Package loci.formats.in

Class SlidebookReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.SlidebookReader

All Implemented Interfaces:

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

public class SlidebookReader
extends FormatReader

SlidebookReader is the file format reader for 3I Slidebook files. The strategies employed by this reader are highly suboptimal, as we have very little information on the Slidebook format.

Author:

Melissa Linkert melissa at glencoesoftware.com

Field Summary

Fields

Modifier and Type	Field	Description
private boolean	adjust
private Map<Integer,String>	imageDescriptions
private boolean	isSpool
private Map<Integer,Integer>	metadataInPlanes
private List<Long>	metadataOffsets
private List<Double>	ndFilters
private List<Long>	pixelLengths
private List<Long>	pixelOffsets
private long[][]	planeOffset
static final int	SLD_MAGIC_BYTES_1_0
static final int	SLD_MAGIC_BYTES_1_1
static final int	SLD_MAGIC_BYTES_1_2
static final int	SLD_MAGIC_BYTES_2_0
static final int	SLD_MAGIC_BYTES_2_1
static final long	SLD_MAGIC_BYTES_3

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
SlidebookReader()	Constructs a new Slidebook reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
private boolean	isGreaterThanEpsilon(double v)	Returns true if the given double is greater than epsilon (defined here as 0.000001), i.e.
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 String	readCString()
private boolean	withinPixels(long offset)

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, 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, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, 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

SLD_MAGIC_BYTES_1_0

public static final int SLD_MAGIC_BYTES_1_0

See Also:

• Constant Field Values

SLD_MAGIC_BYTES_1_1

public static final int SLD_MAGIC_BYTES_1_1

See Also:

• Constant Field Values

SLD_MAGIC_BYTES_1_2

public static final int SLD_MAGIC_BYTES_1_2

See Also:

• Constant Field Values

SLD_MAGIC_BYTES_2_0

public static final int SLD_MAGIC_BYTES_2_0

See Also:

• Constant Field Values

SLD_MAGIC_BYTES_2_1

public static final int SLD_MAGIC_BYTES_2_1

See Also:

• Constant Field Values

SLD_MAGIC_BYTES_3

public static final long SLD_MAGIC_BYTES_3

See Also:

• Constant Field Values

metadataOffsets

private List<Long> metadataOffsets

pixelOffsets

private List<Long> pixelOffsets

pixelLengths

private List<Long> pixelLengths

ndFilters

private List<Double> ndFilters

imageDescriptions

private Map<Integer,String> imageDescriptions

planeOffset

private long[][] planeOffset

adjust

private boolean adjust

isSpool

private boolean isSpool

metadataInPlanes

private Map<Integer,Integer> metadataInPlanes

Constructor Details

SlidebookReader

public SlidebookReader()

Constructs a new Slidebook reader.

Method Details

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

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

withinPixels

private boolean withinPixels(long offset)

isGreaterThanEpsilon

private boolean isGreaterThanEpsilon(double v)

Returns true if the given double is greater than epsilon (defined here as 0.000001), i.e. positive and not a very, very small number. Returns false if the given double is negative or less than epsilon. See also: http://en.wikipedia.org/wiki/(%CE%B5,_%CE%B4)-definition_of_limit

readCString

private String readCString()
                    throws IOException

Throws:

IOException