loci.formats.in.LeicaMicrosystemsMetadata

Class MetadataTempBuffer

java.lang.Object

loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

public class MetadataTempBuffer
extends java.lang.Object

This class is used to temporarily store metadata information extracted from Leica XML before it is written to the reader's MetadataStore

Author:

Melissa Linkert melissa at glencoesoftware.com, Constanze Wendlandt constanze.wendlandt at leica-microsystems.com

Field Summary

Fields

Modifier and Type	Field and Description
double[]	acquiredDate
java.util.ArrayList<java.util.ArrayList<java.lang.Boolean>>	activeDetector
boolean	alternateCenter
java.util.List<java.util.ArrayList<ome.xml.model.primitives.Color>>	channelColors
java.lang.String[][]	channelNames
int[][]	channelPrios
java.util.ArrayList<java.util.ArrayList<Channel>>	channels
java.lang.String[]	corrections
java.util.ArrayList<java.util.ArrayList<ome.units.quantity.Length>>	cutIns
java.util.ArrayList<java.util.ArrayList<ome.units.quantity.Length>>	cutOuts
java.lang.String[]	descriptions
java.util.ArrayList<java.util.HashMap<java.lang.Integer,java.lang.String>>	detectorIndexes
java.util.ArrayList<java.util.ArrayList<java.lang.String>>	detectorModels
java.lang.Double[][]	detectorOffsets
private java.util.ArrayList<java.util.ArrayList<Dimension>>	dimensions
java.lang.Double[][]	expTimes
java.lang.Double[][]	exWaves
java.util.List<ome.units.quantity.Length>	fieldPosX
java.util.List<ome.units.quantity.Length>	fieldPosY
java.util.ArrayList<java.util.ArrayList<java.lang.String>>	filterModels
boolean[]	flipX
boolean[]	flipY
java.lang.Double[][]	gains
java.lang.String[]	imageNames
ROI[][]	imageROIs
java.lang.String[]	immersions
boolean[]	inverseRgb
java.util.ArrayList<java.util.ArrayList<java.lang.Boolean>>	laserActive
java.util.ArrayList<java.util.ArrayList<java.lang.Boolean>>	laserFrap
java.util.ArrayList<java.util.ArrayList<java.lang.Double>>	laserIntensity
java.util.ArrayList<java.util.ArrayList<java.lang.Double>>	laserWavelength
java.lang.Double[]	lensNA
java.lang.Double[]	magnification
java.lang.String[]	microscopeModels
java.lang.String[]	objectiveModels
java.util.List<java.lang.Double>	physicalSizeXs
java.util.List<java.lang.Double>	physicalSizeYs
java.lang.Double[]	pinholes
ome.units.quantity.Length[]	posX
ome.units.quantity.Length[]	posY
ome.units.quantity.Length[]	posZ
java.lang.Double[]	refractiveIndex
java.lang.String[]	serialNumber
boolean[]	swapXY
long[]	tileBytesInc
int[]	tileCount
java.lang.Double[][]	timestamps
java.lang.Double[]	tSteps
java.lang.Double[]	zooms
java.lang.Double[]	zSteps

Constructor Summary

Constructors

Constructor and Description
MetadataTempBuffer(int len) Constructs a MetadataTempBuffer for a given number of images.

Method Summary

Modifier and Type	Method and Description
void	addChannelDimension(int coreIndex) Adds channel dimension
void	addDimension(int imageIndex, Dimension dimension) Inserts dimension to buffer and optionally adapts other dimension-dependent values
void	addMissingDimensions(int imageIndex) Adds Z, T and S dimension if they haven't been added already
private <T> java.util.ArrayList<java.util.ArrayList<T>>	ArrayListOfArrayLists(int rows, java.lang.Class<T> type)
private <T,S> java.util.ArrayList<java.util.HashMap<T,S>>	ArrayListOfHashMaps(int rows, java.lang.Class<T> key, java.lang.Class<S> value)
private long	getChannelDimensionBytesInc(int coreIndex)
Dimension	getDimension(int imageIndex, Dimension.DimensionKey key)
java.lang.String	getDimensionOrder(int imageIndex) Returns the dimension order as a string
java.util.ArrayList<Dimension>	getDimensions(int imageIndex)
private void	sortDimensions(int coreIndex) Sorts list of existing dimensions by increasing bytesInc, beginning with X and Y, ending with stage position

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

channelColors

public java.util.List<java.util.ArrayList<ome.xml.model.primitives.Color>> channelColors

channelPrios

public int[][] channelPrios

physicalSizeXs

public java.util.List<java.lang.Double> physicalSizeXs

physicalSizeYs

public java.util.List<java.lang.Double> physicalSizeYs

fieldPosX

public java.util.List<ome.units.quantity.Length> fieldPosX

fieldPosY

public java.util.List<ome.units.quantity.Length> fieldPosY

descriptions

public java.lang.String[] descriptions

microscopeModels

public java.lang.String[] microscopeModels

serialNumber

public java.lang.String[] serialNumber

pinholes

public java.lang.Double[] pinholes

zooms

public java.lang.Double[] zooms

zSteps

public java.lang.Double[] zSteps

tSteps

public java.lang.Double[] tSteps

lensNA

public java.lang.Double[] lensNA

flipX

public boolean[] flipX

flipY

public boolean[] flipY

swapXY

public boolean[] swapXY

expTimes

public java.lang.Double[][] expTimes

gains

public java.lang.Double[][] gains

detectorOffsets

public java.lang.Double[][] detectorOffsets

channelNames

public java.lang.String[][] channelNames

detectorModels

public java.util.ArrayList<java.util.ArrayList<java.lang.String>> detectorModels

exWaves

public java.lang.Double[][] exWaves

activeDetector

public java.util.ArrayList<java.util.ArrayList<java.lang.Boolean>> activeDetector

detectorIndexes

public java.util.ArrayList<java.util.HashMap<java.lang.Integer,java.lang.String>> detectorIndexes

immersions

public java.lang.String[] immersions

corrections

public java.lang.String[] corrections

objectiveModels

public java.lang.String[] objectiveModels

magnification

public java.lang.Double[] magnification

posX

public ome.units.quantity.Length[] posX

posY

public ome.units.quantity.Length[] posY

posZ

public ome.units.quantity.Length[] posZ

refractiveIndex

public java.lang.Double[] refractiveIndex

cutIns

public java.util.ArrayList<java.util.ArrayList<ome.units.quantity.Length>> cutIns

cutOuts

public java.util.ArrayList<java.util.ArrayList<ome.units.quantity.Length>> cutOuts

filterModels

public java.util.ArrayList<java.util.ArrayList<java.lang.String>> filterModels

timestamps

public java.lang.Double[][] timestamps

laserIntensity

public java.util.ArrayList<java.util.ArrayList<java.lang.Double>> laserIntensity

laserWavelength

public java.util.ArrayList<java.util.ArrayList<java.lang.Double>> laserWavelength

laserActive

public java.util.ArrayList<java.util.ArrayList<java.lang.Boolean>> laserActive

laserFrap

public java.util.ArrayList<java.util.ArrayList<java.lang.Boolean>> laserFrap

imageROIs

public ROI[][] imageROIs

alternateCenter

public boolean alternateCenter

imageNames

public java.lang.String[] imageNames

acquiredDate

public double[] acquiredDate

tileCount

public int[] tileCount

tileBytesInc

public long[] tileBytesInc

inverseRgb

public boolean[] inverseRgb

dimensions

private java.util.ArrayList<java.util.ArrayList<Dimension>> dimensions

channels

public java.util.ArrayList<java.util.ArrayList<Channel>> channels

Constructor Detail

MetadataTempBuffer

public MetadataTempBuffer(int len)

Constructs a MetadataTempBuffer for a given number of images.

Parameters:

len - Number of images (one per XLIF)

Method Detail

getDimension

public Dimension getDimension(int imageIndex,
                              Dimension.DimensionKey key)

addDimension

public void addDimension(int imageIndex,
                         Dimension dimension)

Inserts dimension to buffer and optionally adapts other dimension-dependent values

Parameters:

imageIndex -

dimension -

getDimensionOrder

public java.lang.String getDimensionOrder(int imageIndex)

Returns the dimension order as a string

Parameters:

imageIndex -

Returns:

dimension order string, as it is expected in CoreMetadata.dimensionOrder

sortDimensions

private void sortDimensions(int coreIndex)

Sorts list of existing dimensions by increasing bytesInc, beginning with X and Y, ending with stage position

Parameters:

coreIndex -

getDimensions

public java.util.ArrayList<Dimension> getDimensions(int imageIndex)

addMissingDimensions

public void addMissingDimensions(int imageIndex)

Adds Z, T and S dimension if they haven't been added already

Parameters:

imageIndex -

addChannelDimension

public void addChannelDimension(int coreIndex)

Adds channel dimension

Parameters:

coreIndex -

sizeC - total number of channels

bytesInc -

getChannelDimensionBytesInc

private long getChannelDimensionBytesInc(int coreIndex)

ArrayListOfArrayLists

private <T> java.util.ArrayList<java.util.ArrayList<T>> ArrayListOfArrayLists(int rows,
                                                                              java.lang.Class<T> type)

ArrayListOfHashMaps

private <T,S> java.util.ArrayList<java.util.HashMap<T,S>> ArrayListOfHashMaps(int rows,
                                                                              java.lang.Class<T> key,
                                                                              java.lang.Class<S> value)