loci.formats.in

Class ICSReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.ICSReader

All Implemented Interfaces:

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

Method Summary

Modifier and Type	Method and Description
private boolean	checkUnit(java.lang.String actual, java.lang.String... expected) Verifies that a unit matches the expected value.
void	close(boolean fileOnly) Closes the currently open file.
private boolean	compareTokens(java.lang.String[] tokens, int tokenIndex, java.lang.String[] regexes, int regexesIndex)
private java.lang.String	concatenateTokens(java.lang.String[] tokens, int start, int stop)
int	fileGroupOption(java.lang.String id) Returns an indication of whether the files in a multi-file dataset can be handled individually.
(package private) java.lang.String[]	findKeyValue(java.lang.String[] tokens, java.lang.String[][] regexesArray)
private java.lang.String[]	findKeyValueForCategory(java.lang.String[] tokens, java.lang.String[][] regexesArray)
private java.lang.String[]	findKeyValueOther(java.lang.String[] tokens, java.lang.String[][] regexesArray)
java.lang.String[]	getDomains() Returns the list of domains represented by the current file.
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
protected void	initFile(java.lang.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(java.lang.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 java.lang.Double[]	splitDoubles(java.lang.String v) Splits the given string into a list of Doubles.
private java.lang.String[]	tokenize(java.lang.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, 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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Detail

NL

public static final java.lang.String NL

Newline characters.

See Also:

Constant Field Values

DATE_FORMATS

public static final java.lang.String[] DATE_FORMATS

DOCUMENT_KEYS

private static final java.lang.String[][] DOCUMENT_KEYS

HISTORY_KEYS

private static final java.lang.String[][] HISTORY_KEYS

LAYOUT_KEYS

private static final java.lang.String[][] LAYOUT_KEYS

PARAMETER_KEYS

private static final java.lang.String[][] PARAMETER_KEYS

REPRESENTATION_KEYS

private static final java.lang.String[][] REPRESENTATION_KEYS

SENSOR_KEYS

private static final java.lang.String[][] SENSOR_KEYS

VIEW_KEYS

private static final java.lang.String[][] VIEW_KEYS

OTHER_KEYS

private static java.lang.String[][] OTHER_KEYS

currentIcsId

private java.lang.String currentIcsId

Current filename.

currentIdsId

private java.lang.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 java.util.zip.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 java.lang.String labels

Dimensional reordering for lifetime data

channelLengths

private java.util.Vector<java.lang.Integer> channelLengths

The length of each channel axis.

channelTypes

private java.util.Vector<java.lang.String> channelTypes

The type of each channel axis.

prevImage

private int prevImage

hasInstrumentData

private boolean hasInstrumentData

storedRGB

private boolean storedRGB

Constructor Detail

ICSReader

public ICSReader()

Constructs a new ICSReader.

Method Detail

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

getDomains

public java.lang.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(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

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

reopenFile

public void reopenFile()
                throws java.io.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:

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

tokenize

private java.lang.String[] tokenize(java.lang.String line)

findKeyValue

java.lang.String[] findKeyValue(java.lang.String[] tokens,
                                java.lang.String[][] regexesArray)

concatenateTokens

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

findKeyValueForCategory

private java.lang.String[] findKeyValueForCategory(java.lang.String[] tokens,
                                                   java.lang.String[][] regexesArray)

findKeyValueOther

private java.lang.String[] findKeyValueOther(java.lang.String[] tokens,
                                             java.lang.String[][] regexesArray)

compareTokens

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

splitDoubles

private java.lang.Double[] splitDoubles(java.lang.String v)

Splits the given string into a list of Doubles.

checkUnit

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

Verifies that a unit matches the expected value.