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Public Member Functions | Private Member Functions | Private Attributes | List of all members
Mantid::Algorithms::FitPeaks Class Referencefinal

#include <FitPeaks.h>

Inheritance diagram for Mantid::Algorithms::FitPeaks:
Mantid::API::Algorithm Mantid::API::IAlgorithm Mantid::Kernel::IPropertyManager

Public Member Functions

const std::string category () const override
 Algorithm's category for identification. More...
 
 FitPeaks ()
 
const std::string name () const override
 Algorithm's name. More...
 
const std::string summary () const override
 Summary of algorithms purpose. More...
 
std::map< std::string, std::string > validateInputs () override
 Validate inputs. More...
 
int version () const override
 Algorithm's version. More...
 
- Public Member Functions inherited from Mantid::API::Algorithm
 Algorithm ()
 Constructor. More...
 
 Algorithm (const Algorithm &)=delete
 
Algorithmoperator= (const Algorithm &)=delete
 
 ~Algorithm () override
 Virtual destructor. More...
 
void initialize () override
 Initialization method invoked by the framework. More...
 
bool execute () override final
 The actions to be performed by the algorithm on a dataset. More...
 
void addTimer (const std::string &name, const Kernel::time_point_ns &begin, const Kernel::time_point_ns &end)
 
void executeAsChildAlg () override
 Execute as a Child Algorithm. More...
 
std::map< std::string, std::string > validateInputs () override
 Perform validation of ALL the input properties of the algorithm. More...
 
ExecutionState executionState () const override
 Gets the current execution state. More...
 
ResultState resultState () const override
 Gets the current result State. More...
 
bool isInitialized () const override
 Has the Algorithm already been initialized. More...
 
bool isExecuted () const override
 Has the Algorithm already been executed successfully. More...
 
bool isRunning () const override
 True if the algorithm is running. More...
 
bool isReadyForGarbageCollection () const override
 True if the algorithm is ready for garbage collection. More...
 
bool isChild () const override
 To query whether algorithm is a child. More...
 
void setChild (const bool isChild) override
 To set whether algorithm is a child. More...
 
void enableHistoryRecordingForChild (const bool on) override
 Change the state of the history recording flag. More...
 
bool isRecordingHistoryForChild ()
 
void setAlwaysStoreInADS (const bool doStore) override
 Do we ALWAYS store in the AnalysisDataService? This is set to true for python algorithms' child algorithms. More...
 
bool getAlwaysStoreInADS () const override
 Returns true if we always store in the AnalysisDataService. More...
 
void setRethrows (const bool rethrow) override
 Set whether the algorithm will rethrow exceptions. More...
 
Poco::ActiveResult< bool > executeAsync () override
 Asynchronous execution. More...
 
void addObserver (const Poco::AbstractObserver &observer) const override
 Add an observer for a notification. More...
 
void removeObserver (const Poco::AbstractObserver &observer) const override
 Remove an observer. More...
 
void cancel () override
 Raises the cancel flag. More...
 
bool getCancel () const
 Returns the cancellation state. More...
 
Kernel::LoggergetLogger () const
 Returns a reference to the logger. More...
 
void setLogging (const bool value) override
 Logging can be disabled by passing a value of false. More...
 
bool isLogging () const override
 returns the status of logging, True = enabled More...
 
void setLoggingOffset (const int value) override
 gets the logging priority offset More...
 
int getLoggingOffset () const override
 returns the logging priority offset More...
 
void setAlgStartupLogging (const bool enabled) override
 disable Logging of start and end messages More...
 
bool getAlgStartupLogging () const override
 get the state of Logging of start and end messages More...
 
void setChildStartProgress (const double startProgress) const override
 setting the child start progress More...
 
void setChildEndProgress (const double endProgress) const override
 setting the child end progress More...
 
std::string toString () const override
 Serialize an object to a string. More...
 
::Json::Value toJson () const override
 Serialize an object to a json object. More...
 
virtual std::shared_ptr< AlgorithmcreateChildAlgorithm (const std::string &name, const double startProgress=-1., const double endProgress=-1., const bool enableLogging=true, const int &version=-1)
 Create a Child Algorithm. More...
 
void setupAsChildAlgorithm (const Algorithm_sptr &algorithm, const double startProgress=-1., const double endProgress=-1., const bool enableLogging=true)
 Setup algorithm as child algorithm. More...
 
void trackAlgorithmHistory (std::shared_ptr< AlgorithmHistory > parentHist)
 set whether we wish to track the child algorithm's history and pass it the parent object to fill. More...
 
void findWorkspaces (WorkspaceVector &workspaces, unsigned int direction, bool checkADS=false) const
 Populate lists of the workspace properties for a given direction (InOut workspaces are included in both input/output) More...
 
virtual bool checkGroups ()
 Check the input workspace properties for groups. More...
 
virtual bool processGroups ()
 Process WorkspaceGroup inputs. More...
 
void copyNonWorkspaceProperties (IAlgorithm *alg, int periodNum)
 Copy all the non-workspace properties from this to alg. More...
 
const Parallel::Communicator & communicator () const
 Returns a const reference to the (MPI) communicator of the algorithm. More...
 
void setCommunicator (const Parallel::Communicator &communicator)
 Sets the (MPI) communicator of the algorithm. More...
 
void declareProperty (std::unique_ptr< Kernel::Property > p, const std::string &doc="") override
 Add a property to the list of managed properties. More...
 
void declareOrReplaceProperty (std::unique_ptr< Kernel::Property > p, const std::string &doc="") override
 Add or replace property in the list of managed properties. More...
 
void resetProperties () override
 Reset property values back to initial values (blank or default values) More...
 
void setProperties (const std::string &propertiesJson, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false) override
 Set the ordered list of properties by one string of values, separated by semicolons. More...
 
void setProperties (const ::Json::Value &jsonValue, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false) override
 Sets all the declared properties from a json object. More...
 
void setPropertiesWithString (const std::string &propertiesString, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >()) override
 Sets all the declared properties from a string. More...
 
void setPropertyValue (const std::string &name, const std::string &value) override
 Set the value of a property by string N.B. More...
 
void setPropertyValueFromJson (const std::string &name, const Json::Value &value) override
 Set the value of a property by Json::Value object. More...
 
void setPropertyOrdinal (const int &index, const std::string &value) override
 Set the value of a property by an index N.B. More...
 
virtual void copyPropertiesFrom (const Algorithm &alg)
 Make m_properties point to the same PropertyManager as alg.m_properties. More...
 
bool existsProperty (const std::string &name) const override
 Checks whether the named property is already in the list of managed property. More...
 
bool validateProperties () const override
 Validates all the properties in the collection. More...
 
size_t propertyCount () const override
 Count the number of properties under management. More...
 
std::string getPropertyValue (const std::string &name) const override
 Get the value of a property as a string. More...
 
const std::vector< Kernel::Property * > & getProperties () const override
 Get the list of managed properties. More...
 
std::vector< std::string > getDeclaredPropertyNames () const noexcept override
 Return the list of declared property names. More...
 
TypedValue getProperty (const std::string &name) const override
 Get the value of a property. More...
 
std::string asString (bool withDefaultValues=false) const override
 Return the property manager serialized as a string. More...
 
::Json::Value asJson (bool withDefaultValues=false) const override
 Return the property manager serialized as a json object. More...
 
bool isDefault (const std::string &name) const
 
void removeProperty (const std::string &name, const bool delproperty=true) override
 Removes the property from management. More...
 
std::unique_ptr< Kernel::PropertytakeProperty (const size_t index) override
 Removes the property from management and returns a pointer to it. More...
 
void clear () override
 Clears all properties under management. More...
 
void afterPropertySet (const std::string &) override
 Override this method to perform a custom action right after a property was set. More...
 
void filterByTime (const Types::Core::DateAndTime &, const Types::Core::DateAndTime &) override
 
void splitByTime (std::vector< Kernel::SplittingInterval > &, std::vector< Kernel::PropertyManager * >) const override
 
void filterByProperty (const Kernel::TimeSeriesProperty< bool > &, const std::vector< std::string > &) override
 
Kernel::PropertygetPointerToProperty (const std::string &name) const override
 Get a property by name. More...
 
Kernel::PropertygetPointerToPropertyOrdinal (const int &index) const override
 Get a property by an index. More...
 
virtual void declareProperty (std::unique_ptr< Property > p, const std::string &doc="")=0
 Function to declare properties (i.e. store them) More...
 
template<typename T >
void declareProperty (const std::string &name, T value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc="", const unsigned int direction=Direction::Input)
 Add a property of the template type to the list of managed properties. More...
 
template<typename T >
void declareProperty (const std::string &name, T value, const std::string &doc, const unsigned int direction=Direction::Input)
 Add a property to the list of managed properties with no validator. More...
 
template<typename T >
void declareProperty (const std::string &name, T value, const unsigned int direction)
 Add a property of the template type to the list of managed properties. More...
 
void declareProperty (const std::string &name, const char *value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc=std::string(), const unsigned int direction=Direction::Input)
 Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...
 
void declareProperty (const std::string &name, const char *value, const std::string &doc, IValidator_sptr validator=std::make_shared< NullValidator >(), const unsigned int direction=Direction::Input)
 Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...
 
void declareProperty (const std::string &name, const char *value, const unsigned int direction)
 Add a property of string type to the list of managed properties. More...
 
const std::string category () const override
 function to return a category of the algorithm. More...
 
const std::vector< std::string > categories () const override
 Function to return all of the categories that contain this algorithm. More...
 
const std::string categorySeparator () const override
 Function to return the separator token for the category string. More...
 
const std::vector< std::string > seeAlso () const override
 Function to return all of the seeAlso (these are not validated) algorithms related to this algorithm.A default implementation is provided. More...
 
const std::string alias () const override
 function to return any aliases to the algorithm; A default implementation is provided More...
 
const std::string aliasDeprecated () const override
 Expiration date (in ISO8601 format) for the algorithm aliases; default implementation for no expiration date. More...
 
const std::string helpURL () const override
 function to return URL for algorithm documentation; A default implementation is provided. More...
 
template<typename T , typename = typename std::enable_if<std::is_convertible<T *, MatrixWorkspace *>::value>::type>
std::tuple< std::shared_ptr< T >, Indexing::SpectrumIndexSet > getWorkspaceAndIndices (const std::string &name) const
 
template<typename T1 , typename T2 , typename = typename std::enable_if<std::is_convertible<T1 *, MatrixWorkspace *>::value>::type, typename = typename std::enable_if<std::is_convertible<T2 *, std::string *>::value || std::is_convertible<T2 *, std::vector<int64_t> *>::value>::type>
void setWorkspaceInputProperties (const std::string &name, const std::shared_ptr< T1 > &wksp, IndexType type, const T2 &list)
 
template<typename T1 , typename T2 , typename = typename std::enable_if<std::is_convertible<T1 *, MatrixWorkspace *>::value>::type, typename = typename std::enable_if<std::is_convertible<T2 *, std::string *>::value || std::is_convertible<T2 *, std::vector<int64_t> *>::value>::type>
void setWorkspaceInputProperties (const std::string &name, const std::string &wsName, IndexType type, const T2 &list)
 
const std::string workspaceMethodName () const override
 
const std::vector< std::string > workspaceMethodOn () const override
 
const std::string workspaceMethodInputProperty () const override
 
AlgorithmID getAlgorithmID () const override
 Algorithm ID. More...
 
virtual void addObserver (const Poco::AbstractObserver &observer) const =0
 Add an observer for a notification. More...
 
virtual const std::string alias () const =0
 function to return any aliases of the algorithm. More...
 
virtual const std::string aliasDeprecated () const =0
 Expiration date (in ISO8601 format) for the algorithm aliases. Empty if no expiration date. More...
 
virtual void cancel ()=0
 Raises the cancel flag. More...
 
virtual const std::vector< std::string > categories () const =0
 Function to return all of the categories that contain this algorithm. More...
 
virtual const std::string category () const =0
 function to return a category of the algorithm. More...
 
virtual const std::string categorySeparator () const =0
 Function to return the separator token for the category string. More...
 
virtual void enableHistoryRecordingForChild (const bool on)=0
 If true history will be recorded for a child. More...
 
virtual bool execute ()=0
 System execution. More...
 
virtual void executeAsChildAlg ()=0
 Execute as a Child Algorithm, with try/catch. More...
 
virtual Poco::ActiveResult< bool > executeAsync ()=0
 Asynchronous execution of the algorithm. More...
 
virtual ExecutionState executionState () const =0
 Gets the current execution state. More...
 
virtual AlgorithmID getAlgorithmID () const =0
 Algorithm ID. More...
 
virtual bool getAlgStartupLogging () const =0
 get the state of Logging of start and end messages More...
 
virtual bool getAlwaysStoreInADS () const =0
 To query whether the output is stored in the analysis data service. More...
 
virtual int getLoggingOffset () const =0
 returns the logging priority offset More...
 
virtual const std::string helpURL () const =0
 function to return an optional URL for documentation. More...
 
virtual void initialize ()=0
 Initialization method invoked by the framework. More...
 
virtual bool isChild () const =0
 To query whether algorithm is a child. Default to false. More...
 
virtual bool isExecuted () const =0
 Check whether the algorithm has been executed sucessfully. More...
 
virtual bool isInitialized () const =0
 Check whether the algorithm is initialized properly. More...
 
virtual bool isLogging () const =0
 returns the status of logging, True = enabled More...
 
virtual bool isReadyForGarbageCollection () const =0
 True if the algorithm is ready for garbage collection. More...
 
virtual bool isRunning () const =0
 True if the algorithm is running. More...
 
virtual const std::string name () const =0
 function to return a name of the algorithm, must be overridden in all algorithms More...
 
virtual void removeObserver (const Poco::AbstractObserver &observer) const =0
 Remove an observer. More...
 
virtual ResultState resultState () const =0
 Gets the currnet result State. More...
 
virtual const std::vector< std::string > seeAlso () const =0
 Function to return all of the seeAlso algorithms related to this algorithm. More...
 
virtual void setAlgStartupLogging (const bool enabled)=0
 disable Logging of start and end messages More...
 
virtual void setAlwaysStoreInADS (const bool doStore)=0
 Set whether we always store the output in the analysis data service. More...
 
virtual void setChild (const bool isChild)=0
 To set whether algorithm is a child. More...
 
virtual void setChildEndProgress (const double endProgress) const =0
 setting the child end progress More...
 
virtual void setChildStartProgress (const double startProgress) const =0
 setting the child start progress More...
 
virtual void setLogging (const bool value)=0
 Logging can be disabled by passing a value of false. More...
 
virtual void setLoggingOffset (const int value)=0
 gets the logging priority offset More...
 
virtual void setRethrows (const bool rethrow)=0
 To query whether an algorithm should rethrow exceptions when executing. More...
 
virtual const std::string summary () const =0
 function returns a summary message that will be displayed in the default GUI, and in the help. More...
 
virtual ::Json::Value toJson () const =0
 Serialize an algorithm as Json. More...
 
virtual std::string toString () const =0
 Serialize an algorithm. More...
 
virtual std::map< std::string, std::string > validateInputs ()=0
 Method checking errors on ALL the inputs, before execution. More...
 
virtual int version () const =0
 function to return a version of the algorithm, must be overridden in all algorithms More...
 
Algorithms As Methods
- Public Member Functions inherited from Mantid::Kernel::IPropertyManager
virtual ::Json::Value asJson (bool withDefaultValues=false) const =0
 Return the property manager serialized as a json object. More...
 
virtual std::string asString (bool withDefaultValues=false) const =0
 Return the property manager serialized as a string. More...
 
virtual void declareOrReplaceProperty (std::unique_ptr< Property > p, const std::string &doc="")=0
 Function to declare properties (i.e. store them) More...
 
void declareProperty (const std::string &name, const char *value, const std::string &doc, IValidator_sptr validator=std::make_shared< NullValidator >(), const unsigned int direction=Direction::Input)
 Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...
 
void declareProperty (const std::string &name, const char *value, const unsigned int direction)
 Add a property of string type to the list of managed properties. More...
 
void declareProperty (const std::string &name, const char *value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc=std::string(), const unsigned int direction=Direction::Input)
 Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More...
 
template<typename T >
void declareProperty (const std::string &name, T value, const std::string &doc, const unsigned int direction=Direction::Input)
 Add a property to the list of managed properties with no validator. More...
 
template<typename T >
void declareProperty (const std::string &name, T value, const unsigned int direction)
 Add a property of the template type to the list of managed properties. More...
 
template<typename T >
void declareProperty (const std::string &name, T value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc="", const unsigned int direction=Direction::Input)
 Add a property of the template type to the list of managed properties. More...
 
virtual void declareProperty (std::unique_ptr< Property > p, const std::string &doc="")=0
 Function to declare properties (i.e. store them) More...
 
virtual bool existsProperty (const std::string &name) const =0
 Checks whether the named property is already in the list of managed property. More...
 
virtual void filterByProperty (const TimeSeriesProperty< bool > &, const std::vector< std::string > &)=0
 
virtual void filterByTime (const Types::Core::DateAndTime &, const Types::Core::DateAndTime &)=0
 
virtual std::vector< std::string > getDeclaredPropertyNames () const noexcept=0
 Get the list of managed property names. More...
 
virtual PropertygetPointerToProperty (const std::string &name) const =0
 Get a pointer to property by name. More...
 
virtual const std::vector< Property * > & getProperties () const =0
 Get the list of managed properties. More...
 
std::vector< Property * > getPropertiesInGroup (const std::string &group) const
 Get the list of managed properties in a given group. More...
 
virtual TypedValue getProperty (const std::string &name) const =0
 Get the value of a property. More...
 
virtual std::string getPropertyValue (const std::string &name) const =0
 Get the value of a property as a string. More...
 
virtual size_t propertyCount () const =0
 Returns the number of properties under management. More...
 
virtual void removeProperty (const std::string &name, const bool delproperty=true)=0
 Removes the property from management. More...
 
virtual void resetProperties ()=0
 
virtual void setProperties (const ::Json::Value &jsonValue, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false)=0
 Sets all the properties from a json object. More...
 
virtual void setProperties (const std::string &propertiesJson, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false)=0
 Sets all properties from a string. More...
 
virtual void setPropertiesWithString (const std::string &propertiesString, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >())=0
 Sets all the declared properties from a string. More...
 
IPropertyManagersetProperty (const std::string &name, const char *value)
 Specialised version of setProperty template method to handle const char *. More...
 
IPropertyManagersetProperty (const std::string &name, const std::string &value)
 Specialised version of setProperty template method to handle std::string. More...
 
template<typename T >
IPropertyManagersetProperty (const std::string &name, const T &value)
 Templated method to set the value of a PropertyWithValue. More...
 
template<typename T >
IPropertyManagersetProperty (const std::string &name, std::unique_ptr< T > value)
 Templated method to set the value of a PropertyWithValue from a std::unique_ptr. More...
 
void setPropertyGroup (const std::string &name, const std::string &group)
 Set the group for a given property. More...
 
virtual void setPropertyOrdinal (const int &index, const std::string &value)=0
 Set the value of a property by an index. More...
 
void setPropertySettings (const std::string &name, std::unique_ptr< IPropertySettings > settings)
 
virtual void setPropertyValue (const std::string &name, const std::string &value)=0
 Sets property value from a string. More...
 
virtual void setPropertyValueFromJson (const std::string &name, const Json::Value &value)=0
 Sets property value from a Json::Value. More...
 
virtual void splitByTime (std::vector< SplittingInterval > &, std::vector< PropertyManager * >) const =0
 
virtual std::unique_ptr< PropertytakeProperty (const size_t index)=0
 Removes the property from management and returns a pointer to it. More...
 
void updatePropertyValues (const IPropertyManager &other)
 Update values of the existing properties. More...
 
virtual bool validateProperties () const =0
 Validates all the properties in the collection. More...
 
virtual ~IPropertyManager ()=default
 

Private Member Functions

void calculateFittedPeaks (std::vector< std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > > fit_results)
 calculate peak+background for fitted More...
 
void convertParametersNameToIndex ()
 Convert peak function's parameter names to parameter index for fast access. More...
 
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. More...
 
bool decideToEstimatePeakParams (const bool firstPeakInSpectrum, const API::IPeakFunction_sptr &peak_function)
 Decide whether to estimate peak parameters. More...
 
void exec () override
 Main exec method. More...
 
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 More...
 
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 More...
 
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) More...
 
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)
 Fit an individual peak. More...
 
std::vector< std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > > fitPeaks ()
 suites of method to fit peaks More...
 
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)
 fit peaks in a same spectrum More...
 
void generateCalculatedPeaksWS ()
 Generate workspace for calculated values. More...
 
void generateFittedParametersValueWorkspaces ()
 Generate output workspaces. More...
 
void generateOutputPeakPositionWS ()
 main method to create output workspaces More...
 
std::vector< double > getExpectedPeakPositions (size_t wi)
 methods to retrieve fit range and peak centers More...
 
std::pair< double, double > getPeakFitWindow (size_t wi, size_t ipeak)
 get the peak fit window More...
 
std::string getPeakHeightParameterName (const API::IPeakFunction_const_sptr &peak_function)
 Get the parameter name for peak height (I or height or etc) More...
 
void getRangeData (size_t iws, const std::pair< double, double > &fit_window, 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 More...
 
void init () override
 Init. More...
 
bool isObservablePeakProfile (const std::string &peakprofile)
 check whether FitPeaks supports observation on a certain peak profile's parameters (width!) More...
 
void processInputFitRanges ()
 process inputs for peak fitting range More...
 
void processInputFunctions ()
 process inputs for peak and background functions More...
 
void processInputPeakCenters ()
 peak centers More...
 
void processInputPeakTolerance ()
 process inputs about fitted peak positions' tolerance More...
 
void processInputs ()
 process inputs (main and child algorithms) More...
 
void processOutputs (std::vector< std::shared_ptr< FitPeaksAlgorithm::PeakFitResult > > fit_result_vec)
 Set the workspaces and etc to output properties. More...
 
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. More...
 
void reduceByBackground (const API::IBackgroundFunction_sptr &bkgd_func, const std::vector< double > &vec_x, std::vector< double > &vec_y)
 Reduce background. More...
 
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) More...
 
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. More...
 

Private Attributes

API::IBackgroundFunction_sptr m_bkgdFunction
 Background function. More...
 
double m_bkgdSimga
 
bool m_calculateWindowInstrument
 flag to calcualte peak fit window from instrument resolution More...
 
bool m_constrainPeaksPosition
 
std::string m_costFunction
 Cost function. More...
 
API::ITableWorkspace_sptr m_fitErrorTable
 table workspace for fitted parameters' fitting error. This is optional More...
 
int m_fitIterations
 Fit iterations. More...
 
bool m_fitPeaksFromRight
 Fit from right or left. More...
 
API::ITableWorkspace_sptr m_fittedParamTable
 output analysis workspaces table workspace for fitted parameters More...
 
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 More...
 
bool m_highBackground
 flag for high background More...
 
std::vector< size_t > m_initParamIndexes
 input starting parameters' indexes in peak function More...
 
std::vector< double > m_initParamValues
 input peak parameters' starting values corresponding to above peak parameter names More...
 
DataObjects::EventWorkspace_const_sptr m_inputEventWS
 event workspace for input More...
 
bool m_inputIsDSpace
 
API::MatrixWorkspace_sptr m_inputMatrixWS
 mandatory input and output workspaces More...
 
API::IBackgroundFunction_sptr m_linearBackgroundFunction
 Linear background function for high background fitting. More...
 
std::string m_minimizer
 Minimzer. More...
 
double m_minPeakHeight
 minimum peak height without background and it also serves as the criteria for observed peak parameter More...
 
size_t m_numPeaksToFit
 
API::MatrixWorkspace_sptr m_outputPeakPositionWorkspace
 output workspace for peak positions More...
 
bool m_partialSpectra
 flag whether the peak center workspace has only a subset of spectra to fit More...
 
bool m_partialWindowSpectra
 
std::vector< double > m_peakCenters
 Designed peak positions and tolerance. More...
 
API::MatrixWorkspace_const_sptr m_peakCenterWorkspace
 
API::IPeakFunction_sptr m_peakFunction
 Peak profile name. More...
 
std::vector< std::string > m_peakParamNames
 input peak parameters' names More...
 
bool m_peakPosTolCase234
 peak positon tolerance case b, c and d More...
 
std::vector< double > m_peakPosTolerances
 
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. More...
 
double m_peakWidthPercentage
 flag to estimate peak width from More...
 
std::vector< std::vector< double > > m_peakWindowVector
 peak windows More...
 
API::MatrixWorkspace_const_sptr m_peakWindowWorkspace
 
API::ITableWorkspace_const_sptr m_profileStartingValueTable
 table workspace for profile parameters' starting value More...
 
bool m_rawPeaksTable
 flag to show that the pamarameters in table are raw parameters or effective parameters More...
 
size_t m_startWorkspaceIndex
 start index More...
 
size_t m_stopWorkspaceIndex
 stop index (workspace index of the last spectrum included) More...
 
bool m_uniformPeakPositions
 
bool m_uniformPeakWindows
 
bool m_uniformProfileStartingValue
 flag for profile startng value being uniform or not More...
 

Additional Inherited Members

- Public Types inherited from Mantid::API::Algorithm
using WorkspaceVector = std::vector< std::shared_ptr< Workspace > >
 
- Static Public Member Functions inherited from Mantid::API::Algorithm
static IAlgorithm_sptr fromString (const std::string &input)
 De-serialize an object from a string. More...
 
static IAlgorithm_sptr fromJson (const Json::Value &input)
 De-serialize an object from a Json. More...
 
static IAlgorithm_sptr fromHistory (const AlgorithmHistory &history)
 Construct an object from a history entry. More...
 
- Public Attributes inherited from Mantid::API::Algorithm
bool calledByAlias = false
 Flag to indicate if the algorithm is called by its alias. More...
 
- Protected Member Functions inherited from Mantid::API::Algorithm
void exec (Parallel::ExecutionMode executionMode)
 Runs the algorithm with the specified execution mode. More...
 
virtual void execDistributed ()
 Runs the algorithm in distributed execution mode. More...
 
virtual void execMasterOnly ()
 Runs the algorithm in master-only execution mode. More...
 
virtual Parallel::ExecutionMode getParallelExecutionMode (const std::map< std::string, Parallel::StorageMode > &storageModes) const
 Get correct execution mode based on input storage modes for an MPI run. More...
 
virtual const std::string workspaceMethodOnTypes () const
 Returns a semi-colon separated list of workspace types to attach this algorithm. More...
 
void cacheWorkspaceProperties ()
 Go through the properties and cache the input/output workspace properties for later use. More...
 
void cacheInputWorkspaceHistories ()
 Cache the histories of any input workspaces so they can be copied over after algorithm completion. More...
 
void setExecutionState (const ExecutionState state)
 Sets the current execution state. More...
 
void setResultState (const ResultState state)
 Sets the result execution state. More...
 
void store ()
 Stores any output workspaces into the AnalysisDataService. More...
 
void progress (double p, const std::string &msg="", double estimatedTime=0.0, int progressPrecision=0)
 Sends ProgressNotification. More...
 
void interruption_point ()
 This is called during long-running operations, and check if the algorithm has requested that it be cancelled. More...
 
Poco::NotificationCenter & notificationCenter () const
 Return a reference to the algorithm's notification dispatcher. More...
 
void handleChildProgressNotification (const Poco::AutoPtr< ProgressNotification > &pNf)
 Observation slot for child algorithm progress notification messages, these are scaled and then signalled for this algorithm. More...
 
const Poco::AbstractObserver & progressObserver () const
 Return a reference to the algorithm's object that is reporting progress. More...
 
bool isWorkspaceProperty (const Kernel::Property *const prop) const
 checks the property is a workspace property More...
 
bool trackingHistory ()
 get whether we are tracking the history for this algorithm, More...
 
virtual void fillHistory ()
 Copy workspace history for input workspaces to output workspaces and record the history for ths algorithm. More...
 
virtual void setOtherProperties (IAlgorithm *alg, const std::string &propertyName, const std::string &propertyValue, int periodNum)
 Virtual method to set the non workspace properties for this algorithm. More...
 
template<typename T , const int AllowedIndexTypes = static_cast<int>(IndexType::WorkspaceIndex), typename... WSPropArgs, typename = typename std::enable_if<std::is_convertible<T *, MatrixWorkspace *>::value>::type>
void declareWorkspaceInputProperties (const std::string &propertyName, const std::string &doc, WSPropArgs &&...wsPropArgs)
 
- Protected Member Functions inherited from Mantid::Kernel::IPropertyManager
virtual void afterPropertySet (const std::string &)
 Override this method to perform a custom action right after a property was set. More...
 
virtual void clear ()=0
 Clears all properties under management. More...
 
virtual PropertygetPointerToPropertyOrdinal (const int &index) const =0
 Get a property by an index. More...
 
template<typename T >
getValue (const std::string &name) const
 Templated method to get the value of a property. More...
 
template<>
MANTID_KERNEL_DLL PropertyManager_sptr getValue (const std::string &name) const
 
template<>
MANTID_KERNEL_DLL PropertyManager_const_sptr getValue (const std::string &name) const
 
- Static Protected Member Functions inherited from Mantid::API::Algorithm
template<typename NumT >
static bool isEmpty (const NumT toCheck)
 checks that the value was not set by users, uses the value in empty double/int. More...
 
- Protected Attributes inherited from Mantid::API::Algorithm
std::atomic< bool > m_cancel
 Set to true to stop execution. More...
 
std::atomic< bool > m_parallelException
 Set if an exception is thrown, and not caught, within a parallel region. More...
 
std::vector< IWorkspaceProperty * > m_inputWorkspaceProps
 All the WorkspaceProperties that are Input or InOut. Set in execute() More...
 
std::shared_ptr< AlgorithmHistorym_history
 Pointer to the history for the algorithm being executed. More...
 
Kernel::Logger m_log
 Logger for this algorithm. More...
 
Kernel::Loggerg_log
 
std::shared_ptr< AlgorithmHistorym_parentHistory
 Pointer to the parent history object (if set) More...
 
std::vector< WorkspaceVectorm_unrolledInputWorkspaces
 One vector of workspaces for each input workspace property. More...
 
size_t m_groupSize
 Size of the group(s) being processed. More...
 
bool m_usingBaseProcessGroups = false
 distinguish between base processGroups() and overriden/algorithm specific versions More...
 
- Static Protected Attributes inherited from Mantid::API::Algorithm
static size_t g_execCount = 0
 Counter to keep track of algorithm execution order. More...
 

Detailed Description

Definition at line 65 of file FitPeaks.h.

Constructor & Destructor Documentation

◆ FitPeaks()

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

Definition at line 197 of file FitPeaks.cpp.

Member Function Documentation

◆ calculateFittedPeaks()

void Mantid::Algorithms::FitPeaks::calculateFittedPeaks ( 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 1272 of file FitPeaks.cpp.

References Mantid::API::FunctionValues::getCalculated(), getPeakFitWindow(), m_bkgdFunction, m_fittedParamTable, m_fittedPeakWS, 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().

◆ category()

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

Algorithm's category for identification.

Implements Mantid::API::IAlgorithm.

Definition at line 79 of file FitPeaks.h.

◆ 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 810 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 1657 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 1118 of file FitPeaks.cpp.

References m_initParamIndexes, and m_initParamValues.

Referenced by fitSpectrumPeaks().

◆ exec()

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

◆ 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

◆ 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 1615 of file FitPeaks.cpp.

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

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

◆ 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 1460 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 
)
private

Fit an individual peak.

Definition at line 1431 of file FitPeaks.cpp.

References fitFunctionHighBackground(), fitFunctionSD(), m_highBackground, m_inputMatrixWS, and m_minPeakHeight.

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 842 of file FitPeaks.cpp.

References fitSpectrumPeaks(), getExpectedPeakPositions(), Mantid::Kernel::SingletonHolder< T >::Instance(), m_bkgdFunction, m_numPeaksToFit, 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 
)
private

◆ 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 1782 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 1740 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 1682 of file FitPeaks.cpp.

References getExpectedPeakPositions(), m_numPeaksToFit, m_outputPeakPositionWorkspace, m_startWorkspaceIndex, and m_stopWorkspaceIndex.

Referenced by exec().

◆ getExpectedPeakPositions()

std::vector< double > Mantid::Algorithms::FitPeaks::getExpectedPeakPositions ( size_t  wi)
private

methods to retrieve fit range and peak centers

Get the expected peak's position.

Definition at line 1818 of file FitPeaks.cpp.

References m_numPeaksToFit, m_peakCenters, m_peakCenterWorkspace, m_startWorkspaceIndex, m_stopWorkspaceIndex, and m_uniformPeakPositions.

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

◆ getPeakFitWindow()

std::pair< double, double > Mantid::Algorithms::FitPeaks::getPeakFitWindow ( size_t  wi,
size_t  ipeak 
)
private

◆ 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 2077 of file FitPeaks.cpp.

References name().

◆ getRangeData()

void Mantid::Algorithms::FitPeaks::getRangeData ( size_t  iws,
const std::pair< double, double > &  fit_window,
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

Definition at line 1903 of file FitPeaks.cpp.

References Mantid::Algorithms::PeakParameterHelper::findXIndex(), and m_inputMatrixWS.

Referenced by fitFunctionHighBackground().

◆ init()

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

◆ 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 1379 of file FitPeaks.cpp.

Referenced by processInputs().

◆ name()

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

Algorithm's name.

Implements Mantid::API::Algorithm.

Definition at line 70 of file FitPeaks.h.

Referenced by getPeakHeightParameterName(), and validateInputs().

◆ processInputFitRanges()

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

◆ processInputFunctions()

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

◆ processInputPeakCenters()

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

peak centers

Processing peaks centers and fitting tolerance information from input.

the parameters that are set including

  1. m_peakCenters/m_peakCenterWorkspace/m_uniformPeakPositions (bool)/m_partialSpectra (bool)
  2. m_peakPosTolerances (vector)
  3. m_numPeaksToFit

Definition at line 712 of file FitPeaks.cpp.

References Mantid::Kernel::Logger::debug(), Mantid::Kernel::Logger::error(), Mantid::API::Algorithm::g_log, Mantid::API::Algorithm::getProperty(), Mantid::API::Algorithm::getPropertyValue(), m_inputMatrixWS, m_numPeaksToFit, m_partialSpectra, 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

  1. m_peakPosTolerances (vector)

Definition at line 771 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_numPeaksToFit, m_peakPosTolCase234, and m_peakPosTolerances.

Referenced by processInputs().

◆ processInputs()

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

◆ processOutputs()

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

◆ 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 1158 of file FitPeaks.cpp.

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

Referenced by fitSpectrumPeaks().

◆ reduceByBackground()

void Mantid::Algorithms::FitPeaks::reduceByBackground ( const API::IBackgroundFunction_sptr bkgd_func,
const std::vector< double > &  vec_x,
std::vector< double > &  vec_y 
)
private

Reduce background.

Reduce Y value with given background function.

Parameters
bkgd_func:: bacground function pointer
vec_x:: vector of X valye
vec_y:: (input/output) vector Y to be reduced by background function

Definition at line 1950 of file FitPeaks.cpp.

Referenced by fitFunctionHighBackground().

◆ 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 1707 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 73 of file FitPeaks.h.

◆ validateInputs()

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

◆ version()

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

Algorithm's version.

Implements Mantid::API::Algorithm.

Definition at line 76 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 1975 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

◆ m_bkgdSimga

double Mantid::Algorithms::FitPeaks::m_bkgdSimga
private

Definition at line 276 of file FitPeaks.h.

Referenced by processInputs().

◆ m_calculateWindowInstrument

bool Mantid::Algorithms::FitPeaks::m_calculateWindowInstrument
private

flag to calcualte peak fit window from instrument resolution

Definition at line 257 of file FitPeaks.h.

Referenced by getPeakFitWindow(), and processInputFitRanges().

◆ m_constrainPeaksPosition

bool Mantid::Algorithms::FitPeaks::m_constrainPeaksPosition
private

Definition at line 249 of file FitPeaks.h.

Referenced by fitFunctionSD(), and processInputs().

◆ m_costFunction

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

Cost function.

Definition at line 218 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 198 of file FitPeaks.h.

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

◆ m_fitIterations

int Mantid::Algorithms::FitPeaks::m_fitIterations
private

Fit iterations.

Definition at line 222 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 220 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 196 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 205 of file FitPeaks.h.

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

◆ m_highBackground

bool Mantid::Algorithms::FitPeaks::m_highBackground
private

flag for high background

Definition at line 275 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 226 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 263 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 191 of file FitPeaks.h.

◆ m_inputIsDSpace

bool Mantid::Algorithms::FitPeaks::m_inputIsDSpace
private

Definition at line 189 of file FitPeaks.h.

Referenced by processInputFitRanges(), and processInputs().

◆ m_inputMatrixWS

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

◆ m_linearBackgroundFunction

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

Linear background function for high background fitting.

Definition at line 213 of file FitPeaks.h.

Referenced by fitFunctionHighBackground(), and processInputFunctions().

◆ m_minimizer

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

Minimzer.

Definition at line 216 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 272 of file FitPeaks.h.

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

◆ m_numPeaksToFit

size_t Mantid::Algorithms::FitPeaks::m_numPeaksToFit
private

◆ m_outputPeakPositionWorkspace

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

output workspace for peak positions

Definition at line 193 of file FitPeaks.h.

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

◆ m_partialSpectra

bool Mantid::Algorithms::FitPeaks::m_partialSpectra
private

flag whether the peak center workspace has only a subset of spectra to fit

Definition at line 243 of file FitPeaks.h.

Referenced by processInputFitRanges(), and processInputPeakCenters().

◆ m_partialWindowSpectra

bool Mantid::Algorithms::FitPeaks::m_partialWindowSpectra
private

Definition at line 255 of file FitPeaks.h.

Referenced by processInputFitRanges().

◆ m_peakCenters

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

Designed peak positions and tolerance.

Definition at line 229 of file FitPeaks.h.

Referenced by getExpectedPeakPositions(), processInputFitRanges(), and processInputPeakCenters().

◆ m_peakCenterWorkspace

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

◆ m_peakFunction

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

◆ m_peakParamNames

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

input peak parameters' names

Definition at line 260 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 280 of file FitPeaks.h.

Referenced by processInputPeakTolerance(), and processSinglePeakFitResult().

◆ m_peakPosTolerances

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

Definition at line 244 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 248 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 235 of file FitPeaks.h.

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

◆ m_peakWindowVector

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

peak windows

Definition at line 252 of file FitPeaks.h.

Referenced by getPeakFitWindow(), and processInputFitRanges().

◆ m_peakWindowWorkspace

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

Definition at line 253 of file FitPeaks.h.

Referenced by getPeakFitWindow(), and processInputFitRanges().

◆ m_profileStartingValueTable

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

table workspace for profile parameters' starting value

Definition at line 265 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 201 of file FitPeaks.h.

Referenced by generateFittedParametersValueWorkspaces(), and writeFitResult().

◆ m_startWorkspaceIndex

size_t Mantid::Algorithms::FitPeaks::m_startWorkspaceIndex
private

◆ m_stopWorkspaceIndex

size_t Mantid::Algorithms::FitPeaks::m_stopWorkspaceIndex
private

◆ m_uniformPeakPositions

bool Mantid::Algorithms::FitPeaks::m_uniformPeakPositions
private

◆ m_uniformPeakWindows

bool Mantid::Algorithms::FitPeaks::m_uniformPeakWindows
private

Definition at line 254 of file FitPeaks.h.

Referenced by getPeakFitWindow(), and processInputFitRanges().

◆ m_uniformProfileStartingValue

bool Mantid::Algorithms::FitPeaks::m_uniformProfileStartingValue
private

flag for profile startng value being uniform or not

Definition at line 267 of file FitPeaks.h.

Referenced by processInputFunctions().


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