def _reduce_single_angle(self, scale=1):
"""
Reduce a single angle.
"""
n_spectra = self.reflected_beam.n_spectra
n_tpixels = np.size(self.reflected_beam.m_topandtail, 1)
n_ypixels = np.size(self.reflected_beam.m_topandtail, 2)
# calculate omega and two_theta depending on the mode.
mode = self.reflected_beam.mode
# we'll need the wavelengths to calculate Q.
wavelengths = self.reflected_beam.m_lambda
m_twotheta = np.zeros((n_spectra, n_tpixels, n_ypixels))
detector_z_difference = (self.reflected_beam.detector_z -
self.direct_beam.detector_z)
beampos_z_difference = (self.reflected_beam.m_beampos -
self.direct_beam.m_beampos)
Y_PIXEL_SPACING = self.reflected_beam.cat.y_pixels_per_mm[0]
total_z_deflection = (detector_z_difference +
beampos_z_difference * Y_PIXEL_SPACING)
if mode in ['FOC', 'POL', 'POLANAL', 'MT']:
# omega_nom.shape = (N, )
omega_nom = np.degrees(
np.arctan(total_z_deflection / self.reflected_beam.detector_y)
/ 2.)
'''
Wavelength specific angle of incidence correction
This involves:
1) working out the trajectory of the neutrons through the
collimation system.
2) where those neutrons intersect the sample.
3) working out the elevation of the neutrons when they hit the
sample.
4) correcting the angle of incidence.
'''
speeds = general.wavelength_velocity(wavelengths)
collimation_distance = self.reflected_beam.cat.collimation_distance
s2_sample_distance = (self.reflected_beam.cat.sample_distance -
self.reflected_beam.cat.slit2_distance)
# work out the trajectories of the neutrons for them to pass
# through the collimation system.
trajectories = find_trajectory(collimation_distance / 1000., 0,
speeds)
# work out where the beam hits the sample
res = parabola_line_intersection_point(s2_sample_distance / 1000,
0, trajectories, speeds,
omega_nom[:, np.newaxis])
intersect_x, intersect_y, x_prime, elevation = res
# correct the angle of incidence with a wavelength dependent
# elevation.
omega_corrected = omega_nom[:, np.newaxis] - elevation
m_twotheta += np.arange(n_ypixels * 1.)[np.newaxis, np.newaxis, :]
m_twotheta -= self.direct_beam.m_beampos[:, np.newaxis, np.newaxis]
m_twotheta *= Y_PIXEL_SPACING
m_twotheta += detector_z_difference
m_twotheta /= (self.reflected_beam.detector_y[:, np.newaxis,
np.newaxis])
m_twotheta = np.arctan(m_twotheta)
m_twotheta = np.degrees(m_twotheta)
# you may be reflecting upside down, reverse the sign.
upside_down = np.sign(omega_corrected[:, 0])
m_twotheta *= upside_down[:, np.newaxis, np.newaxis]
omega_corrected *= upside_down[:, np.newaxis]
elif mode in ['SB', 'DB']:
# the angle of incidence is half the two theta of the reflected
# beam
omega = np.arctan(
total_z_deflection / self.reflected_beam.detector_y) / 2.
# work out two theta for each of the detector pixels
m_twotheta += np.arange(n_ypixels * 1.)[np.newaxis, np.newaxis, :]
m_twotheta -= self.direct_beam.m_beampos[:, np.newaxis, np.newaxis]
m_twotheta += detector_z_difference
m_twotheta -= (
self.reflected_beam.detector_y[:, np.newaxis, np.newaxis] *
np.tan(omega[:, np.newaxis, np.newaxis]))
m_twotheta /= (self.reflected_beam.detector_y[:, np.newaxis,
np.newaxis])
m_twotheta = np.arctan(m_twotheta)
m_twotheta += omega[:, np.newaxis, np.newaxis]
# still in radians at this point
# add an extra dimension, because omega_corrected needs to be the
# angle of incidence for each wavelength. I.e. should be
# broadcastable to (N, T)
omega_corrected = np.degrees(omega)[:, np.newaxis]
m_twotheta = np.degrees(m_twotheta)
'''
--Specular Reflectivity--
Use the (constant wavelength) spectra that have already been integrated
over 2theta (in processnexus) to calculate the specular reflectivity.
Beware: this is because m_topandtail has already been divided through
by monitor counts and error propagated (at the end of processnexus).
Thus, the 2theta pixels are correlated to some degree. If we use the 2D
plot to calculate reflectivity
(sum {Iref_{2theta, lambda}}/I_direct_{lambda}) then the error bars in
the reflectivity turn out much larger than they should be.
'''
ydata, ydata_sd = EP.EPdiv(self.reflected_beam.m_spec,
self.reflected_beam.m_spec_sd,
self.direct_beam.m_spec,
self.direct_beam.m_spec_sd)
# calculate the 1D Qz values.
xdata = general.q(omega_corrected, wavelengths)
xdata_sd = (self.reflected_beam.m_lambda_fwhm /
self.reflected_beam.m_lambda)**2
xdata_sd += (self.reflected_beam.domega[:, np.newaxis] /
omega_corrected)**2
xdata_sd = np.sqrt(xdata_sd) * xdata
'''
---Offspecular reflectivity---
normalise the counts in the reflected beam by the direct beam
spectrum this gives a reflectivity. Also propagate the errors,
leaving the fractional variance (dr/r)^2.
--Note-- that adjacent y-pixels (same wavelength) are correlated in
this treatment, so you can't just sum over them.
i.e. (c_0 / d) + ... + c_n / d) != (c_0 + ... + c_n) / d
'''
m_ref, m_ref_sd = EP.EPdiv(
self.reflected_beam.m_topandtail,
self.reflected_beam.m_topandtail_sd,
self.direct_beam.m_spec[:, :, np.newaxis],
self.direct_beam.m_spec_sd[:, :, np.newaxis])
# you may have had divide by zero's.
m_ref = np.where(np.isinf(m_ref), 0, m_ref)
m_ref_sd = np.where(np.isinf(m_ref_sd), 0, m_ref_sd)
# calculate the Q values for the detector pixels. Each pixel has
# different 2theta and different wavelength, ASSUME that they have the
# same angle of incidence
qx, qy, qz = general.q2(omega_corrected[:, :, np.newaxis], m_twotheta,
0, wavelengths[:, :, np.newaxis])
reduction = {}
reduction['x'] = self.x = xdata
reduction['x_err'] = self.x_err = xdata_sd
reduction['y'] = self.y = ydata / scale
reduction['y_err'] = self.y_err = ydata_sd / scale
reduction['omega'] = omega_corrected
reduction['m_twotheta'] = m_twotheta
reduction['m_ref'] = self.m_ref = m_ref
reduction['m_ref_err'] = self.m_ref_err = m_ref_sd
reduction['qz'] = self.m_qz = qz
reduction['qx'] = self.m_qx = qx
reduction['nspectra'] = self.n_spectra = n_spectra
reduction['start_time'] = self.reflected_beam.start_time
reduction['datafile_number'] = self.datafile_number = (
self.reflected_beam.datafile_number)
fnames = []
datasets = []
datafilename = self.reflected_beam.datafilename
datafilename = os.path.basename(datafilename.split('.nx.hdf')[0])
for i in range(n_spectra):
data_tup = self.data(scanpoint=i)
datasets.append(ReflectDataset(data_tup))
if self.save:
for i, dataset in enumerate(datasets):
fname = '{0}_{1}.dat'.format(datafilename, i)
fnames.append(fname)
with open(fname, 'wb') as f:
dataset.save(f)
fname = '{0}_{1}.xml'.format(datafilename, i)
with open(fname, 'wb') as f:
dataset.save_xml(f, start_time=reduction['start_time'][i])
reduction['fname'] = fnames
return datasets, deepcopy(reduction)
def _reduce_single_angle(self, scale=1):
"""
Reduce a single angle.
"""
n_spectra = self.reflected_beam.n_spectra
n_tpixels = np.size(self.reflected_beam.m_topandtail, 1)
n_xpixels = np.size(self.reflected_beam.m_topandtail, 2)
# we'll need the wavelengths to calculate Q.
wavelengths = self.reflected_beam.m_lambda
m_twotheta = np.zeros((n_spectra, n_tpixels, n_xpixels))
detrot_difference = (self.reflected_beam.detector_z -
self.direct_beam.detector_z)
# difference in pixels between reflected position and direct beam
# at the two different detrots.
QZ_PIXEL_SPACING = self.reflected_beam.cat.qz_pixel_size[0]
dy = self.reflected_beam.detector_y
# convert that pixel difference to angle (in small angle approximation)
# higher `som` leads to lower m_beampos. i.e. higher two theta
# is at lower pixel values
beampos_2theta_diff = -(self.reflected_beam.m_beampos -
self.direct_beam.m_beampos)
beampos_2theta_diff *= QZ_PIXEL_SPACING / dy[0]
beampos_2theta_diff = np.degrees(beampos_2theta_diff)
total_2theta_deflection = detrot_difference + beampos_2theta_diff
# omega_nom.shape = (N, )
omega_nom = total_2theta_deflection / 2.0
omega_corrected = omega_nom[:, np.newaxis]
m_twotheta += np.arange(n_xpixels * 1.0)[np.newaxis, np.newaxis, :]
m_twotheta -= self.direct_beam.m_beampos[:, np.newaxis, np.newaxis]
# minus sign in following line because higher two theta is at lower
# pixel values
m_twotheta *= -QZ_PIXEL_SPACING / dy[:, np.newaxis, np.newaxis]
m_twotheta = np.degrees(m_twotheta)
m_twotheta += detrot_difference
# you may be reflecting upside down, reverse the sign.
upside_down = np.sign(omega_corrected[:, 0])
m_twotheta *= upside_down[:, np.newaxis, np.newaxis]
omega_corrected *= upside_down[:, np.newaxis]
"""
--Specular Reflectivity--
Use the (constant wavelength) spectra that have already been integrated
over 2theta (in processnexus) to calculate the specular reflectivity.
Beware: this is because m_topandtail has already been divided through
by monitor counts and error propagated (at the end of processnexus).
Thus, the 2theta pixels are correlated to some degree. If we use the 2D
plot to calculate reflectivity
(sum {Iref_{2theta, lambda}}/I_direct_{lambda}) then the error bars in
the reflectivity turn out much larger than they should be.
"""
ydata, ydata_sd = EP.EPdiv(
self.reflected_beam.m_spec,
self.reflected_beam.m_spec_sd,
self.direct_beam.m_spec,
self.direct_beam.m_spec_sd,
)
# calculate the 1D Qz values.
xdata = general.q(omega_corrected, wavelengths)
xdata_sd = (self.reflected_beam.m_lambda_fwhm /
self.reflected_beam.m_lambda)**2
xdata_sd += (self.reflected_beam.domega[:, np.newaxis] /
omega_corrected)**2
xdata_sd = np.sqrt(xdata_sd) * xdata
"""
---Offspecular reflectivity---
normalise the counts in the reflected beam by the direct beam
spectrum this gives a reflectivity. Also propagate the errors,
leaving the fractional variance (dr/r)^2.
--Note-- that adjacent y-pixels (same wavelength) are correlated in
this treatment, so you can't just sum over them.
i.e. (c_0 / d) + ... + c_n / d) != (c_0 + ... + c_n) / d
"""
m_ref, m_ref_sd = EP.EPdiv(
self.reflected_beam.m_topandtail,
self.reflected_beam.m_topandtail_sd,
self.direct_beam.m_spec[:, :, np.newaxis],
self.direct_beam.m_spec_sd[:, :, np.newaxis],
)
# you may have had divide by zero's.
m_ref = np.where(np.isinf(m_ref), 0, m_ref)
m_ref_sd = np.where(np.isinf(m_ref_sd), 0, m_ref_sd)
# calculate the Q values for the detector pixels. Each pixel has
# different 2theta and different wavelength, ASSUME that they have the
# same angle of incidence
qx, qy, qz = general.q2(
omega_corrected[:, :, np.newaxis],
m_twotheta,
0,
wavelengths[:, :, np.newaxis],
)
reduction = {}
reduction["x"] = self.x = xdata
reduction["x_err"] = self.x_err = xdata_sd
reduction["y"] = self.y = ydata / scale
reduction["y_err"] = self.y_err = ydata_sd / scale
reduction["omega"] = omega_corrected
reduction["m_twotheta"] = m_twotheta
reduction["m_ref"] = self.m_ref = m_ref
reduction["m_ref_err"] = self.m_ref_err = m_ref_sd
reduction["qz"] = self.m_qz = qz
reduction["qx"] = self.m_qx = qx
reduction["nspectra"] = self.n_spectra = n_spectra
reduction["start_time"] = self.reflected_beam.start_time
reduction[
"datafile_number"] = self.datafile_number = self.reflected_beam.datafile_number
fnames = []
datasets = []
datafilename = self.reflected_beam.datafilename
datafilename = os.path.basename(datafilename.split(".nx.hdf")[0])
for i in range(n_spectra):
data_tup = self.data(scanpoint=i)
datasets.append(ReflectDataset(data_tup))
if self.save:
for i, dataset in enumerate(datasets):
fname = "{0}_{1}.dat".format(datafilename, i)
fnames.append(fname)
with open(fname, "wb") as f:
dataset.save(f)
fname = "{0}_{1}.xml".format(datafilename, i)
with open(fname, "wb") as f:
dataset.save_xml(f, start_time=reduction["start_time"][i])
reduction["fname"] = fnames
return datasets, deepcopy(reduction)
def _reduce_single_angle(self, scale=1):
"""
Reduce a single angle.
"""
n_spectra = self.reflected_beam.n_spectra
n_tpixels = np.size(self.reflected_beam.m_topandtail, 1)
n_ypixels = np.size(self.reflected_beam.m_topandtail, 2)
# calculate omega and two_theta depending on the mode.
mode = self.reflected_beam.mode
# we'll need the wavelengths to calculate Q.
wavelengths = self.reflected_beam.m_lambda
m_twotheta = np.zeros((n_spectra, n_tpixels, n_ypixels))
if mode in ['FOC', 'POL', 'POLANAL', 'MT']:
detector_z_difference = (self.reflected_beam.detector_z -
self.direct_beam.detector_z)
beampos_z_difference = (self.reflected_beam.m_beampos
- self.direct_beam.m_beampos)
total_z_deflection = (detector_z_difference
+ beampos_z_difference * Y_PIXEL_SPACING)
# omega_nom.shape = (N, )
omega_nom = np.degrees(np.arctan(total_z_deflection
/ self.reflected_beam.detector_y) / 2.)
'''
Wavelength specific angle of incidence correction
This involves:
1) working out the trajectory of the neutrons through the
collimation system.
2) where those neutrons intersect the sample.
3) working out the elevation of the neutrons when they hit the
sample.
4) correcting the angle of incidence.
'''
speeds = general.wavelength_velocity(wavelengths)
collimation_distance = self.reflected_beam.cat.collimation_distance
s2_sample_distance = (self.reflected_beam.cat.sample_distance
- self.reflected_beam.cat.slit2_distance)
# work out the trajectories of the neutrons for them to pass
# through the collimation system.
trajectories = pm.find_trajectory(collimation_distance / 1000.,
0, speeds)
# work out where the beam hits the sample
res = pm.parabola_line_intersection_point(s2_sample_distance / 1000,
0,
trajectories,
speeds,
omega_nom[:, np.newaxis])
intersect_x, intersect_y, x_prime, elevation = res
# correct the angle of incidence with a wavelength dependent
# elevation.
omega_corrected = omega_nom[:, np.newaxis] - elevation
elif mode == 'SB' or mode == 'DB':
omega = self.reflected_beam.M_beampos + self.reflected_beam.detectorZ[:, np.newaxis]
omega -= self.direct_beam.M_beampos + self.direct_beam.detectorZ
omega /= 2 * self.reflected_beam.detectorY[:, np.newaxis, np.newaxis]
omega = np.arctan(omega)
m_twotheta += np.arange(n_ypixels * 1.)[np.newaxis, np.newaxis, :] * Y_PIXEL_SPACING
m_twotheta += self.reflected_beam.detectorZ[:, np.newaxis, np.newaxis]
m_twotheta -= self.direct_beam.M_beampos[:, :, np.newaxis] + self.direct_beam.detectorZ
m_twotheta -= self.reflected_beam.detectorY[:, np.newaxis, np.newaxis] * np.tan(omega[:, :, np.newaxis])
m_twotheta /= self.reflected_beam.detectorY[:, np.newaxis, np.newaxis]
m_twotheta = np.arctan(m_twotheta)
m_twotheta += omega[:, :, np.newaxis]
'''
--Specular Reflectivity--
Use the (constant wavelength) spectra that have already been integrated
over 2theta (in processnexus) to calculate the specular reflectivity.
Beware: this is because m_topandtail has already been divided through
by monitor counts and error propagated (at the end of processnexus).
Thus, the 2theta pixels are correlated to some degree. If we use the 2D
plot to calculate reflectivity
(sum {Iref_{2theta, lambda}}/I_direct_{lambda}) then the error bars in
the reflectivity turn out much larger than they should be.
'''
ydata, ydata_sd = EP.EPdiv(self.reflected_beam.m_spec,
self.reflected_beam.m_spec_sd,
self.direct_beam.m_spec,
self.direct_beam.m_spec_sd)
# calculate the 1D Qz values.
xdata = general.q(omega_corrected, wavelengths)
xdata_sd = (self.reflected_beam.m_lambda_fwhm
/ self.reflected_beam.m_lambda) ** 2
xdata_sd += (self.reflected_beam.domega[:, np.newaxis]
/ omega_corrected) ** 2
xdata_sd = np.sqrt(xdata_sd) * xdata
'''
---Offspecular reflectivity---
normalise the counts in the reflected beam by the direct beam
spectrum this gives a reflectivity. Also propagate the errors,
leaving the fractional variance (dr/r)^2.
--Note-- that adjacent y-pixels (same wavelength) are correlated in this
treatment, so you can't just sum over them.
i.e. (c_0 / d) + ... + c_n / d) != (c_0 + ... + c_n) / d
'''
m_ref, m_ref_sd = EP.EPdiv(self.reflected_beam.m_topandtail,
self.reflected_beam.m_topandtail_sd,
self.direct_beam.m_spec[:, :, np.newaxis],
self.direct_beam.m_spec_sd[:, :, np.newaxis])
# you may have had divide by zero's.
m_ref = np.where(np.isinf(m_ref), 0, m_ref)
m_ref_sd = np.where(np.isinf(m_ref_sd), 0, m_ref_sd)
# calculate the Q values for the detector pixels. Each pixel has
# different 2theta and different wavelength, ASSUME that they have the
# same angle of incidence
qx, qy, qz = general.q2(omega_corrected[:, :, np.newaxis],
m_twotheta,
0,
wavelengths[:, :, np.newaxis])
reduction = {}
reduction['xdata'] = self.xdata = xdata
reduction['xdata_sd'] = self.xdata_sd = xdata_sd
reduction['ydata'] = self.ydata = ydata
reduction['ydata_sd'] = self.ydata_sd = ydata_sd
reduction['m_ref'] = self.m_ref = m_ref
reduction['m_ref_sd'] = self.m_ref_sd = m_ref_sd
reduction['qz'] = self.m_qz = qz
reduction['qy'] = self.m_qy = qy
reduction['nspectra'] = self.n_spectra = n_spectra
reduction['datafile_number'] = self.datafile_number = (
self.reflected_beam.datafile_number)
fnames = []
if self.save:
for i in range(n_spectra):
data_tup = self.data(scanpoint=i)
dataset = ReflectDataset(data_tup)
fname = 'PLP{0:07d}_{1}.dat'.format(self.datafile_number, i)
fnames.append(fname)
with open(fname, 'wb') as f:
dataset.save(f)
fname = 'PLP{0:07d}_{1}.xml'.format(self.datafile_number, i)
with open(fname, 'wb') as f:
dataset.save_xml(f)
reduction['fname'] = fnames
return deepcopy(reduction)
def reduce_xrdml(f, bkg=None, scale=None, sample_length=None):
"""
Reduces a Panalytical XRDML file
Parameters
----------
f: file-like object or string
The specular reflectivity (XRDML) file of interest
bkg: list
A list of file-like objects or strings that contain background
measurements. The background is assumed to have the same number of
points as the specular reflectivity curve. The backgrounds are
averaged and subtracted from the specular reflectivity
scale: float, None
The direct beam intensity (cps). If `scale is None` then the dataset
is scaled by the point with maximum intensity below Q = 0.0318 (Q_crit
for Si at 8.048 keV).
sample_length: None or float
If None then no footprint correction is done. Otherwise the transverse
footprint of the sample (mm).
Returns
-------
dataset: refnx.dataset.ReflectDataset
The specular reflectivity as a function of momentum transfer, Q.
"""
spec = parse_xrdml_file(f)
reflectivity = spec["intensities"] / spec["count_time"]
reflectivity_s = np.sqrt(reflectivity) / spec["count_time"]
# do the background subtraction
if bkg is not None:
bkgds = [parse_xrdml_file(fi) for fi in bkg]
bkgd_refs = np.r_[[bkgd["intensities"] for bkgd in bkgds]]
bkgd_refs_s = np.r_[[
np.sqrt(bkgd["intensities"]) / bkgd["count_time"] for bkgd in bkgds
]]
bkgd_refs_var = bkgd_refs_s**2
weights = 1.0 / bkgd_refs_var
numerator = np.sum(bkgd_refs * weights, axis=0)
denominator = np.sum(weights, axis=0)
total_bkgd = numerator / denominator
total_bkgd_s = np.sqrt(1 / denominator)
reflectivity, reflectivity_s = EP.EPsub(reflectivity, reflectivity_s,
total_bkgd, total_bkgd_s)
# work out the Q values
qx, qy, qz = general.q2(
spec["omega"],
spec["twotheta"],
np.zeros_like(spec["omega"]),
spec["wavelength"],
)
# do a footprint correction
if sample_length is not None:
footprint_correction = general.beamfrac(
np.array([XRR_BEAMWIDTH_SD]) * 2.35,
np.array([sample_length]),
spec["omega"],
)
reflectivity /= footprint_correction
reflectivity_s /= footprint_correction
# divide by the direct beam intensity
# assumes that the direct beam intensity is enormous, so the counting
# uncertainties in the scale factor are negligible.
if scale is None:
# no scale factor was specifed, so normalise by highest intensity point
# below Qc for Silicon at 8.048 keV
below_qc = qz[qz < 0.0318]
if len(below_qc):
scale = np.max(reflectivity[qz < 0.0318])
reflectivity /= scale
reflectivity_s /= scale
d = ReflectDataset(data=(qz, reflectivity, reflectivity_s))
return d
def process_offspec(f):
"""
Process a 2D XRDML file and return qx, qz, intensity, dintensity
Parameters
----------
f: str or file-like
Returns
-------
qx, qz, intensity, dintensity
"""
x = et.parse(f)
root = x.getroot()
ns = {"xrdml": "http://www.xrdml.com/XRDMeasurement/1.0"}
query = {
"intensities": ".//xrdml:intensities",
"twotheta_start": ".//xrdml:positions[@axis='2Theta']"
"/xrdml:startPosition",
"twotheta_end": ".//xrdml:positions[@axis='2Theta']"
"/xrdml:endPosition",
"omega_start": ".//xrdml:positions[@axis='Omega']"
"/xrdml:startPosition",
"omega_end": ".//xrdml:positions[@axis='Omega']"
"/xrdml:endPosition",
"cnt_time": ".//xrdml:commonCountingTime",
"kAlpha1": ".//xrdml:kAlpha1",
"kAlpha2": ".//xrdml:kAlpha2",
"ratio": ".//xrdml:ratioKAlpha2KAlpha1",
}
res = {key: root.findall(value, ns) for key, value in query.items()}
kAlpha1 = float(res["kAlpha1"][0].text)
kAlpha2 = float(res["kAlpha2"][0].text)
ratio = float(res["ratio"][0].text)
wavelength = (kAlpha1 + ratio * kAlpha2) / (1 + ratio)
intensity = [
np.fromstring(ints.text, sep=" ") for ints in res["intensities"]
]
twotheta_starts = np.array(
[np.fromstring(ints.text, sep=" ") for ints in res["twotheta_start"]])
twotheta_ends = np.array(
[np.fromstring(ints.text, sep=" ") for ints in res["twotheta_end"]])
omega_starts = np.array(
[np.fromstring(ints.text, sep=" ") for ints in res["omega_start"]])
omega_ends = np.array(
[np.fromstring(ints.text, sep=" ") for ints in res["omega_end"]])
cnt_time = np.array(
[np.fromstring(ints.text, sep=" ") for ints in res["cnt_time"]])
intensity = np.array(intensity)
dintensity = np.sqrt(intensity) / cnt_time
intensity /= cnt_time
omegas = []
two_thetas = []
for i in range(len(intensity)):
omega = np.linspace(omega_starts[i], omega_ends[i],
np.size(intensity, 1))
omegas.append(omega)
two_theta = np.linspace(twotheta_starts[i], twotheta_ends[i],
np.size(intensity, 1))
two_thetas.append(two_theta)
omega = np.array(omegas)
twotheta = np.array(two_thetas)
qx, qy, qz = general.q2(omega, twotheta, 0, wavelength)
return qx, qz, intensity, dintensity
def test_q2(self):
qx, qy, qz = general.q2(1., 2., 0., 2.)
assert_almost_equal(qz, 0.1096567037)
def reduce_xrdml(f, bkg=None, scale=1, sample_length=None):
"""
Reduces a Panalytical XRDML file
Parameters
----------
f: file-like object or string
The specular reflectivity (XRDML) file of interest
bkg: list
A list of file-like objects or strings that contain background
measurements. The background is assumed to have the same number of
points as the specular reflectivity curve. The backgrounds are
averaged and subtracted from the specular reflectivity
scale: float
The direct beam intensity (cps)
sample_length: None or float
If None then no footprint correction is done. Otherwise the transverse
footprint of the sample (mm).
Returns
-------
specular_q, specular_r, specular_dr: np.ndarray
The specular reflectivity as a function of momentum transfer, Q.
"""
spec = parse_xrdml_file(f)
reflectivity = spec['intensities'] / spec['count_time']
reflectivity_s = np.sqrt(reflectivity) / spec['count_time']
# do the background subtraction
if bkg is not None:
bkgds = [parse_xrdml_file(fi) for fi in bkg]
bkgd_refs = np.r_[[bkgd['intensities'] for bkgd in bkgds]]
bkgd_refs_s = np.r_[[np.sqrt(bkgd['intensities']) / bkgd['count_time']
for bkgd in bkgds]]
bkgd_refs_var = bkgd_refs_s ** 2
weights = 1. / bkgd_refs_var
numerator = np.sum(bkgd_refs * weights, axis=0)
denominator = np.sum(weights, axis=0)
total_bkgd = numerator / denominator
total_bkgd_s = np.sqrt(1 / denominator)
reflectivity, reflectivity_s = EP.EPsub(reflectivity,
reflectivity_s,
total_bkgd,
total_bkgd_s)
# work out the Q values
qx, qy, qz = general.q2(spec['omega'],
spec['twotheta'],
np.zeros_like(spec['omega']),
spec['wavelength'])
# do a footprint correction
if sample_length is not None:
footprint_correction = general.beamfrac(np.array([XRR_BEAMWIDTH_SD]) *
2.35,
np.array([sample_length]),
spec['omega'])
reflectivity /= footprint_correction
reflectivity_s /= footprint_correction
# divide by the direct beam intensity
# assumes that the direct beam intensity is enormous, so the counting
# uncertainties in the scale factor are negligible.
reflectivity /= scale
reflectivity_s /= scale
return qz, reflectivity, reflectivity_s
def process_offspec(f):
"""
Process a 2D XRDML file and return qx, qz, intensity, dintensity
Parameters
----------
f: str or file-like
Returns
-------
qx, qz, intensity, dintensity
"""
x = et.parse(f)
root = x.getroot()
ns = {'xrdml': 'http://www.xrdml.com/XRDMeasurement/1.0'}
query = {
'intensities': './/xrdml:intensities',
'twotheta_start': './/xrdml:positions[@axis=\'2Theta\']'
'/xrdml:startPosition',
'twotheta_end': './/xrdml:positions[@axis=\'2Theta\']'
'/xrdml:endPosition',
'omega_start': './/xrdml:positions[@axis=\'Omega\']'
'/xrdml:startPosition',
'omega_end': './/xrdml:positions[@axis=\'Omega\']'
'/xrdml:endPosition',
'cnt_time': './/xrdml:commonCountingTime',
'kAlpha1': './/xrdml:kAlpha1',
'kAlpha2': './/xrdml:kAlpha2',
'ratio': './/xrdml:ratioKAlpha2KAlpha1'
}
res = {key: root.findall(value, ns) for key, value in query.items()}
kAlpha1 = float(res['kAlpha1'][0].text)
kAlpha2 = float(res['kAlpha2'][0].text)
ratio = float(res['ratio'][0].text)
wavelength = (kAlpha1 + ratio * kAlpha2) / (1 + ratio)
intensity = [
np.fromstring(ints.text, sep=' ') for ints in res['intensities']
]
twotheta_starts = np.array(
[np.fromstring(ints.text, sep=' ') for ints in res['twotheta_start']])
twotheta_ends = np.array(
[np.fromstring(ints.text, sep=' ') for ints in res['twotheta_end']])
omega_starts = np.array(
[np.fromstring(ints.text, sep=' ') for ints in res['omega_start']])
omega_ends = np.array(
[np.fromstring(ints.text, sep=' ') for ints in res['omega_end']])
cnt_time = np.array(
[np.fromstring(ints.text, sep=' ') for ints in res['cnt_time']])
intensity = np.array(intensity)
dintensity = np.sqrt(intensity) / cnt_time
intensity /= cnt_time
omegas = []
two_thetas = []
for i in range(len(intensity)):
omega = np.linspace(omega_starts[i], omega_ends[i],
np.size(intensity, 1))
omegas.append(omega)
two_theta = np.linspace(twotheta_starts[i], twotheta_ends[i],
np.size(intensity, 1))
two_thetas.append(two_theta)
omega = np.array(omegas)
twotheta = np.array(two_thetas)
qx, qy, qz = general.q2(omega, twotheta, 0, wavelength)
return qx, qz, intensity, dintensity
def reduce_xrdml(f, bkg=None, scale=1, sample_length=None):
"""
Reduces a Panalytical XRDML file
Parameters
----------
f: file-like object or string
The specular reflectivity (XRDML) file of interest
bkg: list
A list of file-like objects or strings that contain background
measurements. The background is assumed to have the same number of
points as the specular reflectivity curve. The backgrounds are
averaged and subtracted from the specular reflectivity
scale: float
The direct beam intensity (cps)
sample_length: None or float
If None then no footprint correction is done. Otherwise the transverse
footprint of the sample (mm).
Returns
-------
specular_q, specular_r, specular_dr: np.ndarray
The specular reflectivity as a function of momentum transfer, Q.
"""
spec = parse_xrdml_file(f)
reflectivity = spec['intensities'] / spec['count_time']
reflectivity_s = np.sqrt(reflectivity) / spec['count_time']
# do the background subtraction
if bkg is not None:
bkgds = [parse_xrdml_file(fi) for fi in bkg]
bkgd_refs = np.r_[[bkgd['intensities'] for bkgd in bkgds]]
bkgd_refs_s = np.r_[[
np.sqrt(bkgd['intensities']) / bkgd['count_time'] for bkgd in bkgds
]]
bkgd_refs_var = bkgd_refs_s**2
weights = 1. / bkgd_refs_var
numerator = np.sum(bkgd_refs * weights, axis=0)
denominator = np.sum(weights, axis=0)
total_bkgd = numerator / denominator
total_bkgd_s = np.sqrt(1 / denominator)
reflectivity, reflectivity_s = EP.EPsub(reflectivity, reflectivity_s,
total_bkgd, total_bkgd_s)
# work out the Q values
qx, qy, qz = general.q2(spec['omega'], spec['twotheta'],
np.zeros_like(spec['omega']), spec['wavelength'])
# do a footprint correction
if sample_length is not None:
footprint_correction = general.beamfrac(
np.array([XRR_BEAMWIDTH_SD]) * 2.35, np.array([sample_length]),
spec['omega'])
reflectivity /= footprint_correction
reflectivity_s /= footprint_correction
# divide by the direct beam intensity
# assumes that the direct beam intensity is enormous, so the counting
# uncertainties in the scale factor are negligible.
reflectivity /= scale
reflectivity_s /= scale
return qz, reflectivity, reflectivity_s
def test_q2(self):
qx, qy, qz = general.q2(1., 2., 0., 2.)
assert_almost_equal(qz, 0.1096567037)