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Apr 8, 2021
Merged

rbf read extra_parameter from file #228

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16 changes: 10 additions & 6 deletions pygem/rbf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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')
Expand Down Expand Up @@ -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'
Expand Down
39 changes: 39 additions & 0 deletions tests/test_datasets/parameters_rbf_extra.prm
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Original file line number Diff line number Diff line change
@@ -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
38 changes: 38 additions & 0 deletions tests/test_datasets/parameters_rbf_radius.prm
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Original file line number Diff line number Diff line change
@@ -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
46 changes: 33 additions & 13 deletions tests/test_rbf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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()
Expand Down Expand Up @@ -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])