Package loci.formats.in

Class MetamorphHandler

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	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 static final org.slf4j.Logger	LOGGER
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	Description
MetamorphHandler()
MetamorphHandler(Hashtable metadata)

Method Summary

Modifier and Type	Method	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()
private Double	parseDouble(String v)	Remove '+' before parsing doubles.
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

Methods inherited from interface org.xml.sax.ContentHandler

declaration

Field Details

LOGGER

private static final org.slf4j.Logger LOGGER

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 Details

MetamorphHandler

public MetamorphHandler()

MetamorphHandler

public MetamorphHandler(Hashtable metadata)

Method Details

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.

parseDouble

private Double parseDouble(String v)

Remove '+' before parsing doubles. Scientific notation values may be stored as -1e+006 or similar.