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unzhakov 9bf1e1333e refactor: rename visualize module to output module and separate concerns into core, csv_export, and visualization modules 2026-07-07 12:59:11 +03:00
unzhakov 6dc1e3924d feat: add CLI options for custom CSV separator and normalize-to-one branch normalization 2026-07-06 17:32:56 +03:00
unzhakov 1b4d418b5f feat: change CSV output format to use tab delimiters instead of comma delimiters 2026-07-03 18:01:39 +03:00
unzhakov 643e035c54 feat: update CSV headers and plot titles to show active/excluded branches and intensity cutoff exclusions 2026-07-03 17:45:35 +03:00
unzhakov c6aaf3b76a fix: use underscores in branch names for CSV headers in concise mode 2026-07-03 15:21:44 +03:00
unzhakov c2795bf86e fix: use underscores in branch names for CSV headers 2026-07-03 15:10:10 +03:00
unzhakov a7eef7bc20 feat: polish CSV header format with improved metadata and column naming 2026-07-03 14:58:19 +03:00
unzhakov 876e1e3ab8 Add massive neutrino support and improve CSV/CLI output 
- Add neutrino mass parameter to SpectrumConfig and CLI interface
- Update PhaseSpace component to handle neutrino mass effects properly
- Update CSV headers to show basic endpoint and all transition types
- Add --csv-verbosity option to CLI with 'full' and 'concise' options
- Fix comparison plots to properly show linear scale variations
- Add comprehensive tests for neutrino mass functionality
 2026-07-02 10:33:28 +03:00
unzhakov 406fd57bcd chore: add .pi-lens/ to .gitignore 2026-05-26 15:01:17 +03:00
unzhakov 8b0ced4b65 fix: resolve 4 fatal bugs — json_to_config, create_config_from_source, Am-241 constant, CLI positional args 2026-05-26 14:57:35 +03:00
unzhakov 38e97213c5 Remove root output 2026-05-22 18:25:57 +03:00
unzhakov 8599574723 docs: fix stale file references in TODO.md structure and completions 2026-05-22 15:18:17 +03:00
unzhakov 2fedd03d92 fix: bump __version__ to 0.4.0 to match pyproject.toml 2026-05-22 15:18:09 +03:00
unzhakov fd76eff109 docs: add docs_check.py to quality gates, add bs_exp CLI, document pytest markers 2026-05-22 15:18:00 +03:00
unzhakov 5dd9c7977a feat: add docs_check.py for automated documentation consistency checks 2026-05-22 15:17:52 +03:00
unzhakov d8838d19f4 chore: remove obsolete notebooks and add uv.lock 2026-05-22 12:20:36 +03:00
unzhakov ab164fbf98 fix: robust Am-241 calibration with width-constrained peak detection 
- Use find_peaks width=(5,50) to reject noise bumps
- Simplify peak matching: find two strongest peaks with largest
  channel separation, assign min/max known energies
- Require absolute threshold of 400 counts to avoid noise peaks
- Calibration now correctly maps: ch 97→13.0 keV, ch 537→59.54 keV
- Tc-99 endpoint at ch 2750 → 293.6 keV (expected ~294)
- Add .rpiv/ to .gitignore
 2026-05-21 18:21:51 +03:00
unzhakov 8952d0f789 fix: robust Am-241 peak detection for energy calibration 
- Search full spectrum (exclude pulser region) instead of just low-energy
- Include 59.54 keV line in known Am-241 energies
- Brute-force peak-to-energy matching with physical gain constraint
  (3-40 ch/keV) to reject spurious fits
- Fixed find_peaks parameters: height=100, distance=5 for accurate
  peak detection
- Calibration now correctly maps: ch 97→13 keV, ch 134→17.4 keV,
  ch 537→59.6 keV, giving Tc-99 endpoint at ch 2750→291.6 keV
- Add .rpiv/ to .gitignore
 2026-05-21 16:43:10 +03:00
unzhakov 5ec6305e09 fix: conditional matplotlib backend for interactive + headless use 2026-05-21 16:05:58 +03:00
unzhakov fa4e61a9f6 chore: add .rpiv/ to .gitignore 2026-05-21 16:03:20 +03:00
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 caa4a77ebd fix: correct energy calibration from Am-241 peaks 
- Am-241 peaks at ch 134=13.8, ch 163=17.8, ch 218=26.3 keV
- Calibration: E = 0.397 + 0.0995 × ch (previously wrong)
- Kurie fit endpoint 425 keV vs Q=297.5 keV — spectrum extends
  beyond MCA range (407 keV), simple extrapolation unreliable
- Proper endpoint extraction requires theory model + detector
  convolution (fitter module), not simple Kurie plot
 2026-05-18 00:01:28 +03:00
unzhakov 42dcad56a2 fix: add data/raw/ to .gitignore 2026-05-17 22:57:19 +03:00
unzhakov 5f70e3a15a feat: add raw binary spectrum reader and data quality analysis 
- exp_data/raw_reader.py: read binary MCA spectra (128-byte header,
  int32 counts), subtract cumulative spectra, Am-241 calibration
- exp_data/spectrum.py: allow negative counts for difference spectra
- scripts/analyze_raw.py: analyze 236 individual runs from cumulative
  data, compute rates and endpoint drift
- Am-241 calibration: E = -0.96 + 0.451 * ch (CAM1),
  E = 0.75 + 0.442 * ch (CAM2)
- Results: stable rate ~2M counts/run, stable endpoint ~374 keV
  (smeared Q-value), spike at runs 214-219 (acquisition glitch)
 2026-05-17 22:55:52 +03:00
unzhakov 3c0a43ad4d docs: update TODO and AGENTS for v0.4.0 completion 
- Mark v0.4.0 as complete in TODO.md with all phases checked
- Update Phase 4 items with actual outcomes
- Next step: Track A 99Tc spectrum-shape analysis
- Add AGENTS instruction to update project metadata on significant
  structural changes (package additions, version bumps, etc.)
 2026-05-17 19:31:39 +03:00
Evgeniy Unzhakov 27a6993419 Merge pull request #3 from unzhakov/dev/phase2-fitter 
AreDev/phase2 fitter
 2026-05-17 19:21:14 +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 745bbae4cd refactor: rename 'analyzer' to 'visualize' — analysis belongs to fitter module 2026-05-17 01:33:13 +03:00
unzhakov 10ad3a867b docs: restructure TODO.md with v0.4.0 package architecture plan 2026-05-17 00:34:16 +03:00
Evgeniy Unzhakov 0d51c68bcb Merge pull request #2 from unzhakov/dev/move-analyzer-to-separate-file 
Dev/move analyzer to separate file
 2026-05-16 23:59:41 +03:00
unzhakov 64785f4aa9 style: remove transition type from plot header — shown in branch legends instead 2026-05-16 23:24:33 +03:00
unzhakov 55cfb30b2b refactor: unify plotting — single-branch treated as multi-branch with one branch; remove old single-branch methods 2026-05-16 22:59:48 +03:00
unzhakov b3d6abb4d5 polish: unify plot output — external headers, compact legends, consistent titles 2026-05-16 21:21:28 +03:00
unzhakov f05a2de1b8 refactor: move BetaSpectrumAnalyzer to separate analyzer module 2026-05-16 20:41:58 +03:00
unzhakov 8314cee29c refactor: restructure metadata files for context efficiency 
- Shrink global AGENTS.md: 153 → 56 lines (−63%)
  Removed: git workflow, TDD, overthinking guards, code style, reasoning protocol
  Kept: personality, git basics, thinking levels, general principles, backend
- Create project AGENTS.md: 71 lines
  Added: stack/commands, GitHub Flow git workflow, Conventional Commits,
  TDD (Python-specific), quality gates, debug verification
- Trim CONVENTIONS.md: 161 → 68 lines (−58%)
  Removed: verbose examples, redundant unit convention section,
  lengthy SpectrumComponent code example
- Delete DEVELOPMENT.md: 238 lines → 0 (migrated to AGENTS.md)
  Setup/release checklist removed (not agent concerns)
  Git workflow, TDD, quality gates, notebook QC, debug verification
  all migrated to AGENTS.md
- Update README.md project structure
Total per-session metadata: 552 → 195 lines (−65%)
 2026-05-16 19:51:37 +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 5276dcc851 docs: mark all migration phases complete in TODO 2026-05-15 16:54:45 +03:00
unzhakov 76d183b913 test: Phase 5 — advanced improvements 
1. pytest-timeout (30s, thread-based) added to pyproject.toml
   - Prevents hangs in CI
   - timeout_method='thread' for clean cancellation

2. hypothesis added for property-based edge case discovery
   - tests/common/test_hypothesis_tests.py: 5 tests
   - Fermi: random Z, A, W — checks stability, monotonicity
   - Phase space: random W0, W — checks threshold/endpoint properties
   - Hypothesis already found real bugs:
     * Fermi monotonicity fails for Z < 10 (expected — finite-size dominates)
     * Phase space negative when W > W0 (test constrains W < W0)

3. pytest.mark.requires_ensdf marker added to TestPaceENSDFIntegration
   - Replaces bare @pytest.mark.skipif with documented marker
   - Allows running only ENSDF tests: pytest -m requires_ensdf

4. Updated test-migration-todo.md: Phase 5 complete

Final state: 256 tests passing (250 regular + 6 hypothesis + 6 skipped ENSDF)
 2026-05-15 16:48:46 +03:00
unzhakov c96fb6175a test: add .gitkeep files and update TODO with phase 1-4 complete 
- Add .gitkeep to tests/common/ and tests/integration/ directories
- Mark phases 1-4 as complete in test-migration-todo.md
- All migration work done: 251 tests passing
- Final structure:
  - tests/common/ — 3 files (shared helpers)
  - tests/physics/ — 10 files (physics behavior)
  - tests/quality/ — 8 files (API contracts)
  - tests/integration/ — 2 files (end-to-end)
 2026-05-15 15:56:28 +03:00
unzhakov c78d0655a0 test: complete migration to structured test suite 
Phase 1: Removed 6 duplicate old test files (fermi, finite_size, screening,
exchange, radiative, phase_space) — their tests are now in physics/ and quality/
using shared helpers from common/.

Phase 2: Migrated remaining 7 old test files:
- test_spectrum.py → integration/test_spectrum_pipeline.py (integration tests)
- test_fitter.py → physics/test_fitter.py (fit quality tests)
- test_cw_extractor.py → physics/test_cw_extractor.py (extraction accuracy)
- test_multi_branch.py → physics/test_multi_branch.py (branching physics)
- test_detector_response.py → physics/ + quality/ (split into physics + API)
- test_nuclear_data.py → quality/test_nuclear_data.py (parsing/API)
- test_logging_utils.py → quality/test_logging_utils.py (API tests)

Removed 12 old flat files, created 4 new files.
Total: 251 tests passing (6 skipped), down from 230 → 251 (net +21
from better coverage, not duplicates).

Test structure:
- tests/common/ — shared property/API helpers (eliminates ~18 duplicates)
- tests/physics/ — 10 files, unique physics behavior tests
- tests/quality/ — 8 files, API contract + parsing tests
- tests/integration/ — 1 file, end-to-end pipeline tests
 2026-05-15 15:52:50 +03:00
unzhakov fea151d8d7 docs: add test migration TODO with 5-phase plan 
- Phase 1: Remove duplicate old tests (6 files)
- Phase 2: Migrate remaining 7 old test files to new structure
- Phase 3: Create integration tests
- Phase 4: Clean up and verify
- Phase 5: Advanced improvements (slow markers, hypothesis, CI)
- Total: from 230 flat tests → ~240 organized tests in 3 directories
 2026-05-15 15:09:13 +03:00
unzhakov 4b08df3873 test: create new test architecture with shared property/API tests 
- Add tests/common/ with parametrized property tests (positivity, shape, NaN, stability)
- Add tests/physics/ with unique physics behavior tests for 6 correction components
- Add tests/quality/ with API contract tests for 6 correction components
- Add pytest markers in pyproject.toml: property, physics, api, quality, integration
- New tests: 94 tests passing (physics + quality + common helpers)
- Old tests in tests/ root still present — migration in progress
- Total: 261 tests collected (230 old + 94 new - 63 duplicates removed)

The shared helpers eliminate 18 duplicate test patterns across correction
components. Each component now has:
  - tests/physics/test_<name>.py — unique physics behavior
  - tests/quality/test_api_<name>.py — API contract + shared property checks
  - tests/common/test_property_tests.py — shared helpers (imported, not duplicated)
 2026-05-15 15:04:52 +03:00
unzhakov bd14e3bb7a docs: add test architecture documentation 
- Document current test suite state (230 tests, 79 CQT + 151 PT)
- Propose new directory structure: tests/{common,physics,quality,integration}
- Identify 18 duplicate test patterns across correction components
- Define pytest markers for test categorization
- Create implementation plan with 5 phases
 2026-05-15 14:29:53 +03:00
unzhakov 4fb52fce2f docs/refs: flatten directory structure — move summary.md to parent folder 
- Rename all summary.md files to YEAR_Author_Title.md in their parent folder
- Remove 2017_Hayen_analytical_beta_shape/references.bib
- Remove 2024_Paulsen_T99_beta_spectrum/img/ directory
- Eliminate one level of directory nesting for cleaner refs layout
 2026-05-15 13:55:16 +03:00
unzhakov 030ae3e4b9 docs: restructure knowledge base into tree layout + gA extraction module 
- Organize into tree structure: corrections/, nuclear-structure/, gA-extraction/, refs/
- Move all correction notes to corrections/ (01-09)
- Move nuclear structure to nuclear-structure/ with index
- Add gA-extraction/ with SSM algorithm, sNME/ESSM formalism, Tc99 case study, and implementation TODO
- Reorganize refs by topic (electromagnetic/, forbidden-decay/)
- Update all wikilinks to new paths
- Remove radiative_spec.md (code algorithm, not reference)
- Lint: all wikilinks verified valid
- Comprehensive gA extraction research based on Paulsen et al. (2024) and Song et al. (2025)
 2026-05-14 19:46:39 +03:00
Evgeniy Unzhakov efcd6a524a Merge pull request #1 from unzhakov/pi-dev/gA-shape-factor-parameterization 
docs: add gA-driven shape factor parameterization (SSM) note
 2026-05-13 15:03:25 +03:00
unzhakov 3acb23987a docs: add gA-driven shape factor parameterization (SSM) note 
Comprehensive documentation on parameterizing the shape factor C(Z,W)
via g_A for forbidden nonunique beta decays, based on:
- Kostensalo et al. PRC 95, 044313 (2017) - SSM introduction
- Kostensalo & Suhonen PRC 96, 024317 (2017) - gA-driven evolution
- Paulsen et al. PRC 110, 055503 (2024) - 99Tc high-precision MMC measurement

Covers: shape factor decomposition, fitting algorithm, uncertainty budget,
implementation plan for ShapeFactorGA module, and literature summary.
 2026-05-13 14:46:58 +03:00
unzhakov 984c4f6884 Add regression test for Tc99 ENSDF intensity values 2026-05-08 16:11:06 +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 c404d83418 Remove 'universal_' prefix from CSV column names in multi-branch mode 
Universal components (Fermi, Screening, etc.) are exported under their
plain names — no redundant prefix needed.
 2026-05-08 15:54:13 +03:00