loci.formats.in

Class CellWorxReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.CellWorxReader

All Implemented Interfaces:

java.io.Closeable, java.lang.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 and Description
protected static java.lang.String	DATE_FORMAT
protected java.lang.String[]	directoryList
protected boolean	doChannels
protected int	fieldCount
private boolean[][]	fieldMap
private java.lang.String	lastFile
private IFormatReader	lastReader
private java.lang.String[][]	logFiles
protected int	nTimepoints
private java.lang.String	plateLogFile
private OMEXMLService	service
protected boolean	subdirectories
private java.util.HashMap<java.lang.Integer,ome.xml.model.primitives.Timestamp>	timestamps
protected java.lang.String[]	wavelengths
protected int	wellCount
protected java.lang.String[][][]	wellFiles
private java.lang.String	zMapFile
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 and Description
CellWorxReader() Constructs a new CellWorx reader.
CellWorxReader(java.lang.String name, java.lang.String[] extensions)

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
int	fileGroupOption(java.lang.String id) Returns an indication of whether the files in a multi-file dataset can be handled individually.
protected void	findPixelsFiles()
protected boolean	foundHTDFile(java.lang.String name)
private java.lang.String	getFile(int seriesIndex, int no) Retrieve the .pnl file corresponding to the given series.
protected java.lang.String	getPlateName(java.lang.String id)
protected IFormatReader	getReader(java.lang.String file, boolean omexml)
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
private int	getWell(int seriesIndex) Retrieve the well index corresponding to the given series.
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(java.lang.String id) Initializes the given file (parsing header information, etc.).
protected void	initReader(IFormatReader reader, java.lang.String file, boolean omexml)
boolean	isThisType(java.lang.String name, boolean open) Checks if a file matches the type of this format reader.
byte[]	openBytes(int no, byte[] buf, int x, int y, int w, int h) Obtains a sub-image of the specified image plane into a pre-allocated byte array.
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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Field Detail

DATE_FORMAT

protected static final java.lang.String DATE_FORMAT

See Also:

Constant Field Values

fieldMap

private boolean[][] fieldMap

wellFiles

protected java.lang.String[][][] wellFiles

logFiles

private java.lang.String[][] logFiles

fieldCount

protected int fieldCount

doChannels

protected boolean doChannels

plateLogFile

private java.lang.String plateLogFile

zMapFile

private java.lang.String zMapFile

lastFile

private java.lang.String lastFile

lastReader

private IFormatReader lastReader

service

private OMEXMLService service

timestamps

private java.util.HashMap<java.lang.Integer,ome.xml.model.primitives.Timestamp> timestamps

directoryList

protected java.lang.String[] directoryList

subdirectories

protected boolean subdirectories

wavelengths

protected java.lang.String[] wavelengths

nTimepoints

protected int nTimepoints

zSteps

protected int zSteps

wellCount

protected int wellCount

Constructor Detail

CellWorxReader

public CellWorxReader()

Constructs a new CellWorx reader.

CellWorxReader

public CellWorxReader(java.lang.String name,
                      java.lang.String[] extensions)

Method Detail

fileGroupOption

public int fileGroupOption(java.lang.String id)
                    throws FormatException,
                           java.io.IOException

Description copied from interface: IFormatReader

Returns an indication of whether the files in a multi-file dataset can be handled individually. This method is only useful for formats and datasets which contain multiple files.

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Parameters:

id - a file in the multi-file dataset

Returns:

an int indicating that we cannot, must, or might group the files. A return value of FormatTools.MUST_GROUP indicates that the files cannot be handled separately; the reader will always detect and read all files in the dataset. FormatTools.CAN_GROUP indicates that the files may be handled separately, but file grouping must then be disabled via IFormatReader.setGroupFiles(boolean). FormatTools.CANNOT_GROUP indicates that the files must be handled separately; the reader will not attempt to read all files in the dataset (this is rare).

Throws:

FormatException

java.io.IOException

See Also:

FormatTools.MUST_GROUP, FormatTools.CAN_GROUP, FormatTools.CANNOT_GROUP

isThisType

public boolean isThisType(java.lang.String name,
                          boolean open)

Description copied from class: FormatReader

Checks if a file matches the type of this format reader. Checks filename suffixes against those known for this format. If the suffix check is inconclusive and the open parameter is true, the file is opened and tested with FormatReader.isThisType(RandomAccessInputStream).

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis.

getSeriesUsedFiles

public java.lang.String[] getSeriesUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned. The first element in the array is expected to be the path passed to IFormatHandler.setId(String), if appropriate based upon 'noPixels'. The remaining elements are expected to be in a consistent order; if a directory listing is necessary to build the list then it should be sorted first.

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,
                        java.io.IOException

Description copied from interface: IFormatReader

Obtains a sub-image of the specified image plane into a pre-allocated byte array.

Specified by:

openBytes in interface IFormatReader

Specified by:

openBytes in class FormatReader

Parameters:

no - the plane index within the current series.

buf - a pre-allocated buffer.

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:

the pre-allocated buffer buf for convenience.

Throws:

FormatException - if there was a problem parsing the metadata of the file.

java.io.IOException - if there was a problem reading the file.

See Also:

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

close

public void close(boolean fileOnly)
           throws java.io.IOException

Description copied from interface: IFormatReader

Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().

Specified by:

close in interface IFormatReader

Overrides:

close in class FormatReader

Throws:

java.io.IOException

initFile

protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.IOException

Description copied from class: FormatReader

Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.

Overrides:

initFile in class FormatReader

Throws:

FormatException - if a parsing error occurs processing the file.

java.io.IOException - if an I/O error occurs processing the file

populateMetadata

protected void populateMetadata()
                         throws FormatException,
                                java.io.IOException

Throws:

FormatException

java.io.IOException

parseHTD

protected void parseHTD()
                 throws FormatException,
                        java.io.IOException

Throws:

FormatException

java.io.IOException

getPlateName

protected java.lang.String getPlateName(java.lang.String id)

findPixelsFiles

protected void findPixelsFiles()
                        throws FormatException

Throws:

FormatException

getWell

private int getWell(int seriesIndex)

Retrieve the well index corresponding to the given series.

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.

getFile

private java.lang.String getFile(int seriesIndex,
                                 int no)

Retrieve the .pnl file corresponding to the given series.

parseWellLogFile

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

Parse metadata from a well log file.

Throws:

java.io.IOException

getReader

protected IFormatReader getReader(java.lang.String file,
                                  boolean omexml)
                           throws FormatException,
                                  java.io.IOException

Throws:

FormatException

java.io.IOException

initReader

protected void initReader(IFormatReader reader,
                          java.lang.String file,
                          boolean omexml)
                   throws FormatException,
                          java.io.IOException

Throws:

FormatException

java.io.IOException

foundHTDFile

protected boolean foundHTDFile(java.lang.String name)