MetamorphHandler (Bio-Formats API)

java.lang.Object
- org.xml.sax.helpers.DefaultHandler
- - loci.common.xml.BaseHandler
  - - loci.formats.in.MetamorphHandler

All Implemented Interfaces:

ContentHandler, DTDHandler, EntityResolver, ErrorHandler
```
public class MetamorphHandler
extends loci.common.xml.BaseHandler
```
MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.

Author:

Melissa Linkert melissa at glencoesoftware.com, Thomas Caswell tcaswell at uchicago.edu

Field Summary

Fields
Modifier and Type	Field and Description
`private String`	`binning`
`private String`	`channelName`
`private Vector<String>`	`channelNames`
`private String`	`date`
`private boolean`	`dualCamera`
`private Vector<Double>`	`exposures`
`private Double`	`gain`
`private String`	`imageName`
`private double`	`lensNA`
`private double`	`lensRI`
`private Hashtable`	`metadata`
`private double`	`pixelSizeX`
`private double`	`pixelSizeY`
`private ome.units.quantity.Length`	`positionX`
`private ome.units.quantity.Length`	`positionY`
`private double`	`readOutRate`
`private String`	`stageLabel`
`private double`	`temperature`
`private Vector<String>`	`timestamps`
`private Vector<Integer>`	`wavelengths`
`private double`	`zoom`
`private Vector<Double>`	`zPositions`

Constructor Summary

Constructors
Constructor and Description

MetamorphHandler()

MetamorphHandler(Hashtable metadata)

Constructors
Constructor and Description
`MetamorphHandler()`
`MetamorphHandler(Hashtable metadata)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private void`	`checkKey(String key, String value)` Check if the value needs to be saved.
`String`	`getBinning()`
`String`	`getChannelName()`
`Vector<String>`	`getChannelNames()`
`String`	`getDate()`
`Vector<Double>`	`getExposures()`
`Double`	`getGain()`
`String`	`getImageName()`
`double`	`getLensNA()`
`double`	`getLensRI()`
`double`	`getPixelSizeX()`
`double`	`getPixelSizeY()`
`double`	`getReadOutRate()`
`String`	`getStageLabel()`
`ome.units.quantity.Length`	`getStagePositionX()`
`ome.units.quantity.Length`	`getStagePositionY()`
`double`	`getTemperature()`
`Vector<String>`	`getTimestamps()`
`Vector<Integer>`	`getWavelengths()`
`double`	`getZoom()`
`Vector<Double>`	`getZPositions()`
`boolean`	`hasDualCamera()`
`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, endDocument, 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

metadata
```
private Hashtable metadata
```

timestamps
```
private Vector<String> timestamps
```

imageName
```
private String imageName
```

date
```
private String date
```

wavelengths
```
private Vector<Integer> wavelengths
```

zPositions
```
private Vector<Double> zPositions
```

pixelSizeX
```
private double pixelSizeX
```

pixelSizeY
```
private double pixelSizeY
```

temperature
```
private double temperature
```

lensNA
```
private double lensNA
```

lensRI
```
private double lensRI
```

binning
```
private String binning
```

readOutRate
```
private double readOutRate
```

zoom
```
private double zoom
```

positionX

private ome.units.quantity.Length positionX

positionY

private ome.units.quantity.Length positionY

exposures
```
private Vector<Double> exposures
```

channelName
```
private String channelName
```

channelNames
```
private Vector<String> channelNames
```

stageLabel
```
private String stageLabel
```

gain
```
private Double gain
```

dualCamera
```
private boolean dualCamera
```

Constructor Detail

MetamorphHandler
```
public MetamorphHandler()
```

MetamorphHandler

public MetamorphHandler(Hashtable metadata)

Method Detail

getGain
```
public Double getGain()
```

getChannelName
```
public String getChannelName()
```

getChannelNames

public Vector<String> getChannelNames()

getStageLabel
```
public String getStageLabel()
```

getTimestamps
```
public Vector<String> getTimestamps()
```

getWavelengths

public Vector<Integer> getWavelengths()

getZPositions
```
public Vector<Double> getZPositions()
```

getDate
```
public String getDate()
```

getImageName
```
public String getImageName()
```

getPixelSizeX
```
public double getPixelSizeX()
```

getPixelSizeY
```
public double getPixelSizeY()
```

getTemperature
```
public double getTemperature()
```

getBinning
```
public String getBinning()
```

getReadOutRate
```
public double getReadOutRate()
```

getZoom
```
public double getZoom()
```

getStagePositionX

public ome.units.quantity.Length getStagePositionX()

getStagePositionY

public ome.units.quantity.Length getStagePositionY()

getLensNA
```
public double getLensNA()
```

getLensRI
```
public double getLensRI()
```

getExposures
```
public Vector<Double> getExposures()
```

hasDualCamera
```
public boolean hasDualCamera()
```

startElement

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

Specified by:: startElement in interface ContentHandler
Overrides:: startElement in class DefaultHandler

checkKey

private void checkKey(String key,
                      String value)

Check if the value needs to be saved.

Class MetamorphHandler

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

metadata

timestamps

imageName

date

wavelengths

zPositions

pixelSizeX

pixelSizeY

temperature

lensNA

lensRI

binning

readOutRate

zoom

positionX

positionY

exposures

channelName

channelNames

stageLabel

gain

dualCamera

Constructor Detail

MetamorphHandler

MetamorphHandler

Method Detail

getGain

getChannelName

getChannelNames

getStageLabel

getTimestamps

getWavelengths

getZPositions

getDate

getImageName

getPixelSizeX

getPixelSizeY

getTemperature

getBinning

getReadOutRate

getZoom

getStagePositionX

getStagePositionY

getLensNA

getLensRI

getExposures

hasDualCamera

startElement

checkKey