ND2Handler (Bio-Formats API)

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 and Description
`private ArrayList<String>`	`binning`
`private String`	`cameraModel`
`private boolean`	`canAdjustDimensions`
`private ArrayList<String>`	`channelNames`
`private Hashtable<String,Integer>`	`colors`
`private List<CoreMetadata>`	`core`
`private String`	`correction`
`private String`	`date`
`private static String`	`DATE_FORMAT`
`private Hashtable<String,String>`	`dyes`
`private ArrayList<Double>`	`emWave`
`private ArrayList<Double>`	`exposureTime`
`private ArrayList<Double>`	`exWave`
`private static int`	`FIELD_INDEX`
`private boolean`	`firstTimeLoop`
`private ArrayList<Double>`	`gain`
`private String`	`immersion`
`private boolean`	`isLossless`
`private static 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 and Description
`ND2Handler(List<CoreMetadata> core, boolean populateXY, int nImages)`
`ND2Handler(List<CoreMetadata> core, int nImages)`

Method Summary

All Methods Instance Methods Concrete 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<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

Field Detail

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 List<CoreMetadata> 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
```

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<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 ".

Class ND2Handler

Field Summary

Constructor Summary

Method Summary

Methods inherited from class loci.common.xml.BaseHandler

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

Methods inherited from class java.lang.Object

Field Detail

LOGGER

DATE_FORMAT

FIELD_INDEX

prefix

prevRuntype

prevElement

metadata

core

isLossless

zs

ts

numSeries

pixelSizeX

pixelSizeY

pixelSizeZ

pinholeSize

voltage

mag

na

objectiveModel

immersion

correction

refractiveIndex

channelNames

modality

binning

speed

gain

temperature

exposureTime

exWave

emWave

power

rois

posX

posY

posZ

posNames

cameraModel

date

colors

dyes

realColors

nXFields

nYFields

populateXY

nImages

validLoopState

canAdjustDimensions

firstTimeLoop

Constructor Detail

ND2Handler

ND2Handler

Method Detail

getXFields

getCoreMetadataList

populateROIs

getDate

getMetadata

getSeriesCount

isLossless

getZSections

getTimepoints

getPixelSizeX

getPixelSizeY

getPixelSizeZ

getPinholeSize

getVoltage

getMagnification

getNumericalAperture

getObjectiveModel

getImmersion