loci.formats.in

Class BaseZeissReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BaseZeissReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

Direct Known Subclasses:

ZeissTIFFReader, ZeissZVIReader

public abstract class BaseZeissReader
extends FormatReader

BaseZeissReader contains common functionality required by readers for Zeiss AxioVision formats.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static class	BaseZeissReader.Charset
static class	BaseZeissReader.Context
(package private) static class	BaseZeissReader.DrawStyle Line drawing styles.
(package private) static class	BaseZeissReader.FeatureType Feature types.
(package private) static class	BaseZeissReader.FillStyle Fill styles.
(package private) class	BaseZeissReader.Layer Layer class representing an AxioVision layer; used to contain a collection of shapes.
(package private) static class	BaseZeissReader.LineEndPositions
(package private) static class	BaseZeissReader.LineEndStyle Line ending styles.
(package private) static class	BaseZeissReader.PointStyle Point styles.
(package private) class	BaseZeissReader.Shape Shape class representing the metadata within an AxioVision Shape ROI
class	BaseZeissReader.Tag Content of a single tag from a Tags block.
(package private) static class	BaseZeissReader.TextAlignment

Field Summary

Fields

Modifier and Type	Field and Description
protected int	bpp Number of bytes per pixel.
protected int[]	channelColors
protected Set<Integer>	channelIndices
protected Map<Integer,String>	channelName
protected int	cIndex
protected int	colCount
protected int[][]	coordinates
protected Map<Integer,Double>	detectorGain
protected Map<Integer,Double>	detectorOffset
protected Map<Integer,ome.units.quantity.Length>	emWavelength
protected Map<Integer,String>	exposureTime
protected Map<Integer,ome.units.quantity.Length>	exWavelength
protected String	imageDescription
protected String[]	imageFiles
protected boolean	isJPEG
protected boolean	isZlib
protected int	lastPlane
ArrayList<BaseZeissReader.Layer>	layers
protected int	nextChName
protected int	nextEmWave
protected int	nextExWave
protected int[]	offsets
protected Double	physicalSizeX
protected Double	physicalSizeY
protected Double	physicalSizeZ
protected int	rawCount
protected int	realHeight
protected int	realWidth
protected List<String>	roiIDs
protected int	rowCount
protected Map<Integer,ome.units.quantity.Length>	stageX
protected Map<Integer,ome.units.quantity.Length>	stageY
protected List<String>	tagsToParse
protected Set<Integer>	tileIndices
protected Map<Integer,Integer>	tiles
protected int	timepoint
protected Set<Integer>	timepointIndices
protected Map<Integer,String>	timestamps
protected Set<Integer>	zIndices

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
BaseZeissReader(String name, String suffix) Constructs a new ZeissZVI reader.
BaseZeissReader(String name, String[] suffixes) Constructs a new ZeissZVI reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
protected void	countImages()
protected void	fillMetadataPass1(MetadataStore store) Read and store basic dimensions in model
protected void	fillMetadataPass2(MetadataStore store) Read and store basic dimensions in model
protected void	fillMetadataPass3(MetadataStore store) Read and store basic dimensions in model
protected void	fillMetadataPass4(MetadataStore store) Read and store basic dimensions in model
protected void	fillMetadataPass5(MetadataStore store) Read and store basic dimensions in model
protected void	fillMetadataPass6(MetadataStore store) Read and store basic dimensions in model
protected void	fillMetadataPass7(MetadataStore store) Store basic dimensions in model
short[][]	get16BitLookupTable() Gets the 16-bit color lookup table associated with the most recently opened image.
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
int	getOptimalTileHeight() Returns the optimal sub-image height for use with openBytes.
protected void	initFileMain(String id)
protected void	initVars(String id)
protected static int	parseColor(byte r, byte g, byte b)
protected static int	parseInt(String number) Parse an Integer from a String.
protected static int	parseInt(String number, int defaultnum) Parse an Integer from a String.
(package private) void	parseMainTags(int image, MetadataStore store, ArrayList<BaseZeissReader.Tag> tags)
private long	parseTimestamp(String s) Parse timestamp from string.
protected void	storeROIs(MetadataStore store) Store basic dimensions in model

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, 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, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, initFile, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, 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

bpp

protected int bpp

Number of bytes per pixel.

imageFiles

protected String[] imageFiles

offsets

protected int[] offsets

coordinates

protected int[][] coordinates

timestamps

protected Map<Integer,String> timestamps

exposureTime

protected Map<Integer,String> exposureTime

cIndex

protected int cIndex

isJPEG

protected boolean isJPEG

isZlib

protected boolean isZlib

realWidth

protected int realWidth

realHeight

protected int realHeight

tagsToParse

protected List<String> tagsToParse

nextEmWave

protected int nextEmWave

nextExWave

protected int nextExWave

nextChName

protected int nextChName

stageX

protected final Map<Integer,ome.units.quantity.Length> stageX

stageY

protected final Map<Integer,ome.units.quantity.Length> stageY

timepoint

protected int timepoint

channelColors

protected int[] channelColors

lastPlane

protected int lastPlane

tiles

protected final Map<Integer,Integer> tiles

detectorGain

protected final Map<Integer,Double> detectorGain

detectorOffset

protected final Map<Integer,Double> detectorOffset

emWavelength

protected final Map<Integer,ome.units.quantity.Length> emWavelength

exWavelength

protected final Map<Integer,ome.units.quantity.Length> exWavelength

channelName

protected final Map<Integer,String> channelName

physicalSizeX

protected Double physicalSizeX

physicalSizeY

protected Double physicalSizeY

physicalSizeZ

protected Double physicalSizeZ

rowCount

protected int rowCount

colCount

protected int colCount

rawCount

protected int rawCount

imageDescription

protected String imageDescription

channelIndices

protected Set<Integer> channelIndices

zIndices

protected Set<Integer> zIndices

timepointIndices

protected Set<Integer> timepointIndices

tileIndices

protected Set<Integer> tileIndices

roiIDs

protected List<String> roiIDs

layers

public ArrayList<BaseZeissReader.Layer> layers

Constructor Detail

BaseZeissReader

public BaseZeissReader(String name,
                       String suffix)

Constructs a new ZeissZVI reader.

BaseZeissReader

public BaseZeissReader(String name,
                       String[] suffixes)

Constructs a new ZeissZVI reader.

Method Detail

initFileMain

protected void initFileMain(String id)
                     throws FormatException,
                            IOException

Throws:

FormatException

IOException

initVars

protected void initVars(String id)
                 throws FormatException,
                        IOException

Throws:

FormatException

IOException

countImages

protected void countImages()

fillMetadataPass1

protected void fillMetadataPass1(MetadataStore store)
                          throws FormatException,
                                 IOException

Read and store basic dimensions in model

Parameters:

store -

Throws:

FormatException

IOException

fillMetadataPass2

protected void fillMetadataPass2(MetadataStore store)
                          throws FormatException,
                                 IOException

Read and store basic dimensions in model

Parameters:

store -

Throws:

FormatException

IOException

fillMetadataPass3

protected void fillMetadataPass3(MetadataStore store)
                          throws FormatException,
                                 IOException

Read and store basic dimensions in model

Parameters:

store -

Throws:

FormatException

IOException

fillMetadataPass4

protected void fillMetadataPass4(MetadataStore store)
                          throws FormatException,
                                 IOException

Read and store basic dimensions in model

Parameters:

store -

Throws:

FormatException

IOException

fillMetadataPass5

protected void fillMetadataPass5(MetadataStore store)
                          throws FormatException,
                                 IOException

Read and store basic dimensions in model

Parameters:

store -

Throws:

FormatException

IOException

fillMetadataPass6

protected void fillMetadataPass6(MetadataStore store)
                          throws FormatException,
                                 IOException

Read and store basic dimensions in model

Parameters:

store -

Throws:

FormatException

IOException

fillMetadataPass7

protected void fillMetadataPass7(MetadataStore store)
                          throws FormatException,
                                 IOException

Store basic dimensions in model

Parameters:

store -

Throws:

FormatException

IOException

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

storeROIs

protected void storeROIs(MetadataStore store)
                  throws FormatException,
                         IOException

Store basic dimensions in model

Parameters:

store -

Throws:

FormatException

IOException

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   IOException

Description copied from interface: IFormatReader

Gets the 8-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.INT8 or FormatTools.UINT8, this method will return null.

Specified by:

get8BitLookupTable in interface IFormatReader

Overrides:

get8BitLookupTable in class FormatReader

Throws:

FormatException

IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
                                     IOException

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

Throws:

FormatException

IOException

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

parseMainTags

void parseMainTags(int image,
                   MetadataStore store,
                   ArrayList<BaseZeissReader.Tag> tags)
            throws FormatException,
                   IOException

Throws:

FormatException

IOException

parseInt

protected static int parseInt(String number)

Parse an Integer from a String.

Parameters:

number - the number to parse

Returns:

an Integer. 0 if number was null.

parseInt

protected static int parseInt(String number,
                              int defaultnum)

Parse an Integer from a String.

Parameters:

number - the number to parse

defaultnum - the number to return if number is null or empty

Returns:

an Integer. 0 if number was null.

parseTimestamp

private long parseTimestamp(String s)

Parse timestamp from string. Note this may be ZVI-specific due to the use of locale-specific date formats in the TIFF XML.

Parameters:

s -

Returns:

a timestamp

parseColor

protected static int parseColor(byte r,
                                byte g,
                                byte b)