loci.formats.in
Class FlexReader

java.lang.Object
  extended by loci.formats.FormatHandler
      extended by loci.formats.FormatReader
          extended by loci.formats.in.BaseTiffReader
              extended by loci.formats.in.FlexReader
All Implemented Interfaces:
IFormatHandler, IFormatReader, StatusReporter

public class FlexReader
extends BaseTiffReader

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, SVN


Nested Class Summary
 class FlexReader.FlexHandler
          SAX handler for parsing XML.
 
Field Summary
protected  double[] factors
          Scale factor for each image.
protected static int FLEX
          Custom IFD entry for Flex XML.
static SAXParserFactory SAX_FACTORY
          Factory for generating SAX parsers.
 
Fields inherited from class loci.formats.in.BaseTiffReader
ifds
 
Fields inherited from class loci.formats.FormatReader
collectMetadata, core, filterMetadata, group, in, metadata, metadataStore, normalizeData, saveOriginalMetadata, series, THUMBNAIL_DIMENSION
 
Fields inherited from class loci.formats.FormatHandler
currentId, debug, debugLevel, format, statusListeners, suffixes
 
Fields inherited from interface loci.formats.IFormatReader
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
 
Constructor Summary
FlexReader()
          Constructs a new Flex reader.
 
Method Summary
protected  void initStandardMetadata()
          Parses standard metadata.
 boolean isThisType(byte[] block)
          Checks if the given block is a valid header for this file format.
 byte[] openBytes(int no, byte[] buf)
          Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).
 
Methods inherited from class loci.formats.in.BaseTiffReader
get16BitLookupTable, get8BitLookupTable, getImageCreationDate, getImageDescription, getImageName, getMetadataValue, getTiffDimensions, initFile, initMetadata, initMetadataStore, put, put, put, put, put, put, put, put, put, put, putInt, swapIfRequired
 
Methods inherited from class loci.formats.FormatReader
addMeta, checkBytes, close, close, fileGroupOption, getChannelDimLengths, getChannelDimLengths, getChannelDimTypes, getChannelDimTypes, getCoreMetadata, getCoreMetadata, getCurrentFile, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getEffectiveSizeC, getImageCount, getImageCount, getIndex, getIndex, getMeta, getMetadata, getMetadata, getMetadataStore, getMetadataStore, getMetadataStoreRoot, getMetadataStoreRoot, getMetadataValue, getPixelType, getPixelType, getRGBChannelCount, getRGBChannelCount, getSeries, getSeries, getSeriesCount, getSeriesCount, getSizeC, getSizeC, getSizeT, getSizeT, getSizeX, getSizeX, getSizeY, getSizeY, getSizeZ, getSizeZ, getThumbSizeX, getThumbSizeX, getThumbSizeY, getThumbSizeY, getUsedFiles, getUsedFiles, getZCTCoords, getZCTCoords, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isInterleaved, isInterleaved, isLittleEndian, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOrderCertain, isOriginalMetadataPopulated, isRGB, isRGB, isUsedFile, openBytes, openBytes, openBytes, openImage, openImage, openThumbBytes, openThumbBytes, openThumbImage, openThumbImage, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setSeries, setSeries
 
Methods inherited from class loci.formats.FormatHandler
addStatusListener, debug, getFormat, getStatusListeners, getSuffixes, isThisType, isThisType, removeStatusListener, setDebug, setDebugLevel, setId, status, status, status, trace, trace
 
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, getSuffixes, isThisType, isThisType, setId
 
Methods inherited from interface loci.formats.StatusReporter
addStatusListener, getStatusListeners, removeStatusListener
 

Field Detail

FLEX

protected static final int FLEX
Custom IFD entry for Flex XML.

See Also:
Constant Field Values

SAX_FACTORY

public static final SAXParserFactory SAX_FACTORY
Factory for generating SAX parsers.


factors

protected double[] factors
Scale factor for each image.

Constructor Detail

FlexReader

public FlexReader()
Constructs a new Flex reader.

Method Detail

isThisType

public boolean isThisType(byte[] block)
Description copied from interface: IFormatReader
Checks if the given block is a valid header for this file format.

Specified by:
isThisType in interface IFormatReader
Overrides:
isThisType in class BaseTiffReader

openBytes

public byte[] openBytes(int no,
                        byte[] buf)
                 throws FormatException,
                        IOException
Description copied from interface: IFormatReader
Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).

Specified by:
openBytes in interface IFormatReader
Overrides:
openBytes in class BaseTiffReader
Parameters:
no - the image index within the file.
buf - a pre-allocated buffer.
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.

initStandardMetadata

protected void initStandardMetadata()
                             throws FormatException,
                                    IOException
Description copied from class: BaseTiffReader
Parses standard metadata. NOTE: Absolutely no calls to the metadata store should be made in this method or methods that override this method. Data will be overwritten if you do so.

Overrides:
initStandardMetadata in class BaseTiffReader
Throws:
FormatException
IOException