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

Browse Source 
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:
unzhakov
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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tests/physics/test_cw_extractor.py
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# tests/test_cw_extractor.py — Tests for C(W) shape factor extraction
"""
Why test this?
--------------
The C(W) extractor is the core scientific tool for extracting the shape factor
from measured beta spectra. It must correctly handle:
1. Energy unit conversions (keV ↔ m_e units)
2. Theoretical factor computation (Fermi, screening, radiative, etc.)
3. Normalization of extracted C(W)
4. Kurie plot endpoint determination
5. g_V, g_A extraction from C(W) data
We test with synthetic data where the true answer is known, so we can verify
the extraction recovers the correct values.
"""
import numpy as np
import pytest
from beta_spectrum import (
BetaSpectrum,
CWExtractor,
CWExtractionResult,
GVAExtractionResult,
SpectrumConfig,
T_to_W,
W_to_T,
)
class TestCWExtractionBasic:
"""Basic C(W) extraction tests."""
def _make_synthetic_data(
self,
endpoint_keV: float = 294.0,
n_points: int = 100,
seed: int = 42,
):
"""Create synthetic beta spectrum with C(W) = 1 (allowed decay)."""
np.random.seed(seed)
# Energy grid
energies_keV = np.linspace(5, endpoint_keV * 0.98, n_points)
# Build theoretical spectrum with C(W) = 1
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=endpoint_keV / 1000.0,
transition_type="F1",
use_screening=True,
use_exchange=True,
use_finite_size=True,
use_radiative=True,
)
spectrum = BetaSpectrum.from_config(config)
W, E_MeV = spectrum.get_energy_grid(config)
# Interpolate to our energy grid
from scipy.interpolate import interp1d
flux_interp = interp1d(
E_MeV * 1000, spectrum(W), kind="linear", fill_value=0.0, bounds_error=False
)
flux_theory = flux_interp(energies_keV)
# Add noise (Poisson-like)
noise_std = np.sqrt(np.maximum(flux_theory, 1e-10))
flux = flux_theory + np.random.normal(0, noise_std, len(flux_theory))
flux = np.maximum(flux, 0.0) # Flux cannot be negative
flux_errors = np.sqrt(np.maximum(flux, 1e-10))
return energies_keV, flux, flux_errors, config
def test_CW_extraction_allowed_decay(self):
"""For allowed decay (C(W)=1), extracted C(W) should be ~1."""
energies_keV, flux, flux_errors, config = self._make_synthetic_data()
extractor = CWExtractor(config, flux, energies_keV, flux_errors)
result = extractor.extract_CW(endpoint_keV=294.0)
# C(W) should be close to 1 in mid-energy region
mid_mask = (energies_keV > 50) & (energies_keV < 200)
if np.any(mid_mask):
avg_cw = np.mean(result.cw_values[mid_mask])
assert (
abs(avg_cw - 1.0) < 0.3
), f"Allowed decay C(W) should be ~1, got {avg_cw}"
def test_CW_extraction_preserves_endpoint(self):
"""Extracted C(W) should report correct endpoint."""
energies_keV, flux, flux_errors, config = self._make_synthetic_data()
extractor = CWExtractor(config, flux, energies_keV, flux_errors)
result = extractor.extract_CW(endpoint_keV=294.0)
assert (
abs(result.endpoint_keV - 294.0) < 1.0
), f"Endpoint should be ~294 keV, got {result.endpoint_keV}"
def test_CW_extraction_errors_positive(self):
"""C(W) uncertainties should be positive."""
energies_keV, flux, flux_errors, config = self._make_synthetic_data()
extractor = CWExtractor(config, flux, energies_keV, flux_errors)
result = extractor.extract_CW(endpoint_keV=294.0)
assert np.all(result.cw_errors > 0), "All errors should be positive"
def test_CW_extraction_clipped(self):
"""C(W) values should be clipped to [0.01, 10.0]."""
energies_keV, flux, flux_errors, config = self._make_synthetic_data()
extractor = CWExtractor(config, flux, energies_keV, flux_errors)
result = extractor.extract_CW(endpoint_keV=294.0)
assert np.all(result.cw_values >= 0.01), "C(W) should be >= 0.01"
assert np.all(result.cw_values <= 10.0), "C(W) should be <= 10.0"
class TestCWParametrization:
"""Test C(W) parametrization fitting."""
def _make_CW_data(
self,
endpoint_keV: float = 294.0,
n_points: int = 60,
seed: int = 42,
):
"""Create synthetic C(W) data with known parametrization."""
np.random.seed(seed)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=endpoint_keV / 1000.0,
transition_type="F1",
use_screening=True,
use_exchange=True,
use_finite_size=True,
use_radiative=True,
)
# Generate C(W) values with known form
W = np.linspace(T_to_W(0.05), T_to_W(endpoint_keV * 0.95), n_points)
E_keV = np.array([W_to_T(w) for w in W])
# Linear C(W): C(W) = 1.0 + 0.5*(W-1)
true_a0, true_a1 = 1.0, 0.5
cw_true = true_a0 + true_a1 * (W - 1.0)
cw_noise = cw_true + np.random.normal(0, 0.05, len(W))
# C(W) = flux / (C0 * phase_space * Fermi * corrections * (W0-W)^2)
# So: flux = C(W) * C0 * phase_space * Fermi * corrections * (W0-W)^2
p = np.sqrt(np.maximum(W**2 - 1.0, 0.0))
from beta_spectrum.components.fermi import FermiFunction
F = FermiFunction(Z=config.Z_parent, A=config.A_number)(W)
C0 = 1.0 # Normalization
endpoint_factor = (T_to_W(endpoint_keV / 1000.0) - W) ** 2
flux_synthetic = cw_noise * C0 * p * W * F * endpoint_factor
flux_synthetic = np.maximum(flux_synthetic, 0)
flux_errors = np.sqrt(np.maximum(flux_synthetic, 1.0))
return E_keV, flux_synthetic, flux_errors, config, true_a0, true_a1
def test_constant_parametrization(self):
"""Fit C(W) = a₀ with known constant value."""
np.random.seed(42)
energies_keV = np.linspace(10, 250, 50)
W = np.array([T_to_W(e / 1000.0) for e in energies_keV])
cw_true = np.full_like(W, 1.0)
cw = cw_true + np.random.normal(0, 0.05, len(W))
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F1",
use_screening=True,
use_exchange=True,
use_finite_size=True,
use_radiative=True,
)
extractor = CWExtractor(
config, cw, energies_keV, flux_errors=np.ones_like(cw) * 0.05
)
cw_result = CWExtractionResult(
energies_W=W.copy(),
energies_keV=energies_keV.copy(),
cw_values=cw.copy(),
cw_errors=np.ones_like(cw) * 0.05,
flux=cw.copy(),
flux_errors=np.ones_like(cw) * 0.05,
endpoint_W=T_to_W(0.294),
endpoint_keV=294.0,
)
result = extractor.fit_CW_parametrization(cw_result, parametrization="constant")
assert (
abs(result.parameters[0] - 1.0) < 0.1
), f"Constant C(W) should be ~1, got {result.parameters[0]}"
def test_linear_parametrization(self):
"""Fit C(W) = a₀ + a₁·(W-1) with known coefficients."""
np.random.seed(42)
energies_keV = np.linspace(10, 250, 50)
W = np.array([T_to_W(e / 1000.0) for e in energies_keV])
true_a0, true_a1 = 1.0, 0.5
cw = true_a0 + true_a1 * (W - 1.0) + np.random.normal(0, 0.05, len(W))
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F1",
use_screening=True,
use_exchange=True,
use_finite_size=True,
use_radiative=True,
)
extractor = CWExtractor(
config, cw, energies_keV, flux_errors=np.ones_like(cw) * 0.05
)
cw_result = CWExtractionResult(
energies_W=W.copy(),
energies_keV=energies_keV.copy(),
cw_values=cw.copy(),
cw_errors=np.ones_like(cw) * 0.05,
flux=cw.copy(),
flux_errors=np.ones_like(cw) * 0.05,
endpoint_W=T_to_W(0.294),
endpoint_keV=294.0,
)
result = extractor.fit_CW_parametrization(cw_result, parametrization="linear")
assert (
abs(result.parameters[0] - true_a0) < 0.15
), f"a₀: expected {true_a0}, got {result.parameters[0]}"
assert (
abs(result.parameters[1] - true_a1) < 0.5
), f"a₁: expected {true_a1}, got {result.parameters[1]}"
def test_quadratic_parametrization(self):
"""Fit C(W) = a₀ + a₁·(W-1) + a₂·(W-1)² with known coefficients."""
np.random.seed(42)
energies_keV = np.linspace(10, 250, 60)
W = np.array([T_to_W(e / 1000.0) for e in energies_keV])
true_a0, true_a1, true_a2 = 1.0, 0.3, -0.1
cw = true_a0 + true_a1 * (W - 1.0) + true_a2 * (W - 1.0) ** 2
cw += np.random.normal(0, 0.03, len(W))
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F1",
use_screening=True,
use_exchange=True,
use_finite_size=True,
use_radiative=True,
)
extractor = CWExtractor(
config, cw, energies_keV, flux_errors=np.ones_like(cw) * 0.03
)
cw_result = CWExtractionResult(
energies_W=W.copy(),
energies_keV=energies_keV.copy(),
cw_values=cw.copy(),
cw_errors=np.ones_like(cw) * 0.03,
flux=cw.copy(),
flux_errors=np.ones_like(cw) * 0.03,
endpoint_W=T_to_W(0.294),
endpoint_keV=294.0,
)
result = extractor.fit_CW_parametrization(
cw_result, parametrization="quadratic"
)
assert abs(result.parameters[0] - true_a0) < 0.15
assert abs(result.parameters[1] - true_a1) < 0.5
assert abs(result.parameters[2] - true_a2) < 0.5
def test_invalid_parametrization(self):
"""Invalid parametrization should raise ValueError."""
np.random.seed(42)
energies_keV = np.linspace(10, 250, 30)
W = np.array([T_to_W(e / 1000.0) for e in energies_keV])
cw = np.ones_like(W)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
)
extractor = CWExtractor(config, cw, energies_keV)
cw_result = CWExtractionResult(
energies_W=W.copy(),
energies_keV=energies_keV.copy(),
cw_values=cw.copy(),
cw_errors=np.ones_like(cw) * 0.05,
flux=cw.copy(),
flux_errors=np.ones_like(cw) * 0.05,
endpoint_W=T_to_W(0.294),
endpoint_keV=294.0,
)
with pytest.raises(ValueError, match="Unknown parametrization"):
extractor.fit_CW_parametrization(cw_result, parametrization="invalid")
class TestGVAExtraction:
"""Test g_V, g_A extraction from C(W) data."""
def test_gV_gA_pure_fermi(self):
"""For pure Fermi transition, g_A ≈ 0."""
np.random.seed(42)
energies_keV = np.linspace(10, 250, 50)
W = np.array([T_to_W(e / 1000.0) for e in energies_keV])
# Pure Fermi: C(W) = g_V² (constant)
true_gV = 0.5
cw = true_gV**2 + np.random.normal(0, 0.02, len(W))
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F1",
use_screening=True,
use_exchange=True,
use_finite_size=True,
use_radiative=True,
)
extractor = CWExtractor(
config, cw, energies_keV, flux_errors=np.ones_like(cw) * 0.02
)
cw_result = CWExtractionResult(
energies_W=W.copy(),
energies_keV=energies_keV.copy(),
cw_values=cw.copy(),
cw_errors=np.ones_like(cw) * 0.02,
flux=cw.copy(),
flux_errors=np.ones_like(cw) * 0.02,
endpoint_W=T_to_W(0.294),
endpoint_keV=294.0,
)
result = extractor.fit_gV_gA(cw_result, M_F=1.0, M_GT=0.0)
assert isinstance(result, GVAExtractionResult)
assert (
abs(result.g_V - true_gV) < 0.15
), f"g_V: expected {true_gV}, got {result.g_V}"
def test_gV_gA_pure_gt(self):
"""For pure Gamow-Teller, g_V ≈ 0."""
np.random.seed(42)
energies_keV = np.linspace(10, 250, 50)
W = np.array([T_to_W(e / 1000.0) for e in energies_keV])
# Pure GT: C(W) = g_A² (constant)
true_gA = 0.8
cw = true_gA**2 + np.random.normal(0, 0.02, len(W))
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F1",
use_screening=True,
use_exchange=True,
use_finite_size=True,
use_radiative=True,
)
extractor = CWExtractor(
config, cw, energies_keV, flux_errors=np.ones_like(cw) * 0.02
)
cw_result = CWExtractionResult(
energies_W=W.copy(),
energies_keV=energies_keV.copy(),
cw_values=cw.copy(),
cw_errors=np.ones_like(cw) * 0.02,
flux=cw.copy(),
flux_errors=np.ones_like(cw) * 0.02,
endpoint_W=T_to_W(0.294),
endpoint_keV=294.0,
)
result = extractor.fit_gV_gA(cw_result, M_F=0.0, M_GT=1.0)
assert isinstance(result, GVAExtractionResult)
assert (
abs(result.g_A - true_gA) < 0.15
), f"g_A: expected {true_gA}, got {result.g_A}"
def test_gV_gA_mixed_transition(self):
"""For mixed transition, extract both g_V and g_A."""
np.random.seed(42)
energies_keV = np.linspace(10, 250, 50)
W = np.array([T_to_W(e / 1000.0) for e in energies_keV])
# Mixed: C(W) = g_V² + g_A² (constant for simplicity)
true_gV, true_gA = 0.4, 0.6
cw = true_gV**2 + true_gA**2 + np.random.normal(0, 0.02, len(W))
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F1",
use_screening=True,
use_exchange=True,
use_finite_size=True,
use_radiative=True,
)
extractor = CWExtractor(
config, cw, energies_keV, flux_errors=np.ones_like(cw) * 0.02
)
cw_result = CWExtractionResult(
energies_W=W.copy(),
energies_keV=energies_keV.copy(),
cw_values=cw.copy(),
cw_errors=np.ones_like(cw) * 0.02,
flux=cw.copy(),
flux_errors=np.ones_like(cw) * 0.02,
endpoint_W=T_to_W(0.294),
endpoint_keV=294.0,
)
result = extractor.fit_gV_gA(cw_result, M_F=1.0, M_GT=1.0)
assert isinstance(result, GVAExtractionResult)
# Check that sum of squares is correct
reconstructed = result.g_V**2 + result.g_A**2
expected = true_gV**2 + true_gA**2
assert (
abs(reconstructed - expected) < 0.15
), f"g_V²+g_A²: expected {expected}, got {reconstructed}"
def test_gV_gA_summary(self):
"""summary() should return a non-empty string with key info."""
np.random.seed(42)
energies_keV = np.linspace(10, 250, 50)
W = np.array([T_to_W(e / 1000.0) for e in energies_keV])
cw = np.full_like(W, 0.5)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
)
extractor = CWExtractor(config, cw, energies_keV)
cw_result = CWExtractionResult(
energies_W=W.copy(),
energies_keV=energies_keV.copy(),
cw_values=cw.copy(),
cw_errors=np.ones_like(cw) * 0.02,
flux=cw.copy(),
flux_errors=np.ones_like(cw) * 0.02,
endpoint_W=T_to_W(0.294),
endpoint_keV=294.0,
)
result = extractor.fit_gV_gA(cw_result, M_F=1.0, M_GT=0.0)
summary = result.summary()
assert "g_V" in summary
assert "g_A" in summary
assert "χ²" in summary
assert "p-value" in summary
class TestKurieAnalysis:
"""Test Kurie plot analysis."""
def test_kurie_analysis_allowed_decay(self):
"""Kurie analysis on allowed decay should produce reasonable C(W)."""
np.random.seed(42)
energies_keV = np.linspace(5, 280, 80)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
transition_type="F1",
use_screening=True,
use_exchange=True,
use_finite_size=True,
use_radiative=True,
)
spectrum = BetaSpectrum.from_config(config)
W, E_MeV = spectrum.get_energy_grid(config)
flux_theory = spectrum(W)
# Interpolate to our energy grid
from scipy.interpolate import interp1d
flux_interp = interp1d(
E_MeV * 1000, flux_theory, kind="linear", fill_value=0.0, bounds_error=False
)
flux = flux_interp(energies_keV)
# Add noise
flux += np.random.normal(0, 0.02 * np.max(flux), len(flux))
extractor = CWExtractor(config, flux, energies_keV)
cw_result, fit_result = extractor.kurie_analysis(endpoint_keV=294.0)
assert isinstance(cw_result, CWExtractionResult)
assert cw_result.fit_result is not None
assert np.all(cw_result.cw_values > 0)
def test_kurie_plot_values(self):
"""Kurie plot should produce valid values."""
np.random.seed(42)
energies_keV = np.linspace(10, 250, 50)
W = np.array([T_to_W(e / 1000.0) for e in energies_keV])
cw = np.ones_like(W) * 1.0
cw_result = CWExtractionResult(
energies_W=W.copy(),
energies_keV=energies_keV.copy(),
cw_values=cw.copy(),
cw_errors=np.ones_like(cw) * 0.05,
flux=cw.copy(),
flux_errors=np.ones_like(cw) * 0.05,
endpoint_W=T_to_W(0.294),
endpoint_keV=294.0,
)
E_plot, kurie = cw_result.kurie_plot()
assert len(E_plot) == len(energies_keV)
assert len(kurie) == len(energies_keV)
assert np.all(kurie >= 0), "Kurie values should be non-negative"
class TestEdgeCases:
"""Test edge cases and error handling."""
def test_not_enough_points_for_fit(self):
"""Fitting with too few points should raise ValueError."""
np.random.seed(42)
energies_keV = np.array([10.0, 20.0, 30.0])
W = np.array([T_to_W(e / 1000.0) for e in energies_keV])
cw = np.ones_like(W)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
)
extractor = CWExtractor(config, cw, energies_keV)
cw_result = CWExtractionResult(
energies_W=W.copy(),
energies_keV=energies_keV.copy(),
cw_values=cw.copy(),
cw_errors=np.ones_like(cw) * 0.05,
flux=cw.copy(),
flux_errors=np.ones_like(cw) * 0.05,
endpoint_W=T_to_W(0.294),
endpoint_keV=294.0,
)
with pytest.raises(ValueError, match="Not enough data points"):
extractor.fit_CW_parametrization(cw_result, parametrization="quadratic")
def test_not_enough_points_for_gV_gA(self):
"""g_V/g_A fit with too few points should raise ValueError."""
np.random.seed(42)
energies_keV = np.array([10.0, 20.0, 30.0])
W = np.array([T_to_W(e / 1000.0) for e in energies_keV])
cw = np.ones_like(W)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
)
extractor = CWExtractor(config, cw, energies_keV)
cw_result = CWExtractionResult(
energies_W=W.copy(),
energies_keV=energies_keV.copy(),
cw_values=cw.copy(),
cw_errors=np.ones_like(cw) * 0.05,
flux=cw.copy(),
flux_errors=np.ones_like(cw) * 0.05,
endpoint_W=T_to_W(0.294),
endpoint_keV=294.0,
)
with pytest.raises(ValueError, match="Not enough data points"):
extractor.fit_gV_gA(cw_result, M_F=1.0, M_GT=1.0)
def test_default_uncertainties(self):
"""Default uncertainties should be sqrt(flux)."""
np.random.seed(42)
energies_keV = np.linspace(10, 250, 30)
flux = np.array(
[
100.0,
200.0,
150.0,
180.0,
120.0,
90.0,
80.0,
70.0,
60.0,
50.0,
45.0,
40.0,
35.0,
30.0,
25.0,
20.0,
18.0,
15.0,
12.0,
10.0,
8.0,
7.0,
6.0,
5.0,
4.0,
3.0,
2.0,
1.5,
1.0,
0.5,
]
)
config = SpectrumConfig(
Z_parent=43,
Z_daughter=44,
A_number=99,
endpoint_MeV=0.294,
)
extractor = CWExtractor(config, flux, energies_keV)
expected_unc = np.sqrt(np.maximum(flux, 1.0))
np.testing.assert_allclose(extractor.flux_errors, expected_unc)
tests/physics/test_fitter.py
+1 -1
View File
@@ -18,7 +18,7 @@ We test:
import numpy as np
from beta_spectrum import CurveFitter, FitConfig
from fitter.fit_engine import CurveFitter, FitConfig
class TestBasicFitting:
tests/physics/test_multi_branch.py
+1 -1
View File
@@ -30,10 +30,10 @@ import pytest
from beta_spectrum import (
BetaSpectrum,
BetaSpectrumAnalyzer,
BranchConfig,
SpectrumConfig,
)
from beta_spectrum.visualize import BetaSpectrumAnalyzer
from beta_spectrum.utils import T_to_W
# ---------------------------------------------------------------------------