loci.formats.in

Class IvisionReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.IvisionReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, ICompressedTileReader, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class IvisionReader
extends FormatReader

IvisionReader is the file format reader for IVision (.IPM) files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	IvisionReader.IvisionHandler

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	binX
private java.lang.String	binY
private boolean	color16
private java.lang.String	creationDate
static java.lang.String	DATE_FORMAT
private java.lang.String	deltaT
private java.lang.String	exposureTime
private java.lang.String	gain
private boolean	hasPaddingByte
private long	imageOffset
private java.lang.Double	lensNA
private byte[]	lut
private java.lang.Double	magnification
private java.lang.String	offset
private java.lang.Double	refractiveIndex
private boolean	squareRoot
private java.lang.String	wavelength

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 and Description
IvisionReader() Constructs a new Ivision reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
boolean	isThisType(loci.common.RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
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, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, fileGroupOption, flattenHashtables, get16BitLookupTable, 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, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, 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, isSingleFile, isThisType, 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.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Field Detail

DATE_FORMAT

public static final java.lang.String DATE_FORMAT

See Also:

Constant Field Values

color16

private boolean color16

squareRoot

private boolean squareRoot

lut

private byte[] lut

imageOffset

private long imageOffset

binX

private java.lang.String binX

binY

private java.lang.String binY

creationDate

private java.lang.String creationDate

exposureTime

private java.lang.String exposureTime

gain

private java.lang.String gain

offset

private java.lang.String offset

deltaT

private java.lang.String deltaT

magnification

private java.lang.Double magnification

lensNA

private java.lang.Double lensNA

refractiveIndex

private java.lang.Double refractiveIndex

wavelength

private java.lang.String wavelength

hasPaddingByte

private boolean hasPaddingByte

Constructor Detail

IvisionReader

public IvisionReader()

Constructs a new Ivision reader.

Method Detail

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

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 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.

java.io.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 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