Merge pull request #77 from mtezzele/rbf

RBF parameter handler with read method and tests

Author: mtezzele

docs/source/params.rst

@@ -6,3 +6,7 @@ Params
 .. autoclass:: FFDParameters
     :members:
     :private-members:
+
+.. autoclass:: RBFParameters
+    :members:
+    :private-members:

pygem/params.py

@@ -1,5 +1,5 @@
 """
-Utilities for reading and writing parameters files to perform the Free Form Deformation (FFD)
+Utilities for reading and writing parameters files to perform the desired geometrical morphing.
 """
 import os
 import ConfigParser
@@ -268,13 +268,11 @@ def print_info(self):
 		"""
 		print 'conversion_unit = ' + str(self.conversion_unit) + '\n'
 		print '(lenght_box_x, lenght_box_y, lenght_box_z) = (' + str(self.lenght_box_x) + \
-			', ' + str(self.lenght_box_y) + ', ' + \
-		str(self.lenght_box_z) + ')'
+			', ' + str(self.lenght_box_y) + ', ' + str(self.lenght_box_z) + ')'
 		print 'origin_box = ' + str(self.origin_box)
 		print 'n_control_points = ' + str(self.n_control_points)
 		print '(rot_angle_x, rot_angle_y, rot_angle_z) = (' + str(self.rot_angle_x) + \
-			', ' + str(self.rot_angle_y) + ', ' + \
-		str(self.rot_angle_z) + ')'
+			', ' + str(self.rot_angle_y) + ', ' + str(self.rot_angle_z) + ')'
 		print '\narray_mu_x ='
 		print self.array_mu_x
 		print '\narray_mu_y ='
@@ -297,3 +295,94 @@ def print_info(self):
 		print self.position_vertex_3
 
 
+
+class RBFParameters(object):
+	"""
+	Class that handles the Radial Basis Functions parameters in terms of RBF control points and
+	basis functions.
+
+	:cvar string basis: 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 :class:`~pygem.radialbasis.RBF`.
+		The default value is None.
+	:cvar float radius: is the scaling parameter r that affects the shape of the basis functions.
+		For details see the class :class:`~pygem.radialbasis.RBF`. The default value is None.
+	:cvar int n_control_points: total number of control points.
+	:cvar numpy.ndarray original_control_points: it is an `n_control_points`-by-3 array with the
+		coordinates of the original interpolation control points before the deformation. The
+		default value is None.
+	:cvar numpy.ndarray deformed_control_points: it is an `n_control_points`-by-3 array with the
+		coordinates of the interpolation control points after the deformation. The default value
+		is None.
+	"""
+	def __init__(self):
+		self.basis = None
+		self.radius = None
+		self.n_control_points = None
+		self.original_control_points = None
+		self.deformed_control_points = None
+
+
+	def read_parameters(self, filename='parameters.prm'):
+		"""
+		Reads in the parameters file and fill the self structure.
+
+		:param string filename: parameters file to be read in.
+		"""
+		if not isinstance(filename, basestring):
+			raise TypeError('filename must be a string')
+
+		# Checks if the parameters file exists. If not it writes the default class into filename.
+		# It consists in the vetices of a cube of side one with a vertex in (0, 0, 0) and opposite one
+		# in (1, 1, 1).
+		if not os.path.isfile(filename):
+			self.basis = 'gaussian_spline'
+			self.radius = 0.5
+			self.n_control_points = 8
+			self.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))
+			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)
+			return
+		
+		config = ConfigParser.RawConfigParser()
+		config.read(filename)
+
+		self.basis = config.get('Radial Basis Functions', 'basis function')
+		self.radius = config.getfloat('Radial Basis Functions', 'radius')
+
+		ctrl_points = config.get('Control points', 'original control points')
+		lines = ctrl_points.split('\n')
+		self.n_control_points = len(lines)
+		self.original_control_points = np.zeros((self.n_control_points, 3))
+		for line, i in zip(lines, range(0, self.n_control_points)):
+			values = line.split()
+			self.original_control_points[i] = np.array([float(values[0]), float(values[1]), float(values[2])])
+
+		mod_points = config.get('Control points', 'deformed control points')
+		lines = mod_points.split('\n')
+
+		if len(lines) != self.n_control_points:
+			raise TypeError("The number of control points must be equal both in the 'original control points'" + \
+				" and in the 'deformed control points' section of the parameters file ({0!s})".format(filename))
+
+		self.deformed_control_points = np.zeros((self.n_control_points, 3))
+		for line, i in zip(lines, range(0, self.n_control_points)):
+			values = line.split()
+			self.deformed_control_points[i] = np.array([float(values[0]), float(values[1]), float(values[2])])
+
+
+	def print_info(self):
+		"""
+		This method prints all the RBF parameters on the screen. Its purpose is for debugging.
+		"""
+		print 'basis function = ' + str(self.basis)
+		print 'radius = ' + str(self.radius)
+		print 'n_control_points = ' + str(self.n_control_points)
+		print '\noriginal_control_points ='
+		print self.original_control_points
+		print '\ndeformed_control_points ='
+		print self.deformed_control_points
+

pygem/stlhandler.py

@@ -4,7 +4,7 @@
 import numpy as np
 from mpl_toolkits import mplot3d
 from matplotlib import pyplot
-from stl import mesh
+from stl import mesh, Mode
 import pygem.filehandler as fh
 
 
@@ -49,9 +49,9 @@ def parse(self, filename):
 
 	def write(self, mesh_points, filename, write_bin=False):
 		"""
-		Writes a unv file, called filename, copying all the lines from self.filename but
+		Writes a stl file, called filename, copying all the lines from self.filename but
 		the coordinates. mesh_points is a matrix that contains the new coordinates to
-		write in the unv file.
+		write in the stl file.
 
 		:param numpy.ndarray mesh_points: it is a `n_points`-by-3 matrix containing
 			the coordinates of the points of the mesh.
@@ -75,7 +75,7 @@ def write(self, mesh_points, filename, write_bin=False):
 				data['vectors'][i][j] = mesh_points[3*i + j]
 
 		if not write_bin:
-			stl_mesh.save(self.outfile, mode=1, update_normals=True)
+			stl_mesh.save(self.outfile, mode=Mode.ASCII, update_normals=True)
 		else:
 			stl_mesh.save(self.outfile, update_normals=True)
 

tests/test_datasets/parameters_rbf_bugged_01.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: 0.0   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: 0.0   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
+                         0.5   0.5   0.5

tests/test_datasets/parameters_rbf_bugged_02.prm

@@ -0,0 +1,36 @@
+
+[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_splines
+
+# 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: 0.0   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: 0.0   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

tests/test_datasets/parameters_rbf_default.prm

@@ -0,0 +1,36 @@
+
+[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: 0.0   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: 0.0   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

tests/test_params.py tests/test_ffdparams.pytests/test_params.py renamed to tests/test_ffdparams.py

@@ -0,0 +1,86 @@
+
+from unittest import TestCase
+import unittest
+import pygem.params as rbfp
+import numpy as np
+import filecmp
+import os
+
+
+class TestFFDParameters(TestCase):
+
+
+	def test_class_members_default_basis(self):
+		params = rbfp.RBFParameters()
+		assert params.basis == None
+
+
+	def test_class_members_default_radius(self):
+		params = rbfp.RBFParameters()
+		assert params.radius == None
+
+
+	def test_class_members_default_n_control_points(self):
+		params = rbfp.RBFParameters()
+		assert params.n_control_points == None
+
+
+	def test_class_members_default_original_control_points(self):
+		params = rbfp.RBFParameters()
+		assert params.original_control_points == None
+
+
+	def test_class_members_default_deformed_control_points(self):
+		params = rbfp.RBFParameters()
+		assert params.deformed_control_points == None
+
+
+	def test_read_parameters_basis(self):
+		params = rbfp.RBFParameters()
+		params.read_parameters('tests/test_datasets/parameters_rbf_default.prm')
+		assert params.basis == 'gaussian_spline'
+
+
+	def test_read_parameters_radius(self):
+		params = rbfp.RBFParameters()
+		params.read_parameters('tests/test_datasets/parameters_rbf_default.prm')
+		assert params.radius == 0.5
+
+
+	def test_read_parameters_n_control_points(self):
+		params = rbfp.RBFParameters()
+		params.read_parameters('tests/test_datasets/parameters_rbf_default.prm')
+		assert params.n_control_points == 8
+
+
+	def test_read_parameters_original_control_points(self):
+		params = rbfp.RBFParameters()
+		params.read_parameters('tests/test_datasets/parameters_rbf_default.prm')
+		original_control_points_exact = 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))
+		np.testing.assert_array_almost_equal(params.original_control_points, original_control_points_exact)
+
+
+	def test_read_parameters_deformed_control_points(self):
+		params = rbfp.RBFParameters()
+		params.read_parameters('tests/test_datasets/parameters_rbf_default.prm')
+		deformed_control_points_exact = 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))
+		np.testing.assert_array_almost_equal(params.deformed_control_points, deformed_control_points_exact)
+
+
+	def test_read_parameters_failing_filename_type(self):
+		params = rbfp.RBFParameters()
+		with self.assertRaises(TypeError):
+			params.read_parameters(3)
+
+
+	def test_read_parameters_failing_number_deformed_control_points(self):
+		params = rbfp.RBFParameters()
+		with self.assertRaises(TypeError):
+			params.read_parameters('tests/test_datasets/parameters_rbf_bugged_01.prm')
+
+
+	def test_print_info(self):
+		params = rbfp.RBFParameters()
+		params.print_info()