BioRadReader (Bio-Formats API)

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.

Author:

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

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

(package private) class BioRadReader.BioRadHandler
SAX handler for parsing XML.

(package private) class BioRadReader.Note

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

Field Summary

Fields
Modifier and Type	Field and Description
`private boolean`	`brokenNotes`
`private List<Double>`	`gain`
`private int`	`lastChannel`
`private static boolean`	`LITTLE_ENDIAN` Always little endian.
`private byte[][][]`	`lut`
`static int`	`LUT_LENGTH`
`private static String[]`	`MERGE_NAMES` List of merge types.
`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`
`private List<BioRadReader.Note>`	`noteStrings`
`private List<Double>`	`offset`
`private static int`	`PIC_FILE_ID` Numerical ID of a valid Bio-Rad PIC file.
`static String[]`	`PIC_SUFFIX`
`private String[]`	`picFiles`
`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`
`private List<String>`	`used`

Fields inherited from class loci.formats.FormatReader
core, coreIndex, datasetDescription, domains, 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

BioRadReader()
Constructs a new BioRadReader.

Constructors
Constructor and Description
`BioRadReader()` Constructs a new BioRadReader.

Method Summary

All Methods Instance Methods Concrete 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(loci.common.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.
`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, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, 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, 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, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

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
  - 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 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(loci.common.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
  - 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

Class BioRadReader

Nested Class Summary

Field Summary

Fields inherited from class loci.formats.FormatReader

Fields inherited from class loci.formats.FormatHandler

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.FormatReader

Methods inherited from class loci.formats.FormatHandler

Methods inherited from class java.lang.Object

Methods inherited from interface loci.formats.IFormatHandler

Methods inherited from interface loci.formats.IMetadataConfigurable

Field Detail

PIC_FILE_ID

LITTLE_ENDIAN

MERGE_NAMES

NOTE_NAMES

NOTE_TYPE_LIVE

NOTE_TYPE_FILE1

NOTE_TYPE_NUMBER

NOTE_TYPE_USER

NOTE_TYPE_LINE

NOTE_TYPE_COLLECT

NOTE_TYPE_FILE2

NOTE_TYPE_SCALEBAR

NOTE_TYPE_MERGE

NOTE_TYPE_THRUVIEW

NOTE_TYPE_ARROW

NOTE_TYPE_VARIABLE

NOTE_TYPE_STRUCTURE

NOTE_TYPE_4D_SERIES

STRUCTURE_LABELS_1

STRUCTURE_LABELS_2

STRUCTURE_LABELS_3

STRUCTURE_LABELS_4

STRUCTURE_LABELS_5

STRUCTURE_LABELS_6

PIC_SUFFIX

LUT_LENGTH

used

picFiles

lut

lastChannel

brokenNotes

noteStrings

offset

gain

Constructor Detail

BioRadReader

Method Detail

getOptimalTileHeight

isSingleFile

isThisType

isThisType

fileGroupOption

get8BitLookupTable

getSeriesUsedFiles

openBytes

close

initFile

readNotes

parseNotes

readLookupTables