ViewStructure (Fiji Javadocs 0-SNAPSHOT API)

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

```
public class ViewStructure
extends Object
```
This class stores the links to all Views and initializes the View-dependent error statistics

Author:

Stephan Preibisch

Field Summary

Fields
Modifier and Type	Field and Description
`protected BeadRegistration`	`beadRegister` The object that handles registration
`protected BeadSegmentation`	`beadSegment` The object that handles segmentation
`protected SPIMConfiguration`	`conf` The configuration of the current SPIM registration
`static int`	`DEBUG_ALL`
`static int`	`DEBUG_ERRORONLY`
`static int`	`DEBUG_MAIN`
`protected int`	`debugLevel` The debug level of this view constellation
`protected GlobalErrorStatistics`	`errorStatistics` The global error statistics of this view constellation
`static int`	`firstID`
`protected FusionControl`	`fusionControl` The object that handles fusion
`protected String`	`identification` Arbitrary String for identification
`protected int`	`numChannels` The number of channels in this view constellation
`protected int`	`timePoint` The time point of the current view constellation
`protected ArrayList<ViewDataBeads>`	`views` The link to the Views

Constructor Summary

Constructors
Constructor and Description
`ViewStructure(ArrayList<ViewDataBeads> views, SPIMConfiguration conf, String id, int timePoint, int numChannels)`
`ViewStructure(ArrayList<ViewDataBeads> views, SPIMConfiguration conf, String id, int timePoint, int numChannels, int debugLevel)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`BeadRegistration`	`getBeadRegistration()`
`BeadSegmentation`	`getBeadSegmentation()`
`int`	`getChannelNum(int channelIndex)` Returns the channel id for a certain channelIndex
`int`	`getDebugLevel()` DebugLevel of this view constellation
`FusionControl`	`getFusionControl()`
`GlobalErrorStatistics`	`getGlobalErrorStatistics()` The `GlobalErrorStatistics` collects error details of the registration prodedure
`String`	`getID()` get the identification String of the ViewStructure
`int`	`getNumChannels()` The number of channels in this view collection
`int`	`getNumDimensions()` Gets the number of dimensions from view 1
`int`	`getNumViews()` The number of views in this view collection
`SPIMConfiguration`	`getSPIMConfiguration()` Return the current SPIMConfiguration
`int`	`getTimePoint()` The time point index of the current `ViewStructure`
`ViewDataBeads`	`getViewFromID(int viewID)` For getting a View with a certain ID
`ArrayList<ViewDataBeads>`	`getViews()` Get the views
`static <M extends AbstractAffineModel3D<M>> ViewStructure`	`initViewStructure(SPIMConfiguration conf, int timePointIndex, M model, String id, int debugLevel)` This static methods creates an instance of `ViewStructure` with all `ViewDataBeads` completely instantiated.
`boolean`	`loadDimensions()` Loads the dimensions from the *.dim files in the registration file directory
`boolean`	`loadRegistrations()` Loads the registration matrix and the errors from the *.registration files in the registration file directory
`boolean`	`loadSegmentations()` Loads the bead detections and its correspondences candidates as well as true correspondences from the *.beads.txt files in the registration file directory
`void`	`setDebugLevel(int debugLevel)` DebugLevel of this view constellation
`void`	`setGlobalErrorStatistics(GlobalErrorStatistics errorStatistics)` Sets a new object that collects error details of the registration prodedure
`String`	`toString()`

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

- Field Detail
  - DEBUG_ALL
```
public static final int DEBUG_ALL
```
    See Also:
    
    Constant Field Values
  - DEBUG_MAIN
```
public static final int DEBUG_MAIN
```
    See Also:
    
    Constant Field Values
  - DEBUG_ERRORONLY
```
public static final int DEBUG_ERRORONLY
```
    See Also:
    
    Constant Field Values
  - firstID
```
public static int firstID
```
  - views
```
protected final ArrayList<ViewDataBeads> views
```
    The link to the Views
  - timePoint
```
protected final int timePoint
```
    The time point of the current view constellation
  - numChannels
```
protected final int numChannels
```
    The number of channels in this view constellation
  - identification
```
protected final String identification
```
    Arbitrary String for identification
  - debugLevel
```
protected int debugLevel
```
    The debug level of this view constellation
  - conf
```
protected final SPIMConfiguration conf
```
    The configuration of the current SPIM registration
  - errorStatistics
```
protected GlobalErrorStatistics errorStatistics
```
    The global error statistics of this view constellation
  - beadSegment
```
protected BeadSegmentation beadSegment
```
    The object that handles segmentation
  - beadRegister
```
protected BeadRegistration beadRegister
```
    The object that handles registration
  - fusionControl
```
protected FusionControl fusionControl
```
    The object that handles fusion
- Constructor Detail
  - ViewStructure
```
public ViewStructure(ArrayList<ViewDataBeads> views,
                     SPIMConfiguration conf,
                     String id,
                     int timePoint,
                     int numChannels)
```
  - ViewStructure
```
public ViewStructure(ArrayList<ViewDataBeads> views,
                     SPIMConfiguration conf,
                     String id,
                     int timePoint,
                     int numChannels,
                     int debugLevel)
```
- Method Detail
  - getBeadSegmentation
```
public BeadSegmentation getBeadSegmentation()
```
  - getBeadRegistration
```
public BeadRegistration getBeadRegistration()
```
  - getFusionControl
```
public FusionControl getFusionControl()
```
  - getNumViews
```
public int getNumViews()
```
    The number of views in this view collection
    
    Returns:
    
    the number of views
  - getNumChannels
```
public int getNumChannels()
```
    The number of channels in this view collection
    
    Returns:
    
    the number of channels
  - getChannelNum
```
public int getChannelNum(int channelIndex)
```
    Returns the channel id for a certain channelIndex
    
    Parameters:
    
    channelIndex -
    
    Returns:
    
    the naming of the channel
  - getGlobalErrorStatistics
```
public GlobalErrorStatistics getGlobalErrorStatistics()
```
    The GlobalErrorStatistics collects error details of the registration prodedure
    
    Returns:
    
    The GlobalErrorStatistics object of this ViewStructure
  - setGlobalErrorStatistics
```
public void setGlobalErrorStatistics(GlobalErrorStatistics errorStatistics)
```
    Sets a new object that collects error details of the registration prodedure
    
    Parameters:
    
    errorStatistics - - The GlobalErrorStatistics object of this ViewStructure
  - getDebugLevel
```
public int getDebugLevel()
```
    DebugLevel of this view constellation
    
    Returns:
    
    the current debug level
  - setDebugLevel
```
public void setDebugLevel(int debugLevel)
```
    DebugLevel of this view constellation
    
    Parameters:
    
    debugLevel - - the new debug level of this view constellation
  - getTimePoint
```
public int getTimePoint()
```
    The time point index of the current ViewStructure
    
    Returns:
    
    the id
  - getSPIMConfiguration
```
public SPIMConfiguration getSPIMConfiguration()
```
    Return the current SPIMConfiguration
    
    Returns:
    
    current SPIMConfiguration object
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - getID
```
public String getID()
```
    get the identification String of the ViewStructure
    
    Returns:
    
    String ID
  - getViews
```
public ArrayList<ViewDataBeads> getViews()
```
    Get the views
    
    Returns:
    
    ArrayList containing all Views
  - getViewFromID
```
public ViewDataBeads getViewFromID(int viewID)
```
    For getting a View with a certain ID
    
    Parameters:
    
    viewID - - the ID of the wanted View
    
    Returns:
    
    the View with the respective id or null if it does not exist
  - getNumDimensions
```
public int getNumDimensions()
```
    Gets the number of dimensions from view 1
    
    Returns:
    
    - the numnber of dimensions
  - loadSegmentations
```
public boolean loadSegmentations()
```
    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
  - loadRegistrations
```
public boolean loadRegistrations()
```
    Loads the registration matrix and the errors from the *.registration 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
  - initViewStructure
```
public static <M extends AbstractAffineModel3D<M>> ViewStructure initViewStructure(SPIMConfiguration conf,
                                                                                   int timePointIndex,
                                                                                   M model,
                                                                                   String id,
                                                                                   int debugLevel)
```
    This static methods creates an instance of ViewStructure with all ViewDataBeads completely instantiated. Afterwards processing can start or already processed data can be loaded.
    
    Parameters:
    
    conf - - the SPIMConfiguration object containing all information about the current registration
    
    timePointIndex - - the id of the current time point as the SPIMConfiguration stores the information for all time points
    
    model - - the model to be used for registration
    
    id - - arbitrary id, will be printed with the toString method
    
    debugLevel - - the debug level of the program ViewStructure.DEBUG_ALL, ViewStructure.DEBUG_MAIN or ViewStructure.DEBUG_ERRORONLY
    
    Returns:
    
    an instance of the ViewStructure, completely intialized

Class ViewStructure

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEBUG_ALL

DEBUG_MAIN

DEBUG_ERRORONLY

firstID

views

timePoint

numChannels

identification

debugLevel

conf

errorStatistics

beadSegment

beadRegister

fusionControl

Constructor Detail

ViewStructure

ViewStructure

Method Detail

getBeadSegmentation

getBeadRegistration

getFusionControl

getNumViews

getNumChannels

getChannelNum

getGlobalErrorStatistics

setGlobalErrorStatistics

getDebugLevel

setDebugLevel

getTimePoint

getSPIMConfiguration

toString

getID

getViews

getViewFromID

getNumDimensions

loadSegmentations

loadRegistrations

loadDimensions

initViewStructure