clean up imports and remove hard-coded __init__ refs

src/pg_rad/configs/__init__.py

@@ -1 +0,0 @@
-__all__ = []

src/pg_rad/configs/filepaths.py

@@ -1,3 +1,4 @@
 ATTENUATION_TABLE = 'attenuation_table.csv'
+ISOTOPE_TABLE = 'isotopes.csv'
 TEST_EXP_DATA = 'test_path_coords.csv'
 LOGGING_CONFIG = 'logging.yml'

src/pg_rad/data/__init__.py

@@ -1 +0,0 @@
-__all__ = []

src/pg_rad/data/isotopes.csv

@@ -0,0 +1,6 @@
+isotope,gamma_energy_keV,branching_ratio
+Cs134,604.7,0.976
+Cs134,795.9,0.855
+Cs137,661.657,0.851
+Co60,1173.228,1.0
+Co60,1332.5,1.0

src/pg_rad/dataloader/__init__.py

@@ -1,8 +0,0 @@
-# do not expose internal logger when running mkinit
-__ignore__ = ["logger"]
-
-from pg_rad.dataloader import dataloader
-
-from pg_rad.dataloader.dataloader import (load_data,)
-
-__all__ = ['dataloader', 'load_data']

src/pg_rad/exceptions/__init__.py

@@ -1,10 +0,0 @@
-# do not expose internal logger when running mkinit
-__ignore__ = ["logger"]
-
-from pg_rad.exceptions import exceptions
-
-from pg_rad.exceptions.exceptions import (ConvergenceError, DataLoadError,
-                                          InvalidCSVError, OutOfBoundsError,)
-
-__all__ = ['ConvergenceError', 'DataLoadError', 'InvalidCSVError',
-           'OutOfBoundsError', 'exceptions']

src/pg_rad/inputparser/parser.py

@@ -11,6 +11,7 @@ from pg_rad.exceptions.exceptions import (
     InvalidYAMLError
 )
 from pg_rad.configs import defaults
+from pg_rad.isotopes.isotope import get_isotope
 
 from .specs import (
     MetadataSpec,
@@ -276,7 +277,9 @@ class ConfigParser:
         specs: List[PointSourceSpec] = []
 
         for name, params in source_dict.items():
-            required = {"activity_MBq", "isotope", "position"}
+            required = {
+                "activity_MBq", "isotope", "position", "gamma_energy_keV"
+            }
             if not isinstance(params, dict):
                 raise InvalidConfigValueError(
                     f"sources.{name} is not defined correctly."
@@ -288,7 +291,10 @@ class ConfigParser:
                 raise MissingConfigKeyError(name, missing)
 
             activity = params.get("activity_MBq")
-            isotope = params.get("isotope")
+            isotope_name = params.get("isotope")
+            gamma_energy_keV = params.get("gamma_energy_keV")
+
+            isotope = get_isotope(isotope_name, gamma_energy_keV)
 
             if not isinstance(activity, int | float) or activity <= 0:
                 raise InvalidConfigValueError(

src/pg_rad/isotopes/__init__.py

@@ -1,9 +0,0 @@
-# do not expose internal logger when running mkinit
-__ignore__ = ["logger"]
-
-from pg_rad.isotopes import isotope
-
-from pg_rad.isotopes.isotope import (CS137, Isotope, get_isotope,
-                                     preset_isotopes,)
-
-__all__ = ['CS137', 'Isotope', 'get_isotope', 'isotope', 'preset_isotopes']

src/pg_rad/isotopes/isotope.py

@@ -1,5 +1,8 @@
-from typing import Dict, Type
+from importlib.resources import files
 
+from pandas import read_csv
+
+from pg_rad.configs.filepaths import ISOTOPE_TABLE
 from pg_rad.exceptions.exceptions import InvalidIsotopeError
 from pg_rad.physics.attenuation import get_mass_attenuation_coeff
 
@@ -30,22 +33,35 @@ class Isotope:
         self.mu_mass_air = get_mass_attenuation_coeff(E / 1000)
 
 
-class CS137(Isotope):
+def get_isotope(isotope: str, energy_gamma_keV: float) -> Isotope:
-    def __init__(self):
+    """Lazy factory function to create isotope objects."""
-        super().__init__(
+    path = files('pg_rad.data').joinpath(ISOTOPE_TABLE)
-            name="Cs-137",
+    df = read_csv(path)
-            E=661.66,
+
-            b=0.851
+    isotope_df = df[df['isotope'] == isotope]
+
+    if isotope_df.empty:
+        raise InvalidIsotopeError(f"No data available for isotope {isotope}.")
+
+    tol = 0.01 * energy_gamma_keV
+    closest_energy = isotope_df[
+        (isotope_df['gamma_energy_keV'] >= energy_gamma_keV - tol) &
+        (isotope_df['gamma_energy_keV'] <= energy_gamma_keV + tol)
+    ]
+
+    if closest_energy.empty:
+        available_gammas = ', '.join(
+            str(x)+' keV' for x in isotope_df['gamma_energy_keV'].to_list()
+        )
+        raise InvalidIsotopeError(
+            f"No gamma of {energy_gamma_keV}±{tol} keV "
+            f"found for isotope {isotope}. "
+            f"Available gammas are: {available_gammas}"
         )
 
-
+    matched_row = closest_energy.iloc[0]
-preset_isotopes: Dict[str, Type[Isotope]] = {
+    return Isotope(
-    "Cs137": CS137
+        name=isotope,
-}
+        E=matched_row['gamma_energy_keV'],
-
+        b=matched_row['branching_ratio']
-
+    )
-def get_isotope(isotope_str: str) -> Isotope:
-    """Lazy factory function to create isotope objects."""
-    if isotope_str not in preset_isotopes:
-        raise InvalidIsotopeError(f"Unknown isotope: {isotope_str}")
-    return preset_isotopes[isotope_str]()

src/pg_rad/logger/__init__.py

@@ -1,5 +0,0 @@
-from pg_rad.logger import logger
-
-from pg_rad.logger.logger import (setup_logger,)
-
-__all__ = ['logger', 'setup_logger']

src/pg_rad/main.py

@@ -59,7 +59,7 @@ def main():
             length: 1000
             segments:
                 - straight
-                - turn_left
+                - turn_left: 45
             direction: negative
 
         sources:
@@ -67,6 +67,7 @@ def main():
                 activity_MBq: 100
                 position: [250, 100, 0]
                 isotope: Cs137
+                gamma_energy_keV: 661
 
         detector:
             name: dummy

src/pg_rad/objects/__init__.py

@@ -1,11 +0,0 @@
-# do not expose internal logger when running mkinit
-__ignore__ = ["logger"]
-
-from pg_rad.objects import objects
-from pg_rad.objects import sources
-
-from pg_rad.objects.objects import (BaseObject,)
-from pg_rad.objects.sources import (PointSource,)
-
-__all__ = ['BaseObject', 'PointSource', 'objects',
-           'sources']

src/pg_rad/objects/sources.py

@@ -1,7 +1,7 @@
 import logging
 
 from .objects import BaseObject
-from pg_rad.isotopes.isotope import Isotope, get_isotope
+from pg_rad.isotopes.isotope import Isotope
 
 logger = logging.getLogger(__name__)
 
@@ -12,7 +12,7 @@ class PointSource(BaseObject):
     def __init__(
             self,
             activity_MBq: int,
-            isotope: str,
+            isotope: Isotope,
             position: tuple[float, float, float] = (0, 0, 0),
             name: str | None = None,
             color: str = 'red'
@@ -40,7 +40,7 @@ class PointSource(BaseObject):
         super().__init__(position, name, color)
 
         self.activity = activity_MBq
-        self.isotope: Isotope = get_isotope(isotope)
+        self.isotope = isotope
 
         logger.debug(f"Source created: {self.name}")
 

src/pg_rad/path/__init__.py

@@ -1,8 +0,0 @@
-# do not expose internal logger when running mkinit
-__ignore__ = ["logger"]
-
-from pg_rad.path import path
-
-from pg_rad.path.path import (Path, PathSegment, path_from_RT90,)
-
-__all__ = ['Path', 'PathSegment', 'path', 'path_from_RT90']

src/pg_rad/physics/__init__.py

@@ -1,12 +0,0 @@
-# do not expose internal logger when running mkinit
-__ignore__ = ["logger"]
-from pg_rad.physics import attenuation
-from pg_rad.physics import fluence
-
-from pg_rad.physics.attenuation import (get_mass_attenuation_coeff,)
-from pg_rad.physics.fluence import (calculate_fluence_along_path,
-                                    calculate_fluence_at, phi,)
-
-__all__ = ['attenuation', 'calculate_fluence_along_path',
-           'calculate_fluence_at', 'fluence', 'get_mass_attenuation_coeff',
-           'phi']

src/pg_rad/plotting/__init__.py

@@ -1,7 +0,0 @@
-# do not expose internal logger when running mkinit
-__ignore__ = ["logger"]
-from pg_rad.plotting import landscape_plotter
-
-from pg_rad.plotting.landscape_plotter import (LandscapeSlicePlotter,)
-
-__all__ = ['LandscapeSlicePlotter', 'landscape_plotter']

src/pg_rad/plotting/result_plotter.py

@@ -105,7 +105,7 @@ class ResultPlotter:
         data = [
             [
                 s.name,
-                s.isotope,
+                s.isotope+f" ({s.primary_gamma} keV)",
                 s.activity,
                 "("+", ".join(f"{val:.2f}" for val in s.position)+")",
                 round(s.dist_from_path, 2)

src/pg_rad/simulator/engine.py

@@ -62,6 +62,7 @@ class SimulationEngine:
                 SourceOutput(
                     s.name,
                     s.isotope.name,
+                    s.isotope.E,
                     s.activity,
                     s.pos,
                     dist_to_path)

src/pg_rad/simulator/outputs.py

@@ -13,6 +13,7 @@ class CountRateOutput:
 class SourceOutput:
     name: str
     isotope: str
+    primary_gamma: float
     activity: float
     position: Tuple[float, float, float]
     dist_from_path: float