loci.formats.in

Class FlowSightReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.FlowSightReader

All Implemented Interfaces:

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

public class FlowSightReader
extends FormatReader

Author:

Lee Kamentsky Reader for the Amris ImageStream / FlowSight file format The cif file format is tiff-like, but doesn't adhere to the TIFF standard, so we use the TiffParser where we can, but do not use the TiffReader hierarchy.

Field Summary

Fields

Modifier and Type	Field and Description
private static int	ACQUISITION_TIME_TAG
private static int	BITMASK_COMPRESSION
private static int	CHANNEL_COUNT_TAG
private static int	CHANNEL_DESCS_TAG
private static int	CHANNEL_NAMES_TAG
private java.lang.String[]	channelDescs
private java.lang.String[]	channelNames
private static int	GREYSCALE_COMPRESSION
private long[]	ifdOffsets
private static int	METADATA_XML_TAG
private static int[]	MINIMAL_TAGS The tags that must be present for this reader to function properly
private TiffParser	tiffParser

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
FlowSightReader()

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.
private byte[]	openBitmaskBytes(IFD ifd, int imageWidth, int imageHeight) Decode the whole IFD plane using bitmask compression
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 byte[]	openGreyscaleBytes(IFD ifd, int imageWidth, int imageHeight) Decode the whole IFD plane using greyscale compression
void	reopenFile() Reopen any files that were closed, and which are expected to be open while the reader is open.

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, 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

CHANNEL_COUNT_TAG

private static final int CHANNEL_COUNT_TAG

See Also:

Constant Field Values

ACQUISITION_TIME_TAG

private static final int ACQUISITION_TIME_TAG

See Also:

Constant Field Values

CHANNEL_NAMES_TAG

private static final int CHANNEL_NAMES_TAG

See Also:

Constant Field Values

CHANNEL_DESCS_TAG

private static final int CHANNEL_DESCS_TAG

See Also:

Constant Field Values

METADATA_XML_TAG

private static final int METADATA_XML_TAG

See Also:

Constant Field Values

GREYSCALE_COMPRESSION

private static final int GREYSCALE_COMPRESSION

See Also:

Constant Field Values

BITMASK_COMPRESSION

private static final int BITMASK_COMPRESSION

See Also:

Constant Field Values

MINIMAL_TAGS

private static final int[] MINIMAL_TAGS

The tags that must be present for this reader to function properly

tiffParser

private transient TiffParser tiffParser

ifdOffsets

private long[] ifdOffsets

channelNames

private java.lang.String[] channelNames

channelDescs

private java.lang.String[] channelDescs

Constructor Detail

FlowSightReader

public FlowSightReader()

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

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

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

reopenFile

public void reopenFile()
                throws java.io.IOException

Description copied from interface: IFormatReader

Reopen any files that were closed, and which are expected to be open while the reader is open. This assumes that IFormatHandler.setId(java.lang.String) has been called, but close(false) has not been called.

Specified by:

reopenFile in interface IFormatReader

Overrides:

reopenFile in class FormatReader

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.

openBitmaskBytes

private byte[] openBitmaskBytes(IFD ifd,
                                int imageWidth,
                                int imageHeight)
                         throws FormatException

Decode the whole IFD plane using bitmask compression

Parameters:

ifd - - the IFD to decode

imageWidth - the width of the IFD plane

imageHeight - the height of the IFD plane

Returns:

a byte array of length imageWidth * imageHeight containing the uncompressed data

Throws:

FormatException

openGreyscaleBytes

private byte[] openGreyscaleBytes(IFD ifd,
                                  int imageWidth,
                                  int imageHeight)
                           throws FormatException

Decode the whole IFD plane using greyscale compression

Parameters:

ifd -

imageWidth -

imageHeight -

Returns:

a byte array

Throws:

FormatException