Merge pull request #78 from mtezzele/write

write method in the RBFParameters class and tests

Author: mtezzele

pygem/params.py

@@ -324,11 +324,11 @@ def __init__(self):
 		self.deformed_control_points = None
 
 
-	def read_parameters(self, filename='parameters.prm'):
+	def read_parameters(self, filename='parameters_rbf.prm'):
 		"""
 		Reads in the parameters file and fill the self structure.
 
-		:param string filename: parameters file to be read in.
+		:param string filename: parameters file to be read in. Default value is parameters_rbf.prm.
 		"""
 		if not isinstance(filename, basestring):
 			raise TypeError('filename must be a string')
@@ -344,7 +344,7 @@ def read_parameters(self, filename='parameters.prm'):
 				0., 1., 1., 1., 0., 1., 1., 1., 0., 1., 1., 1.]).reshape((8, 3))
 			self.deformed_control_points = np.array([0., 0., 0., 0., 0., 1., 0., 1., 0., 1., 0., 0., \
 				0., 1., 1., 1., 0., 1., 1., 1., 0., 1., 1., 1.]).reshape((8, 3))
-			#self.write_parameters(filename)
+			self.write_parameters(filename)
 			return
 
 		config = ConfigParser.RawConfigParser()
@@ -374,6 +374,56 @@ def read_parameters(self, filename='parameters.prm'):
 			self.deformed_control_points[i] = np.array([float(values[0]), float(values[1]), float(values[2])])
 
 
+	def write_parameters(self, filename='parameters_rbf.prm'):
+		"""
+		This method writes a parameters file (.prm) called `filename` and fills it with all
+		the parameters class members. Default value is parameters_rbf.prm.
+		
+		:param string filename: parameters file to be written out.
+		"""
+		if not isinstance(filename, basestring):
+			raise TypeError("filename must be a string")
+
+		with open(filename, 'w') as output_file:
+			output_file.write('\n[Radial Basis Functions]\n')
+			output_file.write('# This section describes the radial basis functions shape.\n')
+
+			output_file.write('\n# basis funtion is the name of the basis functions to use in the transformation. ' + \
+				'The functions\n')
+			output_file.write('# implemented so far are: gaussian_spline, multi_quadratic_biharmonic_spline,\n')
+			output_file.write('# inv_multi_quadratic_biharmonic_spline, thin_plate_spline, beckert_wendland_c2_basis.\n')
+			output_file.write('# For a comprehensive list with details see the class RBF.\n')
+			output_file.write('basis function: ' + str(self.basis) + '\n')
+
+			output_file.write('\n# radius is the scaling parameter r that affects the shape of the basis functions. ' + \
+				'See the documentation\n')
+			output_file.write('# of the class RBF for details.\n')
+			output_file.write('radius: ' + str(self.radius) + '\n')
+
+			output_file.write('\n\n[Control points]\n')
+			output_file.write('# This section describes the RBF control points.\n')
+			
+			output_file.write('\n# original control points collects the coordinates of the interpolation ' + \
+				'control points before the deformation.\n')
+			output_file.write('original control points:')
+			offset = 1
+			for i in range(0, self.n_control_points):
+					output_file.write(offset * ' ' + str(self.original_control_points[i][0]) + '   ' + \
+						str(self.original_control_points[i][1]) + '   ' + \
+						str(self.original_control_points[i][2]) + '\n')
+					offset = 25
+
+			output_file.write('\n# deformed control points collects the coordinates of the interpolation ' + \
+				'control points after the deformation.\n')
+			output_file.write('deformed control points:')
+			offset = 1
+			for i in range(0, self.n_control_points):
+					output_file.write(offset * ' ' + str(self.deformed_control_points[i][0]) + '   ' + \
+						str(self.deformed_control_points[i][1]) + '   ' + \
+						str(self.deformed_control_points[i][2]) + '\n')
+					offset = 25
+
+
 	def print_info(self):
 		"""
 		This method prints all the RBF parameters on the screen. Its purpose is for debugging.

tests/test_datasets/parameters_rbf_bugged_01.prm

@@ -12,6 +12,7 @@ basis function: gaussian_spline
 # of the class RBF for details.
 radius: 0.5
 
+
 [Control points]
 # This section describes the RBF control points.
 

tests/test_datasets/parameters_rbf_bugged_02.prm

@@ -12,6 +12,7 @@ basis function: gaussian_splines
 # of the class RBF for details.
 radius: 0.5
 
+
 [Control points]
 # This section describes the RBF control points.
 

tests/test_datasets/parameters_rbf_cube.prm

@@ -0,0 +1,37 @@
+
+[Radial Basis Functions]
+# This section describes the radial basis functions shape.
+
+# basis funtion is the name of the basis functions to use in the transformation. The functions
+# implemented so far are: gaussian_spline, multi_quadratic_biharmonic_spline,
+# inv_multi_quadratic_biharmonic_spline, thin_plate_spline, beckert_wendland_c2_basis.
+# For a comprehensive list with details see the class RBF.
+basis function: gaussian_spline
+
+# radius is the scaling parameter r that affects the shape of the basis functions. See the documentation
+# of the class RBF for details.
+radius: 0.5
+
+
+[Control points]
+# This section describes the RBF control points.
+
+# original control points collects the coordinates of the interpolation control points before the deformation.
+original control points: -.1   0.0   0.0
+                         0.0   0.0   1.0
+                         0.0   1.0   0.0
+                         1.0   0.0   0.0
+                         0.0   1     1.0
+                         1.0   0.0   1.0
+                         1.0   1.0   0
+                         1.0   1.0   1.0
+
+# deformed control points collects the coordinates of the interpolation control points after the deformation.
+deformed control points: 0.1   0.2   .3
+                         0.0   0.0   1.0
+                         0.0   1.0   0.0
+                         1.0   0.0   0.0
+                         0.0   .8   1.0
+                         1.0   0.0   1.0
+                         1.0   1.0   0.0
+                         1.2   1.2   1.2

tests/test_datasets/parameters_rbf_cube_out_true.prm

@@ -0,0 +1,37 @@
+
+[Radial Basis Functions]
+# This section describes the radial basis functions shape.
+
+# basis funtion is the name of the basis functions to use in the transformation. The functions
+# implemented so far are: gaussian_spline, multi_quadratic_biharmonic_spline,
+# inv_multi_quadratic_biharmonic_spline, thin_plate_spline, beckert_wendland_c2_basis.
+# For a comprehensive list with details see the class RBF.
+basis function: gaussian_spline
+
+# radius is the scaling parameter r that affects the shape of the basis functions. See the documentation
+# of the class RBF for details.
+radius: 0.5
+
+
+[Control points]
+# This section describes the RBF control points.
+
+# original control points collects the coordinates of the interpolation control points before the deformation.
+original control points: -0.1   0.0   0.0
+                         0.0   0.0   1.0
+                         0.0   1.0   0.0
+                         1.0   0.0   0.0
+                         0.0   1.0   1.0
+                         1.0   0.0   1.0
+                         1.0   1.0   0.0
+                         1.0   1.0   1.0
+
+# deformed control points collects the coordinates of the interpolation control points after the deformation.
+deformed control points: 0.1   0.2   0.3
+                         0.0   0.0   1.0
+                         0.0   1.0   0.0
+                         1.0   0.0   0.0
+                         0.0   0.8   1.0
+                         1.0   0.0   1.0
+                         1.0   1.0   0.0
+                         1.2   1.2   1.2

tests/test_datasets/parameters_rbf_default.prm

@@ -12,6 +12,7 @@ basis function: gaussian_spline
 # of the class RBF for details.
 radius: 0.5
 
+
 [Control points]
 # This section describes the RBF control points.
 

tests/test_rbfparams.py

@@ -7,7 +7,7 @@
 import os
 
 
-class TestFFDParameters(TestCase):
+class TestRBFParameters(TestCase):
 
 
 	def test_class_members_default_basis(self):
@@ -81,6 +81,64 @@ def test_read_parameters_failing_number_deformed_control_points(self):
 			params.read_parameters('tests/test_datasets/parameters_rbf_bugged_01.prm')
 
 
+	def test_read_parameters_filename_default(self):
+		params = rbfp.RBFParameters()
+		params.read_parameters()
+		outfilename = 'parameters_rbf.prm'
+		outfilename_expected = 'tests/test_datasets/parameters_rbf_default.prm'
+		
+		self.assertTrue(filecmp.cmp(outfilename, outfilename_expected))
+		os.remove(outfilename)
+
+
+	def test_write_parameters_failing_filename_type(self):
+		params = rbfp.RBFParameters()
+		with self.assertRaises(TypeError):
+			params.write_parameters(5)
+
+	
+	def test_write_parameters_filename_default_existance(self):
+		params = rbfp.RBFParameters()
+		params.basis = 'inv_multi_quadratic_biharmonic_spline'
+		params.radius = 0.1
+		params.n_control_points = 3
+		params.original_control_points = np.array([0., 0., 0., 0., 0., 1., 0., 1., 0.]).reshape((3, 3))
+		params.deformed_control_points = np.array([0., 0., 0., 0., 0., 1., 0., 1., 0.]).reshape((3, 3))
+		params.write_parameters()
+		outfilename = 'parameters_rbf.prm'
+		assert os.path.isfile(outfilename)
+		os.remove(outfilename)
+
+
+	def test_write_parameters_filename_default(self):
+		params = rbfp.RBFParameters()
+		params.basis = 'gaussian_spline'
+		params.radius = 0.5
+		params.n_control_points = 8
+		params.original_control_points = np.array([0., 0., 0., 0., 0., 1., 0., 1., 0., 1., 0., 0., \
+			0., 1., 1., 1., 0., 1., 1., 1., 0., 1., 1., 1.]).reshape((8, 3))
+		params.deformed_control_points = np.array([0., 0., 0., 0., 0., 1., 0., 1., 0., 1., 0., 0., \
+			0., 1., 1., 1., 0., 1., 1., 1., 0., 1., 1., 1.]).reshape((8, 3))
+		params.write_parameters()
+		outfilename = 'parameters_rbf.prm'
+		outfilename_expected = 'tests/test_datasets/parameters_rbf_default.prm'
+		
+		self.assertTrue(filecmp.cmp(outfilename, outfilename_expected))
+		os.remove(outfilename)
+	
+	
+	def test_write_parameters(self):
+		params = rbfp.RBFParameters()
+		params.read_parameters('tests/test_datasets/parameters_rbf_cube.prm')
+		
+		outfilename = 'tests/test_datasets/parameters_rbf_cube_out.prm'
+		outfilename_expected = 'tests/test_datasets/parameters_rbf_cube_out_true.prm'
+		params.write_parameters(outfilename)
+
+		self.assertTrue(filecmp.cmp(outfilename, outfilename_expected))
+		os.remove(outfilename)
+	
+
 	def test_print_info(self):
 		params = rbfp.RBFParameters()
 		params.print_info()