loci.formats.in

Class LegacyND2Reader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.LegacyND2Reader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class LegacyND2Reader
extends FormatReader

LegacyND2Reader is a file format reader for Nikon ND2 files that uses the Nikon ND2 SDK - it is only usable on Windows machines.

Field Summary

Fields

Modifier and Type	Field and Description
private static int	BRIGHT_FIELD
private static int	LASER_SCAN_CONFOCAL
private static boolean	libraryFound
private static int	MULTI_PHOTON
private static java.lang.String	NO_NIKON_MSG
private static int	SPIN_DISK_CONFOCAL
private static int	SWEPT_FIELD_CONFOCAL
private static java.lang.String	URL_NIKON_ND2
private static int	WIDE_FIELD Modality types.

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
LegacyND2Reader()

Method Summary

Modifier and Type	Method and Description
int	getBytesPerPixel(int s)
java.lang.String	getChannelName(int s, int z, int c, int t)
int	getChannels(int s)
double	getDT(int s, int z, int c, int t)
double	getDX(int s, int z, int c, int t)
double	getDY(int s, int z, int c, int t)
double	getDZ(int s, int z, int c, int t)
int	getHeight(int s)
byte[]	getImage(byte[] buf, int s, int z, int c, int t)
double	getMagnification(int s, int z, int c, int t)
int	getModality(int s, int z, int c, int t)
double	getNA(int s, int z, int c, int t)
int	getNumSeries()
java.lang.String	getObjectiveName(int s, int z, int c, int t)
int	getTFrames(int s)
double	getWavelength(int s, int z, int c, int t)
int	getWidth(int s)
int	getZSlices(int s)
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
boolean	isThisType(java.lang.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.
void	openFile(java.lang.String filename)

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, 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, 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, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, 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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Detail

WIDE_FIELD

private static final int WIDE_FIELD

Modality types.

See Also:

Constant Field Values

BRIGHT_FIELD

private static final int BRIGHT_FIELD

See Also:

Constant Field Values

LASER_SCAN_CONFOCAL

private static final int LASER_SCAN_CONFOCAL

See Also:

Constant Field Values

SPIN_DISK_CONFOCAL

private static final int SPIN_DISK_CONFOCAL

See Also:

Constant Field Values

SWEPT_FIELD_CONFOCAL

private static final int SWEPT_FIELD_CONFOCAL

See Also:

Constant Field Values

MULTI_PHOTON

private static final int MULTI_PHOTON

See Also:

Constant Field Values

URL_NIKON_ND2

private static final java.lang.String URL_NIKON_ND2

NO_NIKON_MSG

private static final java.lang.String NO_NIKON_MSG

libraryFound

private static boolean libraryFound

Constructor Detail

LegacyND2Reader

public LegacyND2Reader()

Method Detail

isThisType

public boolean isThisType(java.lang.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,
                        java.io.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.

java.io.IOException - if there was a problem reading the file.

See Also:

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

initFile

protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.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.

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

openFile

public void openFile(java.lang.String filename)

getNumSeries

public int getNumSeries()

getWidth

public int getWidth(int s)

getHeight

public int getHeight(int s)

getZSlices

public int getZSlices(int s)

getTFrames

public int getTFrames(int s)

getChannels

public int getChannels(int s)

getBytesPerPixel

public int getBytesPerPixel(int s)

getImage

public byte[] getImage(byte[] buf,
                       int s,
                       int z,
                       int c,
                       int t)

getDX

public double getDX(int s,
                    int z,
                    int c,
                    int t)

getDY

public double getDY(int s,
                    int z,
                    int c,
                    int t)

getDZ

public double getDZ(int s,
                    int z,
                    int c,
                    int t)

getDT

public double getDT(int s,
                    int z,
                    int c,
                    int t)

getWavelength

public double getWavelength(int s,
                            int z,
                            int c,
                            int t)

getChannelName

public java.lang.String getChannelName(int s,
                                       int z,
                                       int c,
                                       int t)

getMagnification

public double getMagnification(int s,
                               int z,
                               int c,
                               int t)

getNA

public double getNA(int s,
                    int z,
                    int c,
                    int t)

getObjectiveName

public java.lang.String getObjectiveName(int s,
                                         int z,
                                         int c,
                                         int t)

getModality

public int getModality(int s,
                       int z,
                       int c,
                       int t)