FV1000Reader (Bio-Formats API)

java.lang.Object
- loci.formats.FormatHandler
- - loci.formats.FormatReader
  - - loci.formats.in.FV1000Reader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable
```
public class FV1000Reader
extends FormatReader
```
FV1000Reader is the file format reader for Fluoview FV 1000 OIB and Fluoview FV 1000 OIF files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

(package private) class FV1000Reader.ChannelData

(package private) class FV1000Reader.PlaneData

Nested Classes
Modifier and Type	Class and Description
`(package private) class`	`FV1000Reader.ChannelData`
`(package private) class`	`FV1000Reader.PlaneData`

Field Summary

Fields
Modifier and Type	Field and Description
`private static int`	`ARROW`
`private List<FV1000Reader.ChannelData>`	`channels`
`private static int`	`CIRCLE`
`private String[]`	`code`
`private static int`	`COLOR_BAR`
`private String`	`creationDate`
`static String`	`DATE_FORMAT`
`private static int`	`ELLIPSE`
`private Map<Integer,String>`	`filenames`
`private static int`	`FREE_LINE`
`private static int`	`FREE_SHAPE`
`static String`	`FV1000_MAGIC_STRING_1`
`static String`	`FV1000_MAGIC_STRING_2`
`static String[]`	`FV1000_SUFFIXES`
`private static int`	`GRID`
`private ArrayList<IFDList>`	`ifds`
`private List<String>`	`illuminations`
`private int`	`imageDepth`
`private boolean`	`isOIB` Flag indicating this is an OIB dataset.
`private int`	`lastChannel`
`private String`	`lensNA`
`private String`	`line`
`private static int`	`LINE`
`private short[][][]`	`lut`
`private List<String>`	`lutNames`
`private String`	`magnification`
`private static int`	`NUM_DIMENSIONS`
`private String`	`objectiveName`
`static String[]`	`OIB_SUFFIX`
`private Map<String,String>`	`oibMapping` File mappings for OIB file.
`static String[]`	`OIF_SUFFIX`
`private IniParser`	`parser`
`private String`	`pinholeSize`
`private Double[]`	`pixelSize`
`private double`	`pixelSizeT`
`private String`	`pixelSizeX`
`private String`	`pixelSizeY`
`private double`	`pixelSizeZ`
`private List<FV1000Reader.PlaneData>`	`planes`
`private POIService`	`poi`
`private static int`	`POINT` ROI types.
`private static int`	`POLYGON`
`private static int`	`POLYLINE`
`private List<String>`	`previewNames`
`private String`	`ptyEnd`
`private String`	`ptyPattern`
`private String`	`ptyStart`
`private static int`	`RECTANGLE`
`private Map<Integer,String>`	`roiFilenames`
`private static String`	`ROTATION`
`private static int`	`SCALE`
`private String[]`	`size`
`private String`	`thumbId` Name of thumbnail file.
`private BMPReader`	`thumbReader` Helper reader for thumbnail.
`private List<String>`	`tiffs` Names of every TIFF file to open.
`private List<String>`	`usedFiles` Used file list.
`private int`	`validBits`
`private List<Double>`	`wavelengths`
`private String`	`workingDistance`

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

FV1000Reader()
Constructs a new FV1000 reader.

Constructors
Constructor and Description
`FV1000Reader()` Constructs a new FV1000 reader.

Method Summary

Methods
Modifier and Type	Method and Description
`private void`	`addPtyFiles()`
`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.
`private String`	`findOIFFile(String baseFile)`
`short[][]`	`get16BitLookupTable()` Gets the 16-bit color lookup table associated with the most recently opened image.
`private RandomAccessInputStream`	`getFile(String name)`
`private IniList`	`getIniFile(String filename)`
`int`	`getOptimalTileHeight()` Returns the optimal sub-image height for use with openBytes.
`int`	`getOptimalTileWidth()` Returns the optimal sub-image width for use with openBytes.
`private RandomAccessInputStream`	`getPlane(int seriesIndex, int planeIndex)`
`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.).
`private void`	`initPOIService()`
`private boolean`	`isPreviewName(String name)`
`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.
`private String`	`mapOIBFiles()`
`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 int`	`parseROIFile(String filename, MetadataStore store, int nextROI, int plane)`
`private void`	`populateMetadataStore(MetadataStore store, String path)`
`private String`	`removeGST(String s)`
`private String`	`replaceExtension(String name, String oldExt, String newExt)`
`private String`	`sanitizeFile(String file, String path)`
`private String`	`sanitizeValue(String value)`
`private static int[]`	`scanFormat(String pattern, String string)`

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, get8BitLookupTable, 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, 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
  - FV1000_MAGIC_STRING_1
```
public static final String FV1000_MAGIC_STRING_1
```
    See Also:
    Constant Field Values
  - FV1000_MAGIC_STRING_2
```
public static final String FV1000_MAGIC_STRING_2
```
    See Also:
    Constant Field Values
  - OIB_SUFFIX
```
public static final String[] OIB_SUFFIX
```
  - OIF_SUFFIX
```
public static final String[] OIF_SUFFIX
```
  - FV1000_SUFFIXES
```
public static final String[] FV1000_SUFFIXES
```
  - DATE_FORMAT
```
public static final String DATE_FORMAT
```
    See Also:
    Constant Field Values
  - NUM_DIMENSIONS
```
private static final int NUM_DIMENSIONS
```
    See Also:
    Constant Field Values
  - POINT
```
private static final int POINT
```
    ROI types.
    
    See Also:
    Constant Field Values
  - LINE
```
private static final int LINE
```
    See Also:
    Constant Field Values
  - POLYLINE
```
private static final int POLYLINE
```
    See Also:
    Constant Field Values
  - RECTANGLE
```
private static final int RECTANGLE
```
    See Also:
    Constant Field Values
  - CIRCLE
```
private static final int CIRCLE
```
    See Also:
    Constant Field Values
  - ELLIPSE
```
private static final int ELLIPSE
```
    See Also:
    Constant Field Values
  - POLYGON
```
private static final int POLYGON
```
    See Also:
    Constant Field Values
  - FREE_SHAPE
```
private static final int FREE_SHAPE
```
    See Also:
    Constant Field Values
  - FREE_LINE
```
private static final int FREE_LINE
```
    See Also:
    Constant Field Values
  - GRID
```
private static final int GRID
```
    See Also:
    Constant Field Values
  - ARROW
```
private static final int ARROW
```
    See Also:
    Constant Field Values
  - COLOR_BAR
```
private static final int COLOR_BAR
```
    See Also:
    Constant Field Values
  - SCALE
```
private static final int SCALE
```
    See Also:
    Constant Field Values
  - ROTATION
```
private static final String ROTATION
```
    See Also:
    Constant Field Values
  - parser
```
private IniParser parser
```
  - tiffs
```
private List<String> tiffs
```
    Names of every TIFF file to open.
  - thumbId
```
private String thumbId
```
    Name of thumbnail file.
  - thumbReader
```
private BMPReader thumbReader
```
    Helper reader for thumbnail.
  - usedFiles
```
private List<String> usedFiles
```
    Used file list.
  - isOIB
```
private boolean isOIB
```
    Flag indicating this is an OIB dataset.
  - oibMapping
```
private Map<String,String> oibMapping
```
    File mappings for OIB file.
  - code
```
private String[] code
```
  - size
```
private String[] size
```
  - pixelSize
```
private Double[] pixelSize
```
  - imageDepth
```
private int imageDepth
```
  - previewNames
```
private List<String> previewNames
```
  - pixelSizeX
```
private String pixelSizeX
```
  - pixelSizeY
```
private String pixelSizeY
```
  - validBits
```
private int validBits
```
  - illuminations
```
private List<String> illuminations
```
  - wavelengths
```
private List<Double> wavelengths
```
  - pinholeSize
```
private String pinholeSize
```
  - magnification
```
private String magnification
```
  - lensNA
```
private String lensNA
```
  - objectiveName
```
private String objectiveName
```
  - workingDistance
```
private String workingDistance
```
  - creationDate
```
private String creationDate
```
  - channels
```
private List<FV1000Reader.ChannelData> channels
```
  - lutNames
```
private List<String> lutNames
```
  - filenames
```
private Map<Integer,String> filenames
```
  - roiFilenames
```
private Map<Integer,String> roiFilenames
```
  - planes
```
private List<FV1000Reader.PlaneData> planes
```
  - poi
```
private transient POIService poi
```
  - lut
```
private short[][][] lut
```
  - lastChannel
```
private int lastChannel
```
  - pixelSizeZ
```
private double pixelSizeZ
```
  - pixelSizeT
```
private double pixelSizeT
```
  - ptyStart
```
private String ptyStart
```
  - ptyEnd
```
private String ptyEnd
```
  - ptyPattern
```
private String ptyPattern
```
  - line
```
private String line
```
  - ifds
```
private ArrayList<IFDList> ifds
```
- Constructor Detail
  - FV1000Reader
```
public FV1000Reader()
```
    Constructs a new FV1000 reader.
- Method Detail
  - getOptimalTileWidth
```
public int getOptimalTileWidth()
```
    Description copied from interface: IFormatReader
    
    Returns the optimal sub-image width for use with openBytes.
    
    Specified by:
    
    getOptimalTileWidth in interface IFormatReader
    
    Overrides:
    
    getOptimalTileWidth in class FormatReader
  - 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
  - get16BitLookupTable
```
public short[][] get16BitLookupTable()
```
    Description copied from interface: IFormatReader
    
    Gets the 16-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.INT16 or FormatTools.UINT16, this method will return null.
    
    Specified by:
    
    get16BitLookupTable in interface IFormatReader
    
    Overrides:
    
    get16BitLookupTable 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)
  - 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
  - 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
  - populateMetadataStore
```
private void populateMetadataStore(MetadataStore store,
                         String path)
                            throws FormatException,
                                   IOException
```
    Throws:
    
    FormatException
    
    IOException
  - parseROIFile
```
private int parseROIFile(String filename,
               MetadataStore store,
               int nextROI,
               int plane)
                  throws FormatException,
                         IOException
```
    Throws:
    
    FormatException
    
    IOException
  - addPtyFiles
```
private void addPtyFiles()
                  throws FormatException
```
    Throws:
    
    FormatException
  - findOIFFile
```
private String findOIFFile(String baseFile)
                    throws FormatException
```
    Throws:
    
    FormatException
  - mapOIBFiles
```
private String mapOIBFiles()
                    throws FormatException,
                           IOException
```
    Throws:
    
    FormatException
    
    IOException
  - sanitizeValue
```
private String sanitizeValue(String value)
```
  - sanitizeFile
```
private String sanitizeFile(String file,
                  String path)
```
  - removeGST
```
private String removeGST(String s)
```
  - initPOIService
```
private void initPOIService()
                     throws FormatException,
                            IOException
```
    Throws:
    
    FormatException
    
    IOException
  - getFile
```
private RandomAccessInputStream getFile(String name)
                                 throws FormatException,
                                        IOException
```
    Throws:
    
    FormatException
    
    IOException
  - getPlane
```
private RandomAccessInputStream getPlane(int seriesIndex,
                               int planeIndex)
```
  - isPreviewName
```
private boolean isPreviewName(String name)
```
  - replaceExtension
```
private String replaceExtension(String name,
                      String oldExt,
                      String newExt)
```
  - scanFormat
```
private static int[] scanFormat(String pattern,
               String string)
                         throws FormatException
```
    Throws:
    
    FormatException
  - getIniFile
```
private IniList getIniFile(String filename)
                    throws FormatException,
                           IOException
```
    Throws:
    
    FormatException
    
    IOException

Class FV1000Reader

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

FV1000_MAGIC_STRING_1

FV1000_MAGIC_STRING_2

OIB_SUFFIX

OIF_SUFFIX

FV1000_SUFFIXES

DATE_FORMAT

NUM_DIMENSIONS

POINT

LINE

POLYLINE

RECTANGLE

CIRCLE

ELLIPSE

POLYGON

FREE_SHAPE

FREE_LINE

GRID

ARROW

COLOR_BAR

SCALE

ROTATION

parser

tiffs

thumbId

thumbReader

usedFiles

isOIB

oibMapping

code

size

pixelSize

imageDepth

previewNames

pixelSizeX

pixelSizeY

validBits

illuminations

wavelengths

pinholeSize

magnification

lensNA

objectiveName

workingDistance

creationDate

channels

lutNames

filenames

roiFilenames

planes

poi

lut

lastChannel

pixelSizeZ

pixelSizeT

ptyStart

ptyEnd

ptyPattern

line

ifds

Constructor Detail

FV1000Reader

Method Detail

getOptimalTileWidth

getOptimalTileHeight

isSingleFile

isThisType