loci.formats.in

Class FluoviewReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BaseTiffReader

loci.formats.in.FluoviewReader

All Implemented Interfaces:

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

public class FluoviewReader
extends BaseTiffReader

FluoviewReader is the file format reader for Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.

Source code:

Trac, SVN

Author:

Eric Kjellman egkjellman at wisc.edu, Melissa Linkert linkert at wisc.edu, Curtis Rueden ctrueden at wisc.edu

Field Summary

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

Constructors

Constructor and Description
FluoviewReader() Constructs a new Fluoview TIFF reader.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes currently open file(s) and frees allocated memory.
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(byte[] block) Checks if the given block is a valid header for this file format.
boolean	isThisType(String name, boolean open) Checks if a file matches the type of this format handler.
byte[]	openBytes(int no) Obtains the specified image from the current file as a byte array.
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	openImage(int no) Obtains the specified image from the current file.

Methods inherited from class loci.formats.in.BaseTiffReader

get16BitLookupTable, get8BitLookupTable, getImageCreationDate, getImageDescription, getImageName, getMetadataValue, getTiffDimensions, initFile, initMetadata, put, put, put, put, put, put, put, put, put, put, putInt, swapIfRequired

Methods inherited from class loci.formats.FormatReader

addMeta, checkBytes, 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, 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

Constructor Detail

FluoviewReader

public FluoviewReader()

Constructs a new Fluoview TIFF reader.

Method Detail

isThisType

public boolean isThisType(byte[] block)

Description copied from interface: loci.formats.IFormatReader

Checks if the given block is a valid header for this file format.

Specified by:

isThisType in interface loci.formats.IFormatReader

Overrides:

isThisType in class BaseTiffReader

openBytes

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

Description copied from interface: loci.formats.IFormatReader

Obtains the specified image from the current file as a byte array.

Specified by:

openBytes in interface loci.formats.IFormatReader

Overrides:

openBytes in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

openBytes

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

Description copied from interface: loci.formats.IFormatReader

Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).

Specified by:

openBytes in interface loci.formats.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:

loci.formats.FormatException - if there was a problem parsing the metadata of the file.

IOException - if there was a problem reading the file.

openImage

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

Description copied from interface: loci.formats.IFormatReader

Obtains the specified image from the current file.

Specified by:

openImage in interface loci.formats.IFormatReader

Overrides:

openImage in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

close

public void close()
           throws IOException

Description copied from interface: loci.formats.IFormatHandler

Closes currently open file(s) and frees allocated memory.

Specified by:

close in interface loci.formats.IFormatHandler

Overrides:

close in class loci.formats.FormatReader

Throws:

IOException

isThisType

public boolean isThisType(String name,
                 boolean open)

Description copied from class: loci.formats.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 loci.formats.IFormatHandler

Overrides:

isThisType in class loci.formats.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.

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

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