Remove utils module

docs/source/_summaries/pygem.params.ffdparams.FFDParameters.save_points.rst

@@ -0,0 +1,6 @@
+pygem.params.ffdparams.FFDParameters.save_points
+================================================
+
+.. currentmodule:: pygem.params.ffdparams
+
+.. automethod:: FFDParameters.save_points

docs/source/_summaries/pygem.params.rbfparams.RBFParameters.plot_points.rst

@@ -0,0 +1,6 @@
+pygem.params.rbfparams.RBFParameters.plot_points
+================================================
+
+.. currentmodule:: pygem.params.rbfparams
+
+.. automethod:: RBFParameters.plot_points

docs/source/_summaries/pygem.params.rbfparams.RBFParameters.save_points.rst

@@ -0,0 +1,6 @@
+pygem.params.rbfparams.RBFParameters.save_points
+================================================
+
+.. currentmodule:: pygem.params.rbfparams
+
+.. automethod:: RBFParameters.save_points

docs/source/ffdparams.rst

@@ -15,7 +15,7 @@ FFDParameters
     FFDParameters.position_vertices
     FFDParameters.read_parameters
     FFDParameters.write_parameters
-    FFDParameters.save
+    FFDParameters.save_points
     FFDParameters.build_bounding_box
     FFDParameters.reset_deformation
 

docs/source/rbfparams.rst

@@ -12,7 +12,8 @@ RBFParameters
 	RBFParameters.n_control_points
 	RBFParameters.read_parameters
 	RBFParameters.write_parameters
-	RBFParameters.save
+	RBFParameters.save_points
+	RBFParameters.plot_points
 
 .. autoclass:: RBFParameters
 	:members:

pygem/params/ffdparams.py

@@ -334,7 +334,7 @@ def __str__(self):
         string += '\nposition_vertices = {}\n'.format(self.position_vertices)
         return string
 
-    def save(self, filename, write_deformed=True):
+    def save_points(self, filename, write_deformed=True):
         """
         Method that writes a vtk file containing the FFD lattice. This method
         allows to visualize where the FFD control points are located before the
@@ -354,34 +354,38 @@ def save(self, filename, write_deformed=True):
         >>> params.read_parameters(
         >>>     filename='tests/test_datasets/parameters_test_ffd_sphere.prm')
         >>> params.save('tests/test_datasets/box_test_sphere.vtk')
+
+        .. note::
+            In order to visualize the points in Paraview, please select the
+            **Point Gaussian** representation.
+
         """
         x = np.linspace(0, self.lenght_box[0], self.n_control_points[0])
         y = np.linspace(0, self.lenght_box[1], self.n_control_points[1])
         z = np.linspace(0, self.lenght_box[2], self.n_control_points[2])
 
-        lattice_y_coords, lattice_x_coords, lattice_z_coords = np.meshgrid(
-            y, x, z)
+        lattice_y_coords, lattice_x_coords, lattice_z_coords = np.meshgrid(y, x,
+                                                                           z)
 
         if write_deformed:
             box_points = np.array([
-                lattice_x_coords.ravel() +
-                self.array_mu_x.ravel() * self.lenght_box[0],
-                lattice_y_coords.ravel() +
+                lattice_x_coords.ravel() + self.array_mu_x.ravel() *
+                self.lenght_box[0], lattice_y_coords.ravel() +
                 self.array_mu_y.ravel() * self.lenght_box[1],
-                lattice_z_coords.ravel() +
-                self.array_mu_z.ravel() * self.lenght_box[2]
+                lattice_z_coords.ravel() + self.array_mu_z.ravel() *
+                self.lenght_box[2]
             ])
         else:
             box_points = np.array([
-                lattice_x_coords.ravel(),
-                lattice_y_coords.ravel(),
+                lattice_x_coords.ravel(), lattice_y_coords.ravel(),
                 lattice_z_coords.ravel()
             ])
 
         n_rows = box_points.shape[1]
 
-        box_points = np.dot(self.rotation_matrix, box_points) + np.transpose(
-            np.tile(self.origin_box, (n_rows, 1)))
+        box_points = np.dot(
+            self.rotation_matrix,
+            box_points) + np.transpose(np.tile(self.origin_box, (n_rows, 1)))
 
         points = vtk.vtkPoints()
 

pygem/params/rbfparams.py

@@ -9,6 +9,7 @@
 import os
 import numpy as np
 import vtk
+import matplotlib.pyplot as plt
 
 
 class RBFParameters(object):
@@ -193,7 +194,7 @@ def __str__(self):
         string += '{}\n'.format(self.deformed_control_points)
         return string
 
-    def save(self, filename, write_deformed=True):
+    def save_points(self, filename, write_deformed=True):
         """
         Method that writes a vtk file containing the control points. This method
         allows to visualize where the RBF control points are located before the
@@ -212,7 +213,12 @@ def save(self, filename, write_deformed=True):
         >>> params = RBFParameters()
         >>> params.read_parameters(
         >>>     filename='tests/test_datasets/parameters_rbf_cube.prm')
-        >>> params.save('tests/test_datasets/box_cube.vtk')
+        >>> params.save_points('tests/test_datasets/box_cube.vtk')
+
+        .. note::
+            In order to visualize the points in Paraview, please select the
+            **Point Gaussian** representation.
+
         """
         box_points = self.deformed_control_points if write_deformed else self.original_control_points
         points = vtk.vtkPoints()
@@ -227,3 +233,44 @@ def save(self, filename, write_deformed=True):
         writer.SetFileName(filename)
         writer.SetInputData(data)
         writer.Write()
+
+
+    def plot_points(self, filename=None):
+        """
+        Method to plot the control points. It is possible to save the resulting
+        figure.
+
+        :param str filename: if None the figure is shown, otherwise it is saved
+            on the specified `filename`. Default is None.
+        """
+        fig = plt.figure(1)
+        axes = fig.add_subplot(111, projection='3d')
+        orig = axes.scatter(
+            self.original_control_points[:, 0],
+            self.original_control_points[:, 1],
+            self.original_control_points[:, 2],
+            c='blue',
+            marker='o')
+        defor = axes.scatter(
+            self.deformed_control_points[:, 0],
+            self.deformed_control_points[:, 1],
+            self.deformed_control_points[:, 2],
+            c='red',
+            marker='x')
+
+        axes.set_xlabel('X axis')
+        axes.set_ylabel('Y axis')
+        axes.set_zlabel('Z axis')
+
+        plt.legend(
+            (orig, defor), ('Original', 'Deformed'),
+            scatterpoints=1,
+            loc='lower left',
+            ncol=2,
+            fontsize=10)
+
+        # Show the plot to the screen
+        if filename is None:
+            plt.show()
+        else:
+            fig.savefig(filename)