plot stl argument and sphinx extensions

docs/source/code.rst

@@ -11,6 +11,3 @@ Code Documentation
    ffd_parameters
    file_handler
 
-
-.. automodule:: pygem
-    :members:

docs/source/conf.py

@@ -42,6 +42,11 @@
     'sphinx.ext.ifconfig',
 ]
 
+intersphinx_mapping = {'python': ('http://docs.python.org/2', None),
+                       'numpy': ('http://docs.scipy.org/doc/numpy/', None),
+                       'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
+                       'matplotlib': ('http://matplotlib.sourceforge.net/', None)}
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

pygem/file_handler.py

@@ -61,7 +61,7 @@ def parse(self, filename):
 
 		:return: mesh_points: it is a `n_points`-by-3 matrix containing the coordinates of
 			the points of the mesh
-		:rtype: float numpy.ndarray
+		:rtype: numpy.ndarray
 
 		.. todo::
 
@@ -119,7 +119,7 @@ def write(self, mesh_points, filename):
 		the coordinates. mesh_points is a matrix that contains the new coordinates to
 		write in the unv file.
 
-		:param ndarray mesh_points: it is a `n_points`-by-3 matrix containing
+		:param numpy.ndarray mesh_points: it is a `n_points`-by-3 matrix containing
 			the coordinates of the points of the mesh
 		:param string filename: name of the output file.
 
@@ -164,7 +164,7 @@ def parse(self, filename):
 
 		:return: mesh_points: it is a `n_points`-by-3 matrix containing the coordinates of
 			the points of the mesh
-		:rtype: float numpy.ndarray
+		:rtype: numpy.ndarray
 
 		.. todo::
 
@@ -197,7 +197,7 @@ def write(self, mesh_points, filename):
 		the coordinates. mesh_points is a matrix that contains the new coordinates to
 		write in the vtk file.
 
-		:param ndarray mesh_points: it is a `n_points`-by-3 matrix containing
+		:param numpy.ndarray mesh_points: it is a `n_points`-by-3 matrix containing
 			the coordinates of the points of the mesh
 		:param string filename: name of the output file.
 
@@ -226,13 +226,11 @@ def write(self, mesh_points, filename):
 		writer = vtk.vtkDataSetWriter()
 		writer.SetFileName(self.outfile)
 
-
 		if vtk.VTK_MAJOR_VERSION <= 5:
 			writer.SetInput(data)
 		else:
 			writer.SetInputData(data)
 
-		#writer.SetInputData(data)
 		writer.Write()
 
 
@@ -302,11 +300,13 @@ def write(self, mesh_points, filename):
 		stl_mesh.save(self.outfile, mode=1, update_normals=True)
 
 
-	def plot(self, plot_file=None):
+	def plot(self, plot_file=None, save_fig=False):
 		"""
 		Method to plot an stl file. If `plot_file` is not given it plots `self.infile`.
 
 		:param string plot_file: the stl filename you want to plot.
+		:param bool save_fig: a flag to save the figure in png or not. If True the
+			plot is not shown.
 		"""
 		if plot_file is None:
 			plot_file = self.infile
@@ -326,7 +326,10 @@ def plot(self, plot_file=None):
 		axes.auto_scale_xyz(scale, scale, scale)
 
 		# Show the plot to the screen
-		pyplot.show()
+		if not save_fig:
+			pyplot.show()
+		else:
+			figure.savefig(plot_file.split('.')[0] + '.png')
 
 
 

pygem/free_form.py

@@ -10,10 +10,10 @@ class FFD(object):
 	"""
 	Class that handles the Free Form Deformation on the mesh points.
 
-	:param class ffd_parameters: parameters of the Free Form Deformation.
+	:param FFDParameters ffd_parameters: parameters of the Free Form Deformation.
 	:param numpy.ndarray original_mesh_points: coordinates of the original points of the mesh.
 
-	:cvar class parameters: parameters of the Free Form Deformation.
+	:cvar FFDParameters parameters: parameters of the Free Form Deformation.
 	:cvar numpy.ndarray original_mesh_points: coordinates of the original points of the mesh.
 		The shape is `n_points`-by-3.
 	:cvar numpy.ndarray modified_mesh_points: coordinates of the points of the deformed mesh.

test.py

@@ -1,3 +1,7 @@
+
+import matplotlib
 import nose
 
+matplotlib.use('agg')
+
 nose.main()

tests/test_file_handler.py

@@ -407,6 +407,16 @@ def test_stl_write_comparison(self):
 		os.remove(outfilename)
 
 
+	def test_stl_plot_save_fig(self):
+		stl_handler = fh.StlHandler()
+		mesh_points = stl_handler.parse('tests/test_datasets/test_sphere.stl')
+		stl_handler.plot(save_fig=True)
+		if not os.path.isfile('tests/test_datasets/test_sphere.png'):
+			assert False
+		else:
+			os.remove('tests/test_datasets/test_sphere.png')
+
+
 	def test_stl_plot_failing_outfile_type(self):
 		stl_handler = fh.StlHandler()
 		with self.assertRaises(TypeError):