loci.formats.in

Class BaseTiffReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BaseTiffReader

All Implemented Interfaces:

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

Direct Known Subclasses:

FlexReader, FluoviewReader, GelReader, ImarisTiffReader, ImprovisionTiffReader, IPWReader, MetamorphReader, NikonReader, OMETiffReader, SEQReader, TCSReader, TiffReader, ZeissLSMReader

public abstract class BaseTiffReader
extends loci.formats.FormatReader

BaseTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.

Source code:

Trac, SVN

Author:

Curtis Rueden ctrueden at wisc.edu, Melissa Linkert linkert at wisc.edu

Field Summary

Fields

Modifier and Type	Field and Description
protected Hashtable[]	ifds List of IFDs for the current TIFF.

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
BaseTiffReader(String name, String suffix) Constructs a new BaseTiffReader.
BaseTiffReader(String name, String[] suffixes) Constructs a new BaseTiffReader.

Method Summary

Methods

Modifier and Type	Method and Description
short[][]	get16BitLookupTable() Gets the 16-bit color lookup table associated with the most recently opened image.
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
protected String	getImageCreationDate() Retrieves the image creation date.
protected String	getImageDescription() Retrieves the image description.
protected String	getImageName() Retrieves the image name from the TIFF.
Object	getMetadataValue(String field) Obtains the specified metadata field's value for the current file.
int[]	getTiffDimensions() Gets the dimensions of the given (possibly multi-page) TIFF file.
protected void	initFile(String id) Initializes the given file (parsing header information, etc.).
protected void	initMetadata() Populates the metadata hashtable and metadata store.
protected void	initMetadataStore() Populates the metadata store using the data parsed in 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.
byte[]	openBytes(int no, byte[] buf) Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel).
protected void	put(String key, boolean value)
protected void	put(String key, byte value)
protected void	put(String key, char value)
protected void	put(String key, double value)
protected void	put(String key, float value)
protected void	put(String key, Hashtable ifd, int tag)
protected void	put(String key, int value)
protected void	put(String key, long value)
protected void	put(String key, Object value)
protected void	put(String key, short value)
protected void	putInt(String key, Hashtable ifd, int tag)
protected byte[]	swapIfRequired(byte[] byteArray) Examines a byte array to see if it needs to be byte swapped and modifies the byte array directly.

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

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getSuffixes, isThisType, isThisType, setId

Methods inherited from interface loci.formats.StatusReporter

addStatusListener, getStatusListeners, removeStatusListener

Field Detail

ifds

protected Hashtable[] ifds

List of IFDs for the current TIFF.

Constructor Detail

BaseTiffReader

public BaseTiffReader(String name,
              String suffix)

Constructs a new BaseTiffReader.

BaseTiffReader

public BaseTiffReader(String name,
              String[] suffixes)

Constructs a new BaseTiffReader.

Method Detail

getTiffDimensions

public int[] getTiffDimensions()
                        throws loci.formats.FormatException,
                               IOException

Gets the dimensions of the given (possibly multi-page) TIFF file.

Throws:

loci.formats.FormatException

IOException

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.

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws loci.formats.FormatException,
                                   IOException

Description copied from interface: loci.formats.IFormatReader

Gets the 8-bit color lookup table associated with the most recently opened image. If no images have been opened, or if isIndexed() returns false, then this returns null. Also, if getPixelType() returns anything other than INT8 or UINT8, this method will return null.

Specified by:

get8BitLookupTable in interface loci.formats.IFormatReader

Overrides:

get8BitLookupTable in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws loci.formats.FormatException,
                                     IOException

Description copied from interface: loci.formats.IFormatReader

Gets the 16-bit color lookup table associated with the most recently opened image. If no images have been opened, or if isIndexed() returns false, then this returns null. Also, if getPixelType() returns anything other than INT16 or UINT16, this method will return null.

Specified by:

get16BitLookupTable in interface loci.formats.IFormatReader

Overrides:

get16BitLookupTable in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

getMetadataValue

public Object getMetadataValue(String field)

Description copied from interface: loci.formats.IFormatReader

Obtains the specified metadata field's value for the current file.

Specified by:

getMetadataValue in interface loci.formats.IFormatReader

Overrides:

getMetadataValue in class loci.formats.FormatReader

Parameters:

field - the name associated with the metadata field

Returns:

the value, or null if the field doesn't exist

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).

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.

initMetadata

protected void initMetadata()
                     throws loci.formats.FormatException,
                            IOException

Populates the metadata hashtable and metadata store.

Throws:

loci.formats.FormatException

IOException

initStandardMetadata

protected void initStandardMetadata()
                             throws loci.formats.FormatException,
                                    IOException

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.

Throws:

loci.formats.FormatException

IOException

initMetadataStore

protected void initMetadataStore()

Populates the metadata store using the data parsed in 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.

getImageName

protected String getImageName()

Retrieves the image name from the TIFF.

Returns:

the image name.

getImageCreationDate

protected String getImageCreationDate()

Retrieves the image creation date.

Returns:

the image creation date.

getImageDescription

protected String getImageDescription()

Retrieves the image description.

Returns:

the image description.

swapIfRequired

protected byte[] swapIfRequired(byte[] byteArray)
                         throws loci.formats.FormatException,
                                IOException

Examines a byte array to see if it needs to be byte swapped and modifies the byte array directly.

Parameters:

byteArray - The byte array to check and modify if required.

Returns:

the byteArray either swapped or not for convenience.

Throws:

IOException - if there is an error read from the file.

loci.formats.FormatException - if there is an error during metadata parsing.

put

protected void put(String key,
       Object value)

put

protected void put(String key,
       int value)

put

protected void put(String key,
       boolean value)

put

protected void put(String key,
       byte value)

put

protected void put(String key,
       char value)

put

protected void put(String key,
       double value)

put

protected void put(String key,
       float value)

put

protected void put(String key,
       long value)

put

protected void put(String key,
       short value)

put

protected void put(String key,
       Hashtable ifd,
       int tag)

putInt

protected void putInt(String key,
          Hashtable ifd,
          int tag)

initFile

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

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

Throws:

loci.formats.FormatException

IOException