loci.formats.in

Class SlideBook6Reader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.SlideBook6Reader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class SlideBook6Reader
extends FormatReader

SlideBook6Reader is a file format reader for 3i SlideBook SLD files that uses the SlideBook SBReadFile SDK via the (Windows only) dlls: SBReadFile.dll and SlideBook6Reader.dll

Author:

Richard Myers, richard at intelligent-imaging.com

Field Summary

Fields

Modifier and Type	Field and Description
private static String	GENERAL_3I_MSG
private static boolean	initialized
private static boolean	libraryFound
private static String	NO_3I_MSG
static int	SLD_MAGIC_BYTES_1_0
static int	SLD_MAGIC_BYTES_1_1
static int	SLD_MAGIC_BYTES_1_2
static int	SLD_MAGIC_BYTES_2_0
static int	SLD_MAGIC_BYTES_2_1
static long	SLD_MAGIC_BYTES_3
private static String	URL_3I_SLD

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
SlideBook6Reader()

Method Summary

Methods

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
void	closeFile()
int	getBytesPerPixel(int inCapture)
String	getChannelName(int inCapture, int inChannel)
int	getElapsedTime(int inCapture, int inTimepoint)
int	getExposureTime(int inCapture, int inChannel)
String	getImageComments(int inCapture)
String	getImageName(int inCapture)
String	getLensName(int inCapture)
double	getMagnification(int inCapture)
int	getMontageColumn(int inCapture, int inPosition)
int	getMontageRow(int inCapture, int inPosition)
int	getNumCaptures()
int	getNumChannels(int inCapture)
int	getNumPositions(int inCapture)
int	getNumTimepoints(int inCapture)
int	getNumXColumns(int inCapture)
int	getNumYRows(int inCapture)
int	getNumZPlanes(int inCapture)
float	getVoxelSize(int inCapture)
double	getXPosition(int inCapture, int inPosition)
double	getYPosition(int inCapture, int inPosition)
double	getZPosition(int inCapture, int inPosition, int inZPlane)
protected void	initFile(String id) Initializes the given file (parsing header information, etc.).
private static boolean	isLibraryFound()
boolean	isThisType(RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
boolean	isThisType(String file, boolean open) Checks if a file matches the type of this format reader.
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.
boolean	openFile(String path)
boolean	readImagePlaneBuf(byte[] outPlaneBuffer, int inCapture, int inPosition, int inTimepoint, int inZ, int inChannel)

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, 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, getLineCap, getMarker, getMedium, getMetadataOptions, 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, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

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

Field Detail

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

URL_3I_SLD

private static final String URL_3I_SLD

See Also:

Constant Field Values

NO_3I_MSG

private static final String NO_3I_MSG

See Also:

Constant Field Values

GENERAL_3I_MSG

private static final String GENERAL_3I_MSG

See Also:

Constant Field Values

initialized

private static boolean initialized

libraryFound

private static boolean libraryFound

Constructor Detail

SlideBook6Reader

public SlideBook6Reader()

Method Detail

isLibraryFound

private static boolean isLibraryFound()

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Throws:

IOException

isThisType

public boolean isThisType(String file,
                 boolean open)

Description copied from class: FormatReader

Checks if a file matches the type of this format reader. Checks filename suffixes against those known for this format. If the suffix check is inconclusive and the open parameter is true, the file is opened and tested with FormatReader.isThisType(RandomAccessInputStream).

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis.

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

openFile

public boolean openFile(String path)

closeFile

public void closeFile()

getNumCaptures

public int getNumCaptures()

getNumPositions

public int getNumPositions(int inCapture)

getNumTimepoints

public int getNumTimepoints(int inCapture)

getNumChannels

public int getNumChannels(int inCapture)

getNumXColumns

public int getNumXColumns(int inCapture)

getNumYRows

public int getNumYRows(int inCapture)

getNumZPlanes

public int getNumZPlanes(int inCapture)

getElapsedTime

public int getElapsedTime(int inCapture,
                 int inTimepoint)

getExposureTime

public int getExposureTime(int inCapture,
                  int inChannel)

getVoxelSize

public float getVoxelSize(int inCapture)

getXPosition

public double getXPosition(int inCapture,
                  int inPosition)

getYPosition

public double getYPosition(int inCapture,
                  int inPosition)

getZPosition

public double getZPosition(int inCapture,
                  int inPosition,
                  int inZPlane)

getMontageRow

public int getMontageRow(int inCapture,
                int inPosition)

getMontageColumn

public int getMontageColumn(int inCapture,
                   int inPosition)

getChannelName

public String getChannelName(int inCapture,
                    int inChannel)

getLensName

public String getLensName(int inCapture)

getMagnification

public double getMagnification(int inCapture)

getImageName

public String getImageName(int inCapture)

getImageComments

public String getImageComments(int inCapture)

getBytesPerPixel

public int getBytesPerPixel(int inCapture)

readImagePlaneBuf

public boolean readImagePlaneBuf(byte[] outPlaneBuffer,
                        int inCapture,
                        int inPosition,
                        int inTimepoint,
                        int inZ,
                        int inChannel)