LeicaHandler (Bio-Formats API)

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 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<Length>`	`xPos`
`private List<Length>`	`yPos`
`private Double`	`zoom`
`private List<Length>`	`zPos`

Constructor Summary

Constructors
Constructor and Description

LeicaHandler(MetadataStore store, MetadataLevel level)

Constructors
Constructor and Description
`LeicaHandler(MetadataStore store, MetadataLevel level)`

Method Summary

Methods
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<Length> xPos
```

yPos
```
private List<Length> yPos
```

zPos
```
private List<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)

Class LeicaHandler

Nested Class Summary

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

LOGGER

nameStack

elementName

collection

count

numChannels

extras

lutNames

xPos

yPos

zPos

physicalSizeX

physicalSizeY

numDatasets

globalMetadata

store

nextChannel

zoom

pinhole

detectorIndices

filterWheelName

nextFilter

nextROI

roi

alternateCenter

linkedInstruments

detectorChannel

core

canParse

firstStamp

bytesPerAxis

multiBands

detectors

lasers

channels

level

laserCount

Constructor Detail

LeicaHandler

Method Detail

getCoreMetadataList

getGlobalMetadata

getLutNames

endElement

startElement

getSeriesHashtable

storeSeriesHashtable

parseDouble

storeKeyValue