fix: targetting and add shape to ndarray

bsb/config/types.py

@@ -789,13 +789,32 @@ class ndarray(TypeHandler):
     :rtype: Callable
     """
 
-    def __init__(self, dtype=None):
+    def __init__(self, shape: builtins.tuple[builtins.int, ...] = None, dtype=None):
+        """
+        :param shape: shape of the array, optional.
+        :param dtype: data-type, optional
+        """
+        if shape is not None:
+            for dim in shape:
+                if dim < 0:
+                    raise TypeError(
+                        f"Ndarray shape must all be positive. Provided {shape}."
+                    )
+        self.shape = shape
         self.dtype = dtype
 
     def __call__(self, value):
+        result = np.array(value, copy=False)
         if self.dtype is not None:
-            return np.array(value, copy=False, dtype=self.dtype)
-        return np.array(value, copy=False)
+            result = np.asarray(result, dtype=self.dtype)
+        if self.shape is not None:
+            try:
+                result = result.reshape(self.shape)
+            except Exception:
+                raise TypeError(
+                    "Couldn't cast {} into an array of shape {}".format(value, self.shape)
+                )
+        return result
 
     @property
     def __name__(self):

bsb/connectivity/geometric/geometric_shapes.py

@@ -577,15 +577,15 @@ class Ellipsoid(GeometricShape, classmap_entry="ellipsoid"):
     """
 
     origin = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[0.0, 0.0, 0.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[0.0, 0.0, 0.0]
     )
     """The coordinates of the center of the ellipsoid."""
     lambdas = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[1.0, 0.5, 2.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[1.0, 0.5, 2.0]
     )
     """The length of the three semi-axes."""
 
-    @config.property(type=types.ndarray(), required=True)
+    @config.property(type=types.ndarray(shape=(3,)), required=True)
     def v0(self):
         """The versor on which the first semi-axis lies."""
         return self._v0
@@ -594,7 +594,7 @@ def v0(self):
     def v0(self, value):
         self._v0 = np.copy(value) / np.linalg.norm(value)
 
-    @config.property(type=types.ndarray(), required=True)
+    @config.property(type=types.ndarray(shape=(3,)), required=True)
     def v1(self):
         """The versor on which the second semi-axis lies."""
         return self._v1
@@ -603,7 +603,7 @@ def v1(self):
     def v1(self, value):
         self._v1 = np.copy(value) / np.linalg.norm(value)
 
-    @config.property(type=types.ndarray(), required=True)
+    @config.property(type=types.ndarray(shape=(3,)), required=True)
     def v2(self):
         """The versor on which the third semi-axis lies."""
         return self._v2
@@ -700,11 +700,11 @@ class Cone(GeometricShape, classmap_entry="cone"):
     """
 
     apex = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[0.0, 1.0, 0.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[0.0, 1.0, 0.0]
     )
     """The coordinates of the apex of the cone."""
     origin = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[0.0, 0.0, 0.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[0.0, 0.0, 0.0]
     )
     """The coordinates of the center of the cone's base."""
     radius = config.attr(type=float, required=False, default=1.0)
@@ -824,11 +824,11 @@ class Cylinder(GeometricShape, classmap_entry="cylinder"):
     """
 
     origin = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[0.0, 0.0, 0.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[0.0, 0.0, 0.0]
     )
     """The coordinates of the center of the bottom circle of the cylinder."""
     top_center = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[0.0, 2.0, 0.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[0.0, 2.0, 0.0]
     )
     """The coordinates of the center of the top circle of the cylinder."""
     radius = config.attr(type=float, required=False, default=1.0)
@@ -936,7 +936,7 @@ class Sphere(GeometricShape, classmap_entry="sphere"):
     """
 
     origin = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[0.0, 0.0, 0.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[0.0, 0.0, 0.0]
     )
     """The coordinates of the center of the sphere."""
     radius = config.attr(type=float, required=False, default=1.0)
@@ -1008,11 +1008,11 @@ class Cuboid(GeometricShape, classmap_entry="cuboid"):
     """
 
     origin = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[0.0, 0.0, 0.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[0.0, 0.0, 0.0]
     )
     """The coordinates of the center of the barycenter of the bottom rectangle."""
     top_center = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[0.0, 1.0, 0.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[0.0, 1.0, 0.0]
     )
     """The coordinates of the center of the barycenter of the top rectangle."""
     side_length_1 = config.attr(type=float, required=False, default=1.0)
@@ -1159,21 +1159,21 @@ class Parallelepiped(GeometricShape, classmap_entry="parallelepiped"):
     """
 
     origin = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[0.0, 0.0, 0.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[0.0, 0.0, 0.0]
     )
     """The coordinates of the left-bottom edge."""
     side_vector_1 = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[1.0, 0.0, 0.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[1.0, 0.0, 0.0]
     )
     """The first vector identifying the parallelepiped (using the right-hand orientation: the 
         thumb)."""
     side_vector_2 = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[0.0, 1.0, 0.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[0.0, 1.0, 0.0]
     )
     """The second vector identifying the parallelepiped (using the right-hand orientation: the 
         index)."""
     side_vector_3 = config.attr(
-        type=types.ndarray(dtype=float), required=True, hint=[0.0, 0.0, 1.0]
+        type=types.ndarray(shape=(3,), dtype=float), required=True, hint=[0.0, 0.0, 1.0]
     )
     """The third vector identifying the parallelepiped (using the right-hand orientation: the 
         middle finger)."""

bsb/core.py

@@ -464,7 +464,7 @@ def place_cells(
         chunk=None,
     ):
         """
-        Place cells inside of the scaffold
+        Place cells inside the scaffold
 
         .. code-block:: python
 

bsb/services/pool.py

@@ -709,7 +709,7 @@ def execute(self, return_results=False):
         """
         Execute the jobs in the queue
 
-        In serial execution this runs all of the jobs in the queue in First In First Out
+        In serial execution this runs all the jobs in the queue in First In First Out
         order. In parallel execution this enqueues all jobs into the MPIPool unless they
         have dependencies that need to complete first.
         """

bsb/simulation/targetting.py

@@ -177,11 +177,14 @@ class CylindricalTargetting(
     Targets all cells in a cylinder along specified axis.
     """
 
-    origin: list[float] = config.attr(type=types.list(type=float, size=2))
+    origin: np.ndarray[float] = config.attr(type=types.ndarray(shape=(2,), dtype=float))
+    """Coordinates of the base of the cylinder for each non main axis"""
     axis: typing.Union[typing.Literal["x"], typing.Literal["y"], typing.Literal["z"]] = (
         config.attr(type=types.in_(["x", "y", "z"]), default="y")
     )
+    """Main axis of the cylinder"""
     radius: float = config.attr(type=float, required=True)
+    """Radius of the cylinder"""
 
     @FractionFilter.filter
     def get_targets(self, adapter, simulation, simdata):
@@ -198,7 +201,7 @@ def get_targets(self, adapter, simulation, simdata):
             model: simdata.populations[model][
                 np.sum(
                     simdata.placement[model].load_positions()[:, axes] - self.origin**2,
-                    axis=0,
+                    axis=1,
                 )
                 < self.radius**2
             ]