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Mantid
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Namespaces | |
| namespace | CalibrationHelpers |
| CalibrationHelpers : This contains helper methods to move source, sample and detector positions/rotations for an instrument according to some calibration information. | |
| namespace | ConnectedComponentMappingTypes |
| Namespace containing useful typedefs. | |
| namespace | FindSXPeaksHelper |
| namespace | PeakStatisticsTools |
| namespace | Prop |
Classes | |
| class | AddPeakHKL |
| AddPeakHKL : Algorithm to add a peaks to a PeaksWorkspace in the HKL frame. More... | |
| class | AnvredCorrection |
| Calculates anvred correction factors for attenuation due to absorption and scattering in a spherical sample. More... | |
| class | BackgroundStrategy |
| BackgroundStrategy : Abstract class used for identifying elements of a IMDWorkspace that are not considered background. More... | |
| class | CalculatePeaksHKL |
| CalculatePeaksHKL : Calculate the HKL value for each peak without any rounding or optimization of the UB Matrix. More... | |
| class | CalculateUMatrix |
| CalculateUMatrix : Algorithm to calculate the U matrix, given lattice parameters and a list of peaks. More... | |
| class | CentroidPeaks |
| Find the centroid of single-crystal peaks in a 2D Workspace, in order to refine their positions. More... | |
| class | ClearUB |
| ClearUB : Clear the UB matrix from a workspace by removing the oriented lattice. More... | |
| class | Cluster |
| Cluster : Image cluster used by connected component labeling. More... | |
| class | ClusterRegister |
| ClusterRegister : A fly-weight ICluster regeister. More... | |
| class | CombinePeaksWorkspaces |
| An algorithm that combines the sets of peaks in two peaks workspaces. More... | |
| class | CompositeCluster |
| CompositeCluster : Cluster made by by merging other IClusters. More... | |
| class | ConnectedComponentLabeling |
| ConnectedComponentLabelling : Implements connected component labeling on MDHistoWorkspaces. More... | |
| class | ConvertPeaksWorkspace |
| ConvertPeaksWorkspace : Bi-directional conversion between a regular PeaksWorkspace (with instrument) and a LeanElasticPeaksWorkspace (no instrument) More... | |
| class | CountReflections |
| CountReflections. More... | |
| class | DataModeHandler |
| Integrates each time slice using the BivariateNormal formula, adding the results to the peak object. More... | |
| class | DiffPeaksWorkspaces |
| An algorithm that subtracts from a workspace (the LHSWorkspace) any peaks that match entries in a second workspace (the RHSWorkspace). More... | |
| class | DisjointElement |
| DisjointElement : Cluster item used in a disjoint-set data structure. More... | |
| class | FilterPeaks |
| FilterPeaks : Filter a peaks workspace based on a set number of queries to provide a new, filtered peaks workspace. More... | |
| class | FindClusterFaces |
| FindClusterFaces : Algorithm to find faces of clusters in an MDHistoWorkspace (image) More... | |
| class | FindSXPeaks |
| Search detector space for single crystal peaks. More... | |
| class | FindUBUsingFFT |
| FindUBUsingFFT : Algorithm to calculate a UB matrix using fast Fourier transforms given a list of peaks and bounds on the lattice parameters. More... | |
| class | FindUBUsingIndexedPeaks |
| FindUBUsingIndexedPeaks : Algorithm to calculate a UB matrix, given a list of peaks that have already been indexed by some means. More... | |
| class | FindUBUsingLatticeParameters |
| FindUBUsingLatticeParameters : Algorithm to calculate a UB matrix, given lattice parameters and a list of peaks. More... | |
| class | FindUBUsingMinMaxD |
| FindUBUsingMinMaxD : Algorithm to calculate a UB matrix, given bounds on the lattice parameters and a list of peaks. More... | |
| class | GoniometerAnglesFromPhiRotation |
| class | HardThresholdBackground |
| HardThresholdBackground : Implementation of BackgroundStrategy using a fixed background signal value as the threshold. More... | |
| class | HasUB |
| HasUB : Determine if a workspace has a UB matrix on any of it's samples. More... | |
| class | ICluster |
| ICluster : Abstract cluster. More... | |
| class | ImplClusterRegister |
| struct | index |
| Peak indexing algorithm, which works by assigning multiple possible HKL values to each peak and then culling these options by comparison with neighbouring peaks. More... | |
| class | IndexPeaks |
| Implements an algorithm for indexing main and satellites peaks in single crystal peaks. More... | |
| class | IndexSXPeaks |
| class | IntegratePeaksHybrid |
| IntegratePeaksHybrid : Integrate single crystal peaks algorithm. More... | |
| class | IntegratePeaksUsingClusters |
| IntegratePeaksUsingClusters : Uses clustering to integrate peaks. More... | |
| class | IntegratePeakTimeSlices |
| class | LoadHKL |
| LoadHKL : Load an ISAW-style .hkl file into a PeaksWorkspace. More... | |
| class | LoadIsawPeaks |
| Load an ISAW-style .peaks or .integrate file into a PeaksWorkspace. More... | |
| class | LoadIsawSpectrum |
| Load incident spectrum and detector efficiency correction file. More... | |
| class | LoadIsawUB |
| Algorithm to load an ISAW-style ASCII UB matrix and lattice parameters file, and place its information into a workspace. More... | |
| class | MaskPeaksWorkspace |
| Find the offsets for each detector. More... | |
| struct | ModulationProperties |
| Tie together the names of the properties for the modulation vectors. More... | |
| class | NormaliseVanadium |
| Calculates anvred correction factors for attenuation due to absorption and scattering in a spherical sample. More... | |
| class | OptimizeCrystalPlacement |
| OptimizeCrystalPlacement. More... | |
| class | OptimizeLatticeForCellType |
| Find the offsets for each detector. More... | |
| class | OrEnabledWhenProperties |
| class | PeakBackground |
| PeakBackground : Extension of HardThresholdBackground to consider regions of the image as background if they are outside the peaks radius limits (no mater what their theshold is). More... | |
| class | PeakCandidate |
| class | PeakClusterProjection |
| PeakClusterProjection : Maps peaks onto IMDHistoWorkspaces and returns the signal value at the peak center. More... | |
| class | PeakHKLErrors |
| class | PeakIntegration |
| Find the offsets for each detector. More... | |
| class | PeakIntensityVsRadius |
| Calculate the integrated intensity of peaks vs integration radius. More... | |
| class | PeaksInRegion |
| PeaksInRegion : Find peaks that are either inside a box region, or that have a radius of sufficent size, that they intersect the box. More... | |
| class | PeaksIntersection |
| PeaksIntersection : Abstract base algorithm class for algorithms that identify peaks interacting with one or more surfaces i.e. More... | |
| class | PeaksOnSurface |
| PeaksOnSurface : Check peak workspace interaction with a single surface. More... | |
| class | PredictFractionalPeaks |
| Using a set of offset vectors, either provided as separate lists or as a set of vectors, predict whether. More... | |
| class | PredictPeaks |
| Using a known crystal lattice and UB matrix, predict where single crystal peaks should be found in detector/TOF space. More... | |
| class | PredictSatellitePeaks |
| PredictSatellitePeaks : Algorithm to create a PeaksWorkspace with peaks corresponding to fractional h,k,and l values. More... | |
| class | SaveHKL |
| Save a PeaksWorkspace to a Gsas-style ASCII .hkl file. More... | |
| class | SaveIsawPeaks |
| Save a PeaksWorkspace to a ISAW-style ASCII .peaks file. More... | |
| class | SaveIsawUB |
| Algorithm to save a UB matrix and lattice parameters to an ISAW-style ASCII file. More... | |
| class | SaveLauenorm |
| Save a PeaksWorkspace to a lauenorm format http://www.ccp4.ac.uk/cvs/viewvc.cgi/laue/doc/lauenorm.ptx?diff_format=s&revision=1.1.1.1&view=markup. More... | |
| class | SCDCalibratePanels |
| SCDCalibratePanels calibrates instrument parameters for Rectangular Detectors. More... | |
| class | SCDCalibratePanels2 |
| SCDCalibratePanels2 : Using input peakworkspace with indexation results to calibrate each individual panels. More... | |
| class | SCDCalibratePanels2ObjFunc |
| SCDCalibratePanels2ObjFunc : TODO: DESCRIPTION. More... | |
| class | SCDPanelErrors |
| class | SelectCellOfType |
| ShowPossibleCells : Algorithm to display a list of possible conventional cells corresponding to the UB saved in the sample associated with the specified PeaksWorkspace, provided the saved UB is for a Niggli reduced cell. More... | |
| class | SelectCellWithForm |
| ShowPossibleCells : Algorithm to display a list of possible conventional cells corresponding to the UB saved in the sample associated with the specified PeaksWorkspace, provided the saved UB is for a Niggli reduced cell. More... | |
| class | SetCrystalLocation |
| SetCrystalLocation. More... | |
| class | SetGoniometer |
| Define the goniometer used in an experiment by giving the axes and directions of rotations. More... | |
| class | SetSpecialCoordinates |
| SetSpecialCoordinates : More... | |
| class | SetUB |
| SetUB : Algorithm to set the UB matrix, given lattice parameters and u and v vectors as defined in: http://horace.isis.rl.ac.uk/Getting_started. More... | |
| class | ShowPeakHKLOffsets |
| class | ShowPossibleCells |
| ShowPossibleCells : Algorithm to display a list of possible conventional cells corresponding to the UB saved in the sample associated with the specified PeaksWorkspace, provided the saved UB is for a Niggli reduced cell. More... | |
| class | SortHKL |
| Save a PeaksWorkspace to a Gsas-style ASCII .hkl file. More... | |
| class | SortPeaksWorkspace |
| SortPeaksWorkspace : Sort a PeaksWorkspace by a range of properties. More... | |
| class | StatisticsOfPeaksWorkspace |
| Statistics of a PeaksWorkspace. More... | |
| class | TransformHKL |
| TransformHKL : Algorithm to adjust the UB saved in the sample associated with the specified PeaksWorkspace, so the HKL values are reordered or otherwise transformed. More... | |
Typedefs | |
| using | MNPOffset = std::tuple< double, double, double, Kernel::V3D > |
| Tie together a modulated peak number with its offset. More... | |
| using | peakvector = std::vector< FindSXPeaksHelper::SXPeak > |
| using | VecV3D = std::vector< Mantid::Kernel::V3D > |
| using | VecVecV3D = std::vector< VecV3D > |
Functions | |
| std::vector< Kernel::V3D > | addModulationVectors (const std::vector< double > &modVector1, const std::vector< double > &modVector2, const std::vector< double > &modVector3) |
| Create a list of valid modulation vectors from the input. More... | |
| std::vector< MNPOffset > | generateOffsetVectors (const std::vector< double > &hOffsets, const std::vector< double > &kOffsets, const std::vector< double > &lOffsets) |
| Calculate a list of HKL offsets from the given lists of offsets. More... | |
| std::vector< MNPOffset > | generateOffsetVectors (const std::vector< Kernel::V3D > &modVectors, const int maxOrder, const bool crossTerms) |
| Calculate a list of HKL offsets from the given modulation vectors. More... | |
| bool MANTID_CRYSTAL_DLL | lineIntersectsSphere (const Mantid::Kernel::V3D &line, const Mantid::Kernel::V3D &lineStart, const Mantid::Kernel::V3D &peakCenter, const double peakRadius) |
| Non-member helper function. More... | |
| V3D | makeV3DFromVector (const VecDouble &vec) |
| double | qConventionFactor () |
| convenience overload to pull the convention from the config service More... | |
| double | qConventionFactor (const std::string &convention) |
| return -1 if convention is "Crystallography" and 1 otherwise. More... | |
| double | SQRT (double v) |
| void | unionElements (DisjointElement *a, DisjointElement *b) |
| Convenience non-member function. More... | |
| std::vector< Kernel::V3D > | validModulationVectors (const std::vector< double > &modVector1, const std::vector< double > &modVector2, const std::vector< double > &modVector3) |
| Create a list of valid modulation vectors from the input. More... | |
| void | writeXmlParameter (ofstream &ostream, const string &name, const double value) |
Variables | |
| const double | MAX_WAVELENGTH = 50.0 |
| const int | MIN_INDEXED_PEAKS = 3 |
| const size_t | NUM_AXES = 6 |
| How many axes (max) to define. More... | |
| const int | NUM_WAVELENGTHS = static_cast<int>(std::ceil(MAX_WAVELENGTH * STEPS_PER_ANGSTROM)) |
| const double | pc [8][19] |
| const double | radtodeg = 180.0 / M_PI |
| const double | radtodeg_half = 180.0 / M_PI / 2. |
| const double | STEPS_PER_ANGSTROM = 100 |
| using Mantid::Crystal::MNPOffset = typedef std::tuple<double, double, double, Kernel::V3D> |
Tie together a modulated peak number with its offset.
Definition at line 23 of file PeakAlgorithmHelpers.h.
| using Mantid::Crystal::peakvector = typedef std::vector<FindSXPeaksHelper::SXPeak> |
Definition at line 23 of file FindSXPeaks.h.
| using Mantid::Crystal::VecV3D = typedef std::vector<Mantid::Kernel::V3D> |
Definition at line 16 of file PeaksIntersection.h.
| using Mantid::Crystal::VecVecV3D = typedef std::vector<VecV3D> |
Definition at line 17 of file PeaksIntersection.h.
| std::vector< Kernel::V3D > Mantid::Crystal::addModulationVectors | ( | const std::vector< double > & | modVector1, |
| const std::vector< double > & | modVector2, | ||
| const std::vector< double > & | modVector3 | ||
| ) |
Create a list of valid modulation vectors from the input.
Direct add modulation a list to return.
| modVector1 | List of 3 doubles specifying an offset |
| modVector2 | List of 3 doubles specifying an offset |
| modVector3 | List of 3 doubles specifying an offset |
Definition at line 107 of file PeakAlgorithmHelpers.cpp.
References modVectors.
| std::vector< MNPOffset > Mantid::Crystal::generateOffsetVectors | ( | const std::vector< double > & | hOffsets, |
| const std::vector< double > & | kOffsets, | ||
| const std::vector< double > & | lOffsets | ||
| ) |
Calculate a list of HKL offsets from the given lists of offsets.
The final offset vector is computed as (hoffsets[i],koffsets[j],loffsets[k]) for each combination of i,j,k.
All offsets are considered order 1
| hOffsets | A list of offsets in the h direction |
| kOffsets | A list of offsets in the k direction |
| lOffsets | A list of offsets in the l direction |
Definition at line 200 of file PeakAlgorithmHelpers.cpp.
| std::vector< MNPOffset > Mantid::Crystal::generateOffsetVectors | ( | const std::vector< Kernel::V3D > & | modVectors, |
| const int | maxOrder, | ||
| const bool | crossTerms | ||
| ) |
Calculate a list of HKL offsets from the given modulation vectors.
| maxOrder | Integer specifying the multiples of the modulation vector. |
| modVectors | A list of modulation vectors form the user |
| crossTerms | If true then compute products of the modulation vectors |
Definition at line 128 of file PeakAlgorithmHelpers.cpp.
References crossTerms, Mantid::Geometry::m, maxOrder, modVectors, and n.
Referenced by Mantid::Crystal::ModulationProperties::create(), and Mantid::Crystal::PredictFractionalPeaks::getModulationInfo().
| bool Mantid::Crystal::lineIntersectsSphere | ( | const Mantid::Kernel::V3D & | line, |
| const Mantid::Kernel::V3D & | lineStart, | ||
| const Mantid::Kernel::V3D & | peakCenter, | ||
| const double | peakRadius | ||
| ) |
Non-member helper function.
Definition at line 88 of file PeaksOnSurface.cpp.
References lineStart, Mantid::Kernel::V3D::norm(), Mantid::Kernel::normalize(), and Mantid::Kernel::V3D::scalar_prod().
Referenced by Mantid::Crystal::PeaksOnSurface::pointInsideAllExtents().
Definition at line 177 of file PeaksOnSurface.cpp.
Referenced by Mantid::Crystal::PeaksOnSurface::exec().
| double Mantid::Crystal::qConventionFactor | ( | ) |
convenience overload to pull the convention from the config service
Definition at line 36 of file PeakAlgorithmHelpers.cpp.
References Mantid::Kernel::SingletonHolder< T >::Instance(), and qConventionFactor().
Referenced by Mantid::Crystal::PredictPeaks::fillPossibleHKLsUsingPeaksWorkspace(), and qConventionFactor().
| double Mantid::Crystal::qConventionFactor | ( | const std::string & | convention | ) |
return -1 if convention is "Crystallography" and 1 otherwise.
Definition at line 26 of file PeakAlgorithmHelpers.cpp.
| double Mantid::Crystal::SQRT | ( | double | v | ) |
Definition at line 134 of file IntegratePeakTimeSlices.cpp.
Referenced by Mantid::Crystal::IntegratePeakTimeSlices::CalculateIsawIntegrateError(), Mantid::Crystal::IntegratePeakTimeSlices::exec(), Mantid::Crystal::IntegratePeakTimeSlices::Fit(), and Mantid::Crystal::IntegratePeakTimeSlices::UpdateOutputWS().
| void Mantid::Crystal::unionElements | ( | DisjointElement * | a, |
| DisjointElement * | b | ||
| ) |
Convenience non-member function.
| a | : Pointer to first disjoint element to join |
| b | : Pointer to second disjoint element to join |
Definition at line 154 of file DisjointElement.cpp.
References Mantid::Crystal::DisjointElement::unionWith().
| std::vector< Kernel::V3D > Mantid::Crystal::validModulationVectors | ( | const std::vector< double > & | modVector1, |
| const std::vector< double > & | modVector2, | ||
| const std::vector< double > & | modVector3 | ||
| ) |
Create a list of valid modulation vectors from the input.
Check each input is a valid modulation and add it to a list to return.
| modVector1 | List of 3 doubles specifying an offset |
| modVector2 | List of 3 doubles specifying an offset |
| modVector3 | List of 3 doubles specifying an offset |
Definition at line 86 of file PeakAlgorithmHelpers.cpp.
References modVectors.
Referenced by Mantid::Crystal::ModulationProperties::create(), and Mantid::Crystal::PredictFractionalPeaks::validateInputs().
| void Mantid::Crystal::writeXmlParameter | ( | ofstream & | ostream, |
| const string & | name, | ||
| const double | value | ||
| ) |
Definition at line 503 of file SCDCalibratePanels.cpp.
References value.
Referenced by Mantid::Crystal::SCDCalibratePanels::saveXmlFile().
| const double Mantid::Crystal::MAX_WAVELENGTH = 50.0 |
Definition at line 48 of file AnvredCorrection.h.
| const int Mantid::Crystal::MIN_INDEXED_PEAKS = 3 |
Definition at line 25 of file FindUBUsingIndexedPeaks.cpp.
Referenced by Mantid::Crystal::FindUBUsingIndexedPeaks::exec().
| const size_t Mantid::Crystal::NUM_AXES = 6 |
How many axes (max) to define.
Definition at line 31 of file SetGoniometer.cpp.
Referenced by Mantid::Crystal::SetGoniometer::exec(), and Mantid::Crystal::SetGoniometer::init().
| const int Mantid::Crystal::NUM_WAVELENGTHS = static_cast<int>(std::ceil(MAX_WAVELENGTH * STEPS_PER_ANGSTROM)) |
Definition at line 52 of file AnvredCorrection.h.
Referenced by Mantid::Crystal::AnvredCorrection::BuildLamdaWeights().
| const double Mantid::Crystal::pc[8][19] |
Definition at line 23 of file AnvredCorrection.h.
Referenced by Mantid::Crystal::AnvredCorrection::calc_Astar(), and Mantid::Crystal::LoadHKL::exec().
| const double Mantid::Crystal::radtodeg = 180.0 / M_PI |
Definition at line 54 of file AnvredCorrection.h.
Referenced by Mantid::Crystal::AnvredCorrection::absor_sphere(), Mantid::Crystal::SaveHKL::absorbSphere(), Mantid::Crystal::AnvredCorrection::calc_Astar(), and Mantid::Crystal::LoadHKL::exec().
| const double Mantid::Crystal::radtodeg_half = 180.0 / M_PI / 2. |
Definition at line 18 of file NormaliseVanadium.h.
| const double Mantid::Crystal::STEPS_PER_ANGSTROM = 100 |
Definition at line 50 of file AnvredCorrection.h.
Referenced by Mantid::Crystal::AnvredCorrection::BuildLamdaWeights(), and Mantid::Crystal::AnvredCorrection::getEventWeight().
1.9.5