BaseZeissReader (Bio-Formats API)

java.lang.Object
- loci.formats.FormatHandler
- - loci.formats.FormatReader
  - - loci.formats.in.BaseZeissReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

Direct Known Subclasses:

ZeissTIFFReader, ZeissZVIReader
```
public abstract class BaseZeissReader
extends FormatReader
```
BaseZeissReader contains common functionality required by readers for Zeiss AxioVision formats.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class BaseZeissReader.Context

class BaseZeissReader.Tag
Content of a single tag from a Tags block.

Nested Classes
Modifier and Type	Class and Description
`static class`	`BaseZeissReader.Context`
`class`	`BaseZeissReader.Tag` Content of a single tag from a Tags block.

Field Summary

Fields
Modifier and Type	Field and Description
`protected int`	`bpp` Number of bytes per pixel.
`protected int[]`	`channelColors`
`protected Set<Integer>`	`channelIndices`
`protected Hashtable<Integer,String>`	`channelName`
`protected int`	`cIndex`
`protected int`	`colCount`
`protected int[][]`	`coordinates`
`protected Hashtable<Integer,Double>`	`detectorGain`
`protected Hashtable<Integer,Double>`	`detectorOffset`
`protected Hashtable<Integer,PositiveInteger>`	`emWavelength`
`protected Hashtable<Integer,String>`	`exposureTime`
`protected Hashtable<Integer,PositiveInteger>`	`exWavelength`
`protected String`	`imageDescription`
`protected String[]`	`imageFiles`
`protected boolean`	`isJPEG`
`protected boolean`	`isZlib`
`protected int`	`lastPlane`
`ArrayList<loci.formats.in.BaseZeissReader.Layer>`	`layers`
`protected int`	`nextChName`
`protected int`	`nextEmWave`
`protected int`	`nextExWave`
`protected int[]`	`offsets`
`protected Double`	`physicalSizeX`
`protected Double`	`physicalSizeY`
`protected Double`	`physicalSizeZ`
`protected int`	`rawCount`
`protected int`	`realHeight`
`protected int`	`realWidth`
`protected Vector<String>`	`roiIDs`
`protected int`	`rowCount`
`protected Hashtable<Integer,Double>`	`stageX`
`protected Hashtable<Integer,Double>`	`stageY`
`protected Vector<String>`	`tagsToParse`
`protected Set<Integer>`	`tileIndices`
`protected Hashtable<Integer,Integer>`	`tiles`
`protected int`	`timepoint`
`protected Set<Integer>`	`timepointIndices`
`protected Hashtable<Integer,String>`	`timestamps`
`protected Set<Integer>`	`zIndices`

Fields inherited from class loci.formats.FormatReader
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler
COMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixes

Fields inherited from interface loci.formats.IFormatReader
CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors
Constructor and Description
`BaseZeissReader(String name, String suffix)` Constructs a new ZeissZVI reader.
`BaseZeissReader(String name, String[] suffixes)` Constructs a new ZeissZVI reader.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`close(boolean fileOnly)` Closes the currently open file.
`protected void`	`countImages()`
`protected void`	`fillMetadataPass1(MetadataStore store)` Read and store basic dimensions in model
`protected void`	`fillMetadataPass2(MetadataStore store)` Read and store basic dimensions in model
`protected void`	`fillMetadataPass3(MetadataStore store)` Read and store basic dimensions in model
`protected void`	`fillMetadataPass4(MetadataStore store)` Read and store basic dimensions in model
`protected void`	`fillMetadataPass5(MetadataStore store)` Read and store basic dimensions in model
`protected void`	`fillMetadataPass6(MetadataStore store)` Read and store basic dimensions in model
`protected void`	`fillMetadataPass7(MetadataStore store)` Store basic dimensions in model
`short[][]`	`get16BitLookupTable()` Gets the 16-bit color lookup table associated with the most recently opened image.
`byte[][]`	`get8BitLookupTable()` Gets the 8-bit color lookup table associated with the most recently opened image.
`int`	`getOptimalTileHeight()` Returns the optimal sub-image height for use with openBytes.
`protected void`	`initFileMain(String id)`
`protected void`	`initVars(String id)`
`protected static int`	`parseColor(byte r, byte g, byte b)`
`protected static int`	`parseInt(String number)` Parse an Integer from a String.
`protected static int`	`parseInt(String number, int defaultnum)` Parse an Integer from a String.
`protected void`	`storeROIs(MetadataStore store)` Store basic dimensions in model

Methods inherited from class loci.formats.FormatReader
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, fileGroupOption, flattenHashtables, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, hasFlattenedResolutions, initFile, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler
checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

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

Methods inherited from interface loci.formats.IFormatHandler
getFormat, getNativeDataType, getSuffixes

Field Detail

bpp
```
protected int bpp
```
Number of bytes per pixel.

imageFiles
```
protected String[] imageFiles
```

offsets
```
protected int[] offsets
```

coordinates
```
protected int[][] coordinates
```

timestamps

protected Hashtable<Integer,String> timestamps

exposureTime

protected Hashtable<Integer,String> exposureTime

cIndex
```
protected int cIndex
```

isJPEG
```
protected boolean isJPEG
```

isZlib
```
protected boolean isZlib
```

realWidth
```
protected int realWidth
```

realHeight
```
protected int realHeight
```

tagsToParse
```
protected Vector<String> tagsToParse
```

nextEmWave
```
protected int nextEmWave
```

nextExWave
```
protected int nextExWave
```

nextChName
```
protected int nextChName
```

stageX

protected Hashtable<Integer,Double> stageX

stageY

protected Hashtable<Integer,Double> stageY

timepoint
```
protected int timepoint
```

channelColors
```
protected int[] channelColors
```

lastPlane
```
protected int lastPlane
```

tiles

protected Hashtable<Integer,Integer> tiles

detectorGain

protected Hashtable<Integer,Double> detectorGain

detectorOffset

protected Hashtable<Integer,Double> detectorOffset

emWavelength

protected Hashtable<Integer,PositiveInteger> emWavelength

exWavelength

protected Hashtable<Integer,PositiveInteger> exWavelength

channelName

protected Hashtable<Integer,String> channelName

physicalSizeX
```
protected Double physicalSizeX
```

physicalSizeY
```
protected Double physicalSizeY
```

physicalSizeZ
```
protected Double physicalSizeZ
```

rowCount
```
protected int rowCount
```

colCount
```
protected int colCount
```

rawCount
```
protected int rawCount
```

imageDescription
```
protected String imageDescription
```

channelIndices
```
protected Set<Integer> channelIndices
```

zIndices
```
protected Set<Integer> zIndices
```

timepointIndices

protected Set<Integer> timepointIndices

tileIndices
```
protected Set<Integer> tileIndices
```

roiIDs
```
protected Vector<String> roiIDs
```

layers

public ArrayList<loci.formats.in.BaseZeissReader.Layer> layers

Constructor Detail

BaseZeissReader

public BaseZeissReader(String name,
               String suffix)

Constructs a new ZeissZVI reader.

BaseZeissReader

public BaseZeissReader(String name,
               String[] suffixes)

Constructs a new ZeissZVI reader.

Method Detail
- initFileMain
```
protected void initFileMain(String id)
                     throws FormatException,
                            IOException
```
  Throws:
  
  FormatException
  
  IOException
- initVars
```
protected void initVars(String id)
                 throws FormatException,
                        IOException
```
  Throws:
  
  FormatException
  
  IOException
- countImages
```
protected void countImages()
```
- fillMetadataPass1
```
protected void fillMetadataPass1(MetadataStore store)
                          throws FormatException,
                                 IOException
```
  Read and store basic dimensions in model
  
  Parameters:
  store -
  
  Throws:
  
  FormatException
  
  IOException
- fillMetadataPass2
```
protected void fillMetadataPass2(MetadataStore store)
                          throws FormatException,
                                 IOException
```
  Read and store basic dimensions in model
  
  Parameters:
  store -
  
  Throws:
  
  FormatException
  
  IOException
- fillMetadataPass3
```
protected void fillMetadataPass3(MetadataStore store)
                          throws FormatException,
                                 IOException
```
  Read and store basic dimensions in model
  
  Parameters:
  store -
  
  Throws:
  
  FormatException
  
  IOException
- fillMetadataPass4
```
protected void fillMetadataPass4(MetadataStore store)
                          throws FormatException,
                                 IOException
```
  Read and store basic dimensions in model
  
  Parameters:
  store -
  
  Throws:
  
  FormatException
  
  IOException
- fillMetadataPass5
```
protected void fillMetadataPass5(MetadataStore store)
                          throws FormatException,
                                 IOException
```
  Read and store basic dimensions in model
  
  Parameters:
  store -
  
  Throws:
  
  FormatException
  
  IOException
- fillMetadataPass6
```
protected void fillMetadataPass6(MetadataStore store)
                          throws FormatException,
                                 IOException
```
  Read and store basic dimensions in model
  
  Parameters:
  store -
  
  Throws:
  
  FormatException
  
  IOException
- fillMetadataPass7
```
protected void fillMetadataPass7(MetadataStore store)
                          throws FormatException,
                                 IOException
```
  Store basic dimensions in model
  
  Parameters:
  store -
  
  Throws:
  
  FormatException
  
  IOException
- getOptimalTileHeight
```
public int getOptimalTileHeight()
```
  Description copied from interface: IFormatReader
  
  Returns the optimal sub-image height for use with openBytes.
  
  Specified by:
  
  getOptimalTileHeight in interface IFormatReader
  
  Overrides:
  
  getOptimalTileHeight in class FormatReader
- storeROIs
```
protected void storeROIs(MetadataStore store)
                  throws FormatException,
                         IOException
```
  Store basic dimensions in model
  
  Parameters:
  store -
  
  Throws:
  
  FormatException
  
  IOException
- get8BitLookupTable
```
public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   IOException
```
  Description copied from interface: IFormatReader
  
  Gets the 8-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT8 or FormatTools.UINT8, this method will return null.
  
  Specified by:
  
  get8BitLookupTable in interface IFormatReader
  
  Overrides:
  
  get8BitLookupTable in class FormatReader
  
  Throws:
  
  FormatException
  
  IOException
- get16BitLookupTable
```
public short[][] get16BitLookupTable()
                              throws FormatException,
                                     IOException
```
  Description copied from interface: IFormatReader
  
  Gets the 16-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT16 or FormatTools.UINT16, this method will return null.
  
  Specified by:
  
  get16BitLookupTable in interface IFormatReader
  
  Overrides:
  
  get16BitLookupTable in class FormatReader
  
  Throws:
  
  FormatException
  
  IOException
- close
```
public void close(boolean fileOnly)
           throws IOException
```
  Description copied from interface: IFormatReader
  
  Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().
  
  Specified by:
  
  close in interface IFormatReader
  
  Overrides:
  
  close in class FormatReader
  
  Throws:
  
  IOException
- parseInt
```
protected static int parseInt(String number)
```
  Parse an Integer from a String.
  
  Parameters:
  number - the number to parse
  
  Returns:
  an Integer. 0 if number was null.
- parseInt
```
protected static int parseInt(String number,
           int defaultnum)
```
  Parse an Integer from a String.
  
  Parameters:
  number - the number to parse
  defaultnum - the number to return if number is null or empty
  
  Returns:
  an Integer. 0 if number was null.
- parseColor
```
protected static int parseColor(byte r,
             byte g,
             byte b)
```

Class BaseZeissReader

Nested Class Summary

Field Summary

Fields inherited from class loci.formats.FormatReader

Fields inherited from class loci.formats.FormatHandler

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.FormatReader

Methods inherited from class loci.formats.FormatHandler

Methods inherited from class java.lang.Object

Methods inherited from interface loci.formats.IFormatHandler

Field Detail

bpp

imageFiles

offsets

coordinates

timestamps

exposureTime

cIndex

isJPEG

isZlib

realWidth

realHeight

tagsToParse

nextEmWave

nextExWave

nextChName

stageX

stageY

timepoint

channelColors

lastPlane

tiles

detectorGain

detectorOffset

emWavelength

exWavelength

channelName

physicalSizeX

physicalSizeY

physicalSizeZ

rowCount

colCount

rawCount

imageDescription

channelIndices

zIndices

timepointIndices

tileIndices

roiIDs

layers

Constructor Detail

BaseZeissReader

BaseZeissReader

Method Detail

initFileMain

initVars

countImages

fillMetadataPass1

fillMetadataPass2

fillMetadataPass3

fillMetadataPass4

fillMetadataPass5

fillMetadataPass6

fillMetadataPass7

getOptimalTileHeight

storeROIs

get8BitLookupTable

get16BitLookupTable

close

parseInt

parseInt

parseColor