AlignTask (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.trakem2.align.AlignTask

```
public final class AlignTask
extends Object
```
Methods collection to be called from the GUI for alignment tasks.

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class AlignTask.ReferenceData

Nested Classes
Modifier and Type	Class and Description
`static class`	`AlignTask.ReferenceData`

Field Summary

Fields
Modifier and Type	Field and Description
`protected static boolean`	`deform`
`protected static boolean`	`deleteDisconnectedTiles`
`static int`	`ELASTIC_BLOCK_CORRESPONDENCES`
`protected static boolean`	`hideDisconnectedTiles`
`protected static boolean`	`largestGraphOnly`
`static int`	`LINEAR_PHASE_CORRELATION`
`static int`	`LINEAR_SIFT_CORRESPONDENCES`
`protected static int`	`mode` The mode used for alignment, which defaults to LINEAR_SIFT_CORRESPONDENCES but can take the values ELASTIC_BLOCK_CORRESPONDENCES and LINEAR_PHASE_CORRELATION.
`static Align.ParamOptimize`	`p_snap` The ParamOptimize object containg all feature extraction and registration model parameters for the "snap" function.
`protected static boolean`	`sloppyOverlapTest`
`protected static boolean`	`tilesAreInPlace`

Constructor Summary

Constructors
Constructor and Description

AlignTask()

Constructors
Constructor and Description
`AlignTask()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`alignMultiLayerMosaic(Layer l, Patch nail)` Align a multi-layer mosaic.
`static Bureaucrat`	`alignMultiLayerMosaicTask(Layer l)`
`static Bureaucrat`	`alignMultiLayerMosaicTask(Layer l, Patch nail)`
`static void`	`alignMultiLayerMosaicTask(List<Layer> layerRange, Patch nail, Align.Param cp, Align.ParamOptimize p, Align.ParamOptimize pcp, boolean tilesAreInPlaceIn, boolean largestGraphOnlyIn, boolean hideDisconnectedTilesIn, boolean deleteDisconnectedTilesIn, boolean deformIn)`
`static void`	`alignPatches(Align.ParamOptimize p, List<Patch> patches, Collection<Patch> fixedPatches, boolean tilesAreInPlaceIn, boolean largestGraphOnlyIn, boolean hideDisconnectedTilesIn, boolean deleteDisconnectedTilesIn)`
`static void`	`alignPatches(Align.ParamOptimize p, List<Patch> patches, Collection<Patch> fixedPatches, boolean tilesAreInPlaceIn, boolean largestGraphOnlyIn, boolean hideDisconnectedTilesIn, boolean deleteDisconnectedTilesIn, boolean sloppyOverlapTest)`
`static void`	`alignPatches(List<Patch> patches, Set<Patch> fixedPatches, int m)`
`static Bureaucrat`	`alignPatchesTask(List<Patch> patches, Set<Patch> fixedPatches)`
`static void`	`alignSelection(Selection selection, int m)`
`static Bureaucrat`	`alignSelectionTask(Selection selection)`
`static void`	`alignTiles(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles, boolean tilesAreInPlaceIn, boolean largestGraphOnlyIn, boolean hideDisconnectedTilesIn, boolean deleteDisconnectedTilesIn)`
`static void`	`alignTiles(Align.ParamOptimize p, List<AbstractAffineTile2D<?>> tiles, List<AbstractAffineTile2D<?>> fixedTiles, boolean tilesAreInPlaceIn, boolean largestGraphOnlyIn, boolean hideDisconnectedTilesIn, boolean deleteDisconnectedTilesIn, boolean sloppyOverlapTest)`
`static AlignTask.ReferenceData`	`createTransformPropertiesTable(List<Displayable> src_vdata, List<Displayable> tgt_vdata, Set<Long> lids_to_operate)` Creates a map only for visible patches that intersect vdata.
`static void`	`montageLayers(Align.ParamOptimize p, List<Layer> layers, boolean tilesAreInPlaceIn, boolean largestGraphOnlyIn, boolean hideDisconnectedTilesIn, boolean deleteDisconnectedTilesIn)`
`static void`	`montageLayers(Align.ParamOptimize p, List<Layer> layers, boolean tilesAreInPlaceIn, boolean largestGraphOnlyIn, boolean hideDisconnectedTilesIn, boolean deleteDisconnectedTilesIn, boolean sloppyOverlapTest)`
`static void`	`montageLayers(ElasticMontage.Param p, List<Layer> layers)`
`static Bureaucrat`	`montageLayersTask(List<Layer> layers)` Montage each layer independently.
`static Bureaucrat`	`registerStackSlices(Patch slice)`
`static Bureaucrat`	`snap(Patch patch, Align.ParamOptimize p_snapIn, boolean setup)` Find the most overlapping image to @param patch in the same layer where @param patch sits, and snap @param patch and all its linked Displayable objects.
`static void`	`transformPatchesAndVectorData(Collection<Patch> patches, AffineTransform a)`
`static void`	`transformPatchesAndVectorData(Collection<Patch> patches, Runnable alignment)` For registering within the same project instance.
`static void`	`transformPatchesAndVectorData(Layer layer, AffineTransform a)`
`static void`	`transformVectorData(AlignTask.ReferenceData rd, Collection<Displayable> vdata, LayerSet target_layerset)`

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

Field Detail
- tilesAreInPlace
```
protected static boolean tilesAreInPlace
```
- sloppyOverlapTest
```
protected static boolean sloppyOverlapTest
```
- largestGraphOnly
```
protected static boolean largestGraphOnly
```
- hideDisconnectedTiles
```
protected static boolean hideDisconnectedTiles
```
- deleteDisconnectedTiles
```
protected static boolean deleteDisconnectedTiles
```
- deform
```
protected static boolean deform
```
- LINEAR_PHASE_CORRELATION
```
public static final int LINEAR_PHASE_CORRELATION
```
  See Also:
  
  Constant Field Values
- LINEAR_SIFT_CORRESPONDENCES
```
public static final int LINEAR_SIFT_CORRESPONDENCES
```
  See Also:
  
  Constant Field Values
- ELASTIC_BLOCK_CORRESPONDENCES
```
public static final int ELASTIC_BLOCK_CORRESPONDENCES
```
  See Also:
  
  Constant Field Values
- mode
```
protected static int mode
```
  The mode used for alignment, which defaults to LINEAR_SIFT_CORRESPONDENCES but can take the values ELASTIC_BLOCK_CORRESPONDENCES and LINEAR_PHASE_CORRELATION.
- p_snap
```
public static final Align.ParamOptimize p_snap
```
  The ParamOptimize object containg all feature extraction and registration model parameters for the "snap" function.

Constructor Detail
- AlignTask
```
public AlignTask()
```

Method Detail

alignSelectionTask

public static final Bureaucrat alignSelectionTask(Selection selection)

alignSelection

public static final void alignSelection(Selection selection,
                                        int m)
                                 throws Exception

Throws:: Exception

alignPatchesTask

public static final Bureaucrat alignPatchesTask(List<Patch> patches,
                                                Set<Patch> fixedPatches)

alignPatches
```
public static final void alignPatches(List<Patch> patches,
                                      Set<Patch> fixedPatches,
                                      int m)
                               throws Exception
```
Parameters:

patches: - the list of Patch instances to align, all belonging to the same Layer.

fixedPatches: - the list of Patch instances to keep locked in place, if any.

m: - LINEAR_SIFT_CORRESPONDENCES, LINEAR_PHASE_CORRELATION or ELASTIC_BLOCK_CORRESPONDENCES.

Throws:

Exception

montageLayersTask
```
public static final Bureaucrat montageLayersTask(List<Layer> layers)
```
Montage each layer independently. Does NOT register layers to each other. Considers visible Patches only.

montageLayers

public static final void montageLayers(Align.ParamOptimize p,
                                       List<Layer> layers,
                                       boolean tilesAreInPlaceIn,
                                       boolean largestGraphOnlyIn,
                                       boolean hideDisconnectedTilesIn,
                                       boolean deleteDisconnectedTilesIn,
                                       boolean sloppyOverlapTest)

montageLayers

public static final void montageLayers(Align.ParamOptimize p,
                                       List<Layer> layers,
                                       boolean tilesAreInPlaceIn,
                                       boolean largestGraphOnlyIn,
                                       boolean hideDisconnectedTilesIn,
                                       boolean deleteDisconnectedTilesIn)

montageLayers

public static final void montageLayers(ElasticMontage.Param p,
                                       List<Layer> layers)
                                throws Exception

Throws:: Exception

transformPatchesAndVectorData

public static final void transformPatchesAndVectorData(Layer layer,
                                                       AffineTransform a)

transformPatchesAndVectorData

public static final void transformPatchesAndVectorData(Collection<Patch> patches,
                                                       AffineTransform a)

createTransformPropertiesTable
```
public static final AlignTask.ReferenceData createTransformPropertiesTable(List<Displayable> src_vdata,
                                                                           List<Displayable> tgt_vdata,
                                                                           Set<Long> lids_to_operate)
```
Creates a map only for visible patches that intersect vdata.

Parameters:

src_vdata - represents the VectorData instances in original form, of the original project and layer set.

tgt_vdata - if not null, it must have the same size as src_data and their elements correspond one-to-one (as in, tgt element a clone of src element at the same index).

lids_to_operate - The id of the layers on which any operation will be done tgt_data enables transformVectorData to apply the transforms to copies of the src_vdata in another project.

transformPatchesAndVectorData

public static final void transformPatchesAndVectorData(Collection<Patch> patches,
                                                       Runnable alignment)

For registering within the same project instance.

transformVectorData

public static final void transformVectorData(AlignTask.ReferenceData rd,
                                             Collection<Displayable> vdata,
                                             LayerSet target_layerset)

alignPatches

public static final void alignPatches(Align.ParamOptimize p,
                                      List<Patch> patches,
                                      Collection<Patch> fixedPatches,
                                      boolean tilesAreInPlaceIn,
                                      boolean largestGraphOnlyIn,
                                      boolean hideDisconnectedTilesIn,
                                      boolean deleteDisconnectedTilesIn,
                                      boolean sloppyOverlapTest)

alignPatches

public static final void alignPatches(Align.ParamOptimize p,
                                      List<Patch> patches,
                                      Collection<Patch> fixedPatches,
                                      boolean tilesAreInPlaceIn,
                                      boolean largestGraphOnlyIn,
                                      boolean hideDisconnectedTilesIn,
                                      boolean deleteDisconnectedTilesIn)

alignTiles

public static final void alignTiles(Align.ParamOptimize p,
                                    List<AbstractAffineTile2D<?>> tiles,
                                    List<AbstractAffineTile2D<?>> fixedTiles,
                                    boolean tilesAreInPlaceIn,
                                    boolean largestGraphOnlyIn,
                                    boolean hideDisconnectedTilesIn,
                                    boolean deleteDisconnectedTilesIn,
                                    boolean sloppyOverlapTest)

alignTiles

public static final void alignTiles(Align.ParamOptimize p,
                                    List<AbstractAffineTile2D<?>> tiles,
                                    List<AbstractAffineTile2D<?>> fixedTiles,
                                    boolean tilesAreInPlaceIn,
                                    boolean largestGraphOnlyIn,
                                    boolean hideDisconnectedTilesIn,
                                    boolean deleteDisconnectedTilesIn)

alignMultiLayerMosaicTask

public static final Bureaucrat alignMultiLayerMosaicTask(Layer l)

alignMultiLayerMosaicTask

public static final Bureaucrat alignMultiLayerMosaicTask(Layer l,
                                                         Patch nail)

alignMultiLayerMosaic

public static final void alignMultiLayerMosaic(Layer l,
                                               Patch nail)

Align a multi-layer mosaic.

Parameters:: l - the current layer

alignMultiLayerMosaicTask

public static final void alignMultiLayerMosaicTask(List<Layer> layerRange,
                                                   Patch nail,
                                                   Align.Param cp,
                                                   Align.ParamOptimize p,
                                                   Align.ParamOptimize pcp,
                                                   boolean tilesAreInPlaceIn,
                                                   boolean largestGraphOnlyIn,
                                                   boolean hideDisconnectedTilesIn,
                                                   boolean deleteDisconnectedTilesIn,
                                                   boolean deformIn)

snap
```
public static final Bureaucrat snap(Patch patch,
                                    Align.ParamOptimize p_snapIn,
                                    boolean setup)
```
Find the most overlapping image to @param patch in the same layer where @param patch sits, and snap @param patch and all its linked Displayable objects. If a null @param p_snap is given, it will use the AlignTask.p_snap. If @param setup is true, it will show a dialog to adjust parameters.

registerStackSlices

public static final Bureaucrat registerStackSlices(Patch slice)

Class AlignTask

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

tilesAreInPlace

sloppyOverlapTest

largestGraphOnly

hideDisconnectedTiles

deleteDisconnectedTiles

deform

LINEAR_PHASE_CORRELATION

LINEAR_SIFT_CORRESPONDENCES

ELASTIC_BLOCK_CORRESPONDENCES

mode

p_snap

Constructor Detail

AlignTask

Method Detail

alignSelectionTask

alignSelection

alignPatchesTask

alignPatches

montageLayersTask

montageLayers

montageLayers

montageLayers

transformPatchesAndVectorData

transformPatchesAndVectorData

createTransformPropertiesTable

transformPatchesAndVectorData

transformVectorData

alignPatches

alignPatches

alignTiles

alignTiles

alignMultiLayerMosaicTask

alignMultiLayerMosaicTask

alignMultiLayerMosaic

alignMultiLayerMosaicTask

snap

registerStackSlices