fixing other init files

Author: guglielmopadula

pygem/bffd.py

@@ -16,6 +16,9 @@ class BFFD(CFFD):
     '''
     Class that handles the Barycenter Free Form Deformation on the mesh points.
  
+    :param list n_control_points: number of control points in the x, y, and z
+        direction. Default is [2, 2, 2].
+        
     :param list n_control_points: number of control points in the x, y, and z
         direction. Default is [2, 2, 2].
         
@@ -33,12 +36,16 @@ class BFFD(CFFD):
         y, normalized with the box length y.
     :cvar numpy.ndarray array_mu_z: collects the displacements (weights) along
         z, normalized with the box length z.
-    :cvar callable linconstraint: it defines the F of the constraint F(x)=c.
-    :cvar numpy.ndarray valconstraint: it defines the c of the constraint F(x)=c.
-    :cvar list indices: it defines the indices of the control points 
-        that are moved to enforce the constraint. The control index is obtained by doing:
-        all_indices=np.arange(n_x*n_y*n_z*3).reshape(n_x,n_y,n_z,3).tolist().
-    :cvar numpy.ndarray M: a SDP weigth matrix. It must be of size len(indices) x len(indices).
+    :cvar callable fun: it defines the F of the constraint F(x)=c. Default is the constant 1 function.
+    :cvar numpy.ndarray fixval: it defines the c of the constraint F(x)=c. Default is 1.
+    :cvar numpy.ndarray mask: a boolean tensor that tells to the class 
+        which control points can be moved, and in what direction, to enforce the constraint. 
+        The tensor has shape (n_x,n_y,n_z,3), where the last dimension indicates movement
+        on x,y,z respectively. Default is all true.
+    :cvar numpy.ndarray weight_matrix: a symmetric positive definite weigth matrix. 
+        It must be of row and column size the number of trues in the mask.
+        It weights the movemement of the control points which have a true flag in the mask.
+        Default is identity.
 
     :Example:
 
@@ -54,8 +61,8 @@ class BFFD(CFFD):
         >>> new_mesh_points = bffd(original_mesh_points)
         >>> assert np.isclose(np.linalg.norm(bffd.linconstraint(new_mesh_points)-b),np.array([0.]))
     '''
-    def __init__(self, n_control_points=None):
-        super().__init__(n_control_points)
+    def __init__(self, n_control_points=None, fun=None, fixval=None, weight_matrix=None, mask=None):
+        super().__init__(n_control_points,fun,fixval,weight_matrix,mask)
 
         def linfun(x):
             return np.mean(x.reshape(-1, 3), axis=0)

pygem/cffd.py

@@ -82,6 +82,14 @@ def __init__(self, n_control_points=None, fun=None, fixval=None, weight_matrix=N
             self.weight_matrix=np.eye(np.sum(self.mask.astype(int)))
 
     def adjust_control_points(self,src_pts):
+        '''
+        Adjust the FFD control points such that F(ffd(src_pts))=c
+            
+        :param np.ndarray src_pts: the points whose deformation we want to be 
+            constrained.
+        :rtype: None.
+        '''
+
         saved_parameters = self._save_parameters()
         indices=np.arange(np.prod(self.n_control_points)*3)[self.mask.reshape(-1)]
         A, b = self._compute_linear_map(src_pts, saved_parameters.copy(),indices)

pygem/vffd.py

@@ -17,6 +17,9 @@ class VFFD(CFFD):
     '''
     Class that handles the Volumetric Free Form Deformation on the mesh points.
  
+    :param list n_control_points: number of control points in the x, y, and z
+        direction. Default is [2, 2, 2].
+        
     :param list n_control_points: number of control points in the x, y, and z
         direction. Default is [2, 2, 2].
         
@@ -34,12 +37,16 @@ class VFFD(CFFD):
         y, normalized with the box length y.
     :cvar numpy.ndarray array_mu_z: collects the displacements (weights) along
         z, normalized with the box length z.
-    :cvar callable linconstraint: it defines the F of the constraint F(x)=c.
-    :cvar numpy.ndarray valconstraint: it defines the c of the constraint F(x)=c.
-    :cvar list indices: it defines the indices of the control points 
-        that are moved to enforce the constraint. The control index is obtained by doing:
-        all_indices=np.arange(n_x*n_y*n_z*3).reshape(n_x,n_y,n_z,3).tolist().
-    :cvar numpy.ndarray M: a SDP weigth matrix. It must be of size len(indices) x len(indices).
+    :cvar callable fun: it defines the F of the constraint F(x)=c. Default is the constant 1 function.
+    :cvar numpy.ndarray fixval: it defines the c of the constraint F(x)=c. Default is 1.
+    :cvar numpy.ndarray mask: a boolean tensor that tells to the class 
+        which control points can be moved, and in what direction, to enforce the constraint. 
+        The tensor has shape (n_x,n_y,n_z,3), where the last dimension indicates movement
+        on x,y,z respectively. Default is all true.
+    :cvar numpy.ndarray weight_matrix: a symmetric positive definite weigth matrix. 
+        It must be of row and column size the number of trues in the mask.
+        It weights the movemement of the control points which have a true flag in the mask.
+        Default is identity.
     :cvar np.ndarray vweight: specifies the weight of every step of the volume enforcement.
 
     :Example:
@@ -59,8 +66,8 @@ class VFFD(CFFD):
         >>> new_mesh_points = vffd(original_mesh_points)
         >>> assert np.isclose(np.linalg.norm(vffd.linconstraint(new_mesh_points)-b),np.array([0.]))
     '''
-    def __init__(self, triangles, n_control_points=None):
-        super().__init__(n_control_points)
+    def __init__(self, triangles, n_control_points=None, fun=None, fixval=None, weight_matrix=None, mask=None ):
+        super().__init__(n_control_points,fun,fixval,weight_matrix,mask)
         self.triangles = triangles
         self.vweight = [1 / 3, 1 / 3, 1 / 3]