refnx - Neutron and X-ray reflectometry analysis in Python

Modules

• refnx.analysis
  • BaseObjective
    • BaseObjective.covar
    • BaseObjective.logl
    • BaseObjective.logp
    • BaseObjective.logpost
    • BaseObjective.nll
    • BaseObjective.nlpost
    • BaseObjective.setp
    • BaseObjective.varying_parameters
  • Bounds
    • Bounds.invcdf
    • Bounds.logp
    • Bounds.rvs
    • Bounds.valid
  • CurveFitter
    • CurveFitter.acf
    • CurveFitter.chain
    • CurveFitter.fit
    • CurveFitter.index_max_prob
    • CurveFitter.initialise
    • CurveFitter.initialise_with_chain
    • CurveFitter.logpost
    • CurveFitter.make_sampler
    • CurveFitter.nvary
    • CurveFitter.reset
    • CurveFitter.sample
  • GlobalObjective
    • GlobalObjective.generative
    • GlobalObjective.logl
    • GlobalObjective.logp
    • GlobalObjective.npoints
    • GlobalObjective.parameters
    • GlobalObjective.plot
    • GlobalObjective.residuals
    • GlobalObjective.weighted
  • Interval
    • Interval.invcdf
    • Interval.lb
    • Interval.logp
    • Interval.rv
    • Interval.rvs
    • Interval.ub
    • Interval.valid
  • MCMCResult
    • MCMCResult.chain
    • MCMCResult.median
    • MCMCResult.name
    • MCMCResult.param
    • MCMCResult.stderr
  • Model
    • Model.fitfunc
    • Model.logp
    • Model.model
    • Model.parameters
  • Objective
    • Objective.chisqr
    • Objective.corner
    • Objective.covar
    • Objective.generative
    • Objective.logl
    • Objective.logp
    • Objective.logpost
    • Objective.nll
    • Objective.npoints
    • Objective.parameters
    • Objective.pgen
    • Objective.plot
    • Objective.prior_transform
    • Objective.residuals
    • Objective.setp
    • Objective.varying_parameters
    • Objective.weighted
  • PDF
    • PDF.invcdf
    • PDF.logp
    • PDF.rvs
    • PDF.valid
  • Parameter
    • Parameter.bounds
    • Parameter.constraint
    • Parameter.corner
    • Parameter.logp
    • Parameter.range
    • Parameter.set_constraint
    • Parameter.setp
    • Parameter.valid
    • Parameter.value
    • Parameter.vary
  • Parameters
    • Parameters.constrained_parameters
    • Parameters.flattened
    • Parameters.logp
    • Parameters.names
    • Parameters.nparam
    • Parameters.nvary
    • Parameters.parameters
    • Parameters.pgen
    • Parameters.pvals
    • Parameters.varying_parameters
  • Transform
  • autocorrelation_chain
  • fitfunc
  • integrated_time
  • is_parameter
  • is_parameters
  • load_chain
  • possibly_create_parameter
  • process_chain
  • pymc_model
  • sequence_to_parameters
• refnx.reflect
  • Component
    • Component.__mul__
    • Component.__or__
    • Component.__str__
    • Component.interfaces
    • Component.is_magnetic
    • Component.logp
    • Component.parameters
    • Component.slabs
  • Erf
    • Erf.__call__
  • Exponential
    • Exponential.__annotations__
    • Exponential.__call__
  • Footprint
    • Footprint.__call__
    • Footprint.parameters
  • FresnelTransform
    • FresnelTransform.__annotations__
    • FresnelTransform.__call__
  • FunctionalForm
    • FunctionalForm.__annotations__
    • FunctionalForm.parameters
    • FunctionalForm.slabs
  • Interface
    • Interface.__annotations__
    • Interface.__call__
  • Linear
    • Linear.__annotations__
    • Linear.__call__
  • LipidLeaflet
    • LipidLeaflet.__annotations__
    • LipidLeaflet.logp
    • LipidLeaflet.make_constraint
    • LipidLeaflet.parameters
    • LipidLeaflet.slabs
    • LipidLeaflet.volfrac_h
    • LipidLeaflet.volfrac_t
  • LipidLeafletGuest
    • LipidLeafletGuest.__annotations__
    • LipidLeafletGuest.logp
    • LipidLeafletGuest.parameters
    • LipidLeafletGuest.slabs
    • LipidLeafletGuest.volfrac_guest
  • MagneticSlab
    • MagneticSlab.__annotations__
    • MagneticSlab.__str__
    • MagneticSlab.is_magnetic
    • MagneticSlab.parameters
    • MagneticSlab.slabs
  • MaterialSLD
    • MaterialSLD.__complex__
    • MaterialSLD.complex
    • MaterialSLD.formula
    • MaterialSLD.parameters
  • MixedReflectModel
    • MixedReflectModel.__call__
    • MixedReflectModel.bkg
    • MixedReflectModel.dq
    • MixedReflectModel.logp
    • MixedReflectModel.model
    • MixedReflectModel.parameters
    • MixedReflectModel.q_offset
    • MixedReflectModel.scales
    • MixedReflectModel.structures
  • MixedSlab
    • MixedSlab.__annotations__
    • MixedSlab.__str__
    • MixedSlab.parameters
    • MixedSlab.slabs
  • Motofit
    • Motofit.dataset
    • Motofit.model
    • Motofit.objective
    • Motofit.fig
    • Motofit.__call__
    • Motofit.code
    • Motofit.curvefitter
    • Motofit.do_fit
    • Motofit.load_data
    • Motofit.load_model
    • Motofit.redraw
    • Motofit.save_model
    • Motofit.set_model
    • Motofit.update_model
  • PolarisedReflectModel
    • PolarisedReflectModel.model
  • ReflectModel
    • ReflectModel.__annotations__
    • ReflectModel.__call__
    • ReflectModel.bkg
    • ReflectModel.dq
    • ReflectModel.logp
    • ReflectModel.model
    • ReflectModel.parameters
    • ReflectModel.q_offset
    • ReflectModel.scale
    • ReflectModel.structure
  • ReflectModelTL
    • ReflectModelTL.__annotations__
    • ReflectModelTL.model
    • ReflectModelTL.q_offset
    • ReflectModelTL.structure
    • ReflectModelTL.t_offset
  • SLD
    • SLD.__annotations__
    • SLD.__complex__
    • SLD.parameters
  • Sinusoidal
    • Sinusoidal.__annotations__
    • Sinusoidal.__call__
  • Slab
    • Slab.__annotations__
    • Slab.__str__
    • Slab.parameters
    • Slab.slabs
  • SpinChannel
    • SpinChannel.DOWN_DOWN
    • SpinChannel.DOWN_UP
    • SpinChannel.UP_DOWN
    • SpinChannel.UP_UP
  • Spline
    • Spline.__annotations__
    • Spline.__call__
    • Spline.logp
    • Spline.parameters
    • Spline.slabs
  • Stack
    • Stack.__annotations__
    • Stack.__ior__
    • Stack.__setitem__
    • Stack.__str__
    • Stack.append
    • Stack.components
    • Stack.interfaces
    • Stack.is_magnetic
    • Stack.parameters
    • Stack.slabs
  • Step
    • Step.__annotations__
    • Step.__call__
  • Structure
    • Structure.__annotations__
    • Structure.__ior__
    • Structure.__or__
    • Structure.__setitem__
    • Structure.__str__
    • Structure.append
    • Structure.components
    • Structure.contract
    • Structure.from_orso
    • Structure.from_slabs
    • Structure.interfaces
    • Structure.is_magnetic
    • Structure.logp
    • Structure.name
    • Structure.overall_sld
    • Structure.parameters
    • Structure.plot
    • Structure.reflectivity
    • Structure.reverse_structure
    • Structure.slabs
    • Structure.sld_profile
    • Structure.solvent
    • Structure.to_orso
  • Tanh
    • Tanh.__annotations__
    • Tanh.__call__
  • abeles
  • available_backends
  • choose_dq_type
  • create_occupancy
  • gui
  • main
  • possibly_create_scatterer
  • reflectivity
  • sld_profile
  • use_reflect_backend
• refnx.dataset
  • Data1D
    • Data1D.filename
    • Data1D.weighted
    • Data1D.metadata
    • Data1D.add_data
    • Data1D.data
    • Data1D.finite_data
    • Data1D.load
    • Data1D.mask
    • Data1D.plot
    • Data1D.refresh
    • Data1D.save
    • Data1D.scale
    • Data1D.sort
    • Data1D.synthesise
    • Data1D.unmasked_data
    • Data1D.x
    • Data1D.x_err
    • Data1D.y
    • Data1D.y_err
  • OrsoDataset
    • OrsoDataset.load
    • OrsoDataset.orso
    • OrsoDataset.refresh
    • OrsoDataset.save
    • OrsoDataset.setup_analysis
    • OrsoDataset.update_model
  • ReflectDataset
    • ReflectDataset.load
    • ReflectDataset.save_xml
  • load_data
• refnx.reduce
  • AutoReducer
    • AutoReducer.match_datasets
    • AutoReducer.match_direct_beam
    • AutoReducer.splice_datasets
  • BatchReducer
    • BatchReducer.load_runs
    • BatchReducer.reduce
    • BatchReducer.select_runs
  • Catalogue
    • Catalogue.datafile_number
  • PlatypusNexus
    • PlatypusNexus.chod
    • PlatypusNexus.correct_for_gravity
    • PlatypusNexus.create_detector_norm
    • PlatypusNexus.detector_average_unwanted_direction
    • PlatypusNexus.estimated_beam_width_at_detector
    • PlatypusNexus.phase_angle
    • PlatypusNexus.time_offset
  • PlatypusReduce
  • PolarisationEfficiency
    • PolarisationEfficiency.custom_efficiencies
    • PolarisationEfficiency.standard_efficiencies
  • PolarisedReduce
    • PolarisedReduce.spin_set_direct
    • PolarisedReduce.reducers
    • PolarisedReduce.reduce
      • PolarisedReduce.spin_set_reflect
  • ReductionOptions
  • SpatzNexus
    • SpatzNexus.chod
    • SpatzNexus.create_detector_norm
    • SpatzNexus.detector_average_unwanted_direction
    • SpatzNexus.estimated_beam_width_at_detector
    • SpatzNexus.phase_angle
    • SpatzNexus.time_offset
  • SpatzReduce
  • SpinChannel
    • SpinChannel.DOWN_DOWN
    • SpinChannel.DOWN_UP
    • SpinChannel.UP_DOWN
    • SpinChannel.UP_UP
  • SpinSet
    • SpinSet.channels
    • SpinSet.sc_opts
    • SpinSet.dd
    • SpinSet.uu
    • SpinSet.du
    • SpinSet.ud
    • SpinSet.dd
    • SpinSet.du
    • SpinSet.plot_spectra
    • SpinSet.process
    • SpinSet.spin_channels
    • SpinSet.ud
    • SpinSet.uu
  • accumulate_HDF_files
  • basename_datafile
  • catalogue
  • create_reflect_nexus
  • datafile_number
  • gui
  • main
  • number_datafile
  • reduce_stitch
  • reduce_xrdml
• refnx.util
  • EPadd
  • EPcos
  • EPdiv
  • EPexp
  • EPlog
  • EPlog10
  • EPmul
  • EPmulk
  • EPpow
  • EPpowk
  • EPsin
  • EPsub
  • EPtan
  • actual_footprint
  • angle
  • beamfrac
  • beamfrackernel
  • div
  • double_chopper_frequency
  • energy_wavelength
  • get_scaling_in_overlap
  • height_of_beam_after_dx
  • neutron_transmission
  • penetration_depth
  • q
  • q2
  • qcrit
  • refplot
  • resolution_double_chopper
  • resolution_single_chopper
  • slit_optimiser
  • tauC
  • transmission_double_chopper
  • transmission_single_chopper
  • velocity_wavelength
  • wavelength
  • wavelength_energy
  • wavelength_velocity
  • xray_energy
  • xray_wavelength