Package loci.formats.in

Class CellWorxReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.CellWorxReader

All Implemented Interfaces:

Closeable, AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

Direct Known Subclasses:

MetaxpressTiffReader

public class CellWorxReader
extends FormatReader

CellWorxReader is the file format reader for CellWorx .pnl files.

Field Summary

Fields

Modifier and Type	Field	Description
protected static final String	DATE_FORMAT
protected String[]	directoryList
protected boolean	doChannels
protected int	fieldCount
protected int	nTimepoints
protected boolean	subdirectories
protected String[]	wavelengths
protected int	wellCount
protected String[][][]	wellFiles
protected int	zSteps

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	Description
CellWorxReader()	Constructs a new CellWorx reader.
CellWorxReader(String name, String[] extensions)

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)
int	fileGroupOption(String id)
protected void	findPixelsFiles()
protected boolean	foundHTDFile(String name)
protected String	getPlateName(String id)
protected IFormatReader	getReader(String file, boolean omexml)
String[]	getSeriesUsedFiles(boolean noPixels)
protected int	getWellColumn(int seriesIndex)	Retrieve the well column corresponding to the given series.
protected int	getWellRow(int seriesIndex)	Retrieve the well row corresponding to the given series.
protected void	initFile(String id)
protected void	initReader(IFormatReader reader, String file, boolean omexml)
boolean	isThisType(String name, boolean open)
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h)
protected void	parseHTD()
protected void	parseWellLogFile(int wellIndex, MetadataStore store)	Parse metadata from a well log file.
protected void	populateMetadata()

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, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, 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, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, 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, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, 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.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

DATE_FORMAT

protected static final String DATE_FORMAT

See Also:

• Constant Field Values

wellFiles

protected String[][][] wellFiles

fieldCount

protected int fieldCount

doChannels

protected boolean doChannels

directoryList

protected String[] directoryList

subdirectories

protected boolean subdirectories

wavelengths

protected String[] wavelengths

nTimepoints

protected int nTimepoints

zSteps

protected int zSteps

wellCount

protected int wellCount

Constructor Details

CellWorxReader

public CellWorxReader()

Constructs a new CellWorx reader.

CellWorxReader

public CellWorxReader(String name,
 String[] extensions)

Method Details

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
IOException

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Throws:

FormatException

IOException

isThisType

public boolean isThisType(String name,
 boolean open)

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

getSeriesUsedFiles

public String[] getSeriesUsedFiles(boolean noPixels)

Specified by:

getSeriesUsedFiles in interface IFormatReader

Overrides:

getSeriesUsedFiles in class FormatReader

openBytes

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

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Throws:

FormatException

IOException

See Also:

• IFormatReader.openBytes(int, byte[], int, int, int, int)

close

public void close(boolean fileOnly)
           throws IOException

Specified by:

close in interface IFormatReader

Overrides:

close in class FormatReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
IOException

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException

populateMetadata

protected void populateMetadata()
                         throws FormatException,
IOException

Throws:

FormatException

IOException

parseHTD

protected void parseHTD()
                 throws FormatException,
IOException

Throws:

FormatException

IOException

getPlateName

protected String getPlateName(String id)

findPixelsFiles

protected void findPixelsFiles()
                        throws FormatException

Throws:

FormatException

getWellRow

protected int getWellRow(int seriesIndex)

Retrieve the well row corresponding to the given series.

getWellColumn

protected int getWellColumn(int seriesIndex)

Retrieve the well column corresponding to the given series.

parseWellLogFile

protected void parseWellLogFile(int wellIndex,
 MetadataStore store)
                         throws IOException

Parse metadata from a well log file.

Throws:

IOException

getReader

protected IFormatReader getReader(String file,
 boolean omexml)
                           throws FormatException,
IOException

Throws:

FormatException

IOException

initReader

protected void initReader(IFormatReader reader,
 String file,
 boolean omexml)
                   throws FormatException,
IOException

Throws:

FormatException

IOException

foundHTDFile

protected boolean foundHTDFile(String name)