Package gda.device.detector

Class EdeDetectorBase

java.lang.Object

gda.factory.ConfigurableBase

gda.factory.FindableConfigurableBase

gda.device.DeviceBase

gda.device.scannable.ScannableBase

gda.device.detector.DetectorBase

gda.device.detector.EdeDetectorBase

All Implemented Interfaces:

Detector, EdeDetector, NexusDetector, Device, Scannable, Configurable, Findable, gda.observable.IObservable, Serializable

Direct Known Subclasses:

EdeDummyDetector, EdeFrelon, XhDetector

public abstract class EdeDetectorBase
extends DetectorBase
implements EdeDetector

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected EdeDetector	currentDetector
protected EdeScanParameters	currentScanParameter
protected DetectorData	detectorData
protected boolean	dropFirstFrame

Fields inherited from class gda.device.detector.DetectorBase

collectionTime

Fields inherited from class gda.device.scannable.ScannableBase

__doc__, DEFAULT_INPUT_NAME, DEFAULT_OUTPUT_FORMAT, extraNames, inputNames, level, outputFormat

Fields inherited from class gda.device.DeviceBase

DEFAULT_PROTECTION_LEVEL_PROPERTY

Fields inherited from interface gda.device.Detector

BUSY, FAULT, IDLE, MONITORING, PAUSED, STANDBY

Fields inherited from interface gda.device.detector.EdeDetector

CALIBRATION_PROP_KEY, EXCLUDED_PIXELS_PROP_NAME, INITIAL_NO_OF_ROIS, ROIS_PROP_NAME

Fields inherited from interface gda.device.Scannable

ATTR_NEXUS_CATEGORY, ATTR_NX_CLASS, DEFAULT_INPUT_NAME, VALUE_UNAVAILABLE

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	EdeDetectorBase()

Method Summary

Modifier and Type	Method	Description
void	atScanStart()	Called for every Scannable at the start of a group of nested scans (or a single scan if that is the case)
void	configure()	Default implementation for classes that do not have to do any specific configuration. Classes that do their own configuration should *not* call this superclass function, as it may cause the object to appear configured before it really is.
protected abstract void	configureDetectorForCollection()
org.eclipse.january.dataset.DoubleDataset	createDatasetForPixel()
abstract DetectorStatus	fetchStatus()	fetch detector status from hardware.
double	getAccumulationReadoutTime()
int	getCompressionLevel()
DetectorData	getDetectorData()
DetectorSetupType	getDetectorSetupType()
CalibrationDetails	getEnergyCalibration()	Returns the function used to convert channel number to energy.
double[]	getEnergyForChannels()
Integer[]	getExcludedPixels()	Return array of 'dead pixel' locations.
int	getLowerChannel()
int	getMaxNumFramesToRead()
abstract int	getMaxPixel()	detector's maximum pixel size in energy direction.
int	getNumberOfRois()
abstract int	getNumberScansInFrame(double frameTime, double scanTime, int numberOfFrames)	calculate the number of scans (TFG2 term) or accumulations in a single frame based on detector clock rate.
abstract String	getOrbitWaitMethod()
Integer[]	getPixels()
int	getRoiFor(int elementIndex)
Roi[]	getRois()	Returns the regions in use, as defined by calls to setRois or setNumberRois
int	getStatus()	Returns the current collecting state of the device.
abstract int	getSynchroniseBeamOrbitDelay()
abstract boolean	getSynchroniseToBeamOrbit()
int	getUpperChannel()
boolean	isCheckForExcludedStrips()
boolean	isDropFirstFrame()
boolean	isEnergyCalibrationSet()
void	prepareDetectorwithScanParameters(EdeScanParameters newParameters)
NexusTreeProvider[]	readFrames(int startFrame, int finalFrame)	returns a list of NexusTreeProvider, one for each frame in the specified range.
NexusTreeProvider	readout()	Reads the first frame only.
abstract int[]	readoutFrames(int startFrame, int finalFrame)	implements the read out of frames from the actual detector used.
void	setAccumulationReadoutTime(double timeSec)	Set the accumulation readout time
void	setCheckForExcludedStrips(boolean checkForExcludedStrips)	If set to true, detector data will have counts for 'excluded' pixels set to zero.
void	setCompressionLevel(int compressionLevel)	Compression level to use for datasets in the Nexus file : 0 -> no compression 1 -> LZW compression
void	setDetectorData(DetectorData detectorData)
void	setDetectorSetupType(DetectorSetupType detectorSetupType)
void	setDropFirstFrame(boolean dropFirstFrame)
void	setEnergyCalibration(CalibrationDetails energyCalibration)	Set the energy calibration.
void	setEnergyCalibrationSet(boolean energyCalibrationSet)
void	setExcludedPixels(Integer[] excludedPixels)	Set array of dead pixel locations
void	setLowerChannel(int lowerChannel)
void	setMaxNumFramesToRead(int maxNumberOfFramesToRead)
void	setNumberRois(int numberOfRois)	Set evenly sized regions of interest, ignoring channels outside of the lower and upper channel limits.
abstract void	setOrbitWaitMethod(String methodString)
void	setRois(Roi[] rois)	Ignoring the lower and upper channel properties, explicitly set the regions in use.
abstract void	setSynchroniseBeamOrbitDelay(int synchroniseBeamOrbitDelay)
abstract void	setSynchroniseToBeamOrbit(boolean synchroniseToBeamOrbit)
void	setUpperChannel(int upperChannel)
protected int[][]	unpackRawDataToFrames(int[] scalerData, int numFrames)
void	writeLiveDataFile()

Methods inherited from class gda.device.detector.DetectorBase

asynchronousMoveTo, checkPositionValid, endCollection, getCollectionTime, getDataDimensions, getDescription, getDetectorID, getDetectorType, getPosition, isBusy, prepareForCollection, setCollectionTime, toFormattedString

Methods inherited from class gda.device.scannable.ScannableBase

__call__, __call__, __doc__, __getitem__, __len__, __repr__, __str__, atCommandFailure, atLevelEnd, atLevelMoveStart, atLevelStart, atPointEnd, atPointStart, atScanEnd, atScanLineEnd, atScanLineStart, externalToInternal, getExtraNames, getInputNames, getLevel, getOutputFormat, getScanMetadataAttribute, getScanMetadataAttributeNames, getScanMetadataAttributes, internalToExternal, isAt, moveTo, rawAsynchronousMoveTo, rawGetPosition, setExtraNames, setInputNames, setLevel, setOutputFormat, setScanMetadataAttribute, setScanMetadataAttributes, stop, throwExceptionIfInvalidTarget, toString, validateScannable, valueUnavailableString, waitWhileBusy, waitWhileBusy

Methods inherited from class gda.device.DeviceBase

addIObserver, close, deleteIObserver, deleteIObservers, getAttribute, getName, getProtectionLevel, isBeingObserved, isConfigureAtStartup, notifyIObservers, setAttribute, setConfigureAtStartup, setName, setProtectionLevel

Methods inherited from class gda.factory.ConfigurableBase

isConfigured, reconfigure, setConfigured

Methods inherited from class java.lang.Object

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

Methods inherited from interface gda.factory.Configurable

isConfigureAtStartup, isConfigured, reconfigure

Methods inherited from interface gda.device.Detector

collectData, createsOwnFiles, endCollection, getCollectionTime, getDataDimensions, getDescription, getDetectorID, getDetectorType, getFileStructure, prepareForCollection, setCollectionTime, waitWhileBusy

Methods inherited from interface gda.device.Device

close, getAttribute, getProtectionLevel, setAttribute, setProtectionLevel

Methods inherited from interface gda.device.detector.EdeDetector

configureDetectorForROI, configureDetectorForTimingGroup, fetchDetectorSettings, getLastImageAvailable, getNumberOfSpectra, getNumberScansInFrame, getTemperatures, setNumberScansInFrame

Methods inherited from interface gda.factory.Findable

getName, setName

Methods inherited from interface gda.observable.IObservable

addIObserver, deleteIObserver, deleteIObservers

Methods inherited from interface gda.device.Scannable

asynchronousMoveTo, atCommandFailure, atLevelEnd, atLevelMoveStart, atLevelStart, atPointEnd, atPointStart, atScanEnd, atScanLineEnd, atScanLineStart, checkPositionValid, getExtraNames, getInputNames, getLevel, getOutputFormat, getPosition, getScanMetadataAttribute, getScanMetadataAttributeNames, getScanMetadataAttributes, isAt, isBusy, moveTo, setExtraNames, setInputNames, setLevel, setOutputFormat, setScanMetadataAttribute, setScanMetadataAttributes, stop, toFormattedString

Field Details

detectorData

protected DetectorData detectorData

currentScanParameter

protected EdeScanParameters currentScanParameter

currentDetector

protected EdeDetector currentDetector

dropFirstFrame

protected boolean dropFirstFrame

Constructor Details

EdeDetectorBase

protected EdeDetectorBase()

Method Details

configure

public void configure()
               throws FactoryException

Description copied from class: ConfigurableBase

Default implementation for classes that do not have to do any specific configuration.
Classes that do their own configuration should *not* call this superclass function, as it may cause the object to appear configured before it really is.

Specified by:

configure in interface Configurable

Overrides:

configure in class ConfigurableBase

Throws:

FactoryException - if there is an error in configuration e.g. required variable not set or cannot connect to device

atScanStart

public void atScanStart()
                 throws DeviceException

Description copied from class: ScannableBase

Called for every Scannable at the start of a group of nested scans (or a single scan if that is the case) Default behaviour is to do nothing. Inheriting classes have the option to implement this if their specific behaviour requires it.

Specified by:

atScanStart in interface Scannable

Overrides:

atScanStart in class ScannableBase

Throws:

DeviceException

See Also:

• Scannable.atScanStart()

prepareDetectorwithScanParameters

public void prepareDetectorwithScanParameters(EdeScanParameters newParameters)
                                       throws DeviceException

Specified by:

prepareDetectorwithScanParameters in interface EdeDetector

Throws:

DeviceException

configureDetectorForCollection

protected abstract void configureDetectorForCollection()
                                                throws DeviceException

Throws:

DeviceException

getMaxPixel

public abstract int getMaxPixel()

detector's maximum pixel size in energy direction.

Specified by:

getMaxPixel in interface EdeDetector

Returns:

maximum pixels of camera in energy direction

getNumberScansInFrame

public abstract int getNumberScansInFrame(double frameTime,
 double scanTime,
 int numberOfFrames)
                                   throws DeviceException

calculate the number of scans (TFG2 term) or accumulations in a single frame based on detector clock rate.

Specified by:

getNumberScansInFrame in interface EdeDetector

Parameters:

frameTime -

scanTime -

numberOfFrames -

Returns:

number of accumulations.

Throws:

DeviceException

fetchStatus

public abstract DetectorStatus fetchStatus()
                                    throws DeviceException

fetch detector status from hardware.

Specified by:

fetchStatus in interface EdeDetector

Returns:

DetectorStatus

Throws:

DeviceException

getDetectorData

public DetectorData getDetectorData()

Specified by:

getDetectorData in interface EdeDetector

getPixels

public Integer[] getPixels()

Specified by:

getPixels in interface EdeDetector

getEnergyForChannels

public double[] getEnergyForChannels()

Specified by:

getEnergyForChannels in interface EdeDetector

writeLiveDataFile

public void writeLiveDataFile()
                       throws DeviceException

Specified by:

writeLiveDataFile in interface EdeDetector

Throws:

DeviceException

createDatasetForPixel

public org.eclipse.january.dataset.DoubleDataset createDatasetForPixel()

Specified by:

createDatasetForPixel in interface EdeDetector

getStatus

public int getStatus()
              throws DeviceException

Description copied from interface: Detector

Returns the current collecting state of the device.

Specified by:

getStatus in interface Detector

Returns:

BUSY if the detector has not finished the requested operation(s), IDLE if in an completely idle state and STANDBY if temporarily suspended.

Throws:

DeviceException

readout

public NexusTreeProvider readout()
                          throws DeviceException

Reads the first frame only.

Specified by:

readout in interface Detector

Specified by:

readout in interface NexusDetector

Returns:

the data collected

Throws:

DeviceException

readFrames

public NexusTreeProvider[] readFrames(int startFrame,
 int finalFrame)
                               throws DeviceException

returns a list of NexusTreeProvider, one for each frame in the specified range.

Specified by:

readFrames in interface EdeDetector

Parameters:

startFrame -

finalFrame -

Returns:

list of NexusTreeProvider

Throws:

DeviceException

readoutFrames

public abstract int[] readoutFrames(int startFrame,
 int finalFrame)
                             throws DeviceException

implements the read out of frames from the actual detector used.

Specified by:

readoutFrames in interface EdeDetector

Parameters:

startFrame -

finalFrame -

Returns:

an 1D integer array containing all frames concatenated from start frame to the final frame inclusively.

Throws:

DeviceException

unpackRawDataToFrames

protected int[][] unpackRawDataToFrames(int[] scalerData,
 int numFrames)

setDetectorData

public void setDetectorData(DetectorData detectorData)

isDropFirstFrame

public boolean isDropFirstFrame()

Specified by:

isDropFirstFrame in interface EdeDetector

setDropFirstFrame

public void setDropFirstFrame(boolean dropFirstFrame)

getEnergyCalibration

public CalibrationDetails getEnergyCalibration()

Description copied from interface: EdeDetector

Returns the function used to convert channel number to energy. If not calibrated it should return a simple y = x function.

Specified by:

getEnergyCalibration in interface EdeDetector

Returns:

PolynomialFunction

setEnergyCalibration

public void setEnergyCalibration(CalibrationDetails energyCalibration)

Description copied from interface: EdeDetector

Set the energy calibration. The detector object should persist this between GDA server restarts.

Specified by:

setEnergyCalibration in interface EdeDetector

Parameters:

energyCalibration -

isEnergyCalibrationSet

public boolean isEnergyCalibrationSet()

Specified by:

isEnergyCalibrationSet in interface EdeDetector

setEnergyCalibrationSet

public void setEnergyCalibrationSet(boolean energyCalibrationSet)

getRois

public Roi[] getRois()

Description copied from interface: EdeDetector

Returns the regions in use, as defined by calls to setRois or setNumberRois

Specified by:

getRois in interface EdeDetector

Returns:

the array of regions

setRois

public void setRois(Roi[] rois)

Description copied from interface: EdeDetector

Ignoring the lower and upper channel properties, explicitly set the regions in use.

Specified by:

setRois in interface EdeDetector

Parameters:

rois -

getNumberOfRois

public int getNumberOfRois()

Specified by:

getNumberOfRois in interface EdeDetector

setNumberRois

public void setNumberRois(int numberOfRois)

Description copied from interface: EdeDetector

Set evenly sized regions of interest, ignoring channels outside of the lower and upper channel limits.

Specified by:

setNumberRois in interface EdeDetector

Parameters:

numberOfRois -

getLowerChannel

public int getLowerChannel()

Specified by:

getLowerChannel in interface EdeDetector

setLowerChannel

public void setLowerChannel(int lowerChannel)

Specified by:

setLowerChannel in interface EdeDetector

getUpperChannel

public int getUpperChannel()

Specified by:

getUpperChannel in interface EdeDetector

setUpperChannel

public void setUpperChannel(int upperChannel)

Specified by:

setUpperChannel in interface EdeDetector

getExcludedPixels

public Integer[] getExcludedPixels()

Return array of 'dead pixel' locations.

Specified by:

getExcludedPixels in interface EdeDetector

setExcludedPixels

public void setExcludedPixels(Integer[] excludedPixels)

Set array of dead pixel locations

Specified by:

setExcludedPixels in interface EdeDetector

Parameters:

excludedPixels -

getRoiFor

public int getRoiFor(int elementIndex)

Specified by:

getRoiFor in interface EdeDetector

setSynchroniseToBeamOrbit

public abstract void setSynchroniseToBeamOrbit(boolean synchroniseToBeamOrbit)

Specified by:

setSynchroniseToBeamOrbit in interface EdeDetector

getSynchroniseToBeamOrbit

public abstract boolean getSynchroniseToBeamOrbit()

Specified by:

getSynchroniseToBeamOrbit in interface EdeDetector

setSynchroniseBeamOrbitDelay

public abstract void setSynchroniseBeamOrbitDelay(int synchroniseBeamOrbitDelay)
                                           throws DeviceException

Specified by:

setSynchroniseBeamOrbitDelay in interface EdeDetector

Throws:

DeviceException

getSynchroniseBeamOrbitDelay

public abstract int getSynchroniseBeamOrbitDelay()

Specified by:

getSynchroniseBeamOrbitDelay in interface EdeDetector

setOrbitWaitMethod

public abstract void setOrbitWaitMethod(String methodString)

Specified by:

setOrbitWaitMethod in interface EdeDetector

getOrbitWaitMethod

public abstract String getOrbitWaitMethod()

Specified by:

getOrbitWaitMethod in interface EdeDetector

setDetectorSetupType

public void setDetectorSetupType(DetectorSetupType detectorSetupType)

Specified by:

setDetectorSetupType in interface EdeDetector

getDetectorSetupType

public DetectorSetupType getDetectorSetupType()

Specified by:

getDetectorSetupType in interface EdeDetector

isCheckForExcludedStrips

public boolean isCheckForExcludedStrips()

Returns:

true if excluded pixels are set to zero in the detector data.

setCheckForExcludedStrips

public void setCheckForExcludedStrips(boolean checkForExcludedStrips)

If set to true, detector data will have counts for 'excluded' pixels set to zero. Excluded pixels are those defined by setExcludedPixels(Integer[]) or outside of lower and upper channels.

Note that pixels outside of ROI range are only excluded if currentScanParameter.getIncludeCountsOutsideROIs() also returns true.

Parameters:

checkForExcludedStrips -

setAccumulationReadoutTime

public void setAccumulationReadoutTime(double timeSec)

Description copied from interface: EdeDetector

Set the accumulation readout time

Specified by:

setAccumulationReadoutTime in interface EdeDetector

getAccumulationReadoutTime

public double getAccumulationReadoutTime()

Specified by:

getAccumulationReadoutTime in interface EdeDetector

Returns:

Accumulation readout time (in seconds)

getMaxNumFramesToRead

public int getMaxNumFramesToRead()

Specified by:

getMaxNumFramesToRead in interface EdeDetector

setMaxNumFramesToRead

public void setMaxNumFramesToRead(int maxNumberOfFramesToRead)

getCompressionLevel

public int getCompressionLevel()

setCompressionLevel

public void setCompressionLevel(int compressionLevel)

Compression level to use for datasets in the Nexus file :

0 -> no compression

1 -> LZW compression

Parameters:

compressionLevel -