Mapping.ElutionMapper#
ElutionMapper.py
Optimization of mapping between UV-absorbance and Xray-scattering
Copyright (c) 2018-2024, SAXS Team, KEK-PF
- class ElutionMapper(serial_data, input_sd, pre_recog, callbacks=None)#
Bases:
object- adjust_baselines(opt_params)#
- adjust_both_baselines(opt_params, G_init=0)#
- adjust_both_opt_results(D, E, F, G)#
- adjust_uv_baseline_only()#
- adjust_uv_opt_results(D, E)#
- adjust_xray_baseline_only(G_init=0)#
- adjust_xray_opt_results(F, G)#
- both_baseline_adjuster(params)#
- check_mapping_normality(A, B, std_diff=None)#
note that this method is usually called twice, before and after optimazation
- check_peak_concictency(a_peak_info, x_peak_info, allowance)#
- compute_approximate_std_diff(A, B)#
- compute_area(end_x, floor_end_y, ceil_end_y)#
- compute_curve_for_eval_diff()#
- compute_deviation_scales()#
- compute_initial_params(debug=False)#
- compute_penalty_vector(a_adj, m_adj, x_adj)#
the purpose of introducing a penalty vector is to prevent the optimizer from getting lost into useless cases where both adjustments grow large in the same direction.
- compute_simple_params()#
- compute_std_diff()#
- compute_xray_baseline(opt_params)#
- debug_log_results()#
- determine_mapping_ranges()#
- ensure_peak_consistency(check_raw_info=False)#
- get_adjusted_a_spline()#
- get_adjustment_deviation(debug=False)#
- get_affine_info()#
- get_conc_type()#
- get_conc_vector(conc_factor)#
- get_int_ranges()#
- get_mapped_flow_changes()#
- get_mapped_info()#
- get_min_sci()#
- get_num_peaks()#
- get_opt_params_from_ue(ue)#
- get_opt_params_from_xe(xe)#
- get_sci_list()#
- get_uniformly_scaled_vector()#
- get_uv_value(xe)#
- get_x2a_scale()#
- initialize(sd)#
- make_a_curve(opt_params, helper_info=None, flow_change_exist=False, devel=True)#
- make_elution_curves(opt_params, helper_info, debug=False)#
- make_mapped_adjustment(A, B, D, E)#
- make_mapped_valley_vector(i, prev_stop, x_boundary, p_start, prev_A, prev_B, prev_S, A, B, S, make_inv_mapped_boundaries, with_original_scale=False)#
- make_mapped_vector(xray_x, A, B, S)#
- make_proof_info()#
- make_scaled_xray_curve_y(debug=False)#
- make_uniformly_scaled_vector(scale=None, survey_fh=None)#
- make_uniformly_scaled_vector_in_another_way(scale, adj_spline, survey_fh=None)#
- make_whole_mapped_vector(A, B, scales, make_inv_mapped_boundaries=False, with_original_scale=False)#
- make_x_curve(opt_params)#
- optimize(opt_params=None, curve_make_only=False, sync_options=None, helper_info=None, apply_patch=False)#
- optimize_mapping(devel=False)#
- prepare_env_for_plain_LPM()#
- refine_mapping_ranges()#
- resort_to_simpler_solution()#
- set_opt_params(mapping_params)#
- set_optimize_callback(callback)#
- set_peak_eval_ranges()#
- set_sd_update_callback(callback)#
- set_x_curve_update_callback(callback)#
- uv_baseline_adjuster(params)#
- xray_baseline_adjuster(params)#
- TO_BE_REMOVED = False#
refactoring memo
- optimize
optimize_mapping
- adjust_baselines
- adjust_uv_baseline_only
minimize
- adjust_xray_baseline_only
minimize
- adjust_both_baselines
minimize