MDNormSCD : Generate MD normalization for single crystal diffraction. More...

#include <MDNormSCD.h>

Inheritance diagram for Mantid::MDAlgorithms::MDNormSCD:

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

	MDNormSCD ()

const std::string	name () const override
	Algorithm's name for use in the GUI and help.

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.

const std::string	summary () const override
	Algorithm's summary for use in the GUI and help.

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

Public Member Functions inherited from Mantid::MDAlgorithms::MDNormBase
	MDNormBase ()

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

	Algorithm (const Algorithm &)=delete

Algorithm &	operator= (const Algorithm &)=delete

	~Algorithm () override
	Virtual destructor.

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

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

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.

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

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

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

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

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

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

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

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

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

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

void	enableHistoryRecordingForProcessGroups (const bool on) override
	Change the state of the processGroups history recording flag.

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.

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

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

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

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

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

void	cancel () override
	Raises the cancel flag.

bool	getCancel () const
	Returns the cancellation state.

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

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

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

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

int	getLoggingOffset () const override
	returns the logging priority offset

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

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

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

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

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

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

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.

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

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.

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)

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

virtual bool	processGroups ()
	Process WorkspaceGroup inputs.

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

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

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

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

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.

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.

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

void	clear () override
	Clears all properties under management.

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

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

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

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

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.

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.

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.

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).

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).

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.

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

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

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

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

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

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
	Mechanism for retriving the index property.

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)
	Mechanism for setting the index property with a workspace shared pointer.

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)
	Mechanism for setting the index property with a workspace shared pointer.

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.

Algorithms As Methods
Public Member Functions inherited from Mantid::Kernel::IPropertyManager
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).

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.

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).

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.

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.

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.

virtual void	filterByProperty (Mantid::Kernel::LogFilter *, const std::vector< std::string > &)

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

bool	isPropertyEnabled (const std::string &name) const
	Test if a given property should be enabled.

bool	isPropertyVisible (const std::string &name) const
	Test if a given property should be visible.

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

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

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

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.

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

void	setPropertySettings (const std::string &name, std::unique_ptr< IPropertySettings const > settings)
	Add a PropertySettings instance to the chain of settings for a given property.

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

virtual	~IPropertyManager ()=default

Private Member Functions
void	cacheInputs ()
	Set up starting values for cached variables.

void	exec () override
	Execute the algorithm.

void	init () override
	Initialize the algorithm's properties.

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::MDAlgorithms::MDNormBase
static std::string	getDimensionChars ()

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

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

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

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

Static Public Attributes inherited from Mantid::MDAlgorithms::MDNormBase
static constexpr double	CHARGEBINSIZE = 1.0

static constexpr double	GONIOBINSTEP = 0.25

static constexpr double	MINPROTONCHARGE = 0.1

static constexpr double	STATIONARYANGLIM = 0.1

Protected Member Functions inherited from Mantid::MDAlgorithms::MDNormBase
DataObjects::MDHistoWorkspace_sptr	binInputWS ()
	Runs the BinMD algorithm on the input to provide the output workspace All slicing algorithm properties are passed along.

void	cacheDimensionXValues ()
	Stores the X values from each H,K,L,E dimension as member variables Energy dimension is transformed to final wavevector.

void	calcIntegralsForIntersections (const std::vector< double > &xValues, const API::MatrixWorkspace &integrFlux, size_t sp, std::vector< double > &yValues) const
	Linearly interpolate between the points in integrFlux at xValues and save the results in yValues.

void	calculateIntersections (std::vector< std::array< double, 4 > > &intersections, const double theta, const double phi, const DblMatrix &transform, double lowvalue=std::nan(""), double highvalue=0)
	Calculate the points of intersection for the given detector with cuboid surrounding the detector position in HKL.

void	calculateNormalization (const std::vector< coord_t > &otherValues, const Geometry::SymmetryOperation &so, uint16_t expInfoIndex)
	Computed the normalization for the input workspace (for MDNorm).

void	calculateNormalization (const std::vector< coord_t > &otherValues, uint16_t expInfoIndex)
	Computed the normalization for the input workspace (for MDNormSCD/MDNormDirectSC).

void	calculateNormContinuous (const std::vector< coord_t > &otherValues, uint16_t expInfoIndex, const Geometry::SymmetryOperation *so=nullptr)
	Computes the normalization for the input workspace for the case of a continous rotation.

void	calculateNormInner (const API::SpectrumInfo &spectrumInfo, const std::vector< coord_t > &otherValues, const double protonCharge, const double protonChargeBkgd, const DblMatrix &Qtransform, const std::vector< double > &lowValues=std::vector< double >(), const std::vector< double > &highValues=std::vector< double >())

Mantid::Kernel::DblMatrix	calQTransform (const Kernel::DblMatrix &R, const Mantid::Geometry::SymmetryOperation &so, bool doInvert=true)
	Calculate QTransform = (R * UB * SymmetryOperation * m_W)^-1.

void	createNormalizationWS (const DataObjects::MDHistoWorkspace &dataWS)
	Create & cached the normalization workspace.

void	findIntegratedDimensions (const std::vector< coord_t > &otherDimValues, bool &skipNormalization)
	Checks the normalization workspace against the indices of the original dimensions.

std::vector< coord_t >	getValuesFromOtherDimensions (bool &skipNormalization, uint16_t expInfoIndex=0) const
	Retrieve logged values from non-HKL dimensions.

std::string	inputEnergyMode () const
	Currently looks for the ConvertToMD algorithm in the history.

Protected Member Functions inherited from Mantid::API::Algorithm
virtual const std::string	workspaceMethodOnTypes () const
	Returns a semi-colon separated list of workspace types to attach this algorithm.

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

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

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

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

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

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

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

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

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

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

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

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

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

void	fillHistory (const std::vector< Workspace_sptr > &outputWorkspaces)
	Copy workspace history from input workspaces to provided vector of output workspaces.

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.

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)
	Declare a property which defines the workspace and allowed index types, as well as a property for capturing the indices all at once.

Protected Member Functions inherited from Mantid::Kernel::IPropertyManager
template<typename T >
T	getValue (const std::string &name) const
	Templated method to get the value of a property.

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.

Protected Attributes inherited from Mantid::MDAlgorithms::MDNormBase
bool	m_accumulate
	Flag to accumulate normalization.

API::IMDEventWorkspace_sptr	m_backgroundWS
	Input background workspace.

Kernel::V3D	m_beamDir
	Beam direction.

DataObjects::MDHistoWorkspace_sptr	m_bkgdNormWS

std::vector< std::atomic< signal_t > >	m_bkgdSignalArray

std::string	m_convention
	ki-kf for Inelastic convention; kf-ki for Crystallography convention

bool	m_dEIntegrated

coord_t	m_dEmax

coord_t	m_dEmin

bool	m_diffraction
	Flag indicating if the input workspace is from diffraction.

double	m_Ei
	cached values for incident energy and momentum, final momentum min/max

size_t	m_eIdx

std::vector< double >	m_eX

size_t	m_hIdx
	index of h,k,l, dE dimensions in the output workspaces

bool	m_hIntegrated
	flag for integrated h,k,l, dE dimensions

coord_t	m_hmax

coord_t	m_hmin
	limits for h,k,l, dE dimensions

std::vector< double >	m_hX
	cached X values along dimensions h,k,l. dE

API::IMDEventWorkspace_sptr	m_inputWS
	Input workspace.

double	m_kfmax

double	m_kfmin

double	m_ki

size_t	m_kIdx

bool	m_kIntegrated

coord_t	m_kmax

coord_t	m_kmin

std::vector< double >	m_kX

size_t	m_lIdx

bool	m_lIntegrated

coord_t	m_lmax

coord_t	m_lmin

std::vector< double >	m_lX

DataObjects::MDHistoWorkspace_sptr	m_normWS
	Normalization workspace.

uint16_t	m_numExptInfos
	number of experiment infos

std::unique_ptr< API::Progress >	m_progress
	Progress bar.

Kernel::V3D	m_samplePos
	Sample position.

std::vector< std::atomic< signal_t > >	m_signalArray
	internal array to accumulate signals to avoid copying (serial) each loop

Mantid::Kernel::Matrix< coord_t >	m_transformation
	matrix for transforming from intersections to positions in the normalization workspace

Mantid::Kernel::DblMatrix	m_UB
	UB matrix.

Mantid::Kernel::DblMatrix	m_W
	W matrix.

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

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

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

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

Kernel::Logger	m_log
	Logger for this algorithm.

Kernel::Logger &	g_log

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

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

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

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

bool	m_recordHistoryForProcessGroups = false
	Opt-in for overridden processGroups() implementations that want the parent algorithm history recorded on group outputs.

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