kipe package

kipe: Kalman-based identifiability and parameter estimation.

Subpackages

• kipe.examples package
  • Submodules
    • kipe.examples.fitzhugh_nagumo module
      • NDArray_f64
      • State
      • Parameters
      • FieldSpec
      • Solver
• kipe.fenicsx package
  • Subpackages
    • kipe.fenicsx.examples package
      • Submodules
  • Submodules
    • kipe.fenicsx.forward_solver module
      • SupportsFunctionSpaces
      • describe_function_space()
    • kipe.fenicsx.points module
      • PointSampler
      • build_point_sampler()
    • kipe.fenicsx.sampling module
      • Element
      • Projection
      • MeshSampler
      • build_mesh_sampler()
      • observed_function_space()

Submodules

• kipe.cli module
  • main()
• kipe.estimation module
  • Estimation
    • Estimation.run()
  • estimate()
• kipe.forward_solver module
  • State
  • Parameters
  • FieldSpec
    • FieldSpec.local_size
    • FieldSpec.kind
  • ForwardSolver
    • ForwardSolver.initial_state()
    • ForwardSolver.state_spec
    • ForwardSolver.nominal_parameters()
    • ForwardSolver.propagate()
  • SupportsCheckpoints
    • SupportsCheckpoints.read_checkpoint()
  • ForwardSolverError
  • build_forward_solver()
• kipe.measurements module
  • MeasurementModel
    • MeasurementModel.predict()
    • MeasurementModel.innovation()
  • DifferenceModel
    • DifferenceModel.predict()
    • DifferenceModel.innovation()
  • build_model()
  • ObservationOperator
    • ObservationOperator.fields
    • ObservationOperator.sampler
    • ObservationOperator.model
    • ObservationOperator.size
    • ObservationOperator.global_indices
  • build_observation_operator()
  • Measurement
    • Measurement.name
    • Measurement.operator
    • Measurement.times
    • Measurement.values
    • Measurement.stddev
  • measurement_times()
  • read_numpy()
  • write_numpy()
• kipe.options module
  • StudyFileError
  • OutputOptions
    • OutputOptions.path
    • OutputOptions.log_level
  • ForwardSolverOptions
    • ForwardSolverOptions.factory
    • ForwardSolverOptions.arguments
  • Reparameterization
  • ParameterPrior
    • ParameterPrior.initial
    • ParameterPrior.relative_stddev
    • ParameterPrior.stddev
    • ParameterPrior.reparameterization
  • ParametersOptions
    • ParametersOptions.reparameterization
    • ParametersOptions.select
  • TimeRange
    • TimeRange.start
    • TimeRange.stop
    • TimeRange.step
  • NumpyDataOptions
    • NumpyDataOptions.type
    • NumpyDataOptions.path
  • ArraySamplingOptions
    • ArraySamplingOptions.type
  • DifferenceModelOptions
    • DifferenceModelOptions.type
  • NoiseOptions
    • NoiseOptions.stddev
    • NoiseOptions.seed
  • MeshSamplingOptions
    • MeshSamplingOptions.type
    • MeshSamplingOptions.mesh
    • MeshSamplingOptions.mesh_name
    • MeshSamplingOptions.element
    • MeshSamplingOptions.projection
    • MeshSamplingOptions.padding
  • PointSamplingOptions
    • PointSamplingOptions.type
    • PointSamplingOptions.points
  • SpatialSamplingOptions
  • MeasurementOptions
    • MeasurementOptions.fields
    • MeasurementOptions.data
    • MeasurementOptions.noise
    • MeasurementOptions.times
    • MeasurementOptions.spatial_sampling
    • MeasurementOptions.model
  • RunTruthOptions
    • RunTruthOptions.type
  • CheckpointsTruthOptions
    • CheckpointsTruthOptions.type
    • CheckpointsTruthOptions.path
  • TruthOptions
  • SynthesisNoiseOptions
    • SynthesisNoiseOptions.stddev
  • SynthesisOptions
    • SynthesisOptions.truth
    • SynthesisOptions.noise
    • SynthesisOptions.realizations
  • SigmaPoints
  • EstimationOptions
    • EstimationOptions.sigma_points
    • EstimationOptions.iterations
  • StudyOptions
    • StudyOptions.output
    • StudyOptions.forward_solver
    • StudyOptions.parameters
    • StudyOptions.measurements
    • StudyOptions.synthesis
    • StudyOptions.estimation
  • data_path()
  • estimation_directory()
  • load_study()
  • study_schema()
  • dump_study()
• kipe.parameters module
  • EstimatedParameter
    • EstimatedParameter.name
    • EstimatedParameter.reparameterization
    • EstimatedParameter.initial
    • EstimatedParameter.stddev_theta
    • EstimatedParameter.initial_theta()
    • EstimatedParameter.to_physical()
  • Parameterization
    • Parameterization.parameters
    • Parameterization.names
    • Parameterization.stddev_theta()
    • Parameterization.initial_theta()
    • Parameterization.to_physical()
    • Parameterization.recenter()
    • Parameterization.one_sigma_range()
    • Parameterization.physical_range()
  • build_parameterization()
• kipe.plot module
  • PlotError
  • History
    • History.names
    • History.iteration
    • History.parameters
    • History.lower
    • History.upper
    • History.steps_per_iteration
    • History.iterations
    • History.steps
    • History.iteration_starts()
  • read_history()
  • plot_histories()
  • render_histories()
  • watch_histories()
• kipe.provenance module
  • recorded_run()
  • git_state()
• kipe.roukf module
  • SigmaPointStencil
    • SigmaPointStencil.points
    • SigmaPointStencil.alpha
    • SigmaPointStencil.p_alpha()
  • FilterState
    • FilterState.x
    • FilterState.theta
    • FilterState.L_x
    • FilterState.L_theta
    • FilterState.U_inv
    • FilterState.covariance()
  • sigma_point_stencil()
  • initial_state()
  • sample()
  • mean()
  • sensitivity()
  • gain()
  • update()
• kipe.sampling module
  • SpatialSampler
    • SpatialSampler.size
    • SpatialSampler.global_indices
    • SpatialSampler.sample()
  • ArraySampler
    • ArraySampler.sample()
  • build_sampler()
• kipe.synthesis module
  • synthesize()