Package loci.formats.in.LeicaMicrosystemsMetadata

Class MultipleImagesReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

All Implemented Interfaces:

Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class MultipleImagesReader
extends LMSFileReader

MultipleImagesReader presents a number of image files as one image reference

Nested Class Summary

Nested classes/interfaces inherited from class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

LMSFileReader.ImageFormat

Field Summary

Fields inherited from class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

associatedXmlDoc, log, metaTemp, OLD_PHYSICAL_SIZE_DEFAULT, 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, 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	Description
MultipleImagesReader(XlifDocument xlif, int imageIndex)

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
int	getBitsPerPixel()
LMSFileReader.ImageFormat	getImageFormat()	Returns the file format in which actual image bytes are stored
int	getPixelType()
int	getRGBChannelCount()
int	getSizeC()
boolean	isRGB()
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)
void	reopenFile()
void	setCoreMetadata(CoreMetadata cmd)
void	setMetadataTempBuffer(MetadataTempBuffer metaTemp)
void	setSeries(int no)	Sets the field MultipleImagesReader.series.
void	swapDimensions()	Rearranges frame order from ZSTC order (used in XLIFs) to desired CoreMetadata.dimensionOrder

Methods inherited from class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

addSeriesMeta, addSeriesMetaList, fileExists, getCore, makeFilterMetadata, setCore, translateMetadata, translateMetadata, 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, 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, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, 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, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, 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.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Constructor Details

MultipleImagesReader

public MultipleImagesReader(XlifDocument xlif,
 int imageIndex)
                     throws FormatException,
IOException

Throws:

FormatException

IOException

Method Details

openBytes

public byte[] openBytes(int no,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
IOException

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Throws:

FormatException

IOException

setSeries

public void setSeries(int no)

Sets the field MultipleImagesReader.series. Needs to be called before calling MultipleImagesReader.openBytes()

Specified by:

setSeries in interface IFormatReader

Overrides:

setSeries in class FormatReader

getRGBChannelCount

public int getRGBChannelCount()

Specified by:

getRGBChannelCount in interface IFormatReader

Overrides:

getRGBChannelCount in class FormatReader

getBitsPerPixel

public int getBitsPerPixel()

Specified by:

getBitsPerPixel in interface IFormatReader

Overrides:

getBitsPerPixel in class FormatReader

getPixelType

public int getPixelType()

Specified by:

getPixelType in interface IFormatReader

Overrides:

getPixelType in class FormatReader

getSizeC

public int getSizeC()

Specified by:

getSizeC in interface IFormatReader

Overrides:

getSizeC in class FormatReader

isRGB

public boolean isRGB()

Specified by:

isRGB in interface IFormatReader

Overrides:

isRGB in class FormatReader

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface IFormatReader

Overrides:

close in class LMSFileReader

Throws:

IOException

getImageFormat

public LMSFileReader.ImageFormat getImageFormat()

Description copied from class: LMSFileReader

Returns the file format in which actual image bytes are stored

Specified by:

getImageFormat in class LMSFileReader

setMetadataTempBuffer

public void setMetadataTempBuffer(MetadataTempBuffer metaTemp)

setCoreMetadata

public void setCoreMetadata(CoreMetadata cmd)

swapDimensions

public void swapDimensions()
                    throws FormatException

Rearranges frame order from ZSTC order (used in XLIFs) to desired CoreMetadata.dimensionOrder

Throws:

FormatException

reopenFile

public void reopenFile()
                throws IOException

Specified by:

reopenFile in interface IFormatReader

Overrides:

reopenFile in class FormatReader

Throws:

IOException