loci.formats.in.LeicaMicrosystemsMetadata

Class LMSFileReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

All Implemented Interfaces:

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

Direct Known Subclasses:

LOFReader, MultipleImagesReader, XLEFReader

public abstract class LMSFileReader
extends FormatReader

This class can be extended by readers of Leica Microsystems file formats that include LASX generated XML (e.g. XLEF, LOF)

Author:

Melissa Linkert melissa at glencoesoftware.com, Constanze Wendlandt constanze.wendlandt at leica-microsystems.com

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	LMSFileReader.ImageFormat file format in which actual image bytes are stored

Field Summary

Fields

Modifier and Type	Field and Description
LMSXmlDocument	associatedXmlDoc
static org.slf4j.Logger	log
MetadataTempBuffer	metaTemp
static boolean	OLD_PHYSICAL_SIZE_DEFAULT
static java.lang.String	OLD_PHYSICAL_SIZE_KEY

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

Modifier	Constructor and Description
protected	LMSFileReader(java.lang.String format, java.lang.String suffix)

Method Summary

Modifier and Type	Method and Description
void	addSeriesMeta(java.lang.String key, java.lang.Object value) Adds an entry to the metadata table for the current series.
void	addSeriesMetaList(java.lang.String key, java.lang.Object value) Add the given key/value pair to the current series metadata hashtable.
void	close(boolean fileOnly) Closes the currently open file.
static boolean	fileExists(java.lang.String path) Checks if file at path exists
java.util.List<CoreMetadata>	getCore()
abstract LMSFileReader.ImageFormat	getImageFormat() Returns the file format in which actual image bytes are stored
MetadataStore	makeFilterMetadata() Return a properly configured loci.formats.meta.FilterMetadata.
void	setCore(java.util.ArrayList<CoreMetadata> core)
void	translateMetadata(java.util.List<LMSImageXmlDocument> docs) Extracts metadata from a list of Leica image XML Documents and writes them to the reader's CoreMetadata, MetadataTempBuffer and MetadataStore
void	translateMetadata(LMSImageXmlDocument doc)
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, close, coreIndexToSeries, fileGroupOption, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, 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, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, initFile, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, openBytes, 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

log

public static org.slf4j.Logger log

metaTemp

public MetadataTempBuffer metaTemp

associatedXmlDoc

public LMSXmlDocument associatedXmlDoc

Constructor Detail

LMSFileReader

protected LMSFileReader(java.lang.String format,
                        java.lang.String suffix)

Method Detail

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

getImageFormat

public abstract LMSFileReader.ImageFormat getImageFormat()

Returns the file format in which actual image bytes are stored

getCore

public java.util.List<CoreMetadata> getCore()

setCore

public void setCore(java.util.ArrayList<CoreMetadata> core)

useOldPhysicalSizeCalculation

public boolean useOldPhysicalSizeCalculation()

addSeriesMeta

public void addSeriesMeta(java.lang.String key,
                          java.lang.Object value)

Description copied from class: FormatReader

Adds an entry to the metadata table for the current series.

Overrides:

addSeriesMeta in class FormatReader

addSeriesMetaList

public void addSeriesMetaList(java.lang.String key,
                              java.lang.Object value)

Description copied from class: FormatReader

Add the given key/value pair to the current series metadata hashtable. If the key already exists, a list will be stored in the hashtable and the value will be appended to the list.

Overrides:

addSeriesMetaList in class FormatReader

makeFilterMetadata

public MetadataStore makeFilterMetadata()

Description copied from class: FormatReader

Return a properly configured loci.formats.meta.FilterMetadata.

Overrides:

makeFilterMetadata in class FormatReader

translateMetadata

public void translateMetadata(java.util.List<LMSImageXmlDocument> docs)
                       throws FormatException,
                              java.io.IOException

Extracts metadata from a list of Leica image XML Documents and writes them to the reader's CoreMetadata, MetadataTempBuffer and MetadataStore

Parameters:

docs - List of document nodes representing XML documents

Throws:

FormatException

java.io.IOException

translateMetadata

public void translateMetadata(LMSImageXmlDocument doc)
                       throws FormatException,
                              java.io.IOException

Throws:

FormatException

java.io.IOException

fileExists

public static boolean fileExists(java.lang.String path)

Checks if file at path exists

Parameters:

path - whole file path