Mantid
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RefinePowderInstrumentParameters : Algorithm to refine instrument geometry parameters only. More...
#include <RefinePowderInstrumentParameters.h>
Public Member Functions | |
const std::string | category () const override |
Algorithm's category for identification overriding a virtual method. More... | |
const std::string | name () const override |
Algorithm's name for identification overriding a virtual method. More... | |
RefinePowderInstrumentParameters () | |
Constructor. More... | |
const std::string | summary () const override |
Summary of algorithms purpose. More... | |
int | version () const override |
Algorithm's version for identification overriding a virtual method. More... | |
Public Member Functions inherited from Mantid::API::Algorithm | |
Algorithm () | |
Constructor. More... | |
Algorithm (const Algorithm &)=delete | |
Algorithm & | operator= (const Algorithm &)=delete |
~Algorithm () override | |
Virtual destructor. More... | |
void | initialize () override |
Initialization method invoked by the framework. More... | |
bool | execute () override final |
The actions to be performed by the algorithm on a dataset. More... | |
void | addTimer (const std::string &name, const Kernel::time_point_ns &begin, const Kernel::time_point_ns &end) |
void | executeAsChildAlg () override |
Execute as a Child Algorithm. More... | |
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::Logger & | getLogger () const |
Returns a reference to the logger. More... | |
void | setLogging (const bool value) override |
Logging can be disabled by passing a value of false. More... | |
bool | isLogging () const override |
returns the status of logging, True = enabled More... | |
void | setLoggingOffset (const int value) override |
gets the logging priority offset More... | |
int | getLoggingOffset () const override |
returns the logging priority offset More... | |
void | setAlgStartupLogging (const bool enabled) override |
disable Logging of start and end messages More... | |
bool | getAlgStartupLogging () const override |
get the state of Logging of start and end messages More... | |
void | setChildStartProgress (const double startProgress) const override |
setting the child start progress More... | |
void | setChildEndProgress (const double endProgress) const override |
setting the child end progress More... | |
std::string | toString () const override |
Serialize an object to a string. More... | |
::Json::Value | toJson () const override |
Serialize an object to a json object. More... | |
virtual std::shared_ptr< Algorithm > | createChildAlgorithm (const std::string &name, const double startProgress=-1., const double endProgress=-1., const bool enableLogging=true, const int &version=-1) |
Create a Child Algorithm. More... | |
void | setupAsChildAlgorithm (const Algorithm_sptr &algorithm, const double startProgress=-1., const double endProgress=-1., const bool enableLogging=true) |
Setup algorithm as child algorithm. More... | |
void | trackAlgorithmHistory (std::shared_ptr< AlgorithmHistory > parentHist) |
set whether we wish to track the child algorithm's history and pass it the parent object to fill. More... | |
void | findWorkspaces (WorkspaceVector &workspaces, unsigned int direction, bool checkADS=false) const |
Populate lists of the workspace properties for a given direction (InOut workspaces are included in both input/output) More... | |
virtual bool | checkGroups () |
Check the input workspace properties for groups. More... | |
virtual bool | processGroups () |
Process WorkspaceGroup inputs. More... | |
void | copyNonWorkspaceProperties (IAlgorithm *alg, int periodNum) |
Copy all the non-workspace properties from this to alg. More... | |
const Parallel::Communicator & | communicator () const |
Returns a const reference to the (MPI) communicator of the algorithm. More... | |
void | setCommunicator (const Parallel::Communicator &communicator) |
Sets the (MPI) communicator of the algorithm. More... | |
void | declareProperty (std::unique_ptr< Kernel::Property > p, const std::string &doc="") override |
Add a property to the list of managed properties. More... | |
void | declareOrReplaceProperty (std::unique_ptr< Kernel::Property > p, const std::string &doc="") override |
Add or replace property in the list of managed properties. More... | |
void | resetProperties () override |
Reset property values back to initial values (blank or default values) More... | |
void | setProperties (const std::string &propertiesJson, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false) override |
Set the ordered list of properties by one string of values, separated by semicolons. More... | |
void | setProperties (const ::Json::Value &jsonValue, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false) override |
Sets all the declared properties from a json object. More... | |
void | setPropertiesWithString (const std::string &propertiesString, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >()) override |
Sets all the declared properties from a string. More... | |
void | setPropertyValue (const std::string &name, const std::string &value) override |
Set the value of a property by string N.B. More... | |
void | setPropertyValueFromJson (const std::string &name, const Json::Value &value) override |
Set the value of a property by Json::Value object. More... | |
void | setPropertyOrdinal (const int &index, const std::string &value) override |
Set the value of a property by an index N.B. More... | |
virtual void | copyPropertiesFrom (const Algorithm &alg) |
Make m_properties point to the same PropertyManager as alg.m_properties. More... | |
bool | existsProperty (const std::string &name) const override |
Checks whether the named property is already in the list of managed property. More... | |
bool | validateProperties () const override |
Validates all the properties in the collection. More... | |
size_t | propertyCount () const override |
Count the number of properties under management. More... | |
std::string | getPropertyValue (const std::string &name) const override |
Get the value of a property as a string. More... | |
const std::vector< Kernel::Property * > & | getProperties () const override |
Get the list of managed properties. More... | |
std::vector< std::string > | getDeclaredPropertyNames () const noexcept override |
Return the list of declared property names. More... | |
TypedValue | getProperty (const std::string &name) const override |
Get the value of a property. More... | |
std::string | asString (bool withDefaultValues=false) const override |
Return the property manager serialized as a string. More... | |
::Json::Value | asJson (bool withDefaultValues=false) const override |
Return the property manager serialized as a json object. More... | |
bool | isDefault (const std::string &name) const |
void | removeProperty (const std::string &name, const bool delproperty=true) override |
Removes the property from management. More... | |
std::unique_ptr< Kernel::Property > | takeProperty (const size_t index) override |
Removes the property from management and returns a pointer to it. More... | |
void | clear () override |
Clears all properties under management. More... | |
void | afterPropertySet (const std::string &) override |
Override this method to perform a custom action right after a property was set. More... | |
void | filterByTime (const Types::Core::DateAndTime &, const Types::Core::DateAndTime &) override |
void | splitByTime (std::vector< Kernel::SplittingInterval > &, std::vector< Kernel::PropertyManager * >) const override |
void | filterByProperty (const Kernel::TimeSeriesProperty< bool > &, const std::vector< std::string > &) override |
Kernel::Property * | getPointerToProperty (const std::string &name) const override |
Get a property by name. More... | |
Kernel::Property * | getPointerToPropertyOrdinal (const int &index) const override |
Get a property by an index. More... | |
virtual void | declareProperty (std::unique_ptr< Property > p, const std::string &doc="")=0 |
Function to declare properties (i.e. store them) More... | |
template<typename T > | |
void | declareProperty (const std::string &name, T value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc="", const unsigned int direction=Direction::Input) |
Add a property of the template type to the list of managed properties. More... | |
template<typename T > | |
void | declareProperty (const std::string &name, T value, const std::string &doc, const unsigned int direction=Direction::Input) |
Add a property to the list of managed properties with no validator. More... | |
template<typename T > | |
void | declareProperty (const std::string &name, T value, const unsigned int direction) |
Add a property of the template type to the list of managed properties. More... | |
void | declareProperty (const std::string &name, const char *value, IValidator_sptr validator=std::make_shared< NullValidator >(), const std::string &doc=std::string(), const unsigned int direction=Direction::Input) |
Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More... | |
void | declareProperty (const std::string &name, const char *value, const std::string &doc, IValidator_sptr validator=std::make_shared< NullValidator >(), const unsigned int direction=Direction::Input) |
Specialised version of declareProperty template method to prevent the creation of a PropertyWithValue of type const char* if an argument in quotes is passed (it will be converted to a string). More... | |
void | declareProperty (const std::string &name, const char *value, const unsigned int direction) |
Add a property of string type to the list of managed properties. More... | |
const std::vector< std::string > | categories () const override |
Function to return all of the categories that contain this algorithm. More... | |
const std::string | categorySeparator () const override |
Function to return the separator token for the category string. More... | |
const std::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 Property * | getPointerToProperty (const std::string &name) const =0 |
Get a pointer to property by name. More... | |
virtual const std::vector< Property * > & | getProperties () const =0 |
Get the list of managed properties. More... | |
std::vector< Property * > | getPropertiesInGroup (const std::string &group) const |
Get the list of managed properties in a given group. More... | |
virtual TypedValue | getProperty (const std::string &name) const =0 |
Get the value of a property. More... | |
virtual std::string | getPropertyValue (const std::string &name) const =0 |
Get the value of a property as a string. More... | |
virtual size_t | propertyCount () const =0 |
Returns the number of properties under management. More... | |
virtual void | removeProperty (const std::string &name, const bool delproperty=true)=0 |
Removes the property from management. More... | |
virtual void | resetProperties ()=0 |
virtual void | setProperties (const ::Json::Value &jsonValue, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false)=0 |
Sets all the properties from a json object. More... | |
virtual void | setProperties (const std::string &propertiesJson, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >(), bool createMissing=false)=0 |
Sets all properties from a string. More... | |
virtual void | setPropertiesWithString (const std::string &propertiesString, const std::unordered_set< std::string > &ignoreProperties=std::unordered_set< std::string >())=0 |
Sets all the declared properties from a string. More... | |
IPropertyManager * | setProperty (const std::string &name, const char *value) |
Specialised version of setProperty template method to handle const char *. More... | |
IPropertyManager * | setProperty (const std::string &name, const std::string &value) |
Specialised version of setProperty template method to handle std::string. More... | |
template<typename T > | |
IPropertyManager * | setProperty (const std::string &name, const T &value) |
Templated method to set the value of a PropertyWithValue. More... | |
template<typename T > | |
IPropertyManager * | setProperty (const std::string &name, std::unique_ptr< T > value) |
Templated method to set the value of a PropertyWithValue from a std::unique_ptr. More... | |
void | setPropertyGroup (const std::string &name, const std::string &group) |
Set the group for a given property. More... | |
virtual void | setPropertyOrdinal (const int &index, const std::string &value)=0 |
Set the value of a property by an index. More... | |
void | setPropertySettings (const std::string &name, std::unique_ptr< IPropertySettings > settings) |
virtual void | setPropertyValue (const std::string &name, const std::string &value)=0 |
Sets property value from a string. More... | |
virtual void | setPropertyValueFromJson (const std::string &name, const Json::Value &value)=0 |
Sets property value from a Json::Value. More... | |
virtual void | splitByTime (std::vector< SplittingInterval > &, std::vector< PropertyManager * >) const =0 |
virtual std::unique_ptr< Property > | takeProperty (const size_t index)=0 |
Removes the property from management and returns a pointer to it. More... | |
void | updatePropertyValues (const IPropertyManager &other) |
Update values of the existing properties. More... | |
virtual bool | validateProperties () const =0 |
Validates all the properties in the collection. More... | |
virtual | ~IPropertyManager ()=default |
Public Member Functions inherited from Mantid::API::DeprecatedAlgorithm | |
DeprecatedAlgorithm () | |
Does nothing other than make the compiler happy. More... | |
void | deprecatedDate (const std::string &) |
The date the algorithm was deprecated on. More... | |
std::string | deprecationMsg (const IAlgorithm *) |
This merely prints the deprecation error for people to see. More... | |
void | useAlgorithm (const std::string &, const int version=-1) |
The algorithm to use instead of this one. More... | |
virtual | ~DeprecatedAlgorithm () |
Does nothing other than make the compiler happy. More... | |
Private Member Functions | |
double | calculateD2TOFFunction (const API::IFunction_sptr &func, const API::FunctionDomain1DVector &domain, API::FunctionValues &values, const Mantid::HistogramData::HistogramY &rawY, const Mantid::HistogramData::HistogramE &rawE) |
Calculate the value and chi2. More... | |
double | calculateFunctionStatistic (const API::IFunction_sptr &func, const API::MatrixWorkspace_sptr &dataws, size_t workspaceindex) |
Calculate function's statistic. More... | |
void | calculateThermalNeutronSpecial (const API::IFunction_sptr &m_Function, const Mantid::HistogramData::HistogramX &xVals, std::vector< double > &vec_n) |
Calculate d-space value from peak's miller index for thermal neutron. More... | |
void | doParameterSpaceRandomWalk (std::vector< std::string > parnames, std::vector< double > lowerbounds, std::vector< double > upperbounds, std::vector< double > stepsizes, size_t maxsteps, double stepsizescalefactor, bool fit2) |
Core Monte Carlo random walk on parameter-space. More... | |
void | exec () override |
Main execution. More... | |
bool | fitFunction (const API::IFunction_sptr &func, double &gslchi2) |
Fit function to data. More... | |
void | fitInstrumentParameters () |
Fit instrument geometry parameters by ThermalNeutronDtoTOFFunction. More... | |
DataObjects::TableWorkspace_sptr | genMCResultTable () |
Generate an output table workspace for N best fitting result. More... | |
DataObjects::TableWorkspace_sptr | genOutputInstrumentParameterTable () |
Generate (output) table worksspace for instrument parameters. More... | |
void | genPeakCentersWorkspace (bool montecarlo, size_t numbestfit) |
Generate (output) workspace of peak centers. More... | |
void | genPeaksFromTable (const DataObjects::TableWorkspace_sptr &peakparamws) |
Generate peaks from table (workspace) More... | |
void | getD2TOFFuncParamNames (std::vector< std::string > &parnames) |
Get the names of the parameters of D-TOF conversion function. More... | |
void | importMonteCarloParametersFromTable (const DataObjects::TableWorkspace_sptr &tablews, const std::vector< std::string > ¶meternames, std::vector< double > &stepsizes, std::vector< double > &lowerbounds, std::vector< double > &upperbounds) |
Import the Monte Carlo related parameters from table. More... | |
void | importParametersFromTable (const DataObjects::TableWorkspace_sptr ¶meterWS, std::map< std::string, double > ¶meters) |
Import instrument parameter from table (workspace) More... | |
void | init () override |
Parameter declaration. More... | |
std::string | parseFitParameterWorkspace (API::ITableWorkspace_sptr paramws) |
Parse Fit() output parameter workspace. More... | |
std::string | parseFitResult (API::IAlgorithm_sptr fitalg, double &chi2) |
Parse the fitting result. More... | |
void | refineInstrumentParametersMC (const DataObjects::TableWorkspace_sptr ¶meterWS, bool fit2=false) |
Set up and run a monte carlo simulation to refine the peak parameters. More... | |
Private Attributes | |
std::vector< std::pair< double, double > > | m_BestFitChi2s |
N sets of the homemade chi2 and gsl chi2. More... | |
std::vector< std::pair< double, std::vector< double > > > | m_BestFitParameters |
N sets of the peak parameter values for the best N chi2 for MC. More... | |
double | m_BestGSLChi2 |
Best Chi2 ever. More... | |
std::vector< std::pair< double, std::vector< double > > > | m_BestMCParameters |
N sets of the peak parameter values for the best N chi2 for MC. More... | |
DataObjects::Workspace2D_sptr | m_dataWS |
Output Workspace containing the dspacing ~ TOF peak positions. More... | |
std::map< std::string, double > | m_FuncParameters |
Map for function (instrument parameter) More... | |
Functions::ThermalNeutronDtoTOFFunction_sptr | m_Function |
Modelling function. More... | |
size_t | m_MaxNumberStoredParameters |
Maximum number of data stored. More... | |
size_t | m_MinNumFittedPeaks |
Minimum number of fitted peaks for refinement. More... | |
double | m_MinSigma |
Minimum allowed sigma of a peak. More... | |
std::map< std::string, double > | m_OrigParameters |
Map to store the original (input) parameters. More... | |
std::map< std::vector< int >, double > | m_PeakErrors |
Map for all peaks' error (fitted vs. experimental): [HKL]: Chi^2. More... | |
std::vector< std::string > | m_PeakFunctionParameterNames |
Peak function parameter names. More... | |
std::map< std::vector< int >, Functions::BackToBackExponential_sptr > | m_Peaks |
Map for all peaks to fit individually. More... | |
Additional Inherited Members | |
Public Types inherited from Mantid::API::Algorithm | |
using | WorkspaceVector = std::vector< std::shared_ptr< Workspace > > |
Static Public Member Functions inherited from Mantid::API::Algorithm | |
static IAlgorithm_sptr | fromString (const std::string &input) |
De-serialize an object from a string. More... | |
static IAlgorithm_sptr | fromJson (const Json::Value &input) |
De-serialize an object from a Json. More... | |
static IAlgorithm_sptr | fromHistory (const AlgorithmHistory &history) |
Construct an object from a history entry. More... | |
Public Attributes inherited from Mantid::API::Algorithm | |
bool | calledByAlias = false |
Flag to indicate if the algorithm is called by its alias. More... | |
Protected Member Functions inherited from Mantid::API::Algorithm | |
void | exec (Parallel::ExecutionMode executionMode) |
Runs the algorithm with the specified execution mode. More... | |
virtual void | execDistributed () |
Runs the algorithm in distributed execution mode. More... | |
virtual void | execMasterOnly () |
Runs the algorithm in master-only execution mode. More... | |
virtual Parallel::ExecutionMode | getParallelExecutionMode (const std::map< std::string, Parallel::StorageMode > &storageModes) const |
Get correct execution mode based on input storage modes for an MPI run. More... | |
virtual const std::string | workspaceMethodOnTypes () const |
Returns a semi-colon separated list of workspace types to attach this algorithm. More... | |
void | cacheWorkspaceProperties () |
Go through the properties and cache the input/output workspace properties for later use. More... | |
void | cacheInputWorkspaceHistories () |
Cache the histories of any input workspaces so they can be copied over after algorithm completion. More... | |
void | setExecutionState (const ExecutionState state) |
Sets the current execution state. More... | |
void | setResultState (const ResultState state) |
Sets the result execution state. More... | |
void | store () |
Stores any output workspaces into the AnalysisDataService. More... | |
void | progress (double p, const std::string &msg="", double estimatedTime=0.0, int progressPrecision=0) |
Sends ProgressNotification. More... | |
void | interruption_point () |
This is called during long-running operations, and check if the algorithm has requested that it be cancelled. More... | |
Poco::NotificationCenter & | notificationCenter () const |
Return a reference to the algorithm's notification dispatcher. More... | |
void | handleChildProgressNotification (const Poco::AutoPtr< ProgressNotification > &pNf) |
Observation slot for child algorithm progress notification messages, these are scaled and then signalled for this algorithm. More... | |
const Poco::AbstractObserver & | progressObserver () const |
Return a reference to the algorithm's object that is reporting progress. More... | |
bool | isWorkspaceProperty (const Kernel::Property *const prop) const |
checks the property is a workspace property More... | |
bool | trackingHistory () |
get whether we are tracking the history for this algorithm, More... | |
virtual void | fillHistory () |
Copy workspace history for input workspaces to output workspaces and record the history for ths algorithm. More... | |
virtual void | setOtherProperties (IAlgorithm *alg, const std::string &propertyName, const std::string &propertyValue, int periodNum) |
Virtual method to set the non workspace properties for this algorithm. More... | |
template<typename T , const int AllowedIndexTypes = static_cast<int>(IndexType::WorkspaceIndex), typename... WSPropArgs, typename = typename std::enable_if<std::is_convertible<T *, MatrixWorkspace *>::value>::type> | |
void | declareWorkspaceInputProperties (const std::string &propertyName, const std::string &doc, WSPropArgs &&...wsPropArgs) |
Protected Member Functions inherited from Mantid::Kernel::IPropertyManager | |
virtual void | afterPropertySet (const std::string &) |
Override this method to perform a custom action right after a property was set. More... | |
virtual void | clear ()=0 |
Clears all properties under management. More... | |
virtual Property * | getPointerToPropertyOrdinal (const int &index) const =0 |
Get a property by an index. More... | |
template<typename T > | |
T | getValue (const std::string &name) const |
Templated method to get the value of a property. More... | |
template<> | |
MANTID_KERNEL_DLL PropertyManager_sptr | getValue (const std::string &name) const |
template<> | |
MANTID_KERNEL_DLL PropertyManager_const_sptr | getValue (const std::string &name) const |
Static Protected Member Functions inherited from Mantid::API::Algorithm | |
template<typename NumT > | |
static bool | isEmpty (const NumT toCheck) |
checks that the value was not set by users, uses the value in empty double/int. More... | |
Protected Attributes inherited from Mantid::API::Algorithm | |
std::atomic< bool > | m_cancel |
Set to true to stop execution. More... | |
std::atomic< bool > | m_parallelException |
Set if an exception is thrown, and not caught, within a parallel region. More... | |
std::vector< IWorkspaceProperty * > | m_inputWorkspaceProps |
All the WorkspaceProperties that are Input or InOut. Set in execute() More... | |
std::shared_ptr< AlgorithmHistory > | m_history |
Pointer to the history for the algorithm being executed. More... | |
Kernel::Logger | m_log |
Logger for this algorithm. More... | |
Kernel::Logger & | g_log |
std::shared_ptr< AlgorithmHistory > | m_parentHistory |
Pointer to the parent history object (if set) More... | |
std::vector< WorkspaceVector > | m_unrolledInputWorkspaces |
One vector of workspaces for each input workspace property. More... | |
size_t | m_groupSize |
Size of the group(s) being processed. More... | |
bool | m_usingBaseProcessGroups = false |
distinguish between base processGroups() and overriden/algorithm specific versions More... | |
Static Protected Attributes inherited from Mantid::API::Algorithm | |
static size_t | g_execCount = 0 |
Counter to keep track of algorithm execution order. More... | |
RefinePowderInstrumentParameters : Algorithm to refine instrument geometry parameters only.
This algorithm is the second part of the algorithm suite. It must use the output from FitPowderDiffPeaks() as the inputs.
[ASSUMPTIONS]
Definition at line 41 of file RefinePowderInstrumentParameters.h.
Mantid::CurveFitting::Algorithms::RefinePowderInstrumentParameters::RefinePowderInstrumentParameters | ( | ) |
Constructor.
Definition at line 59 of file RefinePowderInstrumentParameters.cpp.
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Calculate the value and chi2.
Calculate the function.
Definition at line 713 of file RefinePowderInstrumentParameters.cpp.
References Mantid::API::FunctionValues::size(), and Mantid::API::FunctionDomain1D::size().
Referenced by doParameterSpaceRandomWalk(), fitInstrumentParameters(), and refineInstrumentParametersMC().
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Calculate function's statistic.
Definition at line 380 of file RefinePowderInstrumentParameters.cpp.
References Mantid::API::Algorithm::createChildAlgorithm(), Mantid::Kernel::Logger::debug(), Mantid::Kernel::Logger::error(), and Mantid::API::Algorithm::g_log.
Referenced by doParameterSpaceRandomWalk(), and fitInstrumentParameters().
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Calculate d-space value from peak's miller index for thermal neutron.
Calculate thermal neutron's d-spacing double RefinePowderInstrumentParameters::calculateDspaceValue(std::vector<int> hkl, double lattice) { FIXME It only works for the assumption that the lattice is cubical double h = static_cast<double>(hkl[0]); double k = static_cast<double>(hkl[1]); double l = static_cast<double>(hkl[2]);.
Calculate value n for thermal neutron peak profile
double d = lattice/sqrt(h*h+k*k+l*l);
return d; } Calculate value n for thermal neutron peak profile
Definition at line 977 of file RefinePowderInstrumentParameters.cpp.
References Mantid::API::Algorithm::g_log, m_Function, n, and Mantid::Kernel::Logger::warning().
Referenced by refineInstrumentParametersMC().
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Algorithm's category for identification overriding a virtual method.
Reimplemented from Mantid::API::Algorithm.
Definition at line 55 of file RefinePowderInstrumentParameters.h.
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Core Monte Carlo random walk on parameter-space.
Core Monte Carlo random walk on parameter-space Arguments.
Definition at line 486 of file RefinePowderInstrumentParameters.cpp.
References calculateD2TOFFunction(), calculateFunctionStatistic(), Mantid::Kernel::Logger::debug(), Mantid::Kernel::Logger::error(), fitFunction(), Mantid::API::Algorithm::g_log, Mantid::API::Algorithm::getProperty(), m_BestFitChi2s, m_BestFitParameters, m_BestGSLChi2, m_BestMCParameters, m_dataWS, m_FuncParameters, m_Function, m_MaxNumberStoredParameters, name(), Mantid::Kernel::Logger::notice(), and Mantid::Geometry::X.
Referenced by refineInstrumentParametersMC().
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Main execution.
Implements Mantid::API::Algorithm.
Definition at line 125 of file RefinePowderInstrumentParameters.cpp.
References Mantid::Kernel::Logger::error(), fitInstrumentParameters(), Mantid::API::Algorithm::g_log, genMCResultTable(), genOutputInstrumentParameterTable(), genPeakCentersWorkspace(), genPeaksFromTable(), Mantid::API::Algorithm::getProperty(), importParametersFromTable(), m_dataWS, m_FuncParameters, m_MaxNumberStoredParameters, m_MinNumFittedPeaks, m_MinSigma, m_OrigParameters, refineInstrumentParametersMC(), and Mantid::Kernel::IPropertyManager::setProperty().
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Fit function to data.
Definition at line 350 of file RefinePowderInstrumentParameters.cpp.
References Mantid::API::Algorithm::createChildAlgorithm(), Mantid::Kernel::Logger::debug(), Mantid::Kernel::Logger::error(), Mantid::API::Algorithm::g_log, and m_dataWS.
Referenced by doParameterSpaceRandomWalk().
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Fit instrument geometry parameters by ThermalNeutronDtoTOFFunction.
Fit instrument parameters.
It is a straight forward fitting to
Definition at line 203 of file RefinePowderInstrumentParameters.cpp.
References calculateD2TOFFunction(), calculateFunctionStatistic(), Mantid::API::Algorithm::createChildAlgorithm(), Mantid::Kernel::Logger::debug(), Mantid::Kernel::Logger::error(), Mantid::API::Algorithm::g_log, Mantid::API::Algorithm::getProperty(), Mantid::Kernel::getZscore(), Mantid::Kernel::Logger::information(), m_dataWS, m_FuncParameters, m_Function, m_OrigParameters, Mantid::API::FunctionDomain1D::size(), Mantid::Geometry::X, and Mantid::Geometry::Y.
Referenced by exec().
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Generate an output table workspace for N best fitting result.
Generate a Monte Carlo result table containing the N best results Column: chi2, parameter1, parameter2, ... ...
Definition at line 1091 of file RefinePowderInstrumentParameters.cpp.
References m_BestFitChi2s, m_BestFitParameters, and m_PeakFunctionParameterNames.
Referenced by exec().
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Generate (output) table worksspace for instrument parameters.
Generate an output table workspace containing the fitted instrument parameters.
Requirement (1): The output table workspace should be usable by Le Bail Fitting
Definition at line 1121 of file RefinePowderInstrumentParameters.cpp.
References m_FuncParameters.
Referenced by exec().
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Generate (output) workspace of peak centers.
Get peak positions from peak functions Arguments: Output: outWS 1 spectrum .
dspacing - peak center
Definition at line 1003 of file RefinePowderInstrumentParameters.cpp.
References Mantid::DataObjects::create(), Mantid::Geometry::UnitCell::d(), Mantid::Kernel::Logger::error(), Mantid::API::Algorithm::g_log, Mantid::API::Algorithm::getProperty(), height, Mantid::Kernel::Logger::information(), Mantid::Kernel::SingletonHolder< T >::Instance(), m_dataWS, m_FuncParameters, m_MinSigma, m_Peaks, and sigma.
Referenced by exec().
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Generate peaks from table (workspace)
Genearte peaks from input workspace m_Peaks are stored in a map.
(HKL) is the key
Definition at line 747 of file RefinePowderInstrumentParameters.cpp.
References Mantid::Kernel::Logger::error(), Mantid::API::Algorithm::g_log, height, Mantid::Kernel::Logger::information(), m_PeakErrors, m_Peaks, and sigma.
Referenced by exec().
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Get the names of the parameters of D-TOF conversion function.
Definition at line 699 of file RefinePowderInstrumentParameters.cpp.
References m_Function.
Referenced by refineInstrumentParametersMC().
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Import the Monte Carlo related parameters from table.
Import the Monte Carlo related parameters from table Arguments.
Definition at line 870 of file RefinePowderInstrumentParameters.cpp.
References Mantid::Kernel::Logger::error(), and Mantid::API::Algorithm::g_log.
Referenced by refineInstrumentParametersMC().
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Import instrument parameter from table (workspace)
Import TableWorkspace containing the instrument parameters for fitting the diffrotometer geometry parameters.
Definition at line 830 of file RefinePowderInstrumentParameters.cpp.
References Mantid::Kernel::Logger::error(), Mantid::API::Algorithm::g_log, and value.
Referenced by exec().
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Parameter declaration.
Implements Mantid::API::Algorithm.
Definition at line 67 of file RefinePowderInstrumentParameters.cpp.
References Mantid::API::Algorithm::declareProperty(), Mantid::Kernel::Direction::InOut, Mantid::Kernel::Direction::Input, Mantid::API::PropertyMode::Optional, and Mantid::Kernel::Direction::Output.
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Algorithm's name for identification overriding a virtual method.
Implements Mantid::API::Algorithm.
Definition at line 47 of file RefinePowderInstrumentParameters.h.
Referenced by doParameterSpaceRandomWalk().
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Parse Fit() output parameter workspace.
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Parse the fitting result.
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Set up and run a monte carlo simulation to refine the peak parameters.
Refine instrument parameters by Monte Carlo method.
Definition at line 418 of file RefinePowderInstrumentParameters.cpp.
References calculateD2TOFFunction(), calculateThermalNeutronSpecial(), doParameterSpaceRandomWalk(), Mantid::API::Algorithm::g_log, getD2TOFFuncParamNames(), Mantid::API::Algorithm::getProperty(), importMonteCarloParametersFromTable(), m_BestFitParameters, m_dataWS, m_Function, m_PeakFunctionParameterNames, Mantid::Kernel::Logger::notice(), Mantid::Geometry::X, and Mantid::Geometry::Y.
Referenced by exec().
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Summary of algorithms purpose.
Implements Mantid::API::Algorithm.
Definition at line 49 of file RefinePowderInstrumentParameters.h.
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Algorithm's version for identification overriding a virtual method.
Implements Mantid::API::Algorithm.
Definition at line 52 of file RefinePowderInstrumentParameters.h.
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N sets of the homemade chi2 and gsl chi2.
Definition at line 151 of file RefinePowderInstrumentParameters.h.
Referenced by doParameterSpaceRandomWalk(), and genMCResultTable().
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N sets of the peak parameter values for the best N chi2 for MC.
It is paired with mPeakFunctionParameterNames
Definition at line 149 of file RefinePowderInstrumentParameters.h.
Referenced by doParameterSpaceRandomWalk(), genMCResultTable(), and refineInstrumentParametersMC().
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Best Chi2 ever.
Definition at line 153 of file RefinePowderInstrumentParameters.h.
Referenced by doParameterSpaceRandomWalk().
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N sets of the peak parameter values for the best N chi2 for MC.
It is paired with mPeakFunctionParameterNames
Definition at line 146 of file RefinePowderInstrumentParameters.h.
Referenced by doParameterSpaceRandomWalk().
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Output Workspace containing the dspacing ~ TOF peak positions.
Definition at line 129 of file RefinePowderInstrumentParameters.h.
Referenced by doParameterSpaceRandomWalk(), exec(), fitFunction(), fitInstrumentParameters(), genPeakCentersWorkspace(), and refineInstrumentParametersMC().
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Map for function (instrument parameter)
Definition at line 138 of file RefinePowderInstrumentParameters.h.
Referenced by doParameterSpaceRandomWalk(), exec(), fitInstrumentParameters(), genOutputInstrumentParameterTable(), and genPeakCentersWorkspace().
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Modelling function.
Definition at line 165 of file RefinePowderInstrumentParameters.h.
Referenced by calculateThermalNeutronSpecial(), doParameterSpaceRandomWalk(), fitInstrumentParameters(), getD2TOFFuncParamNames(), and refineInstrumentParametersMC().
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Maximum number of data stored.
Definition at line 162 of file RefinePowderInstrumentParameters.h.
Referenced by doParameterSpaceRandomWalk(), and exec().
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Minimum number of fitted peaks for refinement.
Definition at line 159 of file RefinePowderInstrumentParameters.h.
Referenced by exec().
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Minimum allowed sigma of a peak.
Definition at line 156 of file RefinePowderInstrumentParameters.h.
Referenced by exec(), and genPeakCentersWorkspace().
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Map to store the original (input) parameters.
Definition at line 140 of file RefinePowderInstrumentParameters.h.
Referenced by exec(), and fitInstrumentParameters().
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Map for all peaks' error (fitted vs. experimental): [HKL]: Chi^2.
Definition at line 135 of file RefinePowderInstrumentParameters.h.
Referenced by genPeaksFromTable().
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Peak function parameter names.
Definition at line 143 of file RefinePowderInstrumentParameters.h.
Referenced by genMCResultTable(), and refineInstrumentParametersMC().
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Map for all peaks to fit individually.
Definition at line 132 of file RefinePowderInstrumentParameters.h.
Referenced by genPeakCentersWorkspace(), and genPeaksFromTable().