Improve error handling. Add alignment feature for point sources

src/pg_rad/exceptions/exceptions.py

@@ -31,3 +31,7 @@ class DimensionError(ValueError):
 
 class InvalidIsotopeError(ValueError):
     """Raised if attempting to load an isotope that is not valid."""
+
+
+class InvalidConfigValueError(ValueError):
+    """Raised if a config key has an incorrect type or value."""

src/pg_rad/inputparser/parser.py

@@ -4,7 +4,11 @@ from typing import Any, Dict, List, Union
 
 import yaml
 
-from pg_rad.exceptions.exceptions import MissingConfigKeyError, DimensionError
+from pg_rad.exceptions.exceptions import (
+    MissingConfigKeyError,
+    DimensionError,
+    InvalidConfigValueError
+)
 from pg_rad.configs import defaults
 
 from .specs import (
@@ -14,7 +18,7 @@ from .specs import (
     PathSpec,
     ProceduralPathSpec,
     CSVPathSpec,
-    SourceSpec,
+    PointSourceSpec,
     AbsolutePointSourceSpec,
     RelativePointSourceSpec,
     DetectorSpec,
@@ -98,19 +102,23 @@ class ConfigParser:
     def _parse_options(self) -> SimulationOptionsSpec:
         options = self.config.get("options", {})
 
-        allowed = {"air_density", "seed"}
+        allowed = {"air_density_kg_per_m3", "seed"}
         self._warn_unknown_keys(
             section="options",
             provided=set(options.keys()),
             allowed=allowed,
         )
 
-        air_density = options.get("air_density", defaults.DEFAULT_AIR_DENSITY)
+        air_density = options.get(
+            "air_density_kg_per_m3",
+            defaults.DEFAULT_AIR_DENSITY
+        )
         seed = options.get("seed")
 
         if not isinstance(air_density, float) or air_density <= 0:
             raise ValueError(
-                "options.air_density must be a positive float in kg/m^3."
+                "options.air_density_kg_per_m3 must be a positive float "
+                "in kg/m^3."
             )
         if (
             seed is not None or
@@ -230,9 +238,9 @@ class ConfigParser:
     def _is_turn(segment_type: str) -> bool:
         return segment_type in {"turn_left", "turn_right"}
 
-    def _parse_point_sources(self) -> List[SourceSpec]:
+    def _parse_point_sources(self) -> List[PointSourceSpec]:
         source_dict = self.config.get("sources", {})
-        specs: List[SourceSpec] = []
+        specs: List[PointSourceSpec] = []
 
         for name, params in source_dict.items():
 
@@ -245,7 +253,7 @@ class ConfigParser:
             isotope = params.get("isotope")
 
             if not isinstance(activity, int | float) or activity <= 0:
-                raise ValueError(
+                raise InvalidConfigValueError(
                     f"sources.{name}.activity_MBq must be positive value "
                     "in MegaBequerels."
                 )
@@ -270,6 +278,16 @@ class ConfigParser:
                 )
 
             elif isinstance(position, dict):
+                alignment = position.get("acquisition_alignment")
+                if alignment not in {'best', 'worst', None}:
+                    raise InvalidConfigValueError(
+                        f"sources.{name}.acquisition_alignment must be "
+                        "'best' or 'worst', with 'best' aligning source "
+                        f"{name} in the middle of the two nearest acquisition "
+                        "points, and 'worst' aligning exactly perpendicular "
+                        "to the nearest acquisition point."
+                    )
+
                 specs.append(
                     RelativePointSourceSpec(
                         name=name,
@@ -278,12 +296,13 @@ class ConfigParser:
                         along_path=float(position["along_path"]),
                         dist_from_path=float(position["dist_from_path"]),
                         side=position["side"],
-                        z=position.get("z", defaults.DEFAULT_SOURCE_HEIGHT)
+                        z=position.get("z", defaults.DEFAULT_SOURCE_HEIGHT),
+                        alignment=alignment
                     )
                 )
 
             else:
-                raise ValueError(
+                raise InvalidConfigValueError(
                     f"Invalid position format for source '{name}'."
                     )
 
@@ -295,7 +314,7 @@ class ConfigParser:
 
         missing = required - det_dict.keys()
         if missing:
-            raise MissingConfigKeyError(missing)
+            raise MissingConfigKeyError("detector", missing)
 
         name = det_dict.get("name")
         is_isotropic = det_dict.get("is_isotropic")
@@ -303,19 +322,23 @@ class ConfigParser:
 
         default_detectors = defaults.DETECTOR_EFFICIENCIES
 
-        if eff is None and name in default_detectors.keys():
+        if name in default_detectors.keys() and not eff:
             eff = default_detectors[name]
-        elif eff is not None:
+        elif eff:
             pass
         else:
             raise ValueError(
-                f"The detector {name} is not in the library, and no "
+                f"The detector {name} not found in library. Either "
-                "efficiency was defined. Either specify detector efficiency "
+                f"specify {name}.efficiency or "
-                "or choose one from the following list: "
+                "choose a detector from the following list: "
-                f"{default_detectors.keys()}"
+                f"{default_detectors.keys()}."
             )
 
-        return DetectorSpec(name=name, eff=eff, is_isotropic=is_isotropic)
+        return DetectorSpec(
+            name=name,
+            efficiency=eff,
+            is_isotropic=is_isotropic
+        )
 
     def _warn_unknown_keys(self, section: str, provided: set, allowed: set):
         unknown = provided - allowed

src/pg_rad/inputparser/specs.py

@@ -1,5 +1,6 @@
 from abc import ABC
 from dataclasses import dataclass
+from typing import Literal
 
 
 @dataclass
@@ -42,31 +43,32 @@ class CSVPathSpec(PathSpec):
 
 
 @dataclass
-class SourceSpec(ABC):
+class PointSourceSpec(ABC):
     activity_MBq: float
     isotope: str
     name: str
 
 
 @dataclass
-class AbsolutePointSourceSpec(SourceSpec):
+class AbsolutePointSourceSpec(PointSourceSpec):
     x: float
     y: float
     z: float
 
 
 @dataclass
-class RelativePointSourceSpec(SourceSpec):
+class RelativePointSourceSpec(PointSourceSpec):
     along_path: float
     dist_from_path: float
     side: str
     z: float
+    alignment: Literal["best", "worst"] | None
 
 
 @dataclass
 class DetectorSpec:
     name: str
-    eff: float | None
+    efficiency: float
     is_isotropic: bool
 
 
@@ -76,5 +78,5 @@ class SimulationSpec:
     runtime: RuntimeSpec
     options: SimulationOptionsSpec
     path: PathSpec
-    point_sources: list[SourceSpec]
+    point_sources: list[PointSourceSpec]
     detector: DetectorSpec

src/pg_rad/landscape/builder.py

@@ -1,5 +1,7 @@
 import logging
-from typing import Self
+from typing import Literal, Self
+
+import numpy as np
 
 from .landscape import Landscape
 from pg_rad.dataloader.dataloader import load_data
@@ -113,11 +115,25 @@ class LandscapeBuilder:
                 pos = (s.x, s.y, s.z)
             elif isinstance(s, RelativePointSourceSpec):
                 path = self.get_path()
+
+                if s.alignment:
+                    along_path = self._align_relative_source(
+                        s.along_path,
+                        path,
+                        s.alignment
+                    )
+                    logger.info(
+                        f"Because source {s.name} was set to align with path "
+                        f"({s.alignment} alignment), it was moved to be at "
+                        f"{along_path} m along the path from {s.along_path} m."
+                    )
+                else:
+                    along_path = s.along_path
                 pos = rel_to_abs_source_position(
                     x_list=path.x_list,
                     y_list=path.y_list,
                     path_z=path.z,
-                    along_path=s.along_path,
+                    along_path=along_path,
                     side=s.side,
                     dist_from_path=s.dist_from_path)
             if any(
@@ -158,6 +174,48 @@ class LandscapeBuilder:
             max_size = max(self._path.size)
             self.set_landscape_size((max_size, max_size))
 
+    def _align_relative_source(
+        self,
+        along_path: float,
+        path: "Path",
+        mode: Literal["best", "worst"],
+    ) -> tuple[float, float, float]:
+        """Given the arc length at which the point source is placed,
+            align the source relative to the waypoints of the path. Here,
+            'best' means the point source is moved such that it is
+            perpendicular to the midpoint between two acuisition points.
+            'worst' means the point source is moved such that it is
+            perpendicular to the nearest acquisition point.
+
+            The distance to the path is not affected by this algorithm.
+
+            For more details on alignment, see
+            Fig. 4 and page 24 in Bukartas (2021).
+
+        Args:
+            along_path (float): Current arc length position of the source.
+            path (Path): The path to align to.
+            mode (Literal["best", "worst"]): Alignment mode.
+
+        Returns:
+            along_new (float): The updated arc length position.
+        """
+        ds = np.hypot(
+            path.x_list[1] - path.x_list[0],
+            path.y_list[1] - path.y_list[0],
+        )
+
+        if mode == "worst":
+            along_new = round(along_path / ds) * ds
+
+        elif mode == "best":
+            along_new = (round(along_path / ds - 0.5) + 0.5) * ds
+
+        else:
+            raise ValueError(f"Unknown alignment mode: {mode}")
+
+        return along_new
+
     def build(self):
         landscape = Landscape(
             name=self.name,

src/pg_rad/landscape/director.py

@@ -22,7 +22,7 @@ class LandscapeDirector:
     def build_test_landscape():
         fp = files('pg_rad.data').joinpath(TEST_EXP_DATA)
         source = PointSource(
-            activity_MBq=100E9,
+            activity_MBq=100E6,
             isotope="CS137",
             position=(0, 0, 0)
         )