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:
- 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
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.FormatReader |
collectMetadata, core, filterMetadata, group, in, metadata, metadataStore, normalizeData, saveOriginalMetadata, series, THUMBNAIL_DIMENSION |
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 |
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.
FlexReader
public FlexReader()
- Constructs a new Flex reader.
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