Package loci.formats.in

Class MetamorphReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

loci.formats.in.MinimalTiffReader

loci.formats.in.BaseTiffReader

loci.formats.in.MetamorphReader

All Implemented Interfaces:

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

public class MetamorphReader
extends BaseTiffReader

Reader is the file format reader for Metamorph STK files.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	LONG_DATE_FORMAT
static final String[]	ND_SUFFIX
static final String	SHORT_DATE_FORMAT
static final String[]	STK_SUFFIX
static final Pattern	WELL_COORDS

Fields inherited from class loci.formats.in.BaseTiffReader

DATE_FORMATS

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
MetamorphReader()	Constructs a new Metamorph reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
static String	decodeDate(int julian)	Converts a Julian date value into a human-readable string.
static String	decodeTime(int millis)	Converts a time value in milliseconds into a human-readable string.
int	fileGroupOption(String id)
String[]	getDomains()
String[]	getSeriesUsedFiles(boolean noPixels)
protected Length[]	getStageX()
protected Length[]	getStageY()
protected void	initFile(String id)
protected void	initStandardMetadata()
static String	intFormat(int myint, int digits)	Formats an integer value with leading 0s if needed.
static String	intFormatMax(int myint, int maxint)	Formats an integer with leading 0 using maximum sequence number.
boolean	isSingleFile(String id)
boolean	isThisType(String name, boolean open)
boolean	isThisType(RandomAccessInputStream stream)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)

Methods inherited from class loci.formats.in.BaseTiffReader

getExifTagName, getImageCreationDate, initMetadata, initMetadataStore, 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, 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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, 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, 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, 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.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

SHORT_DATE_FORMAT

public static final String SHORT_DATE_FORMAT

See Also:

• Constant Field Values

LONG_DATE_FORMAT

public static final String LONG_DATE_FORMAT

See Also:

• Constant Field Values

ND_SUFFIX

public static final String[] ND_SUFFIX

STK_SUFFIX

public static final String[] STK_SUFFIX

WELL_COORDS

public static final Pattern WELL_COORDS

Constructor Details

MetamorphReader

public MetamorphReader()

Constructs a new Metamorph reader.

Method Details

getDomains

public String[] getDomains()

Specified by:

getDomains in interface IFormatReader

Overrides:

getDomains in class FormatReader

isThisType

public boolean isThisType(String name,
 boolean open)

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

isThisType

public boolean isThisType(RandomAccessInputStream stream)
                   throws IOException

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class MinimalTiffReader

Throws:

IOException

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
IOException

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

IOException

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
IOException

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Throws:

FormatException

IOException

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

openBytes

public byte[] openBytes(int no,
 byte[] buf,
 int x,
 int y,
 int w,
 int h)
                 throws FormatException,
IOException

Specified by:

openBytes in interface IFormatReader

Overrides:

openBytes in class MinimalTiffReader

Throws:

FormatException

IOException

See Also:

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

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface IFormatReader

Overrides:

close in class MinimalTiffReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Overrides:

initFile in class BaseTiffReader

Throws:

FormatException

IOException

initStandardMetadata

protected void initStandardMetadata()
                             throws FormatException,
IOException

Overrides:

initStandardMetadata in class BaseTiffReader

Throws:

FormatException

IOException

getStageX

protected Length[] getStageX()

getStageY

protected Length[] getStageY()

decodeDate

public static String decodeDate(int julian)

Converts a Julian date value into a human-readable string.

decodeTime

public static String decodeTime(int millis)

Converts a time value in milliseconds into a human-readable string. Note that the date and time are handled separately, so this method is only concerned with the time of day. The time of day in milliseconds is stored as a 32-bit int in Metamorph files, but is expected to be a positive integer less than the number of milliseconds in one day.

Parameters:

millis - milliseconds elapsed in the relevant day

See Also:

• decodeDate(int)

intFormat

public static String intFormat(int myint,
 int digits)

Formats an integer value with leading 0s if needed.

intFormatMax

public static String intFormatMax(int myint,
 int maxint)

Formats an integer with leading 0 using maximum sequence number.

Parameters:

myint - integer to format

maxint - max of "myint"

Returns:

String