first changes to documentation and modification of class names

docs/source/code.rst

@@ -5,6 +5,7 @@ Code Documentation
 .. toctree::
    :maxdepth: 2
 
+
    affine_trans
    ffd
    ffd_parameters

docs/source/free_form.rst

@@ -0,0 +1,7 @@
+Free Form Deformation
+=====================
+
+.. automodule:: pygem.free_form
+
+.. autoclass:: FFD
+    :members:

pygem/ffd_parameters.py

@@ -8,7 +8,7 @@
 
 class FFDParameters(object):
 	"""
-	Class that handle the Free Form Deformation parameters in terms of FFD bounding box and
+	Class that handles the Free Form Deformation parameters in terms of FFD bounding box and
 	weight of the FFD control points.
 
 	:param list n_control_points: number of control points in the x, y, and z direction.
@@ -102,9 +102,10 @@ def __init__(self, n_control_points=None):
 
 	def read_parameters_file(self, filename=None):
 		"""
+		Reads in the parameters file and fill the self structure.
+
+		:param string filename: parameters file to be read in.
 
-		.. todo::
-			DOCS
 		"""
 		if not isinstance(filename, basestring):
 			raise TypeError("filename must be a string")

pygem/ffd.py → pygem/free_form.py

@@ -8,7 +8,13 @@
 
 class FFD(object):
 	"""
-	DOCS
+	Class that handles the Free Form Deformation on the mesh points.
+
+	:param class ffd_parameters: parameters of the Free Form Deformation.
+	:param numpy.ndarray original_mesh_points: coordinates of the original points of the mesh.
+
+	:return: modified_mesh_points: coordinates of the modified points of the mesh.
+	:rtype: numpy.ndarray
     """
 
 	def __init__(self, ffd_parameters, original_mesh_points):
@@ -77,9 +83,11 @@ def perform(self):
 			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, \
+		modified_mesh_points = self._transform_points(shift_mesh_points + reference_frame_mesh_points, \
 									  inverse_transformation) + translation
 
+		return modified_mesh_points
+
 
 	def _transform_points(self, original_points, transformation):
 		"""

tests/test_ffd.py

@@ -1,7 +1,7 @@
 
 from unittest import TestCase
 import unittest
-import pygem.ffd as ffd
+import pygem.free_form as ffd
 import pygem.ffd_parameters as ffdp
 import pygem.file_handler as fh
 import numpy as np