ProcessForDeconvolution (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- spim.process.fusion.deconvolution.ProcessForDeconvolution

```
public class ProcessForDeconvolution
extends Object
```
Fused individual images for each input stack, uses the exporter directly

Author:

Stephan Preibisch (stephan.preibisch@gmx.de)

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class ProcessForDeconvolution.WeightType

Nested Classes
Modifier and Type	Class and Description
`static class`	`ProcessForDeconvolution.WeightType`

Field Summary

Fields
Modifier and Type Field and Description

static boolean debugImport

static String[] files

protected SpimData2 spimData

protected List<ViewId> viewIdsToProcess

Fields
Modifier and Type	Field and Description
`static boolean`	`debugImport`
`static String[]`	`files`
`protected SpimData2`	`spimData`
`protected List<ViewId>`	`viewIdsToProcess`

Constructor Summary

Constructors
Constructor and Description
`ProcessForDeconvolution(SpimData2 spimData, List<ViewId> viewIdsToProcess, BoundingBoxGUI bb, int[] blendingBorder, int[] blendingRange)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected ExtractPSF<FloatType>`	`assignOtherChannel(Channel channel, HashMap<Channel,ChannelPSF> extractPSFLabels)`
`protected void`	`displayWeights(double osemspeedup, ArrayList<RandomAccessibleInterval<FloatType>> weights, RandomAccessibleInterval<FloatType> overlapImg, ImgFactory<FloatType> imgFactory)`
`boolean`	`fuseStacksAndGetPSFs(TimePoint timepoint, Channel channel, ImgFactory<FloatType> imgFactory, int osemIndex, double osemspeedup, ProcessForDeconvolution.WeightType weightType, HashMap<Channel,ChannelPSF> extractPSFLabels, long[] psfSize, HashMap<Channel,ArrayList<Pair<Pair<Angle,Illumination>,String>>> psfFiles, boolean transformLoadedPSFs)` Fuses one stack, i.e.
`double`	`getAvgOverlappingViews()`
`protected Blending`	`getBlending(Interval interval, int[] blendingBorder, int[] blendingRange, ViewDescription desc)`
`ExtractPSF<FloatType>`	`getExtractPSF()`
`protected ArrayList<double[]>`	`getLocationsOfCorrespondingBeads(TimePoint tp, ViewDescription inputData, String label)`
`int`	`getMinOverlappingViews()`
`HashMap<ViewId,RandomAccessibleInterval<FloatType>>`	`getTransformedImgs()`
`HashMap<ViewId,RandomAccessibleInterval<FloatType>>`	`getTransformedWeights()`
`ArrayList<ViewDescription>`	`getViewDescriptions()`

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

Field Detail

spimData
```
protected final SpimData2 spimData
```

viewIdsToProcess

protected final List<ViewId> viewIdsToProcess

files
```
public static String[] files
```

debugImport
```
public static boolean debugImport
```

Constructor Detail

ProcessForDeconvolution

public ProcessForDeconvolution(SpimData2 spimData,
                               List<ViewId> viewIdsToProcess,
                               BoundingBoxGUI bb,
                               int[] blendingBorder,
                               int[] blendingRange)

Method Detail

getExtractPSF

public ExtractPSF<FloatType> getExtractPSF()

getTransformedImgs

public HashMap<ViewId,RandomAccessibleInterval<FloatType>> getTransformedImgs()

getTransformedWeights

public HashMap<ViewId,RandomAccessibleInterval<FloatType>> getTransformedWeights()

getViewDescriptions

public ArrayList<ViewDescription> getViewDescriptions()

getMinOverlappingViews
```
public int getMinOverlappingViews()
```

getAvgOverlappingViews

public double getAvgOverlappingViews()

fuseStacksAndGetPSFs

public boolean fuseStacksAndGetPSFs(TimePoint timepoint,
                                    Channel channel,
                                    ImgFactory<FloatType> imgFactory,
                                    int osemIndex,
                                    double osemspeedup,
                                    ProcessForDeconvolution.WeightType weightType,
                                    HashMap<Channel,ChannelPSF> extractPSFLabels,
                                    long[] psfSize,
                                    HashMap<Channel,ArrayList<Pair<Pair<Angle,Illumination>,String>>> psfFiles,
                                    boolean transformLoadedPSFs)

Fuses one stack, i.e. all angles/illuminations for one timepoint and channel

Parameters:: timepoint -; channel -
Returns:

assignOtherChannel

protected ExtractPSF<FloatType> assignOtherChannel(Channel channel,
                                                   HashMap<Channel,ChannelPSF> extractPSFLabels)

getLocationsOfCorrespondingBeads

protected ArrayList<double[]> getLocationsOfCorrespondingBeads(TimePoint tp,
                                                               ViewDescription inputData,
                                                               String label)

displayWeights

protected void displayWeights(double osemspeedup,
                              ArrayList<RandomAccessibleInterval<FloatType>> weights,
                              RandomAccessibleInterval<FloatType> overlapImg,
                              ImgFactory<FloatType> imgFactory)

getBlending

protected Blending getBlending(Interval interval,
                               int[] blendingBorder,
                               int[] blendingRange,
                               ViewDescription desc)

Class ProcessForDeconvolution

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

spimData

viewIdsToProcess

files

debugImport

Constructor Detail

ProcessForDeconvolution

Method Detail

getExtractPSF

getTransformedImgs

getTransformedWeights

getViewDescriptions

getMinOverlappingViews

getAvgOverlappingViews

fuseStacksAndGetPSFs

assignOtherChannel

getLocationsOfCorrespondingBeads

displayWeights

getBlending