Package loci.formats.in

Class ICSReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.ICSReader

All Implemented Interfaces:

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

public class ICSReader
extends FormatReader

ICSReader is the file format reader for ICS (Image Cytometry Standard) files. More information on ICS can be found at http://libics.sourceforge.net TODO : remove sub-C logic once N-dimensional support is in place see http://dev.loci.wisc.edu/trac/java/ticket/398

Author:

Melissa Linkert melissa at glencoesoftware.com

Field Summary

Fields

Modifier and Type	Field	Description
private Vector<Integer>	channelLengths	The length of each channel axis.
private Vector<String>	channelTypes	The type of each channel axis.
private String	currentIcsId	Current filename.
private String	currentIdsId
private byte[]	data	Image data.
static final String[]	DATE_FORMATS
private static final String[][]	DOCUMENT_KEYS
private boolean	gzip	Whether or not the pixels are GZIP-compressed.
private GZIPInputStream	gzipStream
private boolean	hasInstrumentData
private static final String[][]	HISTORY_KEYS
private boolean	invertY	Whether or not the image is inverted along the Y axis.
private String	labels	Dimensional reordering for lifetime data
private static final String[][]	LAYOUT_KEYS
private boolean	lifetime	Whether or not the channels represent lifetime histogram bins.
static final String	NL	Newline characters.
private long	offset	Offset to pixel data.
private static String[][]	OTHER_KEYS
private static final String[][]	PARAMETER_KEYS
private int	prevImage
private static final String[][]	REPRESENTATION_KEYS
private static final String[][]	SENSOR_KEYS
private boolean	storedRGB
private boolean	versionTwo	Flag indicating whether current file is v2.0.
private static final String[][]	VIEW_KEYS

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
ICSReader()	Constructs a new ICSReader.

Method Summary

Modifier and Type	Method	Description
private boolean	checkUnit(String actual, String... expected)	Verifies that a unit matches the expected value.
void	close(boolean fileOnly)	Closes the currently open file.
private boolean	compareTokens(String[] tokens, int tokenIndex, String[] regexes, int regexesIndex)
private String	concatenateTokens(String[] tokens, int start, int stop)
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
(package private) String[]	findKeyValue(String[] tokens, String[][] regexesArray)
private String[]	findKeyValueForCategory(String[] tokens, String[][] regexesArray)
private String[]	findKeyValueOther(String[] tokens, String[][] regexesArray)
String[]	getDomains()	Returns the list of domains represented by the current file.
String[]	getSeriesUsedFiles(boolean noPixels)	Returns an array of filenames needed to open the current series.
protected void	initFile(String id)	Initializes the given file (parsing header information, etc.).
boolean	isInterleaved(int subC)	Gets whether or not the given sub-channel is interleaved.
boolean	isSingleFile(String id)	Returns true if the named file is expected to be the only file in the dataset.
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.
void	reopenFile()	Reopen any files that were closed, and which are expected to be open while the reader is open.
private Double[]	splitDoubles(String v)	Splits the given string into a list of Doubles.
private String[]	tokenize(String line)

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, 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, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, readPlane, 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

NL

public static final String NL

Newline characters.

See Also:

• Constant Field Values

DATE_FORMATS

public static final String[] DATE_FORMATS

DOCUMENT_KEYS

private static final String[][] DOCUMENT_KEYS

HISTORY_KEYS

private static final String[][] HISTORY_KEYS

LAYOUT_KEYS

private static final String[][] LAYOUT_KEYS

PARAMETER_KEYS

private static final String[][] PARAMETER_KEYS

REPRESENTATION_KEYS

private static final String[][] REPRESENTATION_KEYS

SENSOR_KEYS

private static final String[][] SENSOR_KEYS

VIEW_KEYS

private static final String[][] VIEW_KEYS

OTHER_KEYS

private static String[][] OTHER_KEYS

currentIcsId

private String currentIcsId

Current filename.

currentIdsId

private String currentIdsId

versionTwo

private boolean versionTwo

Flag indicating whether current file is v2.0.

data

private byte[] data

Image data.

offset

private long offset

Offset to pixel data.

gzip

private boolean gzip

Whether or not the pixels are GZIP-compressed.

gzipStream

private GZIPInputStream gzipStream

invertY

private boolean invertY

Whether or not the image is inverted along the Y axis.

lifetime

private boolean lifetime

Whether or not the channels represent lifetime histogram bins.

labels

private String labels

Dimensional reordering for lifetime data

channelLengths

private Vector<Integer> channelLengths

The length of each channel axis.

channelTypes

private Vector<String> channelTypes

The type of each channel axis.

prevImage

private int prevImage

hasInstrumentData

private boolean hasInstrumentData

storedRGB

private boolean storedRGB

Constructor Details

ICSReader

public ICSReader()

Constructs a new ICSReader.

Method Details

isSingleFile

public boolean isSingleFile(String id)
                     throws FormatException,
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

IOException

getDomains

public String[] getDomains()

Description copied from interface: IFormatReader

Returns the list of domains represented by the current file.

Specified by:

getDomains in interface IFormatReader

Overrides:

getDomains in class FormatReader

isInterleaved

public boolean isInterleaved(int subC)

Description copied from interface: IFormatReader

Gets whether or not the given sub-channel is interleaved. This method exists because some data with multiple rasterized sub-dimensions within C have one sub-dimension interleaved, and the other not—e.g., SDTReader handles spectral-lifetime data with interleaved lifetime bins and non-interleaved spectral channels.

Specified by:

isInterleaved in interface IFormatReader

Overrides:

isInterleaved in class FormatReader

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
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

IOException

See Also:

• FormatTools.MUST_GROUP
• FormatTools.CAN_GROUP
• FormatTools.CANNOT_GROUP

openBytes

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

IOException - if there was a problem reading the file.

See Also:

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

getSeriesUsedFiles

public 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 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:

IOException

reopenFile

public void reopenFile()
                throws IOException

Description copied from interface: IFormatReader

Reopen any files that were closed, and which are expected to be open while the reader is open. This assumes that IFormatHandler.setId(java.lang.String) has been called, but close(false) has not been called.

Specified by:

reopenFile in interface IFormatReader

Overrides:

reopenFile in class FormatReader

Throws:

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
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.

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

tokenize

private String[] tokenize(String line)

findKeyValue

String[] findKeyValue(String[] tokens,
 String[][] regexesArray)

concatenateTokens

private String concatenateTokens(String[] tokens,
 int start,
 int stop)

findKeyValueForCategory

private String[] findKeyValueForCategory(String[] tokens,
 String[][] regexesArray)

findKeyValueOther

private String[] findKeyValueOther(String[] tokens,
 String[][] regexesArray)

compareTokens

private boolean compareTokens(String[] tokens,
 int tokenIndex,
 String[] regexes,
 int regexesIndex)

splitDoubles

private Double[] splitDoubles(String v)

Splits the given string into a list of Doubles.

checkUnit

private boolean checkUnit(String actual,
 String... expected)

Verifies that a unit matches the expected value.