loci.formats.in

Class ZeissZVIReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.BaseZeissReader

loci.formats.in.ZeissZVIReader

All Implemented Interfaces:

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

public class ZeissZVIReader
extends BaseZeissReader

ZeissZVIReader is the file format reader for Zeiss ZVI files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested classes/interfaces inherited from class loci.formats.in.BaseZeissReader

BaseZeissReader.Charset, BaseZeissReader.Context, BaseZeissReader.DrawStyle, BaseZeissReader.FeatureType, BaseZeissReader.FillStyle, BaseZeissReader.Layer, BaseZeissReader.LineEndPositions, BaseZeissReader.LineEndStyle, BaseZeissReader.PointStyle, BaseZeissReader.Shape, BaseZeissReader.Tag, BaseZeissReader.TextAlignment

Field Summary

Fields

Modifier and Type	Field and Description
protected loci.common.RandomAccessInputStream	currentPlane
protected int	currentPlaneIndex
protected java.lang.String[]	files
protected POIService	poi
private static long	ROI_SIGNATURE
static int	ZVI_MAGIC_BYTES

Fields inherited from class loci.formats.in.BaseZeissReader

acquisitionDate, bpp, channelColors, channelIndices, channelName, cIndex, colCount, coordinates, detectorGain, detectorOffset, emWavelength, exposureTime, exWavelength, imageDescription, imageFiles, isJPEG, isZlib, lastPlane, layers, nextChName, nextEmWave, nextExWave, offsets, physicalSizeX, physicalSizeY, physicalSizeZ, rawCount, realHeight, realWidth, roiIDs, rowCount, stageX, stageY, tagsToParse, tileIndices, tiles, timepoint, timepointIndices, timestamps, zIndices

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
ZeissZVIReader() 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	fillMetadataPass3(MetadataStore store) Read and store basic dimensions in model
protected void	fillMetadataPass5(MetadataStore store) Read and store basic dimensions in model
private int	getImageNumber(java.lang.String dirName, int defaultNumber)
private java.lang.String	getNextTag(loci.common.RandomAccessInputStream s)
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
private void	initPOIService()
protected void	initVars(java.lang.String id)
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.
private void	parseROIs(loci.common.RandomAccessInputStream s, int imageNum, java.lang.String name, MetadataStore store) Parse ROI data from the given RandomAccessInputStream and store it in the given MetadataStore.
protected java.lang.String	parseROIString(loci.common.RandomAccessInputStream s)
private void	parseTags(int image, java.lang.String file, MetadataStore store) Parse all of the tags in a stream.

Methods inherited from class loci.formats.in.BaseZeissReader

fillMetadataPass2, fillMetadataPass4, fillMetadataPass6, fillMetadataPass7, get16BitLookupTable, get8BitLookupTable, getOptimalTileHeight, initFileMain, parseColor, parseInt, parseInt, parseMainTags, storeROIs

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, 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, 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

ZVI_MAGIC_BYTES

public static final int ZVI_MAGIC_BYTES

See Also:

Constant Field Values

ROI_SIGNATURE

private static final long ROI_SIGNATURE

See Also:

Constant Field Values

poi

protected transient POIService poi

files

protected java.lang.String[] files

currentPlane

protected transient loci.common.RandomAccessInputStream currentPlane

currentPlaneIndex

protected transient int currentPlaneIndex

Constructor Detail

ZeissZVIReader

public ZeissZVIReader()

Constructs a new ZeissZVI 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 BaseZeissReader

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

initVars

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

Overrides:

initVars in class BaseZeissReader

Throws:

FormatException

java.io.IOException

initPOIService

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

Throws:

FormatException

java.io.IOException

fillMetadataPass1

protected void fillMetadataPass1(MetadataStore store)
                          throws FormatException,
                                 java.io.IOException

Description copied from class: BaseZeissReader

Read and store basic dimensions in model

Overrides:

fillMetadataPass1 in class BaseZeissReader

Throws:

FormatException

java.io.IOException

fillMetadataPass3

protected void fillMetadataPass3(MetadataStore store)
                          throws FormatException,
                                 java.io.IOException

Description copied from class: BaseZeissReader

Read and store basic dimensions in model

Overrides:

fillMetadataPass3 in class BaseZeissReader

Throws:

FormatException

java.io.IOException

fillMetadataPass5

protected void fillMetadataPass5(MetadataStore store)
                          throws FormatException,
                                 java.io.IOException

Description copied from class: BaseZeissReader

Read and store basic dimensions in model

Overrides:

fillMetadataPass5 in class BaseZeissReader

Throws:

FormatException

java.io.IOException

countImages

protected void countImages()

Overrides:

countImages in class BaseZeissReader

getImageNumber

private int getImageNumber(java.lang.String dirName,
                           int defaultNumber)

getNextTag

private java.lang.String getNextTag(loci.common.RandomAccessInputStream s)
                             throws java.io.IOException

Throws:

java.io.IOException

parseTags

private void parseTags(int image,
                       java.lang.String file,
                       MetadataStore store)
                throws FormatException,
                       java.io.IOException

Parse all of the tags in a stream.

Throws:

FormatException

java.io.IOException

parseROIs

private void parseROIs(loci.common.RandomAccessInputStream s,
                       int imageNum,
                       java.lang.String name,
                       MetadataStore store)
                throws java.io.IOException

Parse ROI data from the given RandomAccessInputStream and store it in the given MetadataStore.

Throws:

java.io.IOException

parseROIString

protected java.lang.String parseROIString(loci.common.RandomAccessInputStream s)
                                   throws java.io.IOException

Throws:

java.io.IOException