Package gda.scan

Class EdeScan

java.lang.Object

gda.scan.ScanBase

gda.scan.ConcurrentScanChild

gda.scan.EdeScan

All Implemented Interfaces:

EnergyDispersiveExafsScan, IConcurrentScanChild, NestableScan, Scan, ScanChild, Serializable

Direct Known Subclasses:

EdeScanWithTFGTrigger

public class EdeScan
extends ConcurrentScanChild
implements EnergyDispersiveExafsScan

Runs a single set of timing groups for EDE through the XSTRIP DAServer interface.

So this: moves sample to correct position, waits for top-up to pass (if required), opens/closes shutter, runs the timing groups through the TFG unit and writes data to given Nexus file.

Also holds data in memory for quick retrieval for online data.

This starts immediately and does not take sample environment triggering

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class gda.scan.ConcurrentScanChild

ConcurrentScanChild.PointPositionInLine

Nested classes/interfaces inherited from class gda.scan.ScanBase

ScanBase.ParentScanComponent

Nested classes/interfaces inherited from interface gda.scan.Scan

Scan.ScanStatus

Field Summary

Fields

Modifier and Type	Field	Description
protected EdeScanPosition	motorPositions
protected final List<ScanDataPoint>	rawData
protected EdeScanParameters	scanParameters
protected EdeScanType	scanType
protected final EdeDetector	theDetector
protected final TopupChecker	topupChecker

Fields inherited from class gda.scan.ConcurrentScanChild

allChildScans, allScanObjects, detectorReadoutTask, scannableLevels

Fields inherited from class gda.scan.ScanBase

allDetectors, allScannables, callCollectDataOnDetectors, child, command, currentPointCount, GDA_SCANBASE_FIRST_SCAN_NUMBER_FOR_TEST, GDA_SCANBASE_PRINT_TIMESTAMP_TO_TERMINAL, instrument, isChild, name, numberOfChildScans, parent, parentComponent, permissionLevel, scanDataPointPipeline, stepId, totalNumberOfPoints

Constructor Summary

Constructors

Constructor	Description
EdeScan(EdeScanParameters scanParameters, EdeScanPosition motorPositions, EdeScanType scanType, EdeDetector theDetector, Integer repetitionNumber, Scannable shutter, TopupChecker topupChecker)

Method Summary

Modifier and Type	Method	Description
protected void	addDetectorsToScanDataPoint(int lowFrame, Object[] detData, int thisFrame, ScanDataPoint thisPoint)
void	addScannableToMonitorDuringScan(Scannable scannableToMonitorDuringScan)
protected void	collectDetectorData()
void	doCollection()	The method in which the work of the scan is performed.
org.eclipse.january.dataset.DoubleDataset	extractDetectorDataSet(int spectrumIndex)
org.eclipse.january.dataset.DoubleDataset	extractEnergyDetectorDataSet()
org.eclipse.january.dataset.DoubleDataset	extractLastDetectorDataSet()
void	fastShutterMoveTo(String position)	Move the fast shutter to specified position (e.g.
String	getCommand()
List<ScanDataPoint>	getData()
List<ScanDataPoint>	getDataPoints(int firstFrame, int lastFrame)
EdeDetector	getDetector()
int	getDimension()	default implementation.
Scannable	getFastShutter()
String	getHeaderDescription()
EdeScanPosition	getMotorPositions()
int	getNumberOfAvailablePoints()
Collection<Scannable>	getScannablesToMonitorDuringScan()
EdeScanParameters	getScanParameters()
EdeScanType	getScanType()
double	getSleepTimeAfterCollection()
int	getTotalNumberOfPoints()	The total number of points in the multi-dimesional scan i.e.
boolean	gsUseFastShutter()
boolean	isIncludeGroupNumberInSDPLabel()
protected ScanObject	isScannableToBeMoved(Scannable scannable)	Asks if the given scannable is part of the array of scannables which this scan is to operate in its moveToStarts and moveBySteps methods.
boolean	isSmartstop()
boolean	isUseNexusTreeWriter()
protected void	moveSampleIntoPosition()
protected void	moveShutter(String position)
protected void	pollDetectorAndFetchData()
protected NexusTreeProvider[]	readDetectors(int lowFrame, int highFrame)
void	setFastShutter(Scannable fastShutter)
void	setIncludeCyclePlotLabel(boolean includeGroupNumberInSDPLabel)
void	setMotorPositions(EdeScanPosition motorPositions)
void	setNoOfSecPerSpectrumToPublish(double noOfSecPerSpectrumToPublish)
void	setProgressUpdater(gda.observable.IObserver progressUpdater)
void	setScannablesToMonitorDuringScan(Collection<Scannable> scannablesToMonitorDuringScan)
void	setScanParameters(EdeScanParameters scanParameters)
void	setScanType(EdeScanType scanType)
void	setSmartstop(boolean smartstop)
void	setStatus(Scan.ScanStatus status)	To allow nests of scans to share a common status with each other.
void	setUseFastShutter(boolean useFastShutter)
void	setUseNexusTreeWriter(boolean useNexusTreeWriter)
void	setWaitTimeAfterCollection(double waitTimeAfterCollection)	How long to wait for after collection has finished
protected boolean	smartStopDetected()	Log and display a message about current cycle to be skipped if smart stop has been selected.
String	toString()
protected void	validate()
protected void	waitAfterCollection()	Sleep for waitTimeAfterCollection seconds - if smart stop is not set to true.
protected void	waitBeforeCycle()	For 'light It' measurement wait for required time if TimingGroup.getPreceedingTimeDelay() is > 0.

Methods inherited from class gda.scan.ConcurrentScanChild

acquirePoint, cancelReadoutAndPublishCompletion, checkAllMovesComplete, generateDevicesToMoveByLevel, getAllChildScans, getAllDetectors, getAllScannables, getAllScanObjects, getChild, getPointPositionInLine, getScannableLevels, isMustBeFinal, isReadoutConcurrent, isScannableActuallyToBeMoved, readoutDetectorsAndPublish, reorderAllScanObjects, setAllChildScans, setAllDetectors, setAllScannables, setAllScanObjects, setChild, setCommand, setMustBeFinal, setPointPositionInLine, setScannableLevels, setTotalNumberOfPoints, setUp, waitForDetectorReadoutAndPublishCompletion

Methods inherited from class gda.scan.ScanBase

callAtCommandFailureHooks, callDetectorsEndCollection, callScannablesAtScanEnd, callScannablesAtScanLineEnd, callScannablesAtScanLineStart, callScannablesAtScanStart, checkStartStopStep, checkThreadInterrupted, collectData, createScanDataPoint, createScanDataPointPipeline, createScanDataPointPipeline, endScan, generateRandomName, getDataWriter, getDetectors, getDimensions, getName, getNumberOfChildScans, getParent, getPositionCallableThreadPoolSize, getScanDataPointPipeline, getScanDataPointQueueLength, getScanInformation, getScannables, getScanNumber, getScanPlotSettings, getStatus, getStepId, getStepIds, isChild, isFinishEarlyRequested, isLineScanNeedsDoing, notifyServer, notifyServer, numberOfScannablesThatCanProvidePositionCallables, pause, prepareDevicesForCollection, prepareForCollection, prepareScanForCollection, prepareScanNumber, prepareStaticVariables, readDevicesAndPublishScanDataPoint, reorderScannables, representThrowable, requestFinishEarly, resume, run, runScan, scanRunning, sendScanEvent, setChild, setDataWriter, setDetectors, setIsChild, setLineScanNeedsDoing, setNumberOfChildScans, setParent, setPositionCallableThreadPoolSize, setScanDataPointPipeline, setScanDataPointQueueLength, setScanIdentifierInScanDataPoint, setScannables, setScanNumber, setScanPlotSettings, setStatus, setStepId, shutdownScandataPipeline, signalScanComplete, signalScanStarted, sortArguments, waitIfPaused, wasScanExplicitlyHalted, wrappedException

Methods inherited from class java.lang.Object

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

Methods inherited from interface gda.scan.Scan

getDataWriter, getDetectors, getName, getScanDataPointPipeline, getScanInformation, getScannables, getScanNumber, getScanPlotSettings, getStatus, getStepId, isChild, isFinishEarlyRequested, pause, prepareForCollection, requestFinishEarly, resume, run, runScan, setChild, setDataWriter, setDetectors, setIsChild, setScanDataPointPipeline, setScannables, setScanPlotSettings, setStepId

Methods inherited from interface gda.scan.ScanChild

getParent, setParent

Field Details

theDetector

protected final EdeDetector theDetector

rawData

protected final List<ScanDataPoint> rawData

scanParameters

protected EdeScanParameters scanParameters

motorPositions

protected EdeScanPosition motorPositions

scanType

protected EdeScanType scanType

topupChecker

protected final TopupChecker topupChecker

Constructor Details

EdeScan

public EdeScan(EdeScanParameters scanParameters,
 EdeScanPosition motorPositions,
 EdeScanType scanType,
 EdeDetector theDetector,
 Integer repetitionNumber,
 Scannable shutter,
 TopupChecker topupChecker)

Parameters:

scanParameters - - timing parameters of the data collection

motorPositions - -

scanType -

theDetector -

repetitionNumber - - if this is a negative number then frame index columns will not be added to the output. Useful for single spectrum scans where such indexing is meaningless.

shutter -

Method Details

toString

public String toString()

Overrides:

toString in class Object

getHeaderDescription

public String getHeaderDescription()

Specified by:

getHeaderDescription in interface EnergyDispersiveExafsScan

getDimension

public int getDimension()

Description copied from class: ScanBase

default implementation. Classes that derive from ScanBase which want to support the reporting of scan dimensions -@see getDimensions need to override this method

Specified by:

getDimension in interface Scan

Overrides:

getDimension in class ScanBase

Returns:

the number of points of this scan object - the whole scan execution can be a hierarchy of parent scan objects and layers of child scan objects

See Also:

• ConcurrentScan

getNumberOfAvailablePoints

public int getNumberOfAvailablePoints()

setProgressUpdater

public void setProgressUpdater(gda.observable.IObserver progressUpdater)

Specified by:

setProgressUpdater in interface EnergyDispersiveExafsScan

getDataPoints

public List<ScanDataPoint> getDataPoints(int firstFrame,
 int lastFrame)

isScannableToBeMoved

protected ScanObject isScannableToBeMoved(Scannable scannable)

Description copied from class: ConcurrentScanChild

Asks if the given scannable is part of the array of scannables which this scan is to operate in its moveToStarts and moveBySteps methods. If true returns the ScanObject else returns null.

Overrides:

isScannableToBeMoved in class ConcurrentScanChild

Parameters:

scannable -

Returns:

the ScanObject

fastShutterMoveTo

public void fastShutterMoveTo(String position)
                       throws DeviceException,
InterruptedException

Move the fast shutter to specified position (e.g. "Open" , "Close" ) moveTo doesn't block so sleep until shutter has actually moved to the new position is also implemented here

Parameters:

position -

Throws:

DeviceException

InterruptedException

Since:

28/1/2016.

moveShutter

protected void moveShutter(String position)
                    throws DeviceException,
InterruptedException

Throws:

DeviceException

InterruptedException

doCollection

public void doCollection()
                  throws Exception

Description copied from interface: Scan

The method in which the work of the scan is performed. This method assumes that the data handler has already been created and the baton claimed.

Specified by:

doCollection in interface Scan

Specified by:

doCollection in class ScanBase

Throws:

Exception

smartStopDetected

protected boolean smartStopDetected()

Log and display a message about current cycle to be skipped if smart stop has been selected.

Returns:

true if smartStop is active.

waitAfterCollection

protected void waitAfterCollection()
                            throws InterruptedException

Sleep for waitTimeAfterCollection seconds - if smart stop is not set to true. (To be run after data collection to implement 'wait time between cycles').

Throws:

InterruptedException

waitBeforeCycle

protected void waitBeforeCycle()
                        throws InterruptedException

For 'light It' measurement wait for required time if TimingGroup.getPreceedingTimeDelay() is > 0.

Throws:

InterruptedException

collectDetectorData

protected void collectDetectorData()
                            throws Exception

Throws:

Exception

pollDetectorAndFetchData

protected void pollDetectorAndFetchData()
                                 throws DeviceException,
Exception

Throws:

DeviceException

Exception

moveSampleIntoPosition

protected void moveSampleIntoPosition()
                               throws DeviceException,
InterruptedException

Throws:

DeviceException

InterruptedException

getCommand

public String getCommand()

Specified by:

getCommand in interface IConcurrentScanChild

Overrides:

getCommand in class ConcurrentScanChild

Returns:

Returns the command.

getTotalNumberOfPoints

public int getTotalNumberOfPoints()

Description copied from interface: IConcurrentScanChild

The total number of points in the multi-dimesional scan i.e. the number of ScanDataPoints which would need displaying/recording

Specified by:

getTotalNumberOfPoints in interface IConcurrentScanChild

Specified by:

getTotalNumberOfPoints in interface Scan

Overrides:

getTotalNumberOfPoints in class ScanBase

Returns:

the total number of nodes at which data will be collected in this scan. This includes all the dimensions in a multi-dimensional scan.

validate

protected void validate()
                 throws IllegalArgumentException

Throws:

IllegalArgumentException

getScannablesToMonitorDuringScan

public Collection<Scannable> getScannablesToMonitorDuringScan()

setScannablesToMonitorDuringScan

public void setScannablesToMonitorDuringScan(Collection<Scannable> scannablesToMonitorDuringScan)

addScannableToMonitorDuringScan

public void addScannableToMonitorDuringScan(Scannable scannableToMonitorDuringScan)

addDetectorsToScanDataPoint

protected void addDetectorsToScanDataPoint(int lowFrame,
 Object[] detData,
 int thisFrame,
 ScanDataPoint thisPoint)
                                    throws DeviceException

Throws:

DeviceException

readDetectors

protected NexusTreeProvider[] readDetectors(int lowFrame,
 int highFrame)
                                     throws Exception,
DeviceException

Throws:

Exception

DeviceException

isIncludeGroupNumberInSDPLabel

public boolean isIncludeGroupNumberInSDPLabel()

setIncludeCyclePlotLabel

public void setIncludeCyclePlotLabel(boolean includeGroupNumberInSDPLabel)

extractLastDetectorDataSet

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

extractEnergyDetectorDataSet

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

Specified by:

extractEnergyDetectorDataSet in interface EnergyDispersiveExafsScan

extractDetectorDataSet

public org.eclipse.january.dataset.DoubleDataset extractDetectorDataSet(int spectrumIndex)

Specified by:

extractDetectorDataSet in interface EnergyDispersiveExafsScan

getData

public List<ScanDataPoint> getData()

Specified by:

getData in interface EnergyDispersiveExafsScan

getScanParameters

public EdeScanParameters getScanParameters()

Specified by:

getScanParameters in interface EnergyDispersiveExafsScan

setScanParameters

public void setScanParameters(EdeScanParameters scanParameters)

Specified by:

setScanParameters in interface EnergyDispersiveExafsScan

getMotorPositions

public EdeScanPosition getMotorPositions()

setMotorPositions

public void setMotorPositions(EdeScanPosition motorPositions)

getScanType

public EdeScanType getScanType()

Specified by:

getScanType in interface EnergyDispersiveExafsScan

setScanType

public void setScanType(EdeScanType scanType)

Specified by:

setScanType in interface EnergyDispersiveExafsScan

getDetector

public EdeDetector getDetector()

Specified by:

getDetector in interface EnergyDispersiveExafsScan

isSmartstop

public boolean isSmartstop()

setSmartstop

public void setSmartstop(boolean smartstop)

gsUseFastShutter

public boolean gsUseFastShutter()

setUseFastShutter

public void setUseFastShutter(boolean useFastShutter)

getFastShutter

public Scannable getFastShutter()

setFastShutter

public void setFastShutter(Scannable fastShutter)

isUseNexusTreeWriter

public boolean isUseNexusTreeWriter()

setUseNexusTreeWriter

public void setUseNexusTreeWriter(boolean useNexusTreeWriter)

setNoOfSecPerSpectrumToPublish

public void setNoOfSecPerSpectrumToPublish(double noOfSecPerSpectrumToPublish)

getSleepTimeAfterCollection

public double getSleepTimeAfterCollection()

setWaitTimeAfterCollection

public void setWaitTimeAfterCollection(double waitTimeAfterCollection)

How long to wait for after collection has finished

Parameters:

waitTimeAfterCollection - (time in seconds)

setStatus

void setStatus(Scan.ScanStatus status)

To allow nests of scans to share a common status with each other.

Parameters:

status -