#include <FitPeaks.h>

Inheritance diagram for Mantid::Algorithms::FitPeaks:

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

	FitPeaks ()

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

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

std::map< std::string, std::string >	validateInputs () override
	Validate inputs.

int	version () const override
	Algorithm's version.

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.

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::string	category () const override
	function to return a category of the algorithm.

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::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	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.

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 > settings)

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

virtual	~IPropertyManager ()=default

Private Member Functions
void	calculateFittedPeaks (const std::vector< std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > > &fit_results)
	calculate peak+background for fitted

double	calculateSignalToNoiseRatio (size_t iws, const std::pair< double, double > &range, const API::IBackgroundFunction_sptr &bkgd_function)
	calculate signal-to-noise ratio in histogram range

double	calculateSignalToSigmaRatio (const size_t &iws, const std::pair< double, double > &peakWindow, const API::IPeakFunction_sptr &peakFunction)

void	checkPeakIndices (std::size_t const &, std::size_t const &)

void	checkPeakWindowEdgeOrder (double const &, double const &)

void	checkWorkspaceIndices (std::size_t const &)
	Get the expected peak's position.

void	convertParametersNameToIndex ()
	Convert peak function's parameter names to parameter index for fast access.

API::MatrixWorkspace_sptr	createMatrixWorkspace (const std::vector< double > &vec_x, const std::vector< double > &vec_y, const std::vector< double > &vec_e)
	Create a single spectrum workspace for fitting.

bool	decideToEstimatePeakParams (const bool firstPeakInSpectrum, const API::IPeakFunction_sptr &peak_function)
	Decide whether to estimate peak parameters.

void	exec () override
	Main exec method.

bool	fitBackground (const size_t &ws_index, const std::pair< double, double > &fit_window, const double &expected_peak_pos, const API::IBackgroundFunction_sptr &bkgd_func)
	fit background

double	fitFunctionHighBackground (const API::IAlgorithm_sptr &fit, const std::pair< double, double > &fit_window, const size_t &ws_index, const double &expected_peak_center, bool observe_peak_shape, const API::IPeakFunction_sptr &peakfunction, const API::IBackgroundFunction_sptr &bkgdfunc)
	fit a single peak with high background

double	fitFunctionMD (API::IFunction_sptr fit_function, const API::MatrixWorkspace_sptr &dataws, const size_t wsindex, const std::pair< double, double > &vec_xmin, const std::pair< double, double > &vec_xmax)

double	fitFunctionSD (const API::IAlgorithm_sptr &fit, const API::IPeakFunction_sptr &peak_function, const API::IBackgroundFunction_sptr &bkgd_function, const API::MatrixWorkspace_sptr &dataws, size_t wsindex, const std::pair< double, double > &peak_range, const double &expected_peak_center, bool estimate_peak_width, bool estimate_background)
	Methods to fit functions (general)

double	fitIndividualPeak (size_t wi, const API::IAlgorithm_sptr &fitter, const double expected_peak_center, const std::pair< double, double > &fitwindow, const bool estimate_peak_width, const API::IPeakFunction_sptr &peakfunction, const API::IBackgroundFunction_sptr &bkgdfunc, const std::shared_ptr< FitPeaksAlgorithm::PeakFitPreCheckResult > &pre_check_result)
	Fit an individual peak.

std::vector< std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > >	fitPeaks ()
	suites of method to fit peaks

void	fitSpectrumPeaks (size_t wi, const std::vector< double > &expected_peak_centers, const std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > &fit_result, std::vector< std::vector< double > > &lastGoodPeakParameters, const std::shared_ptr< FitPeaksAlgorithm::PeakFitPreCheckResult > &pre_check_result)
	fit peaks in a same spectrum

void	generateCalculatedPeaksWS ()
	Generate workspace for calculated values.

void	generateFittedParametersValueWorkspaces ()
	Generate output workspaces.

void	generateOutputPeakPositionWS ()
	main method to create output workspaces

std::string	getPeakHeightParameterName (const API::IPeakFunction_const_sptr &peak_function)
	Get the parameter name for peak height (I or height or etc)

void	getRangeData (size_t iws, const std::pair< double, double > &range, std::vector< double > &vec_x, std::vector< double > &vec_y, std::vector< double > &vec_e)
	get vector X, Y and E in a given range

size_t	histRangeToDataPointCount (size_t iws, const std::pair< double, double > &range)
	convert a histogram range to index boundaries

void	histRangeToIndexBounds (size_t iws, const std::pair< double, double > &range, size_t &left_index, size_t &right_index)
	convert a histogram range to index boundaries

void	init () override
	Init.

bool	isObservablePeakProfile (const std::string &peakprofile)
	check whether FitPeaks supports observation on a certain peak profile's parameters (width!)

void	logNoOffset (const size_t &priority, const std::string &msg)

double	numberCounts (size_t iws)
	sum up all counts in histogram

double	numberCounts (size_t iws, const std::pair< double, double > &range)
	sum up all counts in histogram range

void	processInputFitRanges ()
	process inputs for peak fitting range

void	processInputFunctions ()
	process inputs for peak and background functions

void	processInputPeakCenters ()
	peak centers

void	processInputPeakTolerance ()
	process inputs about fitted peak positions' tolerance

void	processInputs ()
	process inputs (main and child algorithms)

void	processOutputs (std::vector< std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > > fit_result_vec)
	Set the workspaces and etc to output properties.

bool	processSinglePeakFitResult (size_t wsindex, size_t peakindex, const double cost, const std::vector< double > &expected_peak_positions, const FitPeaksAlgorithm::FitFunction &fitfunction, const std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > &fit_result)
	Process the result from fitting a single peak.

void	setupParameterTableWorkspace (const API::ITableWorkspace_sptr &table_ws, const std::vector< std::string > &param_names, bool with_chi2)
	Set up parameter table (parameter value or error)

void	writeFitResult (size_t wi, const std::vector< double > &expected_positions, const std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > &fit_result)
	Write result of peak fit per spectrum to output analysis workspaces.

Private Attributes
API::IBackgroundFunction_sptr	m_bkgdFunction
	Background function.

bool	m_constrainPeaksPosition

std::string	m_costFunction
	Cost function.

API::ITableWorkspace_sptr	m_fitErrorTable
	table workspace for fitted parameters' fitting error. This is optional

int	m_fitIterations
	Fit iterations.

bool	m_fitPeaksFromRight
	Fit from right or left.

API::ITableWorkspace_sptr	m_fittedParamTable
	output analysis workspaces table workspace for fitted parameters

API::MatrixWorkspace_sptr	m_fittedPeakWS
	matrix workspace contained calcalated peaks+background from fitted result it has same number of spectra of input workspace even if only part of spectra to have peaks to fit

std::function< std::vector< double >(std::size_t const &)>	m_getExpectedPeakPositions

std::function< std::pair< double, double >(std::size_t const &, std::size_t const &)>	m_getPeakFitWindow

bool	m_highBackground
	flag for high background

std::vector< size_t >	m_initParamIndexes
	input starting parameters' indexes in peak function

std::vector< double >	m_initParamValues
	input peak parameters' starting values corresponding to above peak parameter names

DataObjects::EventWorkspace_const_sptr	m_inputEventWS
	event workspace for input

bool	m_inputIsDSpace

API::MatrixWorkspace_sptr	m_inputMatrixWS
	mandatory input and output workspaces

API::IBackgroundFunction_sptr	m_linearBackgroundFunction
	Linear background function for high background fitting.

std::string	m_minimizer
	Minimzer.

double	m_minPeakHeight
	minimum peak height without background and it also serves as the criteria for observed peak parameter

double	m_minPeakTotalCount

double	m_minSignalToNoiseRatio

double	m_minSignalToSigmaRatio

std::size_t	m_numPeaksToFit
	the number of peaks to fit in all spectra

std::size_t	m_numSpectraToFit
	total number of spectra to be fit

API::MatrixWorkspace_sptr	m_outputPeakPositionWorkspace
	output workspace for peak positions

std::vector< double >	m_peakCenters
	Designed peak positions and tolerance.

API::MatrixWorkspace_const_sptr	m_peakCenterWorkspace

API::IPeakFunction_sptr	m_peakFunction
	Peak profile name.

std::vector< std::string >	m_peakParamNames
	input peak parameters' names

bool	m_peakPosTolCase234
	peak positon tolerance case b, c and d

std::vector< double >	m_peakPosTolerances
	tolerances for fitting peak positions

Algorithms::PeakParameterHelper::EstimatePeakWidth	m_peakWidthEstimateApproach
	Flag for observing peak width: there are 3 states (1) no estimation (2) from 'observation' (3) calculated from instrument resolution.

double	m_peakWidthPercentage
	flag to estimate peak width from

std::vector< std::vector< double > >	m_peakWindowVector
	peak windows

API::MatrixWorkspace_const_sptr	m_peakWindowWorkspace

API::ITableWorkspace_const_sptr	m_profileStartingValueTable
	table workspace for profile parameters' starting value

bool	m_rawPeaksTable
	flag to show that the pamarameters in table are raw parameters or effective parameters

std::size_t	m_startWorkspaceIndex
	start index

std::size_t	m_stopWorkspaceIndex
	stop index (workspace index of the last spectrum included)

bool	m_uniformPeakPositions

bool	m_uniformProfileStartingValue
	flag for profile startng value being uniform or not

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.

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.

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::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

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

Detailed Description

Definition at line 101 of file FitPeaks.h.

Constructor & Destructor Documentation

◆ FitPeaks()

Mantid::Algorithms::FitPeaks::FitPeaks ( )

Definition at line 262 of file FitPeaks.cpp.

Member Function Documentation

◆ calculateFittedPeaks()

void Mantid::Algorithms::FitPeaks::calculateFittedPeaks ( const std::vector< std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > > & fit_results )

private

calculate peak+background for fitted

calculate fitted peaks with background in the output workspace The current version gets the peak parameters and background parameters from fitted parameter table

Definition at line 1494 of file FitPeaks.cpp.

References Mantid::API::FunctionValues::getCalculated(), m_bkgdFunction, m_fittedParamTable, m_fittedPeakWS, m_getPeakFitWindow, m_numPeaksToFit, m_peakFunction, m_startWorkspaceIndex, m_stopWorkspaceIndex, PARALLEL_CHECK_INTERRUPT_REGION, PARALLEL_END_INTERRUPT_REGION, PARALLEL_FOR_IF, PARALLEL_START_INTERRUPT_REGION, and Mantid::Kernel::threadSafe().

Referenced by processOutputs().

◆ calculateSignalToNoiseRatio()

double Mantid::Algorithms::FitPeaks::calculateSignalToNoiseRatio	(	size_t	iws,
		const std::pair< double, double > &	range,
		const API::IBackgroundFunction_sptr &	bkgd_function
	)

private

calculate signal-to-noise ratio in histogram range

Calculate signal-to-noise ratio in a histogram range.

Parameters

iws	:: histogram index in workspace
range	:: histogram range
bkgd_function	:: background function pointer

Returns: :: signal-to-noise ratio

Definition at line 2187 of file FitPeaks.cpp.

Referenced by fitIndividualPeak().

◆ calculateSignalToSigmaRatio()

double Mantid::Algorithms::FitPeaks::calculateSignalToSigmaRatio	(	const size_t &	iws,
		const std::pair< double, double > &	peakWindow,
		const API::IPeakFunction_sptr &	peakFunction
	)

private

Definition at line 1555 of file FitPeaks.cpp.

References m_inputMatrixWS, sigma, and Mantid::API::FunctionValues::toVector().

Referenced by fitSpectrumPeaks().

◆ category()

const std::string Mantid::Algorithms::FitPeaks::category ( ) const

inlineoverridevirtual

Algorithm's category for identification.

Implements Mantid::API::IAlgorithm.

Definition at line 115 of file FitPeaks.h.

◆ checkPeakIndices()

void Mantid::Algorithms::FitPeaks::checkPeakIndices	(	std::size_t const &	wi,
		std::size_t const &	ipeak
	)

private

Definition at line 2235 of file FitPeaks.cpp.

References m_getExpectedPeakPositions, and m_numPeaksToFit.

Referenced by processInputFitRanges().

◆ checkPeakWindowEdgeOrder()

void Mantid::Algorithms::FitPeaks::checkPeakWindowEdgeOrder	(	double const &	left,
		double const &	right
	)

private

Definition at line 2244 of file FitPeaks.cpp.

References left, and right.

Referenced by processInputFitRanges().

◆ checkWorkspaceIndices()

void Mantid::Algorithms::FitPeaks::checkWorkspaceIndices ( std::size_t const & wi )

private

Get the expected peak's position.

Definition at line 2226 of file FitPeaks.cpp.

References m_startWorkspaceIndex, and m_stopWorkspaceIndex.

Referenced by processInputFitRanges(), and processInputPeakCenters().

◆ convertParametersNameToIndex()

void Mantid::Algorithms::FitPeaks::convertParametersNameToIndex ( )

private

Convert peak function's parameter names to parameter index for fast access.

Convert the input initial parameter name/value to parameter index/value for faster access according to the parameter name and peak profile function Output: m_initParamIndexes will be set up.

Definition at line 946 of file FitPeaks.cpp.

References Mantid::API::Algorithm::g_log, m_initParamIndexes, m_peakFunction, m_peakParamNames, m_profileStartingValueTable, and Mantid::Kernel::Logger::warning().

Referenced by processInputFunctions().

◆ createMatrixWorkspace()

API::MatrixWorkspace_sptr Mantid::Algorithms::FitPeaks::createMatrixWorkspace	(	const std::vector< double > &	vec_x,
		const std::vector< double > &	vec_y,
		const std::vector< double > &	vec_e
	)

private

Create a single spectrum workspace for fitting.

Definition at line 1924 of file FitPeaks.cpp.

Referenced by fitFunctionHighBackground().

◆ decideToEstimatePeakParams()

bool Mantid::Algorithms::FitPeaks::decideToEstimatePeakParams	(	const bool	firstPeakInSpectrum,
		const API::IPeakFunction_sptr &	peak_function
	)

private

Decide whether to estimate peak parameters.

If not, then set the peak parameters from user specified starting value

Parameters

firstPeakInSpectrum	:: flag whether the given peak is the first peak in the spectrum
peak_function	:: peak function to set parameter values to

Returns: :: flag whether the peak width shall be observed

Definition at line 1340 of file FitPeaks.cpp.

References m_initParamIndexes, and m_initParamValues.

Referenced by fitSpectrumPeaks().

◆ exec()

void Mantid::Algorithms::FitPeaks::exec ( )

overrideprivatevirtual

Main exec method.

Implements Mantid::API::Algorithm.

Definition at line 535 of file FitPeaks.cpp.

References fitPeaks(), generateCalculatedPeaksWS(), generateFittedParametersValueWorkspaces(), generateOutputPeakPositionWS(), processInputs(), and processOutputs().

◆ fitBackground()

bool Mantid::Algorithms::FitPeaks::fitBackground	(	const size_t &	ws_index,
		const std::pair< double, double > &	fit_window,
		const double &	expected_peak_pos,
		const API::IBackgroundFunction_sptr &	bkgd_func
	)

private

fit background

Fit background function.

Definition at line 1635 of file FitPeaks.cpp.

References Mantid::Kernel::Logger::debug(), Mantid::Algorithms::PeakParameterHelper::findXIndex(), fitFunctionMD(), Mantid::API::Algorithm::g_log, m_inputMatrixWS, and n.

Referenced by fitFunctionHighBackground().

◆ fitFunctionHighBackground()

double Mantid::Algorithms::FitPeaks::fitFunctionHighBackground	(	const API::IAlgorithm_sptr &	fit,
		const std::pair< double, double > &	fit_window,
		const size_t &	ws_index,
		const double &	expected_peak_center,
		bool	observe_peak_shape,
		const API::IPeakFunction_sptr &	peakfunction,
		const API::IBackgroundFunction_sptr &	bkgdfunc
	)

private

fit a single peak with high background

Fit peak with high background.

Definition at line 1882 of file FitPeaks.cpp.

References createMatrixWorkspace(), fitBackground(), fitFunctionSD(), getRangeData(), m_inputMatrixWS, m_linearBackgroundFunction, and n.

Referenced by fitIndividualPeak().

◆ fitFunctionMD()

double Mantid::Algorithms::FitPeaks::fitFunctionMD	(	API::IFunction_sptr	fit_function,
		const API::MatrixWorkspace_sptr &	dataws,
		const size_t	wsindex,
		const std::pair< double, double > &	vec_xmin,
		const std::pair< double, double > &	vec_xmax
	)

private

Definition at line 1822 of file FitPeaks.cpp.

References Mantid::API::Algorithm::createChildAlgorithm(), m_costFunction, m_fitIterations, and m_minimizer.

Referenced by fitBackground().

◆ fitFunctionSD()

double Mantid::Algorithms::FitPeaks::fitFunctionSD	(	const API::IAlgorithm_sptr &	fit,
		const API::IPeakFunction_sptr &	peak_function,
		const API::IBackgroundFunction_sptr &	bkgd_function,
		const API::MatrixWorkspace_sptr &	dataws,
		size_t	wsindex,
		const std::pair< double, double > &	peak_range,
		const double &	expected_peak_center,
		bool	estimate_peak_width,
		bool	estimate_background
	)

private

Methods to fit functions (general)

Fit function in single domain (mostly applied for fitting peak + background) with estimating peak parameters This is the core fitting algorithm to deal with the simplest situation.

Exceptions

:	Fit.isExecuted is false (cannot be executed)

Definition at line 1726 of file FitPeaks.cpp.

References Mantid::Kernel::Logger::debug(), Mantid::Algorithms::PeakParameterHelper::estimatePeakParameters(), Mantid::Algorithms::PeakParameterHelper::findXIndex(), Mantid::API::Algorithm::g_log, Mantid::Algorithms::PeakParameterHelper::GOOD, Mantid::Algorithms::PeakParameterHelper::LOWPEAK, m_constrainPeaksPosition, m_fitIterations, m_minPeakHeight, m_peakWidthEstimateApproach, m_peakWidthPercentage, Mantid::Algorithms::PeakParameterHelper::NOSIGNAL, and Mantid::Kernel::Logger::warning().

Referenced by fitFunctionHighBackground(), and fitIndividualPeak().

◆ fitIndividualPeak()

double Mantid::Algorithms::FitPeaks::fitIndividualPeak	(	size_t	wi,
		const API::IAlgorithm_sptr &	fitter,
		const double	expected_peak_center,
		const std::pair< double, double > &	fitwindow,
		const bool	estimate_peak_width,
		const API::IPeakFunction_sptr &	peakfunction,
		const API::IBackgroundFunction_sptr &	bkgdfunc,
		const std::shared_ptr< FitPeaksAlgorithm::PeakFitPreCheckResult > &	pre_check_result
	)

private

Fit an individual peak.

Definition at line 1679 of file FitPeaks.cpp.

References calculateSignalToNoiseRatio(), fitFunctionHighBackground(), fitFunctionSD(), histRangeToDataPointCount(), m_highBackground, m_inputMatrixWS, m_minPeakTotalCount, m_minSignalToNoiseRatio, and numberCounts().

Referenced by fitSpectrumPeaks().

◆ fitPeaks()

std::vector< std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > > Mantid::Algorithms::FitPeaks::fitPeaks ( )

private

suites of method to fit peaks

main method to fit peaks among all

Vector to record all the FitResult (only containing specified number of spectra. shift is expected)

Definition at line 978 of file FitPeaks.cpp.

References fitSpectrumPeaks(), logNoOffset(), m_bkgdFunction, m_getExpectedPeakPositions, m_numPeaksToFit, m_numSpectraToFit, m_peakFunction, m_startWorkspaceIndex, m_stopWorkspaceIndex, PARALLEL_CHECK_INTERRUPT_REGION, PARALLEL_CRITICAL, PARALLEL_END_INTERRUPT_REGION, PARALLEL_START_INTERRUPT_REGION, PRAGMA_OMP, Mantid::Kernel::ProgressBase::report(), and writeFitResult().

Referenced by exec().

◆ fitSpectrumPeaks()

void Mantid::Algorithms::FitPeaks::fitSpectrumPeaks	(	size_t	wi,
		const std::vector< double > &	expected_peak_centers,
		const std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > &	fit_result,
		std::vector< std::vector< double > > &	lastGoodPeakParameters,
		const std::shared_ptr< FitPeaksAlgorithm::PeakFitPreCheckResult > &	pre_check_result
	)

private

fit peaks in a same spectrum

Fit peaks across one single spectrum.

Definition at line 1139 of file FitPeaks.cpp.

References Mantid::Algorithms::FitPeaksAlgorithm::FitFunction::bkgdfunction, calculateSignalToSigmaRatio(), Mantid::API::Algorithm::createChildAlgorithm(), decideToEstimatePeakParams(), Mantid::Kernel::Logger::error(), fitIndividualPeak(), Mantid::API::Algorithm::g_log, m_bkgdFunction, m_costFunction, m_fitPeaksFromRight, m_getPeakFitWindow, m_inputMatrixWS, m_minimizer, m_minPeakTotalCount, m_minSignalToSigmaRatio, m_numPeaksToFit, m_peakFunction, m_peakWidthEstimateApproach, numberCounts(), Mantid::Algorithms::FitPeaksAlgorithm::FitFunction::peakfunction, processSinglePeakFitResult(), value, and Mantid::Kernel::Logger::warning().

Referenced by fitPeaks().

◆ generateCalculatedPeaksWS()

void Mantid::Algorithms::FitPeaks::generateCalculatedPeaksWS ( )

private

Generate workspace for calculated values.

Generate the output MatrixWorkspace for calculated peaks (as an option)

FitPeaks::generateCalculatedPeaksWS

Definition at line 2046 of file FitPeaks.cpp.

References Mantid::API::Algorithm::getPropertyValue(), m_fittedPeakWS, and m_inputMatrixWS.

Referenced by exec().

◆ generateFittedParametersValueWorkspaces()

void Mantid::Algorithms::FitPeaks::generateFittedParametersValueWorkspaces ( )

private

Generate output workspaces.

Generate table workspace for fitted parameters' value and optionally the table workspace for those parameters' fitting error.

FitPeaks::generateFittedParametersValueWorkspace

Definition at line 2004 of file FitPeaks.cpp.

References Mantid::API::Algorithm::getProperty(), Mantid::API::Algorithm::getPropertyValue(), m_bkgdFunction, m_fitErrorTable, m_fittedParamTable, m_peakFunction, m_rawPeaksTable, and setupParameterTableWorkspace().

Referenced by exec().

◆ generateOutputPeakPositionWS()

void Mantid::Algorithms::FitPeaks::generateOutputPeakPositionWS ( )

private

main method to create output workspaces

generate output workspace for peak positions

Definition at line 1948 of file FitPeaks.cpp.

References m_getExpectedPeakPositions, m_numPeaksToFit, m_numSpectraToFit, m_outputPeakPositionWorkspace, and m_startWorkspaceIndex.

Referenced by exec().

◆ getPeakHeightParameterName()

std::string Mantid::Algorithms::FitPeaks::getPeakHeightParameterName ( const API::IPeakFunction_const_sptr & peak_function )

private

Get the parameter name for peak height (I or height or etc)

Definition at line 2363 of file FitPeaks.cpp.

◆ getRangeData()

void Mantid::Algorithms::FitPeaks::getRangeData	(	size_t	iws,
		const std::pair< double, double > &	range,
		std::vector< double > &	vec_x,
		std::vector< double > &	vec_y,
		std::vector< double > &	vec_e
	)

private

get vector X, Y and E in a given range

Parameters

iws	:: histogram index in workspace
range	:: histogram range
vec_x	:: (output) vector of X-values
vec_y	:: (output) vector of Y-values
vec_e	:: (output) vector of E-values

Definition at line 2155 of file FitPeaks.cpp.

References histRangeToIndexBounds(), and m_inputMatrixWS.

Referenced by fitFunctionHighBackground(), and numberCounts().

◆ histRangeToDataPointCount()

size_t Mantid::Algorithms::FitPeaks::histRangeToDataPointCount	(	size_t	iws,
		const std::pair< double, double > &	range
	)

private

convert a histogram range to index boundaries

Calculate number of data points in a histogram range.

calculate how many data points are in a histogram range

Parameters

iws	:: histogram index in workspace
range	:: histogram range

Returns: :: number of data points

Definition at line 2112 of file FitPeaks.cpp.

References histRangeToIndexBounds(), and m_inputMatrixWS.

Referenced by fitIndividualPeak().

◆ histRangeToIndexBounds()

void Mantid::Algorithms::FitPeaks::histRangeToIndexBounds	(	size_t	iws,
		const std::pair< double, double > &	range,
		size_t &	left_index,
		size_t &	right_index
	)

private

convert a histogram range to index boundaries

Convert a histogram range to vector index boundaries.

Parameters

iws	:: histogram index in workspace
range	:: histogram range
left_index	:: (output) left index boundary
right_index	:: (output) right index boundary

Definition at line 2131 of file FitPeaks.cpp.

Referenced by getRangeData(), and histRangeToDataPointCount().

◆ init()

void Mantid::Algorithms::FitPeaks::init ( )

overrideprivatevirtual

Init.

initialize the properties

Implements Mantid::API::Algorithm.

Definition at line 269 of file FitPeaks.cpp.

References Mantid::API::Algorithm::declareProperty(), Mantid::EMPTY_DBL(), Mantid::EMPTY_INT(), Mantid::Kernel::Direction::Input, Mantid::PropertyNames::INPUT_WKSP(), Mantid::API::PropertyMode::Optional, Mantid::Kernel::Direction::Output, Mantid::PropertyNames::OUTPUT_WKSP(), and Mantid::Kernel::IPropertyManager::setPropertyGroup().

◆ isObservablePeakProfile()

bool Mantid::Algorithms::FitPeaks::isObservablePeakProfile ( const std::string & peakprofile )

private

check whether FitPeaks supports observation on a certain peak profile's parameters (width!)

check whether a peak profile is allowed to observe peak width and set width

isObservablePeakProfile

Parameters

peakprofile : name of peak profile to check against

Returns: :: flag whether the specified peak profile observable

Definition at line 1627 of file FitPeaks.cpp.

Referenced by processInputs().

◆ logNoOffset()

void Mantid::Algorithms::FitPeaks::logNoOffset	(	const size_t &	priority,
		const std::string &	msg
	)

private

Definition at line 2388 of file FitPeaks.cpp.

References Mantid::API::Algorithm::g_log, Mantid::Kernel::Logger::notice(), and Mantid::Kernel::Logger::warning().

Referenced by fitPeaks(), and processInputs().

◆ name()

const std::string Mantid::Algorithms::FitPeaks::name ( ) const

inlineoverridevirtual

Algorithm's name.

Implements Mantid::API::Algorithm.

Definition at line 106 of file FitPeaks.h.

◆ numberCounts() [1/2]

double Mantid::Algorithms::FitPeaks::numberCounts ( size_t iws )

private

sum up all counts in histogram

Sum up all counts in a histogram.

Parameters

iws	:: histogram index in workspace

Returns: :: total number of counts in the histogram

Definition at line 2085 of file FitPeaks.cpp.

References m_inputMatrixWS.

Referenced by fitIndividualPeak(), and fitSpectrumPeaks().

◆ numberCounts() [2/2]

double Mantid::Algorithms::FitPeaks::numberCounts	(	size_t	iws,
		const std::pair< double, double > &	range
	)

private

sum up all counts in histogram range

Sum up all counts in a histogram range.

Parameters

iws	:: histogram index in workspace
range	:: histogram range

Returns: :: total number of counts in the range

Definition at line 2097 of file FitPeaks.cpp.

References getRangeData().

◆ processInputFitRanges()

void Mantid::Algorithms::FitPeaks::processInputFitRanges ( )

private

process inputs for peak fitting range

process and check for inputs about peak fitting range (i.e., window) Note: What is the output of the method?

Definition at line 688 of file FitPeaks.cpp.

References checkPeakIndices(), checkPeakWindowEdgeOrder(), checkWorkspaceIndices(), Mantid::API::Algorithm::getProperty(), Mantid::API::Algorithm::getPropertyValue(), left, m_getExpectedPeakPositions, m_getPeakFitWindow, m_inputIsDSpace, m_numPeaksToFit, m_peakCenters, m_peakCenterWorkspace, m_peakWidthPercentage, m_peakWindowVector, m_peakWindowWorkspace, m_startWorkspaceIndex, m_stopWorkspaceIndex, m_uniformPeakPositions, and right.

Referenced by processInputs().

◆ processInputFunctions()

void Mantid::Algorithms::FitPeaks::processInputFunctions ( )

private

process inputs for peak and background functions

process inputs for peak profile and background

Definition at line 635 of file FitPeaks.cpp.

References convertParametersNameToIndex(), Mantid::API::Algorithm::g_log, Mantid::API::Algorithm::getProperty(), Mantid::API::Algorithm::getPropertyValue(), m_bkgdFunction, m_highBackground, m_initParamValues, m_linearBackgroundFunction, m_peakFunction, m_peakParamNames, m_profileStartingValueTable, m_uniformProfileStartingValue, and Mantid::Kernel::Logger::warning().

Referenced by processInputs().

◆ processInputPeakCenters()

void Mantid::Algorithms::FitPeaks::processInputPeakCenters ( )

private

peak centers

Processing peaks centers and fitting tolerance information from input.

the parameters that are set including

m_peakCenters/m_peakCenterWorkspace/m_uniformPeakPositions (bool)/m_partialSpectra (bool)
m_peakPosTolerances (vector)
m_numPeaksToFit

Definition at line 827 of file FitPeaks.cpp.

References checkWorkspaceIndices(), Mantid::Kernel::Logger::debug(), Mantid::Kernel::Logger::error(), Mantid::API::Algorithm::g_log, Mantid::API::Algorithm::getProperty(), Mantid::API::Algorithm::getPropertyValue(), m_getExpectedPeakPositions, m_numPeaksToFit, m_peakCenters, m_peakCenterWorkspace, m_startWorkspaceIndex, m_stopWorkspaceIndex, m_uniformPeakPositions, and Mantid::Kernel::Logger::notice().

Referenced by processInputs().

◆ processInputPeakTolerance()

void Mantid::Algorithms::FitPeaks::processInputPeakTolerance ( )

private

process inputs about fitted peak positions' tolerance

Processing peak fitting tolerance information from input.

The parameters that are set including

m_peakPosTolerances (vector)

Definition at line 888 of file FitPeaks.cpp.

References Mantid::Kernel::Logger::error(), Mantid::API::Algorithm::g_log, Mantid::API::Algorithm::getProperty(), Mantid::API::Algorithm::isEmpty(), m_minPeakHeight, m_minPeakTotalCount, m_minSignalToNoiseRatio, m_minSignalToSigmaRatio, m_numPeaksToFit, m_peakPosTolCase234, and m_peakPosTolerances.

Referenced by processInputs().

◆ processInputs()

void Mantid::Algorithms::FitPeaks::processInputs ( )

private

process inputs (main and child algorithms)

Definition at line 556 of file FitPeaks.cpp.

References Mantid::Kernel::Logger::debug(), Mantid::API::Algorithm::g_log, Mantid::API::Algorithm::getProperty(), Mantid::API::Algorithm::getPropertyValue(), Mantid::PropertyNames::INPUT_WKSP(), Mantid::API::Algorithm::isEmpty(), isObservablePeakProfile(), logNoOffset(), m_bkgdFunction, m_constrainPeaksPosition, m_costFunction, m_fitIterations, m_fitPeaksFromRight, m_highBackground, m_inputIsDSpace, m_inputMatrixWS, m_minimizer, m_numPeaksToFit, m_numSpectraToFit, m_peakFunction, m_peakWidthEstimateApproach, m_peakWidthPercentage, m_startWorkspaceIndex, m_stopWorkspaceIndex, processInputFitRanges(), processInputFunctions(), processInputPeakCenters(), and processInputPeakTolerance().

Referenced by exec().

◆ processOutputs()

void Mantid::Algorithms::FitPeaks::processOutputs ( std::vector< std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > > fit_result_vec )

private

Set the workspaces and etc to output properties.

set up output workspaces

Definition at line 2061 of file FitPeaks.cpp.

References calculateFittedPeaks(), Mantid::Kernel::Logger::debug(), Mantid::API::Algorithm::g_log, m_fitErrorTable, m_fittedParamTable, m_fittedPeakWS, m_outputPeakPositionWorkspace, Mantid::PropertyNames::OUTPUT_WKSP(), Mantid::Kernel::IPropertyManager::setProperty(), and Mantid::Kernel::Logger::warning().

Referenced by exec().

◆ processSinglePeakFitResult()

bool Mantid::Algorithms::FitPeaks::processSinglePeakFitResult	(	size_t	wsindex,
		size_t	peakindex,
		const double	cost,
		const std::vector< double > &	expected_peak_positions,
		const FitPeaksAlgorithm::FitFunction &	fitfunction,
		const std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > &	fit_result
	)

private

Process the result from fitting a single peak.

retrieve the fitted peak information from functions and set to output vectors

Parameters

wsindex	:: workspace index
peakindex	:: index of peak in given peak position vector
cost	:: cost function value (i.e., chi^2)
expected_peak_positions	:: vector of the expected peak positions
fitfunction	:: pointer to function to retrieve information from
fit_result	:: (output) PeakFitResult instance to set the fitting result to

Returns: :: whether the peak fiting is good or not

Definition at line 1380 of file FitPeaks.cpp.

References Mantid::Kernel::Logger::debug(), fabs, Mantid::API::Algorithm::g_log, m_getPeakFitWindow, m_inputMatrixWS, m_minPeakHeight, m_numPeaksToFit, m_peakPosTolCase234, m_peakPosTolerances, and Mantid::Algorithms::FitPeaksAlgorithm::FitFunction::peakfunction.

Referenced by fitSpectrumPeaks().

◆ setupParameterTableWorkspace()

void Mantid::Algorithms::FitPeaks::setupParameterTableWorkspace	(	const API::ITableWorkspace_sptr &	table_ws,
		const std::vector< std::string > &	param_names,
		bool	with_chi2
	)

private

Set up parameter table (parameter value or error)

FitPeaks::generateParameterTable

Parameters

table_ws,:	an empty workspace
param_names
with_chi2,:	flag to append chi^2 to the table

Definition at line 1972 of file FitPeaks.cpp.

References m_fittedParamTable, m_numPeaksToFit, m_startWorkspaceIndex, and m_stopWorkspaceIndex.

Referenced by generateFittedParametersValueWorkspaces().

◆ summary()

const std::string Mantid::Algorithms::FitPeaks::summary ( ) const

inlineoverridevirtual

Summary of algorithms purpose.

Implements Mantid::API::Algorithm.

Definition at line 109 of file FitPeaks.h.

◆ validateInputs()

std::map< std::string, std::string > Mantid::Algorithms::FitPeaks::validateInputs ( void )

overridevirtual

Validate inputs.

Implements Mantid::API::IAlgorithm.

Definition at line 451 of file FitPeaks.cpp.

References Mantid::API::Algorithm::getProperty(), Mantid::API::Algorithm::getPropertyValue(), Mantid::API::Algorithm::isDefault(), m_peakFunction, and m_profileStartingValueTable.

◆ version()

int Mantid::Algorithms::FitPeaks::version ( ) const

inlineoverridevirtual

Algorithm's version.

Implements Mantid::API::Algorithm.

Definition at line 112 of file FitPeaks.h.

◆ writeFitResult()

void Mantid::Algorithms::FitPeaks::writeFitResult	(	size_t	wi,
		const std::vector< double > &	expected_positions,
		const std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > &	fit_result
	)

private

Write result of peak fit per spectrum to output analysis workspaces.

Write result of peak fit per spectrum to output analysis workspaces including (1) output peak position workspace (2) parameter table workspace and optionally (3) fitting error/uncertainty workspace.

FitPeaks::writeFitResult

Parameters

wi
expected_positions	:: vector for expected peak positions
fit_result	:: PeakFitResult instance

Definition at line 2261 of file FitPeaks.cpp.

References Mantid::Kernel::Logger::error(), Mantid::API::Algorithm::g_log, m_bkgdFunction, m_fitErrorTable, m_fittedParamTable, m_numPeaksToFit, m_outputPeakPositionWorkspace, m_peakFunction, m_rawPeaksTable, and m_startWorkspaceIndex.

Referenced by fitPeaks().

Member Data Documentation

◆ m_bkgdFunction

API::IBackgroundFunction_sptr Mantid::Algorithms::FitPeaks::m_bkgdFunction

private

Background function.

Definition at line 264 of file FitPeaks.h.

Referenced by calculateFittedPeaks(), fitPeaks(), fitSpectrumPeaks(), generateFittedParametersValueWorkspaces(), processInputFunctions(), processInputs(), and writeFitResult().

◆ m_constrainPeaksPosition

bool Mantid::Algorithms::FitPeaks::m_constrainPeaksPosition

private

Definition at line 310 of file FitPeaks.h.

Referenced by fitFunctionSD(), and processInputs().

◆ m_costFunction

std::string Mantid::Algorithms::FitPeaks::m_costFunction

private

Cost function.

Definition at line 271 of file FitPeaks.h.

Referenced by fitFunctionMD(), fitSpectrumPeaks(), and processInputs().

◆ m_fitErrorTable

API::ITableWorkspace_sptr Mantid::Algorithms::FitPeaks::m_fitErrorTable

private

table workspace for fitted parameters' fitting error. This is optional

Definition at line 251 of file FitPeaks.h.

Referenced by generateFittedParametersValueWorkspaces(), processOutputs(), and writeFitResult().

◆ m_fitIterations

int Mantid::Algorithms::FitPeaks::m_fitIterations

private

Fit iterations.

Definition at line 275 of file FitPeaks.h.

Referenced by fitFunctionMD(), fitFunctionSD(), and processInputs().

◆ m_fitPeaksFromRight

bool Mantid::Algorithms::FitPeaks::m_fitPeaksFromRight

private

Fit from right or left.

Definition at line 273 of file FitPeaks.h.

Referenced by fitSpectrumPeaks(), and processInputs().

◆ m_fittedParamTable

API::ITableWorkspace_sptr Mantid::Algorithms::FitPeaks::m_fittedParamTable

private

output analysis workspaces table workspace for fitted parameters

Definition at line 249 of file FitPeaks.h.

Referenced by calculateFittedPeaks(), generateFittedParametersValueWorkspaces(), processOutputs(), setupParameterTableWorkspace(), and writeFitResult().

◆ m_fittedPeakWS

API::MatrixWorkspace_sptr Mantid::Algorithms::FitPeaks::m_fittedPeakWS

private

matrix workspace contained calcalated peaks+background from fitted result it has same number of spectra of input workspace even if only part of spectra to have peaks to fit

Definition at line 258 of file FitPeaks.h.

Referenced by calculateFittedPeaks(), generateCalculatedPeaksWS(), and processOutputs().

◆ m_getExpectedPeakPositions

std::function<std::vector<double>(std::size_t const &)> Mantid::Algorithms::FitPeaks::m_getExpectedPeakPositions

private

Definition at line 288 of file FitPeaks.h.

Referenced by checkPeakIndices(), fitPeaks(), generateOutputPeakPositionWS(), processInputFitRanges(), and processInputPeakCenters().

◆ m_getPeakFitWindow

std::function<std::pair<double, double>(std::size_t const &, std::size_t const &)> Mantid::Algorithms::FitPeaks::m_getPeakFitWindow

private

Definition at line 289 of file FitPeaks.h.

Referenced by calculateFittedPeaks(), fitSpectrumPeaks(), processInputFitRanges(), and processSinglePeakFitResult().

◆ m_highBackground

bool Mantid::Algorithms::FitPeaks::m_highBackground

private

flag for high background

Definition at line 338 of file FitPeaks.h.

Referenced by fitIndividualPeak(), processInputFunctions(), and processInputs().

◆ m_initParamIndexes

std::vector<size_t> Mantid::Algorithms::FitPeaks::m_initParamIndexes

private

input starting parameters' indexes in peak function

Definition at line 279 of file FitPeaks.h.

Referenced by convertParametersNameToIndex(), and decideToEstimatePeakParams().

◆ m_initParamValues

std::vector<double> Mantid::Algorithms::FitPeaks::m_initParamValues

private

input peak parameters' starting values corresponding to above peak parameter names

Definition at line 320 of file FitPeaks.h.

Referenced by decideToEstimatePeakParams(), and processInputFunctions().

◆ m_inputEventWS

DataObjects::EventWorkspace_const_sptr Mantid::Algorithms::FitPeaks::m_inputEventWS

private

event workspace for input

Definition at line 244 of file FitPeaks.h.

◆ m_inputIsDSpace

bool Mantid::Algorithms::FitPeaks::m_inputIsDSpace

private

Definition at line 242 of file FitPeaks.h.

Referenced by processInputFitRanges(), and processInputs().

◆ m_inputMatrixWS

API::MatrixWorkspace_sptr Mantid::Algorithms::FitPeaks::m_inputMatrixWS

private

mandatory input and output workspaces

Definition at line 241 of file FitPeaks.h.

Referenced by calculateSignalToSigmaRatio(), fitBackground(), fitFunctionHighBackground(), fitIndividualPeak(), fitSpectrumPeaks(), generateCalculatedPeaksWS(), getRangeData(), histRangeToDataPointCount(), numberCounts(), processInputs(), and processSinglePeakFitResult().

◆ m_linearBackgroundFunction

API::IBackgroundFunction_sptr Mantid::Algorithms::FitPeaks::m_linearBackgroundFunction

private

Linear background function for high background fitting.

Definition at line 266 of file FitPeaks.h.

Referenced by fitFunctionHighBackground(), and processInputFunctions().

◆ m_minimizer

std::string Mantid::Algorithms::FitPeaks::m_minimizer

private

Minimzer.

Definition at line 269 of file FitPeaks.h.

Referenced by fitFunctionMD(), fitSpectrumPeaks(), and processInputs().

◆ m_minPeakHeight

double Mantid::Algorithms::FitPeaks::m_minPeakHeight

private

minimum peak height without background and it also serves as the criteria for observed peak parameter

Definition at line 329 of file FitPeaks.h.

Referenced by fitFunctionSD(), processInputPeakTolerance(), and processSinglePeakFitResult().

◆ m_minPeakTotalCount

double Mantid::Algorithms::FitPeaks::m_minPeakTotalCount

private

Definition at line 333 of file FitPeaks.h.

Referenced by fitIndividualPeak(), fitSpectrumPeaks(), and processInputPeakTolerance().

◆ m_minSignalToNoiseRatio

double Mantid::Algorithms::FitPeaks::m_minSignalToNoiseRatio

private

Definition at line 332 of file FitPeaks.h.

Referenced by fitIndividualPeak(), and processInputPeakTolerance().

◆ m_minSignalToSigmaRatio

double Mantid::Algorithms::FitPeaks::m_minSignalToSigmaRatio

private

Definition at line 335 of file FitPeaks.h.

Referenced by fitSpectrumPeaks(), and processInputPeakTolerance().

◆ m_numPeaksToFit

std::size_t Mantid::Algorithms::FitPeaks::m_numPeaksToFit

private

the number of peaks to fit in all spectra

Definition at line 285 of file FitPeaks.h.

Referenced by calculateFittedPeaks(), checkPeakIndices(), fitPeaks(), fitSpectrumPeaks(), generateOutputPeakPositionWS(), processInputFitRanges(), processInputPeakCenters(), processInputPeakTolerance(), processInputs(), processSinglePeakFitResult(), setupParameterTableWorkspace(), and writeFitResult().

◆ m_numSpectraToFit

std::size_t Mantid::Algorithms::FitPeaks::m_numSpectraToFit

private

total number of spectra to be fit

Definition at line 303 of file FitPeaks.h.

Referenced by fitPeaks(), generateOutputPeakPositionWS(), and processInputs().

◆ m_outputPeakPositionWorkspace

API::MatrixWorkspace_sptr Mantid::Algorithms::FitPeaks::m_outputPeakPositionWorkspace

private

output workspace for peak positions

Definition at line 246 of file FitPeaks.h.

Referenced by generateOutputPeakPositionWS(), processOutputs(), and writeFitResult().

◆ m_peakCenters

std::vector<double> Mantid::Algorithms::FitPeaks::m_peakCenters

private

Designed peak positions and tolerance.

Definition at line 282 of file FitPeaks.h.

Referenced by processInputFitRanges(), and processInputPeakCenters().

◆ m_peakCenterWorkspace

API::MatrixWorkspace_const_sptr Mantid::Algorithms::FitPeaks::m_peakCenterWorkspace

private

Definition at line 283 of file FitPeaks.h.

Referenced by processInputFitRanges(), and processInputPeakCenters().

◆ m_peakFunction

API::IPeakFunction_sptr Mantid::Algorithms::FitPeaks::m_peakFunction

private

Peak profile name.

Definition at line 262 of file FitPeaks.h.

Referenced by calculateFittedPeaks(), convertParametersNameToIndex(), fitPeaks(), fitSpectrumPeaks(), generateFittedParametersValueWorkspaces(), processInputFunctions(), processInputs(), validateInputs(), and writeFitResult().

◆ m_peakParamNames

std::vector<std::string> Mantid::Algorithms::FitPeaks::m_peakParamNames

private

input peak parameters' names

Definition at line 317 of file FitPeaks.h.

Referenced by convertParametersNameToIndex(), and processInputFunctions().

◆ m_peakPosTolCase234

bool Mantid::Algorithms::FitPeaks::m_peakPosTolCase234

private

peak positon tolerance case b, c and d

Definition at line 342 of file FitPeaks.h.

Referenced by processInputPeakTolerance(), and processSinglePeakFitResult().

◆ m_peakPosTolerances

std::vector<double> Mantid::Algorithms::FitPeaks::m_peakPosTolerances

private

tolerances for fitting peak positions

Definition at line 305 of file FitPeaks.h.

Referenced by processInputPeakTolerance(), and processSinglePeakFitResult().

◆ m_peakWidthEstimateApproach

Algorithms::PeakParameterHelper::EstimatePeakWidth Mantid::Algorithms::FitPeaks::m_peakWidthEstimateApproach

private

Flag for observing peak width: there are 3 states (1) no estimation (2) from 'observation' (3) calculated from instrument resolution.

Definition at line 309 of file FitPeaks.h.

Referenced by fitFunctionSD(), fitSpectrumPeaks(), and processInputs().

◆ m_peakWidthPercentage

double Mantid::Algorithms::FitPeaks::m_peakWidthPercentage

private

flag to estimate peak width from

Definition at line 295 of file FitPeaks.h.

Referenced by fitFunctionSD(), processInputFitRanges(), and processInputs().

◆ m_peakWindowVector

std::vector<std::vector<double> > Mantid::Algorithms::FitPeaks::m_peakWindowVector

private

peak windows

Definition at line 313 of file FitPeaks.h.

Referenced by processInputFitRanges().

◆ m_peakWindowWorkspace

API::MatrixWorkspace_const_sptr Mantid::Algorithms::FitPeaks::m_peakWindowWorkspace

private

Definition at line 314 of file FitPeaks.h.

Referenced by processInputFitRanges().

◆ m_profileStartingValueTable

API::ITableWorkspace_const_sptr Mantid::Algorithms::FitPeaks::m_profileStartingValueTable

private

table workspace for profile parameters' starting value

Definition at line 322 of file FitPeaks.h.

Referenced by convertParametersNameToIndex(), processInputFunctions(), and validateInputs().

◆ m_rawPeaksTable

bool Mantid::Algorithms::FitPeaks::m_rawPeaksTable

private

flag to show that the pamarameters in table are raw parameters or effective parameters

Definition at line 254 of file FitPeaks.h.

Referenced by generateFittedParametersValueWorkspaces(), and writeFitResult().

◆ m_startWorkspaceIndex

std::size_t Mantid::Algorithms::FitPeaks::m_startWorkspaceIndex

private

start index

Definition at line 299 of file FitPeaks.h.

Referenced by calculateFittedPeaks(), checkWorkspaceIndices(), fitPeaks(), generateOutputPeakPositionWS(), processInputFitRanges(), processInputPeakCenters(), processInputs(), setupParameterTableWorkspace(), and writeFitResult().

◆ m_stopWorkspaceIndex

std::size_t Mantid::Algorithms::FitPeaks::m_stopWorkspaceIndex

private

stop index (workspace index of the last spectrum included)

Definition at line 301 of file FitPeaks.h.

Referenced by calculateFittedPeaks(), checkWorkspaceIndices(), fitPeaks(), processInputFitRanges(), processInputPeakCenters(), processInputs(), and setupParameterTableWorkspace().

◆ m_uniformPeakPositions

bool Mantid::Algorithms::FitPeaks::m_uniformPeakPositions

private

Definition at line 286 of file FitPeaks.h.

Referenced by processInputFitRanges(), and processInputPeakCenters().

◆ m_uniformProfileStartingValue

bool Mantid::Algorithms::FitPeaks::m_uniformProfileStartingValue

private

flag for profile startng value being uniform or not

Definition at line 324 of file FitPeaks.h.

Referenced by processInputFunctions().

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

Framework/Algorithms/inc/MantidAlgorithms/FitPeaks.h
Framework/Algorithms/src/FitPeaks.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FitPeaks()

Member Function Documentation

◆ calculateFittedPeaks()

◆ calculateSignalToNoiseRatio()

◆ calculateSignalToSigmaRatio()

◆ category()

◆ checkPeakIndices()

◆ checkPeakWindowEdgeOrder()

◆ checkWorkspaceIndices()

◆ convertParametersNameToIndex()

◆ createMatrixWorkspace()

◆ decideToEstimatePeakParams()

◆ exec()

◆ fitBackground()

◆ fitFunctionHighBackground()

◆ fitFunctionMD()

◆ fitFunctionSD()

◆ fitIndividualPeak()

◆ fitPeaks()

◆ fitSpectrumPeaks()

◆ generateCalculatedPeaksWS()

◆ generateFittedParametersValueWorkspaces()

◆ generateOutputPeakPositionWS()

◆ getPeakHeightParameterName()

◆ getRangeData()

◆ histRangeToDataPointCount()

◆ histRangeToIndexBounds()

◆ init()

◆ isObservablePeakProfile()

◆ logNoOffset()

◆ name()

◆ numberCounts() [1/2]

◆ numberCounts() [2/2]

◆ processInputFitRanges()

◆ processInputFunctions()

◆ processInputPeakCenters()

◆ processInputPeakTolerance()

◆ processInputs()

◆ processOutputs()

◆ processSinglePeakFitResult()

◆ setupParameterTableWorkspace()

◆ summary()

◆ validateInputs()

◆ version()

◆ writeFitResult()

Member Data Documentation

◆ m_bkgdFunction

◆ m_constrainPeaksPosition

◆ m_costFunction

◆ m_fitErrorTable

◆ m_fitIterations

◆ m_fitPeaksFromRight

◆ m_fittedParamTable

◆ m_fittedPeakWS

◆ m_getExpectedPeakPositions

◆ m_getPeakFitWindow

◆ m_highBackground

◆ m_initParamIndexes

◆ m_initParamValues

◆ m_inputEventWS

◆ m_inputIsDSpace

◆ m_inputMatrixWS

◆ m_linearBackgroundFunction

◆ m_minimizer

◆ m_minPeakHeight

◆ m_minPeakTotalCount

◆ m_minSignalToNoiseRatio

◆ m_minSignalToSigmaRatio

◆ m_numPeaksToFit

◆ m_numSpectraToFit

◆ m_outputPeakPositionWorkspace

◆ m_peakCenters

◆ m_peakCenterWorkspace

◆ m_peakFunction