loci.formats.in

Class TiffReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.MinimalTiffReader

loci.formats.in.BaseTiffReader

loci.formats.in.TiffReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class TiffReader
extends BaseTiffReader

TiffReader is the file format reader for regular TIFF files, not of any specific TIFF variant.

Author:

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

Field Summary

Fields

Modifier and Type	Field and Description
private String	calibrationUnit
static String[]	COMPANION_SUFFIXES
private String	companionFile
private String	description
static int	IMAGEJ_TAG
private static org.slf4j.Logger	LOGGER Logger for this class.
private Double	physicalSizeZ
static String[]	TIFF_SUFFIXES
private ome.units.quantity.Time	timeIncrement
private Integer	xOrigin
private Integer	yOrigin

Fields inherited from class loci.formats.in.BaseTiffReader

DATE_FORMATS

Fields inherited from class loci.formats.in.MinimalTiffReader

equalStrips, ifds, lastPlane, noSubresolutions, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, 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
TiffReader() Constructs a new Tiff reader.

Method Summary

Modifier and Type	Method and Description
private boolean	checkCommentImageJ(String comment)
private boolean	checkCommentMetamorph(String comment)
void	close(boolean fileOnly) Closes the currently open file.
String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
protected void	initMetadataStore() Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself.
protected void	initStandardMetadata() Parses standard metadata.
private void	parseCommentGeneric(String comment)
private void	parseCommentImageJ(String comment)
private void	parseCommentMetamorph(String comment)
private double	parseDouble(String s)
private int	parseInt(String s)
private void	populateMetadataStoreImageJ(MetadataStore store) Checks the original metadata table for ImageJ-specific information to propagate into the metadata store.

Methods inherited from class loci.formats.in.BaseTiffReader

getExifTagName, getImageCreationDate, initFile, initMetadata, put, put, put, put, put, put, put, put, put, put, putInt, putString

Methods inherited from class loci.formats.in.MinimalTiffReader

get16BitLookupTable, get8BitLookupTable, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, initTiffParser, isThisType, openBytes, openThumbBytes, reopenFile, setResolutionLevel

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, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, 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, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, 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, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

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

Field Detail

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

TIFF_SUFFIXES

public static final String[] TIFF_SUFFIXES

COMPANION_SUFFIXES

public static final String[] COMPANION_SUFFIXES

IMAGEJ_TAG

public static final int IMAGEJ_TAG

See Also:

Constant Field Values

companionFile

private String companionFile

description

private String description

calibrationUnit

private String calibrationUnit

physicalSizeZ

private Double physicalSizeZ

timeIncrement

private ome.units.quantity.Time timeIncrement

xOrigin

private Integer xOrigin

yOrigin

private Integer yOrigin

Constructor Detail

TiffReader

public TiffReader()

Constructs a new Tiff reader.

Method Detail

getSeriesUsedFiles

public 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.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

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 MinimalTiffReader

Throws:

IOException

initStandardMetadata

protected void initStandardMetadata()
                             throws FormatException,
                                    IOException

Description copied from class: BaseTiffReader

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.

Overrides:

initStandardMetadata in class BaseTiffReader

Throws:

FormatException

IOException

initMetadataStore

protected void initMetadataStore()
                          throws FormatException

Description copied from class: BaseTiffReader

Populates the metadata store using the data parsed in BaseTiffReader.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.

Overrides:

initMetadataStore in class BaseTiffReader

Throws:

FormatException

checkCommentImageJ

private boolean checkCommentImageJ(String comment)

checkCommentMetamorph

private boolean checkCommentMetamorph(String comment)

parseCommentImageJ

private void parseCommentImageJ(String comment)
                         throws FormatException,
                                IOException

Throws:

FormatException

IOException

populateMetadataStoreImageJ

private void populateMetadataStoreImageJ(MetadataStore store)

Checks the original metadata table for ImageJ-specific information to propagate into the metadata store.

parseCommentMetamorph

private void parseCommentMetamorph(String comment)

parseCommentGeneric

private void parseCommentGeneric(String comment)

parseInt

private int parseInt(String s)

parseDouble

private double parseDouble(String s)