loci.formats.in

Class GelReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.MinimalTiffReader

loci.formats.in.BaseTiffReader

loci.formats.in.GelReader

All Implemented Interfaces:

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

public class GelReader
extends BaseTiffReader

GelReader is the file format reader for Molecular Dynamics GEL TIFF files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DATE_FORMAT
static java.lang.String	DATE_TIME_FORMAT
private long	fmt
static java.lang.String[]	FORMATS
private static int	LINEAR
private static int	MD_FILE_UNITS
private static int	MD_FILETAG
private static int	MD_LAB_NAME
private static int	MD_PREP_DATE
private static int	MD_PREP_TIME
private static int	MD_SAMPLE_INFO
private static int	MD_SCALE_PIXEL
private static int	SQUARE_ROOT
static java.lang.String	TIME_FORMAT

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 and Description
GelReader() Constructs a new GEL reader.

Method Summary

Modifier and Type	Method and Description
protected void	initMetadata() Populates the metadata hashtable and metadata store.
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.

Methods inherited from class loci.formats.in.BaseTiffReader

getExifTagName, getImageCreationDate, initFile, initMetadataStore, initStandardMetadata, put, put, put, put, put, put, put, put, put, put, putDouble, putInt, putString

Methods inherited from class loci.formats.in.MinimalTiffReader

close, copyTile, get16BitLookupTable, get8BitLookupTable, getCompressedByteCount, getIFDs, getOptimalTileHeight, getOptimalTileWidth, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, getTileIndex, 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, 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, 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, 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

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Field Detail

DATE_FORMAT

public static final java.lang.String DATE_FORMAT

See Also:

Constant Field Values

TIME_FORMAT

public static final java.lang.String TIME_FORMAT

See Also:

Constant Field Values

DATE_TIME_FORMAT

public static final java.lang.String DATE_TIME_FORMAT

See Also:

Constant Field Values

FORMATS

public static final java.lang.String[] FORMATS

MD_FILETAG

private static final int MD_FILETAG

See Also:

Constant Field Values

MD_SCALE_PIXEL

private static final int MD_SCALE_PIXEL

See Also:

Constant Field Values

MD_LAB_NAME

private static final int MD_LAB_NAME

See Also:

Constant Field Values

MD_SAMPLE_INFO

private static final int MD_SAMPLE_INFO

See Also:

Constant Field Values

MD_PREP_DATE

private static final int MD_PREP_DATE

See Also:

Constant Field Values

MD_PREP_TIME

private static final int MD_PREP_TIME

See Also:

Constant Field Values

MD_FILE_UNITS

private static final int MD_FILE_UNITS

See Also:

Constant Field Values

SQUARE_ROOT

private static final int SQUARE_ROOT

See Also:

Constant Field Values

LINEAR

private static final int LINEAR

See Also:

Constant Field Values

fmt

private long fmt

Constructor Detail

GelReader

public GelReader()

Constructs a new GEL 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)

initMetadata

protected void initMetadata()
                     throws FormatException,
                            java.io.IOException

Description copied from class: BaseTiffReader

Populates the metadata hashtable and metadata store.

Overrides:

initMetadata in class BaseTiffReader

Throws:

FormatException

java.io.IOException