loci.formats.in

Class BioRadReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BioRadReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class BioRadReader
extends FormatReader

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

Source code:

Trac, Gitweb

Author:

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

Field Summary

Fields

Modifier and Type	Field and Description
static int	LUT_LENGTH
static String[]	NOTE_NAMES List of note types.
static int	NOTE_TYPE_4D_SERIES
static int	NOTE_TYPE_ARROW
static int	NOTE_TYPE_COLLECT
static int	NOTE_TYPE_FILE1
static int	NOTE_TYPE_FILE2
static int	NOTE_TYPE_LINE
static int	NOTE_TYPE_LIVE
static int	NOTE_TYPE_MERGE
static int	NOTE_TYPE_NUMBER
static int	NOTE_TYPE_SCALEBAR
static int	NOTE_TYPE_STRUCTURE
static int	NOTE_TYPE_THRUVIEW
static int	NOTE_TYPE_USER
static int	NOTE_TYPE_VARIABLE
static String[]	PIC_SUFFIX
static String[]	STRUCTURE_LABELS_1 Structure labels.
static String[]	STRUCTURE_LABELS_2
static String[]	STRUCTURE_LABELS_3
static String[]	STRUCTURE_LABELS_4
static String[]	STRUCTURE_LABELS_5
static String[]	STRUCTURE_LABELS_6

Fields inherited from class loci.formats.FormatReader

core, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler

COMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixes

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
BioRadReader() Constructs a new BioRadReader.

Method Summary

Methods

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
int	fileGroupOption(String id) Returns an int indicating that we cannot, must, or might group the files in a given dataset.
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 this is a single-file format.
boolean	isThisType(RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
boolean	isThisType(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, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, close, coreIndexToSeries, get16BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadata, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getNamingConvention, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataCollected, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, seriesToCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataCollected, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler

checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

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

Field Detail

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

Constructor Detail

BioRadReader

public BioRadReader()

Constructs a new BioRadReader.

Method Detail

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 this is a single-file format.

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

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(RandomAccessInputStream stream)
                   throws IOException

Description copied from interface: IFormatReader

Checks if the given stream is a valid stream for this file format.

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

Throws:

IOException

fileGroupOption

public int fileGroupOption(String id)
                    throws FormatException,
                           IOException

Description copied from interface: IFormatReader

Returns an int indicating that we cannot, must, or might group the files in a given dataset.

Specified by:

fileGroupOption in interface IFormatReader

Overrides:

fileGroupOption in class FormatReader

Throws:

FormatException

IOException

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.

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 image index within the file.

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