loci.ome.io

Class OmeroReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.ome.io.OmeroReader

All Implemented Interfaces:

Closeable, AutoCloseable, loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable

public class OmeroReader
extends loci.formats.FormatReader

Implementation of IFormatReader for use in export from an OMERO Beta 4.2.x database.

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_PORT

Fields inherited from class loci.formats.FormatReader

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

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
OmeroReader()

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly)
protected void	initFile(String id)
boolean	isThisType(String name, boolean open)
static void	main(String[] args) A simple command line tool for downloading images from OMERO.
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)
protected static String	parsePoints(String str) Parse Points String obtained from convertPoints and extract Coordinates as String
static void	saveOmeroRoiToMetadataStore(List<omero.model.Roi> rois, loci.formats.meta.MetadataStore store) Converts omero.model.Roi to ome.xml.model.* and updates the MetadataStore
void	setEncrypted(boolean encrypted)
void	setGroupID(Long groupID)
void	setGroupName(String group)
void	setPassword(String password)
void	setPort(int port)
void	setServer(String server)
void	setSessionID(String sessionID)
void	setUsername(String username)

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, coreIndexToSeries, fileGroupOption, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, 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, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

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

Field Detail

DEFAULT_PORT

public static final int DEFAULT_PORT

See Also:

Constant Field Values

Constructor Detail

OmeroReader

public OmeroReader()

Method Detail

setServer

public void setServer(String server)

setPort

public void setPort(int port)

setUsername

public void setUsername(String username)

setPassword

public void setPassword(String password)

setSessionID

public void setSessionID(String sessionID)

setEncrypted

public void setEncrypted(boolean encrypted)

setGroupName

public void setGroupName(String group)

setGroupID

public void setGroupID(Long groupID)

isThisType

public boolean isThisType(String name,
                          boolean open)

Specified by:

isThisType in interface loci.formats.IFormatReader

Overrides:

isThisType in class loci.formats.FormatReader

openBytes

public byte[] openBytes(int no,
                        byte[] buf,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws loci.formats.FormatException,
                        IOException

Specified by:

openBytes in interface loci.formats.IFormatReader

Specified by:

openBytes in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface loci.formats.IFormatReader

Overrides:

close in class loci.formats.FormatReader

Throws:

IOException

initFile

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

Overrides:

initFile in class loci.formats.FormatReader

Throws:

loci.formats.FormatException

IOException

main

public static void main(String[] args)
                 throws Exception

A simple command line tool for downloading images from OMERO.

Throws:

Exception

saveOmeroRoiToMetadataStore

public static void saveOmeroRoiToMetadataStore(List<omero.model.Roi> rois,
                                               loci.formats.meta.MetadataStore store)

Converts omero.model.Roi to ome.xml.model.* and updates the MetadataStore

parsePoints

protected static String parsePoints(String str)

Parse Points String obtained from convertPoints and extract Coordinates as String