loci.formats.in
Class OMETiffReader

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

public class OMETiffReader
extends BaseTiffReader

OMETiffReader is the file format reader for OME-TIFF files.

Source code:
Trac, SVN


Field Summary
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
OMETiffReader()
           
 
Method Summary
 String[] getUsedFiles()
          Returns an array of filenames needed to open this dataset.
protected  void initMetadataStore()
          Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself.
protected  void initStandardMetadata()
          Parses standard metadata.
 boolean isThisType(String name, boolean open)
          Checks if a file matches the type of this format handler.
 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, isThisType, 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, 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, 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, setId
 
Methods inherited from interface loci.formats.StatusReporter
addStatusListener, getStatusListeners, removeStatusListener
 

Field Detail

SAX_FACTORY

public static final SAXParserFactory SAX_FACTORY
Factory for generating SAX parsers.

Constructor Detail

OMETiffReader

public OMETiffReader()
Method Detail

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

initMetadataStore

protected void initMetadataStore()
Description copied from class: BaseTiffReader
Populates the metadata store using the data parsed in BaseTiffReader.initStandardMetadata() along with some further parsing done in the method itself. All calls to the active MetadataStore should be made in this method and only in this method. This is especially important for sub-classes that override the getters for pixel set array size, etc.

Overrides:
initMetadataStore in class BaseTiffReader

getUsedFiles

public String[] getUsedFiles()
Description copied from interface: IFormatReader
Returns an array of filenames needed to open this dataset.

Specified by:
getUsedFiles in interface IFormatReader
Overrides:
getUsedFiles in class FormatReader

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.

isThisType

public boolean isThisType(String name,
                          boolean open)
Description copied from class: FormatHandler
Checks if a file matches the type of this format handler. The default implementation checks filename suffixes against those known for this format (the open parameter does nothing).

Specified by:
isThisType in interface IFormatHandler
Overrides:
isThisType in class FormatHandler
open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis. Does nothing in the default implementation.