refactor: rename visualize module to output module and separate concerns into core, csv_export, and visualization modules

beta_spectrum/__init__.py

@@ -11,7 +11,7 @@ from .components.exchange import ExchangeCorrection
 from .components.radiative import RadiativeCorrection
 
 from .spectrum import BetaSpectrum, SpectrumConfig, BranchConfig
-from .visualize import BetaSpectrumAnalyzer
+from .output import BetaSpectrumAnalyzer
 from .nuclear_data import (
     DecayInfo,
     BranchInfo,

beta_spectrum/cli.py

@@ -155,7 +155,7 @@ def _build_parser() -> argparse.ArgumentParser:
     log_group.add_argument(
         "--csv-separator",
         type=str,
-        default=',',
+        default=",",
         help="CSV column separator (default: ','). Use 'tab' for tab separation.",
     )
     log_group.add_argument(
@@ -183,7 +183,7 @@ def _run(args: argparse.Namespace) -> None:
         BranchConfig,
         SpectrumConfig,
     )
-    from beta_spectrum.visualize import BetaSpectrumAnalyzer
+    from beta_spectrum.output import BetaSpectrumAnalyzer
 
     # Determine logging level
     if args.quiet:

beta_spectrum/nuclear_data.py

@@ -471,7 +471,7 @@ def decay_info_to_config(
     e_step_MeV: float = 0.001,
     intensity_cutoff: float = 0.0,
     neutrino_mass_MeV: float = 0.0,
-    csv_separator: str = ',',
+    csv_separator: str = ",",
     normalize_to_one: bool = False,
 ) -> SpectrumConfig:
     """
@@ -698,7 +698,7 @@ def create_config_from_source(
         e_step = kwargs.get("e_step_MeV", 0.001)
         intensity_cutoff = kwargs.get("intensity_cutoff", 0.0)
         neutrino_mass = kwargs.get("neutrino_mass_MeV", 0.0)
-        csv_separator = kwargs.get("csv_separator", ',')
+        csv_separator = kwargs.get("csv_separator", ",")
         normalize_to_one = kwargs.get("normalize_to_one", False)
         info = get_decay_info_from_paceENSDF(nuclide, decay_type, decay_index)
         return decay_info_to_config(

beta_spectrum/output/__init__.py

@@ -0,0 +1,23 @@
+"""
+Output module — BetaSpectrumAnalyzer class and related functionality.
+
+Introspection, analysis, visualization and export tools for BetaSpectrum.
+All nuclides (single- and multi-branch) are treated uniformly as one or more
+branches — single-branch is just a special case with one branch.
+"""
+
+from __future__ import annotations
+
+from .core import BetaSpectrumAnalyzer, _UnifiedBranch
+from .csv_export import CSVEmitter
+from .visualization import Visualizer
+
+# Re-export the main class for backward compatibility
+BetaSpectrumAnalyzer = BetaSpectrumAnalyzer
+
+__all__ = [
+    "BetaSpectrumAnalyzer",
+    "CSVEmitter",
+    "Visualizer",
+    "_UnifiedBranch",
+]

beta_spectrum/output/core.py

@@ -0,0 +1,285 @@
+"""
+Core analyzer module — BetaSpectrumAnalyzer base class.
+
+Core introspection and analysis tools for BetaSpectrum.
+All nuclides (single- and multi-branch) are treated uniformly as one or more
+branches — single-branch is just a special case with one branch.
+"""
+
+from __future__ import annotations
+
+import logging
+from dataclasses import dataclass
+from typing import TYPE_CHECKING, Any, Dict, List, Optional
+
+import numpy as np
+
+from beta_spectrum.utils import T_to_W
+
+if TYPE_CHECKING:
+    from beta_spectrum.spectrum import BetaSpectrum, SpectrumConfig
+
+
+class BetaSpectrumAnalyzer:
+    """
+    Introspection, analysis and debugging tools for BetaSpectrum.
+
+    Parameters
+    ----------
+    spectrum : BetaSpectrum
+        The spectrum to analyze.
+    config : SpectrumConfig
+        Configuration used to create the spectrum.
+    logger : logging.Logger, optional
+        Logger for progress output.
+    """
+
+    def __init__(
+        self,
+        spectrum: BetaSpectrum,
+        config: SpectrumConfig,
+        logger: Optional[logging.Logger] = None,
+    ):
+        """
+        Initialize analyzer with a spectrum and configuration.
+        """
+        self.spectrum = spectrum
+        self.config = config
+        self.W, self.energies_MeV = spectrum.get_energy_grid(config)
+        self._components_cache: Optional[Dict[str, np.ndarray]] = None
+        self._branch_spectra_cache: Optional[List[np.ndarray]] = None
+        self._logger = logger
+        self._is_multi = spectrum._is_multi
+        self._timestamp: Optional[str] = None
+
+        # Unified branch view: single-branch treated as one-branch multi-branch
+        if not self._is_multi and self.spectrum.branch_spectra == []:
+            self._unified_branches: List[_UnifiedBranch] = [
+                _UnifiedBranch(
+                    endpoint_MeV=config.endpoint_MeV,
+                    transition_type=config.transition_type,
+                    intensity=1.0,
+                )
+            ]
+        else:
+            self._unified_branches = [
+                _UnifiedBranch(
+                    endpoint_MeV=b.endpoint_MeV,
+                    transition_type=b.transition_type,
+                    intensity=b.intensity,
+                )
+                for b in self.spectrum.branches
+            ]
+
+    @property
+    def components(self) -> Dict[str, np.ndarray]:
+        if self._components_cache is None:
+            raw = self.spectrum.calculate_components(self.W)
+            # Normalize keys: single-branch has bare names,
+            # multi-branch has branch_0., branch_1., etc.
+            # We keep the raw keys for export_to_csv compatibility.
+            self._components_cache = raw
+        assert self._components_cache is not None
+        return self._components_cache
+
+    @property
+    def branch_spectra(self) -> List[np.ndarray]:
+        """Intensity-weighted branch spectra."""
+        if self._branch_spectra_cache is None:
+            self._branch_spectra_cache = self.spectrum.get_branch_normalized_spectra(
+                self.W
+            )
+        assert self._branch_spectra_cache is not None
+        return self._branch_spectra_cache
+
+    def total_spectrum(self, normalize: bool = True) -> np.ndarray:
+        """Calculate the total spectrum."""
+        total = self.spectrum(self.W)
+
+        if normalize:
+            integral = np.trapezoid(total, self.energies_MeV)
+            total = total / integral
+
+        return total
+
+    # ---------------------------------------------------------------------------
+    # Unified branch view
+    # ---------------------------------------------------------------------------
+
+    @property
+    def _n_branches(self) -> int:
+        """Number of branches (unified view)."""
+        return len(self._unified_branches)
+
+    def _get_branch_spectrum(self, i: int) -> np.ndarray:
+        """Get the spectrum array for branch i."""
+        if i < len(self.spectrum.branch_spectra):
+            bs_obj = self.spectrum.branch_spectra[i]
+            # branch_spectra stores BetaSpectrum objects — call them to get arrays
+            if hasattr(bs_obj, "__call__"):
+                val = bs_obj(self.W)
+                # Clamp to zero beyond endpoint (phase space goes negative)
+                W0 = T_to_W(self._unified_branches[i].endpoint_MeV)
+                return np.where(self.W <= W0, val, 0.0)
+            return np.asarray(bs_obj)
+        # Single-branch: the spectrum itself is the only branch
+        return self.spectrum(self.W)
+
+    def _get_component_key(self, i: int, name: str) -> str:
+        """Get the canonical key for a per-branch component."""
+        if self._is_multi:
+            return f"branch_{i}.{name}"
+        return name
+
+    def _has_component(self, i: int, name: str) -> bool:
+        """Check if branch i has a given component."""
+        key = self._get_component_key(i, name)
+        return key in self.components
+
+    def _get_component(self, i: int, name: str) -> np.ndarray:
+        """Get a per-branch component array."""
+        key = self._get_component_key(i, name)
+        return self.components[key]
+
+    def _element_symbol(self, Z: int) -> str:
+        """Return chemical symbol for atomic number Z."""
+        symbols = [
+            "",
+            "H",
+            "He",
+            "Li",
+            "Be",
+            "B",
+            "C",
+            "N",
+            "O",
+            "F",
+            "Ne",
+            "Na",
+            "Mg",
+            "Al",
+            "Si",
+            "P",
+            "S",
+            "Cl",
+            "Ar",
+            "K",
+            "Ca",
+            "Sc",
+            "Ti",
+            "V",
+            "Cr",
+            "Mn",
+            "Fe",
+            "Co",
+            "Ni",
+            "Cu",
+            "Zn",
+            "Ga",
+            "Ge",
+            "As",
+            "Se",
+            "Br",
+            "Kr",
+            "Rb",
+            "Sr",
+            "Y",
+            "Zr",
+            "Nb",
+            "Mo",
+            "Tc",
+            "Ru",
+            "Rh",
+            "Pd",
+            "Ag",
+            "Cd",
+            "In",
+            "Sn",
+            "Sb",
+            "Te",
+            "I",
+            "Xe",
+            "Cs",
+            "Ba",
+            "La",
+            "Ce",
+            "Pr",
+            "Nd",
+            "Pm",
+            "Sm",
+            "Eu",
+            "Gd",
+            "Tb",
+            "Dy",
+            "Ho",
+            "Er",
+            "Tm",
+            "Yb",
+            "Lu",
+            "Hf",
+            "Ta",
+            "W",
+            "Re",
+            "Os",
+            "Ir",
+            "Pt",
+            "Au",
+            "Hg",
+            "Tl",
+            "Pb",
+            "Bi",
+            "Po",
+            "At",
+            "Rn",
+            "Fr",
+            "Ra",
+            "Ac",
+            "Th",
+            "Pa",
+            "U",
+            "Np",
+            "Pu",
+            "Am",
+            "Cm",
+            "Bk",
+            "Cf",
+            "Es",
+        ]
+        return symbols[Z] if Z < len(symbols) else f"Z{Z}"
+
+    def get_data(self) -> Dict[str, Any]:
+        """Get all numerical data for custom analysis."""
+        return {
+            "energies_MeV": self.energies_MeV,
+            "energies_W": self.W,
+            "spectrum": self.total_spectrum(normalize=True),
+            "components": self.components,
+            "config": self.config,
+        }
+
+    def export_to_csv(
+        self, filename: str, source_type: str = "unknown", csv_verbosity: str = "full"
+    ) -> None:
+        """Export spectrum data to CSV with metadata header."""
+        from .csv_export import CSVEmitter
+
+        CSVEmitter.export_to_csv(self, filename, source_type, csv_verbosity)
+
+    def plot_analysis(
+        self,
+        save_path: Optional[str] = None,
+        show_components: bool = True,
+    ) -> None:
+        """Create visualization of the spectrum and all correction factors."""
+        from .visualization import Visualizer
+
+        Visualizer.plot_analysis(self, save_path, show_components)
+
+
+@dataclass
+class _UnifiedBranch:
+    """Unified branch view for both single- and multi-branch modes."""
+
+    endpoint_MeV: float
+    transition_type: str
+    intensity: float

beta_spectrum/output/csv_export.py

@@ -0,0 +1,219 @@
+"""
+CSV export module — CSV export functionality for BetaSpectrumAnalyzer.
+"""
+
+from __future__ import annotations
+
+import pandas as pd
+from datetime import datetime, timezone
+from typing import TYPE_CHECKING, Dict
+
+import numpy as np
+
+from beta_spectrum.logging_utils import get_git_short_hash
+
+if TYPE_CHECKING:
+    from beta_spectrum.output.core import BetaSpectrumAnalyzer
+
+
+class CSVEmitter:
+    """CSV export functionality for BetaSpectrumAnalyzer."""
+
+    @staticmethod
+    def export_to_csv(
+        analyzer: BetaSpectrumAnalyzer,
+        filename: str,
+        source_type: str = "unknown",
+        csv_verbosity: str = "full",
+    ) -> None:
+        """Export spectrum data to CSV with metadata header.
+
+        Parameters
+        ----------
+        analyzer : BetaSpectrumAnalyzer
+            The analyzer instance to export data from.
+        filename : str
+            Output CSV file path.
+        source_type : str
+            Source type (paceENSDF, json, etc.).
+        csv_verbosity : str
+            Verbosity level: 'full' (all components) or 'concise' (total spectrum and normalized branch components only).
+        """
+        total = analyzer.total_spectrum(normalize=True)
+        components = analyzer.components
+
+        # Only include enabled corrections that are not basic components
+        # Basic components (phase_space and fermi) are always used and should not be listed
+        enabled = []
+        if analyzer.config.use_screening:
+            enabled.append("screening")
+        if analyzer.config.use_finite_size:
+            enabled.append("finite_size")
+        if analyzer.config.use_charge_dist:
+            enabled.append("charge_dist")
+        if analyzer.config.use_radiative:
+            enabled.append("radiative")
+        if analyzer.config.use_exchange:
+            enabled.append("exchange")
+
+        parent_symbol = analyzer._element_symbol(analyzer.config.Z_parent)
+        daughter_symbol = analyzer._element_symbol(analyzer.config.Z_daughter)
+
+        # Get git commit hash
+        git_commit = get_git_short_hash()
+
+        # Format source line with paceENSDF URL if applicable
+        if source_type == "paceENSDF":
+            source_line = "# source: paceENSDF (https://pypi.org/project/paceENSDF/)"
+        else:
+            source_line = f"# source: {source_type}"
+
+        header_lines = [
+            f"# beta-spectrum v{__import__('beta_spectrum').__version__}(build.{git_commit})",
+            f"# timestamp: {datetime.now(timezone.utc).isoformat()}",
+            source_line,
+            f"# nuclide: {parent_symbol}{analyzer.config.A_number} -> {daughter_symbol}{analyzer.config.A_number} (Z={analyzer.config.Z_parent}->{analyzer.config.Z_daughter})",
+            f"# basic_endpoint: {analyzer.config.endpoint_MeV * 1000:.1f} keV",
+        ]
+
+        # Add neutrino mass info if non-zero
+        if analyzer.config.neutrino_mass_MeV > 0:
+            header_lines.append(
+                f"# neutrino_mass_MeV: {analyzer.config.neutrino_mass_MeV:.6f} (non-zero neutrino mass effects included)"
+            )
+        else:
+            header_lines.append(
+                f"# neutrino_mass_MeV: {analyzer.config.neutrino_mass_MeV:.6f}"
+            )
+
+        header_lines.append(f"# corrections: {', '.join(enabled)}")
+        header_lines.append(f"# e_step: {analyzer.config.e_step_MeV:.4f} MeV")
+        header_lines.append(f"# n_points: {len(analyzer.energies_MeV)}")
+
+        # Add normalization mode
+        if analyzer.config.normalize_to_one:
+            header_lines.append("# branch normalization: to_one (ignoring intensity)")
+        else:
+            header_lines.append("# branch normalization: intensity")
+
+        # Separate branches into active and excluded lists
+        active_branches = []
+        excluded_branches = []
+
+        for i, branch in enumerate(analyzer._unified_branches):
+            branch_endpoint_keV = branch.endpoint_MeV * 1000
+            neutrino_mass_keV = analyzer.config.neutrino_mass_MeV * 1000
+
+            # Check if branch is excluded due to neutrino mass
+            if branch_endpoint_keV <= neutrino_mass_keV:
+                excluded_branches.append(
+                    f"  branch_{i + 1}: E₀={branch_endpoint_keV:.1f} keV, transition={branch.transition_type}, intensity={branch.intensity:.4f} - excluded: endpoint < m_nu"
+                )
+            # Check if branch is excluded due to intensity cutoff
+            elif branch.intensity < analyzer.config.intensity_cutoff:
+                excluded_branches.append(
+                    f"  branch_{i + 1}: E₀={branch_endpoint_keV:.1f} keV, transition={branch.transition_type}, intensity={branch.intensity:.4f} - excluded: intensity < cutoff"
+                )
+            else:
+                active_branches.append(
+                    f"  branch_{i + 1}: E₀={branch_endpoint_keV:.1f} keV, transition={branch.transition_type}, intensity={branch.intensity:.4f}"
+                )
+
+        # Add active branches list
+        if active_branches:
+            header_lines.append("# active branches:")
+            for branch_info in active_branches:
+                header_lines.append(f"# {branch_info}")
+
+        # Add excluded branches list if there are any
+        if excluded_branches:
+            header_lines.append("# excluded branches:")
+            for branch_info in excluded_branches:
+                header_lines.append(f"# {branch_info}")
+
+        # Create data dictionary with concise column headers
+        data: Dict[str, np.ndarray] = {
+            "energy_MeV": analyzer.energies_MeV,
+        }
+
+        # Only add total_spectrum if not normalizing to one
+        if not analyzer.config.normalize_to_one:
+            data["total_spectrum"] = total
+
+        if csv_verbosity == "full":
+            # Per-branch spectra and components with concise branch naming
+            for i in range(analyzer._n_branches):
+                # Get branch spectrum
+                branch_spectrum = analyzer._get_branch_spectrum(i)
+
+                if analyzer.config.normalize_to_one:
+                    # Normalize to 1, ignoring intensity
+                    sum_spectrum = np.sum(branch_spectrum)
+                    if sum_spectrum > 0:
+                        normalized_spectrum = branch_spectrum / sum_spectrum
+                    else:
+                        normalized_spectrum = branch_spectrum
+                else:
+                    # Use original spectrum with intensity
+                    normalized_spectrum = (
+                        branch_spectrum * analyzer._unified_branches[i].intensity
+                    )
+
+                data[f"branch_{i + 1}_spectrum"] = normalized_spectrum
+
+                for comp_name in ["PhaseSpace", "Radiative"]:
+                    key = analyzer._get_component_key(i, comp_name)
+                    if key in components:
+                        data[f"branch_{i + 1}_{comp_name}"] = components[key]
+
+            # Universal components (no prefix)
+            for name, values in components.items():
+                if not name.startswith("branch_"):
+                    data[name] = values
+        elif csv_verbosity == "concise":
+            # Only total spectrum and normalized branch components with concise naming
+            for i in range(analyzer._n_branches):
+                branch_spectrum = analyzer._get_branch_spectrum(i)
+                # Check if branch is degenerate (neutrino mass >= branch endpoint)
+                branch_endpoint_keV = analyzer._unified_branches[i].endpoint_MeV * 1000
+                neutrino_mass_keV = analyzer.config.neutrino_mass_MeV * 1000
+                if branch_endpoint_keV <= neutrino_mass_keV:
+                    # Branch is degenerate, spectrum should be all zeros
+                    data[f"branch_{i + 1}"] = np.zeros_like(branch_spectrum)
+                else:
+                    # Branch is valid, normalize as usual
+                    if analyzer.config.normalize_to_one:
+                        # Normalize to 1, ignoring intensity
+                        sum_spectrum = np.sum(branch_spectrum)
+                        if sum_spectrum > 0:
+                            data[f"branch_{i + 1}"] = branch_spectrum / sum_spectrum
+                        else:
+                            data[f"branch_{i + 1}"] = branch_spectrum
+                    else:
+                        # Normalize as usual with intensity
+                        sum_spectrum = np.sum(branch_spectrum)
+                        if sum_spectrum > 0:
+                            data[f"branch_{i + 1}"] = (
+                                branch_spectrum
+                                / sum_spectrum
+                                * analyzer._unified_branches[i].intensity
+                            )
+                        else:
+                            data[f"branch_{i + 1}"] = branch_spectrum
+
+        df = pd.DataFrame(data)
+        # Determine separator
+        separator = (
+            "\t"
+            if analyzer.config.csv_separator == "tab"
+            else analyzer.config.csv_separator
+        )
+        df.to_csv(filename, index=False, float_format="%.4e", sep=separator)
+
+        with open(filename, "r") as f:
+            content = f.read()
+        with open(filename, "w") as f:
+            f.write("\n".join(header_lines) + "\n" + content)
+
+        if analyzer._logger:
+            analyzer._logger.info("CSV exported to %s", filename)

beta_spectrum/output/visualization.py

@@ -0,0 +1,444 @@
+"""
+Visualization module — Plotting functionality for BetaSpectrumAnalyzer.
+"""
+
+from __future__ import annotations
+
+from datetime import datetime, timezone
+from typing import TYPE_CHECKING, Dict, Optional
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+from beta_spectrum.logging_utils import get_git_short_hash
+from beta_spectrum.utils import T_to_W
+
+if TYPE_CHECKING:
+    from matplotlib.figure import Figure
+
+    from beta_spectrum.output.core import BetaSpectrumAnalyzer
+
+
+class Visualizer:
+    """Visualization functionality for BetaSpectrumAnalyzer."""
+
+    @staticmethod
+    def plot_analysis(
+        analyzer: BetaSpectrumAnalyzer,
+        save_path: Optional[str] = None,
+        show_components: bool = True,
+    ) -> None:
+        """
+        Create visualization of the spectrum and all correction factors.
+
+        Parameters
+        ----------
+        analyzer : BetaSpectrumAnalyzer
+            The analyzer instance to visualize.
+        save_path : str, optional
+            Path to save the figure.
+        show_components : bool
+            If True, show full debug view.
+            If False, show only the spectrum plot.
+        """
+        total = analyzer.total_spectrum(normalize=True)
+        components = analyzer.components
+        analyzer._timestamp = datetime.now(timezone.utc).strftime(
+            "%Y-%m-%d %H:%M:%S UTC"
+        )
+
+        if show_components:
+            Visualizer._plot_debug_view(analyzer, total, components, save_path)
+        else:
+            Visualizer._plot_spectra_view(analyzer, total, components, save_path)
+
+    @staticmethod
+    def _build_figure_header(analyzer: BetaSpectrumAnalyzer, fig: "Figure") -> None:
+        """Add a compact header with nuclide info, e_step, commit and timestamp outside axes."""
+        parent = analyzer._element_symbol(analyzer.config.Z_parent)
+        daughter = analyzer._element_symbol(analyzer.config.Z_daughter)
+        e_step_keV = analyzer.config.e_step_MeV * 1000
+        header = (
+            f"{parent}{analyzer.config.A_number} -> {daughter}{analyzer.config.A_number}  "
+            f"|  E₀={analyzer.config.endpoint_MeV * 1000:.1f} keV  "
+            f"|  ΔE={e_step_keV:.1f} keV"
+        )
+        fig.text(
+            0.01,
+            0.98,
+            header,
+            transform=fig.transFigure,
+            fontsize=9,
+            verticalalignment="top",
+            horizontalalignment="left",
+            fontfamily="monospace",
+        )
+
+        # Add neutrino mass info to header if non-zero
+        if analyzer.config.neutrino_mass_MeV > 0:
+            nu_mass_text = f"|  m_ν={analyzer.config.neutrino_mass_MeV:.6f} MeV"
+            fig.text(
+                0.01,
+                0.96,
+                nu_mass_text,
+                transform=fig.transFigure,
+                fontsize=8,
+                verticalalignment="top",
+                horizontalalignment="left",
+                fontfamily="monospace",
+                color="red",
+            )
+
+        id_text = f"{get_git_short_hash(6)}  |  {analyzer._timestamp}"
+        fig.text(
+            0.01,
+            0.01,
+            id_text,
+            transform=fig.transFigure,
+            fontsize=8,
+            verticalalignment="bottom",
+            horizontalalignment="left",
+            fontfamily="monospace",
+            color="gray",
+        )
+
+    @staticmethod
+    def _build_figure_title(analyzer: BetaSpectrumAnalyzer, fig: "Figure") -> str:
+        """Build a unified figure title."""
+        parent = analyzer._element_symbol(analyzer.config.Z_parent)
+        daughter = analyzer._element_symbol(analyzer.config.Z_daughter)
+        n = analyzer.config.A_number
+        title = f"Beta-decay: {n}{parent} -> {n}{daughter}"
+        if analyzer._n_branches > 1:
+            # Count active branches (not excluded by neutrino mass or intensity cutoff)
+            active_branches = 0
+            for i, branch in enumerate(analyzer._unified_branches):
+                branch_endpoint_keV = branch.endpoint_MeV * 1000
+                neutrino_mass_keV = analyzer.config.neutrino_mass_MeV * 1000
+                is_excluded_by_mass = branch_endpoint_keV <= neutrino_mass_keV
+                is_excluded_by_intensity = (
+                    branch.intensity < analyzer.config.intensity_cutoff
+                )
+                if not is_excluded_by_mass and not is_excluded_by_intensity:
+                    active_branches += 1
+
+            if active_branches < analyzer._n_branches:
+                title += f" ({active_branches} of {analyzer._n_branches} branches)"
+            else:
+                title += f" ({analyzer._n_branches} branches)"
+        return title
+
+    @staticmethod
+    def _format_branch_label(analyzer: BetaSpectrumAnalyzer, i: int) -> str:
+        """Abbreviated branch label for legend."""
+        branch = analyzer._unified_branches[i]
+        e0 = branch.endpoint_MeV * 1000
+        intensity_pct = branch.intensity * 100
+
+        # Check if branch is excluded
+        branch_endpoint_keV = branch.endpoint_MeV * 1000
+        neutrino_mass_keV = analyzer.config.neutrino_mass_MeV * 1000
+        is_excluded_by_mass = branch_endpoint_keV <= neutrino_mass_keV
+        is_excluded_by_intensity = branch.intensity < analyzer.config.intensity_cutoff
+
+        if is_excluded_by_mass:
+            return f"Br. {i + 1}: {e0:.1f} keV ({intensity_pct:.1f}%) - excluded (endpoint < m_nu)"
+        elif is_excluded_by_intensity:
+            return f"Br. {i + 1}: {e0:.1f} keV ({intensity_pct:.1f}%) - excluded (intensity < cutoff)"
+        else:
+            return f"Br. {i + 1}: {e0:.1f} keV ({intensity_pct:.1f}%)"
+
+    @staticmethod
+    def _plot_spectra_view(
+        analyzer: BetaSpectrumAnalyzer,
+        total: np.ndarray,
+        components: Dict[str, np.ndarray],
+        save_path: Optional[str],
+    ) -> None:
+        """Plot total spectrum with individual branch decomposition."""
+        fig, ax = plt.subplots(figsize=(12, 7))
+
+        branch_colors = [
+            "#1f77b4",
+            "#ff7f0e",
+            "#2ca02c",
+            "#d62728",
+            "#9467bd",
+            "#8c564b",
+            "#e377c2",
+            "#7f7f7f",
+            "#bcbd22",
+            "#17becf",
+        ]
+
+        e_step_keV = analyzer.config.e_step_MeV * 1000
+
+        # Compute branch contributions (universal * intensity * branch_spectrum)
+        branch_contribs = []
+        # Universal components are shared (no per-branch key prefix)
+        universal_names = [
+            "Fermi",
+            "Screening",
+            "FiniteSizeL0",
+            "ChargeDistributionU",
+            "Exchange",
+        ]
+        for i in range(analyzer._n_branches):
+            universal_product = np.ones_like(analyzer.W)
+            for name in universal_names:
+                key = analyzer._get_component_key(i, name)
+                if key in components:
+                    universal_product *= components[key]
+                elif name in components:  # fallback: universal components
+                    universal_product *= components[name]
+            bs = analyzer._get_branch_spectrum(i)
+            contrib = universal_product * analyzer._unified_branches[i].intensity * bs
+            branch_contribs.append(contrib)
+
+        total_raw = sum(branch_contribs)
+
+        ax.plot(
+            analyzer.energies_MeV,
+            total_raw,
+            "k-",
+            lw=2.5,
+            label="Total spectrum",
+            zorder=10,
+        )
+
+        # Only plot active branches (not excluded by neutrino mass or intensity cutoff)
+        active_branch_indices = []
+        for i in range(analyzer._n_branches):
+            branch_endpoint_keV = analyzer._unified_branches[i].endpoint_MeV * 1000
+            neutrino_mass_keV = analyzer.config.neutrino_mass_MeV * 1000
+            is_excluded_by_mass = branch_endpoint_keV <= neutrino_mass_keV
+            is_excluded_by_intensity = (
+                analyzer._unified_branches[i].intensity
+                < analyzer.config.intensity_cutoff
+            )
+            if not is_excluded_by_mass and not is_excluded_by_intensity:
+                active_branch_indices.append(i)
+
+        for i in active_branch_indices:
+            contrib = branch_contribs[i]
+            color = branch_colors[i % len(branch_colors)]
+            ax.plot(
+                analyzer.energies_MeV,
+                contrib,
+                color=color,
+                lw=1.5,
+                alpha=0.7,
+                label=Visualizer._format_branch_label(analyzer, i),
+            )
+
+        ax.set_xlabel(r"Electron kinetic energy $E$ [MeV]", fontsize=12)
+        ax.set_ylabel(f"Normalized Counts / {e_step_keV:.1f} keV", fontsize=12)
+        fig.suptitle(
+            Visualizer._build_figure_title(analyzer, fig),
+            fontsize=14,
+            fontweight="bold",
+        )
+        ax.set_yscale("log")
+        ax.grid(True, alpha=0.3)
+        ax.legend(
+            loc="best",
+            fontsize=9,
+            ncol=min(2, len(active_branch_indices) + 1),
+        )
+
+        Visualizer._build_figure_header(analyzer, fig)
+
+        plt.tight_layout()
+
+        if save_path:
+            fig.savefig(save_path, dpi=150, bbox_inches="tight")
+            print(f"Figure saved to {save_path}")
+
+    @staticmethod
+    def _plot_debug_view(
+        analyzer: BetaSpectrumAnalyzer,
+        total: np.ndarray,
+        components: Dict[str, np.ndarray],
+        save_path: Optional[str],
+    ) -> None:
+        """Debug view: vertical layout with 4 panels."""
+        n_branches = analyzer._n_branches
+        e_step_keV = analyzer.config.e_step_MeV * 1000
+
+        fig, axes = plt.subplots(4, 1, figsize=(12, 16), sharex=True)
+        fig.suptitle(
+            Visualizer._build_figure_title(analyzer, fig),
+            fontsize=14,
+            fontweight="bold",
+        )
+
+        branch_colors = [
+            "#1f77b4",
+            "#ff7f0e",
+            "#2ca02c",
+            "#d62728",
+            "#9467bd",
+            "#8c564b",
+            "#e377c2",
+            "#7f7f7f",
+            "#bcbd22",
+            "#17becf",
+        ]
+
+        # Panel 1: Total spectrum + per-branch spectra
+        branch_contribs = []
+        universal_names = [
+            "Fermi",
+            "Screening",
+            "FiniteSizeL0",
+            "ChargeDistributionU",
+            "Exchange",
+        ]
+        for i in range(n_branches):
+            universal_product = np.ones_like(analyzer.W)
+            for name in universal_names:
+                key = analyzer._get_component_key(i, name)
+                if key in components:
+                    universal_product *= components[key]
+                elif name in components:
+                    universal_product *= components[name]
+            bs = analyzer._get_branch_spectrum(i)
+            contrib = universal_product * analyzer._unified_branches[i].intensity * bs
+            branch_contribs.append(contrib)
+
+        total_raw = sum(branch_contribs)
+
+        ax = axes[0]
+        ax.plot(
+            analyzer.energies_MeV,
+            total_raw,
+            "k-",
+            lw=2,
+            label="Total spectrum",
+            zorder=10,
+        )
+
+        # Only plot active branches (not excluded by neutrino mass or intensity cutoff)
+        active_branch_indices = []
+        for i in range(n_branches):
+            branch_endpoint_keV = analyzer._unified_branches[i].endpoint_MeV * 1000
+            neutrino_mass_keV = analyzer.config.neutrino_mass_MeV * 1000
+            is_excluded_by_mass = branch_endpoint_keV <= neutrino_mass_keV
+            is_excluded_by_intensity = (
+                analyzer._unified_branches[i].intensity
+                < analyzer.config.intensity_cutoff
+            )
+            if not is_excluded_by_mass and not is_excluded_by_intensity:
+                active_branch_indices.append(i)
+
+        for i in active_branch_indices:
+            contrib = branch_contribs[i]
+            color = branch_colors[i % len(branch_colors)]
+            ax.plot(
+                analyzer.energies_MeV,
+                contrib,
+                color=color,
+                lw=1.5,
+                alpha=0.7,
+                label=Visualizer._format_branch_label(analyzer, i),
+            )
+        ax.set_yscale("log")
+        ax.set_ylabel(f"Normalized Counts / {e_step_keV:.1f} keV", fontsize=10)
+        ax.set_title("Spectrum", fontsize=11)
+        ax.grid(True, alpha=0.3)
+        ax.legend(fontsize=8, loc="best", ncol=min(2, len(active_branch_indices) + 1))
+
+        # Panel 2: Fermi function + all phase spaces
+        ax = axes[1]
+        if "Fermi" in components:
+            fermi_vals = components["Fermi"]
+            fermi_scaled = fermi_vals / np.max(fermi_vals)
+            ax.plot(
+                analyzer.energies_MeV,
+                fermi_scaled,
+                "r-",
+                lw=1.5,
+                label="Fermi",
+                alpha=0.8,
+            )
+        for i in active_branch_indices:
+            color = branch_colors[i % len(branch_colors)]
+            branch = analyzer._unified_branches[i]
+            key = analyzer._get_component_key(i, "PhaseSpace")
+            if key in components:
+                ps_vals = components[key]
+                W0_branch = T_to_W(branch.endpoint_MeV)
+                mask = analyzer.W <= W0_branch
+                ps_masked = np.where(mask, ps_vals, 0.0)
+                ps_max = np.max(ps_masked)
+                if ps_max > 0:
+                    ps_scaled = ps_masked / ps_max
+                else:
+                    ps_scaled = ps_masked
+                ax.plot(
+                    analyzer.energies_MeV,
+                    ps_scaled,
+                    color=color,
+                    lw=1.5,
+                    alpha=0.7,
+                    label=f"PS Br. {i + 1}",
+                )
+        ax.set_ylabel("Normalized Factor", fontsize=10)
+        ax.set_title("Fermi & Phase Space", fontsize=11)
+        ax.grid(True, alpha=0.3)
+        ax.legend(fontsize=8, loc="best")
+
+        # Panel 3: Universal W0-independent corrections
+        ax = axes[2]
+        universal_components = [
+            "Screening",
+            "FiniteSizeL0",
+            "ChargeDistributionU",
+            "Exchange",
+        ]
+        colors = ["green", "orange", "purple", "brown"]
+        for name, color in zip(universal_components, colors):
+            if name in components:
+                values = components[name]
+                values_scaled = values / np.max(values)
+                ax.plot(
+                    analyzer.energies_MeV,
+                    values_scaled,
+                    color=color,
+                    lw=1.5,
+                    label=name,
+                    alpha=0.8,
+                )
+        ax.set_ylabel("Normalized Factor", fontsize=10)
+        ax.set_title("Universal Corrections", fontsize=11)
+        ax.grid(True, alpha=0.3)
+        ax.legend(fontsize=8, loc="best")
+
+        # Panel 4: W0-dependent corrections (Radiative for each branch)
+        ax = axes[3]
+        for i in active_branch_indices:
+            color = branch_colors[i % len(branch_colors)]
+            key = analyzer._get_component_key(i, "Radiative")
+            if key in components:
+                rad_vals = components[key]
+                ax.plot(
+                    analyzer.energies_MeV,
+                    rad_vals,
+                    color=color,
+                    lw=1.5,
+                    alpha=0.7,
+                    label=f"Br. {i + 1}",
+                )
+        ax.set_ylabel("Radiative Correction", fontsize=10)
+        ax.set_xlabel(r"Electron kinetic energy $E$ [MeV]", fontsize=10)
+        ax.set_title("Radiative Corrections", fontsize=11)
+        ax.grid(True, alpha=0.3)
+        ax.legend(fontsize=8, loc="best", ncol=min(2, len(active_branch_indices) + 1))
+
+        Visualizer._build_figure_header(analyzer, fig)
+
+        plt.tight_layout()
+
+        if save_path:
+            fig.savefig(save_path, dpi=150, bbox_inches="tight")
+            print(f"Figure saved to {save_path}")

beta_spectrum/spectrum.py

@@ -89,8 +89,10 @@ class SpectrumConfig:
     )
 
     # CSV output options
-    csv_separator: str = ','  # Default separator for CSV output
+    csv_separator: str = ","  # Default separator for CSV output
-    normalize_to_one: bool = False  # If True, normalize each branch to 1, ignoring intensity
+    normalize_to_one: bool = (
+        False  # If True, normalize each branch to 1, ignoring intensity
+    )
 
 
 class BetaSpectrum:

beta_spectrum/visualize/__init__.py

@@ -1,868 +0,0 @@
-"""
-Visualize module — BetaSpectrumAnalyzer class.
-
-Visualization and plotting tools for BetaSpectrum.
-All nuclides (single- and multi-branch) are treated uniformly as one or more
-branches — single-branch is just a special case with one branch.
-"""
-
-from __future__ import annotations
-
-import logging
-import pandas as pd
-from datetime import datetime, timezone
-from dataclasses import dataclass
-from typing import TYPE_CHECKING, Any, Dict, List, Optional
-
-import numpy as np
-import matplotlib.pyplot as plt
-
-from beta_spectrum.logging_utils import get_git_short_hash
-from beta_spectrum.utils import T_to_W
-
-if TYPE_CHECKING:
-    from matplotlib.figure import Figure
-
-    from beta_spectrum.spectrum import BetaSpectrum, SpectrumConfig
-
-
-class BetaSpectrumAnalyzer:
-    """
-    Introspection, analysis and debugging tools for BetaSpectrum.
-
-    Parameters
-    ----------
-    spectrum : BetaSpectrum
-        The spectrum to analyze.
-    config : SpectrumConfig
-        Configuration used to create the spectrum.
-    logger : logging.Logger, optional
-        Logger for progress output.
-    """
-
-    def __init__(
-        self,
-        spectrum: BetaSpectrum,
-        config: SpectrumConfig,
-        logger: Optional[logging.Logger] = None,
-    ):
-        """
-        Initialize analyzer with a spectrum and configuration.
-        """
-        self.spectrum = spectrum
-        self.config = config
-        self.W, self.energies_MeV = spectrum.get_energy_grid(config)
-        self._components_cache: Optional[Dict[str, np.ndarray]] = None
-        self._branch_spectra_cache: Optional[List[np.ndarray]] = None
-        self._logger = logger
-        self._is_multi = spectrum._is_multi
-
-        # Unified branch view: single-branch treated as one-branch multi-branch
-        if not self._is_multi and self.spectrum.branch_spectra == []:
-            self._unified_branches: List[_UnifiedBranch] = [
-                _UnifiedBranch(
-                    endpoint_MeV=config.endpoint_MeV,
-                    transition_type=config.transition_type,
-                    intensity=1.0,
-                )
-            ]
-        else:
-            self._unified_branches = [
-                _UnifiedBranch(
-                    endpoint_MeV=b.endpoint_MeV,
-                    transition_type=b.transition_type,
-                    intensity=b.intensity,
-                )
-                for b in self.spectrum.branches
-            ]
-
-    @property
-    def components(self) -> Dict[str, np.ndarray]:
-        if self._components_cache is None:
-            raw = self.spectrum.calculate_components(self.W)
-            # Normalize keys: single-branch has bare names,
-            # multi-branch has branch_0., branch_1., etc.
-            # We keep the raw keys for export_to_csv compatibility.
-            self._components_cache = raw
-        assert self._components_cache is not None
-        return self._components_cache
-
-    @property
-    def branch_spectra(self) -> List[np.ndarray]:
-        """Intensity-weighted branch spectra."""
-        if self._branch_spectra_cache is None:
-            self._branch_spectra_cache = self.spectrum.get_branch_normalized_spectra(
-                self.W
-            )
-        assert self._branch_spectra_cache is not None
-        return self._branch_spectra_cache
-
-    def total_spectrum(self, normalize: bool = True) -> np.ndarray:
-        """Calculate the total spectrum."""
-        total = self.spectrum(self.W)
-
-        if normalize:
-            integral = np.trapezoid(total, self.energies_MeV)
-            total = total / integral
-
-        return total
-
-    # ---------------------------------------------------------------------------
-    # Unified branch view
-    # ---------------------------------------------------------------------------
-
-    @property
-    def _n_branches(self) -> int:
-        """Number of branches (unified view)."""
-        return len(self._unified_branches)
-
-    def _get_branch_spectrum(self, i: int) -> np.ndarray:
-        """Get the spectrum array for branch i."""
-        if i < len(self.spectrum.branch_spectra):
-            bs_obj = self.spectrum.branch_spectra[i]
-            # branch_spectra stores BetaSpectrum objects — call them to get arrays
-            if hasattr(bs_obj, "__call__"):
-                val = bs_obj(self.W)
-                # Clamp to zero beyond endpoint (phase space goes negative)
-                W0 = T_to_W(self._unified_branches[i].endpoint_MeV)
-                return np.where(self.W <= W0, val, 0.0)
-            return np.asarray(bs_obj)
-        # Single-branch: the spectrum itself is the only branch
-        return self.spectrum(self.W)
-
-    def _get_component_key(self, i: int, name: str) -> str:
-        """Get the canonical key for a per-branch component."""
-        if self._is_multi:
-            return f"branch_{i}.{name}"
-        return name
-
-    def _has_component(self, i: int, name: str) -> bool:
-        """Check if branch i has a given component."""
-        key = self._get_component_key(i, name)
-        return key in self.components
-
-    def _get_component(self, i: int, name: str) -> np.ndarray:
-        """Get a per-branch component array."""
-        key = self._get_component_key(i, name)
-        return self.components[key]
-
-    # ---------------------------------------------------------------------------
-    # Plotting helpers
-    # ---------------------------------------------------------------------------
-
-    def _build_figure_header(self, fig: "Figure") -> None:
-        """Add a compact header with nuclide info, e_step, commit and timestamp outside axes."""
-        parent = self._element_symbol(self.config.Z_parent)
-        daughter = self._element_symbol(self.config.Z_daughter)
-        e_step_keV = self.config.e_step_MeV * 1000
-        header = (
-            f"{parent}{self.config.A_number} -> {daughter}{self.config.A_number}  "
-            f"|  E₀={self.config.endpoint_MeV * 1000:.1f} keV  "
-            f"|  ΔE={e_step_keV:.1f} keV"
-        )
-        fig.text(
-            0.01,
-            0.98,
-            header,
-            transform=fig.transFigure,
-            fontsize=9,
-            verticalalignment="top",
-            horizontalalignment="left",
-            fontfamily="monospace",
-        )
-
-        # Add neutrino mass info to header if non-zero
-        if self.config.neutrino_mass_MeV > 0:
-            nu_mass_text = f"|  m_ν={self.config.neutrino_mass_MeV:.6f} MeV"
-            fig.text(
-                0.01,
-                0.96,
-                nu_mass_text,
-                transform=fig.transFigure,
-                fontsize=8,
-                verticalalignment="top",
-                horizontalalignment="left",
-                fontfamily="monospace",
-                color="red",
-            )
-
-        id_text = f"{get_git_short_hash(6)}  |  {self._timestamp}"
-        fig.text(
-            0.01,
-            0.01,
-            id_text,
-            transform=fig.transFigure,
-            fontsize=8,
-            verticalalignment="bottom",
-            horizontalalignment="left",
-            fontfamily="monospace",
-            color="gray",
-        )
-
-    def _build_figure_title(self, fig: "Figure") -> str:
-        """Build a unified figure title."""
-        parent = self._element_symbol(self.config.Z_parent)
-        daughter = self._element_symbol(self.config.Z_daughter)
-        n = self.config.A_number
-        title = f"Beta-decay: {n}{parent} -> {n}{daughter}"
-        if self._n_branches > 1:
-            # Count active branches (not excluded by neutrino mass or intensity cutoff)
-            active_branches = 0
-            for i, branch in enumerate(self._unified_branches):
-                branch_endpoint_keV = branch.endpoint_MeV * 1000
-                neutrino_mass_keV = self.config.neutrino_mass_MeV * 1000
-                is_excluded_by_mass = branch_endpoint_keV <= neutrino_mass_keV
-                is_excluded_by_intensity = (
-                    branch.intensity < self.config.intensity_cutoff
-                )
-                if not is_excluded_by_mass and not is_excluded_by_intensity:
-                    active_branches += 1
-
-            if active_branches < self._n_branches:
-                title += f" ({active_branches} of {self._n_branches} branches)"
-            else:
-                title += f" ({self._n_branches} branches)"
-        return title
-
-    def _format_branch_label(self, i: int) -> str:
-        """Abbreviated branch label for legend."""
-        branch = self._unified_branches[i]
-        e0 = branch.endpoint_MeV * 1000
-        intensity_pct = branch.intensity * 100
-
-        # Check if branch is excluded
-        branch_endpoint_keV = branch.endpoint_MeV * 1000
-        neutrino_mass_keV = self.config.neutrino_mass_MeV * 1000
-        is_excluded_by_mass = branch_endpoint_keV <= neutrino_mass_keV
-        is_excluded_by_intensity = branch.intensity < self.config.intensity_cutoff
-
-        if is_excluded_by_mass:
-            return f"Br. {i + 1}: {e0:.1f} keV ({intensity_pct:.1f}%) - excluded (endpoint < m_nu)"
-        elif is_excluded_by_intensity:
-            return f"Br. {i + 1}: {e0:.1f} keV ({intensity_pct:.1f}%) - excluded (intensity < cutoff)"
-        else:
-            return f"Br. {i + 1}: {e0:.1f} keV ({intensity_pct:.1f}%)"
-
-    # ---------------------------------------------------------------------------
-    # Plotting — unified multi-branch approach
-    # ---------------------------------------------------------------------------
-
-    def plot_analysis(
-        self,
-        save_path: Optional[str] = None,
-        show_components: bool = True,
-    ) -> None:
-        """
-        Create visualization of the spectrum and all correction factors.
-
-        Parameters
-        ----------
-        save_path : str, optional
-            Path to save the figure.
-        show_components : bool
-            If True, show full debug view.
-            If False, show only the spectrum plot.
-        """
-        total = self.total_spectrum(normalize=True)
-        components = self.components
-        self._timestamp = datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M:%S UTC")
-
-        if show_components:
-            self._plot_debug_view(total, components, save_path)
-        else:
-            self._plot_spectra_view(total, components, save_path)
-
-    def _plot_spectra_view(
-        self,
-        total: np.ndarray,
-        components: Dict[str, np.ndarray],
-        save_path: Optional[str],
-    ) -> None:
-        """Plot total spectrum with individual branch decomposition."""
-        fig, ax = plt.subplots(figsize=(12, 7))
-
-        branch_colors = [
-            "#1f77b4",
-            "#ff7f0e",
-            "#2ca02c",
-            "#d62728",
-            "#9467bd",
-            "#8c564b",
-            "#e377c2",
-            "#7f7f7f",
-            "#bcbd22",
-            "#17becf",
-        ]
-
-        e_step_keV = self.config.e_step_MeV * 1000
-
-        # Compute branch contributions (universal * intensity * branch_spectrum)
-        branch_contribs = []
-        # Universal components are shared (no per-branch key prefix)
-        universal_names = [
-            "Fermi",
-            "Screening",
-            "FiniteSizeL0",
-            "ChargeDistributionU",
-            "Exchange",
-        ]
-        for i in range(self._n_branches):
-            universal_product = np.ones_like(self.W)
-            for name in universal_names:
-                key = self._get_component_key(i, name)
-                if key in components:
-                    universal_product *= components[key]
-                elif name in components:  # fallback: universal components
-                    universal_product *= components[name]
-            bs = self._get_branch_spectrum(i)
-            contrib = universal_product * self._unified_branches[i].intensity * bs
-            branch_contribs.append(contrib)
-
-        total_raw = sum(branch_contribs)
-
-        ax.plot(
-            self.energies_MeV,
-            total_raw,
-            "k-",
-            lw=2.5,
-            label="Total spectrum",
-            zorder=10,
-        )
-
-        # Only plot active branches (not excluded by neutrino mass or intensity cutoff)
-        active_branch_indices = []
-        for i in range(self._n_branches):
-            branch_endpoint_keV = self._unified_branches[i].endpoint_MeV * 1000
-            neutrino_mass_keV = self.config.neutrino_mass_MeV * 1000
-            is_excluded_by_mass = branch_endpoint_keV <= neutrino_mass_keV
-            is_excluded_by_intensity = (
-                self._unified_branches[i].intensity < self.config.intensity_cutoff
-            )
-            if not is_excluded_by_mass and not is_excluded_by_intensity:
-                active_branch_indices.append(i)
-
-        for i in active_branch_indices:
-            contrib = branch_contribs[i]
-            color = branch_colors[i % len(branch_colors)]
-            ax.plot(
-                self.energies_MeV,
-                contrib,
-                color=color,
-                lw=1.5,
-                alpha=0.7,
-                label=self._format_branch_label(i),
-            )
-
-        ax.set_xlabel(r"Electron kinetic energy $E$ [MeV]", fontsize=12)
-        ax.set_ylabel(f"Normalized Counts / {e_step_keV:.1f} keV", fontsize=12)
-        fig.suptitle(self._build_figure_title(fig), fontsize=14, fontweight="bold")
-        ax.set_yscale("log")
-        ax.grid(True, alpha=0.3)
-        ax.legend(
-            loc="best",
-            fontsize=9,
-            ncol=min(2, len(active_branch_indices) + 1),
-        )
-
-        self._build_figure_header(fig)
-
-        plt.tight_layout()
-
-        if save_path:
-            fig.savefig(save_path, dpi=150, bbox_inches="tight")
-            print(f"Figure saved to {save_path}")
-
-    def _plot_debug_view(
-        self,
-        total: np.ndarray,
-        components: Dict[str, np.ndarray],
-        save_path: Optional[str],
-    ) -> None:
-        """Debug view: vertical layout with 4 panels."""
-        n_branches = self._n_branches
-        e_step_keV = self.config.e_step_MeV * 1000
-
-        fig, axes = plt.subplots(4, 1, figsize=(12, 16), sharex=True)
-        fig.suptitle(self._build_figure_title(fig), fontsize=14, fontweight="bold")
-
-        branch_colors = [
-            "#1f77b4",
-            "#ff7f0e",
-            "#2ca02c",
-            "#d62728",
-            "#9467bd",
-            "#8c564b",
-            "#e377c2",
-            "#7f7f7f",
-            "#bcbd22",
-            "#17becf",
-        ]
-
-        # Panel 1: Total spectrum + per-branch spectra
-        branch_contribs = []
-        universal_names = [
-            "Fermi",
-            "Screening",
-            "FiniteSizeL0",
-            "ChargeDistributionU",
-            "Exchange",
-        ]
-        for i in range(n_branches):
-            universal_product = np.ones_like(self.W)
-            for name in universal_names:
-                key = self._get_component_key(i, name)
-                if key in components:
-                    universal_product *= components[key]
-                elif name in components:
-                    universal_product *= components[name]
-            bs = self._get_branch_spectrum(i)
-            contrib = universal_product * self._unified_branches[i].intensity * bs
-            branch_contribs.append(contrib)
-
-        total_raw = sum(branch_contribs)
-
-        ax = axes[0]
-        ax.plot(
-            self.energies_MeV,
-            total_raw,
-            "k-",
-            lw=2,
-            label="Total spectrum",
-            zorder=10,
-        )
-
-        # Only plot active branches (not excluded by neutrino mass or intensity cutoff)
-        active_branch_indices = []
-        for i in range(n_branches):
-            branch_endpoint_keV = self._unified_branches[i].endpoint_MeV * 1000
-            neutrino_mass_keV = self.config.neutrino_mass_MeV * 1000
-            is_excluded_by_mass = branch_endpoint_keV <= neutrino_mass_keV
-            is_excluded_by_intensity = (
-                self._unified_branches[i].intensity < self.config.intensity_cutoff
-            )
-            if not is_excluded_by_mass and not is_excluded_by_intensity:
-                active_branch_indices.append(i)
-
-        for i in active_branch_indices:
-            contrib = branch_contribs[i]
-            color = branch_colors[i % len(branch_colors)]
-            ax.plot(
-                self.energies_MeV,
-                contrib,
-                color=color,
-                lw=1.5,
-                alpha=0.7,
-                label=self._format_branch_label(i),
-            )
-        ax.set_yscale("log")
-        ax.set_ylabel(f"Normalized Counts / {e_step_keV:.1f} keV", fontsize=10)
-        ax.set_title("Spectrum", fontsize=11)
-        ax.grid(True, alpha=0.3)
-        ax.legend(fontsize=8, loc="best", ncol=min(2, len(active_branch_indices) + 1))
-
-        # Panel 2: Fermi function + all phase spaces
-        ax = axes[1]
-        if "Fermi" in components:
-            fermi_vals = components["Fermi"]
-            fermi_scaled = fermi_vals / np.max(fermi_vals)
-            ax.plot(
-                self.energies_MeV,
-                fermi_scaled,
-                "r-",
-                lw=1.5,
-                label="Fermi",
-                alpha=0.8,
-            )
-        for i in active_branch_indices:
-            color = branch_colors[i % len(branch_colors)]
-            branch = self._unified_branches[i]
-            key = self._get_component_key(i, "PhaseSpace")
-            if key in components:
-                ps_vals = components[key]
-                W0_branch = T_to_W(branch.endpoint_MeV)
-                mask = self.W <= W0_branch
-                ps_masked = np.where(mask, ps_vals, 0.0)
-                ps_max = np.max(ps_masked)
-                if ps_max > 0:
-                    ps_scaled = ps_masked / ps_max
-                else:
-                    ps_scaled = ps_masked
-                ax.plot(
-                    self.energies_MeV,
-                    ps_scaled,
-                    color=color,
-                    lw=1.5,
-                    alpha=0.7,
-                    label=f"PS Br. {i + 1}",
-                )
-        ax.set_ylabel("Normalized Factor", fontsize=10)
-        ax.set_title("Fermi & Phase Space", fontsize=11)
-        ax.grid(True, alpha=0.3)
-        ax.legend(fontsize=8, loc="best")
-
-        # Panel 3: Universal W0-independent corrections
-        ax = axes[2]
-        universal_components = [
-            "Screening",
-            "FiniteSizeL0",
-            "ChargeDistributionU",
-            "Exchange",
-        ]
-        colors = ["green", "orange", "purple", "brown"]
-        for name, color in zip(universal_components, colors):
-            if name in components:
-                values = components[name]
-                values_scaled = values / np.max(values)
-                ax.plot(
-                    self.energies_MeV,
-                    values_scaled,
-                    color=color,
-                    lw=1.5,
-                    label=name,
-                    alpha=0.8,
-                )
-        ax.set_ylabel("Normalized Factor", fontsize=10)
-        ax.set_title("Universal Corrections", fontsize=11)
-        ax.grid(True, alpha=0.3)
-        ax.legend(fontsize=8, loc="best")
-
-        # Panel 4: W0-dependent corrections (Radiative for each branch)
-        ax = axes[3]
-        for i in active_branch_indices:
-            color = branch_colors[i % len(branch_colors)]
-            key = self._get_component_key(i, "Radiative")
-            if key in components:
-                rad_vals = components[key]
-                ax.plot(
-                    self.energies_MeV,
-                    rad_vals,
-                    color=color,
-                    lw=1.5,
-                    alpha=0.7,
-                    label=f"Br. {i + 1}",
-                )
-        ax.set_ylabel("Radiative Correction", fontsize=10)
-        ax.set_xlabel(r"Electron kinetic energy $E$ [MeV]", fontsize=10)
-        ax.set_title("Radiative Corrections", fontsize=11)
-        ax.grid(True, alpha=0.3)
-        ax.legend(fontsize=8, loc="best", ncol=min(2, len(active_branch_indices) + 1))
-
-        self._build_figure_header(fig)
-
-        plt.tight_layout()
-
-        if save_path:
-            fig.savefig(save_path, dpi=150, bbox_inches="tight")
-            print(f"Figure saved to {save_path}")
-
-    def _element_symbol(self, Z: int) -> str:
-        """Return chemical symbol for atomic number Z."""
-        symbols = [
-            "",
-            "H",
-            "He",
-            "Li",
-            "Be",
-            "B",
-            "C",
-            "N",
-            "O",
-            "F",
-            "Ne",
-            "Na",
-            "Mg",
-            "Al",
-            "Si",
-            "P",
-            "S",
-            "Cl",
-            "Ar",
-            "K",
-            "Ca",
-            "Sc",
-            "Ti",
-            "V",
-            "Cr",
-            "Mn",
-            "Fe",
-            "Co",
-            "Ni",
-            "Cu",
-            "Zn",
-            "Ga",
-            "Ge",
-            "As",
-            "Se",
-            "Br",
-            "Kr",
-            "Rb",
-            "Sr",
-            "Y",
-            "Zr",
-            "Nb",
-            "Mo",
-            "Tc",
-            "Ru",
-            "Rh",
-            "Pd",
-            "Ag",
-            "Cd",
-            "In",
-            "Sn",
-            "Sb",
-            "Te",
-            "I",
-            "Xe",
-            "Cs",
-            "Ba",
-            "La",
-            "Ce",
-            "Pr",
-            "Nd",
-            "Pm",
-            "Sm",
-            "Eu",
-            "Gd",
-            "Tb",
-            "Dy",
-            "Ho",
-            "Er",
-            "Tm",
-            "Yb",
-            "Lu",
-            "Hf",
-            "Ta",
-            "W",
-            "Re",
-            "Os",
-            "Ir",
-            "Pt",
-            "Au",
-            "Hg",
-            "Tl",
-            "Pb",
-            "Bi",
-            "Po",
-            "At",
-            "Rn",
-            "Fr",
-            "Ra",
-            "Ac",
-            "Th",
-            "Pa",
-            "U",
-            "Np",
-            "Pu",
-            "Am",
-            "Cm",
-            "Bk",
-            "Cf",
-            "Es",
-        ]
-        return symbols[Z] if Z < len(symbols) else f"Z{Z}"
-
-    # ---------------------------------------------------------------------------
-    # Export
-    # ---------------------------------------------------------------------------
-
-    def export_to_csv(
-        self, filename: str, source_type: str = "unknown", csv_verbosity: str = "full"
-    ) -> None:
-        """Export spectrum data to CSV with metadata header.
-
-        Parameters
-        ----------
-        filename : str
-            Output CSV file path.
-        source_type : str
-            Source type (paceENSDF, json, etc.).
-        csv_verbosity : str
-            Verbosity level: 'full' (all components) or 'concise' (total spectrum and normalized branch components only).
-        """
-        total = self.total_spectrum(normalize=True)
-        components = self.components
-
-        # Only include enabled corrections that are not basic components
-        # Basic components (phase_space and fermi) are always used and should not be listed
-        enabled = []
-        if self.config.use_screening:
-            enabled.append("screening")
-        if self.config.use_finite_size:
-            enabled.append("finite_size")
-        if self.config.use_charge_dist:
-            enabled.append("charge_dist")
-        if self.config.use_radiative:
-            enabled.append("radiative")
-        if self.config.use_exchange:
-            enabled.append("exchange")
-
-        parent_symbol = self._element_symbol(self.config.Z_parent)
-        daughter_symbol = self._element_symbol(self.config.Z_daughter)
-
-        # Get git commit hash
-        git_commit = get_git_short_hash()
-
-        # Format source line with paceENSDF URL if applicable
-        if source_type == "paceENSDF":
-            source_line = "# source: paceENSDF (https://pypi.org/project/paceENSDF/)"
-        else:
-            source_line = f"# source: {source_type}"
-
-        header_lines = [
-            f"# beta-spectrum v{__import__('beta_spectrum').__version__}(build.{git_commit})",
-            f"# timestamp: {datetime.now(timezone.utc).isoformat()}",
-            source_line,
-            f"# nuclide: {parent_symbol}{self.config.A_number} -> {daughter_symbol}{self.config.A_number} (Z={self.config.Z_parent}->{self.config.Z_daughter})",
-            f"# basic_endpoint: {self.config.endpoint_MeV * 1000:.1f} keV",
-        ]
-
-        # Add neutrino mass info if non-zero
-        if self.config.neutrino_mass_MeV > 0:
-            header_lines.append(
-                f"# neutrino_mass_MeV: {self.config.neutrino_mass_MeV:.6f} (non-zero neutrino mass effects included)"
-            )
-        else:
-            header_lines.append(
-                f"# neutrino_mass_MeV: {self.config.neutrino_mass_MeV:.6f}"
-            )
-
-        header_lines.append(f"# corrections: {', '.join(enabled)}")
-        header_lines.append(f"# e_step: {self.config.e_step_MeV:.4f} MeV")
-        header_lines.append(f"# n_points: {len(self.energies_MeV)}")
-
-        # Add normalization mode
-        if self.config.normalize_to_one:
-            header_lines.append("# branch normalization: to_one (ignoring intensity)")
-        else:
-            header_lines.append("# branch normalization: intensity")
-
-        # Separate branches into active and excluded lists
-        active_branches = []
-        excluded_branches = []
-
-        for i, branch in enumerate(self._unified_branches):
-            branch_endpoint_keV = branch.endpoint_MeV * 1000
-            neutrino_mass_keV = self.config.neutrino_mass_MeV * 1000
-
-            # Check if branch is excluded due to neutrino mass
-            if branch_endpoint_keV <= neutrino_mass_keV:
-                excluded_branches.append(
-                    f"  branch_{i + 1}: E₀={branch_endpoint_keV:.1f} keV, transition={branch.transition_type}, intensity={branch.intensity:.4f} - excluded: endpoint < m_nu"
-                )
-            # Check if branch is excluded due to intensity cutoff
-            elif branch.intensity < self.config.intensity_cutoff:
-                excluded_branches.append(
-                    f"  branch_{i + 1}: E₀={branch_endpoint_keV:.1f} keV, transition={branch.transition_type}, intensity={branch.intensity:.4f} - excluded: intensity < cutoff"
-                )
-            else:
-                active_branches.append(
-                    f"  branch_{i + 1}: E₀={branch_endpoint_keV:.1f} keV, transition={branch.transition_type}, intensity={branch.intensity:.4f}"
-                )
-
-        # Add active branches list
-        if active_branches:
-            header_lines.append("# active branches:")
-            for branch_info in active_branches:
-                header_lines.append(f"# {branch_info}")
-
-        # Add excluded branches list if there are any
-        if excluded_branches:
-            header_lines.append("# excluded branches:")
-            for branch_info in excluded_branches:
-                header_lines.append(f"# {branch_info}")
-
-        # Create data dictionary with concise column headers
-        data: Dict[str, np.ndarray] = {
-            "energy_MeV": self.energies_MeV,
-        }
-        
-        # Only add total_spectrum if not normalizing to one
-        if not self.config.normalize_to_one:
-            data["total_spectrum"] = total
-
-        if csv_verbosity == "full":
-            # Per-branch spectra and components with concise branch naming
-            for i in range(self._n_branches):
-                # Get branch spectrum
-                branch_spectrum = self._get_branch_spectrum(i)
-                
-                if self.config.normalize_to_one:
-                    # Normalize to 1, ignoring intensity
-                    sum_spectrum = np.sum(branch_spectrum)
-                    if sum_spectrum > 0:
-                        normalized_spectrum = branch_spectrum / sum_spectrum
-                    else:
-                        normalized_spectrum = branch_spectrum
-                else:
-                    # Use original spectrum with intensity
-                    normalized_spectrum = branch_spectrum * self._unified_branches[i].intensity
-                    
-                data[f"branch_{i + 1}_spectrum"] = normalized_spectrum
-                
-                for comp_name in ["PhaseSpace", "Radiative"]:
-                    key = self._get_component_key(i, comp_name)
-                    if key in components:
-                        data[f"branch_{i + 1}_{comp_name}"] = components[key]
-
-            # Universal components (no prefix)
-            for name, values in components.items():
-                if not name.startswith("branch_"):
-                    data[name] = values
-        elif csv_verbosity == "concise":
-            # Only total spectrum and normalized branch components with concise naming
-            for i in range(self._n_branches):
-                branch_spectrum = self._get_branch_spectrum(i)
-                # Check if branch is degenerate (neutrino mass >= branch endpoint)
-                branch_endpoint_keV = self._unified_branches[i].endpoint_MeV * 1000
-                neutrino_mass_keV = self.config.neutrino_mass_MeV * 1000
-                if branch_endpoint_keV <= neutrino_mass_keV:
-                    # Branch is degenerate, spectrum should be all zeros
-                    data[f"branch_{i + 1}"] = np.zeros_like(branch_spectrum)
-                else:
-                    # Branch is valid, normalize as usual
-                    if self.config.normalize_to_one:
-                        # Normalize to 1, ignoring intensity
-                        sum_spectrum = np.sum(branch_spectrum)
-                        if sum_spectrum > 0:
-                            data[f"branch_{i + 1}"] = branch_spectrum / sum_spectrum
-                        else:
-                            data[f"branch_{i + 1}"] = branch_spectrum
-                    else:
-                        # Normalize as usual with intensity
-                        sum_spectrum = np.sum(branch_spectrum)
-                        if sum_spectrum > 0:
-                            data[f"branch_{i + 1}"] = branch_spectrum / sum_spectrum * self._unified_branches[i].intensity
-                        else:
-                            data[f"branch_{i + 1}"] = branch_spectrum
-
-        df = pd.DataFrame(data)
-        # Determine separator
-        separator = '\t' if self.config.csv_separator == 'tab' else self.config.csv_separator
-        df.to_csv(filename, index=False, float_format="%.4e", sep=separator)
-
-        with open(filename, "r") as f:
-            content = f.read()
-        with open(filename, "w") as f:
-            f.write("\n".join(header_lines) + "\n" + content)
-
-        if self._logger:
-            self._logger.info("CSV exported to %s", filename)
-
-    def get_data(self) -> Dict[str, Any]:
-        """Get all numerical data for custom analysis."""
-        return {
-            "energies_MeV": self.energies_MeV,
-            "energies_W": self.W,
-            "spectrum": self.total_spectrum(normalize=True),
-            "components": self.components,
-            "config": self.config,
-        }
-
-
-@dataclass
-class _UnifiedBranch:
-    """Unified branch view for both single- and multi-branch modes."""
-
-    endpoint_MeV: float
-    transition_type: str
-    intensity: float

tests/physics/test_multi_branch.py

@@ -33,7 +33,7 @@ from beta_spectrum import (
     BranchConfig,
     SpectrumConfig,
 )
-from beta_spectrum.visualize import BetaSpectrumAnalyzer
+from beta_spectrum.output import BetaSpectrumAnalyzer
 from beta_spectrum.utils import T_to_W
 
 # ---------------------------------------------------------------------------
@@ -461,7 +461,7 @@ class TestMultiBranchCSVExport:
         import pandas as pd
 
         # Read CSV (skip comment headers, use comma delimiter by default)
-        df = pd.read_csv(csv_path, comment="#", sep=',')
+        df = pd.read_csv(csv_path, comment="#", sep=",")
 
         # Should have total spectrum column
         assert "total_spectrum" in df.columns
@@ -500,7 +500,7 @@ class TestMultiBranchCSVExport:
 
         import pandas as pd
 
-        df = pd.read_csv(csv_path, comment="#", sep=',')
+        df = pd.read_csv(csv_path, comment="#", sep=",")
 
         assert "total_spectrum" in df.columns
         assert "branch_1_spectrum" in df.columns

tests/quality/test_logging_utils.py

@@ -131,7 +131,7 @@ class TestCSVMetadataHeader:
 
     def test_header_contains_version(self):
         from beta_spectrum.spectrum import BetaSpectrum, SpectrumConfig
-        from beta_spectrum.visualize import BetaSpectrumAnalyzer
+        from beta_spectrum.output import BetaSpectrumAnalyzer
 
         config = SpectrumConfig(
             Z_parent=43,
@@ -159,7 +159,7 @@ class TestCSVMetadataHeader:
 
     def test_header_contains_timestamp(self):
         from beta_spectrum.spectrum import BetaSpectrum, SpectrumConfig
-        from beta_spectrum.visualize import BetaSpectrumAnalyzer
+        from beta_spectrum.output import BetaSpectrumAnalyzer
 
         config = SpectrumConfig(
             Z_parent=43,
@@ -186,7 +186,7 @@ class TestCSVMetadataHeader:
 
     def test_header_contains_nuclide_info(self):
         from beta_spectrum.spectrum import BetaSpectrum, SpectrumConfig
-        from beta_spectrum.visualize import BetaSpectrumAnalyzer
+        from beta_spectrum.output import BetaSpectrumAnalyzer
 
         config = SpectrumConfig(
             Z_parent=43,
@@ -214,7 +214,7 @@ class TestCSVMetadataHeader:
 
     def test_header_contains_git_commit(self):
         from beta_spectrum.spectrum import BetaSpectrum, SpectrumConfig
-        from beta_spectrum.visualize import BetaSpectrumAnalyzer
+        from beta_spectrum.output import BetaSpectrumAnalyzer
 
         config = SpectrumConfig(
             Z_parent=43,
@@ -243,7 +243,7 @@ class TestCSVMetadataHeader:
 
     def test_header_contains_corrections(self):
         from beta_spectrum.spectrum import BetaSpectrum, SpectrumConfig
-        from beta_spectrum.visualize import BetaSpectrumAnalyzer
+        from beta_spectrum.output import BetaSpectrumAnalyzer
 
         config = SpectrumConfig(
             Z_parent=43,