Index

_

__call__() (heterodyne.core.config.PerformanceMonitor method) __init__() (heterodyne.analysis.core.HeterodyneAnalysisCore method) (heterodyne.core.config.ConfigManager method) (heterodyne.core.config.PerformanceMonitor method) (heterodyne.optimization.classical.ClassicalOptimizer method)

A

active_parameters (heterodyne.core.config.InitialParametersConfig attribute) AnalysisSettings (class in heterodyne.core.config) analyze_optimization_results() (heterodyne.optimization.classical.ClassicalOptimizer method)

analyze_per_angle_chi_squared() (heterodyne.analysis.core.HeterodyneAnalysisCore method) angle_filtering (heterodyne.core.config.OptimizationConfig attribute) AngleFilteringConfig (class in heterodyne.core.config) AngleRange (class in heterodyne.core.config)

B

bounds (heterodyne.core.config.ParameterSpaceConfig attribute)

C

cache_file_path (heterodyne.core.config.ExperimentalDataConfig attribute) cache_filename_template (heterodyne.core.config.ExperimentalDataConfig attribute) calculate_c2_heterodyne_parallel() (heterodyne.analysis.core.HeterodyneAnalysisCore method) calculate_c2_single_angle_optimized() (heterodyne.analysis.core.HeterodyneAnalysisCore method) calculate_chi_squared_optimized() (heterodyne.analysis.core.HeterodyneAnalysisCore method) calculate_diffusion_coefficient_numba() (in module heterodyne.core.kernels) calculate_diffusion_coefficient_optimized() (heterodyne.analysis.core.HeterodyneAnalysisCore method) calculate_fraction_coefficient() (heterodyne.analysis.core.HeterodyneAnalysisCore method) calculate_heterodyne_correlation() (heterodyne.analysis.core.HeterodyneAnalysisCore method) calculate_shear_rate_numba() (in module heterodyne.core.kernels) calculate_shear_rate_optimized() (heterodyne.analysis.core.HeterodyneAnalysisCore method) calculate_time_length() (in module heterodyne.core.io_utils) calculate_velocity_coefficient() (heterodyne.analysis.core.HeterodyneAnalysisCore method) classical_optimization (heterodyne.core.config.OptimizationConfig attribute) ClassicalOptimizationConfig (class in heterodyne.core.config)

ClassicalOptimizer (class in heterodyne.optimization.classical) compare_optimization_results() (heterodyne.optimization.classical.ClassicalOptimizer method) compute_chi_squared_batch_numba() (in module heterodyne.core.kernels) compute_g1_correlation_numba() (in module heterodyne.core.kernels) compute_g1_correlation_vectorized() (in module heterodyne.core.kernels) compute_sinc_squared_numba() (in module heterodyne.core.kernels) compute_sinc_squared_numba_flexible() (in module heterodyne.core.kernels) config (heterodyne.core.config.ConfigManager attribute) config_frames_to_python_slice() (in module heterodyne.core.io_utils) ConfigManager (class in heterodyne.core.config) configure_logging() (in module heterodyne.core.config) create_backup() (heterodyne.core.config.ConfigManager method) create_objective_function() (heterodyne.optimization.classical.ClassicalOptimizer method) create_time_integral_matrix_cached (heterodyne.analysis.core.HeterodyneAnalysisCore attribute) create_time_integral_matrix_numba() (in module heterodyne.core.kernels)

D

data_file_name (heterodyne.core.config.ExperimentalDataConfig attribute)

data_folder_path (heterodyne.core.config.ExperimentalDataConfig attribute) DummyType (class in heterodyne.core.kernels)

E

enabled (heterodyne.core.config.AngleFilteringConfig attribute) ensure_dir() (in module heterodyne.core.io_utils)

exchange_key (heterodyne.core.config.ExperimentalDataConfig attribute) ExperimentalDataConfig (class in heterodyne.core.config)

F

fallback_to_all_angles (heterodyne.core.config.AngleFilteringConfig attribute) fatol (heterodyne.core.config.OptimizationMethodConfig attribute)

fit() (heterodyne.analysis.core.HeterodyneAnalysisCore method) format (heterodyne.core.config.LoggingConfig attribute)

G

get() (heterodyne.core.config.ConfigManager method) get_active_parameters() (heterodyne.core.config.ConfigManager method) get_analysis_mode() (heterodyne.core.config.ConfigManager method) get_analysis_settings() (heterodyne.core.config.ConfigManager method) get_angle_filtering_config() (heterodyne.core.config.ConfigManager method) get_available_methods() (heterodyne.optimization.classical.ClassicalOptimizer method) get_config_differences() (heterodyne.core.config.ConfigManager method) get_default_14_parameters() (heterodyne.core.config.ConfigManager method) get_effective_parameter_count() (heterodyne.analysis.core.HeterodyneAnalysisCore method) (heterodyne.core.config.ConfigManager method) get_effective_parameters() (heterodyne.analysis.core.HeterodyneAnalysisCore method)

get_kernel_info() (in module heterodyne.core.kernels) get_method_recommendations() (heterodyne.optimization.classical.ClassicalOptimizer method) get_optimization_counter() (heterodyne.optimization.classical.ClassicalOptimizer method) get_optimization_summary() (heterodyne.optimization.classical.ClassicalOptimizer method) get_output_directory() (in module heterodyne.core.io_utils) get_parameter() (heterodyne.core.config.ConfigManager method) get_parameter_bounds() (heterodyne.core.config.ConfigManager method) (heterodyne.optimization.classical.ClassicalOptimizer method) get_parameter_metadata() (heterodyne.core.config.ConfigManager method) get_static_submode() (heterodyne.core.config.ConfigManager method) get_target_angle_ranges() (heterodyne.core.config.ConfigManager method) get_timing_summary() (heterodyne.core.config.PerformanceMonitor method)

H

heterodyne.analysis.core module heterodyne.core.config module heterodyne.core.io_utils module

heterodyne.core.kernels module heterodyne.optimization.classical module HeterodyneAnalysisCore (class in heterodyne.analysis.core)

I

InitialParametersConfig (class in heterodyne.core.config)

is_angle_filtering_enabled() (heterodyne.core.config.ConfigManager method) is_static_mode_enabled() (heterodyne.core.config.ConfigManager method)

J

jit() (in module heterodyne.core.kernels)

L

level (heterodyne.core.config.LoggingConfig attribute) list_available_templates() (heterodyne.core.config.ConfigManager method) load_config() (heterodyne.core.config.ConfigManager method) load_experimental_data (heterodyne.analysis.core.HeterodyneAnalysisCore attribute)

load_template() (heterodyne.core.config.ConfigManager method) log_filename (heterodyne.core.config.LoggingConfig attribute) log_to_console (heterodyne.core.config.LoggingConfig attribute) log_to_file (heterodyne.core.config.LoggingConfig attribute) LoggingConfig (class in heterodyne.core.config)

M

max (heterodyne.core.config.ParameterBound attribute) max_angle (heterodyne.core.config.AngleRange attribute) maxiter (heterodyne.core.config.OptimizationMethodConfig attribute) memory_efficient_cache() (in module heterodyne.core.kernels) memory_usage (heterodyne.core.config.PerformanceMonitor attribute) merge_configs() (heterodyne.core.config.ConfigManager method) method_options (heterodyne.core.config.ClassicalOptimizationConfig attribute) methods (heterodyne.core.config.ClassicalOptimizationConfig attribute)

min (heterodyne.core.config.ParameterBound attribute) min_angle (heterodyne.core.config.AngleRange attribute) model_description (heterodyne.core.config.AnalysisSettings attribute) module heterodyne.analysis.core heterodyne.core.config heterodyne.core.io_utils heterodyne.core.kernels heterodyne.optimization.classical

N

name (heterodyne.core.config.ParameterBound attribute)

njit() (in module heterodyne.core.kernels)

O

OptimizationConfig (class in heterodyne.core.config)

OptimizationMethodConfig (class in heterodyne.core.config) optimize() (heterodyne.optimization.classical.ClassicalOptimizer method)

P

parameter_names (heterodyne.core.config.InitialParametersConfig attribute) ParameterBound (class in heterodyne.core.config) ParameterSpaceConfig (class in heterodyne.core.config)

PerformanceMonitor (class in heterodyne.core.config) phi_angles_file (heterodyne.core.config.ExperimentalDataConfig attribute) phi_angles_path (heterodyne.core.config.ExperimentalDataConfig attribute)

R

refresh_kernel_functions() (in module heterodyne.core.kernels) reset_optimization_counter() (heterodyne.optimization.classical.ClassicalOptimizer method) reset_timings() (heterodyne.core.config.PerformanceMonitor method) resolve_environment_variables() (heterodyne.core.config.ConfigManager method) restore_from_backup() (heterodyne.core.config.ConfigManager method)

rotation (heterodyne.core.config.LoggingConfig attribute) run_classical_optimization_optimized() (heterodyne.optimization.classical.ClassicalOptimizer method) (in module heterodyne.optimization.classical) run_classical_optimization_optimized_full_signature() (in module heterodyne.optimization.classical) run_optimization() (heterodyne.optimization.classical.ClassicalOptimizer method) run_single_method() (heterodyne.optimization.classical.ClassicalOptimizer method)

S

save_analysis_results() (in module heterodyne.core.io_utils) save_classical_optimization_results() (in module heterodyne.core.io_utils) save_config() (heterodyne.core.config.ConfigManager method) save_fig() (in module heterodyne.core.io_utils) save_json() (in module heterodyne.core.io_utils) save_numpy() (in module heterodyne.core.io_utils) save_pickle() (in module heterodyne.core.io_utils)

save_results_with_config() (heterodyne.analysis.core.HeterodyneAnalysisCore method) set_parameter() (heterodyne.core.config.ConfigManager method) setup_logging() (heterodyne.core.config.ConfigManager method) should_fallback_to_all_angles() (heterodyne.core.config.ConfigManager method) solve_least_squares_batch_numba() (in module heterodyne.core.kernels) start() (heterodyne.core.config.PerformanceMonitor method) static_mode (heterodyne.core.config.AnalysisSettings attribute) static_submode (heterodyne.core.config.AnalysisSettings attribute)

T

target_ranges (heterodyne.core.config.AngleFilteringConfig attribute) time_function() (heterodyne.core.config.PerformanceMonitor method)

timestamped_filename() (in module heterodyne.core.io_utils) timings (heterodyne.core.config.PerformanceMonitor attribute) type (heterodyne.core.config.ParameterBound attribute)

V

validate_config() (heterodyne.core.config.ConfigManager method) validate_heterodyne_parameters() (heterodyne.analysis.core.HeterodyneAnalysisCore method)

validate_method_compatibility() (heterodyne.optimization.classical.ClassicalOptimizer method) validate_parameter_bounds() (heterodyne.core.config.ConfigManager method) validate_parameters() (heterodyne.optimization.classical.ClassicalOptimizer method)

X

xatol (heterodyne.core.config.OptimizationMethodConfig attribute)