GlobalOptimizationType (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- spim.process.interestpointregistration.optimizationtypes.GlobalOptimizationType

Direct Known Subclasses:

AllToAllRegistration, AllToAllRegistrationWithRange, IndividualTimepointRegistration, ReferenceTimepointRegistration
```
public abstract class GlobalOptimizationType
extends Object
```
A certain type of global optimization, must be able to define all view pairs that need to be matched and optimized inidivdually

Author:

Stephan Preibisch (stephan.preibisch@gmx.de)

Field Summary

Fields
Modifier and Type Field and Description

protected boolean considerTimePointsAsUnit

Fields
Modifier and Type	Field and Description
`protected boolean`	`considerTimePointsAsUnit`

Constructor Summary

Constructors
Constructor and Description
`GlobalOptimizationType(SpimData2 spimData, List<ViewId> viewIdsToProcess, List<ChannelProcess> channelsToProcess, boolean considerTimePointsAsUnit)`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addCorrespondences(List<PairwiseMatch> pairs)` Add all correspondences the list for those that are compared here This method can be overwritten if saving, adding & clearing of correspondences is different for a certain type of registration
`protected abstract List<GlobalOptimizationSubset>`	`assembleAllViewPairs()`
`void`	`clearExistingCorrespondences(GlobalOptimizationSubset set)` Clear all lists of existing correspondences for those that are compared here This method can be overwritten if saving, adding & clearing of correspondences is different for a certain type of registration
`boolean`	`considerTimePointsAsUnit()`
`List<GlobalOptimizationSubset>`	`getAllViewPairs()`
`protected static ChannelProcess`	`getChannelProcessForChannel(List<ChannelProcess> cpList, Channel c)`
`Set<ViewId>`	`getFixedTiles()`
`protected HashMap<ViewId,MatchPointList>`	`getInterestPoints(TimePoint timepoint)` Creates lists of input points for the registration, based on the current transformation of the views Note: this always duplicates the location array from the input List> InterestPoint < !!!
`AbstractModel<?>`	`getMapBackModel()` The transformation model used to map back to the reference frame (can be null)
`ViewId`	`getMapBackReferenceTile(GlobalOptimizationSubset set)` In case there is one tile which would be reference tile, return this one - can be null.
`SpimData2`	`getSpimData()`
`boolean`	`isFixedTile(ViewId viewId)`
`protected static boolean`	`isValid(ViewId viewId, MatchPointList list)`
`void`	`saveCorrespondences(GlobalOptimizationSubset set)` Save all lists of existing correspondences for those that are compared here This method can be overwritten if saving, adding & clearing of correspondences is different for a certain type of registration
`void`	`setFixedTiles(Set<ViewId> fixedTiles)`
`void`	`setMapBackModel(AbstractModel<?> model)`
`void`	`setMapBackReferenceTile(GlobalOptimizationSubset set, ViewId referenceTile)`
`void`	`setMapBackReferenceTiles(Map<GlobalOptimizationSubset,ViewId> referenceTiles)`

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

- Field Detail
  - considerTimePointsAsUnit
```
protected final boolean considerTimePointsAsUnit
```
- Constructor Detail
  - GlobalOptimizationType
```
public GlobalOptimizationType(SpimData2 spimData,
                              List<ViewId> viewIdsToProcess,
                              List<ChannelProcess> channelsToProcess,
                              boolean considerTimePointsAsUnit)
```
- Method Detail
  - assembleAllViewPairs
```
protected abstract List<GlobalOptimizationSubset> assembleAllViewPairs()
```
    Returns:
    
    - assembles the list of subsets and points for the registration
  - getAllViewPairs
```
public List<GlobalOptimizationSubset> getAllViewPairs()
```
    Returns:
    
    - the list of all subsets for the global optimization
  - isFixedTile
```
public boolean isFixedTile(ViewId viewId)
```
    Parameters:
    
    viewId -
    
    Returns:
    
    - true if a certain tile is fixed, otherwise false
  - getFixedTiles
```
public Set<ViewId> getFixedTiles()
```
    Returns:
    
    - the set of fixed tiles, can be empty
  - setFixedTiles
```
public void setFixedTiles(Set<ViewId> fixedTiles)
```
    Parameters:
    
    fixedTiles - - the set of fixed tiles, can be empty, but not NULL
  - getMapBackReferenceTile
```
public ViewId getMapBackReferenceTile(GlobalOptimizationSubset set)
```
    In case there is one tile which would be reference tile, return this one - can be null. This will be used to map the entire acquisition back to this frame as good as possible if the user asks for not fixing the first tile but still wants it roughly oriented like this
    
    Parameters:
    
    set - - the current set that will be globally optimized
    
    Returns:
  - setMapBackReferenceTile
```
public void setMapBackReferenceTile(GlobalOptimizationSubset set,
                                    ViewId referenceTile)
```
    Parameters:
    
    set - - for which subset
    
    referenceTile - - set reference tile for mapping back
  - setMapBackReferenceTiles
```
public void setMapBackReferenceTiles(Map<GlobalOptimizationSubset,ViewId> referenceTiles)
```
    Parameters:
    
    referenceTiles - - set all reference tiles
  - getMapBackModel
```
public AbstractModel<?> getMapBackModel()
```
    The transformation model used to map back to the reference frame (can be null)
    
    Returns:
    
    - a new instance of the model
  - setMapBackModel
```
public void setMapBackModel(AbstractModel<?> model)
```
    Parameters:
    
    model - - The transformation model used to map back to the reference frame (can be null)
  - considerTimePointsAsUnit
```
public boolean considerTimePointsAsUnit()
```
    Returns:
    
    - true if timepoints should be considered as one unit
  - getSpimData
```
public SpimData2 getSpimData()
```
  - getInterestPoints
```
protected HashMap<ViewId,MatchPointList> getInterestPoints(TimePoint timepoint)
```
    Creates lists of input points for the registration, based on the current transformation of the views Note: this always duplicates the location array from the input List> InterestPoint < !!!
    
    Parameters:
    
    timepoint -
  - getChannelProcessForChannel
```
protected static ChannelProcess getChannelProcessForChannel(List<ChannelProcess> cpList,
                                                            Channel c)
```
  - addCorrespondences
```
public void addCorrespondences(List<PairwiseMatch> pairs)
```
    Add all correspondences the list for those that are compared here This method can be overwritten if saving, adding & clearing of correspondences is different for a certain type of registration
    
    Parameters:
    
    pairs -
  - saveCorrespondences
```
public void saveCorrespondences(GlobalOptimizationSubset set)
```
    Save all lists of existing correspondences for those that are compared here This method can be overwritten if saving, adding & clearing of correspondences is different for a certain type of registration
    
    Parameters:
    
    set -
  - clearExistingCorrespondences
```
public void clearExistingCorrespondences(GlobalOptimizationSubset set)
```
    Clear all lists of existing correspondences for those that are compared here This method can be overwritten if saving, adding & clearing of correspondences is different for a certain type of registration
    
    Parameters:
    
    set -
  - isValid
```
protected static boolean isValid(ViewId viewId,
                                 MatchPointList list)
```

Class GlobalOptimizationType

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

considerTimePointsAsUnit

Constructor Detail

GlobalOptimizationType

Method Detail

assembleAllViewPairs

getAllViewPairs

isFixedTile

getFixedTiles

setFixedTiles

getMapBackReferenceTile

setMapBackReferenceTile

setMapBackReferenceTiles

getMapBackModel

setMapBackModel

considerTimePointsAsUnit

getSpimData

getInterestPoints

getChannelProcessForChannel

addCorrespondences

saveCorrespondences

clearExistingCorrespondences

isValid