ffd source doc, refactor of members in ffd_parameters and minor fixes

docs/source/code.rst

@@ -5,9 +5,11 @@ Code Documentation
 .. toctree::
    :maxdepth: 2
 
-   file_handler
-   ffd_parameters
    affine_trans
+   ffd
+   ffd_parameters
+   file_handler
+
 
 .. automodule:: pygem
     :members:

docs/source/ffd.rst

@@ -0,0 +1,8 @@
+FFD 
+=================
+
+.. automodule:: pygem.ffd
+
+.. autoclass:: FFD
+    :members:
+    :private-members:

pygem/affine_trans.py

@@ -60,6 +60,7 @@ def affine_points_fit(points_start, points_end):
 	:Example:
 
 	>>> import pygem.affine_trans as at
+
 	>>> # Example of a rotation
 	>>> p_start = np.array([[1,0,0], [0,1,0], [0,0,1], [0,0,0]])
 	>>> p_end = np.array([[0,1,0], [-1,0,0], [0,0,1], [0,0,0]])

pygem/ffd.py

@@ -3,7 +3,6 @@
 """
 import numpy as np
 from scipy import special
-import pygem.ffd_parameters as ffdp
 import pygem.affine_trans as at
 
 
@@ -23,60 +22,63 @@ def perform(self):
 		"""
 		(n_rows_mesh, n_cols_mesh) = self.original_mesh_points.shape
 
-		## translation and then affine transformation
-		translation = np.array([self.parameters.origin_box_x, self.parameters.origin_box_y, self.parameters.origin_box_z])
+		# translation and then affine transformation
+		translation = self.parameters.origin_box
 
 		fisical_frame = np.array([self.parameters.position_vertex_1 - translation, \
 			  self.parameters.position_vertex_2 - translation, \
 			  self.parameters.position_vertex_3 - translation, \
-			  [0,0,0]])
-		reference_frame = np.array([[1,0,0], [0,1,0], [0,0,1], [0,0,0]])
+			  [0, 0, 0]])
+		reference_frame = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1], [0, 0, 0]])
 
 		transformation = at.affine_points_fit(fisical_frame, reference_frame)
 		inverse_transformation = at.affine_points_fit(reference_frame, fisical_frame)
-	
-		##
+
+		# initialization
 		(dim_n_mu, dim_m_mu, dim_t_mu) = self.parameters.array_mu_x.shape
 		bernstein_x = np.zeros((n_rows_mesh, dim_n_mu))
 		bernstein_y = np.zeros((n_rows_mesh, dim_m_mu))
 		bernstein_z = np.zeros((n_rows_mesh, dim_t_mu))
 		shift_mesh_points = np.zeros((n_rows_mesh, n_cols_mesh))
 
-		reference_frame_mesh_points = self._transform_points(self.original_mesh_points - translation, transformation)
+		reference_frame_mesh_points = self._transform_points(self.original_mesh_points - translation, \
+															 transformation)
 
-		for i in range  (0, dim_n_mu):
-			aux1 = np.power((1-reference_frame_mesh_points[:,0]),dim_n_mu-1-i)
-			aux2 = np.power(reference_frame_mesh_points[:,0],i)
-			bernstein_x[:,i] = special.binom(dim_n_mu-1,i) * np.multiply(aux1, aux2)
+		for i in range(0, dim_n_mu):
+			aux1 = np.power((1-reference_frame_mesh_points[:, 0]), dim_n_mu-1-i)
+			aux2 = np.power(reference_frame_mesh_points[:, 0], i)
+			bernstein_x[:, i] = special.binom(dim_n_mu-1, i) * np.multiply(aux1, aux2)
 
-		for i in range  (0, dim_m_mu):
-			aux1 = np.power((1-reference_frame_mesh_points[:,1]),dim_m_mu-1-i)
-			aux2 = np.power(reference_frame_mesh_points[:,1],i)
-			bernstein_y[:,i] = special.binom(dim_m_mu-1,i) * np.multiply(aux1, aux2)
+		for i in range(0, dim_m_mu):
+			aux1 = np.power((1-reference_frame_mesh_points[:, 1]), dim_m_mu-1-i)
+			aux2 = np.power(reference_frame_mesh_points[:, 1], i)
+			bernstein_y[:, i] = special.binom(dim_m_mu-1, i) * np.multiply(aux1, aux2)
 
-		for i in range  (0, dim_t_mu):
-			aux1 = np.power((1-reference_frame_mesh_points[:,2]),dim_t_mu-1-i)
-			aux2 = np.power(reference_frame_mesh_points[:,2],i)
-			bernstein_z[:,i] = special.binom(dim_t_mu-1,i) * np.multiply(aux1, aux2)
+		for i in range(0, dim_t_mu):
+			aux1 = np.power((1-reference_frame_mesh_points[:, 2]), dim_t_mu-1-i)
+			aux2 = np.power(reference_frame_mesh_points[:, 2], i)
+			bernstein_z[:, i] = special.binom(dim_t_mu-1, i) * np.multiply(aux1, aux2)
 
-		for i in range (0, dim_n_mu):
-			for j in range (0, dim_m_mu):
-				for k in range (0, dim_t_mu):
-					aux = np.multiply(bernstein_x[:,i], np.multiply(bernstein_y[:,j], bernstein_z[:,k]))
+		for i in range(0, dim_n_mu):
+			for j in range(0, dim_m_mu):
+				for k in range(0, dim_t_mu):
+					aux = np.multiply(bernstein_x[:, i], np.multiply(bernstein_y[:, j], bernstein_z[:, k]))
 					aux_x = aux * self.parameters.array_mu_x[i, j, k]
 					aux_y = aux * self.parameters.array_mu_y[i, j, k]
 					aux_z = aux * self.parameters.array_mu_z[i, j, k]
-					shift_mesh_points[:,0] += aux_x
-					shift_mesh_points[:,1] += aux_y
-					shift_mesh_points[:,2] += aux_z
+					shift_mesh_points[:, 0] += aux_x
+					shift_mesh_points[:, 1] += aux_y
+					shift_mesh_points[:, 2] += aux_z
 
 		# Splitting points inside and outside the lattice: TODO not very efficient
-		for i in range (0, n_rows_mesh):
-			if (reference_frame_mesh_points[i,0] < 0) or (reference_frame_mesh_points[i,1] < 0) or (reference_frame_mesh_points[i,2] < 0) or \
-				(reference_frame_mesh_points[i,0] > 1) or (reference_frame_mesh_points[i,1] > 1) or (reference_frame_mesh_points[i,2] > 1):
-				shift_mesh_points[i,:] = 0
+		for i in range(0, n_rows_mesh):
+			if (reference_frame_mesh_points[i, 0] < 0) or (reference_frame_mesh_points[i, 1] < 0) \
+			or (reference_frame_mesh_points[i, 2] < 0) or (reference_frame_mesh_points[i, 0] > 1) \
+			or (reference_frame_mesh_points[i, 1] > 1) or (reference_frame_mesh_points[i, 2] > 1):
+				shift_mesh_points[i, :] = 0
 
-		return self._transform_points(shift_mesh_points + reference_frame_mesh_points, inverse_transformation) + translation
+		return self._transform_points(shift_mesh_points + reference_frame_mesh_points, \
+									  inverse_transformation) + translation
 
 
 	def _transform_points(self, original_points, transformation):
@@ -88,6 +90,6 @@ def _transform_points(self, original_points, transformation):
 
 		for i in range(0, n_rows_mesh):
 			single_point = original_points[i]
-			modified_points[i,:] = transformation(single_point)
+			modified_points[i, :] = transformation(single_point)
 
 		return modified_points