Added HeterogeneoysParameter class to the utils.interface submodule. Worked on...

Added HeterogeneoysParameter class to the utils.interface submodule. Worked on heterogeneous mechanical simulations.

data/cellcomplex_production.py

 import numpy as np
+import numpy.linalg as lng
 
 from cellcomplex.property_topomesh.analysis import compute_topomesh_property
 from cellcomplex.property_topomesh.example_topomesh import circle_voronoi_topomesh
@@ -209,3 +210,25 @@ tissue = FaceCellularDomain(points, cells, resolution=.1)
 
 save(tissue, folder_path+'flat_sepal')
 plot(tissue.mesh)
+
+
+# ##############################################################################
+# ##############################################################################
+# -- A new orientation algorithm given only a list of points
+
+points = [[1, 0, 0],
+          [0, 0, 0],
+          [1, 1, 0],
+          [0, 1, 0]]
+
+points = [np.array(p) for p in points]
+oriented_points = [points.pop(0)]
+while len(points) > 0:
+    dist = list(map(lambda x: lng.norm(x - oriented_points[-1]), points))
+    if len(oriented_points) < 2:
+        oriented_points.append(points.pop(dist.index(min(dist))))
+    else:
+
+print(oriented_points)
+
+# End of cellcomplex_production.py

src/bvpy/templates/vforms/linear_elasticity.py

@@ -64,11 +64,11 @@ class LinearElasticForm(ElasticForm):
 
         Parameters
         ----------
-        mu : float or :class:`dolfin.cpp.function.
+        young : float or :class:`dolfin.cpp.function.
                               Expression<dolfin.cpp.function.Expression>`
             First Lame's parameter, can be isotrope (float) or not
             (`Expression<dolfin.cpp.function.Expression>`).
-        lmbda : float or :class:`dolfin.cpp.function.
+        poisson : float or :class:`dolfin.cpp.function.
                                  Expression<dolfin.cpp.function.Expression>`
             Shear parameter, can be isotrope (float)
             or not (`Expression<dolfin.cpp.function.Expression>`).
@@ -130,11 +130,12 @@ class LinearElasticForm(ElasticForm):
 
     def construct_form(self, u, v, sol):
         self.lhs = fe.Constant(self._thickness)\
-                   * fe.inner(self._stress(u), self._strain(v)) * fe.dx
+            * fe.inner(self._stress(u), self._strain(v)) * fe.dx
 
-        self.rhs = fe.dot(self._source_term, v) * fe.dx(domain=v.function_space().mesh())\
-                   + fe.dot(self._neumann, v)\
-                   * fe.ds(domain=v.function_space().mesh())
+        self.rhs = fe.dot(self._source_term, v)\
+            * fe.dx(domain=v.function_space().mesh())\
+            + fe.dot(self._neumann, v)\
+            * fe.ds(domain=v.function_space().mesh())
 
 
 if __name__ == '__main__':

src/bvpy/utils/interface.py

@@ -279,6 +279,91 @@ class FenicsFunctionConverter(object):
         return self._vertex_values
 
 
+class HeterogeneousParameter(fe.UserExpression):
+    """Defines a parameter values for cells given a specific labelling.
+
+    Attributes
+    ----------
+    cdata : :class:<MeshFunctionSizet`dolfin.cpp.MeshFunctionSizet`>
+        The container encapsulating the cell labels to use.
+    values : dict
+        - keys : int
+            The label values.
+        - values : float
+            The corresponding parameter values to use.
+
+    Methods
+    -------
+    eval_cell :
+        Returns the parameter value given a cell.
+    value_shape :
+        Specifies the shape of the parameter field.
+
+    Notes
+    -----
+    This is a daughter class of
+    :class:`UserExpression<dolfin.function.expression.UserExpression>`,
+    checking the doc might be insightful.
+
+    """
+
+    def __init__(self, cdata, values, **kwargs):
+        """Generates an instance of HeterogeneousParameter
+
+        Parameters
+        ----------
+        cdata : :class:<MeshFunctionSizet`dolfin.cpp.MeshFunctionSizet`>
+            The container encapsulating the cell labels to use.
+        values : dict
+            - keys : int
+                The label values.
+            - values : float
+                The corresponding parameter values to use.
+
+        Notes
+        -----
+        The **kwargs is mandatory in the signature,
+        this is a fenics requirement.
+        """
+        assert set(cdata.array()) == values.keys()
+
+        super().__init__(**kwargs)
+
+        self.cdata = cdata
+        self.values = values
+
+    def eval_cell(self, values, x, ufl_cell):
+        """Returns the parameter value given a cell.
+
+        Parameters
+        ----------
+        values : dict
+            - keys : int
+                The label values.
+            - values : float
+                The corresponding parameter values to use.
+        x : list of lists of floats
+            The list of position vectors.
+        ufl_cell : :class:`Cell<ufl.cell.Cell>`
+            Representation of a finite element cell.
+
+        """
+        idx = ufl_cell.index
+        self.values[self.cdata[idx]]
+
+    def value_shape(self):
+        """Specifies the shape of the parameter field.
+
+        Returns
+        -------
+        tuple
+            the shape of the parameter.
+            e.g. : () = scalar, (n,) = vector, (n,m) = tensor...
+
+        """
+        return ()
+
+
 if __name__ == "__main__":
 
     class Test():
@@ -302,4 +387,4 @@ if __name__ == "__main__":
     conv.to_dataframe()
 
     mesh = fe.UnitSquareMesh(1, 1)
-    c = create_expression([-3,3])
+    c = create_expression([-3, 3])

src/bvpy/utils/io.py

@@ -29,6 +29,11 @@ def save(data, filename):
             f.write(data.mesh)
         elif isinstance(data, fe.Function):
             f.write(data)
+        elif isinstance(data, fe.cpp.mesh.MeshFunctionSizet):
+            f.write(data)
+        else:
+            print(f'WARNING - bvpy.utils.io (line 35): {type(data)}\
+                    is not supported by the save function.')
 
 
 def read_tissue_text_file(path):