def __init__(self, direct, reflect=None, data_folder=None, scale=1.,
save=True, **kwds):
self.data_folder = os.path.curdir
if data_folder is not None:
self.data_folder = data_folder
if isinstance(direct, PlatypusNexus):
self.direct_beam = direct
elif type(direct) is str:
direct = os.path.join(self.data_folder, direct)
self.direct_beam = PlatypusNexus(direct)
else:
self.direct_beam = PlatypusNexus(direct)
if reflect is not None:
self.reduce(reflect, save=save, scale=scale, **kwds)
def reduce(self, reflect, scale=1., save=True, **kwds):
"""
Reduction of a single dataset.
The reduction uses the direct beam specified during construction of
this object. This method reduces all the spectra present in the
reflected beam file (see platypusnexus.PlatypusNexus.process for
eventmode specification and other related options), but aggregates
all data in the direct beam spectrum.
Parameters
----------
reflect : string, hdf5 file-handle or PlatypusNexus object
A string containing the path to the specularly reflected hdf5 file,
the hdf5 file itself, or a PlatypusNexus object.
scale : float, optional
Divide all the reflectivity values by this number.
save : bool, optional
If `True` then the reduced dataset is saved to the current
directory, with a name os.path.basename(reflect)
kwds : dict, optional
Options passed directly to `refnx.reduce.platypusnexus.process`,
for processing of individual spectra. Look at that method docstring
for specification of options.
Returns
-------
reduction : dict
Contains the following entries:
- 'x' : np.ndarray
Q values, shape (N, T).
- 'x_sd' : np.ndarray
Uncertainty in Q values (FWHM), shape (N, T).
- 'y' : np.ndarray
Specular Reflectivity, shape (N, T)
- 'y_sd' : np.ndarray
Uncertainty in specular reflectivity (SD), shape (N, T)
- 'm_ref' : np.ndarray
Offspecular reflectivity map, shape (N, T, Y)
- 'm_refSD' : np.ndarray
uncertainty in offspecular reflectivity, shape (N, T, Y)
- 'm_qz' : np.ndarray
Qz for offspecular map, shape (N, T, Y)
- 'm_qy' : np.ndarray
Qy for offspecular map, shape (N, T, Y)
- 'n_spectra' : int
number of reflectivity spectra
- 'datafile_number': int
run number for the reflected beam
N corresponds to the number of spectra
T corresponds to the number of Q (wavelength) bins
Y corresponds to the number of y pixels on the detector.
Notes
-----
All the values returned from this method are also contained as instance
attributes for this object.
"""
keywords = kwds.copy()
keywords['direct'] = False
# get the reflected beam spectrum
if isinstance(reflect, PlatypusNexus):
self.reflected_beam = reflect
else:
reflect = os.path.join(self.data_folder, reflect)
self.reflected_beam = PlatypusNexus(reflect)
self.reflected_beam.process(**keywords)
# get the direct beam spectrum
keywords['direct'] = True
keywords['integrate'] = -1
if 'eventmode' in keywords:
keywords.pop('eventmode')
# got to use the same wavelength bins as the reflected spectrum.
keywords['wavelength_bins'] = self.reflected_beam.m_lambda_hist[0]
self.direct_beam.process(**keywords)
self.save = save
reduction = self._reduce_single_angle(scale)
return reduction
class ReducePlatypus(object):
"""
Reduces Platypus reflectometer data to give the specular reflectivity.
Offspecular data maps are also produced.
Parameters
----------
direct : string, hdf5 file-handle or PlatypusNexus object
A string containing the path to the direct beam hdf5 file,
the hdf5 file itself, or a PlatypusNexus object.
reflect : string, hdf5 file-handle or PlatypusNexus object, optional
A string containing the path to the specularly reflected hdf5 file,
the hdf5 file itself, or a PlatypusNexus object.
data_folder : str, optional
Where is the raw data stored?
scale : float, optional
Divide all specular reflectivity values by this number.
save : bool, optional
If `True` then the reduced dataset is saved to the current
directory, with a name os.path.basename(reflect)
kwds : dict, optional
Options passed directly to `refnx.reduce.platypusnexus.process`,
for processing of individual spectra. Look at that method docstring
for specification of options.
Notes
-----
If `reflect` was specified during construction a reduction will be
done. See ``reduce`` for attributes available from this object on
completion of reduction.
Returns
-------
None
"""
def __init__(self, direct, reflect=None, data_folder=None, scale=1.,
save=True, **kwds):
self.data_folder = os.path.curdir
if data_folder is not None:
self.data_folder = data_folder
if isinstance(direct, PlatypusNexus):
self.direct_beam = direct
else:
direct = os.path.join(self.data_folder, direct)
self.direct_beam = PlatypusNexus(direct)
if reflect is not None:
self.reduce(reflect, save=save, scale=scale, **kwds)
def __call__(self, reflect, scale=1, save=True, **kwds):
return self.reduce(reflect, scale=scale, save=save, **kwds)
def reduce(self, reflect, scale=1., save=True, **kwds):
"""
Reduction of a single dataset.
The reduction uses the direct beam specified during construction of
this object. This method reduces all the spectra present in the
reflected beam file (see platypusnexus.PlatypusNexus.process for
eventmode specification and other related options), but aggregates
all data in the direct beam spectrum.
Parameters
----------
reflect : string, hdf5 file-handle or PlatypusNexus object
A string containing the path to the specularly reflected hdf5 file,
the hdf5 file itself, or a PlatypusNexus object.
scale : float, optional
Divide all the reflectivity values by this number.
save : bool, optional
If `True` then the reduced dataset is saved to the current
directory, with a name os.path.basename(reflect)
kwds : dict, optional
Options passed directly to `refnx.reduce.platypusnexus.process`,
for processing of individual spectra. Look at that method docstring
for specification of options.
Returns
-------
reduction : dict
Contains the following entries:
- 'x' : np.ndarray
Q values, shape (N, T).
- 'x_sd' : np.ndarray
Uncertainty in Q values (FWHM), shape (N, T).
- 'y' : np.ndarray
Specular Reflectivity, shape (N, T)
- 'y_sd' : np.ndarray
Uncertainty in specular reflectivity (SD), shape (N, T)
- 'm_ref' : np.ndarray
Offspecular reflectivity map, shape (N, T, Y)
- 'm_refSD' : np.ndarray
uncertainty in offspecular reflectivity, shape (N, T, Y)
- 'm_qz' : np.ndarray
Qz for offspecular map, shape (N, T, Y)
- 'm_qy' : np.ndarray
Qy for offspecular map, shape (N, T, Y)
- 'n_spectra' : int
number of reflectivity spectra
- 'datafile_number': int
run number for the reflected beam
N corresponds to the number of spectra
T corresponds to the number of Q (wavelength) bins
Y corresponds to the number of y pixels on the detector.
Notes
-----
All the values returned from this method are also contained as instance
attributes for this object.
"""
keywords = kwds.copy()
keywords['direct'] = False
# get the reflected beam spectrum
if isinstance(reflect, PlatypusNexus):
self.reflected_beam = reflect
else:
reflect = os.path.join(self.data_folder, reflect)
self.reflected_beam = PlatypusNexus(reflect)
self.reflected_beam.process(**keywords)
# get the direct beam spectrum
keywords['direct'] = True
keywords['integrate'] = -1
if 'eventmode' in keywords:
keywords.pop('eventmode')
# got to use the same wavelength bins as the reflected spectrum.
keywords['wavelength_bins'] = self.reflected_beam.m_lambda_hist[0]
self.direct_beam.process(**keywords)
self.save = save
reduction = self._reduce_single_angle(scale)
return reduction
def data(self, scanpoint=0):
"""
The specular reflectivity
Parameters
----------
scanpoint: int
Find a particular specular reflectivity image. scanpoints upto
`self.n_spectra - 1` can be specified.
Returns
-------
(Q, R, dR, dQ): np.ndarray tuple
dR is standard deviation, dQ is FWHM
"""
return (self.xdata[scanpoint],
self.ydata[scanpoint],
self.ydata_sd[scanpoint],
self.xdata_sd[scanpoint])
def data2d(self, scanpoint=0):
"""
The offspecular data
Parameters
----------
scanpoint: int
Find a particular offspecular image. scanpoints upto
self.n_spectra - 1 can be specified.
Returns
-------
(Qz, Qy, R, dR): np.ndarrays
"""
return (self.m_qz[scanpoint],
self.m_qy[scanpoint],
self.m_ref[scanpoint],
self.m_ref_sd[scanpoint])
def scale(self, scale):
"""
Divides the reflectivity values by this scale factor
Parameters
----------
scale: float
Divides the reflectivity values by a constant amount
"""
self.m_ref /= scale
self.m_ref_sd /= scale
self.ydata /= scale
self.ydata_sd /= scale
def write_offspecular(self, f, scanpoint=0):
__template_ref_xml = """<?xml version="1.0"?>
<REFroot xmlns="">
<REFentry time="$time">
<Title>$title</Title>
<User>$user</User>
<REFsample>
<ID>$sample</ID>
</REFsample>
<REFdata axes="Qz:Qy" rank="2" type="POINT" spin="UNPOLARISED" dim="$_numpointsz:$_numpointsy">
<Run filename="$_rnumber" preset="" size="">
</Run>
<R uncertainty="dR">$_r</R>
<Qz uncertainty="dQz" units="1/A">$_qz</Qz>
<dR type="SD">$_dr</dR>
<Qy type="_FWHM" units="1/A">$_qy</Qy>
</REFdata>
</REFentry>
</REFroot>"""
d = dict()
d['time'] = strftime("%a, %d %b %Y %H:%M:%S +0000", gmtime())
d['_rnumber'] = self.reflected_beam.datafile_number
d['_numpointsz'] = np.size(self.m_ref, 1)
d['_numpointsy'] = np.size(self.m_ref, 2)
s = string.Template(__template_ref_xml)
# filename = 'off_PLP{:07d}_{:d}.xml'.format(self._rnumber, index)
d['_r'] = repr(self.m_ref[scanpoint].tolist()).strip(',[]')
d['_qz'] = repr(self.m_qz[scanpoint].tolist()).strip(',[]')
d['_dr'] = repr(self.m_ref_sd[scanpoint].tolist()).strip(',[]')
d['_qy'] = repr(self.m_qy[scanpoint].tolist()).strip(',[]')
thefile = s.safe_substitute(d)
g = f
if not hasattr(f, 'read'):
own_fh = open(f, 'w')
g = own_fh
try:
g.write(thefile)
g.truncate()
finally:
g.close()
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)