loci.formats.in
Class OIFReader

java.lang.Object
  loci.formats.FormatHandler
      loci.formats.FormatReader
          loci.formats.in.OIFReader

All Implemented Interfaces:

loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.StatusReporter

public class OIFReader
extends loci.formats.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()
void	close(boolean fileOnly)
int	fileGroupOption(String id)
String[]	getUsedFiles()
protected void	initFile(String id)
boolean	isThisType(byte[] block)
byte[]	openBytes(int no, byte[] buf)
BufferedImage	openThumbImage(int no)

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)

fileGroupOption

public int fileGroupOption(String id)
                    throws loci.formats.FormatException,
                           IOException

Specified by:

fileGroupOption in interface loci.formats.IFormatReader

Overrides:

fileGroupOption in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

openBytes

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

Throws:

loci.formats.FormatException

IOException

openThumbImage

public BufferedImage openThumbImage(int no)
                             throws loci.formats.FormatException,
                                    IOException

Specified by:

openThumbImage in interface loci.formats.IFormatReader

Overrides:

openThumbImage in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

getUsedFiles

public String[] getUsedFiles()

Specified by:

getUsedFiles in interface loci.formats.IFormatReader

Overrides:

getUsedFiles in class loci.formats.FormatReader

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface loci.formats.IFormatReader

Overrides:

close in class loci.formats.FormatReader

Throws:

IOException

close

public void close()
           throws IOException

Specified by:

close in interface loci.formats.IFormatHandler

Overrides:

close in class loci.formats.FormatReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws loci.formats.FormatException,
                        IOException

Overrides:

initFile in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException