loci.formats.in

Class ZeissCZIReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.ZeissCZIReader

All Implemented Interfaces:

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

public class ZeissCZIReader
extends FormatReader

ZeissCZIReader is the file format reader for Zeiss .czi files.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	ZeissCZIReader.Attachment Segment with ID "ZISRAWATTACH".
(package private) class	ZeissCZIReader.AttachmentDirectory Segment with ID "ZISRAWATTDIR".
(package private) static class	ZeissCZIReader.AttachmentEntry
(package private) static class	ZeissCZIReader.Channel
(package private) static class	ZeissCZIReader.Coordinate
(package private) static class	ZeissCZIReader.DimensionEntry
(package private) class	ZeissCZIReader.Directory Segment with ID "ZISRAWDIRECTORY".
(package private) class	ZeissCZIReader.DirectoryEntry
(package private) class	ZeissCZIReader.FileHeader Segment with ID "ZISRAWFILE".
(package private) class	ZeissCZIReader.Metadata Segment with ID "ZISRAWMETADATA".
(package private) class	ZeissCZIReader.Segment Top-level class that implements logic common to all types of Segment.
(package private) class	ZeissCZIReader.SubBlock Segment with ID "ZISRAWSUBBLOCK".

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	acquiredDate
private int	acquisitions
private java.lang.String	airPressure
private static int	ALIGNMENT
static boolean	ALLOW_AUTOSTITCHING_DEFAULT
static java.lang.String	ALLOW_AUTOSTITCHING_KEY
private int	angles
private static int	BGR_24
private static int	BGR_48
private static int	BGR_FLOAT
private static int	BGRA_8
private java.util.ArrayList<java.lang.String>	binnings
private static int	BUFFER_SIZE
private java.util.ArrayList<ZeissCZIReader.Channel>	channels
private java.lang.String	co2Percent
private static int	COMPLEX
private static int	COMPLEX_FLOAT
private java.lang.String	correctionCollar
private static java.lang.String	CZI_MAGIC_STRING
private java.lang.String	description
private java.util.ArrayList<java.lang.String>	detectorRefs
private java.util.ArrayList<ZeissCZIReader.Attachment>	extraImages
private java.util.ArrayList<java.lang.String>	fieldNames
private java.lang.String	gain
private java.util.ArrayList<java.lang.String>	gains
private static int	GRAY_DOUBLE
private static int	GRAY_FLOAT
private static int	GRAY16
private static int	GRAY32
private static int	GRAY8 Pixel type constants.
private boolean	hasDetectorSettings
private static int	HEADER_SIZE
private java.lang.String	humidity
private java.lang.String[]	illuminationLabels
private int	illuminations
private java.lang.String	imageName
private java.util.ArrayList<java.lang.String>	imageNames
static boolean	INCLUDE_ATTACHMENTS_DEFAULT
static java.lang.String	INCLUDE_ATTACHMENTS_KEY
private java.util.HashMap<ZeissCZIReader.Coordinate,java.util.ArrayList<java.lang.Integer>>	indexIntoPlanes
private static int	JPEG
private static int	JPEGXR
private static int	LZW
private int	maxResolution
private java.lang.String	medium
private int	mosaics
private java.lang.String	objectiveSettingsID
private javax.xml.parsers.DocumentBuilder	parser
private java.lang.String[]	phaseLabels
private int	phases
private java.util.HashMap<java.lang.Integer,java.lang.String>	pixels
private java.util.ArrayList<ZeissCZIReader.SubBlock>	planes
private int	plateColumns
private java.util.ArrayList<java.lang.String>	platePositions
private int	plateRows
private int	positions
private ome.units.quantity.Length[]	positionsX
private ome.units.quantity.Length[]	positionsY
private ome.units.quantity.Length[]	positionsZ
private java.lang.Boolean	prestitched
private int	previousChannel
private java.lang.String	refractiveIndex
static boolean	RELATIVE_POSITIONS_DEFAULT
static java.lang.String	RELATIVE_POSITIONS_KEY
private java.lang.String[]	rotationLabels
private int	rotations
private int	scaleFactor
private int	scanDim
private java.util.ArrayList<ZeissCZIReader.Segment>	segments
private MetadataStore	store
private java.lang.String	temperature
private int[]	tileHeight
private int[]	tileWidth
private ome.units.quantity.Time	timeIncrement
private java.util.ArrayList<java.lang.Double>	timestamps
static boolean	TRIM_DIMENSIONS_DEFAULT
static java.lang.String	TRIM_DIMENSIONS_KEY
private static int	UNCOMPRESSED Compression constants.
private java.lang.String	userDisplayName
private java.lang.String	userEmail
private java.lang.String	userFirstName
private java.lang.String	userInstitution
private java.lang.String	userLastName
private java.lang.String	userMiddleName
private java.lang.String	userName
private java.lang.String	zoom
private static int	ZSTD_0
private static int	ZSTD_1
private ome.units.quantity.Length	zStep

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
ZeissCZIReader() Constructs a new Zeiss .czi reader.

Method Summary

Modifier and Type	Method and Description
boolean	allowAutostitching()
private void	assignPlaneIndices()
private void	calculateDimensions()
private void	calculateDimensions(int coreIndex, boolean xyOnly)
boolean	canReadAttachments()
private boolean	checkPALM(java.lang.String xml)
void	close(boolean fileOnly) Closes the currently open file.
private void	convertPixelType(CoreMetadata ms0, int pixelType)
private void	convertPixelType(int pixelType)
private byte[]	decode12BitCamera(byte[] data, int maxBytes)
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.
protected java.util.ArrayList<java.lang.String>	getAvailableOptions() Returns the list of available metadata options.
java.lang.Byte	getFillColor() Return the fill value for undefined pixels.
private org.w3c.dom.Element	getFirstNode(org.w3c.dom.Element root, java.lang.String name)
private java.lang.String	getFirstNodeValue(org.w3c.dom.Element root, java.lang.String name)
private org.w3c.dom.NodeList	getGrandchildren(org.w3c.dom.Element root, java.lang.String name)
private org.w3c.dom.NodeList	getGrandchildren(org.w3c.dom.Element root, java.lang.String child, java.lang.String name)
int	getOptimalTileHeight() Returns the optimal sub-image height for use with openBytes.
int	getOptimalTileWidth() Returns the optimal sub-image width for use with openBytes.
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.).
boolean	isThisType(loci.common.RandomAccessInputStream stream) Checks if the given stream is a valid stream for this file format.
private java.lang.String	normalizeColor(java.lang.String color)
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	parseObjectives(org.w3c.dom.NodeList objectives)
private int	populateCircles(org.w3c.dom.NodeList circles, int roi, int shape)
private int	populateLines(org.w3c.dom.NodeList lines, int roi, int shape)
private void	populateOriginalMetadata(org.w3c.dom.Element root, java.util.Deque<java.lang.String> nameStack)
private int	populatePolylines(org.w3c.dom.NodeList polylines, int roi, int shape, boolean closed)
private int	populateRectangles(org.w3c.dom.NodeList rectangles, int roi, int shape)
private void	readAttachments()
private ZeissCZIReader.Segment	readSegment(java.lang.String filename)
private void	readSegments(java.lang.String id)
private int	readVarint(loci.common.RandomAccessInputStream stream)
boolean	storeRelativePositions()
private void	translateDisplaySettings(org.w3c.dom.Element root)
private void	translateExperiment(org.w3c.dom.Element root)
private void	translateHardwareSettings(org.w3c.dom.Element root)
private void	translateInformation(org.w3c.dom.Element root)
private void	translateLayers(org.w3c.dom.Element root)
private void	translateMetadata(java.lang.String xml)
private void	translateScaling(org.w3c.dom.Element root)
boolean	trimDimensions()

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, 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, 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

ALLOW_AUTOSTITCHING_KEY

public static final java.lang.String ALLOW_AUTOSTITCHING_KEY

See Also:

Constant Field Values

ALLOW_AUTOSTITCHING_DEFAULT

public static final boolean ALLOW_AUTOSTITCHING_DEFAULT

See Also:

Constant Field Values

INCLUDE_ATTACHMENTS_KEY

public static final java.lang.String INCLUDE_ATTACHMENTS_KEY

See Also:

Constant Field Values

INCLUDE_ATTACHMENTS_DEFAULT

public static final boolean INCLUDE_ATTACHMENTS_DEFAULT

See Also:

Constant Field Values

TRIM_DIMENSIONS_KEY

public static final java.lang.String TRIM_DIMENSIONS_KEY

See Also:

Constant Field Values

TRIM_DIMENSIONS_DEFAULT

public static final boolean TRIM_DIMENSIONS_DEFAULT

See Also:

Constant Field Values

RELATIVE_POSITIONS_KEY

public static final java.lang.String RELATIVE_POSITIONS_KEY

See Also:

Constant Field Values

RELATIVE_POSITIONS_DEFAULT

public static final boolean RELATIVE_POSITIONS_DEFAULT

See Also:

Constant Field Values

ALIGNMENT

private static final int ALIGNMENT

See Also:

Constant Field Values

HEADER_SIZE

private static final int HEADER_SIZE

See Also:

Constant Field Values

CZI_MAGIC_STRING

private static final java.lang.String CZI_MAGIC_STRING

See Also:

Constant Field Values

BUFFER_SIZE

private static final int BUFFER_SIZE

See Also:

Constant Field Values

UNCOMPRESSED

private static final int UNCOMPRESSED

Compression constants.

See Also:

Constant Field Values

JPEG

private static final int JPEG

See Also:

Constant Field Values

LZW

private static final int LZW

See Also:

Constant Field Values

JPEGXR

private static final int JPEGXR

See Also:

Constant Field Values

ZSTD_0

private static final int ZSTD_0

See Also:

Constant Field Values

ZSTD_1

private static final int ZSTD_1

See Also:

Constant Field Values

GRAY8

private static final int GRAY8

Pixel type constants.

See Also:

Constant Field Values

GRAY16

private static final int GRAY16

See Also:

Constant Field Values

GRAY_FLOAT

private static final int GRAY_FLOAT

See Also:

Constant Field Values

BGR_24

private static final int BGR_24

See Also:

Constant Field Values

BGR_48

private static final int BGR_48

See Also:

Constant Field Values

BGR_FLOAT

private static final int BGR_FLOAT

See Also:

Constant Field Values

BGRA_8

private static final int BGRA_8

See Also:

Constant Field Values

COMPLEX

private static final int COMPLEX

See Also:

Constant Field Values

COMPLEX_FLOAT

private static final int COMPLEX_FLOAT

See Also:

Constant Field Values

GRAY32

private static final int GRAY32

See Also:

Constant Field Values

GRAY_DOUBLE

private static final int GRAY_DOUBLE

See Also:

Constant Field Values

store

private MetadataStore store

pixels

private java.util.HashMap<java.lang.Integer,java.lang.String> pixels

segments

private java.util.ArrayList<ZeissCZIReader.Segment> segments

planes

private java.util.ArrayList<ZeissCZIReader.SubBlock> planes

indexIntoPlanes

private java.util.HashMap<ZeissCZIReader.Coordinate,java.util.ArrayList<java.lang.Integer>> indexIntoPlanes

rotations

private int rotations

positions

private int positions

illuminations

private int illuminations

acquisitions

private int acquisitions

mosaics

private int mosaics

phases

private int phases

angles

private int angles

maxResolution

private int maxResolution

imageName

private java.lang.String imageName

acquiredDate

private java.lang.String acquiredDate

description

private java.lang.String description

userDisplayName

private java.lang.String userDisplayName

userName

private java.lang.String userName

userFirstName

private java.lang.String userFirstName

userLastName

private java.lang.String userLastName

userMiddleName

private java.lang.String userMiddleName

userEmail

private java.lang.String userEmail

userInstitution

private java.lang.String userInstitution

temperature

private java.lang.String temperature

airPressure

private java.lang.String airPressure

humidity

private java.lang.String humidity

co2Percent

private java.lang.String co2Percent

correctionCollar

private java.lang.String correctionCollar

medium

private java.lang.String medium

refractiveIndex

private java.lang.String refractiveIndex

timeIncrement

private transient ome.units.quantity.Time timeIncrement

zoom

private java.lang.String zoom

gain

private java.lang.String gain

channels

private java.util.ArrayList<ZeissCZIReader.Channel> channels

binnings

private java.util.ArrayList<java.lang.String> binnings

detectorRefs

private java.util.ArrayList<java.lang.String> detectorRefs

timestamps

private java.util.ArrayList<java.lang.Double> timestamps

gains

private transient java.util.ArrayList<java.lang.String> gains

positionsX

private ome.units.quantity.Length[] positionsX

positionsY

private ome.units.quantity.Length[] positionsY

positionsZ

private ome.units.quantity.Length[] positionsZ

previousChannel

private int previousChannel

prestitched

private java.lang.Boolean prestitched

objectiveSettingsID

private java.lang.String objectiveSettingsID

hasDetectorSettings

private boolean hasDetectorSettings

scanDim

private int scanDim

rotationLabels

private java.lang.String[] rotationLabels

phaseLabels

private java.lang.String[] phaseLabels

illuminationLabels

private java.lang.String[] illuminationLabels

parser

private transient javax.xml.parsers.DocumentBuilder parser

extraImages

private java.util.ArrayList<ZeissCZIReader.Attachment> extraImages

tileWidth

private int[] tileWidth

tileHeight

private int[] tileHeight

scaleFactor

private int scaleFactor

zStep

private transient ome.units.quantity.Length zStep

plateRows

private transient int plateRows

plateColumns

private transient int plateColumns

platePositions

private transient java.util.ArrayList<java.lang.String> platePositions

fieldNames

private transient java.util.ArrayList<java.lang.String> fieldNames

imageNames

private transient java.util.ArrayList<java.lang.String> imageNames

Constructor Detail

ZeissCZIReader

public ZeissCZIReader()

Constructs a new Zeiss .czi 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

See Also:

IFormatReader.isThisType(RandomAccessInputStream)

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

See Also:

IFormatReader.getSeriesUsedFiles(boolean)

get8BitLookupTable

public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   java.io.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

java.io.IOException

get16BitLookupTable

public short[][] get16BitLookupTable()
                              throws FormatException,
                                     java.io.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

java.io.IOException

getFillColor

public java.lang.Byte getFillColor()

Description copied from interface: IFormatReader

Return the fill value for undefined pixels. The default implementation in IFormatReader always returns 0.

Specified by:

getFillColor in interface IFormatReader

Overrides:

getFillColor in class FormatReader

See Also:

If the fill value was set explicitly, use that. Otherwise, return 255 (white) for RGB data with a pyramid, and 0 in all other cases. RGB data with a pyramid can reasonably be assumed to be a brightfield slide.

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

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

getAvailableOptions

protected java.util.ArrayList<java.lang.String> getAvailableOptions()

Description copied from class: FormatReader

Returns the list of available metadata options.

Overrides:

getAvailableOptions in class FormatReader

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

allowAutostitching

public boolean allowAutostitching()

canReadAttachments

public boolean canReadAttachments()

trimDimensions

public boolean trimDimensions()

storeRelativePositions

public boolean storeRelativePositions()

readSegments

private void readSegments(java.lang.String id)
                   throws java.io.IOException

Throws:

java.io.IOException

readAttachments

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

Throws:

FormatException

java.io.IOException

calculateDimensions

private void calculateDimensions()

calculateDimensions

private void calculateDimensions(int coreIndex,
                                 boolean xyOnly)

assignPlaneIndices

private void assignPlaneIndices()

translateMetadata

private void translateMetadata(java.lang.String xml)
                        throws FormatException,
                               java.io.IOException

Throws:

FormatException

java.io.IOException

checkPALM

private boolean checkPALM(java.lang.String xml)
                   throws FormatException,
                          java.io.IOException

Throws:

FormatException

java.io.IOException

translateInformation

private void translateInformation(org.w3c.dom.Element root)
                           throws FormatException

Throws:

FormatException

translateScaling

private void translateScaling(org.w3c.dom.Element root)

translateDisplaySettings

private void translateDisplaySettings(org.w3c.dom.Element root)
                               throws FormatException

Throws:

FormatException

translateLayers

private void translateLayers(org.w3c.dom.Element root)

translateHardwareSettings

private void translateHardwareSettings(org.w3c.dom.Element root)
                                throws FormatException

Throws:

FormatException

populateRectangles

private int populateRectangles(org.w3c.dom.NodeList rectangles,
                               int roi,
                               int shape)

populatePolylines

private int populatePolylines(org.w3c.dom.NodeList polylines,
                              int roi,
                              int shape,
                              boolean closed)

populateLines

private int populateLines(org.w3c.dom.NodeList lines,
                          int roi,
                          int shape)

populateCircles

private int populateCircles(org.w3c.dom.NodeList circles,
                            int roi,
                            int shape)

translateExperiment

private void translateExperiment(org.w3c.dom.Element root)
                          throws FormatException

Throws:

FormatException

getFirstNode

private org.w3c.dom.Element getFirstNode(org.w3c.dom.Element root,
                                         java.lang.String name)

getGrandchildren

private org.w3c.dom.NodeList getGrandchildren(org.w3c.dom.Element root,
                                              java.lang.String name)

getGrandchildren

private org.w3c.dom.NodeList getGrandchildren(org.w3c.dom.Element root,
                                              java.lang.String child,
                                              java.lang.String name)

getFirstNodeValue

private java.lang.String getFirstNodeValue(org.w3c.dom.Element root,
                                           java.lang.String name)

populateOriginalMetadata

private void populateOriginalMetadata(org.w3c.dom.Element root,
                                      java.util.Deque<java.lang.String> nameStack)

readSegment

private ZeissCZIReader.Segment readSegment(java.lang.String filename)
                                    throws java.io.IOException

Throws:

java.io.IOException

convertPixelType

private void convertPixelType(int pixelType)
                       throws FormatException

Throws:

FormatException

convertPixelType

private void convertPixelType(CoreMetadata ms0,
                              int pixelType)
                       throws FormatException

Throws:

FormatException

parseObjectives

private void parseObjectives(org.w3c.dom.NodeList objectives)
                      throws FormatException

Throws:

FormatException

decode12BitCamera

private byte[] decode12BitCamera(byte[] data,
                                 int maxBytes)
                          throws java.io.IOException

Throws:

java.io.IOException

readVarint

private int readVarint(loci.common.RandomAccessInputStream stream)
                throws java.io.IOException

Throws:

java.io.IOException

normalizeColor

private java.lang.String normalizeColor(java.lang.String color)