flimkit 0.12.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- flimkit/FLIM/__init__.py +0 -0
- flimkit/FLIM/assemble.py +254 -0
- flimkit/FLIM/batch.py +681 -0
- flimkit/FLIM/bg_tools.py +51 -0
- flimkit/FLIM/fit_tools.py +244 -0
- flimkit/FLIM/fitters.py +1471 -0
- flimkit/FLIM/irf_tools.py +617 -0
- flimkit/FLIM/models.py +391 -0
- flimkit/GPU/__init__.py +85 -0
- flimkit/GPU/_base.py +391 -0
- flimkit/GPU/cuda.py +10 -0
- flimkit/GPU/mlx_backend.py +381 -0
- flimkit/GPU/mps.py +10 -0
- flimkit/GPU/rocm.py +10 -0
- flimkit/GPU/torch_backend.py +385 -0
- flimkit/UI/app_state.py +10 -0
- flimkit/UI/controller.py +139 -0
- flimkit/UI/expert_settings.py +248 -0
- flimkit/UI/fit_help.py +206 -0
- flimkit/UI/fov_preview.py +1085 -0
- flimkit/UI/gui.py +3919 -0
- flimkit/UI/icon.icns +0 -0
- flimkit/UI/icon.ico +0 -0
- flimkit/UI/icon.png +0 -0
- flimkit/UI/irf_widget.py +103 -0
- flimkit/UI/mode_controller.py +118 -0
- flimkit/UI/modes/__init__.py +0 -0
- flimkit/UI/modes/base.py +3 -0
- flimkit/UI/modes/batch_mode.py +312 -0
- flimkit/UI/modes/fov_mode.py +164 -0
- flimkit/UI/modes/irf_mode.py +80 -0
- flimkit/UI/modes/phasor_mode.py +131 -0
- flimkit/UI/modes/stitch_mode.py +254 -0
- flimkit/UI/phasor_panel.py +1087 -0
- flimkit/UI/progress_window.py +113 -0
- flimkit/UI/project_panel.py +262 -0
- flimkit/UI/results_panel.py +332 -0
- flimkit/UI/roi_tools.py +794 -0
- flimkit/UI/utils.py +217 -0
- flimkit/__init__.py +0 -0
- flimkit/_version.py +41 -0
- flimkit/cli.py +120 -0
- flimkit/configs.py +148 -0
- flimkit/dialogs.py +46 -0
- flimkit/formats/BH/__init__.py +0 -0
- flimkit/formats/BH/reader.py +296 -0
- flimkit/formats/BH/writer.py +86 -0
- flimkit/formats/ISS/__init__.py +0 -0
- flimkit/formats/ISS/fdflim.py +86 -0
- flimkit/formats/ISS/image.py +114 -0
- flimkit/formats/ISS/reader.py +223 -0
- flimkit/formats/PS/__init__.py +0 -0
- flimkit/formats/PS/reader.py +202 -0
- flimkit/formats/PTU/__init__.py +0 -0
- flimkit/formats/PTU/decode.py +27 -0
- flimkit/formats/PTU/phu.py +85 -0
- flimkit/formats/PTU/reader.py +235 -0
- flimkit/formats/PTU/series.py +258 -0
- flimkit/formats/PTU/stitch.py +1182 -0
- flimkit/formats/PTU/tools.py +94 -0
- flimkit/formats/__init__.py +2 -0
- flimkit/formats/flim_file.py +232 -0
- flimkit/formats/phasor.py +132 -0
- flimkit/formats/signal.py +170 -0
- flimkit/image/tools.py +124 -0
- flimkit/interactive.py +1857 -0
- flimkit/mpl_backend.py +22 -0
- flimkit/phasor/__init__.py +40 -0
- flimkit/phasor/filters.py +127 -0
- flimkit/phasor/fret.py +654 -0
- flimkit/phasor/interactive.py +556 -0
- flimkit/phasor/peaks.py +186 -0
- flimkit/phasor/signal.py +90 -0
- flimkit/phasor_launcher.py +314 -0
- flimkit/plugins/__init__.py +137 -0
- flimkit/plugins/bindings.py +116 -0
- flimkit/plugins/builtin/__init__.py +3 -0
- flimkit/plugins/builtin/core_tools.py +28 -0
- flimkit/plugins/loader.py +371 -0
- flimkit/plugins/registry.py +406 -0
- flimkit/project.py +197 -0
- flimkit/synth.py +145 -0
- flimkit/utils/__init__.py +0 -0
- flimkit/utils/batch_fit.py +301 -0
- flimkit/utils/config_manager.py +119 -0
- flimkit/utils/config_snapshot.py +30 -0
- flimkit/utils/crash_handler.py +183 -0
- flimkit/utils/display.py +197 -0
- flimkit/utils/enhanced_outputs.py +345 -0
- flimkit/utils/fancy.py +103 -0
- flimkit/utils/lifetime_image.py +243 -0
- flimkit/utils/misc.py +111 -0
- flimkit/utils/plotting.py +190 -0
- flimkit/utils/roi.py +370 -0
- flimkit/utils/session.py +51 -0
- flimkit/utils/update_check.py +198 -0
- flimkit/utils/xlsx_tools.py +97 -0
- flimkit/utils/xml_utils.py +219 -0
- flimkit-0.12.0.dist-info/METADATA +356 -0
- flimkit-0.12.0.dist-info/RECORD +104 -0
- flimkit-0.12.0.dist-info/WHEEL +5 -0
- flimkit-0.12.0.dist-info/entry_points.txt +2 -0
- flimkit-0.12.0.dist-info/licenses/LICENSE.md +11 -0
- flimkit-0.12.0.dist-info/top_level.txt +1 -0
flimkit/FLIM/fitters.py
ADDED
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import time
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import os
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import numpy as np
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from tqdm import tqdm
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tqdm.disable = True
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from scipy.optimize import least_squares, differential_evolution, nnls
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from scipy.stats.distributions import chi2 as chi2_dist
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from ..FLIM.irf_tools import build_full_irf
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from ..FLIM.fit_tools import (estimate_bg, find_fit_start, find_fit_end, _build_bounds,
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_pack_p0, coates_pileup_correction, bins_from_ns, build_fit_idx,
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find_tail_fit_start, _build_bounds_tail, _pack_p0_tail,
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calibrated_chi2, distribution_dof)
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from ..FLIM.models import (reconvolution_model, _DECost, _DECostLogTau,
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_DECostPoisson, _DECostPoissonLogTau,
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dist_reconvolution_model, build_dist_basis_grid,
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_DECostDist, _DECostDistLogParam,
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_DECostDistPoisson, _DECostDistPoissonLogParam,
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tail_model, tail_basis, unpack_tail_params,
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_DECostTail, _DECostTailLogTau,
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_DECostTailPoisson, _DECostTailPoissonLogTau)
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from ..FLIM.fit_tools import (_build_bounds_dist, _pack_p0_dist)
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from ..configs import MIN_PHOTONS_PERPIX
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_GPU_BACKEND_UNSET = object()
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_gpu_backend_cache = _GPU_BACKEND_UNSET
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_GPU_MAX_DIST_STACK_BYTES = 1_000_000_000
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_FREE_TAU_WARN_PIXELS = 50_000
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_TAU_GRID_POINTS = 1600
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def tau_grid_points():
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override = os.environ.get('FLIMKIT_TAU_GRID_POINTS')
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if override:
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try:
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return max(2, int(override))
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except ValueError:
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pass
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return _TAU_GRID_POINTS
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def _init_gpu_backend():
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global _gpu_backend_cache
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if _gpu_backend_cache is not _GPU_BACKEND_UNSET:
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return _gpu_backend_cache
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try:
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from flimkit.GPU import get_backend
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_gpu_backend_cache = get_backend()
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except Exception:
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_gpu_backend_cache = None
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return _gpu_backend_cache
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def warmup_gpu_backend():
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import threading
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global _gpu_backend_cache
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if _gpu_backend_cache is not _GPU_BACKEND_UNSET:
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return
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def _warmup():
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global _gpu_backend_cache
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if _gpu_backend_cache is not _GPU_BACKEND_UNSET:
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return
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try:
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from flimkit.GPU import get_backend
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_gpu_backend_cache = get_backend()
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except Exception:
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_gpu_backend_cache = None
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threading.Thread(target=_warmup, daemon=True).start()
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def fit_summed(decay, tcspc_res, n_bins, irf_prompt,
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has_tail, fit_bg, fit_sigma,
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n_exp, tau_min_ns, tau_max_ns,
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optimizer='de', n_restarts=8,
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de_popsize=15, de_maxiter=1000,
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workers=-1, polish=True,
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cost_function='poisson',
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sigma_max=3.0,
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irf_shift_bins=2,
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tvb_profile=None, fit_tvb=False,
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fit_start_ns=None, fit_end_ns=None, exclude_ns=None,
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n_sync=None):
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warmup_gpu_backend()
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tau_min = tau_min_ns * 1e-9
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tau_max = tau_max_ns * 1e-9
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if cost_function not in ('chi2', 'poisson'):
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raise ValueError(f"Unknown cost_function: {cost_function!r}")
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decay_work = decay.astype(float)
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if decay_work.max() == 0:
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raise ValueError('Decay has zero maximum - cannot fit.')
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scale = 1.0
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peak_bin = int(np.argmax(decay_work))
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bg_init = estimate_bg(decay_work, peak_bin)
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bg_fixed = bg_init if not fit_bg else 0.0
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fit_end = find_fit_end(decay_work, peak_bin, tau_max, tcspc_res, n_bins)
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standard_fit_end = int(round(44.9455 / (tcspc_res * 1e9)))
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fit_end = min(fit_end, standard_fit_end)
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fit_start = find_fit_start(decay_work, irf_prompt, tcspc_res)
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fit_start = max(0, min(fit_start, fit_end - 10))
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if fit_end_ns is not None:
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fit_end = min(n_bins, bins_from_ns(fit_end_ns, tcspc_res))
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if fit_start_ns is not None:
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fit_start = max(0, min(bins_from_ns(fit_start_ns, tcspc_res), fit_end - 2))
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exclude_bins = [(bins_from_ns(lo, tcspc_res), bins_from_ns(hi, tcspc_res))
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for lo, hi in (exclude_ns or [])]
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fit_idx = build_fit_idx(fit_start, fit_end, n_bins, exclude_bins)
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bg_upper = max(bg_init * 2.0, bg_init + 10.0)
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if fit_tvb and tvb_profile is None:
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raise ValueError('fit_tvb=True requires a tvb_profile.')
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tvb_init = float(bg_init * n_bins) if fit_tvb else 0.0
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tvb_upper = float(decay_work.sum()) if fit_tvb else None
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if fit_tvb:
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print(f" TVB: free scale on measured profile, init={tvb_init:.1f}, upper={tvb_upper:.1f}")
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print(f" Cost function: {cost_function}")
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print(f" bg initial guess = {bg_init:.3f} cts/bin"
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f", upper bound = {bg_upper:.3f} "
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f"({'free param' if fit_bg else 'fixed'})")
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print(f" σ broadening: {'free param (σ≤' + f'{sigma_max:.1f})' if fit_sigma else 'fixed at 0'}")
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print(f" Fit window: bins {fit_start}-{fit_end} "
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f"({fit_start*tcspc_res*1e9:.2f}-{fit_end*tcspc_res*1e9:.2f} ns), "
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f"{len(fit_idx)} bins fitted"
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f"{' (user-set)' if (fit_start_ns is not None or fit_end_ns is not None) else ' (auto)'}")
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if exclude_bins:
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for (lo_b, hi_b), (lo_n, hi_n) in zip(exclude_bins, exclude_ns):
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print(f" Excluded: bins {lo_b}-{hi_b} ({lo_n:.2f}-{hi_n:.2f} ns)")
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if n_sync:
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print(f" Pile-up: in forward model (N_sync={n_sync:,}), data left raw")
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lo, hi = _build_bounds(n_exp, tau_min, tau_max, decay_work.max(),
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has_tail, fit_bg, fit_sigma,
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bg_init=bg_init, bg_upper=bg_upper,
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sigma_max=sigma_max, irf_shift_bins=irf_shift_bins,
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fit_tvb=fit_tvb, tvb_init=tvb_init, tvb_upper=tvb_upper)
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bounds = list(zip(lo, hi))
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if cost_function == 'chi2':
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weights = np.sqrt(np.maximum(decay_work[fit_idx], 1.0))
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def residuals(params):
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model_vals = reconvolution_model(
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params, tcspc_res, n_bins, irf_prompt,
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n_exp, bg_fixed, has_tail, fit_bg, fit_sigma,
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tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
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return (model_vals[fit_idx]
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- decay_work[fit_idx]) / weights
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else:
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def residuals(params):
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model_vals = reconvolution_model(
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params, tcspc_res, n_bins, irf_prompt,
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n_exp, bg_fixed, has_tail, fit_bg, fit_sigma,
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tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
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n = decay_work[fit_idx]
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m = np.maximum(model_vals[fit_idx], 1e-10)
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dev = m - n
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pos = n > 0
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dev[pos] += n[pos] * np.log(n[pos] / m[pos])
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dev = np.maximum(dev, 0.0)
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r = np.sqrt(2.0 * dev)
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r[m < n] *= -1
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return r
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if optimizer == 'lm_multistart':
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n_log = n_exp
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lo_scaled = np.asarray(lo, dtype=float).copy()
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hi_scaled = np.asarray(hi, dtype=float).copy()
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lo_scaled[:n_log] = np.log10(lo_scaled[:n_log])
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hi_scaled[:n_log] = np.log10(hi_scaled[:n_log])
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def to_scaled(params):
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scaled = np.asarray(params, dtype=float).copy()
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scaled[:n_log] = np.log10(scaled[:n_log])
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return scaled
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def from_scaled(params):
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linear = np.asarray(params, dtype=float).copy()
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linear[:n_log] = 10.0 ** linear[:n_log]
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return linear
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def residuals_scaled(params):
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return residuals(from_scaled(params))
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rng = np.random.default_rng(42)
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best_res = None
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best_cost = np.inf
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for i in range(n_restarts + 1):
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tau_ov = None if i == 0 else np.sort(
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np.exp(rng.uniform(np.log(tau_min*1.001),
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np.log(tau_max*0.999), n_exp)))
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p0 = _pack_p0(n_exp, tau_min, tau_max, float(decay_work.max()),
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has_tail, fit_bg, fit_sigma, bg_init,
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tau_override=tau_ov, fit_tvb=fit_tvb, tvb_init=tvb_init)
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try:
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res = least_squares(residuals_scaled, to_scaled(p0),
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bounds=(lo_scaled, hi_scaled), method='trf',
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max_nfev=50000,
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ftol=1e-13, xtol=1e-13, gtol=1e-13)
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except Exception as exc:
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print(f" Restart {i:2d}: failed ({exc})")
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continue
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tag = 'log-spaced' if i == 0 else 'random '
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if res.cost < best_cost:
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best_cost = res.cost
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best_res = res
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print(f" Restart {i:2d} ({tag}): cost={res.cost:.4e} ← best")
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else:
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print(f" Restart {i:2d} ({tag}): cost={res.cost:.4e}")
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if best_res is None:
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raise RuntimeError('All restarts failed.')
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popt_work = from_scaled(best_res.x)
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message = best_res.message
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elif optimizer == 'de':
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print(f" Differential evolution: popsize={de_popsize}, "
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200
|
+
f"maxiter={de_maxiter}, workers={workers}")
|
|
201
|
+
bounds_log = list(bounds)
|
|
202
|
+
for i in range(n_exp):
|
|
203
|
+
lo_tau, hi_tau = bounds[i]
|
|
204
|
+
bounds_log[i] = (np.log10(lo_tau), np.log10(hi_tau))
|
|
205
|
+
if cost_function == 'poisson':
|
|
206
|
+
cost_fn = _DECostPoissonLogTau(
|
|
207
|
+
tcspc_res, n_bins, irf_prompt, n_exp, bg_fixed,
|
|
208
|
+
has_tail, fit_bg, fit_sigma,
|
|
209
|
+
fit_idx, decay_work,
|
|
210
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
|
|
211
|
+
else:
|
|
212
|
+
cost_fn = _DECostLogTau(
|
|
213
|
+
tcspc_res, n_bins, irf_prompt, n_exp, bg_fixed,
|
|
214
|
+
has_tail, fit_bg, fit_sigma,
|
|
215
|
+
fit_idx, decay_work, weights,
|
|
216
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
|
|
217
|
+
de_res = differential_evolution(
|
|
218
|
+
cost_fn, bounds=bounds_log,
|
|
219
|
+
maxiter=de_maxiter, popsize=de_popsize,
|
|
220
|
+
workers=workers, seed=42,
|
|
221
|
+
updating='deferred' if workers != 1 else 'immediate',
|
|
222
|
+
init='sobol',
|
|
223
|
+
disp=False)
|
|
224
|
+
popt_work = de_res.x.copy()
|
|
225
|
+
popt_work[:n_exp] = 10.0 ** popt_work[:n_exp]
|
|
226
|
+
message = f"DE success={de_res.success}, fun={de_res.fun:.4e}"
|
|
227
|
+
if polish:
|
|
228
|
+
print(' Running final LM polish...')
|
|
229
|
+
eps = 1e-10
|
|
230
|
+
popt_work = np.clip(popt_work, np.asarray(lo) + eps, np.asarray(hi) - eps)
|
|
231
|
+
try:
|
|
232
|
+
pol = least_squares(residuals, popt_work, bounds=(lo, hi),
|
|
233
|
+
method='trf', max_nfev=5000,
|
|
234
|
+
ftol=1e-13, xtol=1e-13, gtol=1e-13)
|
|
235
|
+
popt_work = pol.x
|
|
236
|
+
message += f"; polished cost={pol.cost:.4e}"
|
|
237
|
+
except ValueError as e:
|
|
238
|
+
print(f" Warning: LM polish failed ({e}) - using DE result")
|
|
239
|
+
else:
|
|
240
|
+
raise ValueError(f"Unknown optimizer: {optimizer!r}")
|
|
241
|
+
popt_original = popt_work.copy()
|
|
242
|
+
summary = _make_summary(popt_original, decay, tcspc_res, n_bins, irf_prompt,
|
|
243
|
+
n_exp, bg_fixed, has_tail, fit_bg, fit_sigma,
|
|
244
|
+
fit_idx, message, tvb_profile=tvb_profile,
|
|
245
|
+
fit_tvb=fit_tvb, n_sync=n_sync)
|
|
246
|
+
return popt_original, summary
|
|
247
|
+
|
|
248
|
+
|
|
249
|
+
def _make_summary(popt, decay, tcspc_res, n_bins, irf_prompt,
|
|
250
|
+
n_exp, bg_fixed, has_tail, fit_bg, fit_sigma,
|
|
251
|
+
fit_idx, message=None,
|
|
252
|
+
tvb_profile=None, fit_tvb=False, n_sync=None):
|
|
253
|
+
fit_start = int(fit_idx[0])
|
|
254
|
+
fit_end = int(fit_idx[-1]) + 1
|
|
255
|
+
taus = popt[:n_exp]
|
|
256
|
+
amps = popt[n_exp:2*n_exp]
|
|
257
|
+
order = np.argsort(-taus)
|
|
258
|
+
taus = taus[order]
|
|
259
|
+
amps = amps[order]
|
|
260
|
+
idx = 2 * n_exp
|
|
261
|
+
shift = popt[idx]; idx += 1
|
|
262
|
+
if fit_sigma:
|
|
263
|
+
sigma = popt[idx]; idx += 1
|
|
264
|
+
else:
|
|
265
|
+
sigma = 0.0
|
|
266
|
+
if fit_bg:
|
|
267
|
+
bg_fit = popt[idx]; idx += 1
|
|
268
|
+
else:
|
|
269
|
+
bg_fit = bg_fixed
|
|
270
|
+
if fit_tvb:
|
|
271
|
+
tvb_scale = popt[idx]; idx += 1
|
|
272
|
+
else:
|
|
273
|
+
tvb_scale = 0.0
|
|
274
|
+
if has_tail:
|
|
275
|
+
tail_amp = popt[idx]
|
|
276
|
+
tail_tau = popt[idx + 1]
|
|
277
|
+
else:
|
|
278
|
+
tail_amp = tail_tau = 0.0
|
|
279
|
+
model = reconvolution_model(popt, tcspc_res, n_bins, irf_prompt,
|
|
280
|
+
n_exp, bg_fixed, has_tail, fit_bg, fit_sigma,
|
|
281
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
|
|
282
|
+
d_win = decay[fit_idx].astype(float)
|
|
283
|
+
m_win = model[fit_idx]
|
|
284
|
+
sigma_w = np.sqrt(np.maximum(d_win, 1.0))
|
|
285
|
+
chi2 = float(np.sum(((d_win - m_win) / sigma_w)**2))
|
|
286
|
+
dof = max(len(fit_idx) - len(popt), 1)
|
|
287
|
+
rchi2 = chi2 / dof
|
|
288
|
+
p_val = float(1 - chi2_dist.cdf(chi2, df=dof))
|
|
289
|
+
resid = (decay - model) / np.sqrt(np.maximum(model, 1.0))
|
|
290
|
+
sigma_p = np.sqrt(np.maximum(m_win, 1.0))
|
|
291
|
+
chi2_p = float(np.sum(((d_win - m_win) / sigma_p)**2))
|
|
292
|
+
rchi2_p = chi2_p / dof
|
|
293
|
+
calibrated_chi2_p = calibrated_chi2(d_win, m_win)
|
|
294
|
+
peak_bin_loc = int(fit_idx[np.argmax(decay[fit_idx])])
|
|
295
|
+
tail_start = peak_bin_loc + max(1, int(0.05 * (fit_end - peak_bin_loc)))
|
|
296
|
+
tail_idx = fit_idx[fit_idx >= tail_start]
|
|
297
|
+
d_tail = decay[tail_idx].astype(float)
|
|
298
|
+
m_tail = model[tail_idx]
|
|
299
|
+
sw_tail = np.sqrt(np.maximum(d_tail, 1.0))
|
|
300
|
+
chi2_tail = float(np.sum(((d_tail - m_tail) / sw_tail)**2))
|
|
301
|
+
dof_tail = max(len(tail_idx) - len(popt), 1)
|
|
302
|
+
rchi2_tail = chi2_tail / dof_tail
|
|
303
|
+
sp_tail = np.sqrt(np.maximum(m_tail, 1.0))
|
|
304
|
+
chi2_tail_p = float(np.sum(((d_tail - m_tail) / sp_tail)**2))
|
|
305
|
+
rchi2_tail_p = chi2_tail_p / dof_tail
|
|
306
|
+
calibrated_chi2_tail_p = calibrated_chi2(d_tail, m_tail)
|
|
307
|
+
amp_sum = amps.sum() if amps.sum() > 0 else 1.0
|
|
308
|
+
fracs = amps / amp_sum
|
|
309
|
+
tau_amp = float(np.dot(fracs, taus))
|
|
310
|
+
tau_int = float(np.dot(amps, taus**2) / np.dot(amps, taus))
|
|
311
|
+
above = np.where(irf_prompt >= irf_prompt.max() / 2)[0]
|
|
312
|
+
fwhm_pr = (above[-1] - above[0]) if len(above) > 1 else 1
|
|
313
|
+
fwhm_eff = np.sqrt(fwhm_pr**2 + (2.3548 * sigma)**2) * tcspc_res * 1e9
|
|
314
|
+
return dict(
|
|
315
|
+
tcspc_res = tcspc_res,
|
|
316
|
+
taus_ns = taus * 1e9,
|
|
317
|
+
amps = amps,
|
|
318
|
+
fractions = fracs,
|
|
319
|
+
bg_fit = bg_fit,
|
|
320
|
+
tvb_scale = tvb_scale,
|
|
321
|
+
tau_mean_amp_ns = tau_amp * 1e9,
|
|
322
|
+
tau_mean_int_ns = tau_int * 1e9,
|
|
323
|
+
chi2 = chi2,
|
|
324
|
+
reduced_chi2 = rchi2,
|
|
325
|
+
reduced_chi2_tail = rchi2_tail,
|
|
326
|
+
chi2_pearson = chi2_p,
|
|
327
|
+
reduced_chi2_pearson = rchi2_p,
|
|
328
|
+
reduced_chi2_tail_pearson = rchi2_tail_p,
|
|
329
|
+
calibrated_chi2_pearson = calibrated_chi2_p,
|
|
330
|
+
calibrated_chi2_tail_pearson = calibrated_chi2_tail_p,
|
|
331
|
+
tail_start_bin = tail_start,
|
|
332
|
+
p_val = p_val,
|
|
333
|
+
dof = dof,
|
|
334
|
+
fit_window_bins = (fit_start, fit_end),
|
|
335
|
+
fit_window_ns = (fit_start*tcspc_res*1e9, fit_end*tcspc_res*1e9),
|
|
336
|
+
fit_idx = fit_idx,
|
|
337
|
+
irf_shift_bins = shift,
|
|
338
|
+
irf_sigma_bins = sigma,
|
|
339
|
+
irf_fwhm_eff_ns = fwhm_eff,
|
|
340
|
+
tail_amp = tail_amp,
|
|
341
|
+
tail_tau_ns = tail_tau * tcspc_res * 1e9,
|
|
342
|
+
model = model,
|
|
343
|
+
residuals = resid,
|
|
344
|
+
optimizer_msg = message,
|
|
345
|
+
)
|
|
346
|
+
|
|
347
|
+
|
|
348
|
+
def _basis_rows(taus, t_axis, tcspc_res, n_bins, tail, irf_fft=None, t0=0.0):
|
|
349
|
+
if tail:
|
|
350
|
+
return tail_basis(tcspc_res, n_bins, taus, t0)
|
|
351
|
+
basis = np.stack([np.exp(-t_axis / max(tau, 1e-15)) for tau in taus])
|
|
352
|
+
return np.array([np.real(np.fft.ifft(np.fft.fft(b) * irf_fft)) for b in basis])
|
|
353
|
+
|
|
354
|
+
|
|
355
|
+
def fit_summed_tail(decay, tcspc_res, n_bins,
|
|
356
|
+
fit_bg, n_exp, tau_min_ns, tau_max_ns,
|
|
357
|
+
fit_t0=False, t0_range_bins=5.0,
|
|
358
|
+
optimizer='de', n_restarts=8,
|
|
359
|
+
de_popsize=15, de_maxiter=1000,
|
|
360
|
+
workers=-1, polish=True,
|
|
361
|
+
cost_function='poisson',
|
|
362
|
+
tvb_profile=None, fit_tvb=False,
|
|
363
|
+
fit_start_ns=None, fit_end_ns=None, exclude_ns=None,
|
|
364
|
+
n_sync=None):
|
|
365
|
+
tau_min = tau_min_ns * 1e-9
|
|
366
|
+
tau_max = tau_max_ns * 1e-9
|
|
367
|
+
if cost_function not in ('chi2', 'poisson'):
|
|
368
|
+
raise ValueError(f"Unknown cost_function: {cost_function!r}")
|
|
369
|
+
decay_work = decay.astype(float)
|
|
370
|
+
if decay_work.max() == 0:
|
|
371
|
+
raise ValueError('Decay has zero maximum - cannot fit.')
|
|
372
|
+
peak_bin = int(np.argmax(decay_work))
|
|
373
|
+
bg_init = estimate_bg(decay_work, peak_bin)
|
|
374
|
+
bg_fixed = bg_init if not fit_bg else 0.0
|
|
375
|
+
t0_fixed = peak_bin * tcspc_res
|
|
376
|
+
t0_range = float(t0_range_bins) * tcspc_res
|
|
377
|
+
fit_end = find_fit_end(decay_work, peak_bin, tau_max, tcspc_res, n_bins)
|
|
378
|
+
standard_fit_end = int(round(44.9455 / (tcspc_res * 1e9)))
|
|
379
|
+
fit_end = min(fit_end, standard_fit_end)
|
|
380
|
+
fit_start = find_tail_fit_start(decay_work, peak_bin, n_bins)
|
|
381
|
+
fit_start = max(0, min(fit_start, fit_end - 10))
|
|
382
|
+
if fit_end_ns is not None:
|
|
383
|
+
fit_end = min(n_bins, bins_from_ns(fit_end_ns, tcspc_res))
|
|
384
|
+
if fit_start_ns is not None:
|
|
385
|
+
fit_start = max(0, min(bins_from_ns(fit_start_ns, tcspc_res), fit_end - 2))
|
|
386
|
+
exclude_bins = [(bins_from_ns(lo, tcspc_res), bins_from_ns(hi, tcspc_res))
|
|
387
|
+
for lo, hi in (exclude_ns or [])]
|
|
388
|
+
fit_idx = build_fit_idx(fit_start, fit_end, n_bins, exclude_bins)
|
|
389
|
+
bg_upper = max(bg_init * 2.0, bg_init + 10.0)
|
|
390
|
+
if fit_tvb and tvb_profile is None:
|
|
391
|
+
raise ValueError('fit_tvb=True requires a tvb_profile.')
|
|
392
|
+
tvb_init = float(bg_init * n_bins) if fit_tvb else 0.0
|
|
393
|
+
tvb_upper = float(decay_work.sum()) if fit_tvb else None
|
|
394
|
+
if fit_tvb:
|
|
395
|
+
print(f" TVB: free scale on measured profile, init={tvb_init:.1f}, upper={tvb_upper:.1f}")
|
|
396
|
+
print(f" Cost function: {cost_function}")
|
|
397
|
+
print(f" Tail fit: no IRF used, no reconvolution")
|
|
398
|
+
print(f" t0 = {t0_fixed*1e9:.3f} ns (decay peak, bin {peak_bin})"
|
|
399
|
+
f"{f', free within ±{t0_range_bins:.0f} bins' if fit_t0 else ', fixed'}")
|
|
400
|
+
print(f" bg initial guess = {bg_init:.3f} cts/bin"
|
|
401
|
+
f", upper bound = {bg_upper:.3f} "
|
|
402
|
+
f"({'free param' if fit_bg else 'fixed'})")
|
|
403
|
+
print(f" Fit window: bins {fit_start}-{fit_end} "
|
|
404
|
+
f"({fit_start*tcspc_res*1e9:.2f}-{fit_end*tcspc_res*1e9:.2f} ns), "
|
|
405
|
+
f"{len(fit_idx)} bins fitted"
|
|
406
|
+
f"{' (user-set)' if (fit_start_ns is not None or fit_end_ns is not None) else ' (auto)'}")
|
|
407
|
+
if exclude_bins:
|
|
408
|
+
for (lo_b, hi_b), (lo_n, hi_n) in zip(exclude_bins, exclude_ns):
|
|
409
|
+
print(f" Excluded: bins {lo_b}-{hi_b} ({lo_n:.2f}-{hi_n:.2f} ns)")
|
|
410
|
+
if n_sync:
|
|
411
|
+
print(f" Pile-up: in forward model (N_sync={n_sync:,}), data left raw")
|
|
412
|
+
lo, hi = _build_bounds_tail(n_exp, tau_min, tau_max, decay_work.max(), fit_bg,
|
|
413
|
+
bg_init=bg_init, bg_upper=bg_upper,
|
|
414
|
+
fit_t0=fit_t0, t0_init=t0_fixed, t0_range=t0_range,
|
|
415
|
+
fit_tvb=fit_tvb, tvb_init=tvb_init, tvb_upper=tvb_upper)
|
|
416
|
+
bounds = list(zip(lo, hi))
|
|
417
|
+
def _model_of(params):
|
|
418
|
+
return tail_model(params, tcspc_res, n_bins, n_exp, bg_fixed, fit_bg,
|
|
419
|
+
fit_t0=fit_t0, t0_fixed=t0_fixed,
|
|
420
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
|
|
421
|
+
if cost_function == 'chi2':
|
|
422
|
+
weights = np.sqrt(np.maximum(decay_work[fit_idx], 1.0))
|
|
423
|
+
def residuals(params):
|
|
424
|
+
model_vals = _model_of(params)
|
|
425
|
+
return (model_vals[fit_idx] - decay_work[fit_idx]) / weights
|
|
426
|
+
else:
|
|
427
|
+
def residuals(params):
|
|
428
|
+
model_vals = _model_of(params)
|
|
429
|
+
n = decay_work[fit_idx]
|
|
430
|
+
m = np.maximum(model_vals[fit_idx], 1e-10)
|
|
431
|
+
dev = m - n
|
|
432
|
+
pos = n > 0
|
|
433
|
+
dev[pos] += n[pos] * np.log(n[pos] / m[pos])
|
|
434
|
+
dev = np.maximum(dev, 0.0)
|
|
435
|
+
r = np.sqrt(2.0 * dev)
|
|
436
|
+
r[m < n] *= -1
|
|
437
|
+
return r
|
|
438
|
+
if optimizer == 'lm_multistart':
|
|
439
|
+
rng = np.random.default_rng(42)
|
|
440
|
+
best_res = None
|
|
441
|
+
best_cost = np.inf
|
|
442
|
+
for i in range(n_restarts + 1):
|
|
443
|
+
tau_ov = None if i == 0 else np.sort(
|
|
444
|
+
np.exp(rng.uniform(np.log(tau_min*1.001),
|
|
445
|
+
np.log(tau_max*0.999), n_exp)))
|
|
446
|
+
p0 = _pack_p0_tail(n_exp, tau_min, tau_max, float(decay_work.max()),
|
|
447
|
+
fit_bg, bg_init, tau_override=tau_ov,
|
|
448
|
+
fit_t0=fit_t0, t0_init=t0_fixed,
|
|
449
|
+
fit_tvb=fit_tvb, tvb_init=tvb_init)
|
|
450
|
+
try:
|
|
451
|
+
res = least_squares(residuals, p0, bounds=(lo, hi), method='trf',
|
|
452
|
+
max_nfev=50000,
|
|
453
|
+
ftol=1e-13, xtol=1e-13, gtol=1e-13)
|
|
454
|
+
except Exception as exc:
|
|
455
|
+
print(f" Restart {i:2d}: failed ({exc})")
|
|
456
|
+
continue
|
|
457
|
+
tag = 'log-spaced' if i == 0 else 'random '
|
|
458
|
+
if res.cost < best_cost:
|
|
459
|
+
best_cost = res.cost
|
|
460
|
+
best_res = res
|
|
461
|
+
print(f" Restart {i:2d} ({tag}): cost={res.cost:.4e} ← best")
|
|
462
|
+
else:
|
|
463
|
+
print(f" Restart {i:2d} ({tag}): cost={res.cost:.4e}")
|
|
464
|
+
if best_res is None:
|
|
465
|
+
raise RuntimeError('All restarts failed.')
|
|
466
|
+
popt_work = best_res.x
|
|
467
|
+
message = best_res.message
|
|
468
|
+
elif optimizer == 'de':
|
|
469
|
+
print(f" Differential evolution: popsize={de_popsize}, "
|
|
470
|
+
f"maxiter={de_maxiter}, workers={workers}")
|
|
471
|
+
bounds_log = list(bounds)
|
|
472
|
+
for i in range(n_exp):
|
|
473
|
+
lo_tau, hi_tau = bounds[i]
|
|
474
|
+
bounds_log[i] = (np.log10(lo_tau), np.log10(hi_tau))
|
|
475
|
+
if cost_function == 'poisson':
|
|
476
|
+
cost_fn = _DECostTailPoissonLogTau(
|
|
477
|
+
tcspc_res, n_bins, n_exp, bg_fixed, fit_bg,
|
|
478
|
+
fit_idx, decay_work,
|
|
479
|
+
fit_t0=fit_t0, t0_fixed=t0_fixed,
|
|
480
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
|
|
481
|
+
else:
|
|
482
|
+
cost_fn = _DECostTailLogTau(
|
|
483
|
+
tcspc_res, n_bins, n_exp, bg_fixed, fit_bg,
|
|
484
|
+
fit_idx, decay_work, weights,
|
|
485
|
+
fit_t0=fit_t0, t0_fixed=t0_fixed,
|
|
486
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
|
|
487
|
+
de_res = differential_evolution(
|
|
488
|
+
cost_fn, bounds=bounds_log,
|
|
489
|
+
maxiter=de_maxiter, popsize=de_popsize,
|
|
490
|
+
workers=workers, seed=42,
|
|
491
|
+
updating='deferred' if workers != 1 else 'immediate',
|
|
492
|
+
init='sobol',
|
|
493
|
+
disp=False)
|
|
494
|
+
popt_work = de_res.x.copy()
|
|
495
|
+
popt_work[:n_exp] = 10.0 ** popt_work[:n_exp]
|
|
496
|
+
message = f"DE success={de_res.success}, fun={de_res.fun:.4e}"
|
|
497
|
+
if polish:
|
|
498
|
+
print(' Running final LM polish...')
|
|
499
|
+
eps = 1e-10
|
|
500
|
+
popt_work = np.clip(popt_work, np.asarray(lo) + eps, np.asarray(hi) - eps)
|
|
501
|
+
try:
|
|
502
|
+
pol = least_squares(residuals, popt_work, bounds=(lo, hi),
|
|
503
|
+
method='trf', max_nfev=5000,
|
|
504
|
+
ftol=1e-13, xtol=1e-13, gtol=1e-13)
|
|
505
|
+
popt_work = pol.x
|
|
506
|
+
message += f"; polished cost={pol.cost:.4e}"
|
|
507
|
+
except ValueError as e:
|
|
508
|
+
print(f" Warning: LM polish failed ({e}) - using DE result")
|
|
509
|
+
else:
|
|
510
|
+
raise ValueError(f"Unknown optimizer: {optimizer!r}")
|
|
511
|
+
summary = _make_summary_tail(popt_work, decay, tcspc_res, n_bins,
|
|
512
|
+
n_exp, bg_fixed, fit_bg, fit_idx, message,
|
|
513
|
+
fit_t0=fit_t0, t0_fixed=t0_fixed,
|
|
514
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
|
|
515
|
+
return popt_work, summary
|
|
516
|
+
|
|
517
|
+
|
|
518
|
+
def _make_summary_tail(popt, decay, tcspc_res, n_bins,
|
|
519
|
+
n_exp, bg_fixed, fit_bg, fit_idx, message=None,
|
|
520
|
+
fit_t0=False, t0_fixed=0.0,
|
|
521
|
+
tvb_profile=None, fit_tvb=False, n_sync=None):
|
|
522
|
+
fit_start = int(fit_idx[0])
|
|
523
|
+
fit_end = int(fit_idx[-1]) + 1
|
|
524
|
+
taus, amps, t0, bg_fit, tvb_scale = unpack_tail_params(
|
|
525
|
+
popt, n_exp, fit_t0, fit_bg, fit_tvb,
|
|
526
|
+
t0_fixed=t0_fixed, bg_fixed=bg_fixed)
|
|
527
|
+
order = np.argsort(-taus)
|
|
528
|
+
taus = taus[order]
|
|
529
|
+
amps = amps[order]
|
|
530
|
+
model = tail_model(popt, tcspc_res, n_bins, n_exp, bg_fixed, fit_bg,
|
|
531
|
+
fit_t0=fit_t0, t0_fixed=t0_fixed,
|
|
532
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
|
|
533
|
+
d_win = decay[fit_idx].astype(float)
|
|
534
|
+
m_win = model[fit_idx]
|
|
535
|
+
sigma_w = np.sqrt(np.maximum(d_win, 1.0))
|
|
536
|
+
chi2 = float(np.sum(((d_win - m_win) / sigma_w)**2))
|
|
537
|
+
dof = max(len(fit_idx) - len(popt), 1)
|
|
538
|
+
rchi2 = chi2 / dof
|
|
539
|
+
p_val = float(1 - chi2_dist.cdf(chi2, df=dof))
|
|
540
|
+
resid = (decay - model) / np.sqrt(np.maximum(model, 1.0))
|
|
541
|
+
sigma_p = np.sqrt(np.maximum(m_win, 1.0))
|
|
542
|
+
chi2_p = float(np.sum(((d_win - m_win) / sigma_p)**2))
|
|
543
|
+
rchi2_p = chi2_p / dof
|
|
544
|
+
calibrated_chi2_p = calibrated_chi2(d_win, m_win)
|
|
545
|
+
amp_sum = amps.sum() if amps.sum() > 0 else 1.0
|
|
546
|
+
fracs = amps / amp_sum
|
|
547
|
+
tau_amp = float(np.dot(fracs, taus))
|
|
548
|
+
tau_int = float(np.dot(amps, taus**2) / np.dot(amps, taus))
|
|
549
|
+
intensities = amps * taus / tcspc_res
|
|
550
|
+
i_sum = float(intensities.sum())
|
|
551
|
+
return dict(
|
|
552
|
+
fit_model = 'tail',
|
|
553
|
+
tcspc_res = tcspc_res,
|
|
554
|
+
taus_ns = taus * 1e9,
|
|
555
|
+
amps = amps,
|
|
556
|
+
fractions = fracs,
|
|
557
|
+
intensities = intensities,
|
|
558
|
+
intensity_fractions = intensities / (i_sum if i_sum > 0 else 1.0),
|
|
559
|
+
i_sum = i_sum,
|
|
560
|
+
a_sum = float(amps.sum()),
|
|
561
|
+
t0_ns = t0 * 1e9,
|
|
562
|
+
bg_fit = bg_fit,
|
|
563
|
+
tvb_scale = tvb_scale,
|
|
564
|
+
tau_mean_amp_ns = tau_amp * 1e9,
|
|
565
|
+
tau_mean_int_ns = tau_int * 1e9,
|
|
566
|
+
chi2 = chi2,
|
|
567
|
+
reduced_chi2 = rchi2,
|
|
568
|
+
reduced_chi2_tail = rchi2,
|
|
569
|
+
chi2_pearson = chi2_p,
|
|
570
|
+
reduced_chi2_pearson = rchi2_p,
|
|
571
|
+
reduced_chi2_tail_pearson = rchi2_p,
|
|
572
|
+
calibrated_chi2_pearson = calibrated_chi2_p,
|
|
573
|
+
calibrated_chi2_tail_pearson = calibrated_chi2_p,
|
|
574
|
+
tail_start_bin = fit_start,
|
|
575
|
+
p_val = p_val,
|
|
576
|
+
dof = dof,
|
|
577
|
+
fit_idx = fit_idx,
|
|
578
|
+
fit_window_bins = (fit_start, fit_end),
|
|
579
|
+
fit_window_ns = (fit_start*tcspc_res*1e9, fit_end*tcspc_res*1e9),
|
|
580
|
+
model = model,
|
|
581
|
+
residuals = resid,
|
|
582
|
+
optimizer_msg = message,
|
|
583
|
+
)
|
|
584
|
+
|
|
585
|
+
|
|
586
|
+
def fit_per_pixel(stack, tcspc_res, n_bins, irf_prompt,
|
|
587
|
+
has_tail, fit_bg, fit_sigma,
|
|
588
|
+
global_popt, n_exp,
|
|
589
|
+
min_photons=MIN_PHOTONS_PERPIX,
|
|
590
|
+
tau_min_ns=None, tau_max_ns=None,
|
|
591
|
+
correct_pileup=False, n_sync=None,
|
|
592
|
+
fit_idx=None,
|
|
593
|
+
progress_callback=None,
|
|
594
|
+
free_tau=False,
|
|
595
|
+
use_gpu='auto',
|
|
596
|
+
gpu_backend=None,
|
|
597
|
+
tvb_profile=None, fit_tvb=False,
|
|
598
|
+
fit_model='reconv', fit_t0=False, t0_fixed=0.0):
|
|
599
|
+
ny, nx, _ = stack.shape
|
|
600
|
+
_tail = fit_model == 'tail'
|
|
601
|
+
if free_tau:
|
|
602
|
+
n_valid = int((stack.sum(axis=2) >= min_photons).sum())
|
|
603
|
+
if n_valid > _FREE_TAU_WARN_PIXELS:
|
|
604
|
+
print(f' [!] free-tau per-pixel on {n_valid:,} pixels is slow (iterative fit each); '
|
|
605
|
+
f'fixed-tau is ~100x faster - untick free-tau or draw a smaller ROI')
|
|
606
|
+
_n_sync_px = 0
|
|
607
|
+
if correct_pileup:
|
|
608
|
+
if not n_sync:
|
|
609
|
+
raise ValueError('pile-up correction requested but this file exposes no '
|
|
610
|
+
'excitation-pulse count (N_sync); Coates is unavailable here')
|
|
611
|
+
_n_sync_px = int(n_sync / max(ny * nx, 1))
|
|
612
|
+
_max_px = float(stack.sum(axis=2).max())
|
|
613
|
+
if _n_sync_px <= _max_px:
|
|
614
|
+
raise ValueError(
|
|
615
|
+
f'pile-up correction needs more pulses than photons per pixel; got '
|
|
616
|
+
f'{_n_sync_px:,} pulses/px vs {_max_px:,.0f} photons in the brightest pixel. '
|
|
617
|
+
f'Check the N_sync reported by the reader.')
|
|
618
|
+
tvb_on = bool(fit_tvb) and tvb_profile is not None
|
|
619
|
+
if _tail:
|
|
620
|
+
taus_fixed, _, t0_px, _, _ = unpack_tail_params(
|
|
621
|
+
global_popt, n_exp, fit_t0, fit_bg, fit_tvb, t0_fixed=t0_fixed)
|
|
622
|
+
shift = sigma = tamp = 0.0
|
|
623
|
+
ttau = 1.0
|
|
624
|
+
irf_fixed = None
|
|
625
|
+
irf_fft = None
|
|
626
|
+
if fit_idx is None:
|
|
627
|
+
fit_idx = np.arange(int(round(t0_px / tcspc_res)), n_bins, dtype=int)
|
|
628
|
+
else:
|
|
629
|
+
t0_px = 0.0
|
|
630
|
+
idx = 2 * n_exp
|
|
631
|
+
shift = global_popt[idx]; idx += 1
|
|
632
|
+
sigma = global_popt[idx] if fit_sigma else 0.0
|
|
633
|
+
if fit_sigma: idx += 1
|
|
634
|
+
if fit_bg: idx += 1
|
|
635
|
+
tamp = global_popt[idx] if has_tail else 0.0
|
|
636
|
+
ttau = global_popt[idx + 1] if has_tail else 1.0
|
|
637
|
+
taus_fixed = global_popt[:n_exp]
|
|
638
|
+
irf_fixed = build_full_irf(irf_prompt, shift, sigma, tamp, ttau, n_bins)
|
|
639
|
+
irf_fft = np.fft.fft(irf_fixed)
|
|
640
|
+
fit_idx = np.arange(n_bins) if fit_idx is None else np.asarray(fit_idx, dtype=int)
|
|
641
|
+
_windowed = len(fit_idx) != n_bins
|
|
642
|
+
t_axis = np.arange(n_bins, dtype=float) * tcspc_res
|
|
643
|
+
conv_basis = _basis_rows(taus_fixed, t_axis, tcspc_res, n_bins, _tail,
|
|
644
|
+
irf_fft=irf_fft, t0=t0_px)
|
|
645
|
+
A = conv_basis.T
|
|
646
|
+
A_fit = A[fit_idx]
|
|
647
|
+
if _tail and use_gpu is not False:
|
|
648
|
+
print(f' [per-pixel] tail fit uses the CPU path; the projection has to be '
|
|
649
|
+
f'restricted to bins past t0')
|
|
650
|
+
_gpu_windowed_ok = not (_windowed and n_exp == 1 and tvb_on)
|
|
651
|
+
if _windowed and use_gpu is not False and not _tail and n_exp == 1 and tvb_on:
|
|
652
|
+
print(f' [per-pixel] fit window with a time-varying background is not supported '
|
|
653
|
+
f'on the GPU for one-exponential fits, using the CPU path')
|
|
654
|
+
if use_gpu is not False and not _tail and _gpu_windowed_ok:
|
|
655
|
+
_backend = gpu_backend if gpu_backend is not None else (
|
|
656
|
+
None if _gpu_backend_cache is _GPU_BACKEND_UNSET else _gpu_backend_cache
|
|
657
|
+
)
|
|
658
|
+
if _backend is not None:
|
|
659
|
+
if not free_tau or n_exp == 1:
|
|
660
|
+
if n_exp == 1:
|
|
661
|
+
_lo = (tau_min_ns if tau_min_ns is not None
|
|
662
|
+
else max(taus_fixed[0] * 1e9 / 20.0, 0.05)) * 1e-9
|
|
663
|
+
_hi = (tau_max_ns if tau_max_ns is not None
|
|
664
|
+
else min(taus_fixed[0] * 1e9 * 20.0, 45.0)) * 1e-9
|
|
665
|
+
_N_GRID = tau_grid_points()
|
|
666
|
+
_tau_grid = np.logspace(np.log10(_lo), np.log10(_hi), _N_GRID)
|
|
667
|
+
_basis_grid = _basis_rows(_tau_grid, t_axis, tcspc_res, n_bins,
|
|
668
|
+
_tail, irf_fft=irf_fft, t0=t0_px)
|
|
669
|
+
_bb_grid = np.maximum((_basis_grid ** 2).sum(axis=1), 1e-20)
|
|
670
|
+
return _backend.batch_grid_scan_1exp(
|
|
671
|
+
stack, _basis_grid, _bb_grid, _tau_grid,
|
|
672
|
+
min_photons, correct_pileup, _n_sync_px,
|
|
673
|
+
progress_callback,
|
|
674
|
+
tvb_profile=tvb_profile if tvb_on else None,
|
|
675
|
+
fit_tvb=tvb_on,
|
|
676
|
+
fit_idx=fit_idx if _windowed else None,
|
|
677
|
+
)
|
|
678
|
+
else:
|
|
679
|
+
return _backend.batch_fixed_tau(
|
|
680
|
+
stack, A, taus_fixed,
|
|
681
|
+
min_photons, correct_pileup, _n_sync_px,
|
|
682
|
+
progress_callback,
|
|
683
|
+
tvb_profile=tvb_profile if tvb_on else None,
|
|
684
|
+
fit_tvb=tvb_on,
|
|
685
|
+
fit_idx=fit_idx if _windowed else None,
|
|
686
|
+
)
|
|
687
|
+
else:
|
|
688
|
+
_tau_min_s = (tau_min_ns if tau_min_ns is not None
|
|
689
|
+
else taus_fixed.min() * 1e9 * 0.1) * 1e-9
|
|
690
|
+
_tau_max_s = (tau_max_ns if tau_max_ns is not None
|
|
691
|
+
else taus_fixed.max() * 1e9 * 10.0) * 1e-9
|
|
692
|
+
return _backend.batch_free_tau_fit(
|
|
693
|
+
stack, irf_fixed, tcspc_res,
|
|
694
|
+
taus_fixed, _tau_min_s, _tau_max_s,
|
|
695
|
+
n_exp, min_photons, correct_pileup, _n_sync_px,
|
|
696
|
+
tvb_profile=tvb_profile if tvb_on else None,
|
|
697
|
+
fit_tvb=tvb_on,
|
|
698
|
+
fit_idx=fit_idx if _windowed else None,
|
|
699
|
+
)
|
|
700
|
+
if tvb_on:
|
|
701
|
+
B_cpu = np.asarray(tvb_profile, dtype=float)
|
|
702
|
+
A_aug = np.column_stack([A, B_cpu, np.ones(n_bins)])
|
|
703
|
+
maps = dict(
|
|
704
|
+
intensity = stack.sum(axis=2),
|
|
705
|
+
tau_mean_int = np.full((ny, nx), np.nan),
|
|
706
|
+
tau_mean_amp = np.full((ny, nx), np.nan),
|
|
707
|
+
chi2_r = np.full((ny, nx), np.nan),
|
|
708
|
+
calibrated_chi2_r = np.full((ny, nx), np.nan),
|
|
709
|
+
)
|
|
710
|
+
for i in range(n_exp):
|
|
711
|
+
maps[f"alpha_{i+1}"] = np.full((ny, nx), np.nan)
|
|
712
|
+
maps[f"frac_{i+1}"] = np.full((ny, nx), np.nan)
|
|
713
|
+
maps[f"tau_{i+1}"] = (np.full((ny, nx), np.nan)
|
|
714
|
+
if n_exp == 1 or free_tau
|
|
715
|
+
else np.full((ny, nx), taus_fixed[i] * 1e9))
|
|
716
|
+
maps[f"a{i+1}"] = maps[f"alpha_{i+1}"]
|
|
717
|
+
if tvb_on:
|
|
718
|
+
maps['tvb_scale'] = np.full((ny, nx), np.nan)
|
|
719
|
+
fitted = skipped = 0
|
|
720
|
+
t0 = time.time()
|
|
721
|
+
if n_exp == 1:
|
|
722
|
+
_lo = (tau_min_ns if tau_min_ns is not None
|
|
723
|
+
else max(taus_fixed[0] * 1e9 / 20.0, 0.05)) * 1e-9
|
|
724
|
+
_hi = (tau_max_ns if tau_max_ns is not None
|
|
725
|
+
else min(taus_fixed[0] * 1e9 * 20.0, 45.0)) * 1e-9
|
|
726
|
+
_N_GRID = tau_grid_points()
|
|
727
|
+
tau_grid = np.logspace(np.log10(_lo), np.log10(_hi), _N_GRID)
|
|
728
|
+
basis_grid = _basis_rows(tau_grid, t_axis, tcspc_res, n_bins, _tail,
|
|
729
|
+
irf_fft=irf_fft, t0=t0_px)
|
|
730
|
+
basis_fit = basis_grid[:, fit_idx]
|
|
731
|
+
bb_grid = np.maximum((basis_fit ** 2).sum(axis=1), 1e-20)
|
|
732
|
+
if tvb_on:
|
|
733
|
+
_tvb_prof_f = np.asarray(tvb_profile, dtype=float)[fit_idx]
|
|
734
|
+
_tvb_U = np.column_stack([_tvb_prof_f, np.ones(len(fit_idx))])
|
|
735
|
+
_tvb_Up = np.linalg.pinv(_tvb_U)
|
|
736
|
+
_basis_perp = basis_fit - (basis_fit @ _tvb_Up.T) @ _tvb_U.T
|
|
737
|
+
_bb_perp = np.maximum((_basis_perp ** 2).sum(axis=1), 1e-20)
|
|
738
|
+
for yi in tqdm(range(ny), desc=' Per-pixel rows', disable=True):
|
|
739
|
+
if progress_callback is not None:
|
|
740
|
+
progress_callback(yi, ny)
|
|
741
|
+
decay_row = stack[yi, :, :].astype(float)
|
|
742
|
+
ph_counts = decay_row.sum(axis=1)
|
|
743
|
+
valid_xi = np.where(ph_counts >= min_photons)[0]
|
|
744
|
+
skipped += nx - len(valid_xi)
|
|
745
|
+
if len(valid_xi) == 0:
|
|
746
|
+
continue
|
|
747
|
+
if tvb_on:
|
|
748
|
+
dvf = decay_row[valid_xi].astype(float)
|
|
749
|
+
if correct_pileup and _n_sync_px > 0:
|
|
750
|
+
dvf = np.array([coates_pileup_correction(dvf[k], _n_sync_px)
|
|
751
|
+
for k in range(len(valid_xi))])
|
|
752
|
+
dvf_f = dvf[:, fit_idx]
|
|
753
|
+
d_perp = dvf_f - (dvf_f @ _tvb_Up.T) @ _tvb_U.T
|
|
754
|
+
bd_p = d_perp @ _basis_perp.T
|
|
755
|
+
d_sq = (d_perp ** 2).sum(axis=1)
|
|
756
|
+
costs_p = d_sq[:, np.newaxis] - np.maximum(bd_p, 0.0) ** 2 / _bb_perp
|
|
757
|
+
best_g = np.argmin(costs_p, axis=1)
|
|
758
|
+
amp_v = np.maximum(bd_p[np.arange(len(valid_xi)), best_g] / _bb_perp[best_g], 0.0)
|
|
759
|
+
resid_after = dvf_f - amp_v[:, np.newaxis] * basis_fit[best_g]
|
|
760
|
+
vz = resid_after @ _tvb_Up.T
|
|
761
|
+
tvb_v = np.maximum(vz[:, 0], 0.0)
|
|
762
|
+
bg_z = vz[:, 1]
|
|
763
|
+
tau_v = tau_grid[best_g]
|
|
764
|
+
for k, xi in enumerate(valid_xi):
|
|
765
|
+
if amp_v[k] <= 0:
|
|
766
|
+
skipped += 1
|
|
767
|
+
continue
|
|
768
|
+
tau_ns = float(tau_v[k] * 1e9)
|
|
769
|
+
maps['tau_1'][yi, xi] = tau_ns
|
|
770
|
+
maps['tau_mean_amp'][yi, xi] = tau_ns
|
|
771
|
+
maps['tau_mean_int'][yi, xi] = tau_ns
|
|
772
|
+
maps['alpha_1'][yi, xi] = float(amp_v[k])
|
|
773
|
+
maps['frac_1'][yi, xi] = 1.0
|
|
774
|
+
maps['tvb_scale'][yi, xi] = float(tvb_v[k])
|
|
775
|
+
model_px = amp_v[k] * basis_fit[best_g[k]] + tvb_v[k] * _tvb_prof_f + bg_z[k]
|
|
776
|
+
resid = dvf_f[k] - model_px
|
|
777
|
+
chi2_px = float(np.sum(resid ** 2 / np.maximum(model_px, 1.0)))
|
|
778
|
+
maps['chi2_r'][yi, xi] = chi2_px / max(len(fit_idx) - 2, 1)
|
|
779
|
+
maps['calibrated_chi2_r'][yi, xi] = calibrated_chi2(dvf_f[k], model_px)
|
|
780
|
+
fitted += 1
|
|
781
|
+
continue
|
|
782
|
+
dv = decay_row[valid_xi]
|
|
783
|
+
peak_b_v = np.argmax(dv, axis=1)
|
|
784
|
+
bg_v = np.array([estimate_bg(dv[k], int(peak_b_v[k]))
|
|
785
|
+
for k in range(len(valid_xi))])
|
|
786
|
+
dc_v = np.maximum(dv - bg_v[:, np.newaxis], 0.0)
|
|
787
|
+
if correct_pileup and _n_sync_px > 0:
|
|
788
|
+
dc_v = np.array([
|
|
789
|
+
coates_pileup_correction(dc_v[k], _n_sync_px)
|
|
790
|
+
for k in range(len(valid_xi))
|
|
791
|
+
])
|
|
792
|
+
dc_f = dc_v[:, fit_idx]
|
|
793
|
+
bd = dc_f @ basis_fit.T
|
|
794
|
+
amps_g = np.maximum(bd / bb_grid, 0.0)
|
|
795
|
+
dc_sq = (dc_f ** 2).sum(axis=1)
|
|
796
|
+
costs = dc_sq[:, np.newaxis] - np.maximum(bd, 0.0) ** 2 / bb_grid
|
|
797
|
+
best_g = np.argmin(costs, axis=1)
|
|
798
|
+
tau_v = tau_grid[best_g]
|
|
799
|
+
amp_v = amps_g[np.arange(len(valid_xi)), best_g]
|
|
800
|
+
good = amp_v > 0
|
|
801
|
+
skipped += int((~good).sum())
|
|
802
|
+
for k, xi in enumerate(valid_xi):
|
|
803
|
+
if not good[k]:
|
|
804
|
+
continue
|
|
805
|
+
tau_ns = float(tau_v[k] * 1e9)
|
|
806
|
+
maps['tau_1'][yi, xi] = tau_ns
|
|
807
|
+
maps['tau_mean_amp'][yi, xi] = tau_ns
|
|
808
|
+
maps['tau_mean_int'][yi, xi] = tau_ns
|
|
809
|
+
maps['alpha_1'][yi, xi] = float(amp_v[k])
|
|
810
|
+
maps['frac_1'][yi, xi] = 1.0
|
|
811
|
+
best_b = basis_fit[best_g[k]]
|
|
812
|
+
model_px = float(amp_v[k]) * best_b + bg_v[k]
|
|
813
|
+
resid = dv[k][fit_idx] - model_px
|
|
814
|
+
chi2_px = float(np.sum(resid ** 2 / np.maximum(model_px, 1.0)))
|
|
815
|
+
maps['chi2_r'][yi, xi] = chi2_px / max(len(fit_idx) - 2, 1)
|
|
816
|
+
maps['calibrated_chi2_r'][yi, xi] = calibrated_chi2(dv[k][fit_idx], model_px)
|
|
817
|
+
fitted += 1
|
|
818
|
+
elif not free_tau:
|
|
819
|
+
for yi in tqdm(range(ny), desc=' Per-pixel rows', disable=True):
|
|
820
|
+
if progress_callback is not None:
|
|
821
|
+
progress_callback(yi, ny)
|
|
822
|
+
for xi in range(nx):
|
|
823
|
+
decay_px = stack[yi, xi, :]
|
|
824
|
+
if decay_px.sum() < min_photons:
|
|
825
|
+
skipped += 1
|
|
826
|
+
continue
|
|
827
|
+
if tvb_on:
|
|
828
|
+
dfit = decay_px.astype(float)
|
|
829
|
+
if correct_pileup and _n_sync_px > 0:
|
|
830
|
+
dfit = coates_pileup_correction(dfit, _n_sync_px)
|
|
831
|
+
coeffs_px, _ = nnls(A_aug[fit_idx], dfit[fit_idx])
|
|
832
|
+
amps_px = coeffs_px[:n_exp]
|
|
833
|
+
tvb_px = coeffs_px[n_exp]
|
|
834
|
+
bg_px = coeffs_px[n_exp + 1]
|
|
835
|
+
model_px = A_fit @ amps_px + tvb_px * B_cpu[fit_idx] + bg_px
|
|
836
|
+
else:
|
|
837
|
+
bg_px = estimate_bg(decay_px, int(np.argmax(decay_px)))
|
|
838
|
+
data_corr = np.maximum(decay_px - bg_px, 0.0)
|
|
839
|
+
if correct_pileup and _n_sync_px > 0:
|
|
840
|
+
data_corr = coates_pileup_correction(data_corr, _n_sync_px)
|
|
841
|
+
amps_px, _ = nnls(A_fit, data_corr[fit_idx])
|
|
842
|
+
model_px = A_fit @ amps_px + bg_px
|
|
843
|
+
resid = decay_px[fit_idx] - model_px
|
|
844
|
+
chi2_px = float(np.sum(resid**2 / np.maximum(model_px, 1.0)))
|
|
845
|
+
dof_px = max(len(fit_idx) - n_exp, 1)
|
|
846
|
+
amp_sum = amps_px.sum()
|
|
847
|
+
if amp_sum <= 0:
|
|
848
|
+
skipped += 1
|
|
849
|
+
continue
|
|
850
|
+
fracs_px = amps_px / amp_sum
|
|
851
|
+
taus_ns = taus_fixed * 1e9
|
|
852
|
+
tau_amp = float(np.dot(fracs_px, taus_ns))
|
|
853
|
+
denom = np.dot(amps_px, taus_ns)
|
|
854
|
+
tau_int = float(np.dot(amps_px, taus_ns**2) / denom) \
|
|
855
|
+
if denom > 0 else np.nan
|
|
856
|
+
maps['tau_mean_int'][yi, xi] = tau_int
|
|
857
|
+
maps['tau_mean_amp'][yi, xi] = tau_amp
|
|
858
|
+
maps['chi2_r'][yi, xi] = chi2_px / dof_px
|
|
859
|
+
maps['calibrated_chi2_r'][yi, xi] = calibrated_chi2(
|
|
860
|
+
decay_px[fit_idx], model_px)
|
|
861
|
+
for i in range(n_exp):
|
|
862
|
+
maps[f"alpha_{i+1}"][yi, xi] = amps_px[i]
|
|
863
|
+
maps[f"frac_{i+1}"][yi, xi] = fracs_px[i]
|
|
864
|
+
if tvb_on:
|
|
865
|
+
maps['tvb_scale'][yi, xi] = tvb_px
|
|
866
|
+
fitted += 1
|
|
867
|
+
else:
|
|
868
|
+
tau_min_s = (tau_min_ns if tau_min_ns is not None
|
|
869
|
+
else taus_fixed.min() * 1e9 * 0.1) * 1e-9
|
|
870
|
+
tau_max_s = (tau_max_ns if tau_max_ns is not None
|
|
871
|
+
else taus_fixed.max() * 1e9 * 10.0) * 1e-9
|
|
872
|
+
amp_hi = float(stack.max()) * 10.0
|
|
873
|
+
lo_px = np.array([tau_min_s] * n_exp + [0.0] * n_exp)
|
|
874
|
+
hi_px = np.array([tau_max_s] * n_exp + [amp_hi] * n_exp)
|
|
875
|
+
p0_px = np.concatenate([taus_fixed, np.full(n_exp, float(stack.max()) / n_exp)])
|
|
876
|
+
if tvb_on:
|
|
877
|
+
tvb_hi = float(stack.sum(axis=2).max())
|
|
878
|
+
lo_px = np.concatenate([lo_px, [0.0]])
|
|
879
|
+
hi_px = np.concatenate([hi_px, [tvb_hi]])
|
|
880
|
+
p0_px = np.concatenate([p0_px, [float(stack.max())]])
|
|
881
|
+
for yi in tqdm(range(ny), desc=' Per-pixel rows (free-τ)', disable=True):
|
|
882
|
+
if progress_callback is not None:
|
|
883
|
+
progress_callback(yi, ny)
|
|
884
|
+
for xi in range(nx):
|
|
885
|
+
decay_px = stack[yi, xi, :].astype(float)
|
|
886
|
+
if decay_px.sum() < min_photons:
|
|
887
|
+
skipped += 1
|
|
888
|
+
continue
|
|
889
|
+
bg_px = estimate_bg(decay_px, int(np.argmax(decay_px)))
|
|
890
|
+
data_corr = np.maximum(decay_px - bg_px, 0.0)
|
|
891
|
+
if correct_pileup and _n_sync_px > 0:
|
|
892
|
+
data_corr = coates_pileup_correction(data_corr, _n_sync_px)
|
|
893
|
+
def _make_full(p_px):
|
|
894
|
+
taus_p = p_px[:n_exp]
|
|
895
|
+
amps_p = p_px[n_exp:2 * n_exp]
|
|
896
|
+
if _tail:
|
|
897
|
+
full = list(taus_p) + list(amps_p)
|
|
898
|
+
if tvb_on:
|
|
899
|
+
full.append(p_px[2 * n_exp])
|
|
900
|
+
return full
|
|
901
|
+
full = list(taus_p) + list(amps_p) + [shift]
|
|
902
|
+
if fit_sigma:
|
|
903
|
+
full.append(sigma)
|
|
904
|
+
if tvb_on:
|
|
905
|
+
full.append(p_px[2 * n_exp])
|
|
906
|
+
elif fit_bg:
|
|
907
|
+
full.append(bg_px)
|
|
908
|
+
if has_tail:
|
|
909
|
+
full.extend([tamp, ttau])
|
|
910
|
+
return full
|
|
911
|
+
def _eval_model(full_p, _bg):
|
|
912
|
+
if _tail:
|
|
913
|
+
return tail_model(
|
|
914
|
+
full_p, tcspc_res, n_bins, n_exp,
|
|
915
|
+
0.0 if tvb_on else _bg, False,
|
|
916
|
+
fit_t0=False, t0_fixed=t0_px,
|
|
917
|
+
tvb_profile=tvb_profile if tvb_on else None,
|
|
918
|
+
fit_tvb=tvb_on)
|
|
919
|
+
if tvb_on:
|
|
920
|
+
return reconvolution_model(
|
|
921
|
+
full_p, tcspc_res, n_bins, irf_prompt,
|
|
922
|
+
n_exp, 0.0, has_tail, False, fit_sigma,
|
|
923
|
+
tvb_profile=tvb_profile, fit_tvb=True)
|
|
924
|
+
return reconvolution_model(
|
|
925
|
+
full_p, tcspc_res, n_bins, irf_prompt,
|
|
926
|
+
n_exp, _bg, has_tail, False, fit_sigma)
|
|
927
|
+
w_px = np.sqrt(np.maximum(decay_px, 1.0))
|
|
928
|
+
def _resid(p_px, _decay=decay_px, _bg=bg_px, _w=w_px):
|
|
929
|
+
model_vals = _eval_model(np.array(_make_full(p_px)), _bg)
|
|
930
|
+
return (model_vals[fit_idx] - _decay[fit_idx]) / _w[fit_idx]
|
|
931
|
+
try:
|
|
932
|
+
res = least_squares(
|
|
933
|
+
_resid, p0_px,
|
|
934
|
+
bounds=(lo_px, hi_px),
|
|
935
|
+
method='trf', max_nfev=500,
|
|
936
|
+
ftol=1e-8, xtol=1e-8, gtol=1e-8)
|
|
937
|
+
p_sol = res.x
|
|
938
|
+
except Exception:
|
|
939
|
+
skipped += 1
|
|
940
|
+
continue
|
|
941
|
+
taus_sol = p_sol[:n_exp]
|
|
942
|
+
amps_sol = p_sol[n_exp:2 * n_exp]
|
|
943
|
+
amp_sum = amps_sol.sum()
|
|
944
|
+
if amp_sum <= 0:
|
|
945
|
+
skipped += 1
|
|
946
|
+
continue
|
|
947
|
+
order = np.argsort(taus_sol)
|
|
948
|
+
taus_sol = taus_sol[order]
|
|
949
|
+
amps_sol = amps_sol[order]
|
|
950
|
+
fracs_px = amps_sol / amp_sum
|
|
951
|
+
taus_ns = taus_sol * 1e9
|
|
952
|
+
tau_amp = float(np.dot(fracs_px, taus_ns))
|
|
953
|
+
denom = np.dot(amps_sol, taus_ns)
|
|
954
|
+
tau_int = float(np.dot(amps_sol, taus_ns**2) / denom) \
|
|
955
|
+
if denom > 0 else np.nan
|
|
956
|
+
full_sol = np.array(_make_full(p_sol))
|
|
957
|
+
model_sol = _eval_model(full_sol, bg_px)
|
|
958
|
+
resid_sol = decay_px[fit_idx] - model_sol[fit_idx]
|
|
959
|
+
chi2_px = float(np.sum(resid_sol**2 / np.maximum(model_sol[fit_idx], 1.0)))
|
|
960
|
+
dof_px = max(len(fit_idx) - 2 * n_exp, 1)
|
|
961
|
+
maps['tau_mean_int'][yi, xi] = tau_int
|
|
962
|
+
maps['tau_mean_amp'][yi, xi] = tau_amp
|
|
963
|
+
maps['chi2_r'][yi, xi] = chi2_px / dof_px
|
|
964
|
+
maps['calibrated_chi2_r'][yi, xi] = calibrated_chi2(
|
|
965
|
+
decay_px[fit_idx], model_sol[fit_idx])
|
|
966
|
+
for i in range(n_exp):
|
|
967
|
+
maps[f"tau_{i+1}"][yi, xi] = taus_ns[i]
|
|
968
|
+
maps[f"alpha_{i+1}"][yi, xi] = amps_sol[i]
|
|
969
|
+
maps[f"frac_{i+1}"][yi, xi] = fracs_px[i]
|
|
970
|
+
if tvb_on:
|
|
971
|
+
maps['tvb_scale'][yi, xi] = float(p_sol[2 * n_exp])
|
|
972
|
+
fitted += 1
|
|
973
|
+
elapsed = time.time() - t0
|
|
974
|
+
return maps
|
|
975
|
+
|
|
976
|
+
def fit_summed_dist(decay, tcspc_res, n_bins, irf_prompt,
|
|
977
|
+
n_components, dist_type,
|
|
978
|
+
fit_bg, fit_sigma,
|
|
979
|
+
tau_min_ns, tau_max_ns,
|
|
980
|
+
optimizer='de', n_restarts=8,
|
|
981
|
+
de_popsize=15, de_maxiter=1000,
|
|
982
|
+
workers=-1, polish=True,
|
|
983
|
+
cost_function='poisson',
|
|
984
|
+
sigma_max=3.0,
|
|
985
|
+
irf_shift_bins=2,
|
|
986
|
+
tvb_profile=None, fit_tvb=False,
|
|
987
|
+
fit_start_ns=None, fit_end_ns=None, exclude_ns=None,
|
|
988
|
+
n_sync=None):
|
|
989
|
+
tau_min = tau_min_ns * 1e-9
|
|
990
|
+
tau_max = tau_max_ns * 1e-9
|
|
991
|
+
if cost_function not in ('chi2', 'poisson'):
|
|
992
|
+
raise ValueError(f"Unknown cost_function: {cost_function!r}")
|
|
993
|
+
decay_work = decay.astype(float)
|
|
994
|
+
if decay_work.max() == 0:
|
|
995
|
+
raise ValueError('Decay has zero maximum - cannot fit.')
|
|
996
|
+
peak_bin = int(np.argmax(decay_work))
|
|
997
|
+
bg_init = estimate_bg(decay_work, peak_bin)
|
|
998
|
+
bg_fixed = bg_init if not fit_bg else 0.0
|
|
999
|
+
fit_end = find_fit_end(decay_work, peak_bin, tau_max, tcspc_res, n_bins)
|
|
1000
|
+
standard_fit_end = int(round(44.9455 / (tcspc_res * 1e9)))
|
|
1001
|
+
fit_end = min(fit_end, standard_fit_end)
|
|
1002
|
+
fit_start = find_fit_start(decay_work, irf_prompt, tcspc_res)
|
|
1003
|
+
fit_start = max(0, min(fit_start, fit_end - 10))
|
|
1004
|
+
if fit_end_ns is not None:
|
|
1005
|
+
fit_end = min(n_bins, bins_from_ns(fit_end_ns, tcspc_res))
|
|
1006
|
+
if fit_start_ns is not None:
|
|
1007
|
+
fit_start = max(0, min(bins_from_ns(fit_start_ns, tcspc_res), fit_end - 2))
|
|
1008
|
+
exclude_bins = [(bins_from_ns(lo, tcspc_res), bins_from_ns(hi, tcspc_res))
|
|
1009
|
+
for lo, hi in (exclude_ns or [])]
|
|
1010
|
+
fit_idx = build_fit_idx(fit_start, fit_end, n_bins, exclude_bins)
|
|
1011
|
+
bg_upper = max(bg_init * 2.0, bg_init + 10.0)
|
|
1012
|
+
if fit_tvb and tvb_profile is None:
|
|
1013
|
+
raise ValueError('fit_tvb=True requires a tvb_profile.')
|
|
1014
|
+
tvb_init = float(bg_init * n_bins) if fit_tvb else 0.0
|
|
1015
|
+
tvb_upper = float(decay_work.sum()) if fit_tvb else None
|
|
1016
|
+
if fit_tvb:
|
|
1017
|
+
print(f" TVB: free scale on measured profile, init={tvb_init:.1f}, upper={tvb_upper:.1f}")
|
|
1018
|
+
print(f" Cost function: {cost_function}")
|
|
1019
|
+
print(f" bg initial guess = {bg_init:.3f} cts/bin, upper bound = {bg_upper:.3f} "
|
|
1020
|
+
f"({'free param' if fit_bg else 'fixed'})")
|
|
1021
|
+
lo, hi = _build_bounds_dist(
|
|
1022
|
+
n_components, tau_min, tau_max, decay_work.max(),
|
|
1023
|
+
fit_bg, fit_sigma, bg_init=bg_init, bg_upper=bg_upper,
|
|
1024
|
+
sigma_max=sigma_max, irf_shift_bins=irf_shift_bins,
|
|
1025
|
+
fit_tvb=fit_tvb, tvb_init=tvb_init, tvb_upper=tvb_upper)
|
|
1026
|
+
bounds = list(zip(lo, hi))
|
|
1027
|
+
if cost_function == 'chi2':
|
|
1028
|
+
weights = np.sqrt(np.maximum(decay_work[fit_idx], 1.0))
|
|
1029
|
+
def residuals(params):
|
|
1030
|
+
model_vals = dist_reconvolution_model(
|
|
1031
|
+
params, tcspc_res, n_bins, irf_prompt,
|
|
1032
|
+
n_components, dist_type, bg_fixed, fit_bg, fit_sigma,
|
|
1033
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb)
|
|
1034
|
+
return (model_vals[fit_idx] - decay_work[fit_idx]) / weights
|
|
1035
|
+
else:
|
|
1036
|
+
def residuals(params):
|
|
1037
|
+
model_vals = dist_reconvolution_model(
|
|
1038
|
+
params, tcspc_res, n_bins, irf_prompt,
|
|
1039
|
+
n_components, dist_type, bg_fixed, fit_bg, fit_sigma,
|
|
1040
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb)
|
|
1041
|
+
n = decay_work[fit_idx]
|
|
1042
|
+
m = np.maximum(model_vals[fit_idx], 1e-10)
|
|
1043
|
+
dev = m - n
|
|
1044
|
+
pos = n > 0
|
|
1045
|
+
dev[pos] += n[pos] * np.log(n[pos] / m[pos])
|
|
1046
|
+
dev = np.maximum(dev, 0.0)
|
|
1047
|
+
r = np.sqrt(2.0 * dev)
|
|
1048
|
+
r[m < n] *= -1
|
|
1049
|
+
return r
|
|
1050
|
+
if optimizer == 'lm_multistart':
|
|
1051
|
+
rng = np.random.default_rng(42)
|
|
1052
|
+
best_res = None
|
|
1053
|
+
best_cost = np.inf
|
|
1054
|
+
for i in range(n_restarts + 1):
|
|
1055
|
+
if i == 0:
|
|
1056
|
+
p0 = _pack_p0_dist(n_components, tau_min, tau_max,
|
|
1057
|
+
float(decay_work.max()), fit_bg, fit_sigma, bg_init,
|
|
1058
|
+
fit_tvb=fit_tvb, tvb_init=tvb_init)
|
|
1059
|
+
else:
|
|
1060
|
+
tau_ov = np.sort(np.exp(rng.uniform(
|
|
1061
|
+
np.log(tau_min * 1.001), np.log(tau_max * 0.999), n_components)))
|
|
1062
|
+
p0 = _pack_p0_dist(n_components, tau_min, tau_max,
|
|
1063
|
+
float(decay_work.max()), fit_bg, fit_sigma, bg_init,
|
|
1064
|
+
fit_tvb=fit_tvb, tvb_init=tvb_init)
|
|
1065
|
+
p0[:n_components] = tau_ov
|
|
1066
|
+
try:
|
|
1067
|
+
res = least_squares(residuals, p0, bounds=(lo, hi), method='trf',
|
|
1068
|
+
max_nfev=50000, ftol=1e-13, xtol=1e-13, gtol=1e-13)
|
|
1069
|
+
except Exception as exc:
|
|
1070
|
+
print(f" Restart {i:2d}: failed ({exc})")
|
|
1071
|
+
continue
|
|
1072
|
+
if res.cost < best_cost:
|
|
1073
|
+
best_cost = res.cost
|
|
1074
|
+
best_res = res
|
|
1075
|
+
print(f" Restart {i:2d}: cost={res.cost:.4e} ← best")
|
|
1076
|
+
else:
|
|
1077
|
+
print(f" Restart {i:2d}: cost={res.cost:.4e}")
|
|
1078
|
+
if best_res is None:
|
|
1079
|
+
raise RuntimeError('All restarts failed.')
|
|
1080
|
+
popt_work = best_res.x
|
|
1081
|
+
message = best_res.message
|
|
1082
|
+
elif optimizer == 'de':
|
|
1083
|
+
print(f" Differential evolution: popsize={de_popsize}, maxiter={de_maxiter}, workers={workers}")
|
|
1084
|
+
n = n_components
|
|
1085
|
+
bounds_log = list(bounds)
|
|
1086
|
+
for i in range(n):
|
|
1087
|
+
lo_t, hi_t = bounds[i]
|
|
1088
|
+
bounds_log[i] = (np.log10(lo_t), np.log10(hi_t))
|
|
1089
|
+
for i in range(n, 2 * n):
|
|
1090
|
+
lo_w, hi_w = bounds[i]
|
|
1091
|
+
bounds_log[i] = (np.log10(lo_w), np.log10(hi_w))
|
|
1092
|
+
if cost_function == 'poisson':
|
|
1093
|
+
cost_fn = _DECostDistPoissonLogParam(
|
|
1094
|
+
tcspc_res, n_bins, irf_prompt, n_components, dist_type,
|
|
1095
|
+
bg_fixed, fit_bg, fit_sigma, fit_idx, decay_work,
|
|
1096
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
|
|
1097
|
+
else:
|
|
1098
|
+
cost_fn = _DECostDistLogParam(
|
|
1099
|
+
tcspc_res, n_bins, irf_prompt, n_components, dist_type,
|
|
1100
|
+
bg_fixed, fit_bg, fit_sigma, fit_idx, decay_work,
|
|
1101
|
+
weights, tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
|
|
1102
|
+
de_res = differential_evolution(
|
|
1103
|
+
cost_fn, bounds=bounds_log,
|
|
1104
|
+
maxiter=de_maxiter, popsize=de_popsize,
|
|
1105
|
+
workers=workers, seed=42,
|
|
1106
|
+
updating='deferred' if workers != 1 else 'immediate',
|
|
1107
|
+
init='sobol', disp=False)
|
|
1108
|
+
popt_work = de_res.x.copy()
|
|
1109
|
+
popt_work[:n] = 10.0 ** popt_work[:n]
|
|
1110
|
+
popt_work[n:2*n] = 10.0 ** popt_work[n:2*n]
|
|
1111
|
+
message = f"DE success={de_res.success}, fun={de_res.fun:.4e}"
|
|
1112
|
+
if polish:
|
|
1113
|
+
print(' Running final LM polish...')
|
|
1114
|
+
eps = 1e-10
|
|
1115
|
+
popt_work = np.clip(popt_work, np.asarray(lo) + eps, np.asarray(hi) - eps)
|
|
1116
|
+
try:
|
|
1117
|
+
pol = least_squares(residuals, popt_work, bounds=(lo, hi), method='trf',
|
|
1118
|
+
max_nfev=5000, ftol=1e-13, xtol=1e-13, gtol=1e-13)
|
|
1119
|
+
popt_work = pol.x
|
|
1120
|
+
message += f"; polished cost={pol.cost:.4e}"
|
|
1121
|
+
except ValueError as e:
|
|
1122
|
+
print(f" Warning: LM polish failed ({e}) - using DE result")
|
|
1123
|
+
else:
|
|
1124
|
+
raise ValueError(f"Unknown optimizer: {optimizer!r}")
|
|
1125
|
+
summary = _make_summary_dist(
|
|
1126
|
+
popt_work, decay, tcspc_res, n_bins, irf_prompt,
|
|
1127
|
+
n_components, dist_type, bg_fixed, fit_bg, fit_sigma,
|
|
1128
|
+
fit_idx, message, tvb_profile=tvb_profile, fit_tvb=fit_tvb, n_sync=n_sync)
|
|
1129
|
+
return popt_work, summary
|
|
1130
|
+
|
|
1131
|
+
def _make_summary_dist(popt, decay, tcspc_res, n_bins, irf_prompt,
|
|
1132
|
+
n_components, dist_type, bg_fixed, fit_bg, fit_sigma,
|
|
1133
|
+
fit_idx, message=None,
|
|
1134
|
+
tvb_profile=None, fit_tvb=False, n_sync=None):
|
|
1135
|
+
fit_start = int(fit_idx[0])
|
|
1136
|
+
fit_end = int(fit_idx[-1]) + 1
|
|
1137
|
+
tau_centers = popt[:n_components]
|
|
1138
|
+
widths = popt[n_components:2 * n_components]
|
|
1139
|
+
amps = popt[2 * n_components:3 * n_components]
|
|
1140
|
+
idx = 3 * n_components
|
|
1141
|
+
shift = popt[idx]; idx += 1
|
|
1142
|
+
sigma = popt[idx] if fit_sigma else 0.0
|
|
1143
|
+
if fit_sigma:
|
|
1144
|
+
idx += 1
|
|
1145
|
+
if fit_bg:
|
|
1146
|
+
bg_fit = popt[idx]; idx += 1
|
|
1147
|
+
else:
|
|
1148
|
+
bg_fit = bg_fixed
|
|
1149
|
+
if fit_tvb:
|
|
1150
|
+
tvb_scale = popt[idx]; idx += 1
|
|
1151
|
+
else:
|
|
1152
|
+
tvb_scale = 0.0
|
|
1153
|
+
model = dist_reconvolution_model(popt, tcspc_res, n_bins, irf_prompt,
|
|
1154
|
+
n_components, dist_type, bg_fixed, fit_bg, fit_sigma,
|
|
1155
|
+
tvb_profile=tvb_profile, fit_tvb=fit_tvb)
|
|
1156
|
+
d_win = decay[fit_idx].astype(float)
|
|
1157
|
+
m_win = model[fit_idx]
|
|
1158
|
+
sigma_w = np.sqrt(np.maximum(d_win, 1.0))
|
|
1159
|
+
chi2 = float(np.sum(((d_win - m_win) / sigma_w) ** 2))
|
|
1160
|
+
dof = max(len(fit_idx) - len(popt), 1)
|
|
1161
|
+
rchi2 = chi2 / dof
|
|
1162
|
+
sigma_p = np.sqrt(np.maximum(m_win, 1.0))
|
|
1163
|
+
chi2_p = float(np.sum(((d_win - m_win) / sigma_p) ** 2))
|
|
1164
|
+
rchi2_p = chi2_p / dof
|
|
1165
|
+
calibrated_chi2_p = calibrated_chi2(d_win, m_win)
|
|
1166
|
+
peak_bin_loc = int(fit_idx[np.argmax(decay[fit_idx])])
|
|
1167
|
+
tail_start = peak_bin_loc + max(1, int(0.05 * (fit_end - peak_bin_loc)))
|
|
1168
|
+
tail_idx = fit_idx[fit_idx >= tail_start]
|
|
1169
|
+
d_tail = decay[tail_idx].astype(float)
|
|
1170
|
+
m_tail = model[tail_idx]
|
|
1171
|
+
sw_tail = np.sqrt(np.maximum(d_tail, 1.0))
|
|
1172
|
+
chi2_tail = float(np.sum(((d_tail - m_tail) / sw_tail) ** 2))
|
|
1173
|
+
dof_tail = max(len(tail_idx) - len(popt), 1)
|
|
1174
|
+
rchi2_tail = chi2_tail / dof_tail
|
|
1175
|
+
sp_tail = np.sqrt(np.maximum(m_tail, 1.0))
|
|
1176
|
+
chi2_tail_p = float(np.sum(((d_tail - m_tail) / sp_tail) ** 2))
|
|
1177
|
+
rchi2_tail_p = chi2_tail_p / dof_tail
|
|
1178
|
+
calibrated_chi2_tail_p = calibrated_chi2(d_tail, m_tail)
|
|
1179
|
+
resid = (decay - model) / np.sqrt(np.maximum(model, 1.0))
|
|
1180
|
+
from ..FLIM.models import _alpha_gaussian, _alpha_lorentzian, _N_QUAD
|
|
1181
|
+
alpha_fn = _alpha_gaussian if dist_type == 'gaussian' else _alpha_lorentzian
|
|
1182
|
+
tau_num_amp = 0.0; tau_den_amp = 0.0
|
|
1183
|
+
tau_num_int = 0.0; tau_den_int = 0.0
|
|
1184
|
+
for i in range(n_components):
|
|
1185
|
+
tau_c = tau_centers[i]; w = widths[i]; a = max(amps[i], 0.0)
|
|
1186
|
+
spread = 4.0 * w if dist_type == 'gaussian' else 8.0 * max(w / 2.0, 1e-15)
|
|
1187
|
+
tau_lo = max(tau_c - spread, 1e-12)
|
|
1188
|
+
tau_hi = max(tau_c + spread, tau_lo + 1e-12)
|
|
1189
|
+
tau_grid = np.linspace(tau_lo, tau_hi, _N_QUAD)
|
|
1190
|
+
alpha = alpha_fn(tau_grid, tau_c, w)
|
|
1191
|
+
alpha = alpha / max(alpha.sum(), 1e-30)
|
|
1192
|
+
tau_num_amp += a * float(np.dot(alpha, tau_grid))
|
|
1193
|
+
tau_den_amp += a
|
|
1194
|
+
tau_num_int += a * float(np.dot(alpha, tau_grid ** 2))
|
|
1195
|
+
tau_den_int += a * float(np.dot(alpha, tau_grid))
|
|
1196
|
+
tau_mean_amp_ns = (tau_num_amp / max(tau_den_amp, 1e-30)) * 1e9
|
|
1197
|
+
tau_mean_int_ns = (tau_num_int / max(tau_den_int, 1e-30)) * 1e9
|
|
1198
|
+
amp_sum = max(amps.sum(), 1e-30)
|
|
1199
|
+
fractions = amps / amp_sum
|
|
1200
|
+
if dist_type == 'gaussian':
|
|
1201
|
+
fwhms_ns = widths * 2.3548 * 1e9
|
|
1202
|
+
else:
|
|
1203
|
+
fwhms_ns = widths * 1e9
|
|
1204
|
+
above = np.where(irf_prompt >= irf_prompt.max() / 2)[0]
|
|
1205
|
+
fwhm_pr = (above[-1] - above[0]) if len(above) > 1 else 1
|
|
1206
|
+
fwhm_eff = np.sqrt(fwhm_pr ** 2 + (2.3548 * sigma) ** 2) * tcspc_res * 1e9
|
|
1207
|
+
return dict(
|
|
1208
|
+
dist_type = dist_type,
|
|
1209
|
+
n_components = n_components,
|
|
1210
|
+
tcspc_res = tcspc_res,
|
|
1211
|
+
tau_centers_ns = tau_centers * 1e9,
|
|
1212
|
+
widths_ns = widths * 1e9,
|
|
1213
|
+
fwhms_ns = fwhms_ns,
|
|
1214
|
+
amps = amps,
|
|
1215
|
+
fractions = fractions,
|
|
1216
|
+
bg_fit = bg_fit,
|
|
1217
|
+
tvb_scale = tvb_scale,
|
|
1218
|
+
tau_mean_amp_ns = tau_mean_amp_ns,
|
|
1219
|
+
tau_mean_int_ns = tau_mean_int_ns,
|
|
1220
|
+
chi2 = chi2,
|
|
1221
|
+
reduced_chi2 = rchi2,
|
|
1222
|
+
reduced_chi2_tail = rchi2_tail,
|
|
1223
|
+
chi2_pearson = chi2_p,
|
|
1224
|
+
reduced_chi2_pearson = rchi2_p,
|
|
1225
|
+
reduced_chi2_tail_pearson = rchi2_tail_p,
|
|
1226
|
+
calibrated_chi2_pearson = calibrated_chi2_p,
|
|
1227
|
+
calibrated_chi2_tail_pearson = calibrated_chi2_tail_p,
|
|
1228
|
+
tail_start_bin = tail_start,
|
|
1229
|
+
dof = dof,
|
|
1230
|
+
fit_window_bins = (fit_start, fit_end),
|
|
1231
|
+
fit_window_ns = (fit_start * tcspc_res * 1e9, fit_end * tcspc_res * 1e9),
|
|
1232
|
+
fit_idx = fit_idx,
|
|
1233
|
+
irf_shift_bins = shift,
|
|
1234
|
+
irf_sigma_bins = sigma,
|
|
1235
|
+
irf_fwhm_eff_ns = fwhm_eff,
|
|
1236
|
+
model = model,
|
|
1237
|
+
residuals = resid,
|
|
1238
|
+
optimizer_msg = message,
|
|
1239
|
+
)
|
|
1240
|
+
|
|
1241
|
+
|
|
1242
|
+
def fit_per_pixel_dist(stack, tcspc_res, n_bins, irf_prompt,
|
|
1243
|
+
global_popt, n_components, dist_type,
|
|
1244
|
+
fit_bg=True, fit_sigma=False,
|
|
1245
|
+
min_photons=MIN_PHOTONS_PERPIX,
|
|
1246
|
+
tau_min_ns=None, tau_max_ns=None,
|
|
1247
|
+
n_tau_grid=50, n_width_grid=30,
|
|
1248
|
+
progress_callback=None,
|
|
1249
|
+
use_gpu='auto',
|
|
1250
|
+
gpu_backend=None,
|
|
1251
|
+
tvb_profile=None, fit_tvb=False,
|
|
1252
|
+
fit_idx=None) -> dict:
|
|
1253
|
+
from ..GPU._base import fit_window
|
|
1254
|
+
|
|
1255
|
+
ny, nx, _ = stack.shape
|
|
1256
|
+
window = fit_window(fit_idx, n_bins)
|
|
1257
|
+
fit_idx = np.arange(n_bins) if window is None else window
|
|
1258
|
+
n_fit = len(fit_idx)
|
|
1259
|
+
tvb_on = bool(fit_tvb) and tvb_profile is not None
|
|
1260
|
+
if tvb_on and n_components != 1:
|
|
1261
|
+
print(' Per-pixel distribution TVB only supported for unimodal (1 component); ignoring TVB here.')
|
|
1262
|
+
tvb_on = False
|
|
1263
|
+
idx = 3 * n_components
|
|
1264
|
+
shift = global_popt[idx]; idx += 1
|
|
1265
|
+
sigma = global_popt[idx] if fit_sigma else 0.0
|
|
1266
|
+
if fit_sigma:
|
|
1267
|
+
idx += 1
|
|
1268
|
+
tau_centers_g = global_popt[:n_components]
|
|
1269
|
+
widths_g = global_popt[n_components:2 * n_components]
|
|
1270
|
+
irf_fixed = build_full_irf(irf_prompt, shift, sigma, 0.0, 1.0, n_bins)
|
|
1271
|
+
tau_lo = max(tau_centers_g.min() / 5.0, 1e-12) if tau_min_ns is None else tau_min_ns * 1e-9
|
|
1272
|
+
tau_hi = tau_centers_g.max() * 5.0 if tau_max_ns is None else tau_max_ns * 1e-9
|
|
1273
|
+
w_lo = widths_g.min() / 5.0
|
|
1274
|
+
w_hi = widths_g.max() * 5.0
|
|
1275
|
+
tau_grid = np.logspace(np.log10(max(tau_lo, 1e-12)), np.log10(tau_hi), n_tau_grid)
|
|
1276
|
+
width_grid = np.logspace(np.log10(max(w_lo, 1e-12)), np.log10(w_hi), n_width_grid)
|
|
1277
|
+
print(f" Building distribution basis grid ({n_tau_grid}×{n_width_grid})...")
|
|
1278
|
+
basis, param_pairs = build_dist_basis_grid(
|
|
1279
|
+
tcspc_res, n_bins, irf_fixed, tau_grid, width_grid, dist_type)
|
|
1280
|
+
basis_fit = basis[:, fit_idx]
|
|
1281
|
+
bb_grid = np.maximum((basis_fit.astype(np.float64) ** 2).sum(axis=1), 1e-20).astype(np.float32)
|
|
1282
|
+
maps = dict(
|
|
1283
|
+
intensity = stack.sum(axis=2),
|
|
1284
|
+
tau_mean_amp = np.full((ny, nx), np.nan),
|
|
1285
|
+
tau_mean_int = np.full((ny, nx), np.nan),
|
|
1286
|
+
chi2_r = np.full((ny, nx), np.nan),
|
|
1287
|
+
calibrated_chi2_r = np.full((ny, nx), np.nan),
|
|
1288
|
+
)
|
|
1289
|
+
for i in range(n_components):
|
|
1290
|
+
maps[f"tau_center_{i+1}"] = np.full((ny, nx), np.nan)
|
|
1291
|
+
maps[f"width_{i+1}"] = np.full((ny, nx), np.nan)
|
|
1292
|
+
maps[f"alpha_{i+1}"] = np.full((ny, nx), np.nan)
|
|
1293
|
+
maps[f"frac_{i+1}"] = np.full((ny, nx), np.nan)
|
|
1294
|
+
if tvb_on:
|
|
1295
|
+
maps['tvb_scale'] = np.full((ny, nx), np.nan)
|
|
1296
|
+
if n_components == 1:
|
|
1297
|
+
backend = None
|
|
1298
|
+
if use_gpu is not False:
|
|
1299
|
+
backend = gpu_backend if gpu_backend is not None else (
|
|
1300
|
+
None if _gpu_backend_cache is _GPU_BACKEND_UNSET else _gpu_backend_cache
|
|
1301
|
+
)
|
|
1302
|
+
if backend is not None and stack.nbytes > _GPU_MAX_DIST_STACK_BYTES:
|
|
1303
|
+
print(f' [per-pixel] {stack.nbytes/1e9:.1f} GB cube exceeds GPU limit '
|
|
1304
|
+
f'({_GPU_MAX_DIST_STACK_BYTES/1e9:.1f} GB); the distribution scan is not blocked, using the CPU path')
|
|
1305
|
+
backend = None
|
|
1306
|
+
if backend is not None:
|
|
1307
|
+
return backend.batch_dist_scan_unimodal(
|
|
1308
|
+
stack, basis_fit, bb_grid, param_pairs,
|
|
1309
|
+
irf_fixed, tcspc_res, n_bins, dist_type,
|
|
1310
|
+
min_photons, progress_callback,
|
|
1311
|
+
tvb_profile=tvb_profile if tvb_on else None,
|
|
1312
|
+
fit_tvb=tvb_on, fit_idx=fit_idx)
|
|
1313
|
+
flat = stack.reshape(ny * nx, n_bins).astype(np.float32)
|
|
1314
|
+
ph_counts = flat.sum(axis=1)
|
|
1315
|
+
valid_idx = np.where(ph_counts >= min_photons)[0]
|
|
1316
|
+
if tvb_on and valid_idx.size > 0:
|
|
1317
|
+
tvb_fit = np.asarray(tvb_profile, dtype=float)[fit_idx]
|
|
1318
|
+
_U = np.column_stack([tvb_fit, np.ones(n_fit)])
|
|
1319
|
+
_Up = np.linalg.pinv(_U)
|
|
1320
|
+
_bp = basis_fit.astype(np.float64) - (basis_fit.astype(np.float64) @ _Up.T) @ _U.T
|
|
1321
|
+
_bbp = np.maximum((_bp ** 2).sum(axis=1), 1e-20)
|
|
1322
|
+
d_valid = flat[valid_idx][:, fit_idx].astype(np.float64)
|
|
1323
|
+
d_perp = d_valid - (d_valid @ _Up.T) @ _U.T
|
|
1324
|
+
bd = d_perp @ _bp.T
|
|
1325
|
+
costs = (d_perp ** 2).sum(axis=1)[:, None] - np.maximum(bd, 0.0) ** 2 / _bbp[None, :]
|
|
1326
|
+
best_g = np.argmin(costs, axis=1)
|
|
1327
|
+
amp_v = np.maximum(bd[np.arange(len(valid_idx)), best_g] / _bbp[best_g], 0.0)
|
|
1328
|
+
basis_best = basis_fit[best_g].astype(np.float64)
|
|
1329
|
+
resid_after = d_valid - amp_v[:, None] * basis_best
|
|
1330
|
+
vz = resid_after @ _Up.T
|
|
1331
|
+
tvb_v = np.maximum(vz[:, 0], 0.0)
|
|
1332
|
+
bg_z = vz[:, 1]
|
|
1333
|
+
tau_v = param_pairs[best_g, 0]
|
|
1334
|
+
w_v = param_pairs[best_g, 1]
|
|
1335
|
+
model_v = amp_v[:, None] * basis_best + tvb_v[:, None] * tvb_fit[None, :] + bg_z[:, None]
|
|
1336
|
+
chi2_v = ((d_valid - model_v) ** 2 / np.maximum(model_v, 1.0)).sum(axis=1)
|
|
1337
|
+
chi2_v /= distribution_dof(n_fit, 1, True)
|
|
1338
|
+
chi2_cal_v = calibrated_chi2(d_valid, model_v, axis=1)
|
|
1339
|
+
for k, fi in enumerate(valid_idx):
|
|
1340
|
+
if amp_v[k] <= 0:
|
|
1341
|
+
continue
|
|
1342
|
+
yy, xx = divmod(int(fi), nx)
|
|
1343
|
+
maps['tau_center_1'][yy, xx] = tau_v[k] * 1e9
|
|
1344
|
+
maps['width_1'][yy, xx] = w_v[k] * 1e9
|
|
1345
|
+
maps['alpha_1'][yy, xx] = amp_v[k]
|
|
1346
|
+
maps['frac_1'][yy, xx] = 1.0
|
|
1347
|
+
maps['tau_mean_amp'][yy, xx] = tau_v[k] * 1e9
|
|
1348
|
+
maps['tau_mean_int'][yy, xx] = (tau_v[k] + w_v[k] ** 2 / max(tau_v[k], 1e-15)) * 1e9
|
|
1349
|
+
maps['chi2_r'][yy, xx] = chi2_v[k]
|
|
1350
|
+
maps['calibrated_chi2_r'][yy, xx] = chi2_cal_v[k]
|
|
1351
|
+
maps['tvb_scale'][yy, xx] = tvb_v[k]
|
|
1352
|
+
return maps
|
|
1353
|
+
t0 = time.time()
|
|
1354
|
+
for row_i in range(ny):
|
|
1355
|
+
if progress_callback is not None:
|
|
1356
|
+
progress_callback(row_i, ny)
|
|
1357
|
+
xi_range = range(nx)
|
|
1358
|
+
for xi in xi_range:
|
|
1359
|
+
flat_idx = row_i * nx + xi
|
|
1360
|
+
if ph_counts[flat_idx] < min_photons:
|
|
1361
|
+
continue
|
|
1362
|
+
d = flat[flat_idx].astype(np.float64)
|
|
1363
|
+
d_fit = d[fit_idx]
|
|
1364
|
+
bg = estimate_bg(d, int(np.argmax(d)))
|
|
1365
|
+
dc = np.maximum(d_fit - bg, 0.0)
|
|
1366
|
+
bd = basis_fit.astype(np.float64) @ dc
|
|
1367
|
+
amps_g = np.maximum(bd / bb_grid.astype(np.float64), 0.0)
|
|
1368
|
+
costs = (dc ** 2).sum() - np.maximum(bd, 0.0) ** 2 / bb_grid.astype(np.float64)
|
|
1369
|
+
best = int(np.argmin(costs))
|
|
1370
|
+
tau_c_px = float(param_pairs[best, 0])
|
|
1371
|
+
w_px = float(param_pairs[best, 1])
|
|
1372
|
+
amp_px = float(amps_g[best])
|
|
1373
|
+
tau_amp_ns = tau_c_px * 1e9
|
|
1374
|
+
tau_int_ns = (tau_c_px + (w_px ** 2) / max(tau_c_px, 1e-15)) * 1e9
|
|
1375
|
+
model_px = amp_px * basis_fit[best].astype(np.float64) + bg
|
|
1376
|
+
resid_px = d_fit - model_px
|
|
1377
|
+
chi2_px = float(np.sum(resid_px ** 2 / np.maximum(model_px, 1.0)))
|
|
1378
|
+
maps['tau_center_1'][row_i, xi] = tau_c_px * 1e9
|
|
1379
|
+
maps['width_1'][row_i, xi] = w_px * 1e9
|
|
1380
|
+
maps['alpha_1'][row_i, xi] = amp_px
|
|
1381
|
+
maps['frac_1'][row_i, xi] = 1.0
|
|
1382
|
+
maps['tau_mean_amp'][row_i, xi] = tau_amp_ns
|
|
1383
|
+
maps['tau_mean_int'][row_i, xi] = tau_int_ns
|
|
1384
|
+
maps['chi2_r'][row_i, xi] = chi2_px / distribution_dof(n_fit, 1, False)
|
|
1385
|
+
maps['calibrated_chi2_r'][row_i, xi] = calibrated_chi2(d_fit, model_px)
|
|
1386
|
+
else:
|
|
1387
|
+
from ..FLIM.fit_tools import estimate_bg as _ebg
|
|
1388
|
+
from concurrent.futures import ThreadPoolExecutor
|
|
1389
|
+
import multiprocessing
|
|
1390
|
+
flat = stack.reshape(ny * nx, n_bins).astype(np.float32)
|
|
1391
|
+
ph_counts = flat.sum(axis=1)
|
|
1392
|
+
tau_lo_s = max(tau_centers_g.min() / 5.0, 1e-12)
|
|
1393
|
+
tau_hi_s = tau_centers_g.max() * 5.0
|
|
1394
|
+
w_lo_s = widths_g.min() / 5.0
|
|
1395
|
+
w_hi_s = widths_g.max() * 5.0
|
|
1396
|
+
fit_stack_max = float(stack[..., fit_idx].max())
|
|
1397
|
+
amp_hi = fit_stack_max * 10.0
|
|
1398
|
+
lo_px = np.array([tau_lo_s] * n_components + [w_lo_s] * n_components + [0.0] * n_components)
|
|
1399
|
+
hi_px = np.array([tau_hi_s] * n_components + [w_hi_s] * n_components + [amp_hi] * n_components)
|
|
1400
|
+
p0_px = np.concatenate([tau_centers_g, widths_g,
|
|
1401
|
+
np.full(n_components, fit_stack_max / n_components)])
|
|
1402
|
+
def _fit_pixel_dist(flat_idx):
|
|
1403
|
+
d = flat[flat_idx].astype(np.float64)
|
|
1404
|
+
d_fit = d[fit_idx]
|
|
1405
|
+
bg = _ebg(d, int(np.argmax(d)))
|
|
1406
|
+
wt_fit = np.sqrt(np.maximum(d_fit, 1.0))
|
|
1407
|
+
def _resid(p):
|
|
1408
|
+
full_p = np.concatenate([p, [shift]])
|
|
1409
|
+
if fit_sigma:
|
|
1410
|
+
full_p = np.concatenate([full_p, [sigma]])
|
|
1411
|
+
if fit_bg:
|
|
1412
|
+
full_p = np.concatenate([full_p, [bg]])
|
|
1413
|
+
m = dist_reconvolution_model(
|
|
1414
|
+
full_p, tcspc_res, n_bins, irf_prompt,
|
|
1415
|
+
n_components, dist_type, bg, False, False)
|
|
1416
|
+
return (m[fit_idx] - d_fit) / wt_fit
|
|
1417
|
+
try:
|
|
1418
|
+
res = least_squares(_resid, p0_px, bounds=(lo_px, hi_px),
|
|
1419
|
+
method='trf', max_nfev=500,
|
|
1420
|
+
ftol=1e-8, xtol=1e-8, gtol=1e-8)
|
|
1421
|
+
return res.x
|
|
1422
|
+
except Exception:
|
|
1423
|
+
return None
|
|
1424
|
+
n_workers = min(ny * nx, max(1, multiprocessing.cpu_count()))
|
|
1425
|
+
valid_flat = [i for i in range(ny * nx) if ph_counts[i] >= min_photons]
|
|
1426
|
+
n_valid = len(valid_flat)
|
|
1427
|
+
t0 = time.time()
|
|
1428
|
+
with ThreadPoolExecutor(max_workers=n_workers) as pool:
|
|
1429
|
+
futures = [pool.submit(_fit_pixel_dist, i) for i in valid_flat]
|
|
1430
|
+
solutions = []
|
|
1431
|
+
for k, f in enumerate(futures):
|
|
1432
|
+
solutions.append(f.result())
|
|
1433
|
+
if progress_callback is not None and k % max(1, n_valid // 200) == 0:
|
|
1434
|
+
progress_callback(k, n_valid)
|
|
1435
|
+
for sol, flat_idx in zip(solutions, valid_flat):
|
|
1436
|
+
if sol is None:
|
|
1437
|
+
continue
|
|
1438
|
+
yi, xi = divmod(flat_idx, nx)
|
|
1439
|
+
tau_cs = sol[:n_components]
|
|
1440
|
+
ws = sol[n_components:2 * n_components]
|
|
1441
|
+
amp_s = sol[2 * n_components:]
|
|
1442
|
+
amp_sum = max(amp_s.sum(), 1e-30)
|
|
1443
|
+
fracs = amp_s / amp_sum
|
|
1444
|
+
tau_amp_ns = float(np.dot(fracs, tau_cs)) * 1e9
|
|
1445
|
+
tau_int_ns = float(np.dot(amp_s, tau_cs ** 2) / max(np.dot(amp_s, tau_cs), 1e-30)) * 1e9
|
|
1446
|
+
maps['tau_mean_amp'][yi, xi] = tau_amp_ns
|
|
1447
|
+
maps['tau_mean_int'][yi, xi] = tau_int_ns
|
|
1448
|
+
d = flat[flat_idx].astype(np.float64)
|
|
1449
|
+
d_fit = d[fit_idx]
|
|
1450
|
+
bg = _ebg(d, int(np.argmax(d)))
|
|
1451
|
+
full_p = np.concatenate([sol, [shift]])
|
|
1452
|
+
if fit_sigma:
|
|
1453
|
+
full_p = np.concatenate([full_p, [sigma]])
|
|
1454
|
+
if fit_bg:
|
|
1455
|
+
full_p = np.concatenate([full_p, [bg]])
|
|
1456
|
+
model_px = dist_reconvolution_model(
|
|
1457
|
+
full_p, tcspc_res, n_bins, irf_prompt,
|
|
1458
|
+
n_components, dist_type, bg, False, False)
|
|
1459
|
+
model_fit = model_px[fit_idx]
|
|
1460
|
+
resid_fit = d_fit - model_fit
|
|
1461
|
+
chi2_px = float(np.sum(resid_fit ** 2 / np.maximum(model_fit, 1.0)))
|
|
1462
|
+
maps['chi2_r'][yi, xi] = chi2_px / distribution_dof(
|
|
1463
|
+
n_fit, n_components, False)
|
|
1464
|
+
maps['calibrated_chi2_r'][yi, xi] = calibrated_chi2(
|
|
1465
|
+
d_fit, model_fit)
|
|
1466
|
+
for i in range(n_components):
|
|
1467
|
+
maps[f"tau_center_{i+1}"][yi, xi] = tau_cs[i] * 1e9
|
|
1468
|
+
maps[f"width_{i+1}"][yi, xi] = ws[i] * 1e9
|
|
1469
|
+
maps[f"alpha_{i+1}"][yi, xi] = amp_s[i]
|
|
1470
|
+
maps[f"frac_{i+1}"][yi, xi] = fracs[i]
|
|
1471
|
+
return maps
|