Interest_Point_Registration (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- spim.fiji.plugin.Interest_Point_Registration

All Implemented Interfaces:

ij.plugin.PlugIn
```
public class Interest_Point_Registration
extends Object
implements ij.plugin.PlugIn
```
Author:

Stephan Preibisch (stephan.preibisch@gmx.de)

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Interest_Point_Registration.RegistrationType

Nested Classes
Modifier and Type	Class and Description
`static class`	`Interest_Point_Registration.RegistrationType`

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`defaultAlgorithm`
`static int[]`	`defaultChannelLabels`
`static boolean`	`defaultConsiderTimepointAsUnit`
`static boolean[]`	`defaultFixedTiles`
`static int`	`defaultFixTiles`
`static int`	`defaultMapBack`
`static int`	`defaultRange`
`static int`	`defaultReferenceTile`
`static int`	`defaultReferenceTimepointIndex`
`static int`	`defaultRegistrationType`
`static boolean`	`defaultSameFixedViews`
`static boolean`	`defaultSameReferenceView`
`static boolean`	`defaultShowStatistics`
`static String[]`	`fixTilesChoice`
`static String[]`	`mapBackChoice`
`static String[]`	`registrationTypes`
`static ArrayList<InterestPointRegistration>`	`staticAlgorithms`
`static String`	`warningLabel`

Constructor Summary

Constructors
Constructor and Description

Interest_Point_Registration()

Constructors
Constructor and Description
`Interest_Point_Registration()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected boolean`	`askForFixedTiles(GlobalOptimizationSubset subset, GlobalOptimizationType type, Set<ViewId> fixedTiles, String title)`
`protected boolean`	`askForReferenceTile(GlobalOptimizationSubset subset, GlobalOptimizationType type, String title)`
`protected static String[]`	`assembleTimepoints(TimePoints timepoints)`
`static String[]`	`getAllInterestPointLabelsForChannel(SpimData2 spimData, List<ViewId> viewIdsToProcess, Channel channel)` Goes through all ViewDescriptions and checks all available labels for interest point detection
`static String[]`	`getAllInterestPointLabelsForChannel(SpimData2 spimData, List<ViewId> viewIdsToProcess, Channel channel, String doWhat)` Goes through all ViewDescriptions and checks all available labels for interest point detection
`protected ArrayList<ViewSetup>`	`getListOfViewSetupPresentInAllSubsets(List<GlobalOptimizationSubset> subsets, GlobalOptimizationType type)`
`static void`	`main(String[] args)`
`boolean`	`register(SpimData2 data, List<ViewId> viewIds)`
`boolean`	`register(SpimData2 data, List<ViewId> viewIds, String xmlFileName, boolean saveXML)`
`boolean`	`register(SpimData2 data, List<ViewId> viewIds, String clusterExtension, String xmlFileName, boolean saveXML)`
`void`	`run(String arg)`
`boolean`	`setFixedTilesAndReference(int fixTilesIndex, int mapBackIndex, GlobalOptimizationType type)` Assign the right fixed tiles and reference tiles for this type of optimization

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

Field Detail

staticAlgorithms

public static ArrayList<InterestPointRegistration> staticAlgorithms

registrationTypes

public static String[] registrationTypes

fixTilesChoice
```
public static String[] fixTilesChoice
```

mapBackChoice
```
public static String[] mapBackChoice
```

defaultAlgorithm
```
public static int defaultAlgorithm
```

defaultRegistrationType

public static int defaultRegistrationType

defaultChannelLabels

public static int[] defaultChannelLabels

defaultRange
```
public static int defaultRange
```

defaultReferenceTimepointIndex

public static int defaultReferenceTimepointIndex

defaultConsiderTimepointAsUnit

public static boolean defaultConsiderTimepointAsUnit

defaultFixTiles
```
public static int defaultFixTiles
```

defaultMapBack
```
public static int defaultMapBack
```

defaultSameFixedViews

public static boolean defaultSameFixedViews

defaultSameReferenceView

public static boolean defaultSameReferenceView

defaultFixedTiles

public static boolean[] defaultFixedTiles

defaultReferenceTile
```
public static int defaultReferenceTile
```

defaultShowStatistics

public static boolean defaultShowStatistics

warningLabel

public static final String warningLabel

See Also:: Constant Field Values

Constructor Detail
- Interest_Point_Registration
```
public Interest_Point_Registration()
```

Method Detail

run
```
public void run(String arg)
```
Specified by:

run in interface ij.plugin.PlugIn

register

public boolean register(SpimData2 data,
                        List<ViewId> viewIds)

register

public boolean register(SpimData2 data,
                        List<ViewId> viewIds,
                        String xmlFileName,
                        boolean saveXML)

register

public boolean register(SpimData2 data,
                        List<ViewId> viewIds,
                        String clusterExtension,
                        String xmlFileName,
                        boolean saveXML)

setFixedTilesAndReference
```
public boolean setFixedTilesAndReference(int fixTilesIndex,
                                         int mapBackIndex,
                                         GlobalOptimizationType type)
```
Assign the right fixed tiles and reference tiles for this type of optimization

Parameters:

fixTilesIndex - - "Fix first tile", "Select fixed tile", "Do not fix tiles"

mapBackIndex - - "Do not map back (use this if tiles are fixed)", "Map back to first tile using translation model", "Map back to first tile using rigid model", "Map back to user defined tile using translation model", "Map back to user defined tile using rigid model"

askForReferenceTile

protected boolean askForReferenceTile(GlobalOptimizationSubset subset,
                                      GlobalOptimizationType type,
                                      String title)

askForFixedTiles

protected boolean askForFixedTiles(GlobalOptimizationSubset subset,
                                   GlobalOptimizationType type,
                                   Set<ViewId> fixedTiles,
                                   String title)

getListOfViewSetupPresentInAllSubsets

protected ArrayList<ViewSetup> getListOfViewSetupPresentInAllSubsets(List<GlobalOptimizationSubset> subsets,
                                                                     GlobalOptimizationType type)

getAllInterestPointLabelsForChannel

public static String[] getAllInterestPointLabelsForChannel(SpimData2 spimData,
                                                           List<ViewId> viewIdsToProcess,
                                                           Channel channel)

Goes through all ViewDescriptions and checks all available labels for interest point detection

Parameters:: spimData -; channel -
Returns:

getAllInterestPointLabelsForChannel

public static String[] getAllInterestPointLabelsForChannel(SpimData2 spimData,
                                                           List<ViewId> viewIdsToProcess,
                                                           Channel channel,
                                                           String doWhat)

Goes through all ViewDescriptions and checks all available labels for interest point detection

Parameters:: spimData -; channel -; doWhat - - the text for not doing anything with this channel
Returns:

assembleTimepoints

protected static String[] assembleTimepoints(TimePoints timepoints)

main

public static void main(String[] args)

Class Interest_Point_Registration

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

staticAlgorithms

registrationTypes

fixTilesChoice

mapBackChoice

defaultAlgorithm

defaultRegistrationType

defaultChannelLabels

defaultRange

defaultReferenceTimepointIndex

defaultConsiderTimepointAsUnit

defaultFixTiles

defaultMapBack

defaultSameFixedViews

defaultSameReferenceView

defaultFixedTiles

defaultReferenceTile

defaultShowStatistics

warningLabel

Constructor Detail

Interest_Point_Registration

Method Detail

run

register

register

register

setFixedTilesAndReference

askForReferenceTile

askForFixedTiles

getListOfViewSetupPresentInAllSubsets

getAllInterestPointLabelsForChannel

getAllInterestPointLabelsForChannel

assembleTimepoints

main