loci.formats

Class Memoizer

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.Memoizer

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class Memoizer
extends ReaderWrapper

ReaderWrapper implementation which caches the state of the delegate (including and other ReaderWrapper instances) after setId has been called.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	Memoizer.Deser
static class	Memoizer.KryoDeser

Field Summary

Fields

Modifier and Type	Field and Description
static long	DEFAULT_MINIMUM_ELAPSED Default value for minimumElapsed if none is provided in the constructor.
static Integer	VERSION Defines the file format.

Fields inherited from class loci.formats.ReaderWrapper

reader

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
Memoizer() Constructs a memoizer around a new image reader.
Memoizer(IFormatReader r) Constructs a memoizer around the given reader.
Memoizer(IFormatReader r, long minimumElapsed) Constructs a memoizer around the given reader.
Memoizer(IFormatReader r, long minimumElapsed, File directory)
Memoizer(long minimumElapsed) Constructs a memoizer around a new image reader.
Memoizer(long minimumElapsed, File directory)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	cleanup()
void	close()
void	close(boolean fileOnly) Closes the currently open file.
protected Memoizer.Deser	getDeser() Returns a configured Kryo instance.
File	getMemoFile(String id) Constructs a File object from setId string.
MetadataStore	getMetadataStore() Retrieves the current metadata store for this reader.
protected OMEXMLService	getService()
protected IFormatReader	handleMetadataStore(IFormatReader memo) : Serialization: If an unknown MetadataStore implementation is passed in when no memo file exists, then a replacement MetadataStore will be created and set on the ReaderWrapper.reader delegate before calling ReaderWrapper.setId(String).
boolean	isLoadedFromMemo()
boolean	isSavedToMemo()
boolean	isVersionChecking() Returns whether or not version checking is done based upon major/minor version numbers.
IFormatReader	loadMemo()
boolean	saveMemo()
void	setId(String id) Sets the current file name.
void	setMetadataStore(MetadataStore store) Sets the default metadata store for this reader.
void	setVersionChecking(boolean version) Set whether version checking is done based upon major/minor version numbers.
protected org.perf4j.slf4j.Slf4JStopWatch	stopWatch()

Methods inherited from class loci.formats.ReaderWrapper

coreIndexToSeries, duplicate, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCoreIndex, getCoreMetadata, getCoreMetadataList, getCurrentFile, getDatasetStructureDescription, getDimensionOrder, getDomains, getEffectiveSizeC, getFormat, getGlobalMetadata, getImageCount, getIndex, getMetadataOptions, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getNativeDataType, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSuffixes, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, openBytes, openBytes, openBytes, openBytes, openPlane, openThumbBytes, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setMetadataFiltered, setMetadataOptions, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, unwrap, unwrap, unwrap

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

VERSION

public static final Integer VERSION

Defines the file format. Bumping this number will invalidate all other cached items. This should happen when the order and type of objects stored in the memo file changes.

DEFAULT_MINIMUM_ELAPSED

public static final long DEFAULT_MINIMUM_ELAPSED

Default value for minimumElapsed if none is provided in the constructor.

See Also:

Constant Field Values

Constructor Detail

Memoizer

public Memoizer()

Constructs a memoizer around a new image reader.

Memoizer

public Memoizer(long minimumElapsed)

Constructs a memoizer around a new image reader.

Memoizer

public Memoizer(long minimumElapsed,
        File directory)

Memoizer

public Memoizer(IFormatReader r)

Constructs a memoizer around the given reader.

Memoizer

public Memoizer(IFormatReader r,
        long minimumElapsed)

Constructs a memoizer around the given reader.

Memoizer

public Memoizer(IFormatReader r,
        long minimumElapsed,
        File directory)

Method Detail

isLoadedFromMemo

public boolean isLoadedFromMemo()

isSavedToMemo

public boolean isSavedToMemo()

isVersionChecking

public boolean isVersionChecking()

Returns whether or not version checking is done based upon major/minor version numbers.

setVersionChecking

public void setVersionChecking(boolean version)

Set whether version checking is done based upon major/minor version numbers. If 'true' is passed in, then a mismatch between the major/minor version of the calling code (e.g. 4.4) and the major/minor version saved in the memo file (e.g. 5.0) will result in the memo file being invalidated. By default, a mismatch in the Git commit hashes will invalidate the memo file; this method allows for less strict version checking.

cleanup

protected void cleanup()

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Overrides:

close in class ReaderWrapper

Throws:

IOException

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 Closeable.close().

Specified by:

close in interface IFormatReader

Overrides:

close in class ReaderWrapper

Throws:

IOException

setId

public void setId(String id)
           throws FormatException,
                  IOException

Description copied from interface: IFormatHandler

Sets the current file name.

Specified by:

setId in interface IFormatHandler

Overrides:

setId in class ReaderWrapper

Throws:

FormatException

IOException

setMetadataStore

public void setMetadataStore(MetadataStore store)

Description copied from interface: IFormatReader

Sets the default metadata store for this reader.

Specified by:

setMetadataStore in interface IFormatReader

Overrides:

setMetadataStore in class ReaderWrapper

Parameters:

store - a metadata store implementation.

getMetadataStore

public MetadataStore getMetadataStore()

Description copied from interface: IFormatReader

Retrieves the current metadata store for this reader. You can be assured that this method will never return a null metadata store.

Specified by:

getMetadataStore in interface IFormatReader

Overrides:

getMetadataStore in class ReaderWrapper

Returns:

A metadata store implementation.

getDeser

protected Memoizer.Deser getDeser()

Returns a configured Kryo instance. This method can be modified by consumers. The returned instance is not thread-safe.

Returns:

a non-null Kryo instance.

getService

protected OMEXMLService getService()
                            throws MissingLibraryException

Throws:

MissingLibraryException

stopWatch

protected org.perf4j.slf4j.Slf4JStopWatch stopWatch()

getMemoFile

public File getMemoFile(String id)

Constructs a File object from setId string. This method can be modified by consumers, but then existing memo files will not be found.

Parameters:

id - the path passed to setId

Returns:

a filename with

loadMemo

public IFormatReader loadMemo()
                       throws IOException,
                              FormatException

Throws:

IOException

FormatException

saveMemo

public boolean saveMemo()

handleMetadataStore

protected IFormatReader handleMetadataStore(IFormatReader memo)
                                     throws MissingLibraryException

:

• Serialization: If an unknown MetadataStore implementation is passed in when no memo file exists, then a replacement MetadataStore will be created and set on the ReaderWrapper.reader delegate before calling ReaderWrapper.setId(String). This stack will then be serialized, before any values are copied into userMetadataStore.
• Deserialization: If an unknown MetadataStore implementation is set before calling setId(String) then ...

Throws:

MissingLibraryException