Merge pull request #19 from pim-n/feature-fluence-rate

- Added mass attenuation interpolator
- PG fluence rate function that can be called at any position in the landscape
- Rewrote landscape module to pseudo-builder pattern (LandscapeBuilder & LandscapeConstructor)
- Added entry point (CLI)
- Verified installation process and updated instructions accordingly
- Updated tests
- various bugfixes
- various minor improvements

README.md

@@ -31,6 +31,14 @@ With the virtual environment activated, run:
 pip install -e .[dev]
 ```
 
+## Running example landscape
+
+The example landscape can be generated using the command-line interface. Still in the virtual environment, run
+
+```
+pgrad --test --loglevel DEBUG
+```
+
 ## Tests
 
 Tests can be run with `pytest` from the root directory of the repository. With the virtual environment activated, run:

pyproject.toml

@@ -7,6 +7,7 @@ where = ["src"]
 
 [tool.setuptools.package-data]
 "pg_rad.data" = ["*.csv"]
+"pg_rad.configs" = ["*.yml"]
 
 [project]
 name = "pg-rad"
@@ -21,14 +22,19 @@ dependencies = [
     "matplotlib>=3.9.2",
     "numpy>=2",
     "pandas>=2.3.1",
-    "pyyaml>=6.0.2"
+    "pyyaml>=6.0.2",
+    "scipy>=1.15.0"
 ]
 license = "MIT"
 license-files = ["LICEN[CS]E*"]
 
+[project.scripts]
+pgrad = "pg_rad.main:main"
+
 [project.urls]
 Homepage = "https://github.com/pim-n/pg-rad"
 Issues = "https://github.com/pim-n/pg-rad/issues"
 
 [project.optional-dependencies]
+
 dev = ["pytest", "mkinit", "notebook", "mkdocs-material", "mkdocstrings-python", "mkdocs-jupyter"]

src/pg_rad/configs/filepaths.py

@@ -0,0 +1,3 @@
+ATTENUATION_TABLE = 'attenuation_table.csv'
+TEST_EXP_DATA = 'test_path_coords.csv'
+LOGGING_CONFIG = 'logging.yml'

src/pg_rad/data/__init__.py

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

src/pg_rad/data/attenuation_table.csv

@@ -0,0 +1,39 @@
+energy_mev,mu
+1.00000E-03,3.606E+03
+1.50000E-03,1.191E+03
+2.00000E-03,5.279E+02
+3.00000E-03,1.625E+02
+3.20290E-03,1.340E+02
+3.20290E-03,1.485E+02
+4.00000E-03,7.788E+01
+5.00000E-03,4.027E+01
+6.00000E-03,2.341E+01
+8.00000E-03,9.921E+00
+1.00000E-02,5.120E+00
+1.50000E-02,1.614E+00
+2.00000E-02,7.779E-01
+3.00000E-02,3.538E-01
+4.00000E-02,2.485E-01
+5.00000E-02,2.080E-01
+6.00000E-02,1.875E-01
+8.00000E-02,1.662E-01
+1.00000E-01,1.541E-01
+1.50000E-01,1.356E-01
+2.00000E-01,1.233E-01
+3.00000E-01,1.067E-01
+4.00000E-01,9.549E-02
+5.00000E-01,8.712E-02
+6.00000E-01,8.055E-02
+8.00000E-01,7.074E-02
+1.00000E+00,6.358E-02
+1.25000E+00,5.687E-02
+1.50000E+00,5.175E-02
+2.00000E+00,4.447E-02
+3.00000E+00,3.581E-02
+4.00000E+00,3.079E-02
+5.00000E+00,2.751E-02
+6.00000E+00,2.522E-02
+8.00000E+00,2.225E-02
+1.00000E+01,2.045E-02
+1.50000E+01,1.810E-02
+2.00000E+01,1.705E-02

src/pg_rad/exceptions/__init__.py

@@ -4,7 +4,7 @@ __ignore__ = ["logger"]
 from pg_rad.exceptions import exceptions
 
 from pg_rad.exceptions.exceptions import (ConvergenceError, DataLoadError,
-                                          InvalidCSVError,)
+                                          InvalidCSVError, OutOfBoundsError,)
 
 __all__ = ['ConvergenceError', 'DataLoadError', 'InvalidCSVError',
-           'exceptions']
+           'OutOfBoundsError', 'exceptions']

src/pg_rad/exceptions/exceptions.py

@@ -8,3 +8,7 @@ class DataLoadError(Exception):
 
 class InvalidCSVError(DataLoadError):
     """Raised when a file is not a valid CSV."""
+
+
+class OutOfBoundsError(Exception):
+    """Raised when an object is attempted to be placed out of bounds."""

src/pg_rad/isotopes/__init__.py

@@ -2,7 +2,9 @@
 __ignore__ = ["logger"]
 
 from pg_rad.isotopes import isotope
+from pg_rad.isotopes import presets
 
 from pg_rad.isotopes.isotope import (Isotope,)
+from pg_rad.isotopes.presets import (CS137,)
 
-__all__ = ['Isotope', 'isotope']
+__all__ = ['CS137', 'Isotope', 'isotope', 'presets']

src/pg_rad/isotopes/isotope.py

@@ -1,3 +1,6 @@
+from pg_rad.physics import get_mass_attenuation_coeff
+
+
 class Isotope:
     """Represents the essential information of an isotope.
 
@@ -16,8 +19,9 @@ class Isotope:
             raise ValueError("primary_gamma must be a positive energy (keV).")
 
         if not (0 <= b <= 1):
-            raise ValueError("branching_ratio_pg must be a ratio (0 <= b <= 1)")
+            raise ValueError("branching_ratio_pg must be a ratio b in [0,1]")
 
         self.name = name
         self.E = E
         self.b = b
+        self.mu_mass_air = get_mass_attenuation_coeff(E / 1000)

src/pg_rad/isotopes/presets.py

@@ -0,0 +1,10 @@
+from .isotope import Isotope
+
+
+class CS137(Isotope):
+    def __init__(self):
+        super().__init__(
+            name="Cs-137",
+            E=661.66,
+            b=0.851
+        )

src/pg_rad/landscape/__init__.py

@@ -1,8 +1,11 @@
 # do not expose internal logger when running mkinit
 __ignore__ = ["logger"]
 
+from pg_rad.landscape import director
 from pg_rad.landscape import landscape
 
-from pg_rad.landscape.landscape import (Landscape, create_landscape_from_path,)
+from pg_rad.landscape.director import (LandscapeDirector,)
+from pg_rad.landscape.landscape import (Landscape, LandscapeBuilder,)
 
-__all__ = ['Landscape', 'create_landscape_from_path', 'landscape']
+__all__ = ['Landscape', 'LandscapeBuilder', 'LandscapeDirector', 'director',
+           'landscape']

src/pg_rad/landscape/director.py

@@ -0,0 +1,23 @@
+from importlib.resources import files
+import logging
+
+from pg_rad.configs.filepaths import TEST_EXP_DATA
+from pg_rad.isotopes import CS137
+from pg_rad.landscape.landscape import LandscapeBuilder
+from pg_rad.objects import PointSource
+
+
+class LandscapeDirector:
+    def __init__(self):
+        self.logger = logging.getLogger(__name__)
+        self.logger.debug("LandscapeDirector initialized.")
+
+    def build_test_landscape(self):
+        fp = files('pg_rad.data').joinpath(TEST_EXP_DATA)
+        source = PointSource(activity=100E9, isotope=CS137(), pos=(0, 0, 0))
+        lb = LandscapeBuilder("Test landscape")
+        lb.set_air_density(1.243)
+        lb.set_path_from_experimental_data(fp, z=0)
+        lb.set_point_sources(source)
+        landscape = lb.build()
+        return landscape

src/pg_rad/landscape/landscape.py

@@ -1,133 +1,161 @@
 import logging
+from typing import Self
 
-from matplotlib import pyplot as plt
+from pg_rad.dataloader import load_data
-from matplotlib.patches import Circle
+from pg_rad.exceptions import OutOfBoundsError
-import numpy as np
-
-from pg_rad.path import Path
 from pg_rad.objects import PointSource
+from pg_rad.path import Path, path_from_RT90
+from pg_rad.physics.fluence import phi_single_source
 
 logger = logging.getLogger(__name__)
 
 
 class Landscape:
-    """A generic Landscape that can contain a Path and sources.
+    """
-
+    A generic Landscape that can contain a Path and sources.
-    Args:
-        air_density (float, optional): Air density, kg/m^3. Defaults to 1.243.
-        size (int | tuple[int, int, int], optional): Size of the world.
-        Defaults to 500.
-        scale (str, optional): The scale of the size argument passed.
-        Defaults to 'meters'.
     """
     def __init__(
             self,
-            air_density: float = 1.243,
+            name: str,
-            size: int | tuple[int, int, int] = 500,
+            path: Path,
-            scale: str = 'meters'
+            point_sources: list[PointSource] = [],
+            size: tuple[int, int, int] = [500, 500, 50],
+            air_density: float = 1.243
             ):
-        if isinstance(size, int):
+        """Initialize a landscape.
-            self.world = np.zeros((size, size, size))
-        elif isinstance(size, tuple) and len(size) == 3:
-            self.world = np.zeros(size)
-        else:
-            raise TypeError("size must be integer or a tuple of 3 integers.")
-
-        self.air_density = air_density
-        self.scale = scale
-
-        self.path: Path = None
-        self.sources: list[PointSource] = []
-        logger.debug("Landscape initialized.")
-
-    def plot(self, z: float | int = 0):
-        """Plot a slice of the world at a height `z`.
 
         Args:
-            z (int, optional): Height of slice. Defaults to 0.
+            path (Path): A Path object.
+            point_sources (list[PointSource], optional): List of point sources.
+            air_density (float, optional): Air density in kg/m^3.
+                Defaults to 1.243.
+            size (tuple[int, int, int], optional): (x,y,z) dimensions of world
+                in meters. Defaults to [500, 500, 50].
 
-        Returns:
+        Raises:
-            fig, ax: Matplotlib figure objects.
+            TypeError: _description_
         """
-        x_lim, y_lim, _ = self.world.shape
 
-        fig, ax = plt.subplots()
+        self.name = name
-        ax.set_xlim(right=x_lim)
+        self.path = path
-        ax.set_ylim(top=y_lim)
+        self.point_sources = point_sources
-        ax.set_xlabel(f"X [{self.scale}]")
+        self.size = size
-        ax.set_ylabel(f"Y [{self.scale}]")
+        self.air_density = air_density
 
-        if self.path is not None:
+        logger.debug(f"Landscape created: {self.name}")
-            ax.plot(self.path.x_list, self.path.y_list, 'bo-')
 
-        for s in self.sources:
+    def calculate_fluence_at(self, pos: tuple):
-            if np.isclose(s.z, z):
+        total_phi = 0.
-                dot = Circle(
+        for source in self.point_sources:
-                        (s.x, s.y),
+            r = source.distance_to(pos)
-                        radius=5,
+            phi_source = phi_single_source(
-                        color=s.color,
+                r=r,
-                        zorder=5
+                activity=source.activity,
+                branching_ratio=source.isotope.b,
+                mu_mass_air=source.isotope.mu_mass_air,
+                air_density=self.air_density
+            )
+            total_phi += phi_source
+        return total_phi
+
+    def calculate_fluence_along_path(self):
+        pass
+
+
+class LandscapeBuilder:
+    def __init__(self, name: str = "Unnamed landscape"):
+        self.name = name
+        self._path = None
+        self._point_sources = []
+        self._size = None
+        self._air_density = None
+
+        logger.debug(f"LandscapeBuilder initialized: {self.name}")
+
+    def set_air_density(self, air_density) -> Self:
+        """Set the air density of the world."""
+        self._air_density = air_density
+        return self
+
+    def set_landscape_size(self, size: tuple[int, int, int]) -> Self:
+        """Set the size of the landscape in meters (x,y,z)."""
+        if self._path and any(p > s for p, s in zip(self._path.size, size)):
+            raise OutOfBoundsError(
+                "Cannot set landscape size smaller than the path."
             )
 
-                ax.text(
+        self._size = size
-                    s.x + 0.06,
+        logger.debug("Size of the landscape has been updated.")
-                    s.y + 0.06,
+
-                    s.name,
+        return self
-                    color=s.color,
+
-                    fontsize=10,
+    def set_path_from_experimental_data(
-                    ha="left",
+        self,
-                    va="bottom",
+        filename: str,
-                    zorder=6
+        z: int,
+        east_col: str = "East",
+        north_col: str = "North"
+    ) -> Self:
+        df = load_data(filename)
+        self._path = path_from_RT90(
+            df=df,
+            east_col=east_col,
+            north_col=north_col,
+            z=z
         )
 
-                ax.add_patch(dot)
+        # The size of the landscape will be updated if
+        # 1) _size is not set, or
+        # 2) _size is too small to contain the path.
+        needs_resize = (
+            not self._size
+            or any(p > s for p, s in zip(self._path.size, self._size))
+        )
 
-        return fig, ax
+        if needs_resize:
+            if not self._size:
+                logger.debug("Because no Landscape size was set, "
+                             "it will now set to path dimensions.")
+            else:
+                logger.warning(
+                    "Path exceeds current landscape size. "
+                    "Landscape size will be expanded to accommodate path."
+                )
 
-    def add_sources(self, *sources: PointSource):
+            self.set_landscape_size(self._path.size)
+
+        return self
+
+    def set_point_sources(self, *sources):
         """Add one or more point sources to the world.
 
         Args:
             *sources (pg_rad.sources.PointSource): One or more sources,
             passed as Source1, Source2, ...
         Raises:
-            ValueError: If the source is outside the boundaries of the
+            OutOfBoundsError: If any source is outside the boundaries of the
             landscape.
         """
-        max_x, max_y, max_z = self.world.shape[:3]
 
         if any(
-            not (0 <= source.x < max_x and
+            any(p < 0 or p >= s for p, s in zip(source.pos, self._size))
-                 0 <= source.y < max_y and
-                 0 <= source.z < max_z)
             for source in sources
         ):
-            raise ValueError("One or more sources are outside the landscape!")
+            raise OutOfBoundsError(
+                "One or more sources attempted to "
+                "be placed outside the landscape."
+                )
 
-        self.sources.extend(sources)
+        self._point_sources = sources
 
-    def set_path(self, path: Path):
+    def build(self):
-        """
+        landscape = Landscape(
-        Set the path in the landscape.
+            name=self.name,
-        """
+            path=self._path,
-        self.path = path
+            point_sources=self._point_sources,
+            size=self._size,
+            air_density=self._air_density
+        )
 
-
+        logger.info(f"Landscape built successfully: {landscape.name}")
-def create_landscape_from_path(path: Path, max_z: float | int = 50):
-    """Generate a landscape from a path, using its dimensions to determine
-    the size of the landscape.
-
-    Args:
-        path (Path): A Path object describing the trajectory.
-        max_z (int, optional): Height of the world. Defaults to 50 meters.
-
-    Returns:
-        landscape (pg_rad.landscape.Landscape): A landscape with dimensions
-        based on the provided Path.
-    """
-    max_x = np.ceil(max(path.x_list))
-    max_y = np.ceil(max(path.y_list))
-
-    landscape = Landscape(size=(max_x, max_y, max_z))
-    landscape.path = path
         return landscape

src/pg_rad/logger/__init__.py

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

src/pg_rad/logger/logger.py

@@ -1,8 +1,10 @@
-import logging
+import logging.config
-import pathlib
+from importlib.resources import files
 
 import yaml
 
+from pg_rad.configs.filepaths import LOGGING_CONFIG
+
 
 def setup_logger(log_level: str = "WARNING"):
     levels = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]
@@ -10,8 +12,7 @@ def setup_logger(log_level: str = "WARNING"):
     if log_level not in levels:
         raise ValueError(f"Log level must be one of {levels}.")
 
-    base_dir = pathlib.Path(__file__).resolve().parent
+    config_file = files('pg_rad.configs').joinpath(LOGGING_CONFIG)
-    config_file = base_dir / "configs" / "logging.yml"
 
     with open(config_file) as f:
         config = yaml.safe_load(f)

src/pg_rad/logging/__init__.py

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

src/pg_rad/main.py

@@ -0,0 +1,33 @@
+import argparse
+
+from pg_rad.logger import setup_logger
+from pg_rad.landscape import LandscapeDirector
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="pg-rad",
+        description="Primary Gamma RADiation landscape tool"
+    )
+
+    parser.add_argument(
+        "--test",
+        action="store_true",
+        help="Load and run the test landscape"
+    )
+    parser.add_argument(
+        "--loglevel",
+        default="INFO",
+        choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
+    )
+
+    args = parser.parse_args()
+    setup_logger(args.loglevel)
+
+    if args.test:
+        landscape = LandscapeDirector().build_test_landscape()
+        print(landscape.name)
+
+
+if __name__ == "__main__":
+    main()

src/pg_rad/objects/__init__.py

@@ -1,13 +1,11 @@
 # do not expose internal logger when running mkinit
 __ignore__ = ["logger"]
 
-from pg_rad.objects import detectors
 from pg_rad.objects import objects
 from pg_rad.objects import sources
 
-from pg_rad.objects.detectors import (Detector,)
 from pg_rad.objects.objects import (BaseObject,)
 from pg_rad.objects.sources import (PointSource,)
 
-__all__ = ['BaseObject', 'Detector', 'PointSource', 'detectors', 'objects',
+__all__ = ['BaseObject', 'PointSource', 'objects',
            'sources']

src/pg_rad/objects/objects.py

@@ -1,36 +1,42 @@
-import math
 from typing import Self
 
+import numpy as np
+
 
 class BaseObject:
     def __init__(
             self,
-            x: float,
+            pos: tuple[float, float, float] = (0, 0, 0),
-            y: float,
-            z: float,
             name: str = "Unnamed object",
             color: str = 'grey'):
         """
         A generic object.
 
         Args:
-            x (float): X coordinate.
+            pos (tuple[float, float, float]): Position vector (x,y,z).
-            y (float): Y coordinate.
-            z (float): Z coordinate.
             name (str, optional): Name for the object.
             Defaults to "Unnamed object".
             color (str, optional): Matplotlib compatible color string.
             Defaults to "red".
         """
 
-        self.x = x
+        if len(pos) != 3:
-        self.y = y
+            raise ValueError("Position must be tuple of length 3 (x,y,z).")
-        self.z = z
+        self.pos = pos
         self.name = name
         self.color = color
 
-    def distance_to(self, other: Self) -> float:
+    def distance_to(self, other: Self | tuple) -> float:
-        return math.dist(
+        if isinstance(other, tuple) and len(other) == 3:
-            (self.x, self.y, self.z),
+            r = np.linalg.norm(
-            (other.x, other.y, other.z),
+                np.subtract(self.pos, other)
                 )
+        else:
+            try:
+                r = np.linalg.norm(
+                    np.subtract(self.pos, other.pos)
+                    )
+            except AttributeError as e:
+                raise e("other must be an object in the world \
+                    or a position tuple (x,y,z).")
+        return r

src/pg_rad/objects/sources.py

@@ -11,26 +11,23 @@ class PointSource(BaseObject):
 
     def __init__(
             self,
-            x: float,
-            y: float,
-            z: float,
             activity: int,
             isotope: Isotope,
+            pos: tuple[float, float, float] = (0, 0, 0),
             name: str | None = None,
-            color: str = "red"):
+            color: str = 'red'
+            ):
         """A point source.
 
         Args:
-            x (float): X coordinate.
-            y (float): Y coordinate.
-            z (float): Z coordinate.
             activity (int): Activity A in MBq.
             isotope (Isotope): The isotope.
-            name (str | None, optional): Can give the source a unique name.
+            pos (tuple[float, float, float], optional):
-            Defaults to None, making the name sequential.
+                Position of the PointSource.
-            (Source-1, Source-2, etc.).
+            name (str, optional): Can give the source a unique name.
-            color (str, optional): Matplotlib compatible color string.
+                If not provided, point sources are sequentially
-            Defaults to "red".
+                named: Source1, Source2, ...
+            color (str, optional): Matplotlib compatible color string
         """
 
         self.id = PointSource._id_counter
@@ -40,11 +37,10 @@ class PointSource(BaseObject):
         if name is None:
             name = f"Source {self.id}"
 
-        super().__init__(x, y, z, name, color)
+        super().__init__(pos, name, color)
 
         self.activity = activity
         self.isotope = isotope
-        self.color = color
 
         logger.debug(f"Source created: {self.name}")
 

src/pg_rad/path/path.py

@@ -42,14 +42,18 @@ class Path:
     def __init__(
             self,
             coord_list: Sequence[tuple[float, float]],
-            z: float = 0
+            z: float = 0.,
+            z_box: float = 50.
                  ):
         """Construct a path of sequences based on a list of coordinates.
 
         Args:
             coord_list (Sequence[tuple[float, float]]): List of x,y
             coordinates.
-            z (float, optional): Height of the path. Defaults to 0.
+            z (float, optional): position of the path in z-direction in meters.
+                Defaults to 0 meters.
+            z_box (float, optional): How much empty space to set
+                above the path in meters. Defaults to 50 meters.
         """
 
         if len(coord_list) < 2:
@@ -70,6 +74,11 @@ class Path:
             ]
 
         self.z = z
+        self.size = (
+            np.ceil(max(self.x_list)),
+            np.ceil(max(self.y_list)),
+            z + z_box
+        )
 
         logger.debug("Path created.")
 

src/pg_rad/physics/__init__.py

@@ -0,0 +1,10 @@
+# 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 (phi_single_source,)
+
+__all__ = ['attenuation', 'fluence', 'get_mass_attenuation_coeff',
+           'phi_single_source']

src/pg_rad/physics/attenuation.py

@@ -0,0 +1,17 @@
+from importlib.resources import files
+
+from pandas import read_csv
+from scipy.interpolate import interp1d
+
+from pg_rad.configs.filepaths import ATTENUATION_TABLE
+
+
+def get_mass_attenuation_coeff(
+        *args
+        ) -> float:
+    csv = files('pg_rad.data').joinpath(ATTENUATION_TABLE)
+    data = read_csv(csv)
+    x = data["energy_mev"].to_numpy()
+    y = data["mu"].to_numpy()
+    f = interp1d(x, y)
+    return f(*args)

src/pg_rad/physics/fluence.py

@@ -0,0 +1,37 @@
+import numpy as np
+
+
+def phi_single_source(
+        r: float,
+        activity: float | int,
+        branching_ratio: float,
+        mu_mass_air: float,
+        air_density: float,
+        ) -> float:
+    """Compute the contribution of a single point source to the
+    primary photon fluence rate phi at position (x,y,z).
+
+    Args:
+        r (float): [m] Distance to the point source.
+        activity (float | int): [Bq] Activity of the point source.
+        branching_ratio (float): Branching ratio for the photon energy E_gamma.
+        mu_mass_air (float): [cm^2/g] Mass attenuation coefficient for air.
+        air_density (float): [kg/m^3] Air density.
+
+    Returns:
+        phi (float): [s^-1 m^-2] Primary photon fluence rate at distance r from
+        a point source.
+    """
+
+    # Linear photon attenuation coefficient in m^-1.
+    mu_mass_air *= 0.1
+    mu_air = mu_mass_air * air_density
+
+    phi = (
+        activity
+        * branching_ratio
+        * np.exp(-mu_air * r)
+        / (4 * np.pi * r**2)
+    )
+
+    return phi

src/pg_rad/plotting/__init__.py

@@ -0,0 +1,7 @@
+# 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/landscape_plotter.py

@@ -0,0 +1,75 @@
+import logging
+
+from matplotlib import pyplot as plt
+from matplotlib.patches import Circle
+
+from pg_rad.landscape import Landscape
+
+
+logger = logging.getLogger(__name__)
+
+
+class LandscapeSlicePlotter:
+    def plot(self, landscape: Landscape, z: int = 0):
+        """Plot a top-down slice of the landscape at a height z.
+
+        Args:
+            landscape (Landscape): the landscape to plot
+            z (int, optional): Height at which to plot slice. Defaults to 0.
+        """        """
+
+        """
+        self.z = z
+        fig, ax = plt.subplots()
+
+        self._draw_base(ax, landscape)
+        self._draw_path(ax, landscape)
+        self._draw_point_sources(ax, landscape)
+
+        ax.set_aspect("equal")
+        plt.show()
+
+    def _draw_base(self, ax, landscape):
+        width, height = landscape.size[:2]
+        ax.set_xlim(right=width)
+        ax.set_ylim(top=height)
+        ax.set_xlabel("X [m]")
+        ax.set_ylabel("Y [m]")
+        ax.set_title(f"Landscape (top-down, z = {self.z})")
+
+    def _draw_path(self, ax, landscape):
+        if landscape.path.z < self.z:
+            ax.plot(landscape.path.x_list, landscape.path.y_list, 'bo-')
+        else:
+            logger.warning(
+                "Path is above the slice height z."
+                "It will not show on the plot."
+                )
+
+    def _draw_point_sources(self, ax, landscape):
+        for s in landscape.point_sources:
+            if s.z <= self.z:
+                dot = Circle(
+                        (s.x, s.y),
+                        radius=5,
+                        color=s.color,
+                        zorder=5
+                )
+
+                ax.text(
+                    s.x + 0.06,
+                    s.y + 0.06,
+                    s.name,
+                    color=s.color,
+                    fontsize=10,
+                    ha="left",
+                    va="bottom",
+                    zorder=6
+                )
+
+                ax.add_patch(dot)
+            else:
+                logger.warning(
+                    f"Source {s.name} is above slice height z."
+                    "It will not show on the plot."
+                    )

tests/test_attenuation_functions.py

@@ -0,0 +1,29 @@
+import pytest
+
+from pg_rad.physics import get_mass_attenuation_coeff
+
+
+@pytest.mark.parametrize("energy,mu", [
+    (1.00000E-03, 3.606E+03),
+    (1.00000E-02, 5.120E+00),
+    (1.00000E-01, 1.541E-01),
+    (1.00000E+00, 6.358E-02),
+    (1.00000E+01, 2.045E-02) 
+])
+def test_exact_attenuation_retrieval(energy, mu):
+    """
+    Test if retrieval of values that are exactly in the table is correct.
+    """
+    func_mu = get_mass_attenuation_coeff(energy)
+    assert pytest.approx(func_mu, rel=1E-6) == mu
+
+
+@pytest.mark.parametrize("energy,mu", [
+    (0.662, 0.0778)
+])
+def test_attenuation_interpolation(energy, mu):
+    """
+    Test retreival for Cs-137 mass attenuation coefficient.
+    """
+    interp_mu = get_mass_attenuation_coeff(energy)
+    assert pytest.approx(interp_mu, rel=1E-2) == mu

tests/test_fluence_rate.py

@@ -0,0 +1,34 @@
+from math import dist, exp, pi
+
+import pytest
+
+from pg_rad.landscape import LandscapeDirector
+
+
+@pytest.fixture
+def phi_ref():
+    A = 100                             # MBq
+    b = 0.851
+    mu_mass_air = 0.0778                # cm^2/g
+    air_density = 1.243                 # kg/m^3
+    r = dist((0, 0, 0), (10, 10, 0))    # m
+
+    A *= 1E9                            # Convert to Bq
+    mu_mass_air *= 0.1                  # Convert to m^2/kg
+
+    mu_air = mu_mass_air * air_density  # [m^2/kg] x [kg/m^3] = [m^-1]
+
+    # [s^-1] x exp([m^-1] x [m]) / [m^-2] = [s^-1 m^-2]
+    phi = A * b * exp(-mu_air * r) / (4 * pi * r**2)
+    return phi
+
+
+@pytest.fixture
+def test_landscape():
+    landscape = LandscapeDirector().build_test_landscape()
+    return landscape
+
+
+def test_single_source_fluence(phi_ref, test_landscape):
+    phi = test_landscape.calculate_fluence_at((10, 10, 0))
+    assert pytest.approx(phi, rel=1E-3) == phi_ref

tests/test_sources.py

@@ -1,27 +1,36 @@
 import numpy as np
 import pytest
 
-from pg_rad.sources import PointSource
+from pg_rad.objects import PointSource
+from pg_rad.isotopes import CS137
+
 
 @pytest.fixture
 def test_sources():
+    iso = CS137()
     pos_a = np.random.rand(3)
     pos_b = np.random.rand(3)
 
-    a = PointSource(*tuple(pos_a), strength = None)
+    a = PointSource(pos=pos_a, activity=None, isotope=iso)
-    b = PointSource(*tuple(pos_b), strength = None)
+    b = PointSource(pos=pos_b, activity=None, isotope=iso)
 
     return pos_a, pos_b, a, b
 
+
 def test_if_distances_equal(test_sources):
-    """Verify whether from PointSource A to PointSource B is the same as B to A."""
+    """
+    Verify whether distance from PointSource A to B is the same as B to A.
+    """
 
     _, _, a, b = test_sources
 
     assert a.distance_to(b) == b.distance_to(a)
 
+
 def test_distance_calculation(test_sources):
-    """Verify whether distance between two PointSources is calculated correctly."""
+    """
+    Verify whether distance between PointSources is calculated correctly.
+    """
 
     pos_a, pos_b, a, b = test_sources
 
@@ -32,4 +41,4 @@ def test_distance_calculation(test_sources):
     assert np.isclose(
         a.distance_to(b),
         np.sqrt(dx**2 + dy**2 + dz**2),
-        rtol = 1e-12)
+        rtol=1e-12)