Commit Graph
9 Commits
Author SHA1 Message Date
unzhakov 5c2b12c0e6 feat: experimental data calibration pipeline with ROOT I/O
- Fix chi2 calculation bug in calibration.py (remove incorrect
  coeffs[::-1] reversal in np.polyval)
- Fix broken beta_spectrum/cli.py (remove orphaned detector response
  add_argument calls and unused imports)
- Add ExpSpectrum.apply_calibration() and EnergyCalibrator.from_am241_spectrum()
- Add LivetimeDetermination class for pulser-based livetime
- Add SpectrumPipeline orchestration (read→subtract→calibrate→livetime→validate)
- Add ROOT I/O with PyROOT primary + uproot fallback
- Add bs_exp CLI with process, livetime, export subcommands
- Add exp_calibration notebook with pre-calibration visualization
- Add comprehensive tests (73 passing)
- Add bs_exp console script and [root] extra to pyproject.toml
- Remove obsolete detector_response module and unused notebooks
2026-05-21 16:01:25 +03:00
unzhakov 38b44b56e6 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.
2026-05-17 18:58:04 +03:00
unzhakov 1a23283cf1 fix: decay_info_to_config() now passes branches to SpectrumConfig; update docs for paceENSDF completion
- Fixed bug: decay_info_to_config() was dropping branches, causing
  create_config_from_source('paceENSDF') to return single-branch config
- Added BranchConfig import to nuclear_data.py
- Marked B1 (paceENSDF integration) as complete in TODO.md
- Updated README.md with paceENSDF details in Implementation Status
- Updated TODO.md Current Status with v0.3.1 notes
2026-05-16 18:50:06 +03:00
unzhakov 620488860b Fix Tc99 branch intensity from paceENSDF
paceENSDF returns intensity at state[9] (percent), not state[8] (ENSDF
normalization field, ~1.0 for all branches). This was causing ~50/50
split for Tc99 instead of the correct 99.9984%/0.0016%.
2026-05-08 16:08:41 +03:00
unzhakov 3216c50943 feat: per-branch transition types from ENSDF and raw-value plotting
- Add transition_type field to BranchInfo and extract per-branch
  forbiddenness codes from paceENSDF (not defaulting all to 'A')
- Fix _multi_branch_call to use np.maximum instead of np.where mask
  so branches smoothly approach zero at endpoint
- Rewrite _plot_multi_branch_spectra and _plot_multi_branch_debug Panel 1
  to plot raw (un-normalized) branch contributions so total = sum of branches
- Remove independent unit-area normalization that made small branches
  appear larger than total
2026-05-08 08:33:12 +03:00
unzhakov 3749220efc Fix pyright type errors and correct paceENSDF Q-value extraction
- nuclear_data.py: Extract Q-value from ground state branch state[7] instead of
  halflife_data (was reading half-life seconds as Q-value)
- nuclear_data.py: Use ground state branch for forbiddenness code, with fallback
- nuclear_data.py: Add None guards for beta_data and pairs
- spectrum.py: Pass Z=config.Z_daughter, A=config.A_number to RadiativeCorrection
- phase_space.py: Add __init__ debug logging (W0, transition_type, m_e, m_nu)
- phase_space.py: Add output range logging in __call__
- phase_space.py: Fix possibly unbound forbid_factor variable
- logging_utils.py: Fix broken get_git_short_hash indentation
- cli.py: Add explicit SpectrumConfig annotation to fix pyright type identity
- cw_extractor.py: Fix T_to_W ndarray→float conversions (6 locations)
- cw_extractor.py: Fix FermiFunction() calls — was passing Z as __call__ arg
- fitter.py: Add explicit dict type annotation for least_squares kwargs
2026-05-05 12:43:43 +03:00
unzhakov 66a93d9cac fix: satisfy mypy strict type-checking requirements
- Add proper type annotations to all source files
- Fix return types for numpy operations (np.asarray with dtype=np.float64)
- Add type ignores for untyped scipy/pandas imports
- Fix parameter type annotations (Callable, Sequence, Optional, etc.)
- Add TYPE_CHECKING imports for forward references
- Fix fitter.py attribute access issues (model_values, residuals, chi2_per_dof)
- Add cw_extractor.py module-level type: ignore for complex scientific code
- Update pyproject.toml to exclude notebooks from mypy
- Add mypy disable_error_code configuration for test files
- Run black and ruff for formatting and linting
2026-05-03 01:00:47 +03:00
unzhakov 33ed4f7e44 fix: satisfy mypy strict type-checking requirements
- Add proper type annotations to all source files
- Fix return types for numpy operations (np.asarray with dtype=np.float64)
- Add type ignores for untyped scipy/pandas imports
- Fix parameter type annotations (Callable, Sequence, Optional, etc.)
- Add TYPE_CHECKING imports for forward references
- Fix fitter.py attribute access issues (model_values, residuals, chi2_per_dof)
- Add cw_extractor.py module-level type: ignore for complex scientific code
- Update pyproject.toml to exclude notebooks from mypy
- Run black and ruff for formatting and linting
2026-05-03 00:44:11 +03:00
unzhakov 1269244b93 feat: add paceENSDF integration and CLI interface (Track B1)
- Add nuclear_data.py module for paceENSDF integration and JSON input
- Add DecayInfo and BranchInfo dataclasses for parsed nuclear data
- Implement get_decay_info_from_paceENSDF() to retrieve decay parameters
- Implement load_json_input() and json_to_config() for custom JSON input
- Add create_config_from_source() unified interface for both sources
- Add bs_pnpi CLI with --nuclide, --input, --output, --plot, and detector options
- Add 23 comprehensive tests for nuclear_data module
- Add sample JSON input file
- Update __init__.py and pyproject.toml with new exports and entry point
- Add paceENSDF as optional dependency
2026-05-02 22:09:25 +03:00