Merge pull request #228 from ndem0/extra-param-file

rbf read extra_parameter from file

Author: ndem0

pygem/rbf.py

@@ -108,14 +108,14 @@ class RBF(Deformation):
         transformation.
     :cvar float radius: the scaling parameter that affects the shape of the
         basis functions.
-    :cvar dict extra_parameter: the additional parameters that may be passed to
-    	the kernel function.
+    :cvar dict extra: the additional parameters that may be passed to the
+        kernel function.
         
     :Example:
 
         >>> from pygem import RBF
         >>> import numpy as np
-        >>> rbf = RBF('gaussian_spline')
+        >>> rbf = RBF(func='gaussian_spline')
         >>> xv = np.linspace(0, 1, 20)
         >>> yv = np.linspace(0, 1, 20)
         >>> zv = np.linspace(0, 1, 20)
@@ -208,7 +208,7 @@ def _get_weights(self, X, Y):
         """
         npts, dim = X.shape
         H = np.zeros((npts + 3 + 1, npts + 3 + 1))
-        H[:npts, :npts] = self.basis(cdist(X, X), self.radius)#, **self.extra)
+        H[:npts, :npts] = self.basis(cdist(X, X), self.radius, **self.extra)
         H[npts, :npts] = 1.0
         H[:npts, npts] = 1.0
         H[:npts, -3:] = X
@@ -239,8 +239,11 @@ def read_parameters(self, filename='parameters_rbf.prm'):
         config = configparser.RawConfigParser()
         config.read(filename)
 
-        self.basis = config.get('Radial Basis Functions', 'basis function')
-        self.radius = config.getfloat('Radial Basis Functions', 'radius')
+        rbf_settings = dict(config.items('Radial Basis Functions'))
+        
+        self.basis = rbf_settings.pop('basis function')
+        self.radius = float(rbf_settings.pop('radius'))
+        self.extra = {k: eval(v) for k, v in rbf_settings.items()}
 
         ctrl_points = config.get('Control points', 'original control points')
         lines = ctrl_points.split('\n')
@@ -331,6 +334,7 @@ def __str__(self):
         string = ''
         string += 'basis function = {}\n'.format(self.basis)
         string += 'radius = {}\n'.format(self.radius)
+        string += 'extra_parameter = {}\n'.format(self.extra)
         string += '\noriginal control points =\n'
         string += '{}\n'.format(self.original_control_points)
         string += '\ndeformed control points =\n'

tests/test_datasets/parameters_rbf_extra.prm

@@ -0,0 +1,39 @@
+
+[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, polyharmonic_spline.
+# For a comprehensive list with details see the class RBF.
+basis function: polyharmonic_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
+
+# Any additional parameter to pass to the basis function (eg the `k` power for poliharmonic_spline)
+k: 4
+
+[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   2.0

tests/test_datasets/parameters_rbf_radius.prm

@@ -0,0 +1,38 @@
+
+[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, polyharmonic_spline.
+# 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: 2.0
+
+
+
+[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_rbf.py

@@ -51,6 +51,10 @@ def test_class_members_default_radius(self):
         rbf = RBF()
         assert rbf.radius == 0.5
 
+    def test_class_members_default_extra(self):
+        rbf = RBF()
+        assert rbf.extra == {}
+
     def test_class_members_default_n_control_points(self):
         rbf = RBF()
         assert rbf.n_control_points == 8
@@ -68,10 +72,20 @@ def test_read_parameters_basis(self):
         rbf.read_parameters('tests/test_datasets/parameters_rbf_default.prm')
         assert rbf.basis == RBFFactory('gaussian_spline')
 
+    def test_read_parameters_basis2(self):
+        rbf = RBF()
+        rbf.read_parameters('tests/test_datasets/parameters_rbf_extra.prm')
+        assert rbf.basis == RBFFactory('polyharmonic_spline')
+
     def test_read_parameters_radius(self):
         rbf = RBF()
-        rbf.read_parameters('tests/test_datasets/parameters_rbf_default.prm')
-        assert rbf.radius == 0.5
+        rbf.read_parameters('tests/test_datasets/parameters_rbf_radius.prm')
+        assert rbf.radius == 2.0
+
+    def test_read_extra_parameters(self):
+        rbf = RBF()
+        rbf.read_parameters('tests/test_datasets/parameters_rbf_extra.prm')
+        assert rbf.extra == {'k': 4}
 
     def test_read_parameters_n_control_points(self):
         rbf = RBF()
@@ -145,17 +159,23 @@ def test_write_parameters(self):
         
         self.assertTrue(filecmp.cmp(outfilename, outfilename_expected))
         #os.remove(outfilename)
-
-    def test_read_parameters_filename_default(self):
-        params = RBF()
-        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_print_info(self):
-        params = RBF()
-        print(params)
+        rbf = RBF()
+        print(rbf)
+
+    def test_call_dummy_transformation(self):
+        rbf = RBF()
+        rbf.read_parameters('tests/test_datasets/parameters_rbf_default.prm')
+        mesh = self.get_cube_mesh_points()
+        new = rbf(mesh)
+        np.testing.assert_array_almost_equal(new[17], mesh[17])
+
+    def test_call(self):
+        rbf = RBF()
+        rbf.read_parameters('tests/test_datasets/parameters_rbf_extra.prm')
+        mesh = self.get_cube_mesh_points()
+        new = rbf(mesh)
+        np.testing.assert_array_almost_equal(new[17], [8.947368e-01, 5.353524e-17, 8.845331e-03])
+