ome.services.formats
Class OmeroReader

java.lang.Object
  extended by loci.formats.FormatHandler
      extended by loci.formats.FormatReader
          extended by ome.services.formats.OmeroReader
All Implemented Interfaces:
loci.formats.IFormatHandler, loci.formats.IFormatReader, loci.formats.IMetadataConfigurable

public class OmeroReader
extends loci.formats.FormatReader

Implementation of IFormatReader for use in export. This is copied from the OMERO 2.3 Reader available from: https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/ome- io/src/loci/ome/io

Since:
Beta4.1
See Also:
MinimumWriter, ImageConverter, ReadWriteInMemory

Field Summary
 int planes
           
 int sizeC
           
 int sizeT
           
 int sizeX
           
 int sizeY
           
 int sizeZ
           
 
Fields inherited from class loci.formats.FormatReader
core, domains, filterMetadata, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, 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
OmeroReader(RawPixelsStore raw, omero.model.Pixels pix)
           
OmeroReader(omero.api.RawPixelsStorePrx prx, omero.model.Pixels pix)
           
 
Method Summary
 void close()
           
protected  void initFile(String id)
           
 boolean isThisType(loci.common.RandomAccessInputStream stream)
           
 boolean isThisType(String name, boolean open)
           
 byte[] openBytes(int no, byte[] buf, int x1, int y1, int w1, int h1)
           
 
Methods inherited from class loci.formats.FormatReader
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, close, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreMetadata, getCorrection, getCurrentFile, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadata, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, 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

sizeX

public final int sizeX

sizeY

public final int sizeY

sizeZ

public final int sizeZ

sizeT

public final int sizeT

sizeC

public final int sizeC

planes

public final int planes
Constructor Detail

OmeroReader

public OmeroReader(RawPixelsStore raw,
                   omero.model.Pixels pix)

OmeroReader

public OmeroReader(omero.api.RawPixelsStorePrx prx,
                   omero.model.Pixels pix)
Method Detail

isThisType

public boolean isThisType(String name,
                          boolean open)
Specified by:
isThisType in interface loci.formats.IFormatReader
Overrides:
isThisType in class loci.formats.FormatReader

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws IOException
Specified by:
isThisType in interface loci.formats.IFormatReader
Overrides:
isThisType in class loci.formats.FormatReader
Throws:
IOException

openBytes

public byte[] openBytes(int no,
                        byte[] buf,
                        int x1,
                        int y1,
                        int w1,
                        int h1)
                 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()
           throws IOException
Specified by:
close in interface loci.formats.IFormatHandler
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


OmeroJava Api

Version: Beta-4.2.0-r7571-b29

Copyright © 2009 The University of Dundee. All Rights Reserved.