Index A | B | C | D | E | F | G | H | I | J | 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) Add (RATapi.utils.enums.BackgroundActions attribute) addBackground() (API.projectClass.backgroundsClass method) (API.projectClass.projectClass method) addBackgroundParam() (API.projectClass.projectClass method) addBulkIn() (API.projectClass.projectClass method) addBulkOut() (API.projectClass.projectClass method) addContrast() (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) addFileExtension() (API.projectClass.customFileClass static method) addLayer() (API.projectClass.layersClass method) (API.projectClass.projectClass method) addLayerGroup() (API.projectClass.projectClass method) addParameter() (API.projectClass.parametersClass method) (API.projectClass.projectClass method) addParameterGroup() (API.projectClass.projectClass method) addResolution() (API.projectClass.projectClass method) (API.projectClass.resolutionsClass method) addResolutionParam() (API.projectClass.projectClass method) addScalefactor() (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) B background (API.projectClass.projectClass attribute) background_parameters (RATapi.Project attribute) backgrounds (RATapi.Project attribute) backgroundsClass (class in API.projectClass) backgroundsClass() (API.projectClass.backgroundsClass method) 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) boundHandling (controlsClass attribute) (RATapi.Controls attribute) bulk_in (RATapi.Project attribute) bulk_out (RATapi.Project attribute) bulkIn (API.projectClass.projectClass attribute) BulkIn (RATapi.utils.enums.Hydration attribute) bulkOut (API.projectClass.projectClass attribute) BulkOut (RATapi.utils.enums.Hydration attribute) C 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) (RATapi.Project attribute) Contrasts (RATapi.utils.enums.Parallel attribute) contrastsClass (class in API.projectClass) contrastsClass() (API.projectClass.contrastsClass method) controlsClass (class in API) Cpp (RATapi.utils.enums.Languages attribute) createProject() (in module API) crossoverProbability (controlsClass attribute) (RATapi.Controls attribute) custom_files (RATapi.Project attribute) customFile (API.projectClass.projectClass attribute) customFileClass (class in API.projectClass) customFileClass() (API.projectClass.customFileClass method) CustomLayers (RATapi.utils.enums.LayerModels attribute) CustomXY (RATapi.utils.enums.LayerModels attribute) D data (API.projectClass.projectClass attribute) (RATapi.Project attribute) Data (RATapi.utils.enums.TypeOptions attribute) dataClass (class in API.projectClass) dataClass() (API.projectClass.dataClass method) DE (RATapi.utils.enums.Procedures attribute) delete() (API.projectClass.customFileClass method) (API.projectClass.projectClass method) delete_IPC() (RATapi.Controls method) display (controlsClass attribute) (RATapi.Controls attribute) displayBackgroundsObject() (API.projectClass.backgroundsClass method) displayResolutionsObject() (API.projectClass.resolutionsClass method) displayTable() (API.projectClass.customFileClass method) (API.projectClass.dataClass method) (API.projectClass.parametersClass method) domain_contrasts (RATapi.Project attribute) domain_ratios (RATapi.Project attribute) domainContrasts (API.projectClass.domainsClass attribute) domainContrastsClass (class in API.projectClass) domainRatio (API.projectClass.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) domainsClass() (API.projectClass.domainsClass method) DREAM (RATapi.utils.enums.Procedures attribute) DreamOutput (class in RATapi.outputs) DreamParams (class in RATapi.outputs) 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) E EventTypes (class in RATapi.rat_core) F FileHandles (class in RATapi.inputs) Final (RATapi.utils.enums.Display attribute) findParameter() (API.projectClass.layersClass static method) Fold (RATapi.utils.enums.BoundHandling attribute) 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) 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) getDataAndFunctionNames() (API.projectClass.projectClass method) getFitNames() (in module targetFunctions.common) getHandle() (RATapi.wrappers.DylibWrapper method) (RATapi.wrappers.MatlabWrapper method) getIPCFilePath() (API.controlsClass method) getNames() (API.projectClass.backgroundsClass method) (API.projectClass.resolutionsClass method) groupLayersMod() (in module targetFunctions.common.groupLayers) groupLayersModImaginary() (in module targetFunctions.common.groupLayers) H hide_priors() (RATapi.Project method) I initialise_IPC() (RATapi.Controls method) initialiseIPC() (API.controlsClass method) Iter (RATapi.utils.enums.Display attribute) J jumpProbability (controlsClass attribute) (RATapi.Controls attribute) L layers (API.projectClass.projectClass attribute) (RATapi.Project attribute) layersClass (class in API.projectClass) layersClass() (API.projectClass.layersClass method) LivePlot (class in RATapi.utils.plotting) load() (RATapi.Controls class method) (RATapi.Project class method) LocalToBest (RATapi.utils.enums.Strategies attribute) 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) 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) 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 N name (RATapi.Project attribute) (RATapi.rat_core.EventTypes property) nChains (controlsClass attribute) (RATapi.Controls attribute) 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) nsTolerance (controlsClass attribute) (RATapi.Controls attribute) numGenerations (controlsClass attribute) (RATapi.Controls attribute) O Off (RATapi.utils.enums.BoundHandling attribute) (RATapi.utils.enums.Display attribute) P parallel (controlsClass attribute) (RATapi.Controls attribute) parameters (API.projectClass.projectClass attribute) (RATapi.Project attribute) parametersClass (class in API.projectClass) parametersClass() (API.projectClass.parametersClass method) parseClassToStructs() (in module API) parseContrastInput() (API.projectClass.contrastsClass method) (API.projectClass.domainContrastsClass method) 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) 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) processCustomFunction() (in module targetFunctions.domainsTF.customLayers) (in module targetFunctions.domainsTF.customXY) (in module targetFunctions.normalTF.customLayers) (in module targetFunctions.normalTF.customXY) projectClass (class in API.projectClass) projectClass() (API.projectClass.projectClass method) projectClassToR1() (in module utilities.misc) propScale (controlsClass attribute) (RATapi.Controls attribute) pUnitGamma (controlsClass attribute) (RATapi.Controls attribute) Python (RATapi.utils.enums.Languages attribute) 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) 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) Reflect (RATapi.utils.enums.BoundHandling attribute) reflectivityCalculation() (in module targetFunctions) register() (in module RATapi.events) removeBackground() (API.projectClass.backgroundsClass method) (API.projectClass.projectClass method) removeBackgroundParam() (API.projectClass.projectClass method) removeBulkIn() (API.projectClass.projectClass method) removeBulkOut() (API.projectClass.projectClass method) removeContrast() (API.projectClass.projectClass method) removeCustomFile() (API.projectClass.projectClass method) removeData() (API.projectClass.projectClass method) removeDomainContrast() (API.projectClass.domainsClass method) removeDomainRatio() (API.projectClass.domainsClass method) removeLayer() (API.projectClass.projectClass method) removeParameter() (API.projectClass.parametersClass method) (API.projectClass.projectClass method) removeResolution() (API.projectClass.projectClass method) (API.projectClass.resolutionsClass method) removeResolutionParam() (API.projectClass.projectClass method) removeScalefactor() (API.projectClass.projectClass method) resampleMinAngle (controlsClass attribute) (RATapi.Controls attribute) resampleNPoints (controlsClass attribute) (RATapi.Controls attribute) resolution (API.projectClass.projectClass attribute) resolution_parameters (RATapi.Project attribute) resolutions (RATapi.Project attribute) resolutionsClass (class in API.projectClass) resolutionsClass() (API.projectClass.resolutionsClass method) Results (class in RATapi.outputs) run() (in module RATapi) S save() (RATapi.Controls method) (RATapi.Project method) scalefactors (API.projectClass.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) (API.projectClass.projectClass method) setBackgroundParam() (API.projectClass.projectClass method) setBackgroundParamLimits() (API.projectClass.projectClass method) setBackgroundParamName() (API.projectClass.projectClass method) setBackgroundParamValue() (API.projectClass.projectClass method) setBulkIn() (API.projectClass.projectClass method) setBulkOut() (API.projectClass.projectClass method) setContrast() (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) setDataName() (API.projectClass.dataClass method) setDefaultValues() (API.projectClass.contrastsClass static method) (API.projectClass.domainContrastsClass static method) setDomainContrast() (API.projectClass.domainsClass method) setDomainContrastModel() (API.projectClass.domainsClass method) setDomainRatio() (API.projectClass.domainsClass method) setFit() (API.projectClass.parametersClass method) setLayerValue() (API.projectClass.layersClass method) (API.projectClass.projectClass method) setLimits() (API.projectClass.parametersClass method) setName() (API.projectClass.parametersClass method) setParameter() (API.projectClass.parametersClass method) (API.projectClass.projectClass method) setParameterFit() (API.projectClass.projectClass method) setParameterLimits() (API.projectClass.projectClass method) setParameterName() (API.projectClass.projectClass method) setParameterPrior() (API.projectClass.projectClass method) setParameterValue() (API.projectClass.projectClass method) setPrior() (API.projectClass.parametersClass method) setProcedure() (API.controlsClass method) setResolution() (API.projectClass.projectClass method) (API.projectClass.resolutionsClass method) setResolutionName() (API.projectClass.projectClass method) (API.projectClass.resolutionsClass method) setResolutionParam() (API.projectClass.projectClass method) setResolutionParamLimits() (API.projectClass.projectClass method) setResolutionParamName() (API.projectClass.projectClass method) setResolutionParamValue() (API.projectClass.projectClass method) setScalefactor() (API.projectClass.projectClass method) setValue() (API.projectClass.parametersClass method) shiftData() (in module targetFunctions.common) show_priors() (RATapi.Project method) Simplex (RATapi.utils.enums.Procedures attribute) Single (RATapi.utils.enums.Parallel attribute) StandardLayers (RATapi.utils.enums.LayerModels attribute) 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.customLayers (module) targetFunctions.domainsTF.customXY (module) targetFunctions.normalTF.customLayers (module) targetFunctions.normalTF.customXY (module) targetValue (controlsClass attribute) (RATapi.Controls attribute) 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) U Uniform (RATapi.utils.enums.Priors attribute) updateDataName() (API.projectClass.contrastsClass method) updateFreq (controlsClass attribute) (RATapi.Controls attribute) updatePlotFreq (controlsClass attribute) (RATapi.Controls attribute) useLivePlot (class in utilities.plotting) utilities.plotting (module) V validateData() (API.projectClass.dataClass static method) validateFunctionName() (API.projectClass.customFileClass static method) validateLimits() (API.projectClass.parametersClass static method) validatePath() (API.projectClass.customFileClass static method) validatePriors() (API.projectClass.parametersClass static method) W write_script() (RATapi.Project method) writeScript() (API.projectClass.projectClass method) X xTolerance (controlsClass attribute) (RATapi.Controls attribute)
