Package loci.formats.in

Class OIRReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.OIRReader

All Implemented Interfaces:

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

public class OIRReader
extends FormatReader

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

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	OIRReader.Channel
private static class	OIRReader.CZTKey	This is a class that wraps three numbers c,z,t and an object can be used as a key in a hashmap.
(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	Description
private ome.xml.model.primitives.Timestamp	acquisitionDate
private String	baseName
private int	blocksPerPlane
private static final int	BUFFER_SIZE
private ArrayList<OIRReader.Channel>	channels
private final Map<OIRReader.CZTKey,OIRReader.PixelBlock[]>	cztToPixelBlocks
private int	defaultXMLSkip
private ArrayList<OIRReader.Detector>	detectors
private static final String	IDENTIFIER
private ArrayList<OIRReader.Laser>	lasers
private int	lastChannel
private int	minT
private int	minZ
private ArrayList<OIRReader.Objective>	objectives
private int	optimalTileHeight
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 HashMap<Integer,Double>	timestampAdjustments
private Double	tStart
private Double	tStep
private Double	zStart
private Double	zStep

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

Constructor	Description
OIRReader()	Constructs a new OIR reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
private void	copyPixelBlock(OIRReader.PixelBlock block, byte[] buf, int offsetBuf, int offsetBlock, int nBytesPerLinesBuf, int nBytesPerLineBlock, int nLines)
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
private void	findNextXMLBlock(loci.common.RandomAccessInputStream s)
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 int	getBlock(String uid)
private int	getC(String uid)
private Element	getFirstChild(Element root, String tag)
private int	getL(String uid)
int	getOptimalTileHeight()	Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth()	Returns the optimal sub-image width for use with openBytes.
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
private int	getT(String uid)
private int	getZ(String uid)
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
private void	insertChannel(int index, OIRReader.Channel c)	Insert the given Channel into the list of channels, at the given index.
private boolean	isCurrentFile(String file)
boolean	isSingleFile(String id)	Returns true if the named file is expected to be the only file in the dataset.
boolean	isThisType(loci.common.RandomAccessInputStream stream)	Checks if the given stream is a valid stream for this file format.
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(loci.common.RandomAccessInputStream s, String xml, long startFilePointer)
private void	readPixelsFile(String file, loci.common.RandomAccessInputStream s)
private void	readXMLBlock(String file, loci.common.RandomAccessInputStream s)
private boolean	skipPixelBlock(String currentFile, loci.common.RandomAccessInputStream s, 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, flattenHashtables, 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, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, 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.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

Field Details

IDENTIFIER

private static final String IDENTIFIER

See Also:

• Constant Field Values

BUFFER_SIZE

private static final int BUFFER_SIZE

See Also:

• Constant Field Values

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

cztToPixelBlocks

private final Map<OIRReader.CZTKey,OIRReader.PixelBlock[]> cztToPixelBlocks

baseName

private String baseName

lastChannel

private int lastChannel

optimalTileHeight

private int optimalTileHeight

minZ

private int minZ

minT

private int minT

zStart

private transient Double zStart

zStep

private transient Double zStep

tStart

private transient Double tStart

tStep

private transient Double tStep

timestampAdjustments

private transient HashMap<Integer,Double> timestampAdjustments

Constructor Details

OIRReader

public OIRReader()

Constructs a new OIR reader.

Method Details

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
IOException

Description copied from interface: IFormatReader

Returns an indication of whether the files in a multi-file dataset can be handled individually. This method is only useful for formats and datasets which contain multiple files.

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Parameters:

id - a file in the multi-file dataset

Returns:

an int indicating that we cannot, must, or might group the files. A return value of FormatTools.MUST_GROUP indicates that the files cannot be handled separately; the reader will always detect and read all files in the dataset. FormatTools.CAN_GROUP indicates that the files may be handled separately, but file grouping must then be disabled via IFormatReader.setGroupFiles(boolean). FormatTools.CANNOT_GROUP indicates that the files must be handled separately; the reader will not attempt to read all files in the dataset (this is rare).

Throws:

FormatException

IOException

See Also:

• FormatTools.MUST_GROUP
• FormatTools.CAN_GROUP
• FormatTools.CANNOT_GROUP

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
IOException

Description copied from interface: IFormatReader

Returns true if the named file is expected to be the only file in the dataset. For single-file formats, always returns true.

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

IOException

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. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Parameters:

stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.

Returns:

true if the file represented by the stream can be read by this reader; false otherwise.

Throws:

IOException

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

getOptimalTileHeight

public int getOptimalTileHeight()

Description copied from interface: IFormatReader

Returns the optimal sub-image height for use with openBytes.

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class FormatReader

getOptimalTileWidth

public int getOptimalTileWidth()

Description copied from interface: IFormatReader

Returns the optimal sub-image width for use with openBytes.

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

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 plane index within the current series.

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

readPixelsFile

private void readPixelsFile(String file,
 loci.common.RandomAccessInputStream s)
                     throws FormatException,
IOException

Throws:

FormatException

IOException

findNextXMLBlock

private void findNextXMLBlock(loci.common.RandomAccessInputStream s)
                       throws IOException

Throws:

IOException

readXMLBlock

private void readXMLBlock(String file,
 loci.common.RandomAccessInputStream s)
                   throws FormatException,
IOException

Throws:

FormatException

IOException

parseXML

private void parseXML(loci.common.RandomAccessInputStream s,
 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

insertChannel

private void insertChannel(int index,
 OIRReader.Channel c)

Insert the given Channel into the list of channels, at the given index. If the index is greater than the current list length, then the list will be expanded accordingly.

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(String currentFile,
 loci.common.RandomAccessInputStream s,
 boolean store)
                        throws IOException

Throws:

IOException

copyPixelBlock

private void copyPixelBlock(OIRReader.PixelBlock block,
 byte[] buf,
 int offsetBuf,
 int offsetBlock,
 int nBytesPerLinesBuf,
 int nBytesPerLineBlock,
 int nLines)
                     throws IOException

Throws:

IOException

getZ

private int getZ(String uid)

getT

private int getT(String uid)

getC

private int getC(String uid)

getBlock

private int getBlock(String uid)

getL

private int getL(String uid)

isCurrentFile

private boolean isCurrentFile(String file)