# Beta Spectrum Calculation Toolkit

A modular Python package for calculating high-precision **beta decay energy spectra**. It models the spectral shape of nuclear transitions by combining well-established physical corrections into a coherent, configurable pipeline.

Since v0.5.0 the project scope is the spectrum-shape **calculation** alone: detector response modeling, data calibration and fitting/extraction live in separate, dedicated projects.

**Features:**

- Numerical evaluation from near-zero kinetic energies up to the endpoint
- Selective inclusion of higher-order corrections via `SpectrumConfig` toggles
- Clean, composable component architecture
- Built-in visualization and CSV export via `BetaSpectrumAnalyzer`
  - Normal mode: single spectrum plot with nuclear data header
  - Debug mode (`-vv`): 4-panel view with all correction factors
  - All plots include commit hash and UTC timestamp for traceability
- Multi-branch decays with intensity weighting and per-branch endpoints
- Nuclear data retrieval from ENSDF via paceENSDF (`bs_pnpi --nuclide Tc99`)
- Comprehensive scientific reference in [`docs/`](docs/)
- Debug verification workflow: `bs_pnpi -vv` validates all parameters end-to-end

______________________________________________________________________

## Core Concept

The beta spectrum is constructed as a product of independent correction factors:

$$N(W) \\propto p W (W_0 - W)^2 \\times \\prod_i C_i(W)$$

Each $C_i(W)$ is an independently implemented and toggleable component. The phase space and the Fermi function are the unconditional core: every spectrum carries their product, and the higher-order corrections multiply on top of it.

______________________________________________________________________

## Project Structure

```
beta_shape_pnpi/
├── pyproject.toml
├── docs/                          ← Obsidian knowledge base (physics theory)
│   ├── README.md                  ← Vault overview + navigation index
│   ├── 00-beta-spectrum-overview.md
│   ├── 02-phase-space.md
│   └── corrections/               ← One note per correction component
├── beta_spectrum/                 ← theory-only core package
│   ├── __init__.py                ← Public API
│   ├── base.py                    ← Abstract SpectrumComponent base class
│   ├── constants.py               ← Physical constants (natural units, m_e = 1)
│   ├── utils.py                   ← T<->W conversion, momentum, nuclear radius
│   ├── spectrum.py                ← BetaSpectrum + SpectrumConfig + BranchConfig
│   ├── nuclear_data.py            ← paceENSDF integration + JSON input support
│   ├── cli.py                     ← Command-line interface (bs_pnpi)
│   ├── logging_utils.py           ← Structured logging helpers
│   ├── components/
│   │   ├── phase_space.py         ← Phase space shape (p·W·(W₀−W)²)
│   │   ├── fermi.py               ← Coulomb correction (loggamma for stability)
│   │   ├── finite_size.py         ← L0 expansion + charge distribution U term
│   │   ├── screening.py           ← Atomic electron screening (ratio method)
│   │   ├── exchange.py            ← Hayen-2018 empirical fit coefficients
│   │   └── radiative.py           ← Outer radiative corrections, soft-photon resummation
│   ├── data/
│   │   └── exchange_coeff.csv     ← Tabulated coefficients for X(Z,W), Z=2..120
│   └── output/                    ← visualization, CSV export
│       ├── core.py                ← BetaSpectrumAnalyzer
│       ├── csv_export.py          ← CSV export
│       └── visualization.py       ← Plotting built from exported CSV
├── data/
│   └── custom_input_example.json  ← Sample JSON input file
├── notebooks/                     ← Calculator notebook + nbmake conftest
├── output/                        ← Test run outputs (gitignored except .gitkeep)
├── tests/
│   ├── physics/                   ← Physics component tests
│   ├── quality/                   ← Code quality tests (logging, API, nuclear data)
│   ├── integration/               ← CLI and pipeline integration tests
│   └── common/                    ← Shared hypothesis + property tests
├── scripts/                       ← docs_check.py, notebook runners
├── AGENTS.md                      ← Agent instructions: stack, git workflow, TDD, quality gates
├── CONVENTIONS.md                 ← Physics conventions: natural units, energy representation, component design
├── TODO.md                        ← Development roadmap
```

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## Architecture

### `SpectrumComponent` (base class)

Defined in `beta_spectrum/base.py`. All physics corrections inherit from this abstract base and implement:

```python
def __call__(self, W: np.ndarray) -> np.ndarray
```

This makes every component stateless (or minimally stateful), vectorized, and composable.

### `BetaSpectrum`

Defined in `beta_spectrum/spectrum.py`. Orchestrates the calculation:

- Combines components multiplicatively via `__call__(W)`
- Factory method `from_config(config)` for declarative setup
- Generates energy grids with `get_energy_grid(config)`
- Returns individual component values via `calculate_components(W)`

### `BetaSpectrumAnalyzer`

In `beta_spectrum.output`. Provides debugging and visualization tools:

- `total_spectrum(normalize=True/False)` — computed spectrum array; raises `ValueError` when every branch is degenerate (non-positive integral)
- `physical_branch_spectrum(i)` — physical spectrum of branch *i*: the core (phase space × Fermi function) times every enabled higher-order correction, clamped beyond the branch endpoint (unnormalized)
- `universal_factor()` — product of the components shared across all branches (Fermi function and the universal higher-order corrections)
- `plot_analysis(save_path=None, show_components=True)` — plot with two modes:
  - `show_components=True` (debug mode): 4-panel figure (spectrum, components, cumulative effect, deviations)
  - `show_components=False` (normal mode): single spectrum plot with nuclear data header
  - All plots include commit hash and UTC timestamp for traceability
  - Plots are built *from the exported CSV file* (temporary full-verbosity export), so a plot always shows exactly the bytes the CSV export produces
- `export_to_csv(filename)` — export via pandas DataFrame with YAML-style metadata header:
  - the basic spectrum is always the core `phase_space × fermi` (the header carries a `# core:` line); finite size, charge distribution, screening, exchange and radiative are higher-order corrections
  - `branch_{i}_spectrum` columns contain the *physical* branch spectra weighted by intensity and normalized so that the sum of branch columns equals `total_spectrum`
  - with `separate_branches=True` (CLI `--separate-branches`) each branch column integrates to 1 (intensity ignored, no total_spectrum column)
- `parse_spectrum_csv(path)` — read an exported CSV and its metadata header (module function in `beta_spectrum.output.visualization`)
- `get_data()` — return all numerical data for downstream analysis

______________________________________________________________________

## Quick Start

```python
from beta_spectrum import SpectrumConfig, BetaSpectrum
from beta_spectrum.output import BetaSpectrumAnalyzer

config = SpectrumConfig(
    Z_parent=90,       # Thorium-232 (example)
    Z_daughter=91,
    A_number=232,
    endpoint_MeV=4.8,  # Q-value
    transition_type="A",  # Allowed transition (default)
)

spectrum = BetaSpectrum.from_config(config)
W, E_MeV = spectrum.get_energy_grid(config)
values = spectrum(W)

analyzer = BetaSpectrumAnalyzer(spectrum, config)
analyzer.plot_analysis("analysis.png")          # Normal mode (single spectrum plot)
analyzer.plot_analysis("debug.png", show_components=True)  # Debug mode (4-panel)
analyzer.export_to_csv("spectrum.csv")   # Export data to CSV
```

### From the command line

```bash
bs_pnpi --nuclide Tc99 -vv --output spectrum.csv   # ENSDF lookup + debug export
bs_pnpi --input data/custom_input_example.json     # JSON-driven configuration
```

CLI flags (`--e-step`, `--neutrino-mass`, `--intensity-cutoff`, `--csv-separator`, `--separate-branches`) override JSON input values only when explicitly given; every long option has a single-letter alias.

______________________________________________________________________

## Nuclear Data (paceENSDF)

`beta_spectrum.nuclear_data` retrieves decay data automatically: `get_decay_info_from_paceENSDF()`, `decay_info_to_config()`, and `create_config_from_source("paceENSDF", nuclide="Tc99")`. Z, A, endpoint energies, half-life, spin/parity, branch intensities, log*ft and forbiddenness are populated from ENSDF; per-branch endpoints are the measured transition endpoint energies (max endpoint across branches defines the spectrum endpoint). paceENSDF is an optional extra: `pip install ".[ensdf]"`.

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## Implementation Status

For a complete list of implemented and planned features, see [TODO.md](TODO.md). Key highlights:

- **Physics corrections**: phase space, Fermi function, finite size, screening, exchange, radiative (with delta_cut resummation)
- **Multi-branch decay**: intensity-weighted sum of branch spectra, per-branch calculators with branch-specific endpoint, transition type (from ENSDF), and `--intensity-cutoff` CLI filter
- **CLI**: `bs_pnpi` with full paceENSDF integration, structured logging (`-v`/`-vv`/`-q`), `--dry-run`, `--version`, `--log-file`
- **CSV metadata headers** with nuclide, decay and calculation parameters plus software version and git commit hash