Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X A absorption (RATapi.Project attribute) absorption() (in module RATapi.examples) adaptPCR (controlsClass attribute) (RATapi.Controls attribute) adaptPCR() (in module minimisers.DREAM.functions) Add (RATapi.utils.enums.BackgroundActions attribute) addBackground() (API.projectClass.backgroundsClass method) (API.projectClass.projectClass method) addBackgroundParam() (API.projectClass.projectClass method) addContrast() (API.projectClass.domainsClass method) (API.projectClass.projectClass method) addCustomFile() (API.projectClass.customFileClass method) (API.projectClass.projectClass method) addData() (API.projectClass.dataClass method) (API.projectClass.projectClass method) addDomainContrast() (API.projectClass.domainsClass method) addDomainRatio() (API.projectClass.domainsClass method) addLayer() (API.projectClass.layersClass method) (API.projectClass.projectClass method) addLayerGroup() (API.projectClass.projectClass method) addParameter() (API.projectClass.parametersClass method) addResolution() (API.projectClass.projectClass method) (API.projectClass.resolutionsClass method) addResolutionParam() (API.projectClass.projectClass method) AirSubstrate (RATapi.utils.enums.Geometries attribute) allocateLayersForContrast() (in module targetFunctions.common.groupLayers) allocateParamsToLayers() (in module targetFunctions.common.groupLayers) append_data_background() (in module RATapi.inputs) averageReflectivity() (in module targetFunctions.domainsTF) B background (API.projectClass.projectClass attribute) (domainsClass attribute) (projectClass attribute) background_parameters (RATapi.Project attribute) backgroundParams (backgroundsClass attribute) backgrounds (backgroundsClass attribute) (RATapi.Project attribute) backgroundsClass (class in API.projectClass) backSort() (in module targetFunctions.common) BayesResults (class in RATapi.outputs) bayesShadedPlot() (in module utilities.plotting) BestWithJitter (RATapi.utils.enums.Strategies attribute) Bound (RATapi.utils.enums.BoundHandling attribute) boundaryHandling() (in module minimisers.DREAM.postprocessing) boundHandling (controlsClass attribute) (RATapi.Controls attribute) bulk_in (RATapi.Project attribute) bulk_out (RATapi.Project attribute) bulkIn (domainsClass attribute) (projectClass attribute) BulkIn (RATapi.utils.enums.Hydration attribute) bulkOut (domainsClass attribute) (projectClass attribute) BulkOut (RATapi.utils.enums.Hydration attribute) C calcDelta() (in module minimisers.DREAM.postprocessing) calcEllipsoid() (in module minimisers.NS) calcLogLikelihood() (in module minimisers.DREAM.functions) calcLogPrior() (in module minimisers.DREAM.functions) calcProposal() (in module minimisers.DREAM.functions) calcSldDuringFit (controlsClass attribute) (RATapi.Controls attribute) Calculate (RATapi.utils.enums.Procedures attribute) calculation (RATapi.Project attribute) CalculationResults (class in RATapi.outputs) check_allowed_source() (RATapi.Project method) check_allowed_values() (RATapi.Project method) check_contrast_model_allowed_values() (RATapi.Project method) check_indices() (in module RATapi.inputs) chiSquared() (in module targetFunctions.common.costFunctions) ClassList (class in RATapi) clear() (in module RATapi.events) clone() (API.projectClass.projectClass method) ConfidenceIntervals (class in RATapi.outputs) Constant (RATapi.utils.enums.TypeOptions attribute) constructBackground() (in module targetFunctions.common) constructResolution() (in module targetFunctions.common) ContrastParams (class in RATapi.outputs) contrasts (API.projectClass.projectClass attribute) (contrastsClass attribute) (domainsClass attribute) (projectClass attribute) (RATapi.Project attribute) Contrasts (RATapi.utils.enums.Parallel attribute) contrastsClass (class in API.projectClass) controlsClass (class in API) copyProperties() (in module utilities) coreLayersCalculation() (in module targetFunctions.normalTF) cornerPlot() (in module utilities.plotting) Cpp (RATapi.utils.enums.Languages attribute) createProject() (in module API) crossoverProbability (controlsClass attribute) (RATapi.Controls attribute) custom_files (RATapi.Project attribute) customEnum (class in utilities) customEnum() (utilities.customEnum method) customFile (API.projectClass.projectClass attribute) (domainsClass attribute) (projectClass attribute) customFileClass (class in API.projectClass) CustomLayers (RATapi.utils.enums.LayerModels attribute) customLayers() (in module targetFunctions.domainsTF) (in module targetFunctions.normalTF) CustomXY (RATapi.utils.enums.LayerModels attribute) customXY() (in module targetFunctions.domainsTF) (in module targetFunctions.normalTF) D data (API.projectClass.projectClass attribute) (domainsClass attribute) (projectClass attribute) (RATapi.Project attribute) Data (RATapi.utils.enums.TypeOptions attribute) dataClass (class in API.projectClass) DE (RATapi.utils.enums.Procedures attribute) delete() (API.projectClass.projectClass method) (utilities.dyLibWrapper method) (utilities.pythonWrapper method) delete_IPC() (RATapi.Controls method) deopt() (in module minimisers.DE) disp() (utilities.dyLibWrapper method) (utilities.pythonWrapper method) display (controlsClass attribute) (RATapi.Controls attribute) displayTable() (API.projectClass.backgroundsClass method) (API.projectClass.customFileClass method) (API.projectClass.dataClass method) (API.projectClass.parametersClass method) (API.projectClass.resolutionsClass method) domain_contrasts (RATapi.Project attribute) domain_ratios (RATapi.Project attribute) domainContrasts (API.projectClass.domainsClass attribute) (domainsClass attribute) domainContrastsClass (class in API.projectClass) domainRatio (API.projectClass.domainsClass attribute) (domainsClass attribute) Domains (RATapi.utils.enums.Calculations attribute) domains_custom_layers() (in module RATapi.examples) domains_custom_XY() (in module RATapi.examples) domainsClass (class in API.projectClass) drawCR() (in module minimisers.DREAM.functions) drawEllipsoidPoints() (in module minimisers.NS) drawMCMC() (in module minimisers.NS) drawMultiNest() (in module minimisers.NS) DREAM (RATapi.utils.enums.Procedures attribute) DREAM() (in module minimisers.DREAM.functions) DreamOutput (class in RATapi.outputs) DreamParams (class in RATapi.outputs) DREAMWrapper() (in module minimisers.DREAM) DSPC_custom_layers() (in module RATapi.examples) DSPC_custom_XY() (in module RATapi.examples) DSPC_data_background() (in module RATapi.examples) DSPC_function_background() (in module RATapi.examples) DSPC_standard_layers() (in module RATapi.examples) DylibWrapper (class in RATapi.wrappers) dyLibWrapper (class in utilities) dyLibWrapper() (utilities.dyLibWrapper method) E EventTypes (class in RATapi.rat_core) F FileHandles (class in RATapi.inputs) Final (RATapi.utils.enums.Display attribute) fMinSearch() (in module minimisers.simplex) Fold (RATapi.utils.enums.BoundHandling attribute) fromValue() (utilities.customEnum static method) Function (RATapi.utils.enums.TypeOptions attribute) funcTolerance (controlsClass attribute) (RATapi.Controls attribute) fWeight (controlsClass attribute) (RATapi.Controls attribute) G Gaussian (RATapi.utils.enums.Priors attribute) gelman() (in module minimisers.DREAM.functions) geometry (RATapi.Project attribute) get_all_names() (RATapi.Project method) get_all_protected_parameters() (RATapi.Project method) get_contrast_model_field() (RATapi.Project method) get_event_callback() (in module RATapi.events) get_field_string() (in module RATapi.outputs) get_handle() (RATapi.inputs.FileHandles method) get_python_handle() (in module RATapi.inputs) getAllAllowedNames() (API.projectClass.domainsClass method) (API.projectClass.projectClass method) getFitNames() (in module targetFunctions.common) getFittedPriors() (in module minimisers.generalUtils) getHandle() (RATapi.wrappers.DylibWrapper method) (RATapi.wrappers.MatlabWrapper method) (utilities.dyLibWrapper method) (utilities.pythonWrapper method) getIPCFilePath() (API.controlsClass method) getNames() (API.projectClass.backgroundsClass method) (API.projectClass.resolutionsClass method) groupLayersMod() (in module targetFunctions.common.groupLayers) H hide_priors() (RATapi.Project method) I inEllipsoids() (in module minimisers.NS) initialise_IPC() (RATapi.Controls method) initialiseIPC() (API.controlsClass method) initializeDREAM() (in module minimisers.DREAM.functions) isFigure() (in module utilities) isText() (in module utilities) Iter (RATapi.utils.enums.Display attribute) J jumpProbability (controlsClass attribute) (RATapi.Controls attribute) K kde() (in module utilities.misc) kmeans() (in module minimisers.NS) L layers (API.projectClass.projectClass attribute) (domainsClass attribute) (projectClass attribute) (RATapi.Project attribute) layersClass (class in API.projectClass) leftWin() (in module minimisers.DE) LivePlot (class in RATapi.utils.plotting) load() (RATapi.Controls class method) (RATapi.Project class method) LocalToBest (RATapi.utils.enums.Strategies attribute) logPlus() (in module minimisers.NS) M make_controls() (in module RATapi.inputs) make_data_present() (in module RATapi.inputs) make_input() (in module RATapi.inputs) make_problem() (in module RATapi.inputs) make_resample() (in module RATapi.inputs) make_results() (in module RATapi.outputs) makeCell() (in module minimisers.generalUtils) makeEmptyBayesResultsStruct() (in module minimisers.generalUtils) makeSimulationRange() (in module targetFunctions.common) makeSLDProfileXY() (in module RATapi.rat_core) Matlab (RATapi.utils.enums.Languages attribute) MatlabWrapper (class in RATapi.wrappers) maxFuncEvals (controlsClass attribute) (RATapi.Controls attribute) maxIterations (controlsClass attribute) (RATapi.Controls attribute) mchol() (in module minimisers.NS) metropolisRule() (in module minimisers.DREAM.functions) minimisers.DE (module) minimisers.DREAM (module) minimisers.DREAM.functions (module) minimisers.DREAM.postprocessing (module) minimisers.generalUtils (module) minimisers.generalUtils.bayesStats (module) minimisers.NS (module) minimisers.simplex (module) model (RATapi.Project attribute) model_post_init() (RATapi.Controls method) (RATapi.Project method) module RATapi.events RATapi.examples RATapi.inputs RATapi.models RATapi.outputs RATapi.rat_core RATapi.utils.enums RATapi.utils.plotting RATapi.wrappers multrnd() (in module minimisers.DREAM.functions) mustBeScalarOrEmptyLogical() (in module utilities) N name (RATapi.Project attribute) (RATapi.rat_core.EventTypes property) nChains (controlsClass attribute) (RATapi.Controls attribute) nest2pos() (in module minimisers.NS) nestedSampler() (in module minimisers.NS) NestedSamplerOutput (class in RATapi.outputs) nLive (controlsClass attribute) (RATapi.Controls attribute) nMCMC (controlsClass attribute) (RATapi.Controls attribute) None_ (RATapi.utils.enums.Hydration attribute) Normal (RATapi.utils.enums.Calculations attribute) Notify (RATapi.utils.enums.Display attribute) notify() (in module RATapi.events) NS (RATapi.utils.enums.Procedures attribute) nSamples (controlsClass attribute) (RATapi.Controls attribute) nsIntraFun() (in module minimisers.NS) nsTolerance (controlsClass attribute) (RATapi.Controls attribute) numGenerations (controlsClass attribute) (RATapi.Controls attribute) O Off (RATapi.utils.enums.BoundHandling attribute) (RATapi.utils.enums.Display attribute) optimalEllipsoids() (in module minimisers.NS) P packParams() (in module minimisers.generalUtils) packParamsPriors() (in module minimisers.generalUtils) parallel (controlsClass attribute) (RATapi.Controls attribute) parameters (domainsClass attribute) (projectClass attribute) (RATapi.Project attribute) parametersClass (class in API.projectClass) parseClassToStructs() (in module API) parseContrastInput() (API.projectClass.contrastsClass method) (API.projectClass.domainContrastsClass method) percentileConfidenceIntervals() (in module minimisers.generalUtils.bayesStats) plot_chain() (in module RATapi.utils.plotting) plot_contour() (in module RATapi.utils.plotting) plot_corner() (in module RATapi.utils.plotting) plot_hists() (in module RATapi.utils.plotting) plot_one_hist() (in module RATapi.utils.plotting) plot_ref_sld() (in module RATapi.utils.plotting) plotChain() (in module utilities.plotting) plotContours() (in module utilities.plotting) plotEvent() (RATapi.utils.plotting.LivePlot method) plotHists() (in module utilities.plotting) plotRefSLD() (in module utilities.plotting) plotRefSLDHelper() (in module utilities.plotting) Points (RATapi.utils.enums.Parallel attribute) populationSize (controlsClass attribute) (RATapi.Controls attribute) PredictionIntervals (class in RATapi.outputs) procedure (controlsClass attribute) (RATapi.Controls attribute) processBayes() (in module minimisers.generalUtils.bayesStats) processCustomFunction() (in module targetFunctions.domainsTF) (in module targetFunctions.normalTF) projectClass (class in API.projectClass) projectClassToR1() (in module utilities.misc) propScale (controlsClass attribute) (RATapi.Controls attribute) pUnitGamma (controlsClass attribute) (RATapi.Controls attribute) Python (RATapi.utils.enums.Languages attribute) pythonWrapper (class in utilities) pythonWrapper() (utilities.pythonWrapper method) R r1ToProjectClass() (in module utilities.misc) Random (RATapi.utils.enums.Strategies attribute) RandomEitherOrAlgorithm (RATapi.utils.enums.Strategies attribute) RandomWithPerGenerationDither (RATapi.utils.enums.Strategies attribute) RandomWithPerVectorDither (RATapi.utils.enums.Strategies attribute) randSample() (in module utilities.misc) RAT() (in module API) RATapi.events module RATapi.examples module RATapi.inputs module RATapi.models module RATapi.outputs module RATapi.rat_core module RATapi.utils.enums module RATapi.utils.plotting module RATapi.wrappers module RATMain() (in module API) (in module RATapi.rat_core) readOrso() (in module utilities) Reflect (RATapi.utils.enums.BoundHandling attribute) reflectivityCalculation() (in module targetFunctions) refPercentileConfidenceIntervals() (in module minimisers.generalUtils.bayesStats) register() (in module RATapi.events) removeBackground() (API.projectClass.backgroundsClass method) (API.projectClass.projectClass method) removeBackgroundParam() (API.projectClass.projectClass method) removeContrast() (API.projectClass.projectClass method) removeCustomFile() (API.projectClass.customFileClass method) (API.projectClass.projectClass method) removeData() (API.projectClass.dataClass method) (API.projectClass.projectClass method) removeDomainContrast() (API.projectClass.domainsClass method) removeDomainRatio() (API.projectClass.domainsClass method) removeLayer() (API.projectClass.layersClass method) (API.projectClass.projectClass method) removeOutlier() (in module minimisers.DREAM.functions) removeParameter() (API.projectClass.parametersClass method) removeResolution() (API.projectClass.projectClass method) (API.projectClass.resolutionsClass method) removeResolutionParam() (API.projectClass.projectClass method) resampleMinAngle (controlsClass attribute) (RATapi.Controls attribute) resampleNPoints (controlsClass attribute) (RATapi.Controls attribute) rescaleParameters() (in module minimisers.NS) resolution (API.projectClass.projectClass attribute) (domainsClass attribute) (projectClass attribute) resolution_parameters (RATapi.Project attribute) resolutionParams (resolutionsClass attribute) resolutions (RATapi.Project attribute) (resolutionsClass attribute) resolutionsClass (class in API.projectClass) Results (class in RATapi.outputs) run() (in module RATapi) runDE() (in module minimisers.DE) runDREAM() (in module minimisers.DREAM) runNestedSampler() (in module minimisers.NS) runSimplex() (in module minimisers.simplex) S save() (RATapi.Controls method) (RATapi.Project method) scalefactors (domainsClass attribute) (projectClass attribute) (RATapi.Project attribute) sendStopEvent() (API.controlsClass method) (RATapi.Controls method) serialize() (RATapi.Controls method) set_prior_visibility() (RATapi.Project method) setBackground() (API.projectClass.backgroundsClass method) (API.projectClass.projectClass method) setBackgroundName() (API.projectClass.backgroundsClass method) setBackgroundParam() (API.projectClass.projectClass method) setContrast() (API.projectClass.domainsClass method) (API.projectClass.projectClass method) setContrastModel() (API.projectClass.domainsClass method) (API.projectClass.projectClass method) setCustomFile() (API.projectClass.customFileClass method) (API.projectClass.projectClass method) setData() (API.projectClass.dataClass method) (API.projectClass.projectClass method) setDefaultValues() (API.projectClass.contrastsClass method) setDomainContrast() (API.projectClass.domainsClass method) setDomainContrastModel() (API.projectClass.domainsClass method) setDomainRatio() (API.projectClass.domainsClass method) setFit() (API.projectClass.parametersClass method) setLayer() (API.projectClass.layersClass method) (API.projectClass.projectClass method) setLimits() (API.projectClass.parametersClass method) setName() (API.projectClass.parametersClass method) setParameter() (API.projectClass.parametersClass method) setPrior() (API.projectClass.parametersClass method) setProcedure() (API.controlsClass method) setResolution() (API.projectClass.projectClass method) (API.projectClass.resolutionsClass method) setResolutionName() (API.projectClass.resolutionsClass method) setResolutionParam() (API.projectClass.projectClass method) setupDREAM() (in module minimisers.DREAM.functions) setValue() (API.projectClass.parametersClass method) shiftData() (in module targetFunctions.common) show_priors() (RATapi.Project method) Simplex (RATapi.utils.enums.Procedures attribute) simplexIntrafun() (in module minimisers.simplex) simplexXTransform() (in module minimisers.simplex) Single (RATapi.utils.enums.Parallel attribute) splitEllipsoid() (in module minimisers.NS) StandardLayers (RATapi.utils.enums.LayerModels attribute) standardLayers() (in module targetFunctions.domainsTF) (in module targetFunctions.normalTF) start_matlab() (in module RATapi.wrappers) strategy (controlsClass attribute) (RATapi.Controls attribute) SubstrateLiquid (RATapi.utils.enums.Geometries attribute) Subtract (RATapi.utils.enums.BackgroundActions attribute) T targetFunctions (module) targetFunctions.common (module) targetFunctions.common.costFunctions (module) targetFunctions.common.groupLayers (module) targetFunctions.domainsTF (module) targetFunctions.normalTF (module) targetValue (controlsClass attribute) (RATapi.Controls attribute) textProgressBar() (in module utilities) toDomainsClass() (API.projectClass.projectClass method) toProjectClass() (API.projectClass.domainsClass method) toStruct() (API.projectClass.backgroundsClass method) (API.projectClass.contrastsClass method) (API.projectClass.customFileClass method) (API.projectClass.dataClass method) (API.projectClass.domainContrastsClass method) (API.projectClass.domainsClass method) (API.projectClass.layersClass method) (API.projectClass.parametersClass method) (API.projectClass.projectClass method) (API.projectClass.resolutionsClass method) (utilities.customEnum static method) U Uniform (RATapi.utils.enums.Priors attribute) unpackParams() (in module minimisers.generalUtils) updateDataName() (API.projectClass.contrastsClass method) updateFreq (controlsClass attribute) (RATapi.Controls attribute) updatePlotFreq (controlsClass attribute) (RATapi.Controls attribute) useLivePlot (class in utilities.plotting) utilities.exceptions (module) utilities.plotting (module) V validateLimits() (in module utilities) validateLogical() (in module utilities) validateNumber() (in module utilities) validateOption() (in module utilities) validateParameter() (in module utilities) validatePriors() (in module utilities) values() (utilities.customEnum static method) varTable (customFileClass attribute) (dataClass attribute) (layersClass attribute) (parametersClass attribute) W write_script() (RATapi.Project method) writeScript() (API.projectClass.projectClass method) X xTolerance (controlsClass attribute) (RATapi.Controls attribute)
