loci.formats.in

Class OpenlabReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.OpenlabReader

All Implemented Interfaces:

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

public class OpenlabReader
extends loci.formats.FormatReader

OpenlabReader is the file format reader for Openlab LIFF files.

Source code:

Trac, SVN

Author:

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

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	OpenlabReader.LayerInfo Helper class for storing layer info.

Field Summary

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
OpenlabReader() Constructs a new OpenlabReader.

Method Summary

Methods

Modifier and Type	Method and Description
void	close() Closes currently open file(s) and frees allocated memory.
void	close(boolean fileOnly) Closes the currently open file.
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.
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).

Methods inherited from class loci.formats.FormatReader

addMeta, checkBytes, fileGroupOption, 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, 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, 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

OpenlabReader

public OpenlabReader()

Constructs a new OpenlabReader.

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.

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.

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

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: loci.formats.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 loci.formats.IFormatReader

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.

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

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