loci.formats

Class SubResolutionFormatReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.SubResolutionFormatReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

Direct Known Subclasses:

DicomReader, ImarisHDFReader, MinimalTiffReader, NativeND2Reader, OMETiffReader

public abstract class SubResolutionFormatReader
extends FormatReader

Abstract superclass of all biological file format readers that can handle image pyramids.

Field Summary

Fields

Modifier and Type	Field and Description
protected CoreMetadataList	core List of CoreMetadata objects for each series and resolution.

Fields inherited from class loci.formats.FormatReader

coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
SubResolutionFormatReader(java.lang.String format, java.lang.String suffix) Constructs a format reader with the given name and default suffix.
SubResolutionFormatReader(java.lang.String format, java.lang.String[] suffixes) Constructs a format reader with the given name and default suffixes.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
int	coreIndexToSeries(int index) Returns the series corresponding to the specified core index.
protected void	flattenHashtables() Call FormatReader.updateMetadataLists(Hashtable) on all metadata hashtables.
int	getCoreIndex() Return the index into CoreMetadata of the current resolution/series.
java.util.List<CoreMetadata>	getCoreMetadataList() Obtains the core metadata values for the current file.
protected CoreMetadata	getCurrentCore() Get the CoreMetadata corresponding to the current series and resolution
int	getResolution() Get the current resolution level.
int	getResolutionCount() Return the number of resolutions for the current series.
int	getSeries() Gets the currently active series.
int	getSeriesCount() Gets the number of series in this file.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
int	seriesToCoreIndex(int s) Returns the first core index corresponding to the specified series.
void	setCoreIndex(int no) Set the current resolution/series (ignores subresolutions).
void	setResolution(int no) Set the resolution level.
void	setSeries(int no) Activates the specified series.

Methods inherited from class loci.formats.FormatReader

addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, reopenFile, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, updateMetadataLists

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions

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, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Detail

core

protected CoreMetadataList core

List of CoreMetadata objects for each series and resolution.

Constructor Detail

SubResolutionFormatReader

public SubResolutionFormatReader(java.lang.String format,
                                 java.lang.String suffix)

Constructs a format reader with the given name and default suffix.

SubResolutionFormatReader

public SubResolutionFormatReader(java.lang.String format,
                                 java.lang.String[] suffixes)

Constructs a format reader with the given name and default suffixes.

Method Detail

initFile

protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.IOException

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 FormatReader

Throws:

FormatException - if a parsing error occurs processing the file.

java.io.IOException - if an I/O error occurs processing the file

flattenHashtables

protected void flattenHashtables()

Call FormatReader.updateMetadataLists(Hashtable) on all metadata hashtables.

Overrides:

flattenHashtables in class FormatReader

close

public void close(boolean fileOnly)
           throws java.io.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 FormatReader

Throws:

java.io.IOException

getSeriesCount

public int getSeriesCount()

Description copied from interface: IFormatReader

Gets the number of series in this file.

Specified by:

getSeriesCount in interface IFormatReader

Overrides:

getSeriesCount in class FormatReader

See Also:

Note that the value can change depending upon whether resolutions are flattened, and so reader implementations should use the series and resolutions fields internally.

setSeries

public void setSeries(int no)

Description copied from interface: IFormatReader

Activates the specified series. This also resets the resolution to 0.

Specified by:

setSeries in interface IFormatReader

Overrides:

setSeries in class FormatReader

See Also:

Note that the value can change depending upon whether resolutions are flattened, and so reader implementations should use the series and resolutions fields internally.

getSeries

public int getSeries()

Description copied from interface: IFormatReader

Gets the currently active series.

Specified by:

getSeries in interface IFormatReader

Overrides:

getSeries in class FormatReader

getCoreMetadataList

public java.util.List<CoreMetadata> getCoreMetadataList()

Description copied from interface: IFormatReader

Obtains the core metadata values for the current file.

Specified by:

getCoreMetadataList in interface IFormatReader

Overrides:

getCoreMetadataList in class FormatReader

seriesToCoreIndex

public int seriesToCoreIndex(int s)

Description copied from interface: IFormatReader

Returns the first core index corresponding to the specified series.

Specified by:

seriesToCoreIndex in interface IFormatReader

Overrides:

seriesToCoreIndex in class FormatReader

coreIndexToSeries

public int coreIndexToSeries(int index)

Description copied from interface: IFormatReader

Returns the series corresponding to the specified core index.

Specified by:

coreIndexToSeries in interface IFormatReader

Overrides:

coreIndexToSeries in class FormatReader

getResolutionCount

public int getResolutionCount()

Description copied from interface: IPyramidHandler

Return the number of resolutions for the current series. Resolutions are stored in descending order, so the largest resolution is first and the smallest resolution is last.

Specified by:

getResolutionCount in interface IPyramidHandler

Overrides:

getResolutionCount in class FormatReader

setResolution

public void setResolution(int no)

Description copied from interface: IPyramidHandler

Set the resolution level.

Specified by:

setResolution in interface IPyramidHandler

Overrides:

setResolution in class FormatReader

See Also:

IPyramidHandler.getResolutionCount()

getResolution

public int getResolution()

Description copied from interface: IPyramidHandler

Get the current resolution level.

Specified by:

getResolution in interface IPyramidHandler

Overrides:

getResolution in class FormatReader

See Also:

IPyramidHandler.getResolutionCount()

getCoreIndex

public int getCoreIndex()

Description copied from interface: IFormatReader

Return the index into CoreMetadata of the current resolution/series.

Specified by:

getCoreIndex in interface IFormatReader

Overrides:

getCoreIndex in class FormatReader

setCoreIndex

public void setCoreIndex(int no)

Description copied from interface: IFormatReader

Set the current resolution/series (ignores subresolutions). Equivalent to setSeries, but with flattened resolutions always set to false.

Specified by:

setCoreIndex in interface IFormatReader

Overrides:

setCoreIndex in class FormatReader

getCurrentCore

protected CoreMetadata getCurrentCore()

Get the CoreMetadata corresponding to the current series and resolution

Overrides:

getCurrentCore in class FormatReader

Returns:

the CoreMetadata