ome.formats.importer

Class OMEROWrapper

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.MinMaxCalculator

ome.formats.importer.OMEROWrapper

All Implemented Interfaces:

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

public class OMEROWrapper
extends loci.formats.MinMaxCalculator

Author:

Brian Loranger brain at lifesci.dundee.ac.uk, Chris Allan callan at blackcat.ca

Field Summary

Fields

Modifier and Type	Field and Description
Boolean	minMaxSet

Fields inherited from class loci.formats.MinMaxCalculator

chanMax, chanMin, minMaxDone, minMaxStore, planeMax, planeMin

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
OMEROWrapper(ImportConfig config) Wrapper for bio-formats
OMEROWrapper(ImportConfig config, long elapsedTime, File cacheDirectory)

Method Summary

Methods

Modifier and Type	Method and Description
void	close()
ImportConfig	getConfig()
loci.formats.ImageReader	getImageReader() Return the base image reader
loci.formats.in.MetadataOptions	getMetadataOptions()
Set<loci.formats.in.MetadataLevel>	getSupportedMetadataLevels()
boolean	isLeicaReader()
boolean	isMinMaxSet()
boolean	isSPWReader()
ome.util.PixelData	openPlane2D(String id, int planeNumber, byte[] buf) Obtains an object which represents a given sub-image of a plane within the file.
ome.util.PixelData	openPlane2D(String id, int planeNumber, byte[] buf, int x, int y, int w, int h) Obtains an object which represents a given sub-image of a plane within the file.
void	setMetadataOptions(loci.formats.in.MetadataOptions options)
protected void	updateMinMax(int no, byte[] buf, int len)

Methods inherited from class loci.formats.MinMaxCalculator

close, getChannelGlobalMaximum, getChannelGlobalMinimum, getChannelKnownMaximum, getChannelKnownMinimum, getMinMaxStore, getNativeDataType, getPlaneMaximum, getPlaneMinimum, initMinMax, isMinMaxPopulated, makeMinMaxCalculator, openBytes, openBytes, openBytes, openBytes, setMinMaxStore

Methods inherited from class loci.formats.ReaderWrapper

coreIndexToSeries, duplicate, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getCoreIndex, getCoreMetadataList, getCurrentFile, getDatasetStructureDescription, getDimensionOrder, getDomains, getEffectiveSizeC, getFormat, getGlobalMetadata, getImageCount, getIndex, getIndex, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSuffixes, 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, openPlane, openThumbBytes, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, 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

minMaxSet

public Boolean minMaxSet

Constructor Detail

OMEROWrapper

public OMEROWrapper(ImportConfig config)

Wrapper for bio-formats

Parameters:

config - - ImportConfit

OMEROWrapper

public OMEROWrapper(ImportConfig config,
            long elapsedTime,
            File cacheDirectory)

Method Detail

getConfig

public ImportConfig getConfig()

openPlane2D

public ome.util.PixelData openPlane2D(String id,
                             int planeNumber,
                             byte[] buf)
                               throws loci.formats.FormatException,
                                      IOException

Obtains an object which represents a given sub-image of a plane within the file.

Parameters:

id - The path to the file.

planeNumber - The plane or section within the file to obtain.

buf - Pre-allocated buffer which has a length that can fit the entire plane.

Returns:

an object which represents the plane.

Throws:

loci.formats.FormatException - If there is an error parsing the file.

IOException - If there is an error reading from the file or acquiring permissions to read the file.

openPlane2D

public ome.util.PixelData openPlane2D(String id,
                             int planeNumber,
                             byte[] buf,
                             int x,
                             int y,
                             int w,
                             int h)
                               throws loci.formats.FormatException,
                                      IOException

Obtains an object which represents a given sub-image of a plane within the file.

Parameters:

id - The path to the file.

planeNumber - The plane or section within the file to obtain.

buf - Pre-allocated buffer which has a length that can fit the byte count of the sub-image.

x - X coordinate of the upper-left corner of the sub-image

y - Y coordinate of the upper-left corner of the sub-image

w - width of the sub-image

h - height of the sub-image

Returns:

an object which represents the sub-image of the plane.

Throws:

loci.formats.FormatException - If there is an error parsing the file.

IOException - If there is an error reading from the file or acquiring permissions to read the file.

isLeicaReader

public boolean isLeicaReader()

Returns:

true if reader being used is LeicaReader

isMinMaxSet

public boolean isMinMaxSet()
                    throws loci.formats.FormatException,
                           IOException

Returns:

true if min-max is set

Throws:

loci.formats.FormatException

IOException

updateMinMax

protected void updateMinMax(int no,
                byte[] buf,
                int len)
                     throws loci.formats.FormatException,
                            IOException

Overrides:

updateMinMax in class loci.formats.MinMaxCalculator

Throws:

loci.formats.FormatException

IOException

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Overrides:

close in class loci.formats.ReaderWrapper

Throws:

IOException

getImageReader

public loci.formats.ImageReader getImageReader()

Return the base image reader

Returns:

See above.

isSPWReader

public boolean isSPWReader()

Returns:

true if using SPW reader

getMetadataOptions

public loci.formats.in.MetadataOptions getMetadataOptions()

Specified by:

getMetadataOptions in interface loci.formats.IMetadataConfigurable

Overrides:

getMetadataOptions in class loci.formats.ReaderWrapper

setMetadataOptions

public void setMetadataOptions(loci.formats.in.MetadataOptions options)

Specified by:

setMetadataOptions in interface loci.formats.IMetadataConfigurable

Overrides:

setMetadataOptions in class loci.formats.ReaderWrapper

getSupportedMetadataLevels

public Set<loci.formats.in.MetadataLevel> getSupportedMetadataLevels()

Specified by:

getSupportedMetadataLevels in interface loci.formats.IMetadataConfigurable

Overrides:

getSupportedMetadataLevels in class loci.formats.ReaderWrapper