EfficientBayesianBased (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- spim.fiji.plugin.fusion.Fusion
- - spim.process.fusion.deconvolution.EfficientBayesianBased

public class EfficientBayesianBased
extends Fusion

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

protected class EfficientBayesianBased.Correspondence

Nested Classes
Modifier and Type	Class and Description
`protected class`	`EfficientBayesianBased.Correspondence`

Field Summary

Fields
Modifier and Type	Field and Description
`static String[]`	`blocksChoice`
`static String[]`	`computationOnChoice`
`static boolean`	`defaultAdjustBlending`
`static int[]`	`defaultBlendingBorder`
`static int`	`defaultBlendingBorderNumber`
`static int[]`	`defaultBlendingRange`
`static int`	`defaultBlendingRangeNumber`
`static int`	`defaultBlockSizeIndex`
`static int`	`defaultBlockSizeX`
`static int`	`defaultBlockSizeY`
`static int`	`defaultBlockSizeZ`
`static int`	`defaultComputationTypeIndex`
`static String`	`defaultCUDAPath`
`static boolean`	`defaultCUDAPathIsRelative`
`static int`	`defaultDebugInterval`
`static boolean`	`defaultDebugMode`
`static int`	`defaultDisplayPSF`
`static int`	`defaultExtractPSF`
`static int`	`defaultFFTImgType`
`static int`	`defaultIterationType`
`static double`	`defaultLambda`
`static int`	`defaultNumIterations`
`static double`	`defaultOSEMspeedup`
`static int`	`defaultOSEMspeedupIndex`
`static ArrayList<String>`	`defaultPSFFileField`
`static int[]`	`defaultPSFLabelIndex`
`static int`	`defaultPSFSizeX`
`static int`	`defaultPSFSizeY`
`static int`	`defaultPSFSizeZ`
`static boolean`	`defaultSamePSFForAllAnglesIllums`
`static boolean`	`defaultSamePSFForAllChannels`
`static boolean`	`defaultSaveMemory`
`static boolean`	`defaultTransformPSFs`
`static boolean`	`defaultUseTikhonovRegularization`
`static int`	`defaultWeightType`
`static String[]`	`displayPSFChoice`
`static String[]`	`extractPSFChoice`
`static String[]`	`iterationTypeString`
`static boolean`	`makeAllPSFSameSize`
`static String[]`	`osemspeedupChoice`
`static String[]`	`weightsString`

Fields inherited from class spim.fiji.plugin.fusion.Fusion
avgPixels, channelsToProcess, defaultInterpolation, defaultUseBlending, defaultUseContentBased, interpolation, interpolationTypes, newViewsetups, spimData, timepointsToProcess, useBlending, useContentBased, viewIdsToProcess

Constructor Summary

Constructors
Constructor and Description

EfficientBayesianBased(SpimData2 spimData, List<ViewId> viewIdsToProcess)

Constructors
Constructor and Description
`EfficientBayesianBased(SpimData2 spimData, List<ViewId> viewIdsToProcess)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`assembleAvailableCorrespondences(HashMap<Channel,ArrayList<EfficientBayesianBased.Correspondence>> correspondences, HashMap<Channel,Integer> viewsPresent, boolean onlyValid)`
`boolean`	`compressBoundingBoxDialog()` compress the bounding box dialog as much as possible to let more space for extra parameters
`protected Map<ViewSetup,ViewSetup>`	`createNewViewSetups(BoundingBoxGUI bb)` Set up the list of new viewsetups that are created with this fusion.
`protected void`	`displayParametersAndPSFs(BoundingBoxGUI bb, Channel channel, HashMap<Channel,ChannelPSF> extractPSFLabels)`
`boolean`	`fuseData(BoundingBoxGUI bb, ImgExport exporter)` Fuses and saves/displays
`protected boolean`	`getBlending()`
`protected boolean`	`getBlocks()`
`protected boolean`	`getCUDA()`
`protected boolean`	`getDebug()`
`String`	`getDescription()`
`protected boolean`	`getOSEM()`
`protected boolean`	`getPSF()`
`Fusion`	`newInstance(SpimData2 spimData, List<ViewId> viewIdsToProcess)`
`boolean`	`parseAdditionalParameters(GenericDialog gd)` Parse the additional parameters added before within the bounding box dialog
`void`	`queryAdditionalParameters(GenericDialog gd)` Query additional parameters within the bounding box dialog
`boolean`	`queryParameters()` Query the necessary parameters for the fusion (new dialog has to be made)
`void`	`registerAdditionalListeners(BoundingBoxGUI.ManageListeners m)` In case there are some other Listener upon whom the memory needs to be recomputed in the Manual Bounding Box.
`protected boolean`	`reOrderChannels()` Order the channels in a way so that those were the beads are extracted from, are first.
`boolean`	`supports16BitUnsigned()`
`boolean`	`supportsDownsampling()`
`long`	`totalRAM(long fusedSizeMB, int bytePerPixel)`

Methods inherited from class spim.fiji.plugin.fusion.Fusion
computeAvgImageSize, computeMaxNumViews, defineNewViewSetups, getInterpolation, getMaxNumViewsPerTimepoint, getNewViewSetups, getTimepointsToProcess

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

Field Detail

computationOnChoice

public static String[] computationOnChoice

osemspeedupChoice

public static String[] osemspeedupChoice

extractPSFChoice

public static String[] extractPSFChoice

blocksChoice
```
public static String[] blocksChoice
```

displayPSFChoice

public static String[] displayPSFChoice

iterationTypeString

public static String[] iterationTypeString

weightsString
```
public static String[] weightsString
```

defaultBlendingRangeNumber

public static int defaultBlendingRangeNumber

defaultBlendingBorderNumber

public static int defaultBlendingBorderNumber

defaultBlendingRange

public static int[] defaultBlendingRange

defaultBlendingBorder

public static int[] defaultBlendingBorder

makeAllPSFSameSize

public static boolean makeAllPSFSameSize

defaultFFTImgType
```
public static int defaultFFTImgType
```

defaultIterationType
```
public static int defaultIterationType
```

defaultWeightType
```
public static int defaultWeightType
```

defaultSaveMemory

public static boolean defaultSaveMemory

defaultOSEMspeedupIndex

public static int defaultOSEMspeedupIndex

defaultNumIterations
```
public static int defaultNumIterations
```

defaultUseTikhonovRegularization

public static boolean defaultUseTikhonovRegularization

defaultLambda
```
public static double defaultLambda
```

defaultBlockSizeIndex

public static int defaultBlockSizeIndex

defaultBlockSizeX
```
public static int defaultBlockSizeX
```

defaultBlockSizeY
```
public static int defaultBlockSizeY
```

defaultBlockSizeZ
```
public static int defaultBlockSizeZ
```

defaultComputationTypeIndex

public static int defaultComputationTypeIndex

defaultExtractPSF
```
public static int defaultExtractPSF
```

defaultDisplayPSF
```
public static int defaultDisplayPSF
```

defaultDebugMode
```
public static boolean defaultDebugMode
```

defaultAdjustBlending

public static boolean defaultAdjustBlending

defaultDebugInterval
```
public static int defaultDebugInterval
```

defaultOSEMspeedup

public static double defaultOSEMspeedup

defaultSamePSFForAllAnglesIllums

public static boolean defaultSamePSFForAllAnglesIllums

defaultSamePSFForAllChannels

public static boolean defaultSamePSFForAllChannels

defaultTransformPSFs

public static boolean defaultTransformPSFs

defaultPSFFileField

public static ArrayList<String> defaultPSFFileField

defaultPSFLabelIndex

public static int[] defaultPSFLabelIndex

defaultPSFSizeX
```
public static int defaultPSFSizeX
```

defaultPSFSizeY
```
public static int defaultPSFSizeY
```

defaultPSFSizeZ
```
public static int defaultPSFSizeZ
```

defaultCUDAPath
```
public static String defaultCUDAPath
```

defaultCUDAPathIsRelative

public static boolean defaultCUDAPathIsRelative

Constructor Detail

EfficientBayesianBased

public EfficientBayesianBased(SpimData2 spimData,
                              List<ViewId> viewIdsToProcess)

Method Detail
- fuseData
```
public boolean fuseData(BoundingBoxGUI bb,
                        ImgExport exporter)
```
  Description copied from class: Fusion
  
  Fuses and saves/displays
  
  Specified by:
  
  fuseData in class Fusion
  
  Returns:
- queryParameters
```
public boolean queryParameters()
```
  Description copied from class: Fusion
  
  Query the necessary parameters for the fusion (new dialog has to be made)
  
  Specified by:
  
  queryParameters in class Fusion
  
  Returns:
- registerAdditionalListeners
```
public void registerAdditionalListeners(BoundingBoxGUI.ManageListeners m)
```
  Description copied from class: Fusion
  
  In case there are some other Listener upon whom the memory needs to be recomputed in the Manual Bounding Box.
  
  Overrides:
  
  registerAdditionalListeners in class Fusion
- queryAdditionalParameters
```
public void queryAdditionalParameters(GenericDialog gd)
```
  Description copied from class: Fusion
  
  Query additional parameters within the bounding box dialog
  
  Specified by:
  
  queryAdditionalParameters in class Fusion
- parseAdditionalParameters
```
public boolean parseAdditionalParameters(GenericDialog gd)
```
  Description copied from class: Fusion
  
  Parse the additional parameters added before within the bounding box dialog
  
  Specified by:
  
  parseAdditionalParameters in class Fusion
  
  Returns:
- newInstance
```
public Fusion newInstance(SpimData2 spimData,
                          List<ViewId> viewIdsToProcess)
```
  Specified by:
  
  newInstance in class Fusion
  
  Returns:
  
  - a new instance without any special properties
- getDescription
```
public String getDescription()
```
  Specified by:
  
  getDescription in class Fusion
  
  Returns:
  
  - to be displayed in the generic dialog
- supports16BitUnsigned
```
public boolean supports16BitUnsigned()
```
  Specified by:
  
  supports16BitUnsigned in class Fusion
- supportsDownsampling
```
public boolean supportsDownsampling()
```
  Specified by:
  
  supportsDownsampling in class Fusion
- compressBoundingBoxDialog
```
public boolean compressBoundingBoxDialog()
```
  Description copied from class: Fusion
  
  compress the bounding box dialog as much as possible to let more space for extra parameters
  
  Specified by:
  
  compressBoundingBoxDialog in class Fusion
  
  Returns:
- totalRAM
```
public long totalRAM(long fusedSizeMB,
                     int bytePerPixel)
```
  Specified by:
  
  totalRAM in class Fusion
- displayParametersAndPSFs
```
protected void displayParametersAndPSFs(BoundingBoxGUI bb,
                                        Channel channel,
                                        HashMap<Channel,ChannelPSF> extractPSFLabels)
```
- reOrderChannels
```
protected boolean reOrderChannels()
```
  Order the channels in a way so that those were the beads are extracted from, are first. Otherwise, the extracted PSF will not be avaiable for a certain channel that uses PSFs from another channel
  
  Returns:
- getBlending
```
protected boolean getBlending()
```
- getPSF
```
protected boolean getPSF()
```
- getOSEM
```
protected boolean getOSEM()
```
- getDebug
```
protected boolean getDebug()
```
- getBlocks
```
protected boolean getBlocks()
```
- getCUDA
```
protected boolean getCUDA()
```
- assembleAvailableCorrespondences
```
protected void assembleAvailableCorrespondences(HashMap<Channel,ArrayList<EfficientBayesianBased.Correspondence>> correspondences,
                                                HashMap<Channel,Integer> viewsPresent,
                                                boolean onlyValid)
```
  Parameters:
  
  correspondences -
  
  viewsPresent -
  
  onlyValid - - only return a list of correspondence labels if all views have correspondences
- createNewViewSetups
```
protected Map<ViewSetup,ViewSetup> createNewViewSetups(BoundingBoxGUI bb)
```
  Description copied from class: Fusion
  
  Set up the list of new viewsetups that are created with this fusion. This maybe required if the exporter needs to assemble a new XML dataset or append to the current XML dataset. It maps from an old ViewSetup to a new ViewSetup
  
  Specified by:
  
  createNewViewSetups in class Fusion
  
  Parameters:
  
  bb - - the bounding box used for fusing the data
  
  Returns:
  
  the list of new viewsetups (in the order as the viewsetups are processed)

Class EfficientBayesianBased

Nested Class Summary

Field Summary

Fields inherited from class spim.fiji.plugin.fusion.Fusion

Constructor Summary

Method Summary

Methods inherited from class spim.fiji.plugin.fusion.Fusion

Methods inherited from class java.lang.Object

Field Detail

computationOnChoice

osemspeedupChoice

extractPSFChoice

blocksChoice

displayPSFChoice

iterationTypeString

weightsString

defaultBlendingRangeNumber

defaultBlendingBorderNumber

defaultBlendingRange

defaultBlendingBorder

makeAllPSFSameSize

defaultFFTImgType

defaultIterationType

defaultWeightType

defaultSaveMemory

defaultOSEMspeedupIndex

defaultNumIterations

defaultUseTikhonovRegularization

defaultLambda

defaultBlockSizeIndex

defaultBlockSizeX

defaultBlockSizeY

defaultBlockSizeZ

defaultComputationTypeIndex

defaultExtractPSF

defaultDisplayPSF

defaultDebugMode

defaultAdjustBlending

defaultDebugInterval

defaultOSEMspeedup

defaultSamePSFForAllAnglesIllums

defaultSamePSFForAllChannels

defaultTransformPSFs

defaultPSFFileField

defaultPSFLabelIndex

defaultPSFSizeX

defaultPSFSizeY

defaultPSFSizeZ

defaultCUDAPath

defaultCUDAPathIsRelative

Constructor Detail

EfficientBayesianBased

Method Detail

fuseData

queryParameters

registerAdditionalListeners

queryAdditionalParameters

parseAdditionalParameters

newInstance

getDescription

supports16BitUnsigned

supportsDownsampling

compressBoundingBoxDialog

totalRAM

displayParametersAndPSFs

reOrderChannels

getBlending

getPSF

getOSEM

getDebug

getBlocks

getCUDA

assembleAvailableCorrespondences

createNewViewSetups