Package loci.formats.in

Class BioRadReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BioRadReader

All Implemented Interfaces:

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

public class BioRadReader
extends FormatReader

BioRadReader is the file format reader for Bio-Rad PIC files.

Author:

Curtis Rueden ctrueden at wisc.edu, Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	BioRadReader.BioRadHandler	SAX handler for parsing XML.
(package private) class	BioRadReader.Note

Field Summary

Fields

Modifier and Type	Field	Description
private boolean	brokenNotes
private List<Double>	gain
private int	lastChannel
private static final boolean	LITTLE_ENDIAN	Always little endian.
private byte[][][]	lut
static final int	LUT_LENGTH
private static final String[]	MERGE_NAMES	List of merge types.
static final String[]	NOTE_NAMES	List of note types.
static final int	NOTE_TYPE_4D_SERIES
static final int	NOTE_TYPE_ARROW
static final int	NOTE_TYPE_COLLECT
static final int	NOTE_TYPE_FILE1
static final int	NOTE_TYPE_FILE2
static final int	NOTE_TYPE_LINE
static final int	NOTE_TYPE_LIVE
static final int	NOTE_TYPE_MERGE
static final int	NOTE_TYPE_NUMBER
static final int	NOTE_TYPE_SCALEBAR
static final int	NOTE_TYPE_STRUCTURE
static final int	NOTE_TYPE_THRUVIEW
static final int	NOTE_TYPE_USER
static final int	NOTE_TYPE_VARIABLE
private List<BioRadReader.Note>	noteStrings
private List<Double>	offset
private static final int	PIC_FILE_ID	Numerical ID of a valid Bio-Rad PIC file.
static final String[]	PIC_SUFFIX
private String[]	picFiles
static final String[]	STRUCTURE_LABELS_1	Structure labels.
static final String[]	STRUCTURE_LABELS_2
static final String[]	STRUCTURE_LABELS_3
static final String[]	STRUCTURE_LABELS_4
static final String[]	STRUCTURE_LABELS_5
static final String[]	STRUCTURE_LABELS_6
private List<String>	used

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
BioRadReader()	Constructs a new BioRadReader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
int	fileGroupOption(String id)	Returns an indication of whether the files in a multi-file dataset can be handled individually.
byte[][]	get8BitLookupTable()	Gets the 8-bit color lookup table associated with the most recently opened image.
int	getOptimalTileHeight()	Returns the optimal sub-image height for use with openBytes.
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	isSingleFile(String id)	Returns true if the named file is expected to be the only file in the dataset.
boolean	isThisType(String name, boolean open)	Checks if a file matches the type of this format reader.
boolean	isThisType(loci.common.RandomAccessInputStream stream)	Checks if the given stream is a valid stream for this file format.
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.
private boolean	parseNotes(MetadataStore store)
private void	readLookupTables(loci.common.RandomAccessInputStream s)	Read all lookup tables from the given file into the 'lut' variable.
private void	readNotes(loci.common.RandomAccessInputStream s, boolean add)	Read all of the note strings from the given file.

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, 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, 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, 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

PIC_FILE_ID

private static final int PIC_FILE_ID

Numerical ID of a valid Bio-Rad PIC file.

See Also:

• Constant Field Values

LITTLE_ENDIAN

private static final boolean LITTLE_ENDIAN

Always little endian.

See Also:

• Constant Field Values

MERGE_NAMES

private static final String[] MERGE_NAMES

List of merge types.

NOTE_NAMES

public static final String[] NOTE_NAMES

List of note types.

NOTE_TYPE_LIVE

public static final int NOTE_TYPE_LIVE

See Also:

• Constant Field Values

NOTE_TYPE_FILE1

public static final int NOTE_TYPE_FILE1

See Also:

• Constant Field Values

NOTE_TYPE_NUMBER

public static final int NOTE_TYPE_NUMBER

See Also:

• Constant Field Values

NOTE_TYPE_USER

public static final int NOTE_TYPE_USER

See Also:

• Constant Field Values

NOTE_TYPE_LINE

public static final int NOTE_TYPE_LINE

See Also:

• Constant Field Values

NOTE_TYPE_COLLECT

public static final int NOTE_TYPE_COLLECT

See Also:

• Constant Field Values

NOTE_TYPE_FILE2

public static final int NOTE_TYPE_FILE2

See Also:

• Constant Field Values

NOTE_TYPE_SCALEBAR

public static final int NOTE_TYPE_SCALEBAR

See Also:

• Constant Field Values

NOTE_TYPE_MERGE

public static final int NOTE_TYPE_MERGE

See Also:

• Constant Field Values

NOTE_TYPE_THRUVIEW

public static final int NOTE_TYPE_THRUVIEW

See Also:

• Constant Field Values

NOTE_TYPE_ARROW

public static final int NOTE_TYPE_ARROW

See Also:

• Constant Field Values

NOTE_TYPE_VARIABLE

public static final int NOTE_TYPE_VARIABLE

See Also:

• Constant Field Values

NOTE_TYPE_STRUCTURE

public static final int NOTE_TYPE_STRUCTURE

See Also:

• Constant Field Values

NOTE_TYPE_4D_SERIES

public static final int NOTE_TYPE_4D_SERIES

See Also:

• Constant Field Values

STRUCTURE_LABELS_1

public static final String[] STRUCTURE_LABELS_1

Structure labels.

STRUCTURE_LABELS_2

public static final String[] STRUCTURE_LABELS_2

STRUCTURE_LABELS_3

public static final String[] STRUCTURE_LABELS_3

STRUCTURE_LABELS_4

public static final String[] STRUCTURE_LABELS_4

STRUCTURE_LABELS_5

public static final String[] STRUCTURE_LABELS_5

STRUCTURE_LABELS_6

public static final String[] STRUCTURE_LABELS_6

PIC_SUFFIX

public static final String[] PIC_SUFFIX

LUT_LENGTH

public static final int LUT_LENGTH

See Also:

• Constant Field Values

used

private List<String> used

picFiles

private String[] picFiles

lut

private byte[][][] lut

lastChannel

private int lastChannel

brokenNotes

private boolean brokenNotes

noteStrings

private List<BioRadReader.Note> noteStrings

offset

private List<Double> offset

gain

private List<Double> gain

Constructor Details

BioRadReader

public BioRadReader()

Constructs a new BioRadReader.

Method Details

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

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

isThisType

public boolean isThisType(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

Parameters:

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

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws 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:

IOException

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

get8BitLookupTable

public byte[][] get8BitLookupTable()

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

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

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)

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

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

readNotes

private void readNotes(loci.common.RandomAccessInputStream s,
 boolean add)
                throws IOException

Read all of the note strings from the given file. If the 'add' flag is set, the notes will be added to the 'noteStrings' list.

Throws:

IOException

parseNotes

private boolean parseNotes(MetadataStore store)
                    throws FormatException

Throws:

FormatException

readLookupTables

private void readLookupTables(loci.common.RandomAccessInputStream s)
                       throws IOException

Read all lookup tables from the given file into the 'lut' variable.

Throws:

IOException