From ef00d75498bccf3702be48861d199f79ed233c93 Mon Sep 17 00:00:00 2001
From: fsalmoir <fsalmoir@sissa.it>
Date: Tue, 22 Mar 2016 14:55:04 +0100
Subject: [PATCH 1/3] first changes to documentation and modification of class
 names

---
 docs/source/code.rst           |  1 +
 docs/source/free_form.rst      |  7 +++++++
 pygem/ffd_parameters.py        |  7 ++++---
 pygem/{ffd.py => free_form.py} | 12 ++++++++++--
 4 files changed, 22 insertions(+), 5 deletions(-)
 create mode 100644 docs/source/free_form.rst
 rename pygem/{ffd.py => free_form.py} (87%)

diff --git a/docs/source/code.rst b/docs/source/code.rst
index 198197d..e59a760 100644
--- a/docs/source/code.rst
+++ b/docs/source/code.rst
@@ -5,6 +5,7 @@ Code Documentation
 .. toctree::
    :maxdepth: 2
 
+
    affine_trans
    ffd
    ffd_parameters
diff --git a/docs/source/free_form.rst b/docs/source/free_form.rst
new file mode 100644
index 0000000..61e7c3a
--- /dev/null
+++ b/docs/source/free_form.rst
@@ -0,0 +1,7 @@
+Free Form Deformation
+=================
+
+.. automodule:: pygem.free_form
+
+.. autoclass:: FFD
+    :members:
diff --git a/pygem/ffd_parameters.py b/pygem/ffd_parameters.py
index 7b902d4..f8d8bec 100644
--- a/pygem/ffd_parameters.py
+++ b/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")
diff --git a/pygem/ffd.py b/pygem/free_form.py
similarity index 87%
rename from pygem/ffd.py
rename to pygem/free_form.py
index 81574e8..1780673 100644
--- a/pygem/ffd.py
+++ b/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):
 		"""

From 48433e31435595200155b8ec619e147636dd6212 Mon Sep 17 00:00:00 2001
From: fsalmoir <fsalmoir@sissa.it>
Date: Tue, 22 Mar 2016 14:59:44 +0100
Subject: [PATCH 2/3] first changes to documentation and modification of class
 names

---
 tests/test_ffd.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_ffd.py b/tests/test_ffd.py
index 29075c1..408494c 100644
--- a/tests/test_ffd.py
+++ b/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

From 47bdc2b9ede637203517e545583ffb928ada7a20 Mon Sep 17 00:00:00 2001
From: fsalmoir <fsalmoir@sissa.it>
Date: Tue, 22 Mar 2016 16:16:02 +0100
Subject: [PATCH 3/3] first changes to documentation and modification of class
 names

---
 docs/source/ffd.rst       | 8 --------
 docs/source/free_form.rst | 2 +-
 2 files changed, 1 insertion(+), 9 deletions(-)
 delete mode 100644 docs/source/ffd.rst

diff --git a/docs/source/ffd.rst b/docs/source/ffd.rst
deleted file mode 100644
index 0dba69b..0000000
--- a/docs/source/ffd.rst
+++ /dev/null
@@ -1,8 +0,0 @@
-FFD 
-=================
-
-.. automodule:: pygem.ffd
-
-.. autoclass:: FFD
-    :members:
-    :private-members:
diff --git a/docs/source/free_form.rst b/docs/source/free_form.rst
index 61e7c3a..22e8e01 100644
--- a/docs/source/free_form.rst
+++ b/docs/source/free_form.rst
@@ -1,5 +1,5 @@
 Free Form Deformation
-=================
+=====================
 
 .. automodule:: pygem.free_form