Loading PyAETNA/reporting/lightcurve_plots.py +26 −5 Changes for PyAETNA/reporting/lightcurve_plots.py: 26 added lines, 5 removed lines. Original line number Diff line number Diff line Loading @@ -2449,15 +2449,34 @@ def plot_models(plData, plModel, best_params, param_config, # probability density (arbitrary units, increasing to the right), making # it easy to see at a glance whether the residuals are Gaussian, skewed, # or have heavy tails, without leaving the time-series context. _kde_visible = False try: from scipy.stats import gaussian_kde as _gkde if len(residuals) >= 4: _kde_visible = True # determine vertical range to sample over; use entire residual set _res_span = float(residuals.max() - residuals.min()) _margin = 0.15 * _res_span if _res_span > 0 else 1e-6 _y_k = np.linspace(float(residuals.min()) - _margin, float(residuals.max()) + _margin, 300) if is_per_inst_plot and visit_colors is not None: # Plot overall combined KDE in background try: _kde_v = _gkde(residuals)(_y_k) ax_kde.fill_betweenx(_y_k, 0, _kde_v, color='gray', alpha=0.30) ax_kde.plot(_kde_v, _y_k, color='gray', linewidth=1.2, label='Combined') except Exception: pass # Reference Gaussian with same mean and std (red dashed) _mu = float(np.mean(residuals)) _sig = float(np.std(residuals)) if _sig > 0: _gauss = (np.exp(-0.5 * ((_y_k - _mu) / _sig) ** 2) / (_sig * np.sqrt(2.0 * np.pi))) ax_kde.plot(_gauss, _y_k, color='C3', linewidth=1.0, linestyle='--', alpha=0.8, label='Gaussian ref.') # plot separate KDEs for each visit using the same colors for uv in unique_vis: sel = vis_sorted == uv Loading @@ -2469,8 +2488,7 @@ def plot_models(plData, plModel, best_params, param_config, ax_kde.plot(kde(_y_k), _y_k, color=visit_colors[uv], linewidth=1.2, alpha=0.8, label=f'Visit {uv}') except Exception: ax_kde.axhline(np.mean(res_uv), color=visit_colors[uv], linewidth=1.2, alpha=0.8, label=f'Visit {uv}') pass ax_kde.axhline(0, color='k', linestyle='--', linewidth=0.5) ax_kde.set_xlim(left=0) ax_kde.legend(fontsize=6, loc='upper right') Loading @@ -2490,15 +2508,18 @@ def plot_models(plData, plModel, best_params, param_config, ax_kde.axhline(0, color='k', linestyle='--', linewidth=0.5) ax_kde.set_xlim(left=0) except ImportError: # scipy not available — leave the KDE panel blank pass except Exception: pass # silently skip KDE on any numerical failure _kde_visible = False if _kde_visible: # Style: suppress y-tick labels (shared with main panel), minimal x-ticks ax_kde.tick_params(labelleft=False, labelsize=7) ax_kde.set_xlabel('KDE', fontsize=7) ax_kde.xaxis.set_major_locator(plt.MaxNLocator(2)) else: # Hide the axis completely (not even showing the axis or anything) ax_kde.set_visible(False) # Show original BJD on x-axis (plData.time is centered internally by timeCenter) time_center = float(getattr(plData, 'timeCenter', 0.0)) if time_center != 0.0: Loading tests/PyAETNAouts/test_rv_only.log +852 −0 File changed.Preview size limit exceeded, changes collapsed. Show changes tests/PyAETNAouts/test_rv_only.pdf +3.96 KiB (783 KiB) File changed.No diff preview for this file type. View original file View changed file tests/PyAETNAouts/test_rv_only_physics.pdf +430 B (73.3 KiB) File changed.No diff preview for this file type. View original file View changed file tests/PyAETNAouts/test_spectral_mixture.log 0 → 100644 +208 −0 Changes for tests/PyAETNAouts/test_spectral_mixture.log: 208 added lines, 0 removed lines. Original line number Diff line number Diff line 2026-06-25 15:10:54 INFO: Log file reset as requested (reset=True) 2026-06-25 15:10:54 INFO: Starting run using config '/dati/software/pyLib/PyAETNA/tests/test_spectral_mixture.yaml' 2026-06-25 15:10:54 INFO: Data working_dir: /dati/software/pyLib/PyAETNA/tests 2026-06-25 15:10:54 INFO: Data file: test_spectral_mixture.dat 2026-06-25 15:10:54 INFO: Successfully changed to data directory 2026-06-25 15:10:54 INFO: JAX version 0.9.0.1 2026-06-25 15:10:54 INFO: JAX devices: [CpuDevice(id=0), CpuDevice(id=1), CpuDevice(id=2), CpuDevice(id=3), CpuDevice(id=4), CpuDevice(id=5), CpuDevice(id=6), CpuDevice(id=7)] 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: JAX Environment Info: 2026-06-25 15:10:54 INFO: jax: 0.9.0.1 2026-06-25 15:10:54 INFO: jaxlib: 0.9.0.1 2026-06-25 15:10:54 INFO: numpy: 2.4.2 2026-06-25 15:10:54 INFO: python: 3.13.14 (main, Jun 11 2026, 12:30:58) [GCC 11.4.0] 2026-06-25 15:10:54 INFO: device info: cpu-8, 8 local devices" 2026-06-25 15:10:54 INFO: process_count: 1 2026-06-25 15:10:54 INFO: platform: uname_result(system='Linux', node='thX280', release='6.8.0-124-generic', version='#124~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue May 26 21:05:19 UTC ', machine='x86_64') 2026-06-25 15:10:54 INFO: XLA_FLAGS=--xla_force_host_platform_device_count=40 2026-06-25 15:10:54 2026-06-25 15:10:54 2026-06-25 15:10:54 ############################### 2026-06-25 15:10:54 # 2026-06-25 15:10:54 # SAMPLING STARTED 2026-06-25 15:10:54 # 2026-06-25 15:10:54 ############################### 2026-06-25 15:10:54 reset=True: log file deleted and freshly started 2026-06-25 15:10:54 Starting NumPyro sampler... 2026-06-25 15:10:54 walkers_coefficient from YAML: 4 (walkers = first even ≥ 4 × n_free_params, resolved after config parsing) 2026-06-25 15:10:54 No GPU detected. Walkers: 4×n_free_params (TBD), NUTS chains: 2 — CPU parallel mode. 2026-06-25 15:10:54 Available CPU cores: 6 2026-06-25 15:10:54 Loading data from test_spectral_mixture.dat... 2026-06-25 15:10:54 Data loaded: 240 points, 1 visits, 1 instruments 2026-06-25 15:10:54 Loading configuration from /dati/software/pyLib/PyAETNA/tests/test_spectral_mixture.yaml... 2026-06-25 15:10:54 Data types: {'LC': 'LC'} 2026-06-25 15:10:54 GP configuration: 2026-06-25 15:10:54 GP_sm: kernel=SpectralMixture, x_variable=BJD, instruments=['LC'] 2026-06-25 15:10:54 GP-enabled instruments: ['LC'] 2026-06-25 15:10:54 JAX precision: float32 (manual override via mcmc.use_float64) 2026-06-25 15:10:54 2026-06-25 15:10:54 2026-06-25 15:10:54 ========================================================================================== 2026-06-25 15:10:54 PRIOR SUMMARY (v3.0.0 scope-aware) 2026-06-25 15:10:54 ========================================================================================== 2026-06-25 15:10:54 Normalization mode: multiplicative 2026-06-25 15:10:54 2026-06-25 15:10:54 FREE PARAMETERS: 2026-06-25 15:10:54 log_gp_sigma_0_GP_sm ('uniform', -2.0, 1.0) (global) 2026-06-25 15:10:54 log_gp_sigma_1_GP_sm ('uniform', -3.0, 0.0) (global) 2026-06-25 15:10:54 log_gp_sigma_2_GP_sm ('uniform', -3.0, 1.0) (global) 2026-06-25 15:10:54 log_gp_lengthscale_GP_sm ('uniform', 1.802585092994046, 2.802585092994046) (global) 2026-06-25 15:10:54 2026-06-25 15:10:54 FIXED PARAMETERS: 2026-06-25 15:10:54 gp_freq_GP_sm 0.5 2026-06-25 15:10:54 log_jitter -inf 2026-06-25 15:10:54 norm 1.0 2026-06-25 15:10:54 q1 0.3 2026-06-25 15:10:54 q2 0.2 2026-06-25 15:10:54 rho_star 1.0 2026-06-25 15:10:54 2026-06-25 15:10:54 SpectralMixture kernel components in section '1': 3 2026-06-25 15:10:54 ========================================================================================== 2026-06-25 15:10:54 2026-06-25 15:10:54 WARNING: internal_warmup_if_nuts=120 is too low for reliable NUTS adaptation (min=500). Clamping to 500. 2026-06-25 15:10:54 Ensemble walkers: 4 × 4 = 16 → 16 (first even number) 2026-06-25 15:10:54 Sampler config: production_sampler=ESS (no warmup), 16 walkers, 500 samples 2026-06-25 15:10:54 2026-06-25 15:10:54 Fresh start on CPU: direct ESS (16 walkers, no warmup) 2026-06-25 15:10:54 Free params (4): ['log_gp_sigma_0_GP_sm', 'log_gp_sigma_1_GP_sm', 'log_gp_sigma_2_GP_sm', 'log_gp_lengthscale_GP_sm'] 2026-06-25 15:10:54 === DIRECT ESS PRODUCTION (no warmup) === 2026-06-25 15:10:54 Walkers: 16, Samples: 500 2026-06-25 15:10:54 Running 1 pilot sample to trigger JIT compilation… 2026-06-25 15:10:57 JIT compilation + 1 pilot step: 2.9s 2026-06-25 15:10:57 Sampling 500 iterations with checkpoints every 100... 2026-06-25 15:10:57 Checkpoints: PyAETNAouts/test_spectral_mixture.pckl 2026-06-25 15:10:57 Running 1 pilot sample to trigger JIT compilation… 2026-06-25 15:10:58 JIT compilation + 1 pilot sample: 1.2s — all batch rates below reflect true hardware throughput 2026-06-25 15:11:05 Progress: 101/500 (20.2%) | Rate: 79.168 it/s | SS rate (steady-state): 79.168 it/s | ETA: 5s [ESS=1.3s] 2026-06-25 15:11:13 Progress: 201/500 (40.2%) | Rate: 127.940 it/s | SS rate (steady-state): 97.811 it/s | ETA: 3s [ESS=0.8s] 2026-06-25 15:11:23 Progress: 301/500 (60.2%) | Rate: 120.117 it/s | SS rate (steady-state): 104.265 it/s | ETA: 2s [ESS=0.8s] 2026-06-25 15:11:30 Progress: 401/500 (80.2%) | Rate: 103.804 it/s | SS rate (steady-state): 104.150 it/s | ETA: 1s [ESS=1.0s] 2026-06-25 15:11:38 Progress: 500/500 (100.0%) | Rate: 64.486 it/s | SS rate (steady-state): 92.823 it/s | ETA: 0s [ESS=1.5s] 2026-06-25 15:11:38 Steady-state rate: 92.823 it/s | JIT (pilot): 1.2s | Total: 41s 2026-06-25 15:11:38 === END ESS PRODUCTION === 2026-06-25 15:11:38 Total MCMC time: 44s 2026-06-25 15:11:38 Saving to PyAETNAouts/test_spectral_mixture.pckl... 2026-06-25 15:11:38 Sampling finished. 2026-06-25 15:11:38 2026-06-25 15:11:38 2026-06-25 15:11:38 2026-06-25 15:11:38 ############################### 2026-06-25 15:11:38 # 2026-06-25 15:11:38 # REPORTING STARTED 2026-06-25 15:11:38 # 2026-06-25 15:11:38 ############################### 2026-06-25 15:11:38 INFO: Loading: PyAETNAouts//test_spectral_mixture.pckl 2026-06-25 15:11:38 INFO: Loaded 8000 scalar-param samples (16 chains × 500) 2026-06-25 15:11:38 INFO: 2026-06-25 15:11:38 INFO: ========================================================================================== 2026-06-25 15:11:38 INFO: MAP SEARCH (Maximum A Posteriori) 2026-06-25 15:11:38 INFO: ========================================================================================== 2026-06-25 15:11:38 INFO: No potential_energy available - evaluating chain endpoints... 2026-06-25 15:11:39 INFO: Chain 0: energy = -767.971542 (loglike=771.56, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 1: energy = -770.000266 (loglike=773.58, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 2: energy = -769.693652 (loglike=773.28, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 3: energy = -770.747228 (loglike=774.33, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 4: energy = -769.465467 (loglike=773.05, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 5: energy = -769.137485 (loglike=772.72, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 6: energy = -769.794605 (loglike=773.38, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 7: energy = -769.443936 (loglike=773.03, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 8: energy = -768.693777 (loglike=772.28, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 9: energy = -769.657909 (loglike=773.24, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 10: energy = -769.776733 (loglike=773.36, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 11: energy = -769.172531 (loglike=772.76, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 12: energy = -770.069315 (loglike=773.65, logprior=-3.58) 2026-06-25 15:11:40 INFO: Chain 13: energy = -770.540210 (loglike=774.12, logprior=-3.58) 2026-06-25 15:11:40 INFO: Chain 14: energy = -769.020568 (loglike=772.60, logprior=-3.58) 2026-06-25 15:11:40 INFO: Chain 15: energy = -767.797758 (loglike=771.38, logprior=-3.58) 2026-06-25 15:11:40 INFO: Best chain endpoint: chain 3 (energy: -770.7472) 2026-06-25 15:11:40 INFO: Skipping optimization step 2026-06-25 15:11:40 INFO: MAP source: last_samples 2026-06-25 15:11:40 INFO: MAP energy: -770.7472 2026-06-25 15:11:40 INFO: ========================================================================================== 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: Raw sample summary (before rejecting 100 extra warmup): 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: ================================================================================================================================== 2026-06-25 15:11:40 INFO: SAMPLING SUMMARY (raw post-warmup samples) 2026-06-25 15:11:40 INFO: Note: These are the raw collected samples. Use the final summary table below (after discard) for analysis. 2026-06-25 15:11:40 INFO: Parameter Mean Std Q16 Median Q84 ESS ESS/s Rhat 2026-06-25 15:11:40 INFO: ---------------------------------------------------------------------------------------------------------------------------------- 2026-06-25 15:11:40 INFO: log_gp_sigma_0_GP_sm -0.948634 0.235042 -1.177547 -0.951180 -0.721983 5774.7 0.00 0.9999 2026-06-25 15:11:40 INFO: log_gp_sigma_1_GP_sm -2.218044 0.268908 -2.472574 -2.239032 -1.968655 6521.0 0.00 0.9998 2026-06-25 15:11:40 INFO: log_gp_sigma_2_GP_sm -2.033365 0.276201 -2.308544 -2.049645 -1.760629 5892.7 0.00 1.0014 2026-06-25 15:11:40 INFO: log_gp_lengthscale_GP_sm 2.255482 0.080088 2.177416 2.256461 2.331224 5271.9 0.00 0.9994 2026-06-25 15:11:40 INFO: ---------------------------------------------------------------------------------------------------------------------------------- 2026-06-25 15:11:40 INFO: # * = Rhat > 1.01 (warning), ** = Rhat > 1.1 (poor convergence) 2026-06-25 15:11:40 INFO: # 16 chains, 500 samples/chain, 100 warmup iterations 2026-06-25 15:11:40 INFO: ================================================================================================================================== 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: ==================================================================================================================================================================================== 2026-06-25 15:11:40 INFO: MCMC SUMMARY (after rejecting 100 extra warmup) 2026-06-25 15:11:40 INFO: parameter mean std q16 median q84 MAP P(tail) ess ess/s rhat 2026-06-25 15:11:40 INFO: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 2026-06-25 15:11:40 INFO: log_gp_sigma_0_GP_sm -0.945665 0.230655 -1.17131 -0.947608 -0.724881 -1.14262 P(<)=19.3% 4735.0 0.00 1.0001 2026-06-25 15:11:40 INFO: log_gp_sigma_1_GP_sm -2.21627 0.259069 -2.46661 -2.23714 -1.96967 -2.44599 P(<)=18.0% 5164.8 0.00 0.9997 2026-06-25 15:11:40 INFO: log_gp_sigma_2_GP_sm -2.03999 0.275237 -2.31208 -2.05903 -1.76996 -2.20828 P(<)=28.6% 4705.2 0.00 1.0014 2026-06-25 15:11:40 INFO: log_gp_lengthscale_GP_sm 2.25713 0.0789604 2.18059 2.25816 2.33227 2.22088 P(<)=31.6% 4300.9 0.00 0.9990 2026-06-25 15:11:40 INFO: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 2026-06-25 15:11:40 INFO: # * = rhat > 1.01 (warning), ** = rhat > 1.1 (poor convergence) 2026-06-25 15:11:40 INFO: # MAP source: last_samples 2026-06-25 15:11:40 INFO: # P(tail) = P(param < MAP) or P(param > MAP) depending on whether MAP < or > median 2026-06-25 15:11:40 INFO: # num_chains=16, num_samples_per_chain=400, num_warmup=100 2026-06-25 15:11:40 INFO: ==================================================================================================================================================================================== 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: ========================================================================================== 2026-06-25 15:11:40 INFO: GOODNESS-OF-FIT STATISTICS 2026-06-25 15:11:40 INFO: ========================================================================================== 2026-06-25 15:11:40 INFO: OVERALL (all instruments combined): 2026-06-25 15:11:40 INFO: Data points (N): 240 2026-06-25 15:11:40 INFO: Free parameters (k): 4 2026-06-25 15:11:40 INFO: Degrees of freedom: 236 2026-06-25 15:11:40 INFO: Chi-squared: 358.8752 2026-06-25 15:11:40 INFO: Reduced Chi-squared: 1.5207 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: Information Criteria: 2026-06-25 15:11:40 INFO: AIC = 2k - 2*ln(L) = -1533.4945 2026-06-25 15:11:40 INFO: AICc (corrected) = -1533.3250 2026-06-25 15:11:40 INFO: BIC = k*ln(N) - 2*ln(L) = -1519.5719 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: PER-VISIT STATISTICS: 2026-06-25 15:11:40 INFO: Residuals include GP mean (y − total_model where total = det + GP mean). 2026-06-25 15:11:40 INFO: sigma_orig = uncertainties from the data file (SIGMA column). 2026-06-25 15:11:40 INFO: sigma_tot = sqrt(sigma_orig² + jitter²) (jitter-inflated). 2026-06-25 15:11:40 INFO: nRMS = sqrt(chi2/N) = sqrt(mean((r/sigma)²)) [consistent with chi2]. 2026-06-25 15:11:40 INFO: chi2_red uses global n_free_params as a conservative DOF floor. 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: LC (LC): 2026-06-25 15:11:40 INFO: Visit 1 (N = 240): 2026-06-25 15:11:40 INFO: With sigma_orig (chi2_red >> 1 expected when jitter is large): 2026-06-25 15:11:40 INFO: chi2_red = 1.5207 2026-06-25 15:11:40 INFO: RMS (O-C) = 0.006114 2026-06-25 15:11:40 INFO: nRMS = 1.2228 2026-06-25 15:11:40 INFO: median sigma_orig = 0.005000 2026-06-25 15:11:40 INFO: With sigma_tot (chi2_red ~ 1 and nRMS ~ 1 expected by design): 2026-06-25 15:11:40 INFO: chi2_red = 1.5207 2026-06-25 15:11:40 INFO: RMS (O-C) = 0.006114 2026-06-25 15:11:40 INFO: nRMS = 1.2228 2026-06-25 15:11:40 INFO: median sigma_tot = 0.005000 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: ========================================================================================== 2026-06-25 15:11:40 INFO: Generating PDF report: PyAETNAouts//test_spectral_mixture.pdf 2026-06-25 15:11:40 INFO: - Corner plot... 2026-06-25 15:11:40 INFO: - KDE + Trace plots (4 params)... 2026-06-25 15:11:42 INFO: - Chain comparison plot... 2026-06-25 15:11:42 INFO: - Computing model components... 2026-06-25 15:11:42 INFO: Built GP kernel for instrument LC (x_var=BJD) 2026-06-25 15:11:42 INFO: - Pre-computing sample data for best-fit plots (1000 samples)... 2026-06-25 15:11:43 INFO: done in 0.3 s 2026-06-25 15:11:43 INFO: - Skipping per-visit plots (all 1 visits belong to single-visit instruments; redundant with per-instrument) 2026-06-25 15:11:43 INFO: - Per-instrument best-fit lightcurve: LC 2026-06-25 15:11:43 INFO: [band grid] 1000 model samples on 275 grid pts (LC-train+gaps, pad=0.000 d) + GP posterior mean [cached] Loading
PyAETNA/reporting/lightcurve_plots.py +26 −5 Changes for PyAETNA/reporting/lightcurve_plots.py: 26 added lines, 5 removed lines. Original line number Diff line number Diff line Loading @@ -2449,15 +2449,34 @@ def plot_models(plData, plModel, best_params, param_config, # probability density (arbitrary units, increasing to the right), making # it easy to see at a glance whether the residuals are Gaussian, skewed, # or have heavy tails, without leaving the time-series context. _kde_visible = False try: from scipy.stats import gaussian_kde as _gkde if len(residuals) >= 4: _kde_visible = True # determine vertical range to sample over; use entire residual set _res_span = float(residuals.max() - residuals.min()) _margin = 0.15 * _res_span if _res_span > 0 else 1e-6 _y_k = np.linspace(float(residuals.min()) - _margin, float(residuals.max()) + _margin, 300) if is_per_inst_plot and visit_colors is not None: # Plot overall combined KDE in background try: _kde_v = _gkde(residuals)(_y_k) ax_kde.fill_betweenx(_y_k, 0, _kde_v, color='gray', alpha=0.30) ax_kde.plot(_kde_v, _y_k, color='gray', linewidth=1.2, label='Combined') except Exception: pass # Reference Gaussian with same mean and std (red dashed) _mu = float(np.mean(residuals)) _sig = float(np.std(residuals)) if _sig > 0: _gauss = (np.exp(-0.5 * ((_y_k - _mu) / _sig) ** 2) / (_sig * np.sqrt(2.0 * np.pi))) ax_kde.plot(_gauss, _y_k, color='C3', linewidth=1.0, linestyle='--', alpha=0.8, label='Gaussian ref.') # plot separate KDEs for each visit using the same colors for uv in unique_vis: sel = vis_sorted == uv Loading @@ -2469,8 +2488,7 @@ def plot_models(plData, plModel, best_params, param_config, ax_kde.plot(kde(_y_k), _y_k, color=visit_colors[uv], linewidth=1.2, alpha=0.8, label=f'Visit {uv}') except Exception: ax_kde.axhline(np.mean(res_uv), color=visit_colors[uv], linewidth=1.2, alpha=0.8, label=f'Visit {uv}') pass ax_kde.axhline(0, color='k', linestyle='--', linewidth=0.5) ax_kde.set_xlim(left=0) ax_kde.legend(fontsize=6, loc='upper right') Loading @@ -2490,15 +2508,18 @@ def plot_models(plData, plModel, best_params, param_config, ax_kde.axhline(0, color='k', linestyle='--', linewidth=0.5) ax_kde.set_xlim(left=0) except ImportError: # scipy not available — leave the KDE panel blank pass except Exception: pass # silently skip KDE on any numerical failure _kde_visible = False if _kde_visible: # Style: suppress y-tick labels (shared with main panel), minimal x-ticks ax_kde.tick_params(labelleft=False, labelsize=7) ax_kde.set_xlabel('KDE', fontsize=7) ax_kde.xaxis.set_major_locator(plt.MaxNLocator(2)) else: # Hide the axis completely (not even showing the axis or anything) ax_kde.set_visible(False) # Show original BJD on x-axis (plData.time is centered internally by timeCenter) time_center = float(getattr(plData, 'timeCenter', 0.0)) if time_center != 0.0: Loading
tests/PyAETNAouts/test_rv_only.log +852 −0 File changed.Preview size limit exceeded, changes collapsed. Show changes
tests/PyAETNAouts/test_rv_only.pdf +3.96 KiB (783 KiB) File changed.No diff preview for this file type. View original file View changed file
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tests/PyAETNAouts/test_spectral_mixture.log 0 → 100644 +208 −0 Changes for tests/PyAETNAouts/test_spectral_mixture.log: 208 added lines, 0 removed lines. Original line number Diff line number Diff line 2026-06-25 15:10:54 INFO: Log file reset as requested (reset=True) 2026-06-25 15:10:54 INFO: Starting run using config '/dati/software/pyLib/PyAETNA/tests/test_spectral_mixture.yaml' 2026-06-25 15:10:54 INFO: Data working_dir: /dati/software/pyLib/PyAETNA/tests 2026-06-25 15:10:54 INFO: Data file: test_spectral_mixture.dat 2026-06-25 15:10:54 INFO: Successfully changed to data directory 2026-06-25 15:10:54 INFO: JAX version 0.9.0.1 2026-06-25 15:10:54 INFO: JAX devices: [CpuDevice(id=0), CpuDevice(id=1), CpuDevice(id=2), CpuDevice(id=3), CpuDevice(id=4), CpuDevice(id=5), CpuDevice(id=6), CpuDevice(id=7)] 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: device_kind=cpu, platform=cpu 2026-06-25 15:10:54 INFO: JAX Environment Info: 2026-06-25 15:10:54 INFO: jax: 0.9.0.1 2026-06-25 15:10:54 INFO: jaxlib: 0.9.0.1 2026-06-25 15:10:54 INFO: numpy: 2.4.2 2026-06-25 15:10:54 INFO: python: 3.13.14 (main, Jun 11 2026, 12:30:58) [GCC 11.4.0] 2026-06-25 15:10:54 INFO: device info: cpu-8, 8 local devices" 2026-06-25 15:10:54 INFO: process_count: 1 2026-06-25 15:10:54 INFO: platform: uname_result(system='Linux', node='thX280', release='6.8.0-124-generic', version='#124~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue May 26 21:05:19 UTC ', machine='x86_64') 2026-06-25 15:10:54 INFO: XLA_FLAGS=--xla_force_host_platform_device_count=40 2026-06-25 15:10:54 2026-06-25 15:10:54 2026-06-25 15:10:54 ############################### 2026-06-25 15:10:54 # 2026-06-25 15:10:54 # SAMPLING STARTED 2026-06-25 15:10:54 # 2026-06-25 15:10:54 ############################### 2026-06-25 15:10:54 reset=True: log file deleted and freshly started 2026-06-25 15:10:54 Starting NumPyro sampler... 2026-06-25 15:10:54 walkers_coefficient from YAML: 4 (walkers = first even ≥ 4 × n_free_params, resolved after config parsing) 2026-06-25 15:10:54 No GPU detected. Walkers: 4×n_free_params (TBD), NUTS chains: 2 — CPU parallel mode. 2026-06-25 15:10:54 Available CPU cores: 6 2026-06-25 15:10:54 Loading data from test_spectral_mixture.dat... 2026-06-25 15:10:54 Data loaded: 240 points, 1 visits, 1 instruments 2026-06-25 15:10:54 Loading configuration from /dati/software/pyLib/PyAETNA/tests/test_spectral_mixture.yaml... 2026-06-25 15:10:54 Data types: {'LC': 'LC'} 2026-06-25 15:10:54 GP configuration: 2026-06-25 15:10:54 GP_sm: kernel=SpectralMixture, x_variable=BJD, instruments=['LC'] 2026-06-25 15:10:54 GP-enabled instruments: ['LC'] 2026-06-25 15:10:54 JAX precision: float32 (manual override via mcmc.use_float64) 2026-06-25 15:10:54 2026-06-25 15:10:54 2026-06-25 15:10:54 ========================================================================================== 2026-06-25 15:10:54 PRIOR SUMMARY (v3.0.0 scope-aware) 2026-06-25 15:10:54 ========================================================================================== 2026-06-25 15:10:54 Normalization mode: multiplicative 2026-06-25 15:10:54 2026-06-25 15:10:54 FREE PARAMETERS: 2026-06-25 15:10:54 log_gp_sigma_0_GP_sm ('uniform', -2.0, 1.0) (global) 2026-06-25 15:10:54 log_gp_sigma_1_GP_sm ('uniform', -3.0, 0.0) (global) 2026-06-25 15:10:54 log_gp_sigma_2_GP_sm ('uniform', -3.0, 1.0) (global) 2026-06-25 15:10:54 log_gp_lengthscale_GP_sm ('uniform', 1.802585092994046, 2.802585092994046) (global) 2026-06-25 15:10:54 2026-06-25 15:10:54 FIXED PARAMETERS: 2026-06-25 15:10:54 gp_freq_GP_sm 0.5 2026-06-25 15:10:54 log_jitter -inf 2026-06-25 15:10:54 norm 1.0 2026-06-25 15:10:54 q1 0.3 2026-06-25 15:10:54 q2 0.2 2026-06-25 15:10:54 rho_star 1.0 2026-06-25 15:10:54 2026-06-25 15:10:54 SpectralMixture kernel components in section '1': 3 2026-06-25 15:10:54 ========================================================================================== 2026-06-25 15:10:54 2026-06-25 15:10:54 WARNING: internal_warmup_if_nuts=120 is too low for reliable NUTS adaptation (min=500). Clamping to 500. 2026-06-25 15:10:54 Ensemble walkers: 4 × 4 = 16 → 16 (first even number) 2026-06-25 15:10:54 Sampler config: production_sampler=ESS (no warmup), 16 walkers, 500 samples 2026-06-25 15:10:54 2026-06-25 15:10:54 Fresh start on CPU: direct ESS (16 walkers, no warmup) 2026-06-25 15:10:54 Free params (4): ['log_gp_sigma_0_GP_sm', 'log_gp_sigma_1_GP_sm', 'log_gp_sigma_2_GP_sm', 'log_gp_lengthscale_GP_sm'] 2026-06-25 15:10:54 === DIRECT ESS PRODUCTION (no warmup) === 2026-06-25 15:10:54 Walkers: 16, Samples: 500 2026-06-25 15:10:54 Running 1 pilot sample to trigger JIT compilation… 2026-06-25 15:10:57 JIT compilation + 1 pilot step: 2.9s 2026-06-25 15:10:57 Sampling 500 iterations with checkpoints every 100... 2026-06-25 15:10:57 Checkpoints: PyAETNAouts/test_spectral_mixture.pckl 2026-06-25 15:10:57 Running 1 pilot sample to trigger JIT compilation… 2026-06-25 15:10:58 JIT compilation + 1 pilot sample: 1.2s — all batch rates below reflect true hardware throughput 2026-06-25 15:11:05 Progress: 101/500 (20.2%) | Rate: 79.168 it/s | SS rate (steady-state): 79.168 it/s | ETA: 5s [ESS=1.3s] 2026-06-25 15:11:13 Progress: 201/500 (40.2%) | Rate: 127.940 it/s | SS rate (steady-state): 97.811 it/s | ETA: 3s [ESS=0.8s] 2026-06-25 15:11:23 Progress: 301/500 (60.2%) | Rate: 120.117 it/s | SS rate (steady-state): 104.265 it/s | ETA: 2s [ESS=0.8s] 2026-06-25 15:11:30 Progress: 401/500 (80.2%) | Rate: 103.804 it/s | SS rate (steady-state): 104.150 it/s | ETA: 1s [ESS=1.0s] 2026-06-25 15:11:38 Progress: 500/500 (100.0%) | Rate: 64.486 it/s | SS rate (steady-state): 92.823 it/s | ETA: 0s [ESS=1.5s] 2026-06-25 15:11:38 Steady-state rate: 92.823 it/s | JIT (pilot): 1.2s | Total: 41s 2026-06-25 15:11:38 === END ESS PRODUCTION === 2026-06-25 15:11:38 Total MCMC time: 44s 2026-06-25 15:11:38 Saving to PyAETNAouts/test_spectral_mixture.pckl... 2026-06-25 15:11:38 Sampling finished. 2026-06-25 15:11:38 2026-06-25 15:11:38 2026-06-25 15:11:38 2026-06-25 15:11:38 ############################### 2026-06-25 15:11:38 # 2026-06-25 15:11:38 # REPORTING STARTED 2026-06-25 15:11:38 # 2026-06-25 15:11:38 ############################### 2026-06-25 15:11:38 INFO: Loading: PyAETNAouts//test_spectral_mixture.pckl 2026-06-25 15:11:38 INFO: Loaded 8000 scalar-param samples (16 chains × 500) 2026-06-25 15:11:38 INFO: 2026-06-25 15:11:38 INFO: ========================================================================================== 2026-06-25 15:11:38 INFO: MAP SEARCH (Maximum A Posteriori) 2026-06-25 15:11:38 INFO: ========================================================================================== 2026-06-25 15:11:38 INFO: No potential_energy available - evaluating chain endpoints... 2026-06-25 15:11:39 INFO: Chain 0: energy = -767.971542 (loglike=771.56, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 1: energy = -770.000266 (loglike=773.58, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 2: energy = -769.693652 (loglike=773.28, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 3: energy = -770.747228 (loglike=774.33, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 4: energy = -769.465467 (loglike=773.05, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 5: energy = -769.137485 (loglike=772.72, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 6: energy = -769.794605 (loglike=773.38, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 7: energy = -769.443936 (loglike=773.03, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 8: energy = -768.693777 (loglike=772.28, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 9: energy = -769.657909 (loglike=773.24, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 10: energy = -769.776733 (loglike=773.36, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 11: energy = -769.172531 (loglike=772.76, logprior=-3.58) 2026-06-25 15:11:39 INFO: Chain 12: energy = -770.069315 (loglike=773.65, logprior=-3.58) 2026-06-25 15:11:40 INFO: Chain 13: energy = -770.540210 (loglike=774.12, logprior=-3.58) 2026-06-25 15:11:40 INFO: Chain 14: energy = -769.020568 (loglike=772.60, logprior=-3.58) 2026-06-25 15:11:40 INFO: Chain 15: energy = -767.797758 (loglike=771.38, logprior=-3.58) 2026-06-25 15:11:40 INFO: Best chain endpoint: chain 3 (energy: -770.7472) 2026-06-25 15:11:40 INFO: Skipping optimization step 2026-06-25 15:11:40 INFO: MAP source: last_samples 2026-06-25 15:11:40 INFO: MAP energy: -770.7472 2026-06-25 15:11:40 INFO: ========================================================================================== 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: Raw sample summary (before rejecting 100 extra warmup): 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: ================================================================================================================================== 2026-06-25 15:11:40 INFO: SAMPLING SUMMARY (raw post-warmup samples) 2026-06-25 15:11:40 INFO: Note: These are the raw collected samples. Use the final summary table below (after discard) for analysis. 2026-06-25 15:11:40 INFO: Parameter Mean Std Q16 Median Q84 ESS ESS/s Rhat 2026-06-25 15:11:40 INFO: ---------------------------------------------------------------------------------------------------------------------------------- 2026-06-25 15:11:40 INFO: log_gp_sigma_0_GP_sm -0.948634 0.235042 -1.177547 -0.951180 -0.721983 5774.7 0.00 0.9999 2026-06-25 15:11:40 INFO: log_gp_sigma_1_GP_sm -2.218044 0.268908 -2.472574 -2.239032 -1.968655 6521.0 0.00 0.9998 2026-06-25 15:11:40 INFO: log_gp_sigma_2_GP_sm -2.033365 0.276201 -2.308544 -2.049645 -1.760629 5892.7 0.00 1.0014 2026-06-25 15:11:40 INFO: log_gp_lengthscale_GP_sm 2.255482 0.080088 2.177416 2.256461 2.331224 5271.9 0.00 0.9994 2026-06-25 15:11:40 INFO: ---------------------------------------------------------------------------------------------------------------------------------- 2026-06-25 15:11:40 INFO: # * = Rhat > 1.01 (warning), ** = Rhat > 1.1 (poor convergence) 2026-06-25 15:11:40 INFO: # 16 chains, 500 samples/chain, 100 warmup iterations 2026-06-25 15:11:40 INFO: ================================================================================================================================== 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: ==================================================================================================================================================================================== 2026-06-25 15:11:40 INFO: MCMC SUMMARY (after rejecting 100 extra warmup) 2026-06-25 15:11:40 INFO: parameter mean std q16 median q84 MAP P(tail) ess ess/s rhat 2026-06-25 15:11:40 INFO: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 2026-06-25 15:11:40 INFO: log_gp_sigma_0_GP_sm -0.945665 0.230655 -1.17131 -0.947608 -0.724881 -1.14262 P(<)=19.3% 4735.0 0.00 1.0001 2026-06-25 15:11:40 INFO: log_gp_sigma_1_GP_sm -2.21627 0.259069 -2.46661 -2.23714 -1.96967 -2.44599 P(<)=18.0% 5164.8 0.00 0.9997 2026-06-25 15:11:40 INFO: log_gp_sigma_2_GP_sm -2.03999 0.275237 -2.31208 -2.05903 -1.76996 -2.20828 P(<)=28.6% 4705.2 0.00 1.0014 2026-06-25 15:11:40 INFO: log_gp_lengthscale_GP_sm 2.25713 0.0789604 2.18059 2.25816 2.33227 2.22088 P(<)=31.6% 4300.9 0.00 0.9990 2026-06-25 15:11:40 INFO: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 2026-06-25 15:11:40 INFO: # * = rhat > 1.01 (warning), ** = rhat > 1.1 (poor convergence) 2026-06-25 15:11:40 INFO: # MAP source: last_samples 2026-06-25 15:11:40 INFO: # P(tail) = P(param < MAP) or P(param > MAP) depending on whether MAP < or > median 2026-06-25 15:11:40 INFO: # num_chains=16, num_samples_per_chain=400, num_warmup=100 2026-06-25 15:11:40 INFO: ==================================================================================================================================================================================== 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: ========================================================================================== 2026-06-25 15:11:40 INFO: GOODNESS-OF-FIT STATISTICS 2026-06-25 15:11:40 INFO: ========================================================================================== 2026-06-25 15:11:40 INFO: OVERALL (all instruments combined): 2026-06-25 15:11:40 INFO: Data points (N): 240 2026-06-25 15:11:40 INFO: Free parameters (k): 4 2026-06-25 15:11:40 INFO: Degrees of freedom: 236 2026-06-25 15:11:40 INFO: Chi-squared: 358.8752 2026-06-25 15:11:40 INFO: Reduced Chi-squared: 1.5207 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: Information Criteria: 2026-06-25 15:11:40 INFO: AIC = 2k - 2*ln(L) = -1533.4945 2026-06-25 15:11:40 INFO: AICc (corrected) = -1533.3250 2026-06-25 15:11:40 INFO: BIC = k*ln(N) - 2*ln(L) = -1519.5719 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: PER-VISIT STATISTICS: 2026-06-25 15:11:40 INFO: Residuals include GP mean (y − total_model where total = det + GP mean). 2026-06-25 15:11:40 INFO: sigma_orig = uncertainties from the data file (SIGMA column). 2026-06-25 15:11:40 INFO: sigma_tot = sqrt(sigma_orig² + jitter²) (jitter-inflated). 2026-06-25 15:11:40 INFO: nRMS = sqrt(chi2/N) = sqrt(mean((r/sigma)²)) [consistent with chi2]. 2026-06-25 15:11:40 INFO: chi2_red uses global n_free_params as a conservative DOF floor. 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: LC (LC): 2026-06-25 15:11:40 INFO: Visit 1 (N = 240): 2026-06-25 15:11:40 INFO: With sigma_orig (chi2_red >> 1 expected when jitter is large): 2026-06-25 15:11:40 INFO: chi2_red = 1.5207 2026-06-25 15:11:40 INFO: RMS (O-C) = 0.006114 2026-06-25 15:11:40 INFO: nRMS = 1.2228 2026-06-25 15:11:40 INFO: median sigma_orig = 0.005000 2026-06-25 15:11:40 INFO: With sigma_tot (chi2_red ~ 1 and nRMS ~ 1 expected by design): 2026-06-25 15:11:40 INFO: chi2_red = 1.5207 2026-06-25 15:11:40 INFO: RMS (O-C) = 0.006114 2026-06-25 15:11:40 INFO: nRMS = 1.2228 2026-06-25 15:11:40 INFO: median sigma_tot = 0.005000 2026-06-25 15:11:40 INFO: 2026-06-25 15:11:40 INFO: ========================================================================================== 2026-06-25 15:11:40 INFO: Generating PDF report: PyAETNAouts//test_spectral_mixture.pdf 2026-06-25 15:11:40 INFO: - Corner plot... 2026-06-25 15:11:40 INFO: - KDE + Trace plots (4 params)... 2026-06-25 15:11:42 INFO: - Chain comparison plot... 2026-06-25 15:11:42 INFO: - Computing model components... 2026-06-25 15:11:42 INFO: Built GP kernel for instrument LC (x_var=BJD) 2026-06-25 15:11:42 INFO: - Pre-computing sample data for best-fit plots (1000 samples)... 2026-06-25 15:11:43 INFO: done in 0.3 s 2026-06-25 15:11:43 INFO: - Skipping per-visit plots (all 1 visits belong to single-visit instruments; redundant with per-instrument) 2026-06-25 15:11:43 INFO: - Per-instrument best-fit lightcurve: LC 2026-06-25 15:11:43 INFO: [band grid] 1000 model samples on 275 grid pts (LC-train+gaps, pad=0.000 d) + GP posterior mean [cached]
