FlexReader (Bio-Formats API)

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,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<Length>`	`planePositionX`
`private ArrayList<Length>`	`planePositionY`
`private ArrayList<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, 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.

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.
`private String[]`	`findFiles(Location baseFile)` Search for files that correspond to the given file.
`private String[]`	`findFiles(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 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, getLineCap, getMarker, getMedium, getMetadataOptions, 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, getSupportedMetadataLevels, 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, 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
  - 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,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<Length> planePositionX
```
  - planePositionY
```
private ArrayList<Length> planePositionY
```
  - planePositionZ
```
private ArrayList<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(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(Location baseFile,
                 String[] suffixes)
                    throws IOException
```
    Throws:
    
    IOException
  - groupFiles
```
private void groupFiles(String[] fileList,
              MetadataStore store)
                 throws FormatException,
                        IOException
```
    Throws:
    
    FormatException
    
    IOException
  - getFileHandle
```
private 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)

Class FlexReader

Nested Class Summary

Field Summary

Fields inherited from class loci.formats.FormatReader

Fields inherited from class loci.formats.FormatHandler

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.FormatReader

Methods inherited from class loci.formats.FormatHandler

Methods inherited from class java.lang.Object

Methods inherited from interface loci.formats.IFormatHandler

Field Detail

FLEX

FLEX_SUFFIX

MEA_SUFFIX

RES_SUFFIX

MEASUREMENT_SUFFIXES

SUFFIXES

SCREENING

ARCHIVE

serverMap

binX

binY

plateCount

wellCount

fieldCount

wellRows

wellColumns

channelNames

xPositions

yPositions

xSizes

ySizes

cameraIDs

objectiveIDs

lightSourceIDs

lightSourceCombinationIDs

cameraRefs

binnings

objectiveRefs

lightSourceCombinationRefs

filterSets

filterSetMap

acquisitionDates

measurementFiles

plateName

plateBarcode

nRows

nCols

plateAcqStartTime

planePositionX

planePositionY

planePositionZ

planeExposureTime

planeDeltaT

flexFiles

nFiles

effectiveFieldCount

reverseFileMapping

dichroicMap

filterMap

wellNumber

Constructor Detail

FlexReader

Method Detail

fileGroupOption

isSingleFile

getSeriesUsedFiles

getOptimalTileWidth

getOptimalTileHeight

openBytes

close

initFile

initResFile

initMeaFile

initFlexFile

populateMetadataStore

parseResFile

getWell