Package loci.formats.in

Class NDPIReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.MinimalTiffReader

loci.formats.in.BaseTiffReader

loci.formats.in.NDPIReader

All Implemented Interfaces:

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

public class NDPIReader
extends BaseTiffReader

NDPIReader is the file format reader for Hamamatsu .ndpi files.

Field Summary

Fields

Modifier and Type	Field	Description
private static final int	BLUE_MULTIPLIER
private static final int	BYTE_COUNT_HIGH_BYTES
private static final int	CAPTURE_MODE
private static final int	DEFAULT_GAMMA
private static final int	EXPOSURE_RATIO
private static final int	EXPOSURE_TIME
private static final int	FILTER_SET_NAME
private static final int	FIRMWARE_VERSION
private static final int	FOCUS_OFFSET
private static final int	FOCUS_POINT_REGIONS
private static final int	FOCUS_TIME
private static final int	FULLY_AUTO_FOCUS
private static final int	GREEN_MULTIPLIER
private int	initializedPlane
private int	initializedSeries
private String	instrumentModel
private static final int	JPEG_QUALITY
private static final int	LABEL_OBSCURED
private static final int	LAMP_AGE
private Double	magnification
private static final int	MARKER_TAG
private static final int	MARKER_TAG_HIGH_BYTES
private static final int	MAX_SIZE
private static final int	METADATA_TAG
private static final int	OFFSET_HIGH_BYTES
private int	pyramidHeight
private static final int	RED_MULTIPLIER
private static final int	REFERENCE
private static final int	REFOCUS_INTERVAL
private static final int	SCAN_TIME
private static final int	SERIAL_NUMBER
private String	serialNumber
private JPEGTurboService	service
private int	sizeZ
private static final int	SOURCE_LENS
private static final int	THUMB_TAG_2
private static final int	TISSUE_INDEX
private static final int	VERSION
private static final int	WAVELENGTH
private static final int	WRITE_TIME
private static final int	X_POSITION
private static final int	Y_POSITION
private static final int	Z_POSITION

Fields inherited from class loci.formats.in.BaseTiffReader

DATE_FORMATS, LOGGER

Fields inherited from class loci.formats.in.MinimalTiffReader

canSeparateSeries, equalStrips, ifds, lastPlane, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit

Fields inherited from class loci.formats.SubResolutionFormatReader

core

Fields inherited from class loci.formats.FormatReader

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, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
NDPIReader()	Constructs a new NDPI reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
private int	getBitsPerSample(int mode)	Get the number of bits per sample associated with the given capture mode.
private String	getCaptureMode(int mode)	Get the description of the given capture mode.
private int	getIFDIndex(int seriesIndex, int zIndex)
private long[]	getMarkers(IFD ifd)	Get the array of restart markers (offsets) for the given IFD.
int	getOptimalTileHeight()	Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth()	Returns the optimal sub-image width for use with openBytes.
protected int	getPyramidHeight()
Codec	getTileCodec(int no)	Retrieve a codec that can be used to decompress compressed tiles.
CodecOptions	getTileCodecOptions(int no, int x, int y)	Retrieve codec options that can be used to decompressed the specified tile.
int	getTileColumns(int no)	Get the number of columns of tiles in the specified plane in the current series.
int	getTileRows(int no)	Get the number of rows of tiles in the specified plane in the current series.
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
protected void	initMetadataStore()	Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself.
protected void	initStandardMetadata()	Parses standard metadata.
boolean	isThisType(String name, 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.
byte[]	openCompressedBytes(int no, byte[] buf, int x, int y)	Retrieve the specified tile without performing any decompression.
byte[]	openCompressedBytes(int no, int x, int y)	Retrieve the specified tile without performing any decompression.
byte[]	openThumbBytes(int no)	Obtains a thumbnail for the specified image plane from the current file, as a byte array.
private void	resetStream(IFD ifd)
private boolean	useTiffParser(IFD ifd)

Methods inherited from class loci.formats.in.BaseTiffReader

getExifTagName, getImageCreationDate, initMetadata, put, put, put, put, put, put, put, put, put, put, putDouble, putInt, putString

Methods inherited from class loci.formats.in.MinimalTiffReader

copyTile, get16BitLookupTable, get8BitLookupTable, getCompressedByteCount, getIFDs, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, getTileIndex, initTiffParser, isThisType, reopenFile, setResolutionLevel

Methods inherited from class loci.formats.SubResolutionFormatReader

coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution, setSeries

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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, 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, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, 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, readPlane, readPlane, readPlane, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, 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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

MAX_SIZE

private static final int MAX_SIZE

See Also:

• Constant Field Values

OFFSET_HIGH_BYTES

private static final int OFFSET_HIGH_BYTES

See Also:

• Constant Field Values

BYTE_COUNT_HIGH_BYTES

private static final int BYTE_COUNT_HIGH_BYTES

See Also:

• Constant Field Values

VERSION

private static final int VERSION

See Also:

• Constant Field Values

SOURCE_LENS

private static final int SOURCE_LENS

See Also:

• Constant Field Values

X_POSITION

private static final int X_POSITION

See Also:

• Constant Field Values

Y_POSITION

private static final int Y_POSITION

See Also:

• Constant Field Values

Z_POSITION

private static final int Z_POSITION

See Also:

• Constant Field Values

TISSUE_INDEX

private static final int TISSUE_INDEX

See Also:

• Constant Field Values

MARKER_TAG

private static final int MARKER_TAG

See Also:

• Constant Field Values

REFERENCE

private static final int REFERENCE

See Also:

• Constant Field Values

MARKER_TAG_HIGH_BYTES

private static final int MARKER_TAG_HIGH_BYTES

See Also:

• Constant Field Values

FILTER_SET_NAME

private static final int FILTER_SET_NAME

See Also:

• Constant Field Values

EXPOSURE_RATIO

private static final int EXPOSURE_RATIO

See Also:

• Constant Field Values

RED_MULTIPLIER

private static final int RED_MULTIPLIER

See Also:

• Constant Field Values

GREEN_MULTIPLIER

private static final int GREEN_MULTIPLIER

See Also:

• Constant Field Values

BLUE_MULTIPLIER

private static final int BLUE_MULTIPLIER

See Also:

• Constant Field Values

THUMB_TAG_2

private static final int THUMB_TAG_2

See Also:

• Constant Field Values

FOCUS_POINT_REGIONS

private static final int FOCUS_POINT_REGIONS

See Also:

• Constant Field Values

CAPTURE_MODE

private static final int CAPTURE_MODE

See Also:

• Constant Field Values

SERIAL_NUMBER

private static final int SERIAL_NUMBER

See Also:

• Constant Field Values

JPEG_QUALITY

private static final int JPEG_QUALITY

See Also:

• Constant Field Values

REFOCUS_INTERVAL

private static final int REFOCUS_INTERVAL

See Also:

• Constant Field Values

FOCUS_OFFSET

private static final int FOCUS_OFFSET

See Also:

• Constant Field Values

FIRMWARE_VERSION

private static final int FIRMWARE_VERSION

See Also:

• Constant Field Values

METADATA_TAG

private static final int METADATA_TAG

See Also:

• Constant Field Values

LABEL_OBSCURED

private static final int LABEL_OBSCURED

See Also:

• Constant Field Values

WAVELENGTH

private static final int WAVELENGTH

See Also:

• Constant Field Values

LAMP_AGE

private static final int LAMP_AGE

See Also:

• Constant Field Values

EXPOSURE_TIME

private static final int EXPOSURE_TIME

See Also:

• Constant Field Values

FOCUS_TIME

private static final int FOCUS_TIME

See Also:

• Constant Field Values

SCAN_TIME

private static final int SCAN_TIME

See Also:

• Constant Field Values

WRITE_TIME

private static final int WRITE_TIME

See Also:

• Constant Field Values

FULLY_AUTO_FOCUS

private static final int FULLY_AUTO_FOCUS

See Also:

• Constant Field Values

DEFAULT_GAMMA

private static final int DEFAULT_GAMMA

See Also:

• Constant Field Values

initializedSeries

private int initializedSeries

initializedPlane

private int initializedPlane

sizeZ

private int sizeZ

pyramidHeight

private int pyramidHeight

service

private JPEGTurboService service

magnification

private Double magnification

serialNumber

private String serialNumber

instrumentModel

private String instrumentModel

Constructor Details

NDPIReader

public NDPIReader()

Constructs a new NDPI reader.

Method Details

getTileRows

public int getTileRows(int no)

Description copied from interface: ICompressedTileReader

Get the number of rows of tiles in the specified plane in the current series.

Specified by:

getTileRows in interface ICompressedTileReader

Overrides:

getTileRows in class FormatReader

Parameters:

no - plane index

Returns:

tile row count

getTileColumns

public int getTileColumns(int no)

Description copied from interface: ICompressedTileReader

Get the number of columns of tiles in the specified plane in the current series.

Specified by:

getTileColumns in interface ICompressedTileReader

Overrides:

getTileColumns in class FormatReader

Parameters:

no - plane index

Returns:

tile column count

openCompressedBytes

public byte[] openCompressedBytes(int no,
 int x,
 int y)
                           throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve the specified tile without performing any decompression.

Parameters:

no - plane index

x - tile X index (indexed from 0, @see getTileColumns(int))

y - tile Y index (indexed from 0, @see getTileRows(int))

Returns:

compressed tile bytes

Throws:

FormatException

IOException

openCompressedBytes

public byte[] openCompressedBytes(int no,
 byte[] buf,
 int x,
 int y)
                           throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve the specified tile without performing any decompression.

Parameters:

no - plane index

buf - pre-allocated buffer in which to store compressed bytes

x - tile X index (indexed from 0, @see getTileColumns(int))

y - tile Y index (indexed from 0, @see getTileRows(int))

Returns:

compressed tile bytes

Throws:

FormatException

IOException

getTileCodec

public Codec getTileCodec(int no)
                   throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve a codec that can be used to decompress compressed tiles.

Parameters:

no - plane index

Returns:

codec that can be used for compressed tiles in the specified plane

Throws:

FormatException

IOException

See Also:

• ICompressedTileReader.openCompressedBytes(int,int,int)

getTileCodecOptions

public CodecOptions getTileCodecOptions(int no,
 int x,
 int y)
                                 throws FormatException,
IOException

Description copied from interface: ICompressedTileReader

Retrieve codec options that can be used to decompressed the specified tile.

Parameters:

no - plane index

x - tile X index (indexed from 0, @see getTileColumns(int))

y - tile Y index (indexed from 0, @see getTileRows(int))

Returns:

codec options

Throws:

FormatException

IOException

See Also:

• ICompressedTileReader.getTileCodec(int)

isThisType

public boolean isThisType(String name,
 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

Parameters:

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

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:

• IFormatReader.fileGroupOption(String)

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

Overrides:

openBytes in class MinimalTiffReader

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)

openThumbBytes

public byte[] openThumbBytes(int no)
                      throws FormatException,
IOException

Description copied from interface: IFormatReader

Obtains a thumbnail for the specified image plane from the current file, as a byte array.

Specified by:

openThumbBytes in interface IFormatReader

Overrides:

openThumbBytes in class MinimalTiffReader

Throws:

FormatException

IOException

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 MinimalTiffReader

Throws:

IOException

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 MinimalTiffReader

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 MinimalTiffReader

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Description copied from class: SubResolutionFormatReader

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 BaseTiffReader

Throws:

FormatException - if a parsing error occurs processing the file.

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

initStandardMetadata

protected void initStandardMetadata()
                             throws FormatException,
IOException

Description copied from class: BaseTiffReader

Parses standard metadata. NOTE: Absolutely no calls to the metadata store should be made in this method or methods that override this method. Data will be overwritten if you do so.

Overrides:

initStandardMetadata in class BaseTiffReader

Throws:

FormatException

IOException

initMetadataStore

protected void initMetadataStore()
                          throws FormatException

Description copied from class: BaseTiffReader

Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself. All calls to the active MetadataStore should be made in this method and only in this method. This is especially important for sub-classes that override the getters for pixel set array size, etc.

Overrides:

initMetadataStore in class BaseTiffReader

Throws:

FormatException

getPyramidHeight

protected int getPyramidHeight()

getIFDIndex

private int getIFDIndex(int seriesIndex,
 int zIndex)

useTiffParser

private boolean useTiffParser(IFD ifd)
                       throws FormatException

Returns:

true if tiles can be read using TiffParser logic, or false if the JPEGTurboService needs to be used

Throws:

FormatException

getCaptureMode

private String getCaptureMode(int mode)

Get the description of the given capture mode.

getBitsPerSample

private int getBitsPerSample(int mode)

Get the number of bits per sample associated with the given capture mode.

getMarkers

private long[] getMarkers(IFD ifd)
                   throws FormatException

Get the array of restart markers (offsets) for the given IFD. Reads both the marker tag and marker high bytes tag (if present) to build the array of 64-bit offsets.

Throws:

FormatException

resetStream

private void resetStream(IFD ifd)
                  throws IOException,
FormatException

Throws:

IOException

FormatException