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).

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	FlexReader.FilterGroup Stores a grouping of filters.
(package private) class	FlexReader.FlexFile
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
private HashMap<Integer,ome.xml.model.primitives.Timestamp>	acquisitionDates
static String	ARCHIVE
private List<String>	binnings
private int	binX Camera binning values.
private int	binY Camera binning values.
private List<String>	cameraIDs
private List<String>	cameraRefs
private String[]	channelNames
private HashMap<String,String>	dichroicMap
private int	effectiveFieldCount
private int	fieldCount
private HashMap<String,String>	filterMap
private HashMap<String,FlexReader.FilterGroup>	filterSetMap
private List<String>	filterSets
static int	FLEX Custom IFD entry for Flex XML.
static String	FLEX_SUFFIX
private ArrayList<FlexReader.FlexFile>	flexFiles
private HashMap<String,List<String>>	lightSourceCombinationIDs
private List<String>	lightSourceCombinationRefs
private List<String>	lightSourceIDs
static String	MEA_SUFFIX
static String[]	MEASUREMENT_SUFFIXES
private List<String>	measurementFiles
private int	nCols
private int	nFiles
private int	nRows
private List<String>	objectiveIDs
private List<String>	objectiveRefs
private ArrayList<Double>	planeDeltaT
private ArrayList<Double>	planeExposureTime
private ArrayList<ome.units.quantity.Length>	planePositionX
private ArrayList<ome.units.quantity.Length>	planePositionY
private ArrayList<ome.units.quantity.Length>	planePositionZ
private String	plateAcqStartTime
private String	plateBarcode
private int	plateCount
private String	plateName
static String	RES_SUFFIX
private HashMap<String,String>	reverseFileMapping
static String	SCREENING
private static HashMap<String,String[]>	serverMap Mapping from server names stored in the .mea file to actual server names.
static String[]	SUFFIXES
private int	wellColumns
private int	wellCount
private int[][]	wellNumber Specifies the row and column index into 'flexFiles' for a given well.
private int	wellRows
private List<Double>	xPositions
private List<Double>	xSizes
private List<Double>	yPositions
private List<Double>	ySizes

Fields inherited from class loci.formats.FormatReader

core, 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, LOGGER, metadataOptions, 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

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.
private String[]	findFiles(loci.common.Location baseFile) Search for files that correspond to the given file.
private String[]	findFiles(loci.common.Location baseFile, String[] suffixes)
private int	firstWellPlanes() Returns the number of planes in the first well that has data.
private int	getField(String file)
private loci.common.IRandomAccess	getFileHandle(String flexFile)
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.
private int[]	getWell(String file) Returns a two-element array containing the well row and well column corresponding to the given file.
private void	groupFiles(String[] fileList, MetadataStore store)
protected void	initFile(String id) Initializes the given file (parsing header information, etc.).
private void	initFlexFile(String id)
private void	initMeaFile(String id) Initialize the dataset from a .mea file.
private void	initResFile(String id) Initialize the dataset from a .res file.
boolean	isSingleFile(String id) Returns true if this is a single-file format.
private FlexReader.FlexFile	lookupFile(int fileSeries)
private FlexReader.FlexFile	lookupFile(int wellRow, int wellColumn, int field)
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.
private void	parseFlexFile(int currentWell, int wellRow, int wellCol, int field, boolean firstFile, MetadataStore store) Parses XML metadata from the Flex file corresponding to the given well.
private void	parseResFile(String id)
private void	populateCoreMetadata(int wellRow, int wellCol, int field, List<String> imageNames) Populate core metadata using the given list of image names.
private void	populateMetadataStore(MetadataStore store)

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, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, 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, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, 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, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

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

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

serverMap

private static HashMap<String,String[]> serverMap

Mapping from server names stored in the .mea file to actual server names.

binX

private int binX

Camera binning values.

binY

private int binY

Camera binning values.

plateCount

private int plateCount

wellCount

private int wellCount

fieldCount

private int fieldCount

wellRows

private int wellRows

wellColumns

private int wellColumns

channelNames

private String[] channelNames

xPositions

private List<Double> xPositions

yPositions

private List<Double> yPositions

xSizes

private List<Double> xSizes

ySizes

private List<Double> ySizes

cameraIDs

private List<String> cameraIDs

objectiveIDs

private List<String> objectiveIDs

lightSourceIDs

private List<String> lightSourceIDs

lightSourceCombinationIDs

private HashMap<String,List<String>> lightSourceCombinationIDs

cameraRefs

private List<String> cameraRefs

binnings

private List<String> binnings

objectiveRefs

private List<String> objectiveRefs

lightSourceCombinationRefs

private List<String> lightSourceCombinationRefs

filterSets

private List<String> filterSets

filterSetMap

private HashMap<String,FlexReader.FilterGroup> filterSetMap

acquisitionDates

private HashMap<Integer,ome.xml.model.primitives.Timestamp> acquisitionDates

measurementFiles

private List<String> measurementFiles

plateName

private String plateName

plateBarcode

private String plateBarcode

nRows

private int nRows

nCols

private int nCols

plateAcqStartTime

private String plateAcqStartTime

planePositionX

private ArrayList<ome.units.quantity.Length> planePositionX

planePositionY

private ArrayList<ome.units.quantity.Length> planePositionY

planePositionZ

private ArrayList<ome.units.quantity.Length> planePositionZ

planeExposureTime

private ArrayList<Double> planeExposureTime

planeDeltaT

private ArrayList<Double> planeDeltaT

flexFiles

private ArrayList<FlexReader.FlexFile> flexFiles

nFiles

private int nFiles

effectiveFieldCount

private int effectiveFieldCount

reverseFileMapping

private HashMap<String,String> reverseFileMapping

dichroicMap

private HashMap<String,String> dichroicMap

filterMap

private HashMap<String,String> filterMap

wellNumber

private int[][] wellNumber

Specifies the row and column index into 'flexFiles' for a given well.

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

initResFile

private void initResFile(String id)
                  throws FormatException,
                         IOException

Initialize the dataset from a .res file.

Throws:

FormatException

IOException

initMeaFile

private void initMeaFile(String id)
                  throws FormatException,
                         IOException

Initialize the dataset from a .mea file.

Throws:

FormatException

IOException

initFlexFile

private void initFlexFile(String id)
                   throws FormatException,
                          IOException

Throws:

FormatException

IOException

populateMetadataStore

private void populateMetadataStore(MetadataStore store)
                            throws FormatException

Throws:

FormatException

parseResFile

private void parseResFile(String id)
                   throws IOException

Throws:

IOException

getWell

private int[] getWell(String file)

Returns a two-element array containing the well row and well column corresponding to the given file.

getField

private int getField(String file)

firstWellPlanes

private int firstWellPlanes()

Returns the number of planes in the first well that has data. May not be [0][0] as the acquisition may have been column or row offset.

parseFlexFile

private void parseFlexFile(int currentWell,
                           int wellRow,
                           int wellCol,
                           int field,
                           boolean firstFile,
                           MetadataStore store)
                    throws FormatException,
                           IOException

Parses XML metadata from the Flex file corresponding to the given well. If the 'firstFile' flag is set, then the core metadata is also populated.

Throws:

FormatException

IOException

populateCoreMetadata

private void populateCoreMetadata(int wellRow,
                                  int wellCol,
                                  int field,
                                  List<String> imageNames)
                           throws FormatException

Populate core metadata using the given list of image names.

Throws:

FormatException

findFiles

private String[] findFiles(loci.common.Location baseFile)
                    throws IOException

Search for files that correspond to the given file. If the given file is a .mea file, then the corresponding files will be .res and .flex files. If the given file is a .flex file, then the corresponding files will be .res and .mea files.

Throws:

IOException

findFiles

private String[] findFiles(loci.common.Location baseFile,
                           String[] suffixes)
                    throws IOException

Throws:

IOException

groupFiles

private void groupFiles(String[] fileList,
                        MetadataStore store)
                 throws FormatException,
                        IOException

Throws:

FormatException

IOException

getFileHandle

private loci.common.IRandomAccess getFileHandle(String flexFile)
                                         throws IOException

Throws:

IOException

lookupFile

private FlexReader.FlexFile lookupFile(int wellRow,
                                       int wellColumn,
                                       int field)

lookupFile

private FlexReader.FlexFile lookupFile(int fileSeries)

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)