loci.formats.in

Class FlexReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.FlexReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class FlexReader
extends FormatReader

FlexReader is a file format reader for Evotec Flex files. To use it, the LuraWave decoder library, lwf_jsdk2.6.jar, must be available, and a LuraWave license key must be specified in the lurawave.license system property (e.g., -Dlurawave.license=XXXX on the command line).

Source code:

Trac, Gitweb

Nested Class Summary

Nested Classes

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

Fields inherited from class loci.formats.FormatReader

core, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
FlexReader() Constructs a new Flex reader.

Method Summary

Methods

Modifier and Type	Method and Description
static void	appendServerMap(String alias, String realName) Add the path 'realName' to the mapping for the server named 'alias'.
void	close(boolean fileOnly) Closes the currently open file.
int	fileGroupOption(String id) Returns an int indicating that we cannot, must, or might group the files in a given dataset.
int	getOptimalTileHeight() Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth() Returns the optimal sub-image width for use with openBytes.
String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
protected void	initFile(String id) Initializes the given file (parsing header information, etc.).
boolean	isSingleFile(String id) Returns true if this is a single-file format.
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) Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, close, coreIndexToSeries, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadata, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, seriesToCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

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

Field Detail

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 Detail

FlexReader

public FlexReader()

Constructs a new Flex reader.

Method Detail

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
                           IOException

Description copied from interface: IFormatReader

Returns an int indicating that we cannot, must, or might group the files in a given dataset.

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Throws:

FormatException

IOException

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
                            IOException

Description copied from interface: IFormatReader

Returns true if this is a single-file format.

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

IOException

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

getOptimalTileWidth

public int getOptimalTileWidth()

Description copied from interface: IFormatReader

Returns the optimal sub-image width for use with openBytes.

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Description copied from interface: IFormatReader

Returns the optimal sub-image height for use with openBytes.

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

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 image index within the file.

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.

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 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 FormatReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
                        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.

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

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)