loci.formats.in

Class ND2Handler

java.lang.Object

org.xml.sax.helpers.DefaultHandler

loci.common.xml.BaseHandler

loci.formats.in.ND2Handler

All Implemented Interfaces:

org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler

public class ND2Handler
extends loci.common.xml.BaseHandler

DefaultHandler implementation for handling XML produced by Nikon Elements.

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.ArrayList<java.lang.String>	binning
private java.lang.String	cameraModel
private boolean	canAdjustDimensions
private java.util.ArrayList<java.lang.String>	channelNames
private java.util.Hashtable<java.lang.String,java.lang.Integer>	colors
private CoreMetadataList	core
private java.lang.String	correction
private java.lang.String	date
private static java.lang.String	DATE_FORMAT
private java.util.Hashtable<java.lang.String,java.lang.String>	dyes
private java.util.ArrayList<java.lang.Double>	emWave
private java.util.ArrayList<java.lang.Double>	exposureTime
private java.util.ArrayList<java.lang.Double>	exWave
private static int	FIELD_INDEX
private boolean	firstTimeLoop
private java.util.ArrayList<java.lang.Double>	gain
private java.lang.String	immersion
private boolean	isLossless
private static org.slf4j.Logger	LOGGER
private java.lang.Double	mag
private java.util.Hashtable<java.lang.String,java.lang.Object>	metadata
private java.util.ArrayList<java.lang.String>	modality
private java.lang.Double	na
private int	nImages
private int	numSeries
private int	nXFields
private int	nYFields
private java.lang.String	objectiveModel
private java.lang.Double	pinholeSize
private double	pixelSizeX
private double	pixelSizeY
private double	pixelSizeZ
private boolean	populateXY
private java.util.ArrayList<java.lang.String>	posNames
private java.util.ArrayList<ome.units.quantity.Length>	posX
private java.util.ArrayList<ome.units.quantity.Length>	posY
private java.util.ArrayList<ome.units.quantity.Length>	posZ
private java.util.ArrayList<java.lang.Integer>	power
private java.lang.String	prefix
private java.lang.String	prevElement
private java.lang.String	prevRuntype
private java.util.Hashtable<java.lang.String,java.lang.Integer>	realColors
private java.lang.Double	refractiveIndex
private java.util.ArrayList<java.util.Hashtable<java.lang.String,java.lang.String>>	rois
private java.util.ArrayList<java.lang.Double>	speed
private java.util.ArrayList<java.lang.Double>	temperature
private java.util.ArrayList<java.lang.Long>	ts
private java.util.ArrayList<java.lang.Boolean>	validLoopState
private java.lang.Double	voltage
private java.util.ArrayList<java.lang.Long>	zs

Constructor Summary

Constructors

Constructor and Description
ND2Handler(CoreMetadataList core, boolean populateXY, int nImages)
ND2Handler(CoreMetadataList core, int nImages)

Method Summary

Modifier and Type	Method and Description
void	endDocument()
void	endElement(java.lang.String uri, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attributes)
java.util.ArrayList<java.lang.String>	getBinnings()
java.lang.String	getCameraModel()
java.util.Hashtable<java.lang.String,java.lang.Integer>	getChannelColors()
java.util.ArrayList<java.lang.String>	getChannelNames()
CoreMetadataList	getCoreMetadataList()
java.lang.String	getCorrection()
java.lang.String	getDate()
java.util.ArrayList<java.lang.Double>	getEmissionWavelengths()
java.util.ArrayList<java.lang.Double>	getExcitationWavelengths()
java.util.ArrayList<java.lang.Double>	getExposureTimes()
int	getFieldIndex()
java.util.ArrayList<java.lang.Double>	getGains()
java.lang.String	getImmersion()
java.lang.Double	getMagnification()
java.util.Hashtable<java.lang.String,java.lang.Object>	getMetadata()
java.util.ArrayList<java.lang.String>	getModalities()
java.lang.Double	getNumericalAperture()
java.lang.String	getObjectiveModel()
java.lang.Double	getPinholeSize()
double	getPixelSizeX()
double	getPixelSizeY()
double	getPixelSizeZ()
java.util.ArrayList<java.lang.String>	getPositionNames()
java.util.ArrayList<java.lang.Integer>	getPowers()
java.lang.Double	getRefractiveIndex()
java.util.ArrayList<java.util.Hashtable<java.lang.String,java.lang.String>>	getROIs()
int	getSeriesCount()
java.util.ArrayList<java.lang.Double>	getSpeeds()
java.util.ArrayList<java.lang.Double>	getTemperatures()
java.util.ArrayList<java.lang.Long>	getTimepoints()
java.lang.Double	getVoltage()
int	getXFields()
java.util.ArrayList<ome.units.quantity.Length>	getXPositions()
java.util.ArrayList<ome.units.quantity.Length>	getYPositions()
java.util.ArrayList<ome.units.quantity.Length>	getZPositions()
java.util.ArrayList<java.lang.Long>	getZSections()
boolean	isDimensions(java.lang.String key) Returns whether or not the specified key is denotes dimensions.
boolean	isLossless()
void	parseKeyAndValue(java.lang.String key, java.lang.String value, java.lang.String runtype)
private java.lang.Double	parsePixelsSizeZFromKey(java.lang.String key) Parses the physical size from a key.
void	populateROIs(MetadataStore store)
void	startElement(java.lang.String uri, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attributes)

Methods inherited from class loci.common.xml.BaseHandler

resolveEntity

Methods inherited from class org.xml.sax.helpers.DefaultHandler

characters, endElement, endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, setDocumentLocator, skippedEntity, startDocument, startPrefixMapping, unparsedEntityDecl, warning

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

LOGGER

private static final org.slf4j.Logger LOGGER

DATE_FORMAT

private static final java.lang.String DATE_FORMAT

See Also:

Constant Field Values

FIELD_INDEX

private static final int FIELD_INDEX

See Also:

Constant Field Values

prefix

private java.lang.String prefix

prevRuntype

private java.lang.String prevRuntype

prevElement

private java.lang.String prevElement

metadata

private java.util.Hashtable<java.lang.String,java.lang.Object> metadata

core

private CoreMetadataList core

isLossless

private boolean isLossless

zs

private java.util.ArrayList<java.lang.Long> zs

ts

private java.util.ArrayList<java.lang.Long> ts

numSeries

private int numSeries

pixelSizeX

private double pixelSizeX

pixelSizeY

private double pixelSizeY

pixelSizeZ

private double pixelSizeZ

pinholeSize

private java.lang.Double pinholeSize

voltage

private java.lang.Double voltage

mag

private java.lang.Double mag

na

private java.lang.Double na

objectiveModel

private java.lang.String objectiveModel

immersion

private java.lang.String immersion

correction

private java.lang.String correction

refractiveIndex

private java.lang.Double refractiveIndex

channelNames

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

modality

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

binning

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

speed

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

gain

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

temperature

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

exposureTime

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

exWave

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

emWave

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

power

private java.util.ArrayList<java.lang.Integer> power

rois

private java.util.ArrayList<java.util.Hashtable<java.lang.String,java.lang.String>> rois

posX

private java.util.ArrayList<ome.units.quantity.Length> posX

posY

private java.util.ArrayList<ome.units.quantity.Length> posY

posZ

private java.util.ArrayList<ome.units.quantity.Length> posZ

posNames

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

cameraModel

private java.lang.String cameraModel

date

private java.lang.String date

colors

private java.util.Hashtable<java.lang.String,java.lang.Integer> colors

dyes

private java.util.Hashtable<java.lang.String,java.lang.String> dyes

realColors

private java.util.Hashtable<java.lang.String,java.lang.Integer> realColors

nXFields

private int nXFields

nYFields

private int nYFields

populateXY

private boolean populateXY

nImages

private int nImages

validLoopState

private java.util.ArrayList<java.lang.Boolean> validLoopState

canAdjustDimensions

private boolean canAdjustDimensions

firstTimeLoop

private boolean firstTimeLoop

Constructor Detail

ND2Handler

public ND2Handler(CoreMetadataList core,
                  int nImages)

ND2Handler

public ND2Handler(CoreMetadataList core,
                  boolean populateXY,
                  int nImages)

Method Detail

getXFields

public int getXFields()

getCoreMetadataList

public CoreMetadataList getCoreMetadataList()

populateROIs

public void populateROIs(MetadataStore store)

getDate

public java.lang.String getDate()

getMetadata

public java.util.Hashtable<java.lang.String,java.lang.Object> getMetadata()

getSeriesCount

public int getSeriesCount()

isLossless

public boolean isLossless()

getZSections

public java.util.ArrayList<java.lang.Long> getZSections()

getTimepoints

public java.util.ArrayList<java.lang.Long> getTimepoints()

getPixelSizeX

public double getPixelSizeX()

getPixelSizeY

public double getPixelSizeY()

getPixelSizeZ

public double getPixelSizeZ()

getPinholeSize

public java.lang.Double getPinholeSize()

getVoltage

public java.lang.Double getVoltage()

getMagnification

public java.lang.Double getMagnification()

getNumericalAperture

public java.lang.Double getNumericalAperture()

getObjectiveModel

public java.lang.String getObjectiveModel()

getImmersion

public java.lang.String getImmersion()

getCorrection

public java.lang.String getCorrection()

getRefractiveIndex

public java.lang.Double getRefractiveIndex()

getChannelNames

public java.util.ArrayList<java.lang.String> getChannelNames()

getModalities

public java.util.ArrayList<java.lang.String> getModalities()

getBinnings

public java.util.ArrayList<java.lang.String> getBinnings()

getSpeeds

public java.util.ArrayList<java.lang.Double> getSpeeds()

getGains

public java.util.ArrayList<java.lang.Double> getGains()

getTemperatures

public java.util.ArrayList<java.lang.Double> getTemperatures()

getExposureTimes

public java.util.ArrayList<java.lang.Double> getExposureTimes()

getExcitationWavelengths

public java.util.ArrayList<java.lang.Double> getExcitationWavelengths()

getEmissionWavelengths

public java.util.ArrayList<java.lang.Double> getEmissionWavelengths()

getPowers

public java.util.ArrayList<java.lang.Integer> getPowers()

getROIs

public java.util.ArrayList<java.util.Hashtable<java.lang.String,java.lang.String>> getROIs()

getXPositions

public java.util.ArrayList<ome.units.quantity.Length> getXPositions()

getYPositions

public java.util.ArrayList<ome.units.quantity.Length> getYPositions()

getZPositions

public java.util.ArrayList<ome.units.quantity.Length> getZPositions()

getPositionNames

public java.util.ArrayList<java.lang.String> getPositionNames()

getCameraModel

public java.lang.String getCameraModel()

getFieldIndex

public int getFieldIndex()

getChannelColors

public java.util.Hashtable<java.lang.String,java.lang.Integer> getChannelColors()

endElement

public void endElement(java.lang.String uri,
                       java.lang.String localName,
                       java.lang.String qName,
                       org.xml.sax.Attributes attributes)

startElement

public void startElement(java.lang.String uri,
                         java.lang.String localName,
                         java.lang.String qName,
                         org.xml.sax.Attributes attributes)

Specified by:

startElement in interface org.xml.sax.ContentHandler

Overrides:

startElement in class org.xml.sax.helpers.DefaultHandler

endDocument

public void endDocument()

Specified by:

endDocument in interface org.xml.sax.ContentHandler

Overrides:

endDocument in class org.xml.sax.helpers.DefaultHandler

parseKeyAndValue

public void parseKeyAndValue(java.lang.String key,
                             java.lang.String value,
                             java.lang.String runtype)

isDimensions

public boolean isDimensions(java.lang.String key)

Returns whether or not the specified key is denotes dimensions. Full versions of Elements allow the user to choose a language, though it's not clear what all of the choices are. Most keys are always recorded in English, but some are recorded in the language specified by the user.

parsePixelsSizeZFromKey

private java.lang.Double parsePixelsSizeZFromKey(java.lang.String key)

Parses the physical size from a key. The expected format for the key is "- Step ".