Update sources and objects to new position system

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],
-            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

@@ -11,9 +11,7 @@ class PointSource(BaseObject):
 
     def __init__(
             self,
-            x: float,
+            pos: tuple,
-            y: float,
-            z: float,
             activity: int,
             isotope: Isotope,
             name: str | None = None,
@@ -21,9 +19,7 @@ class PointSource(BaseObject):
         """A point source.
 
         Args:
-            x (float): X coordinate.
+            pos (tuple): a position vector of length 3 (x,y,z).
-            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.
@@ -40,11 +36,10 @@ 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}")