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"""Regenerate synthetic data and publication figures; no experimental records."""
from __future__ import annotations
import csv, json, pathlib, sys
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from scipy.constants import h, k as k_B
from lioraen_omega import (phase_model, reflection, sigma, pick_matrices,
    spectral_mass_bound, recover, full_response, quadratic_value, controls)
ROOT=pathlib.Path(__file__).resolve().parents[1]
SEED=16102027

def write_csv(path, header, rows):
    with path.open('w',newline='',encoding='utf-8') as f:
        writer=csv.writer(f);writer.writerow(header);writer.writerows(rows)

def save_fig(name):
    plt.tight_layout()
    plt.savefig(ROOT/'manuscript'/'figures'/f'{name}.pdf',bbox_inches='tight')
    plt.savefig(ROOT/'manuscript'/'figures'/f'{name}.png',dpi=160,bbox_inches='tight')
    plt.close()

def main():
    rng=np.random.default_rng(SEED)
    for directory in ['physics','data','results','manuscript/figures']:
        (ROOT/directory).mkdir(parents=True,exist_ok=True)
    eta=.05;kext=.05;tau=.2;phis=[np.pi/2,-np.pi/2]
    models=[phase_model(p) for p in phis]
    omegas=np.linspace(-1.2,1.2,801)
    values=np.array([[reflection(*model,float(w),1j*tau,eta,kext)
                      for w in omegas] for model in models])
    contrast=np.abs(values[0]-values[1]);index=int(np.argmax(contrast));w0=float(omegas[index])
    std_single=.001; repeats=25;std_mean=std_single/np.sqrt(repeats)
    noisy=values+std_mean/np.sqrt(2)*(rng.normal(size=values.shape)+1j*rng.normal(size=values.shape))
    rows=[]
    for j,w in enumerate(omegas):
        rows.append([w,values[0,j].real,values[0,j].imag,values[1,j].real,
                     values[1,j].imag,contrast[j],noisy[0,j].real,noisy[0,j].imag,
                     noisy[1,j].real,noisy[1,j].imag])
    write_csv(ROOT/'physics'/'phase_scan.csv',
        ['omega_over_Omega0','S_plus_real','S_plus_imag','S_minus_real','S_minus_imag',
         'absolute_contrast','noisy_plus_real','noisy_plus_imag',
         'noisy_minus_real','noisy_minus_imag'],rows)
    plt.figure(figsize=(7.0,4.2))
    plt.plot(omegas,np.abs(values[0]),label=r'$\phi=+\pi/2$')
    plt.plot(omegas,np.abs(values[1]),label=r'$\phi=-\pi/2$')
    plt.xlabel(r'Drive detuning $\omega/\Omega_0$');plt.ylabel('Reflection amplitude magnitude')
    plt.title('Synthetic phase-controlled one-port response');plt.legend()
    save_fig('reflection_phase')
    plt.figure(figsize=(7.0,4.2))
    plt.plot(omegas,contrast)
    plt.xlabel(r'Drive detuning $\omega/\Omega_0$');plt.ylabel(r'$|S_{+}-S_{-}|$')
    plt.title('Synthetic complex-reflection contrast')
    save_fig('phase_contrast')
    # Raw four-setting reconstruction and withheld checks use full resolvents.
    ts=[tau*t for t in controls(1)];H,L,C=models[0];z=w0+1j*eta
    fs=[full_response(H,L,C,z,t) for t in ts]
    cal_records=[];fmeas=[]
    for j,(t,f) in enumerate(zip(ts,fs)):
        sexact=1-1j*kext/f
        sm=sexact+std_mean/np.sqrt(2)*(rng.normal()+1j*rng.normal())
        gm=(1-sm)/(1j*kext);fm=1/gm;fmeas.append(fm)
        cal_records.append([j,t[0].real,t[0].imag,sexact.real,sexact.imag,
                            sm.real,sm.imag,f.real,f.imag,fm.real,fm.imag])
    write_csv(ROOT/'physics'/'raw_control_records.csv',
        ['setting','t_real','t_imag','S_exact_real','S_exact_imag','S_measured_real',
         'S_measured_imag','F_exact_real','F_exact_imag','F_measured_real',
         'F_measured_imag'],cal_records)
    rec=recover(ts,fs);recnoise=recover(ts,fmeas)
    withheld=[]
    for j in range(20):
        t=tau*(rng.normal(size=1)+1j*rng.normal(size=1))
        truth=full_response(H,L,C,z,t);pred=quadratic_value(rec,t)
        noisy_pred=quadratic_value(recnoise,t)
        # An intentional hidden-mode shift only at validation invalidates the model.
        Ldrift=L.copy();Ldrift[0,0]+=.025
        drift=full_response(H,Ldrift,C,z,t)
        withheld.append([j,t[0].real,t[0].imag,truth.real,truth.imag,
                         abs(pred-truth),abs(noisy_pred-truth),abs(pred-drift)])
    write_csv(ROOT/'physics'/'withheld_controls.csv',
        ['index','t_real','t_imag','F_true_real','F_true_imag','exact_prediction_error',
         'noisy_prediction_error','deliberate_drift_error'],withheld)
    # Return-memory cross-pole invariant.
    times=np.linspace(0,10,501)
    mem=np.array([abs(np.exp(.6j*times)+np.exp(1j*p)*np.exp(-.6j*times))**2 for p in phis])
    write_csv(ROOT/'data'/'memory_phase.csv',['time_times_Omega0','plus','minus'],
              zip(times,mem[0],mem[1]))
    plt.figure(figsize=(7,4.2))
    for p,m in zip(phis,mem):
        plt.plot(times,m,label=r'$\phi=+\pi/2$' if p>0 else r'$\phi=-\pi/2$')
    plt.xlabel(r'Dimensionless time $t\Omega_0$');plt.ylabel(r'$|\mathcal{M}_{12}(t)|^2/g^4$')
    plt.legend();plt.title('A phase relation across two spectral poles')
    save_fig('memory_phase')
    ns=np.arange(1,9);profile=np.minimum(ns,3)+2*np.minimum(ns,2)
    write_csv(ROOT/'data'/'rank_profiles.csv',['nodes','seven_state_Hermitian','one_damped_state'],zip(ns,profile,ns))
    plt.figure(figsize=(7,4.2))
    plt.plot(ns,profile,'o-',label='Seven-state Hermitian model (q=3)')
    plt.plot(ns,ns,'s--',label='One damped state, unshifted kernel (q=1)')
    plt.xlabel('Number of distinct sample frequencies');plt.ylabel('Exact kernel rank')
    plt.xticks(ns);plt.legend();plt.title('Completion versus persistent rank growth')
    save_fig('rank_profiles')
    zs=np.linspace(-2,2,8)+.7j;gamma=.4
    vals=[np.array([[1/(z+1j*gamma)]]) for z in zs]
    K,_,_=pick_matrices(zs,vals);Kcorrect,_,_=pick_matrices(zs+1j*gamma,vals)
    eig=np.linalg.eigvalsh(K)[::-1];correct=np.linalg.eigvalsh(Kcorrect)[::-1]
    write_csv(ROOT/'data'/'damping_kernel_spectrum.csv',
        ['index','uncorrected_eigenvalue','known_shift_eigenvalue'],zip(range(1,9),eig,correct))
    plt.figure(figsize=(7,4.2))
    plt.semilogy(range(1,9),np.maximum(abs(eig),1e-18),'o-',label='Unshifted Pick kernel')
    plt.semilogy(range(1,9),np.maximum(abs(correct),1e-18),'s--',label='Known common linewidth shift')
    plt.xlabel('Eigenvalue index');plt.ylabel('Absolute numerical eigenvalue')
    plt.legend();plt.title('One damped mode: two different dimension questions')
    save_fig('damping_spectrum')
    # A nonvacuous but deliberately conservative support witness.
    wz=np.array([-.7+.5j,0+.5j,.7+.5j]);roots=np.array([-.5,.5])
    masses=np.array([1.,1.,1e-6]);poles=np.array([-.5,.5,.9])
    vals=[np.array([[sum(masses/(z-poles))]]) for z in wz]
    Kw,_,_=pick_matrices(wz,vals)
    result=spectral_mass_bound(wz,roots,Kw,1,1.,.2,sample_error=1e-10)
    result['weights']=[[float(a.real),float(a.imag)] for a in result['weights']]
    result.update(actual_outside_mass=1e-6,total_mass=float(sum(masses)),
                  support_radius=1.,band_radius=.2,assumed_sample_error=1e-10)
    assert result['bound']>=result['actual_outside_mass']
    (ROOT/'results'/'spectral_witness.json').write_text(json.dumps(result,indent=2)+'\n')
    occupation=float(1/np.expm1(h*10e6/(k_B*.01)))
    real_null=max(abs(full_response(*models[0],z,[x])-full_response(*models[1],z,[x]))
                  for x in np.linspace(-.5,.5,31))
    report=dict(status='entirely synthetic; no physical experiment',seed=SEED,
        angular_frequency_unit_rad_per_s=float(2*np.pi*1e6),
        parameter_units='Hamiltonian, linewidth, and drive detuning divided by Omega0',
        eta=.05,kappa_external=.05,g=.3,tau=.2,
        visible_detunings=[-.1,.15],hidden_detunings=[-.6,.6],
        maximum_complex_reflection_contrast=float(contrast[index]),
        omega_at_maximum=w0,frequency_grid_points=len(omegas),
        maximum_absolute_reflection=float(abs(values).max()),
        real_control_transpose_null_max=float(real_null),
        assumed_single_record_complex_rms=std_single,repeats=repeats,
        assumed_averaged_complex_rms=std_mean,assumed_systematic_target=.005,
        thermal_example=dict(frequency_Hz=10e6,temperature_K=.01,occupation=occupation),
        control_design_condition=rec['condition'],
        maximum_exact_withheld_error=float(max(row[5] for row in withheld)),
        maximum_noisy_withheld_error=float(max(row[6] for row in withheld)),
        minimum_deliberate_drift_error=float(min(row[7] for row in withheld)),
        maximum_deliberate_drift_error=float(max(row[7] for row in withheld)),
        witness_bound=float(result['bound']))
    assert report['maximum_absolute_reflection']<=1+1e-10
    assert real_null<1e-10
    assert report['maximum_exact_withheld_error']<1e-8
    (ROOT/'physics'/'parameters_and_results.json').write_text(json.dumps(report,indent=2)+'\n')
    tex=(r'\newcommand{\PeakContrast}{'+f"{report['maximum_complex_reflection_contrast']:.4f}"+'}\n'+
         r'\newcommand{\PeakFrequency}{'+f'{w0:.3f}'+'}\n'+
         r'\newcommand{\ThermalOccupation}{'+f'{occupation:.2f}'+'}\n'+
         r'\newcommand{\WitnessBound}{'+f"{result['bound']:.6f}"+'}\n')
    (ROOT/'manuscript'/'generated_numbers.tex').write_text(tex)
    print(json.dumps(report,indent=2))
if __name__=='__main__':main()