Fix setter for SizedAggregator

CADETProcess/dataStructure/aggregator.py

@@ -6,9 +6,29 @@
 class SizedAggregator(Aggregator):
     """Aggregator for sized parameters."""
 
+    def __init__(self, *args, transpose=False, **kwargs):
+        """
+        Initialize a SizedAggregator instance.
+
+        Parameters
+        ----------
+        *args : Any
+            Variable length argument list.
+        transpose : bool, options
+            If False, the parameter shape will be ((n_instances, ) + parameter_shape).
+            Else, it will be (parameter_shape + (n_instances, ))
+            The default is False.
+        **kwargs : Any
+            Arbitrary keyword arguments.
+        """
+        self.transpose = transpose
+
+        super().__init__(*args, **kwargs)
+
     def _parameter_shape(self, instance):
-        values = self._get_parameter_values_from_container(instance)
-        shapes = [np.array(el, ndmin=1).shape for el in values]
+        values = self._get_parameter_values_from_container(instance, transpose=False)
+
+        shapes = [el.shape for el in values]
 
         if len(set(shapes)) > 1:
             raise ValueError("Inconsistent parameter shapes.")
@@ -19,35 +39,91 @@ def _parameter_shape(self, instance):
         return shapes[0]
 
     def _expected_shape(self, instance):
-        return (self._n_instances(instance), ) + self._parameter_shape(instance)
+        if self.transpose:
+            return self._parameter_shape(instance) + (self._n_instances(instance), )
+        else:
+            return (self._n_instances(instance), ) + self._parameter_shape(instance)
 
-    def _get_parameter_values_from_container(self, instance):
+    def _get_parameter_values_from_container(self, instance, transpose=False):
         value = super()._get_parameter_values_from_container(instance)
 
         if value is None or len(value) == 0:
             return
 
-        value = np.array(value, ndmin=2).T
+        value = np.array(value, ndmin=2)
+        if transpose and self.transpose:
+            value = value.T
+
         return value
 
-    def _check(self, instance, value, recursive=False):
+    def _check(self, instance, value, transpose=True, recursive=False):
+        value_array = np.array(value, ndmin=2)
+        if transpose and self.transpose:
+            value_array = value_array.T
+
+        value_shape = value_array.shape
         expected_shape = self._expected_shape(instance)
-        if value.shape != expected_shape:
+
+        if value_shape != expected_shape:
             raise ValueError(
-                f"Expected a array with shape {expected_shape}, got {value.shape}"
+                f"Expected a array with shape {expected_shape}, got {value_shape}"
             )
 
         if recursive:
             super()._check(instance, value, recursive)
 
-    def _prepare(self, instance, value, recursive=False):
-        value = np.array(value)
+    def _prepare(self, instance, value, transpose=False, recursive=False):
+        value = np.array(value, ndmin=2)
+
+        if transpose and self.transpose:
+            value = value.T
 
         if recursive:
             value = super()._prepare(instance, value, recursive)
 
         return value
 
+    def __get__(self, instance, cls):
+        """
+        Retrieve the descriptor value for the given instance.
+
+        Parameters
+        ----------
+        instance : Any
+            Instance to retrieve the descriptor value for.
+        cls : Type[Any], optional
+            Class to which the descriptor belongs. By default None.
+
+        Returns
+        -------
+        np.array
+            Descriptor values aggregated in a numpy array.
+        """
+        if instance is None:
+            return self
+
+        value = super().__get__(instance, cls)
+
+        if value is not None:
+            if self.transpose:
+                value = value.T
+
+        return value
+
+    def __set__(self, instance, value):
+        """
+        Set the descriptor value for the given instance.
+
+        Parameters
+        ----------
+        instance : Any
+            Instance to set the descriptor value for.
+        value : Any
+            Value to set.
+        """
+        value = self._prepare(instance, value, transpose=True)
+        super().__set__(instance, value)
+
 
 class ClassDependentAggregator(Aggregator):
     """Aggregator where parameter name changes depending on instance type."""

CADETProcess/dataStructure/dataStructure.py

@@ -98,7 +98,7 @@ def _container_obj(self, instance):
         return container
 
     def _n_instances(self, instance):
-        return len(self._get_parameter_values_from_container(instance))
+        return len(self._container_obj(instance))
 
     def _get_parameter_values_from_container(self, instance):
         container = self._container_obj(instance)
@@ -131,6 +131,7 @@ def __get__(self, instance, cls):
         value = self._get_parameter_values_from_container(instance)
 
         if value is not None:
+            value = self._prepare(instance, value, recursive=True)
             self._check(instance, value, recursive=True)
 
         return value
@@ -143,17 +144,18 @@ def __set__(self, instance, value):
         ----------
         instance : Any
             Instance to set the descriptor value for.
-        value : Any
-            Value to set.
+        value : Iterable
+            Value to set. Note, this assumes that each element of the value maps to
+            each element of the container.
         """
         if value is not None:
             value = self._prepare(instance, value, recursive=True)
             self._check(instance, value, recursive=True)
 
-        container = self._container_obj(instance)
+        containers = self._container_obj(instance)
 
-        for i, el in enumerate(container):
-            setattr(el, self.parameter_name, value[i])
+        for container_value, container in zip(value, containers):
+            setattr(container, self.parameter_name, container_value)
 
     def _prepare(self, instance, value, recursive=False):
         """
@@ -185,12 +187,21 @@ def _check(self, instance, value, recursive=False):
         ----------
         instance : Any
             Instance to retrieve the descriptor value for.
-        value : Any
-            Value to check.
+        value : Iterable
+            Value to set. Note, this assumes that each element of the value maps to
+            each element of the container.
         recursive : bool, optional
             If True, perform the check recursively. Defaults to False.
 
         """
+        container = self._container_obj(instance)
+
+        if len(value) != len(container):
+            raise ValueError(
+                "Unexpected length. "
+                f"Expected {len(container)} entries, got {len(value)}."
+            )
+
         return
 
 

CADETProcess/processModel/reaction.py

@@ -50,7 +50,7 @@ class Reaction(Structure):
         The equilibrium constant for the reaction.
     """
     is_kinetic = Bool(default=True)
-    stoich = SizedNdArray(size='n_comp', default=0)
+    stoich = SizedNdArray(size='n_comp')
     k_fwd = UnsignedFloat()
     k_bwd = UnsignedFloat()
     k_fwd_min = UnsignedFloat(default=100)
@@ -492,9 +492,9 @@ class MassActionLaw(BulkReactionBase):
 
     k_fwd = Aggregator('k_fwd', 'reactions')
     k_bwd = Aggregator('k_bwd', 'reactions')
-    stoich = SizedAggregator('stoich', 'reactions')
-    exponents_fwd = SizedAggregator('exponents_fwd', 'reactions')
-    exponents_bwd = SizedAggregator('exponents_bwd', 'reactions')
+    stoich = SizedAggregator('stoich', 'reactions', transpose=True)
+    exponents_fwd = SizedAggregator('exponents_fwd', 'reactions', transpose=True)
+    exponents_bwd = SizedAggregator('exponents_bwd', 'reactions', transpose=True)
 
     _parameters = ['stoich', 'exponents_fwd', 'exponents_bwd', 'k_fwd', 'k_bwd']
 
@@ -549,49 +549,62 @@ class MassActionLawParticle(ParticleReactionBase):
     )
     k_fwd_liquid = Aggregator('k_fwd', 'liquid_reactions')
     k_bwd_liquid = Aggregator('k_bwd', 'liquid_reactions')
-    exponents_fwd_liquid = SizedAggregator('exponents_fwd', 'liquid_reactions')
-    exponents_bwd_liquid = SizedAggregator('exponents_bwd', 'liquid_reactions')
+    exponents_fwd_liquid = SizedAggregator(
+        'exponents_fwd', 'liquid_reactions', transpose=True
+    )
+    exponents_bwd_liquid = SizedAggregator(
+        'exponents_bwd', 'liquid_reactions', transpose=True
+    )
 
     stoich_solid = SizedClassDependentAggregator(
         'stoich_solid', 'solid_reactions',
         mapping={
             CrossPhaseReaction: 'stoich_solid',
             None: 'stoich'
-        }
+        },
+        transpose=True
     )
     k_fwd_solid = Aggregator('k_fwd', 'solid_reactions')
     k_bwd_solid = Aggregator('k_bwd', 'solid_reactions')
-    exponents_fwd_solid = SizedAggregator('exponents_fwd', 'solid_reactions')
-    exponents_bwd_solid = SizedAggregator('exponents_bwd', 'solid_reactions')
+    exponents_fwd_solid = SizedAggregator(
+        'exponents_fwd', 'solid_reactions', transpose=True
+    )
+    exponents_bwd_solid = SizedAggregator(
+        'exponents_bwd', 'solid_reactions', transpose=True
+    )
 
     exponents_fwd_liquid_modsolid = SizedClassDependentAggregator(
         'exponents_fwd_liquid_modsolid', 'liquid_reactions',
         mapping={
             CrossPhaseReaction: 'exponents_fwd_liquid_modsolid',
             None: None
-        }
+        },
+        transpose=True,
     )
     exponents_bwd_liquid_modsolid = SizedClassDependentAggregator(
         'exponents_bwd_liquid_modsolid', 'liquid_reactions',
         mapping={
             CrossPhaseReaction: 'exponents_bwd_liquid_modsolid',
             None: None
-        }
+        },
+        transpose=True,
     )
 
     exponents_fwd_solid_modliquid = SizedClassDependentAggregator(
         'exponents_fwd_solid_modliquid', 'solid_reactions',
         mapping={
             CrossPhaseReaction: 'exponents_fwd_solid_modliquid',
             None: None
-        }
+        },
+        transpose=True,
     )
     exponents_bwd_solid_modliquid = SizedClassDependentAggregator(
         'exponents_bwd_solid_modliquid', 'solid_reactions',
         mapping={
             CrossPhaseReaction: 'exponents_bwd_solid_modliquid',
             None: None
-        }
+        },
+        transpose=True,
     )
 
     _parameters = [