loci.formats.in
Class FlexReader

java.lang.Object
  loci.formats.FormatHandler
      loci.formats.FormatReader
          loci.formats.in.BaseTiffReader
              loci.formats.in.FlexReader

All Implemented Interfaces:

loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.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)
byte[]	openBytes(int no, byte[] buf)

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)

Specified by:

isThisType in interface loci.formats.IFormatReader

Overrides:

isThisType in class BaseTiffReader

openBytes

public byte[] openBytes(int no,
                        byte[] buf)
                 throws loci.formats.FormatException,
                        IOException

Specified by:

openBytes in interface loci.formats.IFormatReader

Overrides:

openBytes in class BaseTiffReader

Throws:

loci.formats.FormatException

IOException

initStandardMetadata

protected void initStandardMetadata()
                             throws loci.formats.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:

loci.formats.FormatException

IOException