def Grid(self, delta, **kwargs):
"""Package the PMF as a :class:`gridData.Grid` object.
*delta* should be the original spacing of the points in angstroem.
With a *resample_factor*, the data are interpolated on a new grid
with *resample_factor* times as many bins as in the original
histogram (See :meth:`gridData.Grid.resample_factor`).
*interpolation_order* sets the interpolation order for the
resampling procedure.
.. Warning:: Interpolating can lead to artifacts in the 3D PMF. If
in doubt, **do not resample**.
"""
from gridData import Grid
resample_factor = kwargs.pop('resample_factor', None)
kwargs.setdefault('interpolation_spline_order', 3)
g = Grid(*self.histogramdd(delta), **kwargs)
if not resample_factor:
return g
return g.resample_factor(resample_factor)
def dx4resample(name, factor):
"""Comments"""
gddx = Grid()
gddx.load(name)
gddx.resample_factor(factor)
gddx.export(name, file_format='dx')
class TestGrid:
def __init__(self):
self.griddata = np.arange(1, 28).reshape(3, 3, 3)
self.origin = np.zeros(3)
self.delta = np.ones(3)
self.grid = Grid(self.griddata, origin=self.origin, delta=self.delta)
def test_init(self):
g = Grid(self.griddata, origin=self.origin, delta=1)
assert_array_equal(g.delta, self.delta)
@raises(TypeError)
def test_init_wrong_origin(self):
Grid(self.griddata, origin=np.ones(4), delta=self.delta)
@raises(TypeError)
def test_init_wrong_delta(self):
Grid(self.griddata, origin=self.origin, delta=np.ones(4))
def test_equality(self):
assert self.grid == self.grid
assert self.grid != 'foo'
g = Grid(self.griddata, origin=self.origin + 1, delta=self.delta)
assert self.grid != g
def test_addition(self):
g = self.grid + self.grid
assert_array_equal(g.grid.flat, (2 * self.griddata).flat)
g = 2 + self.grid
assert_array_equal(g.grid.flat, (2 + self.griddata).flat)
g = g + self.grid
assert_array_equal(g.grid.flat, (2 + (2 * self.griddata)).flat)
def test_substraction(self):
g = self.grid - self.grid
assert_array_equal(g.grid.flat, np.zeros(27))
g = 2 - self.grid
assert_array_equal(g.grid.flat, (2 - self.griddata).flat)
def test_multiplication(self):
g = self.grid * self.grid
assert_array_equal(g.grid.flat, (self.griddata**2).flat)
g = 2 * self.grid
assert_array_equal(g.grid.flat, (2 * self.griddata).flat)
def test_division(self):
# __truediv__ is used in py3 by default and py2 if division
# is imported from __future__ to make testing easier lets call
# them explicitely
g = self.grid.__truediv__(self.grid)
assert_array_equal(g.grid.flat, np.ones(27))
g = self.grid.__rtruediv__(2)
assert_array_equal(g.grid.flat, (2 / self.griddata).flat)
def test_old_division(self):
# this is normally ONLY invoked in python 2. To have test
# coverage in python3 as well call it explicitely
g = self.grid.__div__(self.grid)
assert_array_equal(g.grid.flat, np.ones(27))
g = self.grid.__rdiv__(2)
assert_array_equal(g.grid.flat, (2 / self.griddata).flat)
def test_power(self):
g = self.grid**2
assert_array_equal(g.grid.flat, (self.griddata**2).flat)
g = 2**self.grid
assert_array_equal(g.grid.flat, (2**self.griddata).flat)
def test_compatibility_type(self):
assert self.grid.check_compatible(self.grid)
assert self.grid.check_compatible(3)
g = Grid(self.griddata, origin=self.origin - 1, delta=self.delta)
assert self.grid.check_compatible(g)
@raises(TypeError)
def test_wrong_compatibile_type(self):
self.grid.check_compatible("foo")
@raises(NotImplementedError)
def test_non_orthonormal_boxes(self):
delta = np.eye(3)
Grid(self.griddata, origin=self.origin, delta=delta)
def test_centers(self):
# this only checks the edges. If you know an alternative
# algorithm that isn't an exact duplicate of the one in
# g.centers to test this please implement it.
g = Grid(self.griddata, origin=np.ones(3), delta=self.delta)
centers = np.array(list(g.centers()))
assert_array_equal(centers[0], g.origin)
assert_array_equal(centers[-1] - g.origin,
(np.array(g.grid.shape) - 1) * self.delta)
@dec.skipif(module_not_found('scipy'),
"Test skipped because scipy is not available.")
def test_resample_factor(self):
g = self.grid.resample_factor(2)
assert_array_equal(g.delta, np.ones(3) * .5)
assert_array_equal(g.grid.shape, np.ones(3) * 6)
# check that the edges are the same
assert_array_almost_equal(g.grid[::5, ::5, ::5],
self.grid.grid[::2, ::2, ::2])
class TestGrid:
def __init__(self):
self.griddata = np.arange(1, 28).reshape(3, 3, 3)
self.origin = np.zeros(3)
self.delta = np.ones(3)
self.grid = Grid(self.griddata, origin=self.origin, delta=self.delta)
def test_init(self):
g = Grid(self.griddata, origin=self.origin, delta=1)
assert_array_equal(g.delta, self.delta)
@raises(TypeError)
def test_init_wrong_origin(self):
Grid(self.griddata, origin=np.ones(4), delta=self.delta)
@raises(TypeError)
def test_init_wrong_delta(self):
Grid(self.griddata, origin=self.origin, delta=np.ones(4))
def test_equality(self):
assert self.grid == self.grid
assert self.grid != 'foo'
g = Grid(self.griddata, origin=self.origin + 1, delta=self.delta)
assert self.grid != g
def test_addition(self):
g = self.grid + self.grid
assert_array_equal(g.grid.flat, (2 * self.griddata).flat)
g = 2 + self.grid
assert_array_equal(g.grid.flat, (2 + self.griddata).flat)
g = g + self.grid
assert_array_equal(g.grid.flat, (2 + (2 * self.griddata)).flat)
def test_substraction(self):
g = self.grid - self.grid
assert_array_equal(g.grid.flat, np.zeros(27))
g = 2 - self.grid
assert_array_equal(g.grid.flat, (2 - self.griddata).flat)
def test_multiplication(self):
g = self.grid * self.grid
assert_array_equal(g.grid.flat, (self.griddata ** 2).flat)
g = 2 * self.grid
assert_array_equal(g.grid.flat, (2 * self.griddata).flat)
def test_division(self):
# __truediv__ is used in py3 by default and py2 if division
# is imported from __future__ to make testing easier lets call
# them explicitely
g = self.grid.__truediv__(self.grid)
assert_array_equal(g.grid.flat, np.ones(27))
g = self.grid.__rtruediv__(2)
assert_array_equal(g.grid.flat, (2 / self.griddata).flat)
def test_old_division(self):
# this is normally ONLY invoked in python 2. To have test
# coverage in python3 as well call it explicitely
g = self.grid.__div__(self.grid)
assert_array_equal(g.grid.flat, np.ones(27))
g = self.grid.__rdiv__(2)
assert_array_equal(g.grid.flat, (2 / self.griddata).flat)
def test_power(self):
g = self.grid ** 2
assert_array_equal(g.grid.flat, (self.griddata ** 2).flat)
g = 2 ** self.grid
assert_array_equal(g.grid.flat, (2 ** self.griddata).flat)
def test_compatibility_type(self):
assert self.grid.check_compatible(self.grid)
assert self.grid.check_compatible(3)
g = Grid(self.griddata, origin=self.origin - 1, delta=self.delta)
assert self.grid.check_compatible(g)
@raises(TypeError)
def test_wrong_compatibile_type(self):
self.grid.check_compatible("foo")
@raises(NotImplementedError)
def test_non_orthonormal_boxes(self):
delta = np.eye(3)
Grid(self.griddata, origin=self.origin, delta=delta)
def test_centers(self):
# this only checks the edges. If you know an alternative
# algorithm that isn't an exact duplicate of the one in
# g.centers to test this please implement it.
g = Grid(self.griddata, origin=np.ones(3), delta=self.delta)
centers = np.array(list(g.centers()))
assert_array_equal(centers[0], g.origin)
assert_array_equal(centers[-1] - g.origin,
(np.array(g.grid.shape) - 1) * self.delta)
@dec.skipif(module_not_found('scipy'),
"Test skipped because scipy is not available.")
def test_resample_factor(self):
g = self.grid.resample_factor(2)
assert_array_equal(g.delta, np.ones(3) * .5)
assert_array_equal(g.grid.shape, np.ones(3) * 6)
# check that the edges are the same
assert_array_almost_equal(g.grid[::5, ::5, ::5],
self.grid.grid[::2, ::2, ::2])