loci.formats.in

Class FluoviewReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.MinimalTiffReader

loci.formats.in.BaseTiffReader

loci.formats.in.FluoviewReader

All Implemented Interfaces:

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

public class FluoviewReader
extends BaseTiffReader

FluoviewReader is the file format reader for Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.

Author:

Eric Kjellman egkjellman at wisc.edu, Melissa Linkert melissa at glencoesoftware.com, Curtis Rueden ctrueden at wisc.edu

Field Summary

Fields

Modifier and Type	Field and Description
private static int	ACQUISITION_CYCLE_TIME
private static int	ACTUAL_TEMPERATURE
private static java.lang.String	ANDOR_MAGIC_STRING
private static int	BASELINE_CLAMP
private static int	BASELINE_OFFSET
private static int	CAMERA_SERIAL_SETTING
private java.lang.String[]	channelNames
private static int	CHIP_SIZE_X
private static int	CHIP_SIZE_Y
private static int	CLOCKWISE
private java.lang.String	comment
private static int	COUNTER_CLOCKWISE
private java.lang.String	date
private static java.lang.String	DATE_FORMAT Date format
private java.lang.String	detectorManufacturer
private java.lang.String	dimensionOrder
private static int	EM_DAC
private static int	EXPOSURE_TIME
private java.lang.Float	exposureTime
private int	fieldIndex
private double[][]	fieldOffsets
private static java.lang.String	FLUOVIEW_MAGIC_STRING String identifying a Fluoview file.
private java.lang.String[]	gains
private static int	HORIZONTAL_FLIP
private static int	KINETIC_CYCLE_TIME
private java.lang.String[]	lensNA
private java.lang.String	mag
private static int	MMHEADER Private TIFF tags
private static int	MMSTAMP
private java.lang.String	model
private static int	MODEL
private int	montageIndex
private double[][]	montageOffsets
private static int	N_ACCUMULATIONS
private static int	N_FRAMES
private java.lang.String	objectiveManufacturer
private java.lang.String[]	offsets
private static int	PRE_AMP_SETTING
private static int	PRESCANS
private static int	READOUT_TIME
private java.lang.Float	readoutTime
private double[][]	stamps Timestamps for each plane, in seconds.
private java.lang.Float	temperature
private static int	TEMPERATURE
private int	timeIndex
private static int	VERTICAL_CLOCK_VOLTAGE
private static int	VERTICAL_FLIP
private static int	VERTICAL_SHIFT_SPEED
private java.lang.String[]	voltages
private double	voxelC Pixel dimensions for this file.
private double	voxelT Pixel dimensions for this file.
private double	voxelX Pixel dimensions for this file.
private double	voxelY Pixel dimensions for this file.
private double	voxelZ Pixel dimensions for this file.
private double[]	zPositions

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, 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 and Description
FluoviewReader() Constructs a new Fluoview TIFF reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
private int	getField(int seriesIndex)
private int	getImageIndex(int no)
private int	getMontage(int seriesIndex)
private int[]	getPos(int seriesIndex)
private void	initAlternateMetadata()
private void	initAlternateMetadataStore()
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(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	parseComment()
private void	parsePageName()
private void	readStamps()
private byte[]	shortArrayToBytes(short[] s)

Methods inherited from class loci.formats.in.BaseTiffReader

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

Methods inherited from class loci.formats.in.MinimalTiffReader

get16BitLookupTable, get8BitLookupTable, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, initTiffParser, openThumbBytes, 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, fileGroupOption, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, 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, 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, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, 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 Detail

FLUOVIEW_MAGIC_STRING

private static final java.lang.String FLUOVIEW_MAGIC_STRING

String identifying a Fluoview file.

See Also:

Constant Field Values

ANDOR_MAGIC_STRING

private static final java.lang.String ANDOR_MAGIC_STRING

See Also:

Constant Field Values

MMHEADER

private static final int MMHEADER

Private TIFF tags

See Also:

Constant Field Values

MMSTAMP

private static final int MMSTAMP

See Also:

Constant Field Values

TEMPERATURE

private static final int TEMPERATURE

See Also:

Constant Field Values

EXPOSURE_TIME

private static final int EXPOSURE_TIME

See Also:

Constant Field Values

KINETIC_CYCLE_TIME

private static final int KINETIC_CYCLE_TIME

See Also:

Constant Field Values

N_ACCUMULATIONS

private static final int N_ACCUMULATIONS

See Also:

Constant Field Values

ACQUISITION_CYCLE_TIME

private static final int ACQUISITION_CYCLE_TIME

See Also:

Constant Field Values

READOUT_TIME

private static final int READOUT_TIME

See Also:

Constant Field Values

EM_DAC

private static final int EM_DAC

See Also:

Constant Field Values

N_FRAMES

private static final int N_FRAMES

See Also:

Constant Field Values

HORIZONTAL_FLIP

private static final int HORIZONTAL_FLIP

See Also:

Constant Field Values

VERTICAL_FLIP

private static final int VERTICAL_FLIP

See Also:

Constant Field Values

CLOCKWISE

private static final int CLOCKWISE

See Also:

Constant Field Values

COUNTER_CLOCKWISE

private static final int COUNTER_CLOCKWISE

See Also:

Constant Field Values

VERTICAL_CLOCK_VOLTAGE

private static final int VERTICAL_CLOCK_VOLTAGE

See Also:

Constant Field Values

VERTICAL_SHIFT_SPEED

private static final int VERTICAL_SHIFT_SPEED

See Also:

Constant Field Values

PRE_AMP_SETTING

private static final int PRE_AMP_SETTING

See Also:

Constant Field Values

CAMERA_SERIAL_SETTING

private static final int CAMERA_SERIAL_SETTING

See Also:

Constant Field Values

ACTUAL_TEMPERATURE

private static final int ACTUAL_TEMPERATURE

See Also:

Constant Field Values

BASELINE_CLAMP

private static final int BASELINE_CLAMP

See Also:

Constant Field Values

PRESCANS

private static final int PRESCANS

See Also:

Constant Field Values

MODEL

private static final int MODEL

See Also:

Constant Field Values

CHIP_SIZE_X

private static final int CHIP_SIZE_X

See Also:

Constant Field Values

CHIP_SIZE_Y

private static final int CHIP_SIZE_Y

See Also:

Constant Field Values

BASELINE_OFFSET

private static final int BASELINE_OFFSET

See Also:

Constant Field Values

DATE_FORMAT

private static final java.lang.String DATE_FORMAT

Date format

See Also:

Constant Field Values

voxelX

private double voxelX

Pixel dimensions for this file.

voxelY

private double voxelY

Pixel dimensions for this file.

voxelZ

private double voxelZ

Pixel dimensions for this file.

voxelC

private double voxelC

Pixel dimensions for this file.

voxelT

private double voxelT

Pixel dimensions for this file.

dimensionOrder

private java.lang.String dimensionOrder

date

private java.lang.String date

timeIndex

private int timeIndex

fieldIndex

private int fieldIndex

montageIndex

private int montageIndex

stamps

private double[][] stamps

Timestamps for each plane, in seconds.

zPositions

private double[] zPositions

gains

private java.lang.String[] gains

voltages

private java.lang.String[] voltages

offsets

private java.lang.String[] offsets

channelNames

private java.lang.String[] channelNames

lensNA

private java.lang.String[] lensNA

mag

private java.lang.String mag

detectorManufacturer

private java.lang.String detectorManufacturer

objectiveManufacturer

private java.lang.String objectiveManufacturer

comment

private java.lang.String comment

temperature

private java.lang.Float temperature

exposureTime

private java.lang.Float exposureTime

readoutTime

private java.lang.Float readoutTime

model

private java.lang.String model

montageOffsets

private double[][] montageOffsets

fieldOffsets

private double[][] fieldOffsets

Constructor Detail

FluoviewReader

public FluoviewReader()

Constructs a new Fluoview TIFF reader.

Method Detail

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws java.io.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 MinimalTiffReader

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:

java.io.IOException

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

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.

java.io.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 java.io.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:

java.io.IOException

initStandardMetadata

protected void initStandardMetadata()
                             throws FormatException,
                                    java.io.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

java.io.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

initAlternateMetadata

private void initAlternateMetadata()
                            throws FormatException,
                                   java.io.IOException

Throws:

FormatException

java.io.IOException

initAlternateMetadataStore

private void initAlternateMetadataStore()
                                 throws FormatException

Throws:

FormatException

getImageIndex

private int getImageIndex(int no)

readStamps

private void readStamps()
                 throws FormatException,
                        java.io.IOException

Throws:

FormatException

java.io.IOException

shortArrayToBytes

private byte[] shortArrayToBytes(short[] s)

parsePageName

private void parsePageName()

parseComment

private void parseComment()

getMontage

private int getMontage(int seriesIndex)

getField

private int getField(int seriesIndex)

getPos

private int[] getPos(int seriesIndex)