io.scif.formats

Class ScancoISQFormat.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.ScancoISQFormat.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:

ScancoISQFormat

public static class ScancoISQFormat.Metadata
extends AbstractMetadata

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	HEADER_BLOCK Bytes in an ISQ header block
static String	UNIT The unit of the spatial calibration, e.g.
static long	UNIX_EPOCH January 1 1970 as a VMS timestamp, i.e. in 100 nanosecond ticks from November 17, 1858

Constructor Summary

Constructors

Constructor and Description
Metadata()

Method Summary

Modifier and Type	Method and Description
LocalDate	getCreationDate()
int	getDataOffset()
int	getEnergy()
int	getFirstSlicePosition()
int	getHeight()
int	getIntensity()
int	getMaxDataValue()
int	getMeasurementIndex()
int	getMinDataValue()
int	getMuScaling()
int	getPatientIndex()
String	getPatientName()
int	getPhysicalDepth()
int	getPhysicalHeight()
int	getPhysicalWidth()
int	getProjections()
int	getReconstructionAlgorithm()
int	getReferenceLine()
int	getSamples()
int	getSamplingTime()
int	getScanDistance()
int	getScannerId()
int	getScannerType()
int	getSite()
int	getSliceBytes()
int	getSlices()
int	getSliceSpacing()
int	getSliceThickness()
int	getWidth()
void	populateImageMetadata() Generates format-agnostic image metadata structures based on this instance's format-specific metadata.
void	setCreationDate(long vmsTimestamp) Converts the given timestamp to a creation date Timestamp starts from byte 36 of the file
void	setDataOffset(int optionalHeaders) Sets the starting point of image date in the file The 16-bit optional header number is found at byte 508 in the file.
void	setEnergy(int energy)
void	setFirstSlicePosition(int firstSlicePosition)
void	setHeight(int height)
void	setIntensity(int intensity)
void	setMaxDataValue(int maxDataValue)
void	setMeasurementIndex(int measurementIndex)
void	setMinDataValue(int minDataValue)
void	setMuScaling(int muScaling)
void	setPatientIndex(int patientIndex)
void	setPatientName(String patientName)
void	setPhysicalDepth(int physicalDepth)
void	setPhysicalHeight(int physicalHeight)
void	setPhysicalWidth(int physicalWidth)
void	setProjections(int projections)
void	setReconstructionAlgorithm(int reconstructionAlgorithm)
void	setReferenceLine(int referenceLine)
void	setSamples(int samples)
void	setSamplingTime(int samplingTime)
void	setScanDistance(int scanDistance)
void	setScannerId(int scannerId)
void	setScannerType(int scannerType)
void	setSite(int site)
void	setSlices(int slices)
void	setSliceSpacing(int sliceSpacing)
void	setSliceThickness(int sliceThickness)
void	setWidth(int width)

Methods inherited from class io.scif.AbstractMetadata

add, close, 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

Field Detail

UNIT

public static final String UNIT

The unit of the spatial calibration, e.g. "voxel size"

NB (Default)UnitService recognises "µm" as "um"

See Also:

Constant Field Values

HEADER_BLOCK

public static final int HEADER_BLOCK

Bytes in an ISQ header block

See Also:

Constant Field Values

UNIX_EPOCH

public static final long UNIX_EPOCH

January 1 1970 as a VMS timestamp, i.e. in 100 nanosecond ticks from November 17, 1858

See Also:

Constant Field Values

Constructor Detail

Metadata

public Metadata()

Method Detail

getCreationDate

public LocalDate getCreationDate()

getDataOffset

public int getDataOffset()

getEnergy

public int getEnergy()

getFirstSlicePosition

public int getFirstSlicePosition()

getHeight

public int getHeight()

getIntensity

public int getIntensity()

getMaxDataValue

public int getMaxDataValue()

getMeasurementIndex

public int getMeasurementIndex()

getMinDataValue

public int getMinDataValue()

getMuScaling

public int getMuScaling()

getPatientIndex

public int getPatientIndex()

getPatientName

public String getPatientName()

getPhysicalDepth

public int getPhysicalDepth()

getPhysicalHeight

public int getPhysicalHeight()

getPhysicalWidth

public int getPhysicalWidth()

getProjections

public int getProjections()

getReconstructionAlgorithm

public int getReconstructionAlgorithm()

getReferenceLine

public int getReferenceLine()

getSamples

public int getSamples()

getSamplingTime

public int getSamplingTime()

getScanDistance

public int getScanDistance()

getScannerId

public int getScannerId()

getScannerType

public int getScannerType()

getSite

public int getSite()

getSliceSpacing

public int getSliceSpacing()

getSliceThickness

public int getSliceThickness()

getSlices

public int getSlices()

getWidth

public int getWidth()

getSliceBytes

public int getSliceBytes()

setCreationDate

public void setCreationDate(long vmsTimestamp)

Converts the given timestamp to a creation date

Timestamp starts from byte 36 of the file

Parameters:

vmsTimestamp - An eight byte VMS timestamp

setDataOffset

public void setDataOffset(int optionalHeaders)

Sets the starting point of image date in the file

The 16-bit optional header number is found at byte 508 in the file.

Parameters:

optionalHeaders - Number of optional header blocks

setEnergy

public void setEnergy(int energy)

setFirstSlicePosition

public void setFirstSlicePosition(int firstSlicePosition)

setHeight

public void setHeight(int height)

setIntensity

public void setIntensity(int intensity)

setMaxDataValue

public void setMaxDataValue(int maxDataValue)

setMeasurementIndex

public void setMeasurementIndex(int measurementIndex)

setMinDataValue

public void setMinDataValue(int minDataValue)

setMuScaling

public void setMuScaling(int muScaling)

setPatientIndex

public void setPatientIndex(int patientIndex)

setPatientName

public void setPatientName(String patientName)

setPhysicalDepth

public void setPhysicalDepth(int physicalDepth)

setPhysicalHeight

public void setPhysicalHeight(int physicalHeight)

setPhysicalWidth

public void setPhysicalWidth(int physicalWidth)

setProjections

public void setProjections(int projections)

setReconstructionAlgorithm

public void setReconstructionAlgorithm(int reconstructionAlgorithm)

setReferenceLine

public void setReferenceLine(int referenceLine)

setSamples

public void setSamples(int samples)

setSamplingTime

public void setSamplingTime(int samplingTime)

setScanDistance

public void setScanDistance(int scanDistance)

setScannerId

public void setScannerId(int scannerId)

setScannerType

public void setScannerType(int scannerType)

setSite

public void setSite(int site)

setSliceSpacing

public void setSliceSpacing(int sliceSpacing)

setSliceThickness

public void setSliceThickness(int sliceThickness)

setSlices

public void setSlices(int slices)

setWidth

public void setWidth(int width)

populateImageMetadata

public void populateImageMetadata()

Description copied from interface: Metadata

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