Integrate single-crystal peaks in reciprocal-space. More...

#include <IntegratePeaksMD2.h>

Inheritance diagram for Mantid::MDAlgorithms::IntegratePeaksMD2:

Public Member Functions
const std::string	category () const override
	Algorithm's category for identification. More...

const std::string	name () const override
	Algorithm's name for identification. More...

const std::vector< std::string >	seeAlso () const override
	Function to return all of the seeAlso (these are not validated) algorithms related to this algorithm.A default implementation is provided. More...

const std::string	summary () const override
	Summary of algorithms purpose. More...

int	version () const override
	Algorithm's version for identification. More...

Public Member Functions inherited from Mantid::API::Algorithm
	Algorithm ()
	Constructor. More...

	Algorithm (const Algorithm &)=delete

Algorithm &	operator= (const Algorithm &)=delete

	~Algorithm () override
	Virtual destructor. More...

void	initialize () override
	Initialization method invoked by the framework. More...

bool	execute () override final
	The actions to be performed by the algorithm on a dataset. More...

void	addTimer (const std::string &name, const Kernel::time_point_ns &begin, const Kernel::time_point_ns &end)

void	executeAsChildAlg () override
	Execute as a Child Algorithm. More...

ExecutionState	executionState () const override
	Gets the current execution state. More...

ResultState	resultState () const override
	Gets the current result State. More...

bool	isInitialized () const override
	Has the Algorithm already been initialized. More...

bool	isExecuted () const override
	Has the Algorithm already been executed successfully. More...

bool	isRunning () const override
	True if the algorithm is running. More...

bool	isReadyForGarbageCollection () const override
	True if the algorithm is ready for garbage collection. More...

bool	isChild () const override
	To query whether algorithm is a child. More...

void	setChild (const bool isChild) override
	To set whether algorithm is a child. More...

void	enableHistoryRecordingForChild (const bool on) override
	Change the state of the history recording flag. More...

bool	isRecordingHistoryForChild ()

void	setAlwaysStoreInADS (const bool doStore) override
	Do we ALWAYS store in the AnalysisDataService? This is set to true for python algorithms' child algorithms. More...

bool	getAlwaysStoreInADS () const override
	Returns true if we always store in the AnalysisDataService. More...

void	setRethrows (const bool rethrow) override
	Set whether the algorithm will rethrow exceptions. More...

Poco::ActiveResult< bool >	executeAsync () override
	Asynchronous execution. More...

void	addObserver (const Poco::AbstractObserver &observer) const override
	Add an observer for a notification. More...

void	removeObserver (const Poco::AbstractObserver &observer) const override
	Remove an observer. More...

void	cancel () override
	Raises the cancel flag. More...

bool	getCancel () const
	Returns the cancellation state. More...

Kernel::Logger &	getLogger () const
	Returns a reference to the logger. More...

void	setLogging (const bool value) override
	Logging can be disabled by passing a value of false. More...

bool	isLogging () const override
	returns the status of logging, True = enabled More...

void	setLoggingOffset (const int value) override
	gets the logging priority offset More...

int	getLoggingOffset () const override
	returns the logging priority offset More...

void	setAlgStartupLogging (const bool enabled) override
	disable Logging of start and end messages More...

bool	getAlgStartupLogging () const override
	get the state of Logging of start and end messages More...

void	setChildStartProgress (const double startProgress) const override
	setting the child start progress More...

void	setChildEndProgress (const double endProgress) const override
	setting the child end progress More...

std::string	toString () const override
	Serialize an object to a string. More...

::Json::Value	toJson () const override
	Serialize an object to a json object. More...

virtual std::shared_ptr< Algorithm >	createChildAlgorithm (const std::string &name, const double startProgress=-1., const double endProgress=-1., const bool enableLogging=true, const int &version=-1)
	Create a Child Algorithm. More...

void	setupAsChildAlgorithm (const Algorithm_sptr &algorithm, const double startProgress=-1., const double endProgress=-1., const bool enableLogging=true)
	Setup algorithm as child algorithm. More...

void	trackAlgorithmHistory (std::shared_ptr< AlgorithmHistory > parentHist)
	set whether we wish to track the child algorithm's history and pass it the parent object to fill. More...

void	findWorkspaces (WorkspaceVector &workspaces, unsigned int direction, bool checkADS=false) const
	Populate lists of the workspace properties for a given direction (InOut workspaces are included in both input/output) More...

virtual bool	checkGroups ()
	Check the input workspace properties for groups. More...

virtual bool	processGroups ()
	Process WorkspaceGroup inputs. More...

void	copyNonWorkspaceProperties (IAlgorithm *alg, int periodNum)
	Copy all the non-workspace properties from this to alg. More...

const Parallel::Communicator &	communicator () const
	Returns a const reference to the (MPI) communicator of the algorithm. More...

void	setCommunicator (const Parallel::Communicator &communicator)
	Sets the (MPI) communicator of the algorithm. More...

void	declareProperty (std::unique_ptr< Kernel::Property > p, const std::string &doc="") override
	Add a property to the list of managed properties. More...

void	declareOrReplaceProperty (std::unique_ptr< Kernel::Property > p, const std::string &doc="") override
	Add or replace property in the list of managed properties. More...

void	resetProperties () override
	Reset property values back to initial values (blank or default values) More...

void	setProperties (const std::string &propertiesJson, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false) override
	Set the ordered list of properties by one string of values, separated by semicolons. More...

void	setProperties (const ::Json::Value &jsonValue, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false) override
	Sets all the declared properties from a json object. More...

void	setPropertiesWithString (const std::string &propertiesString, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >()) override
	Sets all the declared properties from a string. More...

void	setPropertyValue (const std::string &name, const std::string &value) override
	Set the value of a property by string N.B. More...

void	setPropertyValueFromJson (const std::string &name, const Json::Value &value) override
	Set the value of a property by Json::Value object. More...

void	setPropertyOrdinal (const int &index, const std::string &value) override
	Set the value of a property by an index N.B. More...

virtual void	copyPropertiesFrom (const Algorithm &alg)
	Make m_properties point to the same PropertyManager as alg.m_properties. More...

bool	existsProperty (const std::string &name) const override
	Checks whether the named property is already in the list of managed property. More...

bool	validateProperties () const override
	Validates all the properties in the collection. More...

size_t	propertyCount () const override
	Count the number of properties under management. More...

std::string	getPropertyValue (const std::string &name) const override
	Get the value of a property as a string. More...

const std::vector< Kernel::Property * > &	getProperties () const override
	Get the list of managed properties. More...

std::vector< std::string >	getDeclaredPropertyNames () const noexcept override
	Return the list of declared property names. More...

TypedValue	getProperty (const std::string &name) const override
	Get the value of a property. More...

std::string	asString (bool withDefaultValues=false) const override
	Return the property manager serialized as a string. More...

::Json::Value	asJson (bool withDefaultValues=false) const override
	Return the property manager serialized as a json object. More...

bool	isDefault (const std::string &name) const

void	removeProperty (const std::string &name, const bool delproperty=true) override
	Removes the property from management. More...

std::unique_ptr< Kernel::Property >	takeProperty (const size_t index) override
	Removes the property from management and returns a pointer to it. More...

void	clear () override
	Clears all properties under management. More...

void	afterPropertySet (const std::string &) override
	Override this method to perform a custom action right after a property was set. More...

void	filterByTime (const Types::Core::DateAndTime &, const Types::Core::DateAndTime &) override

void	splitByTime (std::vector< Kernel::SplittingInterval > &, std::vector< Kernel::PropertyManager * >) const override

void	filterByProperty (const Kernel::TimeSeriesProperty< bool > &, const std::vector< std::string > &) override

Kernel::Property *	getPointerToProperty (const std::string &name) const override
	Get a property by name. More...

Kernel::Property *	getPointerToPropertyOrdinal (const int &index) const override
	Get a property by an index. More...

virtual void	declareProperty (std::unique_ptr< Property > p, const std::string &doc="")=0
	Function to declare properties (i.e. store them) More...

template<typename T >
void	declareProperty (const std::string &name, T value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc="", const unsigned int direction=Direction::Input)
	Add a property of the template type to the list of managed properties. More...

template<typename T >
void	declareProperty (const std::string &name, T value, const std::string &doc, const unsigned int direction=Direction::Input)
	Add a property to the list of managed properties with no validator. More...

template<typename T >
void	declareProperty (const std::string &name, T value, const unsigned int direction)
	Add a property of the template type to the list of managed properties. More...

void	declareProperty (const std::string &name, const char *value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc=std::string(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...

void	declareProperty (const std::string &name, const char *value, const std::string &doc, IValidator_sptr validator=std::make_shared< NullValidator >(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...

void	declareProperty (const std::string &name, const char *value, const unsigned int direction)
	Add a property of string type to the list of managed properties. More...

const std::vector< std::string >	categories () const override
	Function to return all of the categories that contain this algorithm. More...

const std::string	categorySeparator () const override
	Function to return the separator token for the category string. More...

const std::string	alias () const override
	function to return any aliases to the algorithm; A default implementation is provided More...

const std::string	aliasDeprecated () const override
	Expiration date (in ISO8601 format) for the algorithm aliases; default implementation for no expiration date. More...

const std::string	helpURL () const override
	function to return URL for algorithm documentation; A default implementation is provided. More...

template<typename T , typename = typename std::enable_if<std::is_convertible<T , MatrixWorkspace >::value>::type>
std::tuple< std::shared_ptr< T >, Indexing::SpectrumIndexSet >	getWorkspaceAndIndices (const std::string &name) const

template<typename T1 , typename T2 , typename = typename std::enable_if<std::is_convertible<T1 , MatrixWorkspace >::value>::type, typename = typename std::enable_if<std::is_convertible<T2 , std::string >::value \|\| std::is_convertible<T2 , std::vector<int64_t> >::value>::type>
void	setWorkspaceInputProperties (const std::string &name, const std::shared_ptr< T1 > &wksp, IndexType type, const T2 &list)

template<typename T1 , typename T2 , typename = typename std::enable_if<std::is_convertible<T1 , MatrixWorkspace >::value>::type, typename = typename std::enable_if<std::is_convertible<T2 , std::string >::value \|\| std::is_convertible<T2 , std::vector<int64_t> >::value>::type>
void	setWorkspaceInputProperties (const std::string &name, const std::string &wsName, IndexType type, const T2 &list)

const std::string	workspaceMethodName () const override

const std::vector< std::string >	workspaceMethodOn () const override

const std::string	workspaceMethodInputProperty () const override

AlgorithmID	getAlgorithmID () const override
	Algorithm ID. More...

virtual void	addObserver (const Poco::AbstractObserver &observer) const =0
	Add an observer for a notification. More...

virtual const std::string	alias () const =0
	function to return any aliases of the algorithm. More...

virtual const std::string	aliasDeprecated () const =0
	Expiration date (in ISO8601 format) for the algorithm aliases. Empty if no expiration date. More...

virtual void	cancel ()=0
	Raises the cancel flag. More...

virtual const std::vector< std::string >	categories () const =0
	Function to return all of the categories that contain this algorithm. More...

virtual const std::string	category () const =0
	function to return a category of the algorithm. More...

virtual const std::string	categorySeparator () const =0
	Function to return the separator token for the category string. More...

virtual void	enableHistoryRecordingForChild (const bool on)=0
	If true history will be recorded for a child. More...

virtual bool	execute ()=0
	System execution. More...

virtual void	executeAsChildAlg ()=0
	Execute as a Child Algorithm, with try/catch. More...

virtual Poco::ActiveResult< bool >	executeAsync ()=0
	Asynchronous execution of the algorithm. More...

virtual ExecutionState	executionState () const =0
	Gets the current execution state. More...

virtual AlgorithmID	getAlgorithmID () const =0
	Algorithm ID. More...

virtual bool	getAlgStartupLogging () const =0
	get the state of Logging of start and end messages More...

virtual bool	getAlwaysStoreInADS () const =0
	To query whether the output is stored in the analysis data service. More...

virtual int	getLoggingOffset () const =0
	returns the logging priority offset More...

virtual const std::string	helpURL () const =0
	function to return an optional URL for documentation. More...

virtual void	initialize ()=0
	Initialization method invoked by the framework. More...

virtual bool	isChild () const =0
	To query whether algorithm is a child. Default to false. More...

virtual bool	isExecuted () const =0
	Check whether the algorithm has been executed sucessfully. More...

virtual bool	isInitialized () const =0
	Check whether the algorithm is initialized properly. More...

virtual bool	isLogging () const =0
	returns the status of logging, True = enabled More...

virtual bool	isReadyForGarbageCollection () const =0
	True if the algorithm is ready for garbage collection. More...

virtual bool	isRunning () const =0
	True if the algorithm is running. More...

virtual const std::string	name () const =0
	function to return a name of the algorithm, must be overridden in all algorithms More...

virtual void	removeObserver (const Poco::AbstractObserver &observer) const =0
	Remove an observer. More...

virtual ResultState	resultState () const =0
	Gets the currnet result State. More...

virtual const std::vector< std::string >	seeAlso () const =0
	Function to return all of the seeAlso algorithms related to this algorithm. More...

virtual void	setAlgStartupLogging (const bool enabled)=0
	disable Logging of start and end messages More...

virtual void	setAlwaysStoreInADS (const bool doStore)=0
	Set whether we always store the output in the analysis data service. More...

virtual void	setChild (const bool isChild)=0
	To set whether algorithm is a child. More...

virtual void	setChildEndProgress (const double endProgress) const =0
	setting the child end progress More...

virtual void	setChildStartProgress (const double startProgress) const =0
	setting the child start progress More...

virtual void	setLogging (const bool value)=0
	Logging can be disabled by passing a value of false. More...

virtual void	setLoggingOffset (const int value)=0
	gets the logging priority offset More...

virtual void	setRethrows (const bool rethrow)=0
	To query whether an algorithm should rethrow exceptions when executing. More...

virtual const std::string	summary () const =0
	function returns a summary message that will be displayed in the default GUI, and in the help. More...

virtual ::Json::Value	toJson () const =0
	Serialize an algorithm as Json. More...

virtual std::string	toString () const =0
	Serialize an algorithm. More...

virtual std::map< std::string, std::string >	validateInputs ()=0
	Method checking errors on ALL the inputs, before execution. More...

virtual int	version () const =0
	function to return a version of the algorithm, must be overridden in all algorithms More...

Algorithms As Methods
Public Member Functions inherited from Mantid::Kernel::IPropertyManager
virtual ::Json::Value	asJson (bool withDefaultValues=false) const =0
	Return the property manager serialized as a json object. More...

virtual std::string	asString (bool withDefaultValues=false) const =0
	Return the property manager serialized as a string. More...

virtual void	declareOrReplaceProperty (std::unique_ptr< Property > p, const std::string &doc="")=0
	Function to declare properties (i.e. store them) More...

void	declareProperty (const std::string &name, const char *value, const std::string &doc, IValidator_sptr validator=std::make_shared< NullValidator >(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...

void	declareProperty (const std::string &name, const char *value, const unsigned int direction)
	Add a property of string type to the list of managed properties. More...

void	declareProperty (const std::string &name, const char *value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc=std::string(), const unsigned int direction=Direction::Input)
	Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...

template<typename T >
void	declareProperty (const std::string &name, T value, const std::string &doc, const unsigned int direction=Direction::Input)
	Add a property to the list of managed properties with no validator. More...

template<typename T >
void	declareProperty (const std::string &name, T value, const unsigned int direction)
	Add a property of the template type to the list of managed properties. More...

template<typename T >
void	declareProperty (const std::string &name, T value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc="", const unsigned int direction=Direction::Input)
	Add a property of the template type to the list of managed properties. More...

virtual void	declareProperty (std::unique_ptr< Property > p, const std::string &doc="")=0
	Function to declare properties (i.e. store them) More...

virtual bool	existsProperty (const std::string &name) const =0
	Checks whether the named property is already in the list of managed property. More...

virtual void	filterByProperty (const TimeSeriesProperty< bool > &, const std::vector< std::string > &)=0

virtual void	filterByTime (const Types::Core::DateAndTime &, const Types::Core::DateAndTime &)=0

virtual std::vector< std::string >	getDeclaredPropertyNames () const noexcept=0
	Get the list of managed property names. More...

virtual Property *	getPointerToProperty (const std::string &name) const =0
	Get a pointer to property by name. More...

virtual const std::vector< Property * > &	getProperties () const =0
	Get the list of managed properties. More...

std::vector< Property * >	getPropertiesInGroup (const std::string &group) const
	Get the list of managed properties in a given group. More...

virtual TypedValue	getProperty (const std::string &name) const =0
	Get the value of a property. More...

virtual std::string	getPropertyValue (const std::string &name) const =0
	Get the value of a property as a string. More...

virtual size_t	propertyCount () const =0
	Returns the number of properties under management. More...

virtual void	removeProperty (const std::string &name, const bool delproperty=true)=0
	Removes the property from management. More...

virtual void	resetProperties ()=0

virtual void	setProperties (const ::Json::Value &jsonValue, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false)=0
	Sets all the properties from a json object. More...

virtual void	setProperties (const std::string &propertiesJson, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false)=0
	Sets all properties from a string. More...

virtual void	setPropertiesWithString (const std::string &propertiesString, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >())=0
	Sets all the declared properties from a string. More...

IPropertyManager *	setProperty (const std::string &name, const char *value)
	Specialised version of setProperty template method to handle const char *. More...

IPropertyManager *	setProperty (const std::string &name, const std::string &value)
	Specialised version of setProperty template method to handle std::string. More...

template<typename T >
IPropertyManager *	setProperty (const std::string &name, const T &value)
	Templated method to set the value of a PropertyWithValue. More...

template<typename T >
IPropertyManager *	setProperty (const std::string &name, std::unique_ptr< T > value)
	Templated method to set the value of a PropertyWithValue from a std::unique_ptr. More...

void	setPropertyGroup (const std::string &name, const std::string &group)
	Set the group for a given property. More...

virtual void	setPropertyOrdinal (const int &index, const std::string &value)=0
	Set the value of a property by an index. More...

void	setPropertySettings (const std::string &name, std::unique_ptr< IPropertySettings > settings)

virtual void	setPropertyValue (const std::string &name, const std::string &value)=0
	Sets property value from a string. More...

virtual void	setPropertyValueFromJson (const std::string &name, const Json::Value &value)=0
	Sets property value from a Json::Value. More...

virtual void	splitByTime (std::vector< SplittingInterval > &, std::vector< PropertyManager * >) const =0

virtual std::unique_ptr< Property >	takeProperty (const size_t index)=0
	Removes the property from management and returns a pointer to it. More...

void	updatePropertyValues (const IPropertyManager &other)
	Update values of the existing properties. More...

virtual bool	validateProperties () const =0
	Validates all the properties in the collection. More...

virtual	~IPropertyManager ()=default

Private Member Functions
void	calcCovar (const std::vector< std::pair< Mantid::Kernel::V3D, double > > &peak_events, const Mantid::Kernel::V3D &pos, const coord_t &radiusSquared, const bool &qAxisIsFixed, const bool &useCentroid, std::vector< Mantid::Kernel::V3D > &eigenvects, std::vector< double > &eigenvals, Mantid::Kernel::V3D &mean, const int maxIter)
	Calculate the covariance matrix of a spherical region and store the eigenvectors and eigenvalues that diagonalise the covariance matrix in the vectors provided. More...

double	calculateDistanceToEdge (const Mantid::Kernel::V3D &QLabFrame)
	Calculate if this Q is on a detector The distance from C to OE is given by dv=C-E*(C.scalar_prod(E)) If dv.norm<integration_radius, one of the detector trajectories on the edge is too close to the peak This method is applied to all masked pixels. More...

void	calculateE1 (const Geometry::DetectorInfo &detectorInfo)
	Calculate if this Q is on a detector. More...

void	checkOverlap (int i, const Mantid::API::IPeaksWorkspace_sptr &peakWS, Mantid::Kernel::SpecialCoordinateSystem CoordinatesToUse, double radius)
	Check if peaks overlap. More...

void	exec () override
	Run the algorithm. More...

template<typename MDE , size_t nd>
void	findEllipsoid (const typename DataObjects::MDEventWorkspace< MDE, nd >::sptr ws, const Mantid::API::CoordTransform &getRadiusSq, const Mantid::Kernel::V3D &pos, const coord_t &radiusSquared, const bool &qAxisBool, const bool &useCentroid, const double &bgDensity, std::vector< Mantid::Kernel::V3D > &eigenvects, std::vector< double > &eigenvals, Mantid::Kernel::V3D &mean, const int maxIter=1)
	Calculate the covariance matrix of a spherical region and store the eigenvectors and eigenvalues that diagonalise the covariance matrix in the vectors provided. More...

void	getPinv (const Mantid::Kernel::V3D &q, Mantid::Kernel::Matrix< double > &Pinv)
	Get the inverse of the matrix P. More...

void	init () override
	Initialise the properties. More...

template<typename MDE , size_t nd>
void	integrate (typename DataObjects::MDEventWorkspace< MDE, nd >::sptr ws)
	Integrate the peaks of the workspace using parameters saved in the algorithm class. More...

void	runMaskDetectors (const Mantid::DataObjects::PeaksWorkspace_sptr &peakWS, const std::string &property, const std::string &values)

std::map< std::string, std::string >	validateInputs () override
	Perform validation of ALL the input properties of the algorithm. More...

Private Attributes
std::vector< Kernel::V3D >	E1Vec
	save for all detector pixels More...

Mantid::API::IMDEventWorkspace_sptr	inWS
	Input MDEventWorkspace. More...

Additional Inherited Members
Public Types inherited from Mantid::API::Algorithm
using	WorkspaceVector = std::vector< std::shared_ptr< Workspace > >

Static Public Member Functions inherited from Mantid::API::Algorithm
static IAlgorithm_sptr	fromString (const std::string &input)
	De-serialize an object from a string. More...

static IAlgorithm_sptr	fromJson (const Json::Value &input)
	De-serialize an object from a Json. More...

static IAlgorithm_sptr	fromHistory (const AlgorithmHistory &history)
	Construct an object from a history entry. More...

Public Attributes inherited from Mantid::API::Algorithm
bool	calledByAlias = false
	Flag to indicate if the algorithm is called by its alias. More...

Protected Member Functions inherited from Mantid::API::Algorithm
void	exec (Parallel::ExecutionMode executionMode)
	Runs the algorithm with the specified execution mode. More...

virtual void	execDistributed ()
	Runs the algorithm in `distributed` execution mode. More...

virtual void	execMasterOnly ()
	Runs the algorithm in `master-only` execution mode. More...

virtual Parallel::ExecutionMode	getParallelExecutionMode (const std::map< std::string, Parallel::StorageMode > &storageModes) const
	Get correct execution mode based on input storage modes for an MPI run. More...

virtual const std::string	workspaceMethodOnTypes () const
	Returns a semi-colon separated list of workspace types to attach this algorithm. More...

void	cacheWorkspaceProperties ()
	Go through the properties and cache the input/output workspace properties for later use. More...

void	cacheInputWorkspaceHistories ()
	Cache the histories of any input workspaces so they can be copied over after algorithm completion. More...

void	setExecutionState (const ExecutionState state)
	Sets the current execution state. More...

void	setResultState (const ResultState state)
	Sets the result execution state. More...

void	store ()
	Stores any output workspaces into the AnalysisDataService. More...

void	progress (double p, const std::string &msg="", double estimatedTime=0.0, int progressPrecision=0)
	Sends ProgressNotification. More...

void	interruption_point ()
	This is called during long-running operations, and check if the algorithm has requested that it be cancelled. More...

Poco::NotificationCenter &	notificationCenter () const
	Return a reference to the algorithm's notification dispatcher. More...

void	handleChildProgressNotification (const Poco::AutoPtr< ProgressNotification > &pNf)
	Observation slot for child algorithm progress notification messages, these are scaled and then signalled for this algorithm. More...

const Poco::AbstractObserver &	progressObserver () const
	Return a reference to the algorithm's object that is reporting progress. More...

bool	isWorkspaceProperty (const Kernel::Property *const prop) const
	checks the property is a workspace property More...

bool	trackingHistory ()
	get whether we are tracking the history for this algorithm, More...

virtual void	fillHistory ()
	Copy workspace history for input workspaces to output workspaces and record the history for ths algorithm. More...

virtual void	setOtherProperties (IAlgorithm *alg, const std::string &propertyName, const std::string &propertyValue, int periodNum)
	Virtual method to set the non workspace properties for this algorithm. More...

template<typename T , const int AllowedIndexTypes = static_cast<int>(IndexType::WorkspaceIndex), typename... WSPropArgs, typename = typename std::enable_if<std::is_convertible<T , MatrixWorkspace >::value>::type>
void	declareWorkspaceInputProperties (const std::string &propertyName, const std::string &doc, WSPropArgs &&...wsPropArgs)

Protected Member Functions inherited from Mantid::Kernel::IPropertyManager
virtual void	afterPropertySet (const std::string &)
	Override this method to perform a custom action right after a property was set. More...

virtual void	clear ()=0
	Clears all properties under management. More...

virtual Property *	getPointerToPropertyOrdinal (const int &index) const =0
	Get a property by an index. More...

template<typename T >
T	getValue (const std::string &name) const
	Templated method to get the value of a property. More...

template<>
MANTID_KERNEL_DLL PropertyManager_sptr	getValue (const std::string &name) const

template<>
MANTID_KERNEL_DLL PropertyManager_const_sptr	getValue (const std::string &name) const

Static Protected Member Functions inherited from Mantid::API::Algorithm
template<typename NumT >
static bool	isEmpty (const NumT toCheck)
	checks that the value was not set by users, uses the value in empty double/int. More...

Protected Attributes inherited from Mantid::API::Algorithm
std::atomic< bool >	m_cancel
	Set to true to stop execution. More...

std::atomic< bool >	m_parallelException
	Set if an exception is thrown, and not caught, within a parallel region. More...

std::vector< IWorkspaceProperty * >	m_inputWorkspaceProps
	All the WorkspaceProperties that are Input or InOut. Set in execute() More...

std::shared_ptr< AlgorithmHistory >	m_history
	Pointer to the history for the algorithm being executed. More...

Kernel::Logger	m_log
	Logger for this algorithm. More...

Kernel::Logger &	g_log

std::shared_ptr< AlgorithmHistory >	m_parentHistory
	Pointer to the parent history object (if set) More...

std::vector< WorkspaceVector >	m_unrolledInputWorkspaces
	One vector of workspaces for each input workspace property. More...

size_t	m_groupSize
	Size of the group(s) being processed. More...

bool	m_usingBaseProcessGroups = false
	distinguish between base processGroups() and overriden/algorithm specific versions More...

Static Protected Attributes inherited from Mantid::API::Algorithm
static size_t	g_execCount = 0
	Counter to keep track of algorithm execution order. More...

Detailed Description

Integrate single-crystal peaks in reciprocal-space.

Author: Janik Zikovsky

Date: 2011-04-13 18:11:53.496539

Definition at line 29 of file IntegratePeaksMD2.h.

Member Function Documentation

◆ calcCovar()

void Mantid::MDAlgorithms::IntegratePeaksMD2::calcCovar	(	const std::vector< std::pair< Mantid::Kernel::V3D, double > > &	peak_events,
		const Mantid::Kernel::V3D &	pos,
		const coord_t &	radiusSquared,
		const bool &	qAxisIsFixed,
		const bool &	useCentroid,
		std::vector< Mantid::Kernel::V3D > &	eigenvects,
		std::vector< double > &	eigenvals,
		Mantid::Kernel::V3D &	mean,
		const int	maxIter
	)

private

Calculate the covariance matrix of a spherical region and store the eigenvectors and eigenvalues that diagonalise the covariance matrix in the vectors provided.

Parameters

peak_events	container of center and signal of events in sphere
pos	V3D of nominal peak centre
radiusSquared	radius squared of spherical region for covarariance
qAxisIsFixed	bool to fix an eigenvector along direction pos
useCentroid	bool to use estimated centroid in variance calc
eigenvects	eigenvectors of covariance matrix of spherical region
eigenvals	eigenvalues of covariance matrix of spherical region
mean	container to hold centroid (fixed at pos if not using)
maxIter	max number of iterations in covariance determination

Definition at line 1009 of file IntegratePeaksMD2.cpp.

Referenced by findEllipsoid().

◆ calculateDistanceToEdge()

double Mantid::MDAlgorithms::IntegratePeaksMD2::calculateDistanceToEdge ( const Mantid::Kernel::V3D & QLabFrame )

private

Calculate if this Q is on a detector The distance from C to OE is given by dv=C-E*(C.scalar_prod(E)) If dv.norm<integration_radius, one of the detector trajectories on the edge is too close to the peak This method is applied to all masked pixels.

If there are masked pixels trajectories inside an integration volume, the peak must be rejected.

Parameters

QLabFrame The Peak center.

Definition at line 1221 of file IntegratePeaksMD2.cpp.

References Mantid::API::E1(), E1Vec, Mantid::Kernel::V3D::norm(), and Mantid::Kernel::V3D::scalar_prod().

Referenced by integrate().

◆ calculateE1()

void Mantid::MDAlgorithms::IntegratePeaksMD2::calculateE1 ( const Geometry::DetectorInfo & detectorInfo )

private

Calculate if this Q is on a detector.

Definition at line 1196 of file IntegratePeaksMD2.cpp.

References Mantid::Geometry::DetectorInfo::detector(), Mantid::API::E1(), E1Vec, Mantid::Geometry::IDetector::getTwoTheta(), Mantid::Geometry::DetectorInfo::isMasked(), Mantid::Geometry::DetectorInfo::isMonitor(), and Mantid::Geometry::DetectorInfo::size().

Referenced by integrate().

◆ category()

const std::string Mantid::MDAlgorithms::IntegratePeaksMD2::category ( ) const

inlineoverridevirtual

Algorithm's category for identification.

Reimplemented from Mantid::API::Algorithm.

Definition at line 48 of file IntegratePeaksMD2.h.

◆ checkOverlap()

void Mantid::MDAlgorithms::IntegratePeaksMD2::checkOverlap	(	int	i,
		const Mantid::API::IPeaksWorkspace_sptr &	peakWS,
		Mantid::Kernel::SpecialCoordinateSystem	CoordinatesToUse,
		double	radius
	)

private

Check if peaks overlap.

Definition at line 1257 of file IntegratePeaksMD2.cpp.

References Mantid::Kernel::V3D::distance(), Mantid::API::Algorithm::g_log, Mantid::Geometry::IPeak::getHKL(), Mantid::Geometry::IPeak::getQLabFrame(), Mantid::Geometry::IPeak::getQSampleFrame(), Mantid::Kernel::HKL, Mantid::Kernel::QLab, Mantid::Kernel::QSample, radius, and Mantid::Kernel::Logger::warning().

Referenced by integrate().

◆ exec()

void Mantid::MDAlgorithms::IntegratePeaksMD2::exec ( )

overrideprivatevirtual

Run the algorithm.

Execute the algorithm.

Implements Mantid::API::Algorithm.

Definition at line 1288 of file IntegratePeaksMD2.cpp.

References CALL_MDEVENT_FUNCTION, Mantid::API::Algorithm::getProperty(), integrate(), and inWS.

◆ findEllipsoid()

template<typename MDE , size_t nd>

void Mantid::MDAlgorithms::IntegratePeaksMD2::findEllipsoid	(	const typename DataObjects::MDEventWorkspace< MDE, nd >::sptr	ws,
		const Mantid::API::CoordTransform &	getRadiusSq,
		const Mantid::Kernel::V3D &	pos,
		const coord_t &	radiusSquared,
		const bool &	qAxisIsFixed,
		const bool &	useCentroid,
		const double &	bgDensity,
		std::vector< Mantid::Kernel::V3D > &	eigenvects,
		std::vector< double > &	eigenvals,
		Mantid::Kernel::V3D &	mean,
		const int	maxIter = `1`
	)

private

Calculate the covariance matrix of a spherical region and store the eigenvectors and eigenvalues that diagonalise the covariance matrix in the vectors provided.

Parameters

ws	input workspace
getRadiusSq	Coord transfrom for sphere
pos	V3D of peak centre
radiusSquared	radius that defines spherical region for covarariance
qAxisIsFixed	bool to fix an eigenvector along direction pos
useCentroid	bool to use estimated centroid in variance calc
bgDensity	background counts per unit volume
eigenvects	eigenvectors of covariance matrix of spherical region
eigenvals	eigenvectors of covariance matrix of spherical region
mean	container to hold centroid (fixed at pos if not using)
maxIter	max number of iterations in covariance determination

Definition at line 934 of file IntegratePeaksMD2.cpp.

References Mantid::API::CoordTransform::apply(), calcCovar(), Mantid::Geometry::d, Mantid::DataObjects::MDEventWorkspace::getBox(), Mantid::DataObjects::MDBoxIterator::getBox(), Mantid::DataObjects::MDBoxBase::getCenter(), Mantid::DataObjects::MDBoxIterator::next(), and Mantid::Kernel::V3D::norm().

◆ getPinv()

void Mantid::MDAlgorithms::IntegratePeaksMD2::getPinv	(	const Mantid::Kernel::V3D &	q,
		Mantid::Kernel::Matrix< double > &	Pinv
	)

private

Get the inverse of the matrix P.

Left multiply a vector by Pinv to transform from Qlab to basis Qhat, and uhat,vhat in plane perpendicular to Q. P is a matrix with columns corresponding to new basis vectors. The inverse of P is equivalent to the transpose (as for any roation matrix)

Parameters

q	Qlab of peak center.
Pinv	3 x 3 matrix with rows correpsonding to new basis vectors

Definition at line 1164 of file IntegratePeaksMD2.cpp.

References Mantid::Kernel::V3D::cross_prod(), Mantid::Kernel::V3D::norm(), Mantid::Kernel::V3D::scalar_prod(), Mantid::Kernel::Matrix< T >::setRow(), and tmp.

Referenced by calcCovar().

◆ init()

void Mantid::MDAlgorithms::IntegratePeaksMD2::init ( )

overrideprivatevirtual

Initialise the properties.

Initialize the algorithm's properties.

Implements Mantid::API::Algorithm.

Definition at line 63 of file IntegratePeaksMD2.cpp.

References Mantid::API::Algorithm::declareProperty(), Mantid::Kernel::Direction::Input, Mantid::Kernel::SingletonHolder< T >::Instance(), Mantid::Kernel::IS_EQUAL_TO, Mantid::API::FileProperty::OptionalSave, Mantid::Kernel::Direction::Output, Mantid::Kernel::IPropertyManager::setPropertyGroup(), and Mantid::Kernel::IPropertyManager::setPropertySettings().

◆ integrate()

template<typename MDE , size_t nd>

void Mantid::MDAlgorithms::IntegratePeaksMD2::integrate ( typename DataObjects::MDEventWorkspace< MDE, nd >::sptr ws )

private

Integrate the peaks of the workspace using parameters saved in the algorithm class.

Parameters

ws	:: MDEventWorkspace to integrate

Peak workspace to integrate

Output peaks workspace, create if needed

Radius to use around peaks

Background (end) radius

Start radius of the background

One percent background correction

Cylinder Length to use around peaks for cylinder

Replace intensity with 0

Definition at line 321 of file IntegratePeaksMD2.cpp.

Referenced by exec().

◆ name()

const std::string Mantid::MDAlgorithms::IntegratePeaksMD2::name ( ) const

inlineoverridevirtual

Algorithm's name for identification.

Implements Mantid::API::Algorithm.

Definition at line 32 of file IntegratePeaksMD2.h.

Referenced by integrate().

◆ runMaskDetectors()

void Mantid::MDAlgorithms::IntegratePeaksMD2::runMaskDetectors	(	const Mantid::DataObjects::PeaksWorkspace_sptr &	peakWS,
		const std::string &	property,
		const std::string &	values
	)

private

Definition at line 1232 of file IntegratePeaksMD2.cpp.

References Mantid::API::Algorithm::createChildAlgorithm().

Referenced by integrate().

◆ seeAlso()

const std::vector< std::string > Mantid::MDAlgorithms::IntegratePeaksMD2::seeAlso ( ) const

inlineoverridevirtual

Function to return all of the seeAlso (these are not validated) algorithms related to this algorithm.A default implementation is provided.

Reimplemented from Mantid::API::Algorithm.

Definition at line 43 of file IntegratePeaksMD2.h.

◆ summary()

const std::string Mantid::MDAlgorithms::IntegratePeaksMD2::summary ( ) const

inlineoverridevirtual

Summary of algorithms purpose.

Implements Mantid::API::Algorithm.

Definition at line 34 of file IntegratePeaksMD2.h.

◆ validateInputs()

std::map< std::string, std::string > Mantid::MDAlgorithms::IntegratePeaksMD2::validateInputs ( void )

overrideprivatevirtual

Perform validation of ALL the input properties of the algorithm.

This is to be overridden by specific algorithms. It will be called in dialogs after parsing all inputs and setting the properties, but BEFORE executing.

Returns: a map where: Key = string name of the the property; Value = string describing the problem with the property.

Reimplemented from Mantid::API::Algorithm.

Definition at line 261 of file IntegratePeaksMD2.cpp.

References Mantid::API::Algorithm::getProperty().

◆ version()

int Mantid::MDAlgorithms::IntegratePeaksMD2::version ( ) const

inlineoverridevirtual

Algorithm's version for identification.

Implements Mantid::API::Algorithm.

Definition at line 42 of file IntegratePeaksMD2.h.

Referenced by integrate().

Member Data Documentation

◆ E1Vec

std::vector<Kernel::V3D> Mantid::MDAlgorithms::IntegratePeaksMD2::E1Vec

private

save for all detector pixels

Definition at line 87 of file IntegratePeaksMD2.h.

Referenced by calculateDistanceToEdge(), and calculateE1().

◆ inWS

Mantid::API::IMDEventWorkspace_sptr Mantid::MDAlgorithms::IntegratePeaksMD2::inWS

private

Input MDEventWorkspace.

Definition at line 61 of file IntegratePeaksMD2.h.

Referenced by exec().

The documentation for this class was generated from the following files:

Framework/MDAlgorithms/inc/MantidMDAlgorithms/IntegratePeaksMD2.h
Framework/MDAlgorithms/src/IntegratePeaksMD2.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ calcCovar()

◆ calculateDistanceToEdge()

◆ calculateE1()

◆ category()

◆ checkOverlap()

◆ exec()

◆ findEllipsoid()

◆ getPinv()

◆ init()

◆ integrate()

◆ name()

◆ runMaskDetectors()

◆ seeAlso()

◆ summary()

◆ validateInputs()

◆ version()

Member Data Documentation

◆ E1Vec

◆ inWS