loci.formats.in

Class LeicaHandler

java.lang.Object

org.xml.sax.helpers.DefaultHandler

loci.common.xml.BaseHandler

loci.formats.in.LeicaHandler

All Implemented Interfaces:

ContentHandler, DTDHandler, EntityResolver, ErrorHandler

public class LeicaHandler
extends loci.common.xml.BaseHandler

SAX handler for parsing XML in Leica LIF and Leica TCS files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	LeicaHandler.Channel
(package private) class	LeicaHandler.Detector
(package private) class	LeicaHandler.Laser
(package private) class	LeicaHandler.MultiBand
(package private) class	LeicaHandler.ROI

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	alternateCenter
private Map<Integer,String>	bytesPerAxis
private boolean	canParse
private Map<String,LeicaHandler.Channel>	channels
private String	collection
private List<CoreMetadata>	core
private int	count
private int	detectorChannel
private List<Integer>	detectorIndices
private List<LeicaHandler.Detector>	detectors
private String	elementName
private int	extras
private String	filterWheelName
private long	firstStamp
private Hashtable	globalMetadata
private int	laserCount
private List<LeicaHandler.Laser>	lasers
private MetadataLevel	level
private boolean	linkedInstruments
private static org.slf4j.Logger	LOGGER Logger for this class.
private Vector<String>	lutNames
private List<LeicaHandler.MultiBand>	multiBands
private Deque<String>	nameStack
private int	nextChannel
private int	nextFilter
private int	nextROI
private int	numChannels
private int	numDatasets
private double	physicalSizeX
private double	physicalSizeY
private Double	pinhole
private LeicaHandler.ROI	roi
private MetadataStore	store
private List<ome.units.quantity.Length>	xPos
private List<ome.units.quantity.Length>	yPos
private Double	zoom
private List<ome.units.quantity.Length>	zPos

Constructor Summary

Constructors

Constructor and Description
LeicaHandler(MetadataStore store, MetadataLevel level)

Method Summary

Modifier and Type	Method and Description
void	endElement(String uri, String localName, String qName)
List<CoreMetadata>	getCoreMetadataList()
Hashtable	getGlobalMetadata()
Vector<String>	getLutNames()
private Hashtable	getSeriesHashtable(int series)
private double	parseDouble(String number)
void	startElement(String uri, String localName, String qName, Attributes attributes)
private void	storeKeyValue(Hashtable h, String key, String value)
private void	storeSeriesHashtable(int series, Hashtable h)

Methods inherited from class loci.common.xml.BaseHandler

resolveEntity

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

characters, endDocument, 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

Logger for this class.

nameStack

private Deque<String> nameStack

elementName

private String elementName

collection

private String collection

count

private int count

numChannels

private int numChannels

extras

private int extras

lutNames

private Vector<String> lutNames

xPos

private List<ome.units.quantity.Length> xPos

yPos

private List<ome.units.quantity.Length> yPos

zPos

private List<ome.units.quantity.Length> zPos

physicalSizeX

private double physicalSizeX

physicalSizeY

private double physicalSizeY

numDatasets

private int numDatasets

globalMetadata

private Hashtable globalMetadata

store

private MetadataStore store

nextChannel

private int nextChannel

zoom

private Double zoom

pinhole

private Double pinhole

detectorIndices

private List<Integer> detectorIndices

filterWheelName

private String filterWheelName

nextFilter

private int nextFilter

nextROI

private int nextROI

roi

private LeicaHandler.ROI roi

alternateCenter

private boolean alternateCenter

linkedInstruments

private boolean linkedInstruments

detectorChannel

private int detectorChannel

core

private List<CoreMetadata> core

canParse

private boolean canParse

firstStamp

private long firstStamp

bytesPerAxis

private Map<Integer,String> bytesPerAxis

multiBands

private List<LeicaHandler.MultiBand> multiBands

detectors

private List<LeicaHandler.Detector> detectors

lasers

private List<LeicaHandler.Laser> lasers

channels

private Map<String,LeicaHandler.Channel> channels

level

private MetadataLevel level

laserCount

private int laserCount

Constructor Detail

LeicaHandler

public LeicaHandler(MetadataStore store,
                    MetadataLevel level)

Method Detail

getCoreMetadataList

public List<CoreMetadata> getCoreMetadataList()

getGlobalMetadata

public Hashtable getGlobalMetadata()

getLutNames

public Vector<String> getLutNames()

endElement

public void endElement(String uri,
                       String localName,
                       String qName)

Specified by:

endElement in interface ContentHandler

Overrides:

endElement in class DefaultHandler

startElement

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

Specified by:

startElement in interface ContentHandler

Overrides:

startElement in class DefaultHandler

getSeriesHashtable

private Hashtable getSeriesHashtable(int series)

storeSeriesHashtable

private void storeSeriesHashtable(int series,
                                  Hashtable h)

parseDouble

private double parseDouble(String number)

storeKeyValue

private void storeKeyValue(Hashtable h,
                           String key,
                           String value)