returns:
    
    - a float[] array with array[ 0 ] == min and array[ 1 ] == max
  - normalizeImage
```
public static float[] normalizeImage(Image<FloatType> image,
                                     float[] minmax)
```
    Normalizes the image to the range [0...1]
    
    Parameters:
    
    image - - the image to normalize
    
    minmax - - null or a predefined min/max range (array[ 0 ] == min and array[ 1 ] == max)
    
    Returns:
    
    - a new float[] array with array[ 0 ] == min and array[ 1 ] == max
  - closeImage
```
public void closeImage()
```
    Closes the input image stack of this view
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - loadRegistration
```
public boolean loadRegistration()
```
    Loads the registration matrix and the errors from the *.registration files in the registration file directory
    
    Returns:
    
    true if successful, false otherwise
  - loadRegistrationTimePoint
```
public boolean loadRegistrationTimePoint(int referenceTimePoint)
```
    Loads the registration matrix and the errors relative to a reference timepoint from the *.registration files in the registration file directory
    
    Returns:
    
    true if successful, false otherwise
  - writeRegistration
```
public boolean writeRegistration()
```
    Writes the registration matrix and the errors into the *.registration files in the registration file directory
    
    Returns:
    
    true if successful, false otherwise
  - writeRegistrationTimeLapse
```
public boolean writeRegistrationTimeLapse(int referenceTimePoint)
```
    Writes the registration matrix and the errors into the *.registration files in the registration file directory
    
    Parameters:
    
    referenceTimePoint - - the reference time point
    
    Returns:
    
    true if successful, false otherwise
  - loadSegmentation
```
public boolean loadSegmentation()
```
    Loads the bead detections and its correspondences candidates as well as true correspondences from the *.beads.txt files in the registration file directory
    
    Returns:
    
    true if successful, false otherwise
  - writeSegmentation
```
public boolean writeSegmentation()
```
    Writes the segmentated beads, correspondence candidates and ransac correspondences into the *.beads.txt files in the registration file directory
    
    Returns:
    
    true if successful, false otherwise
  - loadDimensions
```
public boolean loadDimensions()
```
    Loads the dimensions from the *.dim files in the registration file directory
    
    Returns:
    
    true if successful, false otherwise
  - compareTo
```
public int compareTo(ViewDataBeads o)
```
    Specified by:
    
    compareTo in interface Comparable<ViewDataBeads>

Class ViewDataBeads

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

minmaxset

viewStructure

beads

nuclei

viewError

id

channel

channelIndex

useForRegistration

useForFusion

initialSigma

minPeakValue

minInitialPeakValue

integralRadius1

integralRadius2

integralThreshold

timePoint

angle

illumination

zStretching

imageSize

imageSizeOffset

downSampledImage

currentDownSamplingFactor

mirrorVertically

mirrorHorizontally

Constructor Detail

ViewDataBeads

Method Detail

getUninitializedModel

isConnected

setViewStructure

getViewStructure

getNumViews

getBeadStructure

setBeadStructure

getNucleiStructure

setNucleiStructure

initErrorStatistics

getViewErrorStatistics

getID

setID

getChannel

setChannel

getChannelIndex

setChannelIndex

getTimePoint

setTimePoint

getUseForRegistration

setUseForRegistration

getUseForFusion

setUseForFusion

setIntegralRadius1

setIntegralRadius2

setIntegralThreshold

setInitialSigma

setMinPeakValue

setMinInitialPeakValue

getInitialSigma

getMinPeakValue

getMinInitialPeakValue

getIntegralRadius1

getIntegralRadius2

getIntegralThreshold

getAcqusitionAngle

setAcqusitionAngle

getIllumination

setIllumination

getFileName

setFileName

getName

setName

getTile

getTransform3D