loci.formats.in

Class OIRReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.OIRReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class OIRReader
extends FormatReader

OIRReader is the file format reader for Olympus .oir files.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	OIRReader.Channel
(package private) class	OIRReader.Detector
(package private) class	OIRReader.Laser
(package private) class	OIRReader.Objective
(package private) class	OIRReader.PixelBlock

Field Summary

Fields

Modifier and Type	Field and Description
private ome.xml.model.primitives.Timestamp	acquisitionDate
private String	baseName
private int	blocksPerPlane
private ArrayList<OIRReader.Channel>	channels
private int	defaultXMLSkip
private ArrayList<OIRReader.Detector>	detectors
private ArrayList<OIRReader.Laser>	lasers
private int	lastChannel
private ArrayList<OIRReader.Objective>	objectives
private ome.units.quantity.Length	physicalSizeX
private ome.units.quantity.Length	physicalSizeY
private ome.units.quantity.Length	physicalSizeZ
private HashMap<String,OIRReader.PixelBlock>	pixelBlocks
private String[]	pixelUIDs

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, LOGGER, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
OIRReader() Constructs a new OIR reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
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.
private Element	getFirstChild(Element root, String tag)
protected void	initFile(String id) Initializes the given file (parsing header information, etc.).
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	parseAxis(Element dimensionAxis)
private void	parseChannel(Element channel, boolean appendChannels)
private void	parseFrameProperties(Element root)
private void	parseImageProperties(Element root)
private void	parseLUT(Element root, String uid)
private void	parseOriginalMetadata(Node root)
private void	parseXML(String xml, long startFilePointer)
private byte[]	readPixelBlock(long offset)
private void	readXMLBlock()
private boolean	skipPixelBlock(boolean store)

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, 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, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, reopenFile, 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

pixelBlocks

private HashMap<String,OIRReader.PixelBlock> pixelBlocks

channels

private ArrayList<OIRReader.Channel> channels

lasers

private ArrayList<OIRReader.Laser> lasers

detectors

private ArrayList<OIRReader.Detector> detectors

objectives

private ArrayList<OIRReader.Objective> objectives

physicalSizeX

private ome.units.quantity.Length physicalSizeX

physicalSizeY

private ome.units.quantity.Length physicalSizeY

physicalSizeZ

private ome.units.quantity.Length physicalSizeZ

acquisitionDate

private ome.xml.model.primitives.Timestamp acquisitionDate

defaultXMLSkip

private int defaultXMLSkip

blocksPerPlane

private int blocksPerPlane

pixelUIDs

private String[] pixelUIDs

baseName

private String baseName

lastChannel

private int lastChannel

Constructor Detail

OIRReader

public OIRReader()

Constructs a new OIR reader.

Method Detail

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   IOException

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

Throws:

FormatException

IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
                                     IOException

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

Throws:

FormatException

IOException

openBytes

public byte[] openBytes(int no,
                        byte[] buf,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        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 image index within the file.

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.

IOException - if there was a problem reading the file.

See Also:

IFormatReader.openBytes(int, byte[], int, int, int, int)

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 FormatReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
                        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.

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

readXMLBlock

private void readXMLBlock()
                   throws FormatException,
                          IOException

Throws:

FormatException

IOException

parseXML

private void parseXML(String xml,
                      long startFilePointer)
               throws FormatException,
                      IOException

Throws:

FormatException

IOException

parseLUT

private void parseLUT(Element root,
                      String uid)
               throws FormatException

Throws:

FormatException

parseFrameProperties

private void parseFrameProperties(Element root)
                           throws FormatException

Throws:

FormatException

parseImageProperties

private void parseImageProperties(Element root)
                           throws FormatException

Throws:

FormatException

parseChannel

private void parseChannel(Element channel,
                          boolean appendChannels)

parseAxis

private void parseAxis(Element dimensionAxis)

parseOriginalMetadata

private void parseOriginalMetadata(Node root)

getFirstChild

private Element getFirstChild(Element root,
                              String tag)

skipPixelBlock

private boolean skipPixelBlock(boolean store)
                        throws IOException

Throws:

IOException

readPixelBlock

private byte[] readPixelBlock(long offset)
                       throws IOException

Throws:

IOException