LIFReader (Bio-Formats API)

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

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler
```
public class LIFReader
extends FormatReader
```
LIFReader is the file format reader for Leica LIF files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

(package private) class LIFReader.ROI

Nested Classes
Modifier and Type	Class and Description
`(package private) class`	`LIFReader.ROI`

Field Summary

Fields
Modifier and Type	Field and Description
`private double[]`	`acquiredDate`
`private java.util.List[]`	`activeDetector`
`private boolean`	`alternateCenter`
`private static com.google.common.collect.ImmutableMap<java.lang.String,java.lang.Integer>`	`CHANNEL_PRIORITIES`
`private java.lang.String[][]`	`channelNames`
`private java.lang.String[]`	`corrections`
`private java.util.List[]`	`cutIns`
`private java.util.List[]`	`cutOuts`
`private java.lang.String[]`	`descriptions`
`private java.util.HashMap[]`	`detectorIndexes`
`private java.util.List[]`	`detectorModels`
`private java.lang.Double[][]`	`detectorOffsets`
`private static java.lang.String`	`ENCODING` The encoding used in this file.
`private long`	`endPointer`
`private java.lang.Double[][]`	`expTimes`
`private java.lang.Double[][]`	`exWaves`
`private java.util.List<ome.units.quantity.Length>`	`fieldPosX`
`private java.util.List<ome.units.quantity.Length>`	`fieldPosY`
`private java.util.List[]`	`filterModels`
`private boolean[]`	`flipX`
`private boolean[]`	`flipY`
`private java.lang.Double[][]`	`gains`
`private java.lang.String[]`	`imageNames`
`private LIFReader.ROI[][]`	`imageROIs`
`private java.lang.String[]`	`immersions`
`private java.util.List[]`	`laserActive`
`private java.util.List[]`	`laserFrap`
`private java.util.List[]`	`laserIntensity`
`private java.util.List[]`	`laserWavelength`
`private int`	`lastChannel`
`private java.lang.Double[]`	`lensNA`
`static byte`	`LIF_MAGIC_BYTE`
`static byte`	`LIF_MEMORY_BYTE`
`private static java.lang.String`	`LOGO_FILE`
`private java.util.List<java.lang.String>`	`lutNames`
`private java.lang.Double[]`	`magnification`
`private static long`	`METER_MULTIPLY`
`private java.lang.String[]`	`microscopeModels`
`private java.lang.String[]`	`objectiveModels`
`private java.util.List<java.lang.Long>`	`offsets` Offsets to memory blocks, paired with their corresponding description.
`static boolean`	`OLD_PHYSICAL_SIZE_DEFAULT`
`static java.lang.String`	`OLD_PHYSICAL_SIZE_KEY`
`private java.util.List<java.lang.Double>`	`physicalSizeXs`
`private java.util.List<java.lang.Double>`	`physicalSizeYs`
`private java.lang.Double[]`	`pinholes`
`private ome.units.quantity.Length[]`	`posX`
`private ome.units.quantity.Length[]`	`posY`
`private ome.units.quantity.Length[]`	`posZ`
`private int[][]`	`realChannel`
`private java.lang.Double[]`	`refractiveIndex`
`private java.lang.String[]`	`serialNumber`
`private static java.lang.String`	`STYLESHEET_FILE`
`private boolean[]`	`swapXY`
`private long[]`	`tileBytesInc`
`private int[]`	`tileCount`
`private java.lang.Double[][]`	`timestamps`
`private java.lang.Double[]`	`tSteps`
`private java.lang.Double[]`	`zooms`
`private java.lang.Double[]`	`zSteps`

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

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

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

Constructor Summary

Constructors
Constructor and Description

LIFReader()
Constructs a new Leica LIF reader.

Constructors
Constructor and Description
`LIFReader()` Constructs a new Leica LIF reader.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private void`	`addUserCommentMeta(org.w3c.dom.Element imageNode, int image)`
`private ome.units.quantity.Length`	`checkFlip(boolean flip, ome.units.quantity.Length pos)`
`void`	`close(boolean fileOnly)` Closes the currently open file.
`private static com.google.common.collect.ImmutableMap<java.lang.String,java.lang.Integer>`	`createChannelPriorities()`
`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.
`protected java.util.ArrayList<java.lang.String>`	`getAvailableOptions()` Returns the list of available metadata options.
`private ome.xml.model.primitives.Color`	`getChannelColor(int colorCode)`
`private org.w3c.dom.NodeList`	`getChannelDescriptionNodes(org.w3c.dom.Element root)`
`private int`	`getChannelIndex(org.w3c.dom.Element filterSetting)`
`private org.w3c.dom.NodeList`	`getDimensionDescriptionNodes(org.w3c.dom.Element root)`
`private org.w3c.dom.Element`	`getImageDescription(org.w3c.dom.Element root)`
`private org.w3c.dom.Element`	`getMetadataRoot(java.lang.String xml)`
`private org.w3c.dom.NodeList`	`getNodes(org.w3c.dom.Element root, java.lang.String nodeName)`
`int`	`getOptimalTileHeight()` Returns the optimal sub-image height for use with openBytes.
`java.lang.String[]`	`getSeriesUsedFiles(boolean noPixels)` Returns an array of filenames needed to open the current series.
`private int`	`getTileIndex(int coreIndex)`
`protected void`	`initFile(java.lang.String id)` Initializes the given file (parsing header information, etc.).
`private void`	`initMetadata(java.lang.String xml)` Parses a string of XML and puts the values in a Hashtable.
`boolean`	`isThisType(loci.common.RandomAccessInputStream stream)` Checks if the given stream is a valid stream for this file format.
`byte[]`	`openBytes(int no, byte[] buf, int x, int y, int w, int h)` Obtains a sub-image of the specified image plane into a pre-allocated byte array.
`private void`	`populateOriginalMetadata(org.w3c.dom.Element root, java.util.Deque<java.lang.String> nameStack, int[] key_index, int jj)`
`private void`	`seekStartOfPlane(int no, long dataOffset, long planeSize)`
`private void`	`translateAttachmentNodes(org.w3c.dom.Element imageNode, int image)`
`private void`	`translateDetectors(org.w3c.dom.Element imageNode, int image)`
`private void`	`translateFilterSettings(org.w3c.dom.Element imageNode, int image)`
`private void`	`translateImageNames(org.w3c.dom.Element imageNode, int image)`
`private void`	`translateImageNodes(org.w3c.dom.Element imageNode, int i)`
`private void`	`translateLaserLines(org.w3c.dom.Element imageNode, int image)`
`private void`	`translateMetadata(org.w3c.dom.Element root)`
`private void`	`translateROIs(org.w3c.dom.Element imageNode, int image)`
`private void`	`translateScannerSettings(org.w3c.dom.Element imageNode, int image)`
`private void`	`translateSingleROIs(org.w3c.dom.Element imageNode, int image)`
`private double`	`translateSingleTimestamp(org.w3c.dom.Element timestamp)`
`private double`	`translateSingleTimestamp(java.lang.String timestamp)`
`private void`	`translateTimestamps(org.w3c.dom.Element imageNode, int image)`
`boolean`	`useOldPhysicalSizeCalculation()`

Methods inherited from class loci.formats.FormatReader
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, fileGroupOption, flattenHashtables, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, 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, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists

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

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

Methods inherited from interface loci.formats.IMetadataConfigurable
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from interface loci.formats.ICompressedTileReader
getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Field Detail

OLD_PHYSICAL_SIZE_KEY

public static final java.lang.String OLD_PHYSICAL_SIZE_KEY

See Also:: Constant Field Values

OLD_PHYSICAL_SIZE_DEFAULT
```
public static final boolean OLD_PHYSICAL_SIZE_DEFAULT
```
See Also:

Constant Field Values

LIF_MAGIC_BYTE
```
public static final byte LIF_MAGIC_BYTE
```
See Also:

Constant Field Values

LIF_MEMORY_BYTE
```
public static final byte LIF_MEMORY_BYTE
```
See Also:

Constant Field Values

ENCODING
```
private static final java.lang.String ENCODING
```
The encoding used in this file.

See Also:

Constant Field Values

LOGO_FILE

private static final java.lang.String LOGO_FILE

See Also:: Constant Field Values

STYLESHEET_FILE

private static final java.lang.String STYLESHEET_FILE

See Also:: Constant Field Values

CHANNEL_PRIORITIES

private static final com.google.common.collect.ImmutableMap<java.lang.String,java.lang.Integer> CHANNEL_PRIORITIES

METER_MULTIPLY
```
private static final long METER_MULTIPLY
```
See Also:

Constant Field Values

offsets
```
private java.util.List<java.lang.Long> offsets
```
Offsets to memory blocks, paired with their corresponding description.

realChannel
```
private int[][] realChannel
```

lastChannel
```
private int lastChannel
```

lutNames

private java.util.List<java.lang.String> lutNames

physicalSizeXs

private java.util.List<java.lang.Double> physicalSizeXs

physicalSizeYs

private java.util.List<java.lang.Double> physicalSizeYs

fieldPosX

private java.util.List<ome.units.quantity.Length> fieldPosX

fieldPosY

private java.util.List<ome.units.quantity.Length> fieldPosY

descriptions

private java.lang.String[] descriptions

microscopeModels

private java.lang.String[] microscopeModels

serialNumber

private java.lang.String[] serialNumber

pinholes
```
private java.lang.Double[] pinholes
```

zooms
```
private java.lang.Double[] zooms
```

zSteps
```
private java.lang.Double[] zSteps
```

tSteps
```
private java.lang.Double[] tSteps
```

lensNA
```
private java.lang.Double[] lensNA
```

flipX
```
private boolean[] flipX
```

flipY
```
private boolean[] flipY
```

swapXY
```
private boolean[] swapXY
```

expTimes
```
private java.lang.Double[][] expTimes
```

gains
```
private java.lang.Double[][] gains
```

detectorOffsets

private java.lang.Double[][] detectorOffsets

channelNames

private java.lang.String[][] channelNames

detectorModels

private java.util.List[] detectorModels

exWaves
```
private java.lang.Double[][] exWaves
```

activeDetector

private java.util.List[] activeDetector

detectorIndexes

private java.util.HashMap[] detectorIndexes

immersions
```
private java.lang.String[] immersions
```

corrections
```
private java.lang.String[] corrections
```

objectiveModels

private java.lang.String[] objectiveModels

magnification

private java.lang.Double[] magnification

posX

private ome.units.quantity.Length[] posX

posY

private ome.units.quantity.Length[] posY

posZ

private ome.units.quantity.Length[] posZ

refractiveIndex

private java.lang.Double[] refractiveIndex

cutIns
```
private java.util.List[] cutIns
```

cutOuts
```
private java.util.List[] cutOuts
```

filterModels
```
private java.util.List[] filterModels
```

timestamps

private java.lang.Double[][] timestamps

laserWavelength

private java.util.List[] laserWavelength

laserIntensity

private java.util.List[] laserIntensity

laserActive
```
private java.util.List[] laserActive
```

laserFrap
```
private java.util.List[] laserFrap
```

imageROIs
```
private LIFReader.ROI[][] imageROIs
```

alternateCenter
```
private boolean alternateCenter
```

imageNames
```
private java.lang.String[] imageNames
```

acquiredDate
```
private double[] acquiredDate
```

tileCount
```
private int[] tileCount
```

tileBytesInc
```
private long[] tileBytesInc
```

endPointer
```
private long endPointer
```

Constructor Detail
- LIFReader
```
public LIFReader()
```
  Constructs a new Leica LIF reader.

Method Detail
- createChannelPriorities
```
private static com.google.common.collect.ImmutableMap<java.lang.String,java.lang.Integer> createChannelPriorities()
```
- useOldPhysicalSizeCalculation
```
public boolean useOldPhysicalSizeCalculation()
```
- 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
- isThisType
```
public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws java.io.IOException
```
  Description copied from interface: IFormatReader
  
  Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.
  
  Specified by:
  
  isThisType in interface IFormatReader
  
  Overrides:
  
  isThisType in class FormatReader
  
  Parameters:
  
  stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.
  
  Returns:
  
  true if the file represented by the stream can be read by this reader; false otherwise.
  
  Throws:
  
  java.io.IOException
- get8BitLookupTable
```
public byte[][] get8BitLookupTable()
```
  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
- get16BitLookupTable
```
public short[][] get16BitLookupTable()
```
  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
- openBytes
```
public byte[] openBytes(int no,
                        byte[] buf,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        java.io.IOException
```
  Description copied from interface: IFormatReader
  
  Obtains a sub-image of the specified image plane into a pre-allocated byte array.
  
  Specified by:
  
  openBytes in interface IFormatReader
  
  Specified by:
  
  openBytes in class FormatReader
  
  Parameters:
  
  no - the plane index within the current series.
  
  buf - a pre-allocated buffer.
  
  x - X coordinate of the upper-left corner of the sub-image
  
  y - Y coordinate of the upper-left corner of the sub-image
  
  w - width of the sub-image
  
  h - height of the sub-image
  
  Returns:
  
  the pre-allocated buffer buf for convenience.
  
  Throws:
  
  FormatException - if there was a problem parsing the metadata of the file.
  
  java.io.IOException - if there was a problem reading the file.
  
  See Also:
  
  IFormatReader.openBytes(int, byte[], int, int, int, int)
- seekStartOfPlane
```
private void seekStartOfPlane(int no,
                              long dataOffset,
                              long planeSize)
                       throws java.io.IOException
```
  Throws:
  
  java.io.IOException
- getSeriesUsedFiles
```
public java.lang.String[] getSeriesUsedFiles(boolean noPixels)
```
  Description copied from interface: IFormatReader
  
  Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.
  
  Specified by:
  
  getSeriesUsedFiles in interface IFormatReader
  
  Overrides:
  
  getSeriesUsedFiles in class FormatReader
- close
```
public void close(boolean fileOnly)
           throws java.io.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:
  
  java.io.IOException
- getAvailableOptions
```
protected java.util.ArrayList<java.lang.String> getAvailableOptions()
```
  Description copied from class: FormatReader
  
  Returns the list of available metadata options.
  
  Overrides:
  
  getAvailableOptions in class FormatReader
- initFile
```
protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.IOException
```
  Description copied from class: FormatReader
  
  Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.
  
  Overrides:
  
  initFile in class FormatReader
  
  Throws:
  
  FormatException - if a parsing error occurs processing the file.
  
  java.io.IOException - if an I/O error occurs processing the file
- initMetadata
```
private void initMetadata(java.lang.String xml)
                   throws FormatException,
                          java.io.IOException
```
  Parses a string of XML and puts the values in a Hashtable.
  
  Throws:
  
  FormatException
  
  java.io.IOException
- checkFlip
```
private ome.units.quantity.Length checkFlip(boolean flip,
                                            ome.units.quantity.Length pos)
```
- getMetadataRoot
```
private org.w3c.dom.Element getMetadataRoot(java.lang.String xml)
                                     throws FormatException,
                                            java.io.IOException
```
  Throws:
  
  FormatException
  
  java.io.IOException
- translateMetadata
```
private void translateMetadata(org.w3c.dom.Element root)
                        throws FormatException
```
  Throws:
  
  FormatException
- populateOriginalMetadata
```
private void populateOriginalMetadata(org.w3c.dom.Element root,
                                      java.util.Deque<java.lang.String> nameStack,
                                      int[] key_index,
                                      int jj)
```
- translateImageNames
```
private void translateImageNames(org.w3c.dom.Element imageNode,
                                 int image)
```
- translateDetectors
```
private void translateDetectors(org.w3c.dom.Element imageNode,
                                int image)
                         throws FormatException
```
  Throws:
  
  FormatException
- translateROIs
```
private void translateROIs(org.w3c.dom.Element imageNode,
                           int image)
                    throws FormatException
```
  Throws:
  
  FormatException
- translateSingleROIs
```
private void translateSingleROIs(org.w3c.dom.Element imageNode,
                                 int image)
                          throws FormatException
```
  Throws:
  
  FormatException
- translateLaserLines
```
private void translateLaserLines(org.w3c.dom.Element imageNode,
                                 int image)
                          throws FormatException
```
  Throws:
  
  FormatException
- translateTimestamps
```
private void translateTimestamps(org.w3c.dom.Element imageNode,
                                 int image)
                          throws FormatException
```
  Throws:
  
  FormatException
- translateSingleTimestamp
```
private double translateSingleTimestamp(java.lang.String timestamp)
```
- translateSingleTimestamp
```
private double translateSingleTimestamp(org.w3c.dom.Element timestamp)
```
- translateFilterSettings
```
private void translateFilterSettings(org.w3c.dom.Element imageNode,
                                     int image)
                              throws FormatException
```
  Throws:
  
  FormatException
- translateScannerSettings
```
private void translateScannerSettings(org.w3c.dom.Element imageNode,
                                      int image)
                               throws FormatException
```
  Throws:
  
  FormatException
- translateAttachmentNodes
```
private void translateAttachmentNodes(org.w3c.dom.Element imageNode,
                                      int image)
                               throws FormatException
```
  Throws:
  
  FormatException
- addUserCommentMeta
```
private void addUserCommentMeta(org.w3c.dom.Element imageNode,
                                int image)
                         throws FormatException
```
  Throws:
  
  FormatException
- translateImageNodes
```
private void translateImageNodes(org.w3c.dom.Element imageNode,
                                 int i)
                          throws FormatException
```
  Throws:
  
  FormatException
- getNodes
```
private org.w3c.dom.NodeList getNodes(org.w3c.dom.Element root,
                                      java.lang.String nodeName)
```
- getImageDescription
```
private org.w3c.dom.Element getImageDescription(org.w3c.dom.Element root)
```
- getChannelDescriptionNodes
```
private org.w3c.dom.NodeList getChannelDescriptionNodes(org.w3c.dom.Element root)
```
- getDimensionDescriptionNodes
```
private org.w3c.dom.NodeList getDimensionDescriptionNodes(org.w3c.dom.Element root)
```
- getChannelIndex
```
private int getChannelIndex(org.w3c.dom.Element filterSetting)
```
- getChannelColor
```
private ome.xml.model.primitives.Color getChannelColor(int colorCode)
```
- getTileIndex
```
private int getTileIndex(int coreIndex)
```

Class LIFReader

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

Methods inherited from interface loci.formats.IMetadataConfigurable

Methods inherited from interface loci.formats.ICompressedTileReader

Field Detail

OLD_PHYSICAL_SIZE_KEY

OLD_PHYSICAL_SIZE_DEFAULT

LIF_MAGIC_BYTE

LIF_MEMORY_BYTE

ENCODING

LOGO_FILE

STYLESHEET_FILE

CHANNEL_PRIORITIES

METER_MULTIPLY

offsets

realChannel

lastChannel

lutNames

physicalSizeXs

physicalSizeYs

fieldPosX

fieldPosY

descriptions

microscopeModels

serialNumber

pinholes

zooms

zSteps

tSteps

lensNA

flipX

flipY

swapXY

expTimes

gains

detectorOffsets

channelNames

detectorModels

exWaves

activeDetector

detectorIndexes

immersions

corrections

objectiveModels

magnification

posX

posY

posZ

refractiveIndex

cutIns

cutOuts

filterModels

timestamps

laserWavelength

laserIntensity

laserActive

laserFrap

imageROIs

alternateCenter

imageNames

acquiredDate

tileCount

tileBytesInc

endPointer

Constructor Detail

LIFReader

Method Detail

createChannelPriorities

useOldPhysicalSizeCalculation

getOptimalTileHeight