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 BaseHandler

DefaultHandler implementation for handling XML produced by Nikon Elements.

Source code:

Trac, Gitweb

Constructor Summary

Constructors

Constructor and Description
ND2Handler(List<CoreMetadata> core, boolean populateXY, int nImages)
ND2Handler(List<CoreMetadata> core, int nImages)

Method Summary

Methods

Modifier and Type	Method and 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()
List<CoreMetadata>	getCoreMetadataList()
String	getCorrection()
String	getDate()
ArrayList<Integer>	getEmissionWavelengths()
ArrayList<Integer>	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<Double>	getXPositions()
ArrayList<Double>	getYPositions()
ArrayList<Double>	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)
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

Constructor Detail

ND2Handler

public ND2Handler(List<CoreMetadata> core,
          int nImages)

ND2Handler

public ND2Handler(List<CoreMetadata> core,
          boolean populateXY,
          int nImages)

Method Detail

getXFields

public int getXFields()

getCoreMetadataList

public List<CoreMetadata> 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<Integer> getExcitationWavelengths()

getEmissionWavelengths

public ArrayList<Integer> getEmissionWavelengths()

getPowers

public ArrayList<Integer> getPowers()

getROIs

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

getXPositions

public ArrayList<Double> getXPositions()

getYPositions

public ArrayList<Double> getYPositions()

getZPositions

public ArrayList<Double> 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.