ome.formats.importer
Class OMEROWrapper

java.lang.Object
  extended by loci.formats.ReaderWrapper
      extended by loci.formats.MinMaxCalculator
          extended by ome.formats.importer.OMEROWrapper
All Implemented Interfaces:
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
 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
OMEROWrapper(ImportConfig config)
          Wrapper for bio-formats
 
Method Summary
 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
copyCoreMetadata, duplicate, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCoreMetadata, getCurrentFile, getDimensionOrder, getDomains, getEffectiveSizeC, getFormat, getGlobalMetadata, getImageCount, getIndex, getMetadata, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSuffixes, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, openPlane, openThumbBytes, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, 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
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 loci.formats.IFormatHandler
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


OmeroJava Api

Version: 4.3.4-dbcbce5a-b4

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