loci.formats.in

Class MetamorphHandler

java.lang.Object

org.xml.sax.helpers.DefaultHandler

loci.common.xml.BaseHandler

loci.formats.in.MetamorphHandler

All Implemented Interfaces:

org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.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 java.lang.String	binning
private java.lang.String	channelName
private java.util.Vector<java.lang.String>	channelNames
private java.lang.String	date
private boolean	dualCamera
private java.util.Vector<java.lang.Double>	exposures
private java.lang.Double	gain
private java.lang.String	imageName
private double	lensNA
private double	lensRI
private java.util.Hashtable	metadata
private double	pixelSizeX
private double	pixelSizeY
private ome.units.quantity.Length	positionX
private ome.units.quantity.Length	positionY
private double	readOutRate
private java.lang.String	stageLabel
private double	temperature
private java.util.Vector<java.lang.String>	timestamps
private java.util.Vector<java.lang.Integer>	wavelengths
private double	zoom
private java.util.Vector<java.lang.Double>	zPositions

Constructor Summary

Constructors

Constructor and Description
MetamorphHandler()
MetamorphHandler(java.util.Hashtable metadata)

Method Summary

Modifier and Type	Method and Description
private void	checkKey(java.lang.String key, java.lang.String value) Check if the value needs to be saved.
java.lang.String	getBinning()
java.lang.String	getChannelName()
java.util.Vector<java.lang.String>	getChannelNames()
java.lang.String	getDate()
java.util.Vector<java.lang.Double>	getExposures()
java.lang.Double	getGain()
java.lang.String	getImageName()
double	getLensNA()
double	getLensRI()
double	getPixelSizeX()
double	getPixelSizeY()
double	getReadOutRate()
java.lang.String	getStageLabel()
ome.units.quantity.Length	getStagePositionX()
ome.units.quantity.Length	getStagePositionY()
double	getTemperature()
java.util.Vector<java.lang.String>	getTimestamps()
java.util.Vector<java.lang.Integer>	getWavelengths()
double	getZoom()
java.util.Vector<java.lang.Double>	getZPositions()
boolean	hasDualCamera()
private java.lang.Double	parseDouble(java.lang.String v) Remove '+' before parsing doubles.
void	startElement(java.lang.String uri, java.lang.String localName, java.lang.String qName, org.xml.sax.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 java.util.Hashtable metadata

timestamps

private java.util.Vector<java.lang.String> timestamps

imageName

private java.lang.String imageName

date

private java.lang.String date

wavelengths

private java.util.Vector<java.lang.Integer> wavelengths

zPositions

private java.util.Vector<java.lang.Double> zPositions

pixelSizeX

private double pixelSizeX

pixelSizeY

private double pixelSizeY

temperature

private double temperature

lensNA

private double lensNA

lensRI

private double lensRI

binning

private java.lang.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 java.util.Vector<java.lang.Double> exposures

channelName

private java.lang.String channelName

channelNames

private java.util.Vector<java.lang.String> channelNames

stageLabel

private java.lang.String stageLabel

gain

private java.lang.Double gain

dualCamera

private boolean dualCamera

Constructor Detail

MetamorphHandler

public MetamorphHandler()

MetamorphHandler

public MetamorphHandler(java.util.Hashtable metadata)

Method Detail

getGain

public java.lang.Double getGain()

getChannelName

public java.lang.String getChannelName()

getChannelNames

public java.util.Vector<java.lang.String> getChannelNames()

getStageLabel

public java.lang.String getStageLabel()

getTimestamps

public java.util.Vector<java.lang.String> getTimestamps()

getWavelengths

public java.util.Vector<java.lang.Integer> getWavelengths()

getZPositions

public java.util.Vector<java.lang.Double> getZPositions()

getDate

public java.lang.String getDate()

getImageName

public java.lang.String getImageName()

getPixelSizeX

public double getPixelSizeX()

getPixelSizeY

public double getPixelSizeY()

getTemperature

public double getTemperature()

getBinning

public java.lang.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 java.util.Vector<java.lang.Double> getExposures()

hasDualCamera

public boolean hasDualCamera()

startElement

public void startElement(java.lang.String uri,
                         java.lang.String localName,
                         java.lang.String qName,
                         org.xml.sax.Attributes attributes)

Specified by:

startElement in interface org.xml.sax.ContentHandler

Overrides:

startElement in class org.xml.sax.helpers.DefaultHandler

checkKey

private void checkKey(java.lang.String key,
                      java.lang.String value)

Check if the value needs to be saved.

parseDouble

private java.lang.Double parseDouble(java.lang.String v)

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