SPIMConfiguration (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- mpicbg.spim.io.SPIMConfiguration

public class SPIMConfiguration
extends Object

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class SPIMConfiguration.SegmentationTypes

Nested Classes
Modifier and Type	Class and Description
`static class`	`SPIMConfiguration.SegmentationTypes`

Field Summary

Fields
Modifier and Type	Field and Description
`float`	`alpha`
`String`	`anglePattern`
`int[]`	`angles`
`int`	`background`
`String`	`channelPattern`
`int[]`	`channels`
`int[]`	`channelsFuse`
`int[][]`	`channelsMirror`
`int[]`	`channelsRegister`
`String`	`channelsToFuse`
`String`	`channelsToRegister`
`double`	`circularityFactor`
`boolean`	`collectRegistrationStatistics`
`int`	`cropOffsetX`
`int`	`cropOffsetY`
`int`	`cropOffsetZ`
`int`	`cropSizeX`
`int`	`cropSizeY`
`int`	`cropSizeZ`
`int`	`cutOffRadiusGauss`
`String`	`debugLevel`
`int`	`debugLevelInt`
`int`	`deconvolutionDisplayPSF`
`boolean`	`deconvolutionJustShowOverlap`
`boolean`	`deconvolutionLoadSequentially`
`boolean`	`detectSmallestStructures`
`double`	`differenceThreshold`
`int`	`doFit`
`boolean`	`doGaussKeepImagesOpen`
`boolean`	`extractPSF`
`File[][][][]`	`file`
`float`	`fixedThreshold`
`boolean`	`fuseOnly`
`boolean`	`fuseReferenceTimepoint`
`float`	`fusionSigma1`
`float`	`fusionSigma2`
`int`	`histogramBins`
`float`	`identityRadius`
`int[]`	`illuminations`
`float`	`imageSigma`
`float[]`	`initialSigma`
`String`	`inputdirectory`
`String`	`inputFilePattern`
`ContainerFactory`	`inputImageFactory`
`Multi_View_Deconvolution`	`instance`
`int[]`	`integralImgRadius1`
`int[]`	`integralImgRadius2`
`float[]`	`integralImgThreshold`
`InterpolatorFactory<FloatType>`	`interpolatorFactorOutput`
`boolean`	`isDeconvolution`
`float`	`max_epsilon`
`float`	`maximaTolerance`
`int`	`maxSize`
`float`	`min_inlier_ratio`
`int`	`minBlackBorder`
`float[]`	`minInitialPeakValue`
`float[]`	`minPeakValue`
`int`	`minSize`
`String`	`mirrorChannels`
`boolean`	`multipleImageFusion`
`int`	`neighbors`
`int`	`numberOfThreads`
`int`	`numIterations`
`int`	`numParalellViews`
`String`	`outputdirectory`
`boolean`	`overrideImageZStretching`
`boolean`	`paralellFusion`
`ContainerFactory`	`processImageFactory`
`ArrayList<String>`	`psfFiles`
`double`	`ratioOfDistance`
`boolean`	`readRegistration`
`boolean`	`readSegmentation`
`int`	`referenceTimePoint`
`boolean`	`registerOnly`
`int[]`	`registrationAssignmentForFusion`
`String`	`registrationFiledirectory`
`int`	`scale`
`int`	`scaleSpaceNumberOfThreads`
`SPIMConfiguration.SegmentationTypes`	`segmentation`
`boolean`	`sequentialFusion`
`boolean`	`showImageJWindow`
`boolean`	`showOutputImage`
`float`	`sigma`
`SPIMExperiment`	`spimExperiment`
`int`	`steps`
`int`	`stepsPerOctave`
`OutOfBoundsStrategyFactory<FloatType>`	`strategyFactoryGauss`
`OutOfBoundsStrategyFactory<FloatType>`	`strategyFactoryOutput`
`String`	`tempDir`
`float`	`threshold`
`boolean`	`timeLapseRegistration`
`String`	`timepointPattern`
`int[]`	`timepoints`
`String`	`transformationModel`
`boolean`	`transformPSFs`
`boolean`	`useAssociatedBeads`
`boolean`	`useCenterOfMass`
`boolean`	`useEntropy`
`boolean`	`useFixedThreshold`
`boolean`	`useGaussContentBased`
`boolean`	`useIntegralContentBased`
`boolean`	`useLinearBlening`
`boolean`	`useRANSAC`
`int`	`windowSizeX`
`int`	`windowSizeY`
`int`	`writeOutputImage`
`boolean`	`writeRegistration`
`boolean`	`writeSegmentation`
`double`	`zStretching`

Constructor Summary

Constructors
Constructor and Description

SPIMConfiguration()

Constructors
Constructor and Description
`SPIMConfiguration()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected String[]`	`getDirListing(String directory, String filePatternStart, String filePatternEnd)`
`void`	`getFileNames()`
`void`	`getFilenamesHuisken()`
`int`	`getIndexForTimePoint(int timepoint)`
`AbstractAffineModel3D`	`getModel()`
`static String`	`getReplaceStringAngle(String inputFilePattern)`
`static String`	`getReplaceStringChannels(String inputFilePattern)`
`static String`	`getReplaceStringTimePoints(String inputFilePattern)`
`SPIMExperiment`	`getSpimExperiment()`
`int`	`getTimePointIndex(int timepoint)`
`double`	`getZStretchingHuisken()`
`boolean`	`hasAlternatingIllumination()`
`boolean`	`isHuiskenFormat()`
`void`	`parseAngles()`
`void`	`parseChannels()`
`void`	`parseIlluminations()`
`static ArrayList<Integer>`	`parseIntegerString(String integers)`
`void`	`parseTimePoints()`
`void`	`printProperties()`

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

Field Detail

timepointPattern
```
public String timepointPattern
```

timepoints
```
public int[] timepoints
```

anglePattern
```
public String anglePattern
```

angles
```
public int[] angles
```

illuminations
```
public int[] illuminations
```

inputFilePattern
```
public String inputFilePattern
```

channels
```
public int[] channels
```

channelsRegister
```
public int[] channelsRegister
```

channelsFuse
```
public int[] channelsFuse
```

channelsMirror
```
public int[][] channelsMirror
```

channelPattern
```
public String channelPattern
```

channelsToRegister
```
public String channelsToRegister
```

channelsToFuse
```
public String channelsToFuse
```

mirrorChannels
```
public String mirrorChannels
```

registrationAssignmentForFusion

public int[] registrationAssignmentForFusion

file
```
public File[][][][] file
```

inputdirectory
```
public String inputdirectory
```

outputdirectory
```
public String outputdirectory
```

registrationFiledirectory

public String registrationFiledirectory

debugLevel
```
public String debugLevel
```

debugLevelInt
```
public int debugLevelInt
```

showImageJWindow
```
public boolean showImageJWindow
```

collectRegistrationStatistics

public boolean collectRegistrationStatistics

transformationModel
```
public String transformationModel
```

timeLapseRegistration
```
public boolean timeLapseRegistration
```

fuseReferenceTimepoint
```
public boolean fuseReferenceTimepoint
```

referenceTimePoint
```
public int referenceTimePoint
```

spimExperiment
```
public SPIMExperiment spimExperiment
```

inputImageFactory

public ContainerFactory inputImageFactory

processImageFactory

public ContainerFactory processImageFactory

tempDir
```
public String tempDir
```

strategyFactoryOutput

public OutOfBoundsStrategyFactory<FloatType> strategyFactoryOutput

interpolatorFactorOutput

public InterpolatorFactory<FloatType> interpolatorFactorOutput

strategyFactoryGauss

public OutOfBoundsStrategyFactory<FloatType> strategyFactoryGauss

writeOutputImage
```
public int writeOutputImage
```

showOutputImage
```
public boolean showOutputImage
```

useEntropy
```
public boolean useEntropy
```

useIntegralContentBased
```
public boolean useIntegralContentBased
```

useGaussContentBased
```
public boolean useGaussContentBased
```

useLinearBlening
```
public boolean useLinearBlening
```

paralellFusion
```
public boolean paralellFusion
```

sequentialFusion
```
public boolean sequentialFusion
```

numParalellViews
```
public int numParalellViews
```

multipleImageFusion
```
public boolean multipleImageFusion
```

isDeconvolution
```
public boolean isDeconvolution
```

deconvolutionLoadSequentially

public boolean deconvolutionLoadSequentially

deconvolutionJustShowOverlap

public boolean deconvolutionJustShowOverlap

deconvolutionDisplayPSF
```
public int deconvolutionDisplayPSF
```

extractPSF
```
public boolean extractPSF
```

transformPSFs
```
public boolean transformPSFs
```

psfFiles
```
public ArrayList<String> psfFiles
```

instance

public Multi_View_Deconvolution instance

fuseOnly
```
public boolean fuseOnly
```

registerOnly
```
public boolean registerOnly
```

readSegmentation
```
public boolean readSegmentation
```

writeSegmentation
```
public boolean writeSegmentation
```

readRegistration
```
public boolean readRegistration
```

writeRegistration
```
public boolean writeRegistration
```

overrideImageZStretching

public boolean overrideImageZStretching

zStretching
```
public double zStretching
```

background
```
public int background
```

doFit
```
public int doFit
```

doGaussKeepImagesOpen
```
public boolean doGaussKeepImagesOpen
```

segmentation

public SPIMConfiguration.SegmentationTypes segmentation

threshold
```
public float threshold
```

fixedThreshold
```
public float fixedThreshold
```

useFixedThreshold
```
public boolean useFixedThreshold
```

circularityFactor
```
public double circularityFactor
```

minBlackBorder
```
public int minBlackBorder
```

minSize
```
public int minSize
```

maxSize
```
public int maxSize
```

useCenterOfMass
```
public boolean useCenterOfMass
```

minPeakValue
```
public float[] minPeakValue
```

minInitialPeakValue
```
public float[] minInitialPeakValue
```

identityRadius
```
public float identityRadius
```

maximaTolerance
```
public float maximaTolerance
```

imageSigma
```
public float imageSigma
```

initialSigma
```
public float[] initialSigma
```

stepsPerOctave
```
public int stepsPerOctave
```

steps
```
public int steps
```

detectSmallestStructures

public boolean detectSmallestStructures

scaleSpaceNumberOfThreads
```
public int scaleSpaceNumberOfThreads
```

integralImgRadius1
```
public int[] integralImgRadius1
```

integralImgRadius2
```
public int[] integralImgRadius2
```

integralImgThreshold
```
public float[] integralImgThreshold
```

differenceThreshold
```
public double differenceThreshold
```

ratioOfDistance
```
public double ratioOfDistance
```

neighbors
```
public int neighbors
```

useAssociatedBeads
```
public boolean useAssociatedBeads
```

useRANSAC
```
public boolean useRANSAC
```

max_epsilon
```
public float max_epsilon
```

min_inlier_ratio
```
public float min_inlier_ratio
```

numIterations
```
public int numIterations
```

scale
```
public int scale
```

cropOffsetX
```
public int cropOffsetX
```

cropOffsetY
```
public int cropOffsetY
```

cropOffsetZ
```
public int cropOffsetZ
```

cropSizeX
```
public int cropSizeX
```

cropSizeY
```
public int cropSizeY
```

cropSizeZ
```
public int cropSizeZ
```

numberOfThreads
```
public int numberOfThreads
```

sigma
```
public float sigma
```

cutOffRadiusGauss
```
public int cutOffRadiusGauss
```

histogramBins
```
public int histogramBins
```

windowSizeX
```
public int windowSizeX
```

windowSizeY
```
public int windowSizeY
```

alpha
```
public float alpha
```

fusionSigma1
```
public float fusionSigma1
```

fusionSigma2
```
public float fusionSigma2
```

Constructor Detail
- SPIMConfiguration
```
public SPIMConfiguration()
```

Method Detail

getModel

public AbstractAffineModel3D getModel()

getIndexForTimePoint

public int getIndexForTimePoint(int timepoint)

parseIntegerString

public static ArrayList<Integer> parseIntegerString(String integers)
                                             throws ConfigurationParserException

Throws:: ConfigurationParserException

parseAngles

public void parseAngles()
                 throws ConfigurationParserException

Throws:: ConfigurationParserException

parseChannels

public void parseChannels()
                   throws ConfigurationParserException

Throws:: ConfigurationParserException

parseIlluminations

public void parseIlluminations()
                        throws ConfigurationParserException

Throws:: ConfigurationParserException

getDirListing

protected String[] getDirListing(String directory,
                                 String filePatternStart,
                                 String filePatternEnd)

parseTimePoints

public void parseTimePoints()
                     throws ConfigurationParserException

Throws:: ConfigurationParserException

getReplaceStringChannels

public static String getReplaceStringChannels(String inputFilePattern)

getReplaceStringTimePoints

public static String getReplaceStringTimePoints(String inputFilePattern)

getReplaceStringAngle

public static String getReplaceStringAngle(String inputFilePattern)

isHuiskenFormat
```
public boolean isHuiskenFormat()
```

hasAlternatingIllumination

public boolean hasAlternatingIllumination()

getSpimExperiment

public SPIMExperiment getSpimExperiment()

getZStretchingHuisken
```
public double getZStretchingHuisken()
```

getFilenamesHuisken

public void getFilenamesHuisken()
                         throws ConfigurationParserException

Throws:: ConfigurationParserException

getFileNames

public void getFileNames()
                  throws ConfigurationParserException

Throws:: ConfigurationParserException

getTimePointIndex

public int getTimePointIndex(int timepoint)

printProperties
```
public void printProperties()
```

Class SPIMConfiguration

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

timepointPattern

timepoints

anglePattern

angles

illuminations

inputFilePattern

channels

channelsRegister

channelsFuse

channelsMirror

channelPattern

channelsToRegister

channelsToFuse

mirrorChannels

registrationAssignmentForFusion

file

inputdirectory

outputdirectory

registrationFiledirectory

debugLevel

debugLevelInt

showImageJWindow

collectRegistrationStatistics

transformationModel

timeLapseRegistration

fuseReferenceTimepoint

referenceTimePoint

spimExperiment

inputImageFactory

processImageFactory

tempDir

strategyFactoryOutput

interpolatorFactorOutput

strategyFactoryGauss

writeOutputImage

showOutputImage

useEntropy

useIntegralContentBased

useGaussContentBased

useLinearBlening

paralellFusion

sequentialFusion

numParalellViews

multipleImageFusion

isDeconvolution

deconvolutionLoadSequentially

deconvolutionJustShowOverlap

deconvolutionDisplayPSF

extractPSF

transformPSFs

psfFiles

instance

fuseOnly

registerOnly

readSegmentation

writeSegmentation

readRegistration

writeRegistration

overrideImageZStretching

zStretching

background

doFit

doGaussKeepImagesOpen

segmentation

threshold

fixedThreshold

useFixedThreshold

circularityFactor

minBlackBorder

minSize

maxSize

useCenterOfMass

minPeakValue