loci.formats.in

Class LeicaHandler

java.lang.Object

org.xml.sax.helpers.DefaultHandler

loci.common.xml.BaseHandler

loci.formats.in.LeicaHandler

All Implemented Interfaces:

org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.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 java.util.Map<java.lang.Integer,java.lang.String>	bytesPerAxis
private boolean	canParse
private java.util.Map<java.lang.String,LeicaHandler.Channel>	channels
private java.lang.String	collection
private java.util.List<CoreMetadata>	core
private int	count
private int	detectorChannel
private java.util.List<java.lang.Integer>	detectorIndices
private java.util.List<LeicaHandler.Detector>	detectors
private java.lang.String	elementName
private int	extras
private long	firstStamp
private java.util.Hashtable	globalMetadata
private int	laserCount
private java.util.List<LeicaHandler.Laser>	lasers
private MetadataLevel	level
private boolean	linkedInstruments
private static org.slf4j.Logger	LOGGER Logger for this class.
private java.util.Vector<java.lang.String>	lutNames
private java.util.List<LeicaHandler.MultiBand>	multiBands
private java.util.Deque<java.lang.String>	nameStack
private int	nextChannel
private int	nextFilter
private int	nextROI
private int	numChannels
private int	numDatasets
private double	physicalSizeX
private double	physicalSizeY
private java.lang.Double	pinhole
private LeicaHandler.ROI	roi
private MetadataStore	store
private java.util.List<ome.units.quantity.Length>	xPos
private java.util.List<ome.units.quantity.Length>	yPos
private java.lang.Double	zoom
private java.util.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(java.lang.String uri, java.lang.String localName, java.lang.String qName)
java.util.List<CoreMetadata>	getCoreMetadataList()
java.util.Hashtable	getGlobalMetadata()
java.util.Vector<java.lang.String>	getLutNames()
private java.util.Hashtable	getSeriesHashtable(int series)
private double	parseDouble(java.lang.String number)
void	startElement(java.lang.String uri, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attributes)
private void	storeKeyValue(java.util.Hashtable h, java.lang.String key, java.lang.String value)
private void	storeSeriesHashtable(int series, java.util.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 java.util.Deque<java.lang.String> nameStack

elementName

private java.lang.String elementName

collection

private java.lang.String collection

count

private int count

numChannels

private int numChannels

extras

private int extras

lutNames

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

xPos

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

yPos

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

zPos

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

physicalSizeX

private double physicalSizeX

physicalSizeY

private double physicalSizeY

numDatasets

private int numDatasets

globalMetadata

private java.util.Hashtable globalMetadata

store

private MetadataStore store

nextChannel

private int nextChannel

zoom

private java.lang.Double zoom

pinhole

private java.lang.Double pinhole

detectorIndices

private java.util.List<java.lang.Integer> detectorIndices

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 java.util.List<CoreMetadata> core

canParse

private boolean canParse

firstStamp

private long firstStamp

bytesPerAxis

private java.util.Map<java.lang.Integer,java.lang.String> bytesPerAxis

multiBands

private java.util.List<LeicaHandler.MultiBand> multiBands

detectors

private java.util.List<LeicaHandler.Detector> detectors

lasers

private java.util.List<LeicaHandler.Laser> lasers

channels

private java.util.Map<java.lang.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 java.util.List<CoreMetadata> getCoreMetadataList()

getGlobalMetadata

public java.util.Hashtable getGlobalMetadata()

getLutNames

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

endElement

public void endElement(java.lang.String uri,
                       java.lang.String localName,
                       java.lang.String qName)

Specified by:

endElement in interface org.xml.sax.ContentHandler

Overrides:

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

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

getSeriesHashtable

private java.util.Hashtable getSeriesHashtable(int series)

storeSeriesHashtable

private void storeSeriesHashtable(int series,
                                  java.util.Hashtable h)

parseDouble

private double parseDouble(java.lang.String number)

storeKeyValue

private void storeKeyValue(java.util.Hashtable h,
                           java.lang.String key,
                           java.lang.String value)