Package loci.formats.in

Class FlexReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.FlexReader

All Implemented Interfaces:

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

public class FlexReader
extends FormatReader

FlexReader is a file format reader for Evotec Flex files.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	FlexReader.FlexHandler	SAX handler for parsing XML.
class	FlexReader.MeaHandler	SAX handler for parsing XML from .mea files.
class	FlexReader.ResHandler	SAX handler for parsing XML from .res files.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ARCHIVE
static final int	FLEX	Custom IFD entry for Flex XML.
static final String	FLEX_SUFFIX
static final String	MEA_SUFFIX
static final String[]	MEASUREMENT_SUFFIXES
static final String	RES_SUFFIX
static final String	SCREENING
static final String[]	SUFFIXES

Fields inherited from class loci.formats.FormatReader

core, 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, LOGGER, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor	Description
FlexReader()	Constructs a new Flex reader.

Method Summary

Modifier and Type	Method	Description
static void	appendServerMap(String alias, String realName)	Add the path 'realName' to the mapping for the server named 'alias'.
void	close(boolean fileOnly)
int	fileGroupOption(String id)
int	getOptimalTileHeight()
int	getOptimalTileWidth()
String[]	getSeriesUsedFiles(boolean noPixels)
protected void	initFile(String id)
boolean	isSingleFile(String id)
static void	mapServer(String alias, String realName)	Map the server named 'alias' to the path 'realName'.
static void	mapServer(String alias, String[] realNames)	Map the server named 'alias' to the paths in 'realNames'.
static void	mapServersFromConfigurationFile(String configFile)	Read a configuration file with lines of the form: <server alias>=<real server name> and call mapServer(String, String) accordingly.
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)

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, coreIndexToSeries, 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, 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, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, 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.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

FLEX

public static final int FLEX

Custom IFD entry for Flex XML.

See Also:

• Constant Field Values

FLEX_SUFFIX

public static final String FLEX_SUFFIX

See Also:

• Constant Field Values

MEA_SUFFIX

public static final String MEA_SUFFIX

See Also:

• Constant Field Values

RES_SUFFIX

public static final String RES_SUFFIX

See Also:

• Constant Field Values

MEASUREMENT_SUFFIXES

public static final String[] MEASUREMENT_SUFFIXES

SUFFIXES

public static final String[] SUFFIXES

SCREENING

public static final String SCREENING

See Also:

• Constant Field Values

ARCHIVE

public static final String ARCHIVE

See Also:

• Constant Field Values

Constructor Details

FlexReader

public FlexReader()

Constructs a new Flex reader.

Method Details

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
IOException

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Throws:

FormatException

IOException

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
IOException

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

IOException

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

getOptimalTileWidth

public int getOptimalTileWidth()

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight 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

Specified by:

openBytes in class FormatReader

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 FormatReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException

appendServerMap

public static void appendServerMap(String alias,
 String realName)
                            throws FormatException

Add the path 'realName' to the mapping for the server named 'alias'.

Throws:

FormatException - if 'realName' does not exist

mapServer

public static void mapServer(String alias,
 String realName)

Map the server named 'alias' to the path 'realName'. If other paths were mapped to 'alias', they will be overwritten.

mapServer

public static void mapServer(String alias,
 String[] realNames)

Map the server named 'alias' to the paths in 'realNames'. If other paths were mapped to 'alias', they will be overwritten.

mapServersFromConfigurationFile

public static void mapServersFromConfigurationFile(String configFile)
                                            throws FormatException,
IOException

Read a configuration file with lines of the form: <server alias>=<real server name> and call mapServer(String, String) accordingly.

Throws:

FormatException - if configFile does not exist.

IOException

See Also:

• mapServer(String, String)