Package loci.formats.in

Class FV1000Reader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.FV1000Reader

All Implemented Interfaces:

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

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	Description
(package private) class	FV1000Reader.ChannelData
(package private) class	FV1000Reader.PlaneData

Field Summary

Fields

Modifier and Type	Field	Description
private static final int	ARROW
private List<FV1000Reader.ChannelData>	channels
private static final int	CIRCLE
private String[]	code
private static final int	COLOR_BAR
private String	creationDate
static final String	DATE_FORMAT
private static final int	ELLIPSE
private Map<Integer,String>	filenames
private static final int	FREE_LINE
private static final int	FREE_SHAPE
static final String	FV1000_MAGIC_STRING_1
static final String	FV1000_MAGIC_STRING_2
static final String[]	FV1000_SUFFIXES
private static final 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 final int	LINE
private short[][][]	lut
private List<String>	lutNames
private String	magnification
private static final int	NUM_DIMENSIONS
private String	objectiveName
static final String[]	OIB_SUFFIX
private Map<String,String>	oibMapping	File mappings for OIB file.
static final String[]	OIF_SUFFIX
private loci.common.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 final int	POINT	ROI types.
private static final int	POLYGON
private static final int	POLYLINE
static final String[]	PREVIEWNAME_PREFIXES
private List<String>	previewNames
private String	ptyEnd
private String	ptyPattern
private String	ptyStart
private static final int	RECTANGLE
private Map<Integer,String>	roiFilenames
private static final String	ROTATION
private static final 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, 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
FV1000Reader()	Constructs a new FV1000 reader.

Method Summary

Modifier and Type	Method	Description
private void	addPtyFiles()
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.
private String	findOIFFile(String baseFile)
short[][]	get16BitLookupTable()	Gets the 16-bit color lookup table associated with the most recently opened image.
private loci.common.RandomAccessInputStream	getFile(String name)
private loci.common.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 loci.common.RandomAccessInputStream	getPlane(int seriesIndex, int planeIndex)
private Integer	getPreviewNameIndex(String key)
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 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.
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, 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, 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

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

PREVIEWNAME_PREFIXES

public static final String[] PREVIEWNAME_PREFIXES

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 loci.common.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 Details

FV1000Reader

public FV1000Reader()

Constructs a new FV1000 reader.

Method Details

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 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

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 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)

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

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 loci.common.RandomAccessInputStream getFile(String name)
                                             throws FormatException,
IOException

Throws:

FormatException

IOException

getPlane

private loci.common.RandomAccessInputStream getPlane(int seriesIndex,
 int planeIndex)

getPreviewNameIndex

private Integer getPreviewNameIndex(String key)

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 loci.common.IniList getIniFile(String filename)
                                throws FormatException,
IOException

Throws:

FormatException

IOException