loci.formats.in

Class FV1000Reader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.FV1000Reader

All Implemented Interfaces:

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

Method Summary

Modifier and Type	Method and Description
private void	addPtyFiles()
void	close(boolean fileOnly) Closes the currently open file.
int	fileGroupOption(java.lang.String id) Returns an indication of whether the files in a multi-file dataset can be handled individually.
private java.lang.String	findOIFFile(java.lang.String baseFile)
short[][]	get16BitLookupTable() Gets the 16-bit color lookup table associated with the most recently opened image.
private loci.common.RandomAccessInputStream	getFile(java.lang.String name)
private loci.common.IniList	getIniFile(java.lang.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 java.lang.Integer	getPreviewNameIndex(java.lang.String key)
java.lang.String[]	getSeriesUsedFiles(boolean noPixels) Returns an array of filenames needed to open the current series.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
private void	initPOIService()
private boolean	isPreviewName(java.lang.String name)
boolean	isSingleFile(java.lang.String id) Returns true if the named file is expected to be the only file in the dataset.
boolean	isThisType(loci.common.RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
boolean	isThisType(java.lang.String name, boolean open) Checks if a file matches the type of this format reader.
private java.lang.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(java.lang.String filename, MetadataStore store, int nextROI, int plane)
private void	populateMetadataStore(MetadataStore store, java.lang.String path)
private java.lang.String	removeGST(java.lang.String s)
private java.lang.String	replaceExtension(java.lang.String name, java.lang.String oldExt, java.lang.String newExt)
private java.lang.String	sanitizeFile(java.lang.String file, java.lang.String path)
private java.lang.String	sanitizeValue(java.lang.String value)
private static int[]	scanFormat(java.lang.String pattern, java.lang.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, getCurrentCore, 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, 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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Detail

FV1000_MAGIC_STRING_1

public static final java.lang.String FV1000_MAGIC_STRING_1

See Also:

Constant Field Values

FV1000_MAGIC_STRING_2

public static final java.lang.String FV1000_MAGIC_STRING_2

See Also:

Constant Field Values

OIB_SUFFIX

public static final java.lang.String[] OIB_SUFFIX

OIF_SUFFIX

public static final java.lang.String[] OIF_SUFFIX

FV1000_SUFFIXES

public static final java.lang.String[] FV1000_SUFFIXES

PREVIEWNAME_PREFIXES

public static final java.lang.String[] PREVIEWNAME_PREFIXES

DATE_FORMAT

public static final java.lang.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 java.lang.String ROTATION

See Also:

Constant Field Values

parser

private loci.common.IniParser parser

tiffs

private java.util.List<java.lang.String> tiffs

Names of every TIFF file to open.

thumbId

private java.lang.String thumbId

Name of thumbnail file.

thumbReader

private BMPReader thumbReader

Helper reader for thumbnail.

usedFiles

private java.util.List<java.lang.String> usedFiles

Used file list.

isOIB

private boolean isOIB

Flag indicating this is an OIB dataset.

oibMapping

private java.util.Map<java.lang.String,java.lang.String> oibMapping

File mappings for OIB file.

code

private java.lang.String[] code

size

private java.lang.String[] size

pixelSize

private java.lang.Double[] pixelSize

imageDepth

private int imageDepth

previewNames

private java.util.List<java.lang.String> previewNames

pixelSizeX

private java.lang.String pixelSizeX

pixelSizeY

private java.lang.String pixelSizeY

validBits

private int validBits

illuminations

private java.util.List<java.lang.String> illuminations

wavelengths

private java.util.List<java.lang.Double> wavelengths

pinholeSize

private java.lang.String pinholeSize

magnification

private java.lang.String magnification

lensNA

private java.lang.String lensNA

objectiveName

private java.lang.String objectiveName

workingDistance

private java.lang.String workingDistance

creationDate

private java.lang.String creationDate

channels

private java.util.List<FV1000Reader.ChannelData> channels

lutNames

private java.util.List<java.lang.String> lutNames

filenames

private java.util.Map<java.lang.Integer,java.lang.String> filenames

roiFilenames

private java.util.Map<java.lang.Integer,java.lang.String> roiFilenames

planes

private java.util.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 java.lang.String ptyStart

ptyEnd

private java.lang.String ptyEnd

ptyPattern

private java.lang.String ptyPattern

line

private java.lang.String line

ifds

private java.util.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(java.lang.String id)
                     throws FormatException,
                            java.io.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

java.io.IOException

isThisType

public boolean isThisType(java.lang.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 java.io.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:

java.io.IOException

fileGroupOption

public int fileGroupOption(java.lang.String id)
                    throws FormatException,
                           java.io.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

java.io.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,
                        java.io.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.

java.io.IOException - if there was a problem reading the file.

See Also:

IFormatReader.openBytes(int, byte[], int, int, int, int)

getSeriesUsedFiles

public java.lang.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 java.io.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:

java.io.IOException

initFile

protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.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.

java.io.IOException - if an I/O error occurs processing the file

populateMetadataStore

private void populateMetadataStore(MetadataStore store,
                                   java.lang.String path)
                            throws FormatException,
                                   java.io.IOException

Throws:

FormatException

java.io.IOException

parseROIFile

private int parseROIFile(java.lang.String filename,
                         MetadataStore store,
                         int nextROI,
                         int plane)
                  throws FormatException,
                         java.io.IOException

Throws:

FormatException

java.io.IOException

addPtyFiles

private void addPtyFiles()
                  throws FormatException

Throws:

FormatException

findOIFFile

private java.lang.String findOIFFile(java.lang.String baseFile)
                              throws FormatException

Throws:

FormatException

mapOIBFiles

private java.lang.String mapOIBFiles()
                              throws FormatException,
                                     java.io.IOException

Throws:

FormatException

java.io.IOException

sanitizeValue

private java.lang.String sanitizeValue(java.lang.String value)

sanitizeFile

private java.lang.String sanitizeFile(java.lang.String file,
                                      java.lang.String path)

removeGST

private java.lang.String removeGST(java.lang.String s)

initPOIService

private void initPOIService()
                     throws FormatException,
                            java.io.IOException

Throws:

FormatException

java.io.IOException

getFile

private loci.common.RandomAccessInputStream getFile(java.lang.String name)
                                             throws FormatException,
                                                    java.io.IOException

Throws:

FormatException

java.io.IOException

getPlane

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

getPreviewNameIndex

private java.lang.Integer getPreviewNameIndex(java.lang.String key)

isPreviewName

private boolean isPreviewName(java.lang.String name)

replaceExtension

private java.lang.String replaceExtension(java.lang.String name,
                                          java.lang.String oldExt,
                                          java.lang.String newExt)

scanFormat

private static int[] scanFormat(java.lang.String pattern,
                                java.lang.String string)
                         throws FormatException

Throws:

FormatException

getIniFile

private loci.common.IniList getIniFile(java.lang.String filename)
                                throws FormatException,
                                       java.io.IOException

Throws:

FormatException

java.io.IOException