loci.formats.in

Class InCellReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.InCellReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class InCellReader
extends FormatReader

InCellReader is the file format reader for InCell 1000/2000 datasets.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	InCellReader.Image
(package private) class	InCellReader.InCellHandler SAX handler for parsing XML.
(package private) class	InCellReader.MinimalInCellHandler

Field Summary

Fields

Modifier and Type	Field and Description
private ome.xml.model.enums.Binning	bin
private java.util.List<java.lang.String>	channelNames
private java.util.List<java.lang.Integer>	channelsPerTimepoint
private java.lang.String	colName
private java.lang.String	creationDate
static java.lang.String	CYTELL_MAGIC_STRING
private java.util.List<java.lang.String>	emFilters
private java.util.List<java.lang.Double>	emWaves
private boolean[][]	exclude
private java.util.List<java.lang.String>	exFilters
private java.util.List<java.lang.Double>	exWaves
private int	fieldCount
private java.lang.Double	gain
private InCellReader.Image[][][][]	imageFiles
private int	imageHeight
private int	imagesNumber
private int	imageWidth
static java.lang.String	INCELL_MAGIC_STRING
private static java.lang.String[]	METADATA_SUFFIXES
private java.util.List<java.lang.String>	metadataFiles
private int	offsetPointCounter
private boolean	oneTimepointPerSeries
private static java.lang.String[]	PIXELS_SUFFIXES
private boolean[][]	plateMap
private java.util.Map<java.lang.Integer,ome.units.quantity.Length>	posX
private java.util.Map<java.lang.Integer,ome.units.quantity.Length>	posY
private java.lang.Double	refractive
private java.lang.String	rowName
private java.lang.Double	temperature
private MinimalTiffReader	tiffReader
private int	totalChannels
private int	totalImages
private int	wellCols
private java.util.Map<java.lang.Integer,int[]>	wellCoordinates
private int	wellRows
private ome.units.quantity.Length	x
private ome.units.quantity.Length	y

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
InCellReader() Constructs a new InCell 1000/2000 reader.

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.
short[][]	get16BitLookupTable() Gets the 16-bit color lookup table associated with the most recently opened image.
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
private int	getFieldFromSeries(int series)
int	getOptimalTileHeight() Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth() Returns the optimal sub-image width for use with openBytes.
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
private int	getWellFromSeries(int series)
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
boolean	isSingleFile(java.lang.String id) Returns true if the named file is expected to be the only file in the dataset.
boolean	isThisType(loci.common.RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
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.

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, 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, 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, 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

INCELL_MAGIC_STRING

public static final java.lang.String INCELL_MAGIC_STRING

See Also:

Constant Field Values

CYTELL_MAGIC_STRING

public static final java.lang.String CYTELL_MAGIC_STRING

See Also:

Constant Field Values

PIXELS_SUFFIXES

private static final java.lang.String[] PIXELS_SUFFIXES

METADATA_SUFFIXES

private static final java.lang.String[] METADATA_SUFFIXES

plateMap

private boolean[][] plateMap

imageFiles

private InCellReader.Image[][][][] imageFiles

tiffReader

private MinimalTiffReader tiffReader

emWaves

private java.util.List<java.lang.Double> emWaves

exWaves

private java.util.List<java.lang.Double> exWaves

channelNames

private java.util.List<java.lang.String> channelNames

totalImages

private int totalImages

imagesNumber

private transient int imagesNumber

imageWidth

private int imageWidth

imageHeight

private int imageHeight

creationDate

private java.lang.String creationDate

rowName

private java.lang.String rowName

colName

private java.lang.String colName

fieldCount

private int fieldCount

wellRows

private int wellRows

wellCols

private int wellCols

wellCoordinates

private java.util.Map<java.lang.Integer,int[]> wellCoordinates

posX

private java.util.Map<java.lang.Integer,ome.units.quantity.Length> posX

posY

private java.util.Map<java.lang.Integer,ome.units.quantity.Length> posY

offsetPointCounter

private int offsetPointCounter

exclude

private boolean[][] exclude

channelsPerTimepoint

private java.util.List<java.lang.Integer> channelsPerTimepoint

oneTimepointPerSeries

private boolean oneTimepointPerSeries

totalChannels

private int totalChannels

metadataFiles

private java.util.List<java.lang.String> metadataFiles

bin

private ome.xml.model.enums.Binning bin

x

private ome.units.quantity.Length x

y

private ome.units.quantity.Length y

gain

private java.lang.Double gain

temperature

private java.lang.Double temperature

refractive

private java.lang.Double refractive

exFilters

private java.util.List<java.lang.String> exFilters

emFilters

private java.util.List<java.lang.String> emFilters

Constructor Detail

InCellReader

public InCellReader()

Constructs a new InCell 1000/2000 reader.

Method Detail

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.

isSingleFile

public boolean isSingleFile(java.lang.String id)
                     throws FormatException,
                            java.io.IOException

Description copied from interface: IFormatReader

Returns true if the named file is expected to be the only file in the dataset. For single-file formats, always returns true.

Specified by:

isSingleFile in interface IFormatReader

Overrides:

isSingleFile in class FormatReader

Throws:

FormatException

java.io.IOException

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws java.io.IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Parameters:

stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.

Returns:

true if the file represented by the stream can be read by this reader; false otherwise.

Throws:

java.io.IOException

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

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   java.io.IOException

Description copied from interface: IFormatReader

Gets the 8-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT8 or FormatTools.UINT8, this method will return null.

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class FormatReader

Throws:

FormatException

java.io.IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
                                     java.io.IOException

Description copied from interface: IFormatReader

Gets the 16-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if IFormatReader.isIndexed() returns false, then this may return null. Also, if IFormatReader.getPixelType() returns anything other than FormatTools.INT16 or FormatTools.UINT16, this method will return null.

Specified by:

get16BitLookupTable in interface IFormatReader

Overrides:

get16BitLookupTable in class FormatReader

Throws:

FormatException

java.io.IOException

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)

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

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

getOptimalTileWidth

public int getOptimalTileWidth()

Description copied from interface: IFormatReader

Returns the optimal sub-image width for use with openBytes.

Specified by:

getOptimalTileWidth in interface IFormatReader

Overrides:

getOptimalTileWidth in class FormatReader

getOptimalTileHeight

public int getOptimalTileHeight()

Description copied from interface: IFormatReader

Returns the optimal sub-image height for use with openBytes.

Specified by:

getOptimalTileHeight in interface IFormatReader

Overrides:

getOptimalTileHeight in class FormatReader

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

getFieldFromSeries

private int getFieldFromSeries(int series)

getWellFromSeries

private int getWellFromSeries(int series)