Pixels (Bio-Formats API)

java.lang.Object
- ome.xml.model.AbstractOMEModelObject
- - ome.xml.model.Pixels

All Implemented Interfaces:: OMEModelObject

public class Pixels
extends AbstractOMEModelObject

Field Summary

Fields
Modifier and Type	Field and Description
`private Boolean`	`bigEndian`
`private List<BinData>`	`binDataBlocks`
`private List<Channel>`	`channels`
`private DimensionOrder`	`dimensionOrder`
`private String`	`id`
`private Boolean`	`interleaved`
`private static org.slf4j.Logger`	`LOGGER` Logger for this class.
`private MetadataOnly`	`metadataOnly`
`static String`	`NAMESPACE`
`private Length`	`physicalSizeX`
`private Length`	`physicalSizeY`
`private Length`	`physicalSizeZ`
`private List<Plane>`	`planes`
`private PositiveInteger`	`significantBits`
`private PositiveInteger`	`sizeC`
`private PositiveInteger`	`sizeT`
`private PositiveInteger`	`sizeX`
`private PositiveInteger`	`sizeY`
`private PositiveInteger`	`sizeZ`
`private List<TiffData>`	`tiffDataBlocks`
`private Time`	`timeIncrement`
`private PixelType`	`type`

Constructor Summary

Constructors
Constructor and Description
`Pixels()` Default constructor.
`Pixels(Element element, OMEModel model)` Constructs Pixels recursively from an XML DOM tree.
`Pixels(Pixels orig)` Copy constructor.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addBinData(BinData binData)`
`void`	`addChannel(Channel channel)`
`void`	`addPlane(Plane plane)`
`void`	`addTiffData(TiffData tiffData)`
`Element`	`asXMLElement(Document document)` Takes the entire object hierarchy and produces an XML DOM tree.
`protected Element`	`asXMLElement(Document document, Element Pixels_element)` Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
`List<BinData>`	`copyBinDataList()`
`List<Channel>`	`copyChannelList()`
`List<Plane>`	`copyPlaneList()`
`List<TiffData>`	`copyTiffDataList()`
`Boolean`	`getBigEndian()`
`BinData`	`getBinData(int index)`
`Channel`	`getChannel(int index)`
`DimensionOrder`	`getDimensionOrder()`
`String`	`getID()`
`Boolean`	`getInterleaved()`
`MetadataOnly`	`getMetadataOnly()`
`Length`	`getPhysicalSizeX()`
`static String`	`getPhysicalSizeXUnitXsdDefault()`
`Length`	`getPhysicalSizeY()`
`static String`	`getPhysicalSizeYUnitXsdDefault()`
`Length`	`getPhysicalSizeZ()`
`static String`	`getPhysicalSizeZUnitXsdDefault()`
`Plane`	`getPlane(int index)`
`PositiveInteger`	`getSignificantBits()`
`PositiveInteger`	`getSizeC()`
`PositiveInteger`	`getSizeT()`
`PositiveInteger`	`getSizeX()`
`PositiveInteger`	`getSizeY()`
`PositiveInteger`	`getSizeZ()`
`TiffData`	`getTiffData(int index)`
`Time`	`getTimeIncrement()`
`static String`	`getTimeIncrementUnitXsdDefault()`
`PixelType`	`getType()`
`boolean`	`link(Reference reference, OMEModelObject o)` Link a given OME model object to this model object.
`void`	`removeBinData(BinData binData)`
`void`	`removeChannel(Channel channel)`
`void`	`removePlane(Plane plane)`
`void`	`removeTiffData(TiffData tiffData)`
`void`	`setBigEndian(Boolean bigEndian)`
`BinData`	`setBinData(int index, BinData binData)`
`Channel`	`setChannel(int index, Channel channel)`
`void`	`setDimensionOrder(DimensionOrder dimensionOrder)`
`void`	`setID(String id)`
`void`	`setInterleaved(Boolean interleaved)`
`void`	`setMetadataOnly(MetadataOnly metadataOnly)`
`void`	`setPhysicalSizeX(Length physicalSizeX)`
`void`	`setPhysicalSizeY(Length physicalSizeY)`
`void`	`setPhysicalSizeZ(Length physicalSizeZ)`
`Plane`	`setPlane(int index, Plane plane)`
`void`	`setSignificantBits(PositiveInteger significantBits)`
`void`	`setSizeC(PositiveInteger sizeC)`
`void`	`setSizeT(PositiveInteger sizeT)`
`void`	`setSizeX(PositiveInteger sizeX)`
`void`	`setSizeY(PositiveInteger sizeY)`
`void`	`setSizeZ(PositiveInteger sizeZ)`
`TiffData`	`setTiffData(int index, TiffData tiffData)`
`void`	`setTimeIncrement(Time timeIncrement)`
`void`	`setType(PixelType type)`
`int`	`sizeOfBinDataList()`
`int`	`sizeOfChannelList()`
`int`	`sizeOfPlaneList()`
`int`	`sizeOfTiffDataList()`
`void`	`update(Element element, OMEModel model)` Updates Pixels recursively from an XML DOM tree.

Methods inherited from class ome.xml.model.AbstractOMEModelObject
getChildrenByTagName, stripNamespacePrefix

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NAMESPACE
```
public static final String NAMESPACE
```
See Also:
Constant Field Values

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

sizeT
```
private PositiveInteger sizeT
```

dimensionOrder
```
private DimensionOrder dimensionOrder
```

physicalSizeZ
```
private Length physicalSizeZ
```

physicalSizeY
```
private Length physicalSizeY
```

physicalSizeX
```
private Length physicalSizeX
```

sizeX
```
private PositiveInteger sizeX
```

sizeY
```
private PositiveInteger sizeY
```

sizeZ
```
private PositiveInteger sizeZ
```

bigEndian
```
private Boolean bigEndian
```

timeIncrement
```
private Time timeIncrement
```

significantBits

private PositiveInteger significantBits

sizeC
```
private PositiveInteger sizeC
```

type
```
private PixelType type
```

id
```
private String id
```

interleaved
```
private Boolean interleaved
```

channels
```
private List<Channel> channels
```

binDataBlocks
```
private List<BinData> binDataBlocks
```

tiffDataBlocks
```
private List<TiffData> tiffDataBlocks
```

metadataOnly
```
private MetadataOnly metadataOnly
```

planes
```
private List<Plane> planes
```

Constructor Detail
- Pixels
```
public Pixels()
```
  Default constructor.
- Pixels
```
public Pixels(Element element,
      OMEModel model)
       throws EnumerationException
```
  Constructs Pixels recursively from an XML DOM tree.
  
  Parameters:
  element - Root of the XML DOM tree to construct a model object graph from.
  model - Handler for the OME model which keeps track of instances and references seen during object population.
  
  Throws:
  
  EnumerationException - If there is an error instantiating an enumeration during model object creation.
- Pixels
```
public Pixels(Pixels orig)
```
  Copy constructor.

Method Detail

update
```
public void update(Element element,
          OMEModel model)
            throws EnumerationException
```
Updates Pixels recursively from an XML DOM tree. NOTE: No properties are removed, only added or updated.

Specified by:

update in interface OMEModelObject

Overrides:

update in class AbstractOMEModelObject

Parameters:
element - Root of the XML DOM tree to construct a model object graph from.
model - Handler for the OME model which keeps track of instances and references seen during object population.

Throws:

EnumerationException - If there is an error instantiating an enumeration during model object creation.

link
```
public boolean link(Reference reference,
           OMEModelObject o)
```
Description copied from interface: OMEModelObject

Link a given OME model object to this model object.

Specified by:

link in interface OMEModelObject

Overrides:

link in class AbstractOMEModelObject

Parameters:
reference - The type qualifier for the reference. This should be the corresponding reference type for o. If, for example, o is of type Image, reference MUST be of type ImageRef.
o - Model object to link to.

Returns:
true if this model object was able to handle the reference, false otherwise.

getSizeT
```
public PositiveInteger getSizeT()
```

setSizeT

public void setSizeT(PositiveInteger sizeT)

getDimensionOrder

public DimensionOrder getDimensionOrder()

setDimensionOrder

public void setDimensionOrder(DimensionOrder dimensionOrder)

getPhysicalSizeZ
```
public Length getPhysicalSizeZ()
```

setPhysicalSizeZ

public void setPhysicalSizeZ(Length physicalSizeZ)

getPhysicalSizeY
```
public Length getPhysicalSizeY()
```

setPhysicalSizeY

public void setPhysicalSizeY(Length physicalSizeY)

getPhysicalSizeX
```
public Length getPhysicalSizeX()
```

setPhysicalSizeX

public void setPhysicalSizeX(Length physicalSizeX)

getPhysicalSizeXUnitXsdDefault

public static String getPhysicalSizeXUnitXsdDefault()

getSizeX
```
public PositiveInteger getSizeX()
```

setSizeX

public void setSizeX(PositiveInteger sizeX)

getSizeY
```
public PositiveInteger getSizeY()
```

setSizeY

public void setSizeY(PositiveInteger sizeY)

getSizeZ
```
public PositiveInteger getSizeZ()
```

setSizeZ

public void setSizeZ(PositiveInteger sizeZ)

getPhysicalSizeZUnitXsdDefault

public static String getPhysicalSizeZUnitXsdDefault()

getBigEndian
```
public Boolean getBigEndian()
```

setBigEndian

public void setBigEndian(Boolean bigEndian)

getTimeIncrement
```
public Time getTimeIncrement()
```

setTimeIncrement

public void setTimeIncrement(Time timeIncrement)

getSignificantBits

public PositiveInteger getSignificantBits()

setSignificantBits

public void setSignificantBits(PositiveInteger significantBits)

getSizeC
```
public PositiveInteger getSizeC()
```

setSizeC

public void setSizeC(PositiveInteger sizeC)

getPhysicalSizeYUnitXsdDefault

public static String getPhysicalSizeYUnitXsdDefault()

getType
```
public PixelType getType()
```

setType
```
public void setType(PixelType type)
```

getID
```
public String getID()
```

setID
```
public void setID(String id)
```

getInterleaved
```
public Boolean getInterleaved()
```

setInterleaved

public void setInterleaved(Boolean interleaved)

getTimeIncrementUnitXsdDefault

public static String getTimeIncrementUnitXsdDefault()

sizeOfChannelList
```
public int sizeOfChannelList()
```

copyChannelList

public List<Channel> copyChannelList()

getChannel
```
public Channel getChannel(int index)
```

setChannel

public Channel setChannel(int index,
                 Channel channel)

addChannel

public void addChannel(Channel channel)

removeChannel

public void removeChannel(Channel channel)

sizeOfBinDataList
```
public int sizeOfBinDataList()
```

copyBinDataList

public List<BinData> copyBinDataList()

getBinData
```
public BinData getBinData(int index)
```

setBinData

public BinData setBinData(int index,
                 BinData binData)

addBinData

public void addBinData(BinData binData)

removeBinData

public void removeBinData(BinData binData)

sizeOfTiffDataList
```
public int sizeOfTiffDataList()
```

copyTiffDataList

public List<TiffData> copyTiffDataList()

getTiffData

public TiffData getTiffData(int index)

setTiffData

public TiffData setTiffData(int index,
                   TiffData tiffData)

addTiffData

public void addTiffData(TiffData tiffData)

removeTiffData

public void removeTiffData(TiffData tiffData)

getMetadataOnly
```
public MetadataOnly getMetadataOnly()
```

setMetadataOnly

public void setMetadataOnly(MetadataOnly metadataOnly)

sizeOfPlaneList
```
public int sizeOfPlaneList()
```

copyPlaneList
```
public List<Plane> copyPlaneList()
```

getPlane
```
public Plane getPlane(int index)
```

setPlane

public Plane setPlane(int index,
             Plane plane)

addPlane
```
public void addPlane(Plane plane)
```

removePlane
```
public void removePlane(Plane plane)
```

asXMLElement
```
public Element asXMLElement(Document document)
```
Description copied from interface: OMEModelObject

Takes the entire object hierarchy and produces an XML DOM tree.

Specified by:

asXMLElement in interface OMEModelObject

Specified by:

asXMLElement in class AbstractOMEModelObject

Parameters:
document - Destination document for element creation, etc.

Returns:
XML DOM tree root element for this model object.

asXMLElement
```
protected Element asXMLElement(Document document,
                   Element Pixels_element)
```
Description copied from class: AbstractOMEModelObject

Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.

Overrides:

asXMLElement in class AbstractOMEModelObject

Parameters:
document - Destination document for element creation, etc.
Pixels_element - Element from the subclass. If null a new element will be created of this class.

Returns:
element populated with properties from this class.

Class Pixels

Field Summary

Constructor Summary

Method Summary

Methods inherited from class ome.xml.model.AbstractOMEModelObject

Methods inherited from class java.lang.Object

Field Detail

NAMESPACE

LOGGER

sizeT

dimensionOrder

physicalSizeZ

physicalSizeY

physicalSizeX

sizeX

sizeY

sizeZ

bigEndian

timeIncrement

significantBits

sizeC

type

id

interleaved

channels

binDataBlocks

tiffDataBlocks

metadataOnly

planes

Constructor Detail

Pixels

Pixels

Pixels

Method Detail

update

link

getSizeT

setSizeT

getDimensionOrder

setDimensionOrder

getPhysicalSizeZ

setPhysicalSizeZ

getPhysicalSizeY

setPhysicalSizeY

getPhysicalSizeX

setPhysicalSizeX

getPhysicalSizeXUnitXsdDefault

getSizeX

setSizeX

getSizeY

setSizeY

getSizeZ

setSizeZ

getPhysicalSizeZUnitXsdDefault

getBigEndian

setBigEndian

getTimeIncrement

setTimeIncrement

getSignificantBits

setSignificantBits

getSizeC

setSizeC

getPhysicalSizeYUnitXsdDefault

getType

setType

getID

setID

getInterleaved

setInterleaved

getTimeIncrementUnitXsdDefault

sizeOfChannelList

copyChannelList

getChannel

setChannel

addChannel

removeChannel

sizeOfBinDataList

copyBinDataList

getBinData

setBinData