loci.formats.in
Class OIFReader

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

public class OIFReader
extends FormatReader

OIFReader is the file format reader for Fluoview FV 1000 OIF files.

Source code:
Trac, SVN

Author:
Melissa Linkert linkert at wisc.edu

Field Summary
protected  String[] code
           
protected  int imageDepth
           
protected  String[] size
           
protected  BMPReader thumbReader
          Helper reader to open the thumbnail.
protected  TiffReader[] tiffReader
          Helper reader to open TIFF files.
protected  Vector tiffs
          Names of every TIFF file to open.
protected  Vector usedFiles
          List of files in the current OIF dataset.
 
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
OIFReader()
          Constructs a new OIF reader.
 
Method Summary
 void close()
          Closes currently open file(s) and frees allocated memory.
 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.
 String[] getUsedFiles()
          Returns an array of filenames needed to open this dataset.
protected  void initFile(String id)
          Initializes the given file (parsing header information, etc.).
 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).
 BufferedImage openThumbImage(int no)
          Obtains a thumbnail for the specified image from the current file.
 
Methods inherited from class loci.formats.FormatReader
addMeta, checkBytes, get16BitLookupTable, get8BitLookupTable, getChannelDimLengths, getChannelDimLengths, getChannelDimTypes, getChannelDimTypes, getCoreMetadata, getCoreMetadata, getCurrentFile, getDimensionOrder, getDimensionOrder, getEffectiveSizeC, getEffectiveSizeC, getImageCount, getImageCount, getIndex, getIndex, getMeta, getMetadata, getMetadata, getMetadataStore, getMetadataStore, getMetadataStoreRoot, getMetadataStoreRoot, getMetadataValue, 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, 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

tiffs

protected Vector tiffs
Names of every TIFF file to open.


tiffReader

protected TiffReader[] tiffReader
Helper reader to open TIFF files.


thumbReader

protected BMPReader thumbReader
Helper reader to open the thumbnail.


usedFiles

protected Vector usedFiles
List of files in the current OIF dataset.


size

protected String[] size

code

protected String[] code

imageDepth

protected int imageDepth
Constructor Detail

OIFReader

public OIFReader()
Constructs a new OIF 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.


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

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).

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.

openThumbImage

public BufferedImage openThumbImage(int no)
                             throws FormatException,
                                    IOException
Description copied from interface: IFormatReader
Obtains a thumbnail for the specified image from the current file.

Specified by:
openThumbImage in interface IFormatReader
Overrides:
openThumbImage in class FormatReader
Throws:
FormatException
IOException

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

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 IFormatHandler.close().

Specified by:
close in interface IFormatReader
Overrides:
close in class FormatReader
Throws:
IOException

close

public void close()
           throws IOException
Description copied from interface: IFormatHandler
Closes currently open file(s) and frees allocated memory.

Specified by:
close in interface IFormatHandler
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
IOException