SetupAggregator (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bdv.ij.export.SetupAggregator

Deprecated.
```
@Deprecated
public class SetupAggregator
extends Object
```
Aggregate setups, i.e., SPIM source angles and fused datasets from multiple SequenceDescriptions. Also keeps for each setup the mipmap resolutions and subdivisions to be created. Note, that added setups are assigned new, consecutive ids starting from 0.

Author:

Tobias Pietzsch <tobias.pietzsch@gmail.com>

Field Summary

Fields
Modifier and Type	Field and Description
`protected BasicImgLoader`	`imgLoader` Deprecated. An `ImgLoader` that forwards to wrapped source sequences.
`protected Map<Integer,ExportMipmapInfo>`	`perSetupMipmapInfo` Deprecated.
`protected ArrayList<ViewRegistration>`	`registrations` Deprecated.
`protected ArrayList<BasicSetupImgLoader<?>>`	`setupImgLoaders` Deprecated.
`protected ArrayList<ViewSetupWrapper>`	`setups` Deprecated. Contains `wrappers` around setups in other sequences.
`protected TimePoints`	`timepoints` Deprecated. timepoint id for every timepoint index.

Constructor Summary

Constructors
Constructor and Description

SetupAggregator()
Deprecated.

Create an empty aggregator.

Constructors
Constructor and Description
`SetupAggregator()` Deprecated. Create an empty aggregator.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`int`	`add(BasicViewSetup sourceSetup, AbstractSequenceDescription<?,?,?> sourceSequence, ViewRegistrations sourceRegs, int[][] resolutions, int[][] subdivisions)` Deprecated. Add a new `BasicViewSetup` to the aggregator.
`void`	`addSetup(SpimRegistrationSequence sequence, int setupIndex, int[][] resolutions, int[][] subdivisions)` Deprecated.
`void`	`addSetup(SpimRegistrationSequence sequence, int setupIndex, String resolutionsString, String subdivisionsString)` Deprecated.
`void`	`addSetups(FusionResult fusionResult, int[][] resolutions, int[][] subdivisions)` Deprecated.
`void`	`addSetups(FusionResult fusionResult, String resolutionsString, String subdivisionsString)` Deprecated.
`void`	`addSetups(SpimRegistrationSequence sequence, int[][] resolutions, int[][] subdivisions)` Deprecated.
`void`	`addSetups(SpimRegistrationSequence sequence, String resolutionsString, String subdivisionsString)` Deprecated.
`SpimDataMinimal`	`createSpimData(File basePath)` Deprecated. Create a `SpimDataMinimal` for the setups currently aggregated.
`Map<Integer,ExportMipmapInfo>`	`getPerSetupMipmapInfo()` Deprecated. Get the aggregated per-setup `ExportMipmapInfo`s.

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

- Field Detail
  - timepoints
```
protected TimePoints timepoints
```
    Deprecated.
    
    timepoint id for every timepoint index.
  - registrations
```
protected final ArrayList<ViewRegistration> registrations
```
    Deprecated.
  - setups
```
protected final ArrayList<ViewSetupWrapper> setups
```
    Deprecated.
    
    Contains wrappers around setups in other sequences.
  - setupImgLoaders
```
protected final ArrayList<BasicSetupImgLoader<?>> setupImgLoaders
```
    Deprecated.
  - perSetupMipmapInfo
```
protected final Map<Integer,ExportMipmapInfo> perSetupMipmapInfo
```
    Deprecated.
  - imgLoader
```
protected final BasicImgLoader imgLoader
```
    Deprecated.
    
    An ImgLoader that forwards to wrapped source sequences.
- Constructor Detail
  - SetupAggregator
```
public SetupAggregator()
```
    Deprecated.
    
    Create an empty aggregator.
- Method Detail
  - add
```
public int add(BasicViewSetup sourceSetup,
               AbstractSequenceDescription<?,?,?> sourceSequence,
               ViewRegistrations sourceRegs,
               int[][] resolutions,
               int[][] subdivisions)
```
    Deprecated.
    
    Add a new BasicViewSetup to the aggregator. Adds a setup of the given source AbstractSequenceDescription to the aggregator. A reference to the source sequence is kept and the source ViewRegistrations are copied. In the viewer format, every image is stored in multiple resolutions. The resolutions are described as int[] arrays defining multiple of original pixel size in every dimension. For example {1,1,1} is the original resolution, {4,4,2} is downsampled by factor 4 in X and Y and factor 2 in Z. Each resolution of the image is stored as a chunked three-dimensional array (each chunk corresponds to one cell of a CellImg when the data is loaded). The chunk sizes are defined by the subdivisions parameter which is an array of int[], one per resolution. Each int[] array describes the X,Y,Z chunk size for one resolution.
    
    Parameters:
    
    sourceSetup - the setup to add
    
    sourceSequence - the source sequence to which the given setup refers.
    
    sourceRegs - the view registrations associated with the source sequence. registrations for the given setup are copied.
    
    resolutions - the set of resolutions to store. each nested int[] array defines one resolution.
    
    subdivisions - the set of subdivisions to store. each nested int[] array defines one subdivision.
    
    Returns:
    
    the setup id of the new BasicViewSetup in the aggregator.
  - createSpimData
```
public SpimDataMinimal createSpimData(File basePath)
```
    Deprecated.
    
    Create a SpimDataMinimal for the setups currently aggregated. This can be used to write the sequence (see WriteSequenceToHdf5 and XmlIoAbstractSpimData.toXml(mpicbg.spim.data.generic.AbstractSpimData, File)
    
    Parameters:
    
    basePath -
    
    Returns:
    
    a SpimDataMinimal with the currently aggregated setups.
  - getPerSetupMipmapInfo
```
public Map<Integer,ExportMipmapInfo> getPerSetupMipmapInfo()
```
    Deprecated.
    
    Get the aggregated per-setup ExportMipmapInfos.
  - addSetup
```
@Deprecated
public void addSetup(SpimRegistrationSequence sequence,
                                 int setupIndex,
                                 String resolutionsString,
                                 String subdivisionsString)
```
    Deprecated.
    
    Add the setup (angle) of the given SpimRegistrationSequence to this collection. In the viewer format, every image is stored in multiple resolutions. The resolutions are described as int[] arrays defining multiple of original pixel size in every dimension. For example {1,1,1} is the original resolution, {4,4,2} is downsampled by factor 4 in X and Y and factor 2 in Z. Each resolution of the image is stored as a chunked three-dimensional array (each chunk corresponds to one cell of a CellImg when the data is loaded). The chunk sizes are defined by the subdivisions parameter which is an array of int[], one per resolution. Each int[] array describes the X,Y,Z chunk size for one resolution.
    
    Parameters:
    
    sequence - a registered spim sequence. see Scripting.createSpimRegistrationSequence(String, String, String, String, String, int, boolean, double)
    
    setupIndex - which of the setups of the spim sequence to add.
    
    resolutionsString - the set of resolutions to store, formatted like "{1,1,1}, {2,2,1}, {4,4,4}" where each "{...}" defines one resolution.
    
    subdivisionsString - the set of subdivisions to store, formatted like "{32,32,32}, {16,16,8}, {8,8,8}" where each "{...}" defines one subdivision.
  - addSetup
```
@Deprecated
public void addSetup(SpimRegistrationSequence sequence,
                                 int setupIndex,
                                 int[][] resolutions,
                                 int[][] subdivisions)
```
    Deprecated.
    
    Add the setup (angle) of the given SpimRegistrationSequence to this collection. In the viewer format, every image is stored in multiple resolutions. The resolutions are described as int[] arrays defining multiple of original pixel size in every dimension. For example {1,1,1} is the original resolution, {4,4,2} is downsampled by factor 4 in X and Y and factor 2 in Z. Each resolution of the image is stored as a chunked three-dimensional array (each chunk corresponds to one cell of a CellImg when the data is loaded). The chunk sizes are defined by the subdivisions parameter which is an array of int[], one per resolution. Each int[] array describes the X,Y,Z chunk size for one resolution.
    
    Parameters:
    
    sequence - a registered spim sequence. see Scripting.createSpimRegistrationSequence(String, String, String, String, String, int, boolean, double)
    
    setupIndex - which of the setups of the spim sequence to add.
    
    resolutions - the set of resolutions to store. each nested int[] array defines one resolution.
    
    subdivisions - the set of subdivisions to store. each nested int[] array defines one subdivision.
  - addSetups
```
@Deprecated
public void addSetups(SpimRegistrationSequence sequence,
                                  String resolutionsString,
                                  String subdivisionsString)
```
    Deprecated.
    
    Add all setups (angles) of the given SpimRegistrationSequence to this collection. In the viewer format, every image is stored in multiple resolutions. The resolutions are described as int[] arrays defining multiple of original pixel size in every dimension. For example {1,1,1} is the original resolution, {4,4,2} is downsampled by factor 4 in X and Y and factor 2 in Z. Each resolution of the image is stored as a chunked three-dimensional array (each chunk corresponds to one cell of a CellImg when the data is loaded). The chunk sizes are defined by the subdivisions parameter which is an array of int[], one per resolution. Each int[] array describes the X,Y,Z chunk size for one resolution.
    
    Parameters:
    
    sequence - a registered spim sequence. see Scripting.createSpimRegistrationSequence(String, String, String, String, String, int, boolean, double)
    
    resolutionsString - the set of resolutions to store, formatted like "{1,1,1}, {2,2,1}, {4,4,4}" where each "{...}" defines one resolution.
    
    subdivisionsString - the set of subdivisions to store, formatted like "{32,32,32}, {16,16,8}, {8,8,8}" where each "{...}" defines one subdivision.
  - addSetups
```
@Deprecated
public void addSetups(SpimRegistrationSequence sequence,
                                  int[][] resolutions,
                                  int[][] subdivisions)
```
    Deprecated.
    
    Add all setups (angles) of the given SpimRegistrationSequence to this collection. In the viewer format, every image is stored in multiple resolutions. The resolutions are described as int[] arrays defining multiple of original pixel size in every dimension. For example {1,1,1} is the original resolution, {4,4,2} is downsampled by factor 4 in X and Y and factor 2 in Z. Each resolution of the image is stored as a chunked three-dimensional array (each chunk corresponds to one cell of a CellImg when the data is loaded). The chunk sizes are defined by the subdivisions parameter which is an array of int[], one per resolution. Each int[] array describes the X,Y,Z chunk size for one resolution.
    
    Parameters:
    
    sequence - a registered spim sequence. see Scripting.createSpimRegistrationSequence(String, String, String, String, String, int, boolean, double)
    
    resolutions - the set of resolutions to store. each nested int[] array defines one resolution.
    
    subdivisions - the set of subdivisions to store. each nested int[] array defines one subdivision.
  - addSetups
```
@Deprecated
public void addSetups(FusionResult fusionResult,
                                  String resolutionsString,
                                  String subdivisionsString)
```
    Deprecated.
    
    Add result of SPIM fusion or deconvolution as a setup to this collection. In the viewer format, every image is stored in multiple resolutions. The resolutions are described as int[] arrays defining multiple of original pixel size in every dimension. For example {1,1,1} is the original resolution, {4,4,2} is downsampled by factor 4 in X and Y and factor 2 in Z. Each resolution of the image is stored as a chunked three-dimensional array (each chunk corresponds to one cell of a CellImg when the data is loaded). The chunk sizes are defined by the subdivisions parameter which is an array of int[], one per resolution. Each int[] array describes the X,Y,Z chunk size for one resolution.
    
    Parameters:
    
    fusionResult - a fused spim sequence. Scripting.createFusionResult(SpimRegistrationSequence, String, String, int, double, double, Map)
    
    resolutionsString - the set of resolutions to store, formatted like "{1,1,1}, {2,2,1}, {4,4,4}" where each "{...}" defines one resolution.
    
    subdivisionsString - the set of subdivisions to store, formatted like "{32,32,32}, {16,16,8}, {8,8,8}" where each "{...}" defines one subdivision.
  - addSetups
```
@Deprecated
public void addSetups(FusionResult fusionResult,
                                  int[][] resolutions,
                                  int[][] subdivisions)
```
    Deprecated.
    
    Add result of SPIM fusion or deconvolution as a setup to this collection. In the viewer format, every image is stored in multiple resolutions. The resolutions are described as int[] arrays defining multiple of original pixel size in every dimension. For example {1,1,1} is the original resolution, {4,4,2} is downsampled by factor 4 in X and Y and factor 2 in Z. Each resolution of the image is stored as a chunked three-dimensional array (final each chunk corresponds to one cell of a CellImg when the data is loaded). The chunk sizes are defined by the subdivisions parameter which is an array of int[], one per resolution. Each int[] array describes the X,Y,Z chunk size for one resolution.
    
    Parameters:
    
    fusionResult - a fused spim sequence. Scripting.createSpimRegistrationSequence(String, String, String, String, String, int, boolean, double)
    
    resolutions - the set of resolutions to store. each nested int[] array defines one resolution.
    
    subdivisions - the set of subdivisions to store. each nested int[] array defines one subdivision.

Class SetupAggregator

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

timepoints

registrations

setups

setupImgLoaders

perSetupMipmapInfo

imgLoader

Constructor Detail

SetupAggregator

Method Detail

add

createSpimData

getPerSetupMipmapInfo

addSetup

addSetup

addSetups

addSetups

addSetups

addSetups