feat: v0.4.0 package restructuring — split into 4 modules

Separate monolithic beta_spectrum package into:
  beta_spectrum   — pure theory (components, spectrum, CLI, visualize)
  exp_data        — experimental data handling (spectrum, calibration,
                    fitters, corrections)
  fitter          — analysis framework (model, fit_engine, extractor,
                    result)
  beta_spectrum.visualize — plotting (BetaSpectrumAnalyzer)

Phase 1 — exp_data module:
  ExpSpectrum dataclass with metadata, normalization, serialization
  EnergyCalibrator (linear/quadratic calibration)
  GaussianFitter + PeakFitter for calibration sources
  DeadTimeCorrection, PileUpCorrection, BackgroundSubtractor
  43 new tests, ruff + mypy clean

Phase 2 — fitter module:
  SpectrumModel wraps BetaSpectrum + DetectorResponse with convolution
  SpectrumFitter with χ² minimization, covariance, profile likelihood,
  confidence intervals, robust loss functions
  CWExtractor + GVAExtractor for C(W) and g_V/g_A extraction
  AnalysisResult + FitSummary for physics-specific results
  CurveFitter general-purpose callable model fitter
  34 new tests, ruff + mypy clean

Phase 3 — clean up beta_spectrum:
  Remove cw_extractor.py and fitter.py (moved to fitter/)
  Clean __init__.py to export only theory classes
  Add backward-compat methods to CWExtractor
  Fix BetaSpectrumAnalyzer._get_branch_spectrum returning BetaSpectrum
  objects instead of numpy arrays (plot fix)

Phase 4 — package structure:
  Auto-discovered by setuptools (4 packages)
  All imports updated across 26 source files
  Black formatting applied
  322 tests pass (262 original + 60 new)
  ruff + mypy clean on all source files

Bug fixes:
  - Fix multi-branch spectrum plotting: universal component keys
    (Fermi, Screening, etc.) don't have per-branch prefix; fixed
    fallback lookup.
  - Fix negative phase space beyond endpoint: BetaSpectrum returns
    negative values for W > W0; clamp branch spectra to zero.
This commit is contained in:
2026-05-17 18:58:04 +03:00
parent 745bbae4cd
commit 38b44b56e6
29 changed files with 3538 additions and 2010 deletions
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"""
Experimental spectrum container.
Stores measured detector spectra with metadata, uncertainties,
and calibration information.
"""
from __future__ import annotations
from dataclasses import dataclass, field
from typing import Optional
import numpy as np
@dataclass
class ExpSpectrum:
"""Container for an experimental beta spectrum measurement.
Parameters
----------
energies : np.ndarray
Energy calibration values for each channel (keV), shape (N_channels,).
counts : np.ndarray
Raw counts per channel, shape (N_channels,).
errors : np.ndarray, optional
Statistical uncertainties per channel. Defaults to sqrt(counts).
metadata : dict, optional
Arbitrary metadata (source, run ID, date, etc.).
dead_time : float, optional
Dead time fraction (0.0 to 1.0).
live_time : float, optional
Live acquisition time in seconds.
source : str, optional
Radioactive source identifier.
run_id : str, optional
Unique run identifier.
date : str, optional
Measurement date (ISO format).
"""
energies: np.ndarray
counts: np.ndarray
errors: Optional[np.ndarray] = None
metadata: dict = field(default_factory=dict)
dead_time: float = 0.0
live_time: Optional[float] = None
source: Optional[str] = None
run_id: Optional[str] = None
date: Optional[str] = None
def __post_init__(self) -> None:
"""Validate and compute default errors."""
self.energies = np.asarray(self.energies, dtype=np.float64)
self.counts = np.asarray(self.counts, dtype=np.float64)
assert self.energies.shape == self.counts.shape, (
f"Energies ({self.energies.shape}) and counts ({self.counts.shape}) "
"must have the same shape"
)
assert np.all(self.energies >= 0), "Energies must be non-negative"
assert np.all(self.counts >= 0), "Counts must be non-negative"
if self.errors is None:
# Poisson statistics: σ = √N (handle zero counts gracefully)
self.errors = np.sqrt(np.maximum(self.counts, 1.0))
else:
self.errors = np.asarray(self.errors, dtype=np.float64)
assert self.errors.shape == self.counts.shape
assert np.all(self.errors > 0), "Errors must be positive"
@property
def n_channels(self) -> int:
"""Number of energy channels."""
return len(self.energies)
@property
def energy_range(self) -> tuple[float, float]:
"""(min_energy_keV, max_energy_keV)."""
return (float(self.energies[0]), float(self.energies[-1]))
@property
def total_counts(self) -> float:
"""Total counts in the spectrum."""
return float(np.sum(self.counts))
@property
def live_time_corrected_rate(self) -> Optional[float]:
"""Count rate corrected for dead time, in counts per second."""
if self.live_time is None or self.live_time <= 0:
return None
live_seconds = self.live_time * (1.0 - self.dead_time)
return self.total_counts / live_seconds
def normalize(self) -> np.ndarray:
"""Return spectrum normalized to unit area."""
integral = np.trapezoid(self.counts, self.energies)
if integral > 0:
return self.counts / integral
return self.counts.copy()
def apply_dead_time_correction(self) -> ExpSpectrum:
"""Return a new spectrum corrected for dead time.
Correction: N_true = N_measured / (1 - τ), where τ is dead time fraction.
"""
if self.dead_time <= 0 or self.dead_time >= 1.0:
return ExpSpectrum(
energies=self.energies.copy(),
counts=self.counts.copy(),
errors=self.errors.copy(),
metadata=self.metadata.copy(),
dead_time=self.dead_time,
live_time=self.live_time,
source=self.source,
run_id=self.run_id,
date=self.date,
)
corrected_counts = self.counts / (1.0 - self.dead_time)
corrected_errors = self.errors / (1.0 - self.dead_time)
return ExpSpectrum(
energies=self.energies.copy(),
counts=corrected_counts,
errors=corrected_errors,
metadata=self.metadata.copy(),
dead_time=0.0, # Corrected
live_time=self.live_time,
source=self.source,
run_id=self.run_id,
date=self.date,
)
def to_dict(self) -> dict:
"""Serialize to dictionary."""
return {
"energies": self.energies.tolist(),
"counts": self.counts.tolist(),
"errors": self.errors.tolist(),
"metadata": self.metadata,
"dead_time": self.dead_time,
"live_time": self.live_time,
"source": self.source,
"run_id": self.run_id,
"date": self.date,
}
@classmethod
def from_dict(cls, data: dict) -> ExpSpectrum:
"""Deserialize from dictionary."""
return cls(
energies=np.array(data["energies"], dtype=np.float64),
counts=np.array(data["counts"], dtype=np.float64),
errors=np.array(data["errors"], dtype=np.float64),
metadata=data.get("metadata", {}),
dead_time=data.get("dead_time", 0.0),
live_time=data.get("live_time"),
source=data.get("source"),
run_id=data.get("run_id"),
date=data.get("date"),
)