def test_generate_signal():
data = np.ones((1, 10)) * np.arange(1, 5).reshape(4, 1)
data = data.reshape(2, 2, 10)
pdf = PairDistributionFunction1D(data)
assert isinstance(pdf, PairDistributionFunction1D)
pdf.normalise_signal()
assert np.equal(pdf, np.ones((2, 2, 10)))
def get_pdf(self,
s_min,
s_max=None,
r_min=0,
r_max=20,
r_increment=0.01
):
""" Calculates the pdf from the reduced intensity signal.
Parameters
----------
s_min : float
Minimum scattering vector s for the pdf calculation. Note that s is
defined here as s = 2 sin(theta)/lambda = 1/d.
s_max : float
Maximum scattering vector s for the pdf calculation. Note that s is
defined here as s = 2 sin(theta)/lambda = 1/d.
r_cutoff : list of float
A list with the format [<r_min>, <r_max>], which sets the
limits of the real space axis in the calculated PDF.
r_increment : float
Step size in r in the extracted PDF.
Returns
-------
pdf : PDF1D
A signal of pair distribution functions.
"""
s_scale = self.signal.axes_manager.signal_axes[0].scale
if s_max is None:
s_max = self.signal.axes_manager.signal_axes[0].size * s_scale
print('s_max set to maximum of signal.')
r_values = np.arange(r_min, r_max, r_increment)
r_values = r_values.reshape(1, r_values.size)
s_limits = [int(s_min / s_scale), int(s_max / s_scale)]
#check that these aren't out of bounds
if s_limits[1] > self.signal.axes_manager.signal_axes[0].size:
raise ValueError('User specified s_max is larger than the maximum '
'scattering vector magnitude in the data. Please reduce '
's_max or use s_max=None to use the full scattering range.')
s_values = np.arange(s_limits[0], s_limits[1], 1) * s_scale
s_values = s_values.reshape(s_values.size, 1) # column vector
limited_red_int = self.signal.isig[s_limits[0]:s_limits[1]].data
pdf_sine = np.sin(2 * np.pi * np.matmul(s_values,r_values))
# creates a vector of the pdf
rpdf = PairDistributionFunction1D(8 * np.pi * s_scale
* np.matmul(limited_red_int,pdf_sine))
signal_axis = rpdf.axes_manager.signal_axes[0]
pdf_scaling = r_increment
signal_axis.scale = pdf_scaling
signal_axis.name = 'Radius r'
signal_axis.units = '$Å$'
rpdf = transfer_navigation_axes(rpdf,self.signal)
return rpdf