Package loci.formats.in

Class ND2Handler

java.lang.Object

org.xml.sax.helpers.DefaultHandler

loci.common.xml.BaseHandler

loci.formats.in.ND2Handler

All Implemented Interfaces:

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

Constructor Summary

Constructors

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

Method Summary

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

Methods inherited from interface org.xml.sax.ContentHandler

declaration

Field Details

LOGGER

private static final org.slf4j.Logger LOGGER

DATE_FORMAT

private static final String DATE_FORMAT

See Also:

• Constant Field Values

FIELD_INDEX

private static final int FIELD_INDEX

See Also:

• Constant Field Values

prefix

private String prefix

prevRuntype

private String prevRuntype

prevElement

private String prevElement

metadata

private Hashtable<String,Object> metadata

core

private CoreMetadataList core

isLossless

private boolean isLossless

zs

private ArrayList<Long> zs

ts

private ArrayList<Long> ts

numSeries

private int numSeries

pixelSizeX

private double pixelSizeX

pixelSizeY

private double pixelSizeY

pixelSizeZ

private double pixelSizeZ

pinholeSize

private Double pinholeSize

voltage

private Double voltage

mag

private Double mag

na

private Double na

objectiveModel

private String objectiveModel

immersion

private String immersion

correction

private String correction

refractiveIndex

private Double refractiveIndex

channelNames

private ArrayList<String> channelNames

modality

private ArrayList<String> modality

binning

private ArrayList<String> binning

speed

private ArrayList<Double> speed

gain

private ArrayList<Double> gain

temperature

private ArrayList<Double> temperature

exposureTime

private ArrayList<Double> exposureTime

exWave

private ArrayList<Double> exWave

emWave

private ArrayList<Double> emWave

power

private ArrayList<Integer> power

rois

private ArrayList<Hashtable<String,String>> rois

posX

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

posY

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

posZ

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

posNames

private ArrayList<String> posNames

cameraModel

private String cameraModel

date

private String date

colors

private Hashtable<String,Integer> colors

dyes

private Hashtable<String,String> dyes

realColors

private Hashtable<String,Integer> realColors

nXFields

private int nXFields

nYFields

private int nYFields

populateXY

private boolean populateXY

nImages

private int nImages

validLoopState

private ArrayList<Boolean> validLoopState

canAdjustDimensions

private boolean canAdjustDimensions

firstTimeLoop

private boolean firstTimeLoop

imageMetadataLVExists

public boolean imageMetadataLVExists

Constructor Details

ND2Handler

public ND2Handler(CoreMetadataList core,
 int nImages)

ND2Handler

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

Method Details

getXFields

public int getXFields()

getCoreMetadataList

public CoreMetadataList getCoreMetadataList()

populateROIs

public void populateROIs(MetadataStore store)

getDate

public String getDate()

getMetadata

public Hashtable<String,Object> getMetadata()

getSeriesCount

public int getSeriesCount()

isLossless

public boolean isLossless()

getZSections

public ArrayList<Long> getZSections()

getTimepoints

public ArrayList<Long> getTimepoints()

getPixelSizeX

public double getPixelSizeX()

getPixelSizeY

public double getPixelSizeY()

getPixelSizeZ

public double getPixelSizeZ()

getPinholeSize

public Double getPinholeSize()

getVoltage

public Double getVoltage()

getMagnification

public Double getMagnification()

getNumericalAperture

public Double getNumericalAperture()

getObjectiveModel

public String getObjectiveModel()

getImmersion

public String getImmersion()

getCorrection

public String getCorrection()

getRefractiveIndex

public Double getRefractiveIndex()

getChannelNames

public ArrayList<String> getChannelNames()

getModalities

public ArrayList<String> getModalities()

getBinnings

public ArrayList<String> getBinnings()

getSpeeds

public ArrayList<Double> getSpeeds()

getGains

public ArrayList<Double> getGains()

getTemperatures

public ArrayList<Double> getTemperatures()

getExposureTimes

public ArrayList<Double> getExposureTimes()

getExcitationWavelengths

public ArrayList<Double> getExcitationWavelengths()

getEmissionWavelengths

public ArrayList<Double> getEmissionWavelengths()

getPowers

public ArrayList<Integer> getPowers()

getROIs

public ArrayList<Hashtable<String,String>> getROIs()

getXPositions

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

getYPositions

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

getZPositions

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

getPositionNames

public ArrayList<String> getPositionNames()

getCameraModel

public String getCameraModel()

getFieldIndex

public int getFieldIndex()

getChannelColors

public Hashtable<String,Integer> getChannelColors()

endElement

public void endElement(String uri,
 String localName,
 String qName,
 Attributes attributes)

startElement

public void startElement(String uri,
 String localName,
 String qName,
 Attributes attributes)

Specified by:

startElement in interface ContentHandler

Overrides:

startElement in class DefaultHandler

endDocument

public void endDocument()

Specified by:

endDocument in interface ContentHandler

Overrides:

endDocument in class DefaultHandler

parseKeyAndValue

public void parseKeyAndValue(String key,
 String value,
 String runtype)

isDimensions

public boolean isDimensions(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 Double parsePixelsSizeZFromKey(String key)

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