- 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
- 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
- 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.)
- 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
- 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
- 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
- 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)
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%.
Branch intensity, endpoint, and transition are constant per branch and
already documented in the CSV header. No need to repeat them as columns
for every energy row.
- Cross out B3 in TODO.md with completion details
- Export BranchConfig in __init__.py public API
- Update README to mention per-branch transition types and intensity cutoff
- Add --intensity-cutoff CLI option to filter negligible branches
- Fetch DecayInfo from paceENSDF and construct SpectrumConfig with
branches including per-branch transition types
- Normalize branch intensities to sum to 1.0, filter by cutoff
- Display branch info in dry-run output and logging
- Add intensity_cutoff to SpectrumConfig
- 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
- Fix paceENSDF Q-value extraction (was reading half-life as Q-value)
- Fix RadiativeCorrection Z/A parameters
- Add debug verification workflow (bs_pnpi -vv)
- Add plot output with ID tracking and two display modes
- Fix pyright/mypy type errors across codebase
- Add ./output/ directory for test artifacts
- Update docs and development workflow
- README.md: Add features for plot modes, traceability, debug workflow
- README.md: Update BetaSpectrumAnalyzer docs with show_components param
- README.md: Update Quick Start with both plot modes
- README.md: Add output/ to project structure
- TODO.md: Mark B8.4 plot output as completed
- TODO.md: Update Current Status with B8.4
- Add commit hash (6 chars) and UTC timestamp to all plots via text boxes
- Add nuclear data header (nuclide, endpoint, transition, corrections) to plots
- Two display modes:
- DEBUG (-vv): 4-panel debug view with all correction factors
- Normal (default): single spectrum plot with nuclear data header
- CLI: --plot now passes show_components=(args.verbose >= 2)
- Create ./output/ with .gitkeep for test run outputs
- Add output/* to .gitignore (negated .gitkeep)
- Add §4.5 Debug Verification to DEVELOPMENT.md: final step of each dev iteration
- Run bs_pnpi -vv with full parameter consistency checks
- Required debug logging per component documented
- Example commands and success criteria
- Update Agent Instructions and Release Checklist
- Mark B8.3 debug verification framework as completed in TODO.md
unzhakov
Evgeniy Unzhakov