Package loci.formats.in

Class SlideBook7Reader.CImageGroup

java.lang.Object

loci.formats.in.SlideBook7Reader.ClassDecoder

loci.formats.in.SlideBook7Reader.CImageGroup

Enclosing class:

SlideBook7Reader

class SlideBook7Reader.CImageGroup
extends SlideBook7Reader.ClassDecoder

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	SlideBook7Reader.CImageGroup.CAnnotations
(package private) class	SlideBook7Reader.CImageGroup.CAuxDoubleData
(package private) class	SlideBook7Reader.CImageGroup.CAuxFloatData
(package private) class	SlideBook7Reader.CImageGroup.CAuxSInt32Data
(package private) class	SlideBook7Reader.CImageGroup.CAuxSInt64Data
(package private) class	SlideBook7Reader.CImageGroup.CAuxXmlData
(package private) class	SlideBook7Reader.CImageGroup.CMaskPositions

Field Summary

Fields

Modifier and Type	Field	Description
(package private) ArrayList<SlideBook7Reader.CAlignManipRecord70>	mAlignManipRecordList
(package private) ArrayList<SlideBook7Reader.CImageGroup.CAnnotations>	mAnnotationList
(package private) ArrayList<SlideBook7Reader.CImageGroup.CAuxDoubleData>	mAuxDoubleDataList
(package private) ArrayList<SlideBook7Reader.CImageGroup.CAuxFloatData>	mAuxFloatDataList
(package private) ArrayList<SlideBook7Reader.CImageGroup.CAuxSInt32Data>	mAuxSInt32DataList
(package private) ArrayList<SlideBook7Reader.CImageGroup.CAuxSInt64Data>	mAuxSInt64DataList
(package private) ArrayList<SlideBook7Reader.CImageGroup.CAuxXmlData>	mAuxXmlDataList
(package private) ArrayList<SlideBook7Reader.CChannelRecord70>	mChannelRecordList
(package private) int	mCompressionFlag
(package private) SlideBook7Reader.CCompressionBase	mCompressor
(package private) Integer[]	mElapsedTimes
(package private) SlideBook7Reader.CSBFile70	mFile
(package private) ArrayList<SlideBook7Reader.CFRETManipRecord70>	mFRETManipRecList
(package private) ArrayList<SlideBook7Reader.CHistogramRecord70>	mHistogramRecordList
(package private) ArrayList<SlideBook7Reader.CImageData>	mImageDataList
(package private) SlideBook7Reader.CImageRecord70	mImageRecord
(package private) String	mImageTitle
(package private) int	mLastChannel
(package private) int	mLastTimepoint
(package private) ArrayList<SlideBook7Reader.CImageGroup.CMaskPositions>	mMaskPosList
(package private) ArrayList<SlideBook7Reader.CMaskRecord70>	mMaskRecordList
(package private) SlideBook7Reader.CNpyHeader	mNpyHeader
(package private) ArrayList<SlideBook7Reader.CRatioManipRecord70>	mRatioManipRecordList
(package private) ArrayList<SlideBook7Reader.CRemapChannelLUT70>	mRemapChannelLUTList
(package private) ArrayList<SlideBook7Reader.CRemapManipRecord70>	mRemapManipRecList
(package private) ArrayList<Integer[]>	mSAPositionList
Boolean	mSingleTimepointFile
(package private) ArrayList<SlideBook7Reader.CSBPoint<Float>>	mStagePositions

Constructor Summary

Constructors

Constructor	Description
CImageGroup(SlideBook7Reader.CSBFile70 inFile, String inImageTitle)

Method Summary

Modifier and Type	Method	Description
Boolean	CountImageDataFiles()
int	GetBytesPerPixel()
String	GetChannelName(int inChannel)
int	GetElapsedTime(int inTimepoint)
int	GetExposureTime(int inChannel)
String	GetInfo()
float	GetInterplaneSpacing()
String	GetLensName()
double	GetMagnification()
String	GetName()
int	GetNumChannels()
int	GetNumColumns()
int	GetNumPlanes()
int	GetNumPositions()
int	GetNumRows()
int	GetNumTimepoints()
Boolean	GetSingleTimepointFile()
float	GetVoxelSize()
float	GetXPosition(int inPosition)
float	GetYPosition(int inPosition)
float	GetZPosition(int inPosition, int zplane)
int	IsSFMT(String inPath)
Boolean	Load()
Boolean	LoadAnnotations()
Boolean	LoadAuxData()
Boolean	LoadChannelRecord()
Boolean	LoadElapsedTimes()
Boolean	LoadImageRecord()
Boolean	LoadMaks()
Boolean	LoadSAPositions()
Boolean	LoadStagePosition()

Methods inherited from class loci.formats.in.SlideBook7Reader.ClassDecoder

Decode, Decode, DecodeUnknownString, FindNextClass, GetDoubleArray, GetFloatArray, GetIntegerArray, GetIntegerValue, GetLongArray, GetSBClassName, GetStringArray, GetStringValue, RestoreSpecialCharacters

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

mImageDataList

ArrayList<SlideBook7Reader.CImageData> mImageDataList

mMaskPosList

ArrayList<SlideBook7Reader.CImageGroup.CMaskPositions> mMaskPosList

mAnnotationList

ArrayList<SlideBook7Reader.CImageGroup.CAnnotations> mAnnotationList

mImageRecord

SlideBook7Reader.CImageRecord70 mImageRecord

mChannelRecordList

ArrayList<SlideBook7Reader.CChannelRecord70> mChannelRecordList

mRemapChannelLUTList

ArrayList<SlideBook7Reader.CRemapChannelLUT70> mRemapChannelLUTList

mAlignManipRecordList

ArrayList<SlideBook7Reader.CAlignManipRecord70> mAlignManipRecordList

mRatioManipRecordList

ArrayList<SlideBook7Reader.CRatioManipRecord70> mRatioManipRecordList

mFRETManipRecList

ArrayList<SlideBook7Reader.CFRETManipRecord70> mFRETManipRecList

mRemapManipRecList

ArrayList<SlideBook7Reader.CRemapManipRecord70> mRemapManipRecList

mHistogramRecordList

ArrayList<SlideBook7Reader.CHistogramRecord70> mHistogramRecordList

mMaskRecordList

ArrayList<SlideBook7Reader.CMaskRecord70> mMaskRecordList

mElapsedTimes

Integer[] mElapsedTimes

mSAPositionList

ArrayList<Integer[]> mSAPositionList

mStagePositions

ArrayList<SlideBook7Reader.CSBPoint<Float>> mStagePositions

mAuxFloatDataList

ArrayList<SlideBook7Reader.CImageGroup.CAuxFloatData> mAuxFloatDataList

mAuxDoubleDataList

ArrayList<SlideBook7Reader.CImageGroup.CAuxDoubleData> mAuxDoubleDataList

mAuxSInt32DataList

ArrayList<SlideBook7Reader.CImageGroup.CAuxSInt32Data> mAuxSInt32DataList

mAuxSInt64DataList

ArrayList<SlideBook7Reader.CImageGroup.CAuxSInt64Data> mAuxSInt64DataList

mAuxXmlDataList

ArrayList<SlideBook7Reader.CImageGroup.CAuxXmlData> mAuxXmlDataList

mFile

SlideBook7Reader.CSBFile70 mFile

mImageTitle

String mImageTitle

mNpyHeader

SlideBook7Reader.CNpyHeader mNpyHeader

mCompressor

SlideBook7Reader.CCompressionBase mCompressor

mLastTimepoint

int mLastTimepoint

mLastChannel

int mLastChannel

mSingleTimepointFile

public Boolean mSingleTimepointFile

mCompressionFlag

int mCompressionFlag

Constructor Details

CImageGroup

public CImageGroup(SlideBook7Reader.CSBFile70 inFile,
 String inImageTitle)

Method Details

Load

public Boolean Load()

LoadImageRecord

public Boolean LoadImageRecord()

IsSFMT

public int IsSFMT(String inPath)
           throws IOException

Throws:

IOException

CountImageDataFiles

public Boolean CountImageDataFiles()

LoadChannelRecord

public Boolean LoadChannelRecord()

LoadMaks

public Boolean LoadMaks()

LoadAnnotations

public Boolean LoadAnnotations()

LoadElapsedTimes

public Boolean LoadElapsedTimes()

LoadSAPositions

public Boolean LoadSAPositions()

LoadStagePosition

public Boolean LoadStagePosition()

LoadAuxData

public Boolean LoadAuxData()

GetNumChannels

public int GetNumChannels()

GetNumColumns

public int GetNumColumns()

GetNumRows

public int GetNumRows()

GetNumPlanes

public int GetNumPlanes()

GetNumPositions

public int GetNumPositions()

GetNumTimepoints

public int GetNumTimepoints()

GetElapsedTime

public int GetElapsedTime(int inTimepoint)

GetBytesPerPixel

public int GetBytesPerPixel()

GetName

public String GetName()

GetInfo

public String GetInfo()

GetChannelName

public String GetChannelName(int inChannel)

GetLensName

public String GetLensName()

GetMagnification

public double GetMagnification()

GetVoxelSize

public float GetVoxelSize()

GetInterplaneSpacing

public float GetInterplaneSpacing()

GetExposureTime

public int GetExposureTime(int inChannel)

GetXPosition

public float GetXPosition(int inPosition)

GetYPosition

public float GetYPosition(int inPosition)

GetZPosition

public float GetZPosition(int inPosition,
 int zplane)

GetSingleTimepointFile

public Boolean GetSingleTimepointFile()