loci.formats.in

Class BaseTiffReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.MinimalTiffReader

loci.formats.in.BaseTiffReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

Direct Known Subclasses:

DNGReader, FEITiffReader, FluoviewReader, GelReader, ImaconReader, ImarisTiffReader, ImprovisionTiffReader, IonpathMIBITiffReader, JPKReader, LeicaSCNReader, LEOReader, MetamorphReader, MetamorphTiffReader, NDPIReader, NikonElementsTiffReader, NikonReader, NikonTiffReader, PhotoshopTiffReader, PyramidTiffReader, SEQReader, SimplePCITiffReader, SISReader, SlidebookTiffReader, SVSReader, TiffReader, TrestleReader, VectraReader, VentanaReader

public abstract class BaseTiffReader
extends MinimalTiffReader

BaseTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.

Author:

Curtis Rueden ctrueden at wisc.edu, Melissa Linkert melissa at glencoesoftware.com

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String[]	DATE_FORMATS
protected static org.slf4j.Logger	LOGGER Logger for this class.

Fields inherited from class loci.formats.in.MinimalTiffReader

canSeparateSeries, equalStrips, ifds, lastPlane, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit

Fields inherited from class loci.formats.SubResolutionFormatReader

core

Fields inherited from class loci.formats.FormatReader

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, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
BaseTiffReader(java.lang.String name, java.lang.String suffix) Constructs a new BaseTiffReader.
BaseTiffReader(java.lang.String name, java.lang.String[] suffixes) Constructs a new BaseTiffReader.

Method Summary

Modifier and Type	Method and Description
static java.lang.String	getExifTagName(int tag)
protected java.lang.String	getImageCreationDate() Retrieves the image creation date.
private java.lang.String	getResolutionUnitFromComment(IFD ifd) Extracts the resolution unit symbol from the comment field
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
protected void	initMetadata() Populates the metadata hashtable and metadata store.
protected void	initMetadataStore() Populates the metadata store using the data parsed in initStandardMetadata() along with some further parsing done in the method itself.
protected void	initStandardMetadata() Parses standard metadata.
protected void	put(java.lang.String key, boolean value)
protected void	put(java.lang.String key, byte value)
protected void	put(java.lang.String key, char value)
protected void	put(java.lang.String key, double value)
protected void	put(java.lang.String key, float value)
protected void	put(java.lang.String key, IFD ifd, int tag)
protected void	put(java.lang.String key, int value)
protected void	put(java.lang.String key, long value)
protected void	put(java.lang.String key, java.lang.Object value)
protected void	put(java.lang.String key, short value)
protected void	putDouble(java.lang.String key, IFD ifd, int tag)
protected void	putInt(java.lang.String key, IFD ifd, int tag)
protected void	putString(java.lang.String key, IFD ifd, int tag)

Methods inherited from class loci.formats.in.MinimalTiffReader

close, copyTile, get16BitLookupTable, get8BitLookupTable, getCompressedByteCount, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, getTileIndex, initTiffParser, isThisType, openBytes, openThumbBytes, reopenFile, setResolutionLevel

Methods inherited from class loci.formats.SubResolutionFormatReader

coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution, setSeries

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, fileGroupOption, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, 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, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, 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, readPlane, readPlane, readPlane, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, 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

LOGGER

protected static final org.slf4j.Logger LOGGER

Logger for this class.

DATE_FORMATS

public static final java.lang.String[] DATE_FORMATS

Constructor Detail

BaseTiffReader

public BaseTiffReader(java.lang.String name,
                      java.lang.String suffix)

Constructs a new BaseTiffReader.

BaseTiffReader

public BaseTiffReader(java.lang.String name,
                      java.lang.String[] suffixes)

Constructs a new BaseTiffReader.

Method Detail

initMetadata

protected void initMetadata()
                     throws FormatException,
                            java.io.IOException

Populates the metadata hashtable and metadata store.

Throws:

FormatException

java.io.IOException

initStandardMetadata

protected void initStandardMetadata()
                             throws FormatException,
                                    java.io.IOException

Parses standard metadata. NOTE: Absolutely no calls to the metadata store should be made in this method or methods that override this method. Data will be overwritten if you do so.

Throws:

FormatException

java.io.IOException

initMetadataStore

protected void initMetadataStore()
                          throws FormatException

Populates the metadata store using the data parsed in initStandardMetadata() along with some further parsing done in the method itself. All calls to the active MetadataStore should be made in this method and only in this method. This is especially important for sub-classes that override the getters for pixel set array size, etc.

Throws:

FormatException

getResolutionUnitFromComment

private java.lang.String getResolutionUnitFromComment(IFD ifd)

Extracts the resolution unit symbol from the comment field

Parameters:

ifd - The IFD

Returns:

The unit symbol or null if the information is not available

getImageCreationDate

protected java.lang.String getImageCreationDate()

Retrieves the image creation date.

Returns:

the image creation date.

put

protected void put(java.lang.String key,
                   java.lang.Object value)

put

protected void put(java.lang.String key,
                   int value)

put

protected void put(java.lang.String key,
                   boolean value)

put

protected void put(java.lang.String key,
                   byte value)

put

protected void put(java.lang.String key,
                   char value)

put

protected void put(java.lang.String key,
                   double value)

put

protected void put(java.lang.String key,
                   float value)

put

protected void put(java.lang.String key,
                   long value)

put

protected void put(java.lang.String key,
                   short value)

put

protected void put(java.lang.String key,
                   IFD ifd,
                   int tag)

putInt

protected void putInt(java.lang.String key,
                      IFD ifd,
                      int tag)

putString

protected void putString(java.lang.String key,
                         IFD ifd,
                         int tag)

putDouble

protected void putDouble(java.lang.String key,
                         IFD ifd,
                         int tag)

initFile

protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.IOException

Description copied from class: SubResolutionFormatReader

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 MinimalTiffReader

Throws:

FormatException - if a parsing error occurs processing the file.

java.io.IOException - if an I/O error occurs processing the file

getExifTagName

public static java.lang.String getExifTagName(int tag)