Merge branch 'dev' of github.com:pim-n/pg-rad into dev

src/pg_rad/background/background.py

@@ -11,7 +11,8 @@ def generate_background(
     cps_array: np.ndarray,
     detector: Detector,
     energy_keV: float,
-    lam_inp: int | None = None
+    lam_inp: int | None = None,
+    seed: int | None = None
 
 ) -> np.ndarray:
     """
@@ -23,7 +24,7 @@ def generate_background(
     else:
         lam = lam_inp
 
-    rng = np.random.default_rng()
+    rng = np.random.default_rng(seed=seed)
     return rng.poisson(lam=lam, size=cps_array.shape)
 
 

src/pg_rad/data/angular_efficiencies/LU_NaIR.csv

@@ -0,0 +1,38 @@
+angle,662
+0,0.027
+10,0.162
+20,0.346
+30,0.517
+40,0.662
+50,0.794
+60,0.882
+70,0.947
+80,0.995
+90,1.000
+100,0.970
+110,0.895
+120,0.778
+130,0.649
+140,0.546
+150,0.477
+160,0.387
+170,0.267
+180,0.205
+-180,0.205
+-170,0.266
+-160,0.385
+-150,0.527
+-140,0.671
+-130,0.764
+-120,0.838
+-110,0.763
+-100,0.838
+-90,0.903
+-80,0.904
+-70,0.898
+-60,0.862
+-50,0.717
+-40,0.337
+-30,0.154
+-20,0.253
+-10,0.125

src/pg_rad/data/detectors.csv

@@ -2,3 +2,4 @@ name,type,is_isotropic
 dummy,NaI,true
 LU_NaI_3inch,NaI,true
 LU_HPGe_90,HPGe,false
+LU_NaIR,NaI,false

src/pg_rad/data/field_efficiencies/LU_NaIR.csv

@@ -0,0 +1,3 @@
+energy_keV,field_efficiency_m2
+0,0
+662,0.0216

src/pg_rad/inputparser/parser.py

@@ -125,7 +125,7 @@ class ConfigParser:
             )
 
         if (
-            seed is not None or
+            seed is not None and
             (isinstance(seed, int) and seed <= 0)
         ):
             raise InvalidConfigValueError(

src/pg_rad/landscape/builder.py

@@ -107,7 +107,8 @@ class LandscapeBuilder:
 
     def set_point_sources(
         self,
-        *sources: AbsolutePointSourceSpec | RelativePointSourceSpec
+        *sources: AbsolutePointSourceSpec | RelativePointSourceSpec,
+        bounds_check: bool = False
     ):
         """Add one or more point sources to the world.
 
@@ -148,7 +149,7 @@ class LandscapeBuilder:
 
             # we dont support -x values, but negative y values are possible as
             # the path is centered in the y direction.
-            if not (
+            if bounds_check and not (
                 (0 <= pos[0] <= self._size[0]) and
                 (-0.5 * self._size[1] <= pos[1] <= 0.5 * self._size[1])
             ):

src/pg_rad/main.py

@@ -2,6 +2,7 @@ import argparse
 import logging
 import sys
 
+from numpy.random import SeedSequence
 from pandas.errors import ParserError
 
 from pg_rad.exceptions.exceptions import (
@@ -77,12 +78,22 @@ def main():
                 gamma_energy_keV: 661
 
         detector: LU_NaI_3inch
+
+        options:
+          seed: 1234
         """
     elif args.config:
         input_config = args.config
-
+    else:
+        logger.warning(
+            "No input provided. Try --example or --config path/to/config.yml. "
+        )
+        sys.exit(1)
     try:
         cp = ConfigParser(input_config).parse()
+        if cp.options.seed is None:
+            entr = SeedSequence().entropy
+            cp.options.seed = int(str(entr)[:6])
         landscape = LandscapeDirector.build_from_config(cp)
         output = SimulationEngine(
             landscape=landscape,

src/pg_rad/physics/fluence.py

@@ -109,7 +109,8 @@ def calculate_counts_along_path(
     detector: "Detector",
     velocity: float,
     points_per_segment: int = 10,
-    bkg_cps_input: int | None = None
+    bkg_cps_input: int | None = None,
+    seed: int | None = None
 ) -> Tuple[np.ndarray, np.ndarray]:
     """Compute the counts recorded in each acquisition period in the landscape.
 
@@ -152,14 +153,16 @@ def calculate_counts_along_path(
 
     if bkg_cps_input is None:
         bkg = generate_background(
-            cps, detector, landscape.point_sources[0].isotope.E
+            cps, detector, landscape.point_sources[0].isotope.E,
+            seed=seed
         )
     elif bkg_cps_input == 0:
         bkg = bkg_cps_input
     else:
         bkg = generate_background(
             cps, detector, landscape.point_sources[0].isotope.E,
-            lam_inp=bkg_cps_input
+            lam_inp=bkg_cps_input,
+            seed=seed
         )
 
     cps_with_bg = cps + bkg

src/pg_rad/plotting/result_plotter.py

@@ -116,6 +116,7 @@ class ResultPlotter:
             ["Air density (kg/m^3)", round(self.landscape.air_density, 3)],
             ["Total path length (m)", round(self.landscape.path.length, 3)],
             ["Readout points", len(self.count_rate_res.integrated_counts)],
+            ["Seed", self.count_rate_res.seed],
             ["Mean background cps", round(self.count_rate_res.mean_bkg_cps, 3)]
         ]
 

src/pg_rad/simulator/engine.py

@@ -48,7 +48,8 @@ class SimulationEngine:
                 self.landscape,
                 self.detector,
                 velocity=self.runtime_spec.speed,
-                bkg_cps_input=self.sim_spec.bkg_cps
+                bkg_cps_input=self.sim_spec.bkg_cps,
+                seed=self.sim_spec.seed
             )
         )
 
@@ -59,7 +60,8 @@ class SimulationEngine:
             sub_points,
             cps,
             int_counts,
-            mean_bkg_counts
+            mean_bkg_counts,
+            self.sim_spec.seed
         )
 
     def _calculate_point_source_distance_to_path(self) -> List[SourceOutput]:

src/pg_rad/simulator/outputs.py

@@ -12,6 +12,7 @@ class CountRateOutput:
     cps: List[float]
     integrated_counts: List[float]
     mean_bkg_cps: List[float]
+    seed: int
 
 
 @dataclass