loci.formats.in

Class FilePatternReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.WrappedReader

loci.formats.in.FilePatternReader

All Implemented Interfaces:

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

public class FilePatternReader
extends WrappedReader

Field Summary

Fields

Modifier and Type	Field and Description
private FileStitcher	helper

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, fillColor, 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
FilePatternReader() Constructs a new pattern reader.

Method Summary

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.
java.util.List<CoreMetadata>	getCoreMetadataList() Obtains the core metadata values for the current file.
protected ReaderWrapper	getHelper() Get the helper class that reads images
MetadataStore	getMetadataStore() Retrieves the current metadata store for this reader.
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
java.lang.String[]	getUsedFiles(boolean noPixels) Returns an array of filenames needed to open this dataset.
boolean	hasCompanionFiles() Returns true if this format supports multi-file datasets.
boolean	hasFlattenedResolutions() Return whether or not resolution flattening is enabled.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
boolean	isGroupFiles() Returns true if we should group files in multi-file formats.
boolean	isMetadataFiltered() Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.
boolean	isNormalized() Returns true if we should normalize float data.
boolean	isOriginalMetadataPopulated() Returns true if we should save proprietary metadata in the MetadataStore.
boolean	isSingleFile(java.lang.String id) Returns true if the named file is expected to be the only file in the dataset.
void	setFlattenedResolutions(boolean flattened) Set whether or not to flatten resolutions into individual series.
void	setGroupFiles(boolean group) Specifies whether or not to force grouping in multi-file formats.
void	setMetadataFiltered(boolean filter) Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.
void	setMetadataStore(MetadataStore store) Sets the default metadata store for this reader.
void	setNormalized(boolean normalize) Specifies whether or not to normalize float data.
void	setOriginalMetadataPopulated(boolean populate) Specifies whether or not to save proprietary metadata in the MetadataStore.

Methods inherited from class loci.formats.WrappedReader

callDeferredSetters, close, close, coreIndexToSeries, getBitsPerPixel, getCoreIndex, getDatasetStructureDescription, getDimensionOrder, getDomains, getEffectiveSizeC, getGlobalMetadata, getImageCount, getIndex, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getNativeDataType, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getZCTCoords, isFalseColor, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isOrderCertain, isRGB, isThumbnailSeries, openBytes, openBytes, openBytes, openBytes, openPlane, openThumbBytes, reopenFile, seriesToCoreIndex, setCoreIndex, setResolution, setSeries

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, fileGroupOption, flattenHashtables, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getCompression, getContrastMethod, getCorrection, getCurrentCore, getCurrentFile, getDetectorType, getDimensionOrder, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getIlluminationType, getImmersion, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMicrobeamManipulationType, getMicroscopeType, getNamingConvention, getPixelType, getPulse, getRequiredDirectories, getRotationTransform, getSeriesMeta, getSeriesUsedFiles, getTileColumns, getTileRows, getUsedFiles, getZCTModuloCoords, isThisType, isThisType, isThisType, isThisType, isUsedFile, makeFilterMetadata, readPlane, readPlane, readPlane, setFillColor, setId, updateMetadataLists

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, 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, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Field Detail

helper

private FileStitcher helper

Constructor Detail

FilePatternReader

public FilePatternReader()

Constructs a new pattern reader.

Method Detail

getHelper

protected ReaderWrapper getHelper()

Description copied from class: WrappedReader

Get the helper class that reads images

Specified by:

getHelper in class WrappedReader

setGroupFiles

public void setGroupFiles(boolean group)

Description copied from interface: IFormatReader

Specifies whether or not to force grouping in multi-file formats.

Specified by:

setGroupFiles in interface IFormatReader

Overrides:

setGroupFiles in class FormatReader

See Also:

IFormatReader.fileGroupOption(String), IFormatReader.isGroupFiles()

isGroupFiles

public boolean isGroupFiles()

Description copied from interface: IFormatReader

Returns true if we should group files in multi-file formats.

Specified by:

isGroupFiles in interface IFormatReader

Overrides:

isGroupFiles in class FormatReader

See Also:

IFormatReader.setGroupFiles(boolean), IFormatReader.fileGroupOption(String)

setNormalized

public void setNormalized(boolean normalize)

Description copied from interface: IFormatReader

Specifies whether or not to normalize float data.

Specified by:

setNormalized in interface IFormatReader

Overrides:

setNormalized in class FormatReader

isNormalized

public boolean isNormalized()

Description copied from interface: IFormatReader

Returns true if we should normalize float data.

Specified by:

isNormalized in interface IFormatReader

Overrides:

isNormalized in class FormatReader

setOriginalMetadataPopulated

public void setOriginalMetadataPopulated(boolean populate)

Description copied from interface: IFormatReader

Specifies whether or not to save proprietary metadata in the MetadataStore.

Specified by:

setOriginalMetadataPopulated in interface IFormatReader

Overrides:

setOriginalMetadataPopulated in class FormatReader

isOriginalMetadataPopulated

public boolean isOriginalMetadataPopulated()

Description copied from interface: IFormatReader

Returns true if we should save proprietary metadata in the MetadataStore.

Specified by:

isOriginalMetadataPopulated in interface IFormatReader

Overrides:

isOriginalMetadataPopulated in class FormatReader

setMetadataFiltered

public void setMetadataFiltered(boolean filter)

Description copied from interface: IFormatReader

Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table.

Specified by:

setMetadataFiltered in interface IFormatReader

Overrides:

setMetadataFiltered in class FormatReader

isMetadataFiltered

public boolean isMetadataFiltered()

Description copied from interface: IFormatReader

Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table.

Specified by:

isMetadataFiltered in interface IFormatReader

Overrides:

isMetadataFiltered in class FormatReader

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 FormatReader

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 FormatReader

Returns:

A metadata store implementation.

hasFlattenedResolutions

public boolean hasFlattenedResolutions()

Description copied from interface: IFormatReader

Return whether or not resolution flattening is enabled.

Specified by:

hasFlattenedResolutions in interface IFormatReader

Overrides:

hasFlattenedResolutions in class FormatReader

setFlattenedResolutions

public void setFlattenedResolutions(boolean flattened)

Description copied from interface: IFormatReader

Set whether or not to flatten resolutions into individual series.

Specified by:

setFlattenedResolutions in interface IFormatReader

Overrides:

setFlattenedResolutions in class FormatReader

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   java.io.IOException

Description copied from interface: IFormatReader

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

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class WrappedReader

Throws:

FormatException

java.io.IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
                                     java.io.IOException

Description copied from interface: IFormatReader

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

Specified by:

get16BitLookupTable in interface IFormatReader

Overrides:

get16BitLookupTable in class WrappedReader

Throws:

FormatException

java.io.IOException

getSeriesUsedFiles

public java.lang.String[] getSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class WrappedReader

getUsedFiles

public java.lang.String[] getUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open this dataset. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

Specified by:

getUsedFiles in interface IFormatReader

Overrides:

getUsedFiles in class WrappedReader

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 WrappedReader

isSingleFile

public boolean isSingleFile(java.lang.String id)
                     throws FormatException,
                            java.io.IOException

Description copied from interface: IFormatReader

Returns true if the named file is expected to be the only file in the dataset. For single-file formats, always returns true.

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class WrappedReader

Throws:

FormatException

java.io.IOException

hasCompanionFiles

public boolean hasCompanionFiles()

Description copied from interface: IFormatReader

Returns true if this format supports multi-file datasets.

Specified by:

hasCompanionFiles in interface IFormatReader

Overrides:

hasCompanionFiles in class WrappedReader

initFile

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

Description copied from class: 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 FormatReader

Throws:

FormatException - if a parsing error occurs processing the file.

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