feat: add CLI options for custom CSV separator and normalize-to-one branch normalization

beta_spectrum/cli.py

@@ -152,6 +152,17 @@ def _build_parser() -> argparse.ArgumentParser:
         choices=["full", "concise"],
         help="CSV output verbosity: 'full' (all components) or 'concise' (total spectrum and normalized branch components only) (default: full)",
     )
+    log_group.add_argument(
+        "--csv-separator",
+        type=str,
+        default=',',
+        help="CSV column separator (default: ','). Use 'tab' for tab separation.",
+    )
+    log_group.add_argument(
+        "--normalize-to-one",
+        action="store_true",
+        help="Normalize each branch to 1, ignoring intensity. In this case, total spectrum will not be produced (only energy and branch-wise spectra).",
+    )
 
     return parser
 
@@ -253,6 +264,8 @@ def _run(args: argparse.Namespace) -> None:
                     neutrino_mass_MeV=args.neutrino_mass,
                     branches=branches,
                     intensity_cutoff=args.intensity_cutoff,
+                    csv_separator=args.csv_separator,
+                    normalize_to_one=args.normalize_to_one,
                 )
             else:
                 config = create_config_from_source(
@@ -261,6 +274,8 @@ def _run(args: argparse.Namespace) -> None:
                     e_step_MeV=args.e_step,
                     intensity_cutoff=args.intensity_cutoff,
                     neutrino_mass_MeV=args.neutrino_mass,
+                    csv_separator=args.csv_separator,
+                    normalize_to_one=args.normalize_to_one,
                 )
         else:
             config = create_config_from_source(
@@ -269,6 +284,8 @@ def _run(args: argparse.Namespace) -> None:
                 e_step_MeV=args.e_step,
                 intensity_cutoff=args.intensity_cutoff,
                 neutrino_mass_MeV=args.neutrino_mass,
+                csv_separator=args.csv_separator,
+                normalize_to_one=args.normalize_to_one,
             )
     else:
         logger.info("Source: JSON file=%s", source_value)

beta_spectrum/nuclear_data.py

@@ -471,6 +471,8 @@ 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 = ',',
+    normalize_to_one: bool = False,
 ) -> SpectrumConfig:
     """
     Convert DecayInfo to a SpectrumConfig.
@@ -485,6 +487,10 @@ def decay_info_to_config(
         Minimum branch intensity fraction to include.
     neutrino_mass_MeV : float
         Neutrino mass in MeV.
+    csv_separator : str
+        CSV column separator.
+    normalize_to_one : bool
+        If True, normalize each branch to 1, ignoring intensity.
 
     Returns
     -------
@@ -516,6 +522,8 @@ def decay_info_to_config(
         neutrino_mass_MeV=neutrino_mass_MeV,
         branches=branches,
         intensity_cutoff=intensity_cutoff,
+        csv_separator=csv_separator,
+        normalize_to_one=normalize_to_one,
     )
 
 
@@ -690,12 +698,16 @@ 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", ',')
+        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(
             info,
             e_step_MeV=e_step,
             intensity_cutoff=intensity_cutoff,
             neutrino_mass_MeV=neutrino_mass,
+            csv_separator=csv_separator,
+            normalize_to_one=normalize_to_one,
         )
     elif source == "json":
         if not json_path:

beta_spectrum/spectrum.py

@@ -88,6 +88,10 @@ class SpectrumConfig:
         0.0  # Ignore branches below this fraction (default: 0.0 = all)
     )
     
+    # CSV output options
+    csv_separator: str = ','  # Default separator for CSV output
+    normalize_to_one: bool = False  # If True, normalize each branch to 1, ignoring intensity
+
 
 class BetaSpectrum:
     """
@@ -321,6 +325,8 @@ class BetaSpectrum:
 
         # Create per-branch calculators
         branch_spectra: List[BetaSpectrum] = []
+        if config.branches is None:
+            raise ValueError("branches must be provided for multi-branch mode")
         for i, branch in enumerate(config.branches):
             if logger:
                 logger.info(

beta_spectrum/visualize/__init__.py

@@ -731,7 +731,10 @@ class BetaSpectrumAnalyzer:
         header_lines.append(f"# n_points: {len(self.energies_MeV)}")
 
         # Add normalization mode
-        header_lines.append("# branch normalization: intensity")
+        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 = []
@@ -771,13 +774,31 @@ class BetaSpectrumAnalyzer:
         # Create data dictionary with concise column headers
         data: Dict[str, np.ndarray] = {
             "energy_MeV": self.energies_MeV,
-            "total_spectrum": total,
         }
         
+        # 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):
-                data[f"branch_{i + 1}_spectrum"] = self._get_branch_spectrum(i)
+                # 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:
@@ -799,14 +820,25 @@ class BetaSpectrumAnalyzer:
                     data[f"branch_{i + 1}"] = np.zeros_like(branch_spectrum)
                 else:
                     # Branch is valid, normalize as usual
-                    sum_spectrum = np.sum(branch_spectrum)
+                    if self.config.normalize_to_one:
-                    if sum_spectrum > 0:
+                        # Normalize to 1, ignoring intensity
-                        data[f"branch_{i + 1}"] = branch_spectrum / sum_spectrum
+                        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:
-                        data[f"branch_{i + 1}"] = branch_spectrum
+                        # 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)
-        df.to_csv(filename, index=False, float_format="%.4e", sep='\t')
+        # 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()

tests/physics/test_multi_branch.py

@@ -460,8 +460,8 @@ class TestMultiBranchCSVExport:
 
         import pandas as pd
 
-        # Read CSV (skip comment headers, use tab delimiter)
+        # Read CSV (skip comment headers, use comma delimiter by default)
-        df = pd.read_csv(csv_path, comment="#", sep='\t')
+        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='\t')
+        df = pd.read_csv(csv_path, comment="#", sep=',')
 
         assert "total_spectrum" in df.columns
         assert "branch_1_spectrum" in df.columns