remove mkinit requirement

prepare for release 0.1.0

CITATION.cff

@@ -0,0 +1,26 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: PG-RAD - Primary Gamma RADiation Simulator
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Pim
+    family-names: Nelissen
+    email: pi0274ne-s@student.lu.se
+    affiliation: Lund University
+repository-code: 'https://github.com/pim-n/pg-rad'
+abstract: >-
+  Primary Gamma RADiation (PG-RAD) is a deterministic
+  landscape simulator to simulate vehicle-based gamma source
+  localization scenarios.
+keywords:
+  - gamma spectrometry
+  - mobile gamma spectrometry
+  - emergency preparedness
+  - environmental radiation
+license: MIT
+

docs/config-spec.md

@@ -2,10 +2,7 @@
     To get started quickly, you may copy and modify one of the example configs found [here](quickstart.md#example-configs).
 
 
-The config file must be a [YAML](https://yaml.org/) file. YAML is a serialization language that works with key-value pairs, but in a syntax more readable than some other alternatives. In YAML, the indentation matters. I
-
-
-The remainder of this chapter will explain the different required and optionals keys, what they represent, and allowed values. 
+The config file must be a [YAML](https://yaml.org/) file. YAML is a serialization language that works with key-value pairs, but in a syntax more readable than some other alternatives. The remainder of this chapter will explain the different required and optionals keys, what they represent, and allowed values.
 
 ## Required keys
 
@@ -124,11 +121,11 @@ Like with the lengths, if a turn segment has no angle specified, a random one (w
     Letting PG-RAD randomly assign lengths and angles can cause (expected) issues. That is because of physics restrictions. If the combination of length, angle (radius) and velocity of the vehicle is such that the centrifugal force makes it impossible to take this turn, PG-RAD will raise an error. To fix it, you can 1) reduce the speed; 2) define a smaller angle for the turn; or 3) assign more length to the turn segment.
 
 !!! info
-    For more information about how procedural roads are generated, including the random sampling of lengths and angles, see X
+    For more information about how procedural roads are generated, including the random sampling of lengths and angles, see [this](explainers/prefab_roads.ipynb) explainer.
 
 ### Sources
 
-Currently, the only type of source supported is a point source. Point sources can be added under the `sources` key, where the **subkey is the name** of the source:
+Currently, the only type of source supported is an isotropic point source. However, an arbitrary number of point sources can be added to the landscape. Point sources can be added under the `sources` key, where the **subkey is the name** of the source:
 
 ```yaml
 sources:
@@ -190,21 +187,10 @@ Note that side is relative to the direction of travel. The path will by default
 
 ### Detector
 
-The final required key is the `detector`. Currently, only isotropic detectors are supported. Nonetheless, you must specify it with `name`, `is_isotropic` and `efficiency`:
+The final required key is the `detector`. Currently, custom detectors are not yet supported and you must choose from a list of existing detectors:
 
 ```yaml
-detector:
-  name: test
-  is_isotropic: True
-  efficiency: 0.02
-```
-
-Note there are some existing detectors available, where efficiency is not required and will be looked up by PG-RAD itself:
-
-```yaml
-detector:
-  name: NaIR
-  is_isotropic: True
+detector: LU_HPGe_90
 ```
 
 ## Optional keys

docs/explainers/count_rate_along_path.ipynb

@@ -0,0 +1,121 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "a8d303ad",
+   "metadata": {},
+   "source": [
+    "# Gamma detectors along a path"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "08dda386",
+   "metadata": {},
+   "source": [
+    "## Fluence rate at $\\vec{r}$\n",
+    "\n",
+    "Let $\\vec{r}_{p} = (x_{p},y_{p},z_{p})$ denote the location of a point source $p$. Let $\\vec{r}_{i} = (x_{i},y_{i},z_{i})$ denote an arbitrary point in space. The primary photon fluence rate at $\\vec{r}$ is then given by\n",
+    "\n",
+    "$$\n",
+    "\\dot{\\phi}(r) = \\frac{A n_\\gamma \\exp(-\\mu_{air} r)}{4\\pi r^2}\n",
+    "$$\n",
+    "\n",
+    "where $r = ||\\vec{r}_p - \\vec{r}_i ||$. The units are $\\dot{\\phi} \\sim \\frac{\\text{photons}}{s \\cdot m^2}$\n",
+    "\n",
+    "## Count rate\n",
+    "\n",
+    "Gamma detectors are not perfectly efficient and efficiency is dependent on both photon energy $E_\\gamma$ and incident angle $\\theta$ [1].\n",
+    "\n",
+    "- the field efficiency $\\varepsilon_D (E_\\gamma) \\in [0, 1]$, in units of area $\\text{m}^2$,\n",
+    "- the relative angular efficiency $\\varepsilon_\\theta (E_\\gamma, \\theta) \\in [0, 1]$, dimensionless.\n",
+    "\n",
+    "The total efficiency of the detector is then defined as\n",
+    "\n",
+    "$$\n",
+    "\\varepsilon(E_\\gamma, \\theta) = \\varepsilon_D (E_\\gamma) \\varepsilon_\\theta (E_\\gamma, \\theta) \\; .\n",
+    "$$\n",
+    "\n",
+    "Where $\\varepsilon(E_\\gamma, \\theta) \\sim \\text{m}^2$.\n",
+    "\n",
+    "If the detector $D$ is positioned at $\\vec{r}_i$, the **count rate** becomes\n",
+    "\n",
+    "$$\n",
+    "\\dot{N}(r, E_\\gamma, \\theta) = \\varepsilon(E_\\gamma, \\theta) \\phi(r)\n",
+    "$$\n",
+    "\n",
+    "where $\\dot{N} \\sim \\frac{\\text{counts}}{s}$.\n",
+    "\n",
+    "## Acquisiton time \n",
+    "\n",
+    "The acquisition time window $t_{w}$ is the time during which counts are accumulated in the detector until readout into the digital system. A typical $t_{w}$ in mobile gamma spectrometry is 1 to 10 seconds [2]. \n",
+    "\n",
+    "## Integration of counts\n",
+    "\n",
+    "Suppose an acquisition time of $t_{w}$ seconds and a fixed velocity $v$ in meters per seconds. Let $R(u)$ describe a road of $L$ meters long in the xy-plane, described as a function of arc length $u$ in meters (distance traveled along the road), where $u \\in [0, L]$. The euclidian norm between the point $R(u)$ and point source $\\vec{r}_p$ is then\n",
+    "\n",
+    "$$\n",
+    "r(u) = || \\vec{r}_p - R(u) ||\n",
+    "$$\n",
+    "\n",
+    "Assuming a fixed velocity $v$, the distance traveled during one acquisition window $t_{w}$ is $\\Delta_s \\equiv vt_{w}$ meters. The path is divided into $K = L/\\Delta s$ segments, where the $k$-th segment represents the interval\n",
+    "\n",
+    "$$\n",
+    "u \\in [(k-1) \\Delta_s, k\\Delta_s] \\; , \\; k = 1, 2, \\dots, K\n",
+    "$$\n",
+    "\n",
+    "The total count rate acquired during segment $k$-th is then\n",
+    "\n",
+    "$$\n",
+    "N_{w}(k) = \\frac{1}{v} \\int_{(k-1)\\Delta_s}^{k\\Delta_s} \\underbrace{\\dot{N}(r(u), E_\\gamma, \\theta(u))}_{\\text{CPS}} du\n",
+    "$$\n",
+    "\n",
+    "## Numerical approximation\n",
+    "\n",
+    "Let us divide each segment into $N$ equally spaced points with step size $\\Delta u = \\Delta s / N$. Applying the trapezoidal rule then gives\n",
+    "\n",
+    "$$\n",
+    "N_w(k) \\approx \\frac{\\Delta u}{v}\n",
+    "\\left[\n",
+    "\\frac{\\dot{N}_0 + \\dot{N}_N}{2}\n",
+    "+ \\sum_{n=1}^{N-1} \\dot{N}_n\n",
+    "\\right],\n",
+    "$$\n",
+    "\n",
+    "where\n",
+    "\n",
+    "$$\n",
+    "\\dot{N}_n = \\dot{N}\\big(r(u_n), E_\\gamma, \\theta(u_n)\\big), \\quad\n",
+    "u_n = (k-1)\\Delta s + n \\Delta u.\n",
+    "$$\n",
+    "\n",
+    "## References\n",
+    "\n",
+    "[1] A. Bukartas, ‘Assessment of mobile radiometry data in radiological emergencies using Bayesian statistical methods’, thesis/doccomp, Lund University, 2021. Accessed: Jan. 19, 2026. [Online]. Available: http://lup.lub.lu.se/record/4c298e71-3278-42a7-818a-6f17a5121d56\n",
+    "\n",
+    "[2] R. Finck, A. Bukartas, M. Jönsson, and C. Rääf, ‘Maximum detection distances for gamma emitting point sources in mobile gamma spectrometry’, Applied Radiation and Isotopes, vol. 184, p. 110195, Jun. 2022, doi: 10.1016/j.apradiso.2022.110195.\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": ".venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/quickstart.md

@@ -22,13 +22,18 @@ Primary Gamma RADiation landscape tool
 
 If you get something like `pgrad: command not found`, please consult the [installation guide](installation.md).
 
-You can run a quick test scenario as follows:
+You can run a quick test by running the example landscape as follows:
 
 ```
-pgrad --test
+pgrad --example
 ```
 
-This should produce a plot of a scenario containing a single point source and a path.
+This should produce an output like
+
+```
+INFO: Landscape built successfully: Example landscape
+WARNING: No output produced. Use --save flag to save outputs and/or --showplots to display interactive plots.
+```
 
 ## Running PG-RAD
 
@@ -38,11 +43,11 @@ In order to use the CLI for your own simulations, you need to provide a *config
 pgrad --config path/to/my_config.yml
 ```
 
-where `path/to/my_config.yml` points to your config file.
+where `path/to/my_config.yml` points to your config file. To check the results live, add the `--showplots` flag. If you want to save the results directly, then add the `--save` flag (you can use them at the same time as well).
 
 ## Example configs
 
-The easiest way is to take one of these example configs, and adjust them as needed. Alternatively, there is a detailed guide on how to write your own config file [here](config-spec.md).
+The easiest way to get started is to take one of these example configs, and adjust them as needed. Alternatively, there is a detailed guide on how to write your own config file [here](config-spec.md).
 
 === "Example 1"
 
@@ -61,15 +66,14 @@ The easiest way is to take one of these example configs, and adjust them as need
     sources:
       source1:
       activity_MBq: 1000
-      isotope: CS137
+      isotope: Cs137
+      gamma_energy_keV: 662
       position:
         along_path: 100
         dist_from_path: 50
         side: left
     
-    detector:
-      name: dummy
-      is_isotropic: True
+    detector: dummy
     ```
 
 === "Example 2"
@@ -89,21 +93,21 @@ The easiest way is to take one of these example configs, and adjust them as need
     sources:
       source1:
         activity_MBq: 1000
-        isotope: CS137
+        isotope: Cs137
+        gamma_energy_keV: 662
         position: [104.3, 32.5, 0]
       source2:
         activity_MBq: 100
-        isotope: CS137
+        isotope: Cs137
+        gamma_energy_keV: 662
         position: [0, 0, 0]
         
-    detector:
-      name: dummy
-      is_isotropic: True
+    detector: dummy
     ```
 
 === "Example 3"
 
-    This is an example of a procedural path with random apportionment of total length and random angles being assigned to turns. The parameter `alpha` is optional, and is related to randomness. A higher value leads to more uniform apportionment of lengths and a lower value to more random apportionment. More information about `alpha` can be found [here](pg-rad-config-spec.md).
+    This is an example of a procedural path with random apportionment of total length and random angles being assigned to turns. The parameter `alpha` is optional, and is related to randomness. A higher value leads to more uniform apportionment of lengths and a lower value to more random apportionment. More information about `alpha` can be found [here](explainers/prefab_roads.ipynb).
 
     ``` yaml
     name: Example 3
@@ -121,12 +125,11 @@ The easiest way is to take one of these example configs, and adjust them as need
     sources:
       source1:
         activity_MBq: 1000
-        isotope: CS137
+        isotope: Cs137
+        gamma_energy_keV: 662
         position: [0, 0, 0]
 
-    detector:
-      name: dummy
-      is_isotropic: True
+    detector: dummy
     ```
 
 === "Example 4"
@@ -148,12 +151,11 @@ The easiest way is to take one of these example configs, and adjust them as need
     sources:
       source1:
         activity_MBq: 1000
-        isotope: CS137
+        isotope: Cs137
+        gamma_energy_keV: 662
         position: [0, 0, 0]
         
-    detector:
-      name: dummy
-      is_isotropic: True
+    detector: dummy
     ```
 
 === "Example 5"
@@ -178,10 +180,9 @@ The easiest way is to take one of these example configs, and adjust them as need
     sources:
       source1:
         activity_MBq: 1000
-        isotope: CS137
+        isotope: Cs137
+        gamma_energy_keV: 662
         position: [0, 0, 0]
         
-    detector:
-      name: dummy
-      is_isotropic: True
+    detector: dummy
     ```

pyproject.toml

@@ -6,16 +6,16 @@ build-backend = "setuptools.build_meta"
 where = ["src"]
 
 [tool.setuptools.package-data]
-"pg_rad.data" = ["*.csv"]
+"pg_rad.data" = ["**/*.csv"]
 "pg_rad.configs" = ["*.yml"]
 
 [project]
-name = "pg-rad"
-version = "0.2.1"
+name = "pgrad"
+version = "0.1.0"
 authors = [
   { name="Pim Nelissen", email="pi0274ne-s@student.lu.se" },
 ]
-description = "Primary Gamma RADiation Landscape"
+description = "PG-RAD - Primary Gamma RADiation Simulator"
 readme = "README.md"
 requires-python = ">=3.12.4,<3.13"
 dependencies = [
@@ -37,4 +37,4 @@ Issues = "https://github.com/pim-n/pg-rad/issues"
 
 [project.optional-dependencies]
 
-dev = ["pytest", "mkinit", "notebook", "mkdocs-material", "mkdocstrings-python", "mkdocs-jupyter", "flake8"]
+dev = ["pytest", "notebook", "mkdocs-material", "mkdocstrings-python", "mkdocs-jupyter", "flake8"]

requirements.txt

@@ -1,6 +0,0 @@
-matplotlib>=3.9.2
-notebook>=7.2.1
-numpy>=2
-pandas>=2.3.1
-piecewise_regression==1.5.0
-pyyaml>=6.0.2

src/pg_rad/background/background.py

@@ -9,11 +9,23 @@ from pg_rad.detector.detector import Detector
 
 def generate_background(
     cps_array: np.ndarray,
+    detector: Detector,
+    energy_keV: float,
+    lam_inp: int | None = None,
+    seed: int | None = None
+
 ) -> np.ndarray:
     """
     Generate synthetic background cps for a given detector and energy.
     """
-    pass
+    if not lam_inp:
+        ROI_lo, ROI_hi = get_roi_from_fwhm(detector, energy_keV)
+        lam = get_cps_from_roi(detector, ROI_lo, ROI_hi)
+    else:
+        lam = lam_inp
+
+    rng = np.random.default_rng(seed=seed)
+    return rng.poisson(lam=lam, size=cps_array.shape)
 
 
 def fwhm(A: float, B: float, C: float, E: float) -> float:
@@ -39,8 +51,13 @@ def get_cps_from_roi(
     roi_hi: float
 ) -> float:
 
+    try:
         csv = files('pg_rad.data.backgrounds').joinpath(detector.name+'.csv')
         data = read_csv(csv)
+    except FileNotFoundError:
+        raise NotImplementedError(
+            f"Detector {detector.name} does not have backgrounds implemented."
+        )
 
     # get indices of nearest bins
     idx_min = (data["Energy"] - roi_lo).abs().idxmin()

src/pg_rad/data/angular_efficiencies/LU_HPGe_90.csv

@@ -18,6 +18,7 @@ angle,662,1173,1332
 160,1.113,1.096,1.099
 170,1.091,1.076,1.083
 180,1.076,1.066,1.078
+-180,1.076,1.066,1.078
 -170,1.102,1.091,1.093
 -160,1.122,1.100,1.102
 -150,1.128,1.105,1.093

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/backgrounds/dummy.csv

@@ -0,0 +1,3 @@
+Energy,Data,cps
+0,0,0
+10000,0,0

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 +1,5 @@
+energy_keV,field_efficiency_m2
+0,0
+661.657,0.0261
+1173.228,0.0203
+1332.492,0.0166

src/pg_rad/inputparser/parser.py

@@ -104,7 +104,7 @@ class ConfigParser:
     def _parse_options(self) -> SimulationOptionsSpec:
         options = self.config.get("options", {})
 
-        allowed = {"air_density_kg_per_m3", "seed"}
+        allowed = {"air_density_kg_per_m3", "seed", "bkg_cps"}
         self._warn_unknown_keys(
             section="options",
             provided=set(options.keys()),
@@ -116,23 +116,33 @@ class ConfigParser:
             defaults.DEFAULT_AIR_DENSITY
         )
         seed = options.get("seed")
+        bkg_cps = options.get("bkg_cps")
 
         if not isinstance(air_density, float) or air_density <= 0:
             raise InvalidConfigValueError(
                 "options.air_density_kg_per_m3 must be a positive float "
                 "in kg/m^3."
             )
+
         if (
-            seed is not None or
+            seed is not None and
             (isinstance(seed, int) and seed <= 0)
         ):
             raise InvalidConfigValueError(
                 "Seed must be a positive integer value."
             )
 
+        if bkg_cps is not None and (
+            not isinstance(bkg_cps, int) or bkg_cps < 0
+        ):
+            raise InvalidConfigValueError(
+                "Background CPS must be an integer >= 0."
+            )
+
         return SimulationOptionsSpec(
             air_density=air_density,
             seed=seed,
+            bkg_cps=bkg_cps
         )
 
     def _parse_path(self) -> PathSpec:

src/pg_rad/inputparser/specs.py

@@ -18,6 +18,7 @@ class RuntimeSpec:
 class SimulationOptionsSpec:
     air_density: float
     seed: int | None = None
+    bkg_cps: int | None = None
 
 
 @dataclass

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.
 
@@ -145,8 +146,12 @@ class LandscapeBuilder:
                     along_path=along_path,
                     side=s.side,
                     dist_from_path=s.dist_from_path)
-            if any(
-                p < 0 or p >= s for p, s in zip(pos, self._size)
+
+            # we dont support -x values, but negative y values are possible as
+            # the path is centered in the y direction.
+            if bounds_check and not (
+                (0 <= pos[0] <= self._size[0]) and
+                (-0.5 * self._size[1] <= pos[1] <= 0.5 * self._size[1])
             ):
                 raise OutOfBoundsError(
                     "One or more sources attempted to "

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 (
@@ -17,6 +18,7 @@ from pg_rad.inputparser.parser import ConfigParser
 from pg_rad.landscape.director import LandscapeDirector
 from pg_rad.plotting.result_plotter import ResultPlotter
 from pg_rad.simulator.engine import SimulationEngine
+from pg_rad.utils.export import generate_folder_name, save_results
 
 
 def main():
@@ -29,9 +31,9 @@ def main():
         help="Build from a config file."
     )
     parser.add_argument(
-        "--test",
+        "--example",
         action="store_true",
-        help="Load and run the test landscape."
+        help="Load and run an example landscape."
     )
     parser.add_argument(
         "--loglevel",
@@ -39,18 +41,23 @@ def main():
         choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
     )
     parser.add_argument(
-        "--saveplot",
+        "--showplots",
         action="store_true",
-        help="Save the plot or not."
+        help="Show the plots immediately."
+    )
+    parser.add_argument(
+        "--save",
+        action="store_true",
+        help="Save the outputs"
     )
 
     args = parser.parse_args()
     setup_logger(args.loglevel)
     logger = logging.getLogger(__name__)
 
-    if args.test:
-        test_yaml = """
-        name: Test landscape
+    if args.example:
+        input_config = """
+        name: Example landscape
         speed: 8.33
         acquisition_time: 1
 
@@ -66,27 +73,27 @@ def main():
         sources:
             test_source:
                 activity_MBq: 100
-                position: [250, 100, 0]
+                position: [250, 30, 0]
                 isotope: Cs137
                 gamma_energy_keV: 661
 
         detector: LU_NaI_3inch
+
+        options:
+          seed: 1234
         """
-
-        cp = ConfigParser(test_yaml).parse()
-        landscape = LandscapeDirector.build_from_config(cp)
-        output = SimulationEngine(
-            landscape=landscape,
-            runtime_spec=cp.runtime,
-            sim_spec=cp.options,
-        ).simulate()
-
-        plotter = ResultPlotter(landscape, output)
-        plotter.plot()
-
     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(args.config).parse()
+        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,
@@ -95,7 +102,18 @@ def main():
         ).simulate()
 
         plotter = ResultPlotter(landscape, output)
+        if args.save:
+            folder_name = generate_folder_name(output)
+            save_results(output, folder_name)
+            plotter.save(folder_name)
+        if args.showplots:
             plotter.plot()
+
+        if not (args.save or args.showplots):
+            logger.warning(
+                "No output produced. Use --save flag to save outputs and/or "
+                "--showplots to display interactive plots."
+            )
     except (
         MissingConfigKeyError,
         KeyError
@@ -111,7 +129,8 @@ def main():
         OutOfBoundsError,
         DimensionError,
         InvalidIsotopeError,
-            InvalidConfigValueError
+        InvalidConfigValueError,
+        NotImplementedError
     ) as e:
         logger.critical(e)
         logger.critical(

src/pg_rad/physics/fluence.py

@@ -2,6 +2,8 @@ from typing import Tuple, TYPE_CHECKING
 
 import numpy as np
 
+from pg_rad.background.background import generate_background
+
 if TYPE_CHECKING:
     from pg_rad.landscape.landscape import Landscape
     from pg_rad.detector.detector import Detector
@@ -106,7 +108,10 @@ def calculate_counts_along_path(
     landscape: "Landscape",
     detector: "Detector",
     velocity: float,
+    t_acq: float,
     points_per_segment: int = 10,
+    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.
 
@@ -114,6 +119,7 @@ def calculate_counts_along_path(
         landscape (Landscape): _description_
         detector (Detector): _description_
         points_per_segment (int, optional): _description_. Defaults to 100.
+        bkg_cps_input (int | None, optional): Optional background CPS.
 
     Returns:
         Tuple[np.ndarray, np.ndarray]: Array of acquisition points and
@@ -146,12 +152,41 @@ def calculate_counts_along_path(
         landscape, full_positions, detector
     )
 
-    # reshape so each segment is on a row
-    cps_per_seg = cps.reshape(num_segments, points_per_segment)
+    if bkg_cps_input is None:
+        bkg = generate_background(
+            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,
+            seed=seed
+        )
 
-    du = s[1] - s[0]
-    integrated_counts = np.trapezoid(cps_per_seg, dx=du, axis=1) / velocity
-    int_counts_result = np.zeros(num_points)
-    int_counts_result[1:] = integrated_counts
+    cps_with_bg = cps + bkg
 
-    return original_distances, s, cps, int_counts_result
+    # Integrate along time dimension. see e.g. Bukartas (2021 doccomp.)
+    t = s / abs(velocity)
+
+    # acquisition bins
+    t_bins = np.arange(0, t[-1] + t_acq, t_acq)
+
+    int_counts = np.zeros(len(t_bins) - 1)
+    acq_points = np.zeros(len(t_bins) - 1)
+
+    for i in range(len(t_bins) - 1):
+        mask = (t >= t_bins[i]) & (t < t_bins[i + 1])
+
+        int_counts[i] = np.trapezoid(cps_with_bg[mask], t[mask])
+        acq_points[i] = np.mean(s[mask])
+
+    return (
+        acq_points[:-1],
+        s[:-1],
+        cps_with_bg[:-1],
+        int_counts[:-1],
+        np.mean(bkg)
+        )

src/pg_rad/plotting/landscape_plotter.py

@@ -4,11 +4,10 @@ from matplotlib import pyplot as plt
 from matplotlib.axes import Axes
 from matplotlib.patches import Circle
 
-from numpy import median
-
 from pg_rad.landscape.landscape import Landscape
 
 logger = logging.getLogger(__name__)
+plt.set_loglevel(level='warning')
 
 
 class LandscapeSlicePlotter:
@@ -58,12 +57,7 @@ class LandscapeSlicePlotter:
         ax.set_xlim(right=max(width, .5*height))
 
         # if the road is very flat, we center it vertically (looks better)
-        if median(landscape.path.y_list) == 0:
-            h = max(height, .5*width)
-            ax.set_ylim(bottom=-h//2,
-                        top=h//2)
-        else:
-            ax.set_ylim(top=max(height, .5*width))
+        ax.set_ylim(bottom=-.5*width, top=.5*width)
 
         ax.set_xlabel("X [m]")
         ax.set_ylabel("Y [m]")

src/pg_rad/plotting/result_plotter.py

@@ -10,6 +10,9 @@ from pg_rad.simulator.outputs import SimulationOutput
 from pg_rad.landscape.landscape import Landscape
 
 
+plt.set_loglevel(level='warning')
+
+
 class ResultPlotter:
     def __init__(self, landscape: Landscape, output: SimulationOutput):
         self.landscape = landscape
@@ -23,6 +26,15 @@ class ResultPlotter:
 
         plt.show()
 
+    def save(self, path: str, landscape_z: float = 0) -> None:
+        fig_1 = self._plot_main(landscape_z)
+        fig_2 = self._plot_detector()
+        fig_3 = self._plot_metadata()
+
+        fig_1.savefig(path+"/main.jpg")
+        fig_2.savefig(path+"/detector.jpg")
+        fig_3.savefig(path+"/metadata.jpg")
+
     def _plot_main(self, landscape_z):
         fig = plt.figure(figsize=(12, 8))
         fig.suptitle(self.landscape.name)
@@ -37,10 +49,11 @@ class ResultPlotter:
         self._draw_cps(ax_cps)
 
         ax_counts = fig.add_subplot(gs[0, 1])
-        self._draw_count_rate(ax_counts)
+        self._draw_counts(ax_counts)
 
         ax_landscape = fig.add_subplot(gs[1, :])
         self._plot_landscape(ax_landscape, landscape_z)
+        return fig
 
     def _plot_detector(self):
         det = self.landscape.detector
@@ -61,6 +74,7 @@ class ResultPlotter:
             ]
 
             self._draw_angular_efficiency_polar(ax_polar, det, energies[0])
+        return fig
 
     def _plot_metadata(self):
         fig, axs = plt.subplots(2, 1, figsize=(10, 6))
@@ -68,6 +82,7 @@ class ResultPlotter:
 
         self._draw_table(axs[0])
         self._draw_source_table(axs[1])
+        return fig
 
     def _plot_landscape(self, ax, z):
         lp = LandscapeSlicePlotter()
@@ -77,17 +92,35 @@ class ResultPlotter:
     def _draw_cps(self, ax):
         x = self.count_rate_res.sub_points
         y = self.count_rate_res.cps
-        ax.plot(x, y, color='b')
+        ax.plot(x, y, color='b', label=f'max(CPS) = {y.max():.2f}')
+        ax.legend(handlelength=0, handletextpad=0, fancybox=True)
         ax.set_title('Counts per second (CPS)')
         ax.set_xlabel('Arc length s [m]')
         ax.set_ylabel('CPS [s$^{-1}$]')
 
-    def _draw_count_rate(self, ax):
-        x = self.count_rate_res.acquisition_points
-        y = self.count_rate_res.integrated_counts
-        ax.plot(x, y, color='r', linestyle='--', alpha=0.2)
+    def _draw_counts(self, ax):
+        x = self.count_rate_res.distance[1:]
+        y = self.count_rate_res.integrated_counts[1:]
+
+        yerr = np.sqrt(y)
+        peak_idx = y.argmax()
+
+        ax.fill_between(
+            x,
+            y - yerr,
+            y + yerr,
+            color='red',
+            alpha=0.15,
+        )
+
+        ax.plot(
+            x, y,
+            color='r', linestyle='--', alpha=0.2,
+            label=rf'max(counts)={y[peak_idx]:.2f} $\pm$ {yerr[peak_idx]:.2f}'
+        )
+        ax.legend(handlelength=0, handletextpad=0, fancybox=True)
         ax.scatter(x, y, color='r', marker='x')
-        ax.set_title('Integrated counts')
+        ax.set_title('Counts')
         ax.set_xlabel('Arc length s [m]')
         ax.set_ylabel('N')
 
@@ -99,6 +132,8 @@ 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)]
         ]
 
         ax.table(
@@ -124,7 +159,7 @@ class ResultPlotter:
         # list field efficiencies for each primary gamma in the landscape
         effs = {e: det.get_efficiency(e) for e in source_energies}
         formatted_effs = ", ".join(
-            f"{value:.3f} @ {key:.1f} keV"
+            f"{value:.5f} @ {key:.1f} keV"
             for key, value in effs.items()
         )
         ax.set_axis_off()
@@ -201,6 +236,5 @@ class ResultPlotter:
 
         theta_rad = np.radians(theta_deg)
 
-        print(theta_rad)
         ax.plot(theta_rad, eff)
         ax.set_title(f"Rel. angular efficiency @ {energy_keV:.1f} keV")

src/pg_rad/simulator/engine.py

@@ -3,6 +3,7 @@ from typing import List
 from pg_rad.landscape.landscape import Landscape
 from pg_rad.simulator.outputs import (
     CountRateOutput,
+    DetectorOutput,
     SimulationOutput,
     SourceOutput
 )
@@ -31,21 +32,38 @@ class SimulationEngine:
 
         count_rate_results = self._calculate_count_rate_along_path()
         source_results = self._calculate_point_source_distance_to_path()
+        detector_results = self._generate_detector_output()
 
         return SimulationOutput(
             name=self.landscape.name,
+            size=self.landscape.size,
             count_rate=count_rate_results,
+            detector=detector_results,
             sources=source_results
         )
 
     def _calculate_count_rate_along_path(self) -> CountRateOutput:
-        acq_points, sub_points, cps, int_counts = calculate_counts_along_path(
+        acq_points, sub_points, cps, int_counts, mean_bkg_counts = (
+            calculate_counts_along_path(
                 self.landscape,
                 self.detector,
-            velocity=self.runtime_spec.speed
+                velocity=self.runtime_spec.speed,
+                bkg_cps_input=self.sim_spec.bkg_cps,
+                t_acq=self.runtime_spec.acquisition_time,
+                seed=self.sim_spec.seed
+            )
         )
 
-        return CountRateOutput(acq_points, sub_points, cps, int_counts)
+        return CountRateOutput(
+            self.landscape.path.x_list,
+            self.landscape.path.y_list,
+            acq_points,
+            sub_points,
+            cps,
+            int_counts,
+            mean_bkg_counts,
+            self.sim_spec.seed
+        )
 
     def _calculate_point_source_distance_to_path(self) -> List[SourceOutput]:
 
@@ -69,3 +87,13 @@ class SimulationEngine:
             )
 
         return source_output
+
+    def _generate_detector_output(self) -> DetectorOutput:
+        return DetectorOutput(
+            name=self.detector.name,
+            type=self.detector.type,
+            is_isotropic=self.detector.is_isotropic,
+            field_eff=self.detector.get_efficiency(
+                self.landscape.point_sources[0].isotope.E
+            )
+        )

src/pg_rad/simulator/outputs.py

@@ -5,10 +5,14 @@ from dataclasses import dataclass
 
 @dataclass
 class CountRateOutput:
-    acquisition_points: List[float]
+    x: List[float]
+    y: List[float]
+    distance: List[float]
     sub_points: List[float]
     cps: List[float]
     integrated_counts: List[float]
+    mean_bkg_cps: List[float]
+    seed: int
 
 
 @dataclass
@@ -21,8 +25,18 @@ class SourceOutput:
     dist_from_path: float
 
 
+@dataclass
+class DetectorOutput:
+    name: str
+    type: str
+    is_isotropic: bool
+    field_eff: float
+
+
 @dataclass
 class SimulationOutput:
     name: str
+    size: tuple
+    detector: DetectorOutput
     count_rate: CountRateOutput
     sources: List[SourceOutput]

src/pg_rad/utils/export.py

@@ -0,0 +1,128 @@
+from dataclasses import asdict
+from datetime import datetime as dt
+import json
+import os
+import logging
+import re
+
+from numpy import array, full_like, ndarray, bool_
+from pandas import DataFrame
+
+from pg_rad.simulator.outputs import SimulationOutput
+
+
+logger = logging.getLogger(__name__)
+logging.getLogger("PIL").setLevel(logging.WARNING)
+
+
+class NumpyEncoder(json.JSONEncoder):
+    def default(self, obj):
+        if isinstance(obj, ndarray):
+            return obj.tolist()
+        elif isinstance(obj, bool_):
+            return bool(obj)
+        return super().default(obj)
+
+
+def generate_folder_name(sim: SimulationOutput) -> str:
+    formatted_sim_name = re.sub(r"\s+", '_',  sim.name.lower())
+    folder_name = (
+        formatted_sim_name +
+        '_result_' +
+        dt.today().strftime('%Y%m%d_%H%M')
+    )
+    return folder_name
+
+
+def save_results(sim: SimulationOutput, folder_name: str) -> None:
+    """Parse all simulation output and save to a folder."""
+    if not os.path.exists(folder_name):
+        os.makedirs(folder_name)
+    else:
+        logger.warning("Folder already exists. Overwrite?")
+        ans = input("[type 'n' to cancel overwrite] ")
+        if ans.lower() == 'n':
+            return
+
+    logger.debug(
+        f"Integrated counts: {list(sim.count_rate.integrated_counts)}"
+    )
+    logger.debug(
+        f"Distances: {list(sim.count_rate.distance)}"
+    )
+
+    df = generate_df(sim)
+    csv_name = generate_csv_name(sim)
+    df.to_csv(f"{folder_name}/{csv_name}.csv", index=False)
+    param_dict = generate_sim_param_dict(sim)
+    with open(f"{folder_name}/parameters.json", 'w') as f:
+        json.dump(param_dict, f, cls=NumpyEncoder)
+    logger.info(f"Simulation output saved to {folder_name}!")
+
+
+def generate_sim_param_dict(sim: SimulationOutput) -> dict:
+    """Parse simulation parameters and hyperparameters to dictionary."""
+    d = asdict(sim)
+    d.pop('count_rate')
+    return d
+
+
+def generate_df(sim: SimulationOutput) -> DataFrame:
+    """Parse simulation output to CSV format and the name of CSV."""
+
+    br_array = full_like(
+        sim.count_rate.integrated_counts,
+        sim.count_rate.mean_bkg_cps
+    )
+
+    east_coords = sim.count_rate.x[1:]
+    north_coords = sim.count_rate.y[1:]
+
+    if len(east_coords) != sim.count_rate.integrated_counts.shape:
+        east_coords = None
+        north_coords = None
+        logger.warning(
+            "PG-RAD currently does not support interpolation"
+            " of experimental paths for export. Only ROI_P, ROI_BR and Dist"
+            " will be saved."
+        )
+
+    result_df = DataFrame(
+        {
+            "East": east_coords,
+            "North": north_coords,
+            "ROI_P": sim.count_rate.integrated_counts,
+            "ROI_BR": br_array,
+            "Dist": sim.count_rate.distance
+        }
+    )
+
+    return result_df
+
+
+def generate_csv_name(sim: SimulationOutput) -> str:
+    """Generate CSV name according to Alex' specification"""
+    num_src = len(sim.sources)
+    src_ids = [str(i+1) for i in range(num_src)]
+    bkg_cps = round(sim.count_rate.mean_bkg_cps)
+    source_param_strings = [
+        [
+            str(round(s.activity))+"MBq",
+            str(round(s.dist_from_path))+"m",
+            str(round(s.position[0]))+'_'+str(round(s.position[1]))
+        ]
+        for s in sim.sources
+    ]
+
+    if num_src == 1:
+        src_str = "_".join(source_param_strings[0])
+    else:
+        src_str_array = array(
+            [list(item) for item in zip(*source_param_strings)]
+        )
+
+        src_str = "_".join(src_str_array.flat)
+
+    src_ids_str = "_".join(src_ids)
+    csv_name = f"{src_ids_str}_src_{bkg_cps}_cps_bkg_{src_str}"
+    return csv_name