io.scif.formats

Class ICSFormat.Metadata

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.AbstractHasFormat

io.scif.AbstractHasSource

io.scif.AbstractMetadata

io.scif.formats.ICSFormat.Metadata

All Implemented Interfaces:

HasFormat, HasMetaTable, HasSource, Metadata, SCIFIOPlugin, TypedMetadata, Serializable, Comparable<org.scijava.Prioritized>, org.scijava.Contextual, org.scijava.Identifiable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.plugin.HasPluginInfo, org.scijava.plugin.RichPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Prioritized, org.scijava.Versioned

Enclosing class:

ICSFormat

public static class ICSFormat.Metadata
extends AbstractMetadata

SCIFIO Metadata object for ICS images.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
Metadata()

Method Summary

Modifier and Type	Method and Description
void	addCubeChannel(Map<Integer,String> channelNames)
void	addLaserWavelength(Map<Integer,Integer> wavelengths)
void	addStepChannel(Map<Integer,String> channelNames)
void	close(boolean fileOnly) Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.
String	get(String key) Convenience method to directly access the hashtable.
String	getAuthorLastName()
String[]	getAxes()
int[]	getAxesSizes()
Integer	getBitsPerPixel()
String	getByteOrder()
Map<Integer,String>	getChannelNames()
String	getCompression()
String	getDate()
String	getDescription()
String	getDetectorManufacturer()
String	getDetectorModel()
String	getDichroicModel()
String	getEmissionModel()
Integer[]	getEMSingleton()
Integer[]	getEMWaves()
String	getExcitationModel()
String	getExperimentType()
Double	getExposureTime()
Integer[]	getEXSingleton()
Integer[]	getEXWaves()
String	getFilterSetModel()
Map<Integer,Double>	getGains()
Double[]	getHistoryExtents()
String[]	getHistoryLabels()
String[]	getHistoryUnits()
org.scijava.io.location.Location	getIcsLocation()
org.scijava.io.location.Location	getIdsLocation()
String	getImmersion()
Map<String,String>	getKeyValPairs()
String	getLaserManufacturer()
String	getLaserModel()
Double	getLaserPower()
Double	getLaserRepetitionRate()
Double	getLensNA()
boolean	getLifetime()
Double	getMagnification()
String	getMicroscopeManufacturer()
String	getMicroscopeModel()
String	getObjectiveModel()
String[]	getParameterLabels()
Double[]	getParameterScales()
String[]	getParameterUnits()
Map<Integer,Double>	getPinholes()
String	getRepFormat()
Double[]	getStagePositions()
Double	getStageX()
Double	getStageY()
Double	getStageZ()
Double[]	getTimestamps()
Map<Integer,Integer>	getWavelengths()
Double	getWorkingDistance()
boolean	hasInstrumentData()
boolean	isSigned()
boolean	isVersionTwo()
void	populateImageMetadata() Generates format-agnostic image metadata structures based on this instance's format-specific metadata.
void	put(String key, String value)
void	putAuthorLastName(String lastName)
void	putAxes(String[] axes)
void	putAxesSizes(double[] axesSizes)
void	putBitsPerPixel(Integer bpp)
void	putByteOrder(String byteOrder)
void	putChannelNames(Map<Integer,String> cNames)
void	putCompression(String cmp)
void	putDate(String value)
void	putDescription(String value)
void	putDetectorManufacturer(String detMan)
void	putDetectorModel(String detModel)
void	putDichroicModel(String diModel)
void	putEmissionModel(String emModel)
void	putEMSingleton(Integer[] em)
void	putEMWaves(Integer[] emWaves)
void	putExcitationModel(String exModel)
void	putExperimentType(String value)
void	putExposureTime(Double expTime)
void	putEXSingleton(Integer[] ex)
void	putEXWaves(Integer[] exWaves)
void	putFilterSetModel(String fltrModel)
void	putGains(Map<Integer,Double> gains)
void	putImmersion(String immersion)
void	putLaserManufacturer(String laserMan)
void	putLaserModel(String laserMod)
void	putLaserPower(Double laserPower)
void	putLaserRepetitionRate(Double laserRep)
void	putLensNA(Double lensNA)
void	putLifetime(boolean lifetime)
void	putMagnification(Double mag)
void	putMicroscopeManufacturer(String value)
void	putMicroscopeModel(String value)
void	putObjectiveModel(String objModel)
void	putPhysicalPixelSizes(double[] physSizes)
void	putPinholes(Map<Integer,Double> pins)
void	putPixelSizes(Double[] pixelSizes)
void	putRepFormat(String repFormat)
void	putSigned(boolean signed)
void	putStagePositions(Double[] positions)
void	putStageX(Double stageX)
void	putStageY(Double stageY)
void	putStageZ(Double stageZ)
void	putTimestamps(Double[] timeStamp)
void	putUnits(String[] units)
void	putWavelengths(Map<Integer,Integer> waves)
void	putWorkingDistance(Double wd)
void	setHasInstrumentData(boolean hasInstrumentData)
void	setIcsLocation(org.scijava.io.location.Location icsLocation)
void	setIdsLocation(org.scijava.io.location.Location idsLocation)
void	setKeyValPairs(Map<String,String> keyValPairs)
void	setStoredRGB(boolean rgb)
void	setVersionTwo(boolean versionTwo)
boolean	storedRGB()

Methods inherited from class io.scif.AbstractMetadata

add, createImageMetadata, get, getAll, getDatasetName, getDatasetSize, getDestinationLocation, getImageCount, getSource, getSourceLocation, getTable, isFiltered, setDatasetName, setDestinationLocation, setFiltered, setSource, setSourceLocation, setTable

Methods inherited from class io.scif.AbstractHasSource

close

Methods inherited from class io.scif.AbstractHasFormat

asBrowsableLocation, asBrowsableLocation, getFormat, getFormatName

Methods inherited from class io.scif.AbstractSCIFIOPlugin

getVersion, log

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, getPriority, setInfo, setPriority, toString

Methods inherited from class org.scijava.AbstractContextual

context, getContext

Methods inherited from class java.lang.Object

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

Methods inherited from interface io.scif.HasFormat

getFormat, getFormatName

Methods inherited from interface io.scif.SCIFIOPlugin

getVersion, log

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier

Methods inherited from interface org.scijava.Contextual

context, getContext, setContext

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Methods inherited from interface io.scif.HasSource

close

Constructor Detail

Metadata

public Metadata()

Method Detail

populateImageMetadata

public void populateImageMetadata()

Description copied from interface: Metadata

Generates format-agnostic image metadata structures based on this instance's format-specific metadata.

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: HasSource

Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.

Specified by:

close in interface HasSource

Overrides:

close in class AbstractMetadata

Parameters:

fileOnly - - If true, only the associated source(s) are closed.

Throws:

IOException

storedRGB

public boolean storedRGB()

setStoredRGB

public void setStoredRGB(boolean rgb)

get

public String get(String key)

Convenience method to directly access the hashtable.

setIcsLocation

public void setIcsLocation(org.scijava.io.location.Location icsLocation)

setIdsLocation

public void setIdsLocation(org.scijava.io.location.Location idsLocation)

getIcsLocation

public org.scijava.io.location.Location getIcsLocation()

getIdsLocation

public org.scijava.io.location.Location getIdsLocation()

hasInstrumentData

public boolean hasInstrumentData()

setHasInstrumentData

public void setHasInstrumentData(boolean hasInstrumentData)

isVersionTwo

public boolean isVersionTwo()

setVersionTwo

public void setVersionTwo(boolean versionTwo)

setKeyValPairs

public void setKeyValPairs(Map<String,String> keyValPairs)

getKeyValPairs

public Map<String,String> getKeyValPairs()

put

public void put(String key,
                String value)

putDate

public void putDate(String value)

putDescription

public void putDescription(String value)

putMicroscopeModel

public void putMicroscopeModel(String value)

putMicroscopeManufacturer

public void putMicroscopeManufacturer(String value)

putExperimentType

public void putExperimentType(String value)

putLifetime

public void putLifetime(boolean lifetime)

putPixelSizes

public void putPixelSizes(Double[] pixelSizes)

putUnits

public void putUnits(String[] units)

putAxes

public void putAxes(String[] axes)

putAxesSizes

public void putAxesSizes(double[] axesSizes)

putPhysicalPixelSizes

public void putPhysicalPixelSizes(double[] physSizes)

putTimestamps

public void putTimestamps(Double[] timeStamp)

putChannelNames

public void putChannelNames(Map<Integer,String> cNames)

putPinholes

public void putPinholes(Map<Integer,Double> pins)

putEMWaves

public void putEMWaves(Integer[] emWaves)

putEMSingleton

public void putEMSingleton(Integer[] em)

putEXWaves

public void putEXWaves(Integer[] exWaves)

putEXSingleton

public void putEXSingleton(Integer[] ex)

putWavelengths

public void putWavelengths(Map<Integer,Integer> waves)

putByteOrder

public void putByteOrder(String byteOrder)

putRepFormat

public void putRepFormat(String repFormat)

putCompression

public void putCompression(String cmp)

putSigned

public void putSigned(boolean signed)

putLaserManufacturer

public void putLaserManufacturer(String laserMan)

putLaserModel

public void putLaserModel(String laserMod)

putLaserRepetitionRate

public void putLaserRepetitionRate(Double laserRep)

putLaserPower

public void putLaserPower(Double laserPower)

putDichroicModel

public void putDichroicModel(String diModel)

putExcitationModel

public void putExcitationModel(String exModel)

putEmissionModel

public void putEmissionModel(String emModel)

putFilterSetModel

public void putFilterSetModel(String fltrModel)

putObjectiveModel

public void putObjectiveModel(String objModel)

putImmersion

public void putImmersion(String immersion)

putLensNA

public void putLensNA(Double lensNA)

putWorkingDistance

public void putWorkingDistance(Double wd)

putMagnification

public void putMagnification(Double mag)

putDetectorManufacturer

public void putDetectorManufacturer(String detMan)

putDetectorModel

public void putDetectorModel(String detModel)

putBitsPerPixel

public void putBitsPerPixel(Integer bpp)

putGains

public void putGains(Map<Integer,Double> gains)

putAuthorLastName

public void putAuthorLastName(String lastName)

putStagePositions

public void putStagePositions(Double[] positions)

putStageX

public void putStageX(Double stageX)

putStageY

public void putStageY(Double stageY)

putStageZ

public void putStageZ(Double stageZ)

putExposureTime

public void putExposureTime(Double expTime)

getDate

public String getDate()

getDescription

public String getDescription()

getMicroscopeModel

public String getMicroscopeModel()

getMicroscopeManufacturer

public String getMicroscopeManufacturer()

getLifetime

public boolean getLifetime()

getParameterLabels

public String[] getParameterLabels()

getHistoryLabels

public String[] getHistoryLabels()

getExperimentType

public String getExperimentType()

getParameterScales

public Double[] getParameterScales()

getParameterUnits

public String[] getParameterUnits()

getAxes

public String[] getAxes()

getAxesSizes

public int[] getAxesSizes()

getHistoryExtents

public Double[] getHistoryExtents()

getHistoryUnits

public String[] getHistoryUnits()

getTimestamps

public Double[] getTimestamps()

getChannelNames

public Map<Integer,String> getChannelNames()

addStepChannel

public void addStepChannel(Map<Integer,String> channelNames)

addCubeChannel

public void addCubeChannel(Map<Integer,String> channelNames)

getPinholes

public Map<Integer,Double> getPinholes()

getEMWaves

public Integer[] getEMWaves()

getEMSingleton

public Integer[] getEMSingleton()

getEXWaves

public Integer[] getEXWaves()

getEXSingleton

public Integer[] getEXSingleton()

getWavelengths

public Map<Integer,Integer> getWavelengths()

addLaserWavelength

public void addLaserWavelength(Map<Integer,Integer> wavelengths)

getByteOrder

public String getByteOrder()

getRepFormat

public String getRepFormat()

getCompression

public String getCompression()

isSigned

public boolean isSigned()

getLaserManufacturer

public String getLaserManufacturer()

getLaserModel

public String getLaserModel()

getLaserRepetitionRate

public Double getLaserRepetitionRate()

getLaserPower

public Double getLaserPower()

getDichroicModel

public String getDichroicModel()

getExcitationModel

public String getExcitationModel()

getEmissionModel

public String getEmissionModel()

getFilterSetModel

public String getFilterSetModel()

getObjectiveModel

public String getObjectiveModel()

getImmersion

public String getImmersion()

getLensNA

public Double getLensNA()

getWorkingDistance

public Double getWorkingDistance()

getMagnification

public Double getMagnification()

getDetectorManufacturer

public String getDetectorManufacturer()

getDetectorModel

public String getDetectorModel()

getBitsPerPixel

public Integer getBitsPerPixel()

getGains

public Map<Integer,Double> getGains()

getAuthorLastName

public String getAuthorLastName()

getStagePositions

public Double[] getStagePositions()

getStageX

public Double getStageX()

getStageY

public Double getStageY()

getStageZ

public Double getStageZ()

getExposureTime

public Double getExposureTime()