def _stitch_event_data(
item: sc.DataArray, frames: sc.Dataset, dim: str, new_dim: str,
bins: Union[int, sc.Variable]) -> Union[sc.DataArray, dict]:
edges = sc.flatten(sc.transpose(sc.concat(
[frames["time_min"].data, frames["time_max"].data], 'dummy'),
dims=['frame', 'dummy']),
to=dim)
binned = sc.bin(item, edges=[edges])
for i in range(frames.sizes["frame"]):
# TODO: temporary fix working on the .value because read-only flag is set
binned[dim, i *
2].value.coords[dim] -= frames["time_correction"].data["frame",
i]
erase = None
if new_dim != dim:
binned.bins.coords[new_dim] = binned.bins.coords[dim]
del binned.bins.coords[dim]
erase = [dim]
binned.masks['frame_gaps'] = (
sc.arange(dim, 2 * frames.sizes["frame"] - 1) % 2).astype(bool)
new_edges = sc.concat([(frames["time_min"]["frame", 0] -
frames["time_correction"]["frame", 0]).data,
(frames["time_max"]["frame", -1] -
frames["time_correction"]["frame", -1]).data],
new_dim)
return sc.bin(binned, edges=[new_edges], erase=erase)
def _bin_events(data: DetectorData):
if not bin_by_pixel:
# If loading "raw" data, leave binned by pulse.
return data.event_data
if data.detector_ids is None:
# If detector ids were not found in an associated detector group
# we will just have to bin according to whatever
# ids we have a events for (pixels with no recorded events
# will not have a bin)
event_id = data.event_data.bins.constituents['data'].coords[
_detector_dimension]
data.detector_ids = sc.array(dims=[_detector_dimension],
values=np.unique(event_id.values))
# Events in the NeXus file are effectively binned by pulse
# (because they are recorded chronologically)
# but for reduction it is more useful to bin by detector id
# Broadcast pulse times to events
data.event_data.bins.coords['pulse_time'] = sc.bins_like(
data.event_data, fill_value=data.event_data.coords['pulse_time'])
# TODO Look into using `erase=[_pulse_dimension]` instead of binning
# underlying buffer. Must prove that performance can be unaffected.
da = sc.bin(data.event_data.bins.constituents['data'],
groups=[data.detector_ids])
# Add a single time-of-flight bin
da = sc.DataArray(data=sc.broadcast(da.data,
dims=da.dims + [_time_of_flight],
shape=da.shape + [1]),
coords={_detector_dimension: data.detector_ids})
if pixel_positions_loaded:
# TODO: the name 'position' should probably not be hard-coded but moved
# to a variable that cah be changed in a single place.
da.coords['position'] = data.pixel_positions
return da
def _getitem(self, select: ScippIndex) -> sc.DataArray:
# Note that ._detector_data._load_detector provides a different loading
# facility for NXdetector but handles only loading of detector_number,
# as needed for event data loading
if self._is_events:
# If there is a 'detector_number' field it is used to bin events into
# detector pixels. Note that due to the nature of NXevent_data, which stores
# events from all pixels and random order, we always have to load the entire
# bank. Slicing with the provided 'select' is done while binning.
event_data = self._nxbase[...]
if self.detector_number is None:
# Ideally we would prefer to use np.unique, but a quick experiment shows
# that this can easily be 100x slower, so it is not an option. In
# practice most files have contiguous event_id values within a bank
# (NXevent_data).
id_min = event_data.bins.coords['event_id'].min()
id_max = event_data.bins.coords['event_id'].max()
detector_numbers = sc.arange(dim='detector_number',
start=id_min.value,
stop=id_max.value + 1,
dtype=id_min.dtype)
else:
detector_numbers = self.detector_number[select]
event_data.bins.coords[
'detector_number'] = event_data.bins.coords.pop('event_id')
# After loading raw NXevent_data it is guaranteed that the event table
# is contiguous and that there is no masking. We can therefore use the
# more efficient approach of binning from scratch instead of erasing the
# 'pulse' binning defined by NXevent_data.
return sc.bin(event_data.bins.constituents['data'],
groups=[detector_numbers])
return self._nxbase[select]
def test_bins_arithmetic():
var = sc.Variable(dims=['event'], values=[1.0, 2.0, 3.0, 4.0])
table = sc.DataArray(var, {'x': var})
binned = sc.bin(table, [sc.Variable(dims=['x'], values=[1.0, 5.0])])
hist = sc.DataArray(
data=sc.Variable(dims=['x'], values=[1.0, 2.0]),
coords={'x': sc.Variable(dims=['x'], values=[1.0, 3.0, 5.0])})
binned.bins *= sc.lookup(func=hist, dim='x')
assert sc.is_equal(
binned.bins.data.data,
sc.Variable(dims=['event'], values=[1.0, 2.0, 6.0, 8.0]))
def _bin_event_data_for_ploting(data, frame, bins_per_frame):
"""
Bin event data using `bins_per_frame` to make a meaningful plot.
"""
return sc.bin(data,
edges=[
sc.linspace(dim='tof',
start=frame["time_min"].value,
stop=frame["time_max"].value,
num=bins_per_frame,
unit=frame['time_min'].unit)
]).bins.sum()
def _tof_correction(data: sc.DataArray, dim: str = 'tof') -> sc.DataArray:
"""
A correction for the presense of the chopper with respect to the "true" ToF.
Also fold the two pulses.
TODO: generalise mechanism to fold any number of pulses.
"""
tau = sc.to_unit(
1 / (2 * data.coords['source_chopper'].value['frequency'].data),
data.coords[dim].unit)
chopper_phase = data.coords['source_chopper'].value['phase'].data
tof_offset = tau * chopper_phase / (180.0 * sc.units.deg)
# Make 2 bins, one for each pulse
edges = sc.concat([-tof_offset, tau - tof_offset, 2 * tau - tof_offset],
dim)
data = sc.bin(data, edges=[sc.to_unit(edges, data.coords[dim].unit)])
# Make one offset for each bin
offset = sc.concat([tof_offset, tof_offset - tau], dim)
# Apply the offset on both bins
data.bins.coords[dim] += offset
# Rebin to exclude second (empty) pulse range
return sc.bin(data, edges=[sc.concat([0. * sc.units.us, tau], dim)])
def _check_lambda_inside_resolution(lam,
dlam_over_lam,
data,
event_mode=False,
check_value=True):
dlam = 0.5 * dlam_over_lam * lam
if event_mode:
sum_in_range = sc.bin(data,
edges=[
sc.array(dims=['wavelength'],
values=[(lam - dlam).value,
(lam + dlam).value],
unit=lam.unit)
]).bins.sum().data['wavelength', 0]
else:
sum_in_range = sc.sum(data['wavelength', lam - dlam:lam + dlam]).data
assert sc.isclose(sum_in_range, 1.0 * sc.units.counts).value is check_value
def make_binned_data_array(ndim=1, variances=False, masks=False):
dim_list = ['tof', 'x', 'y', 'z', 'Q_x']
N = 50
M = 10
values = 10.0 * np.random.random(N)
da = sc.DataArray(data=sc.Variable(dims=['position'],
unit=sc.units.counts,
values=values),
coords={
'position':
sc.Variable(
dims=['position'],
values=['site-{}'.format(i) for i in range(N)])
})
if variances:
da.variances = values
bin_list = []
for i in range(ndim):
da.coords[dim_list[i]] = sc.Variable(dims=['position'],
unit=sc.units.m,
values=np.random.random(N))
bin_list.append(
sc.Variable(dims=[dim_list[i]],
unit=sc.units.m,
values=np.linspace(0.1, 0.9, M - i)))
binned = sc.bin(da, bin_list)
if masks:
# Make a checkerboard mask, see https://stackoverflow.com/a/51715491
binned.masks["mask"] = sc.Variable(
dims=binned.dims,
values=(np.indices(binned.shape).sum(axis=0) % 2).astype(np.bool))
return binned
def _do_stitching_on_beamline(wavelengths, dim, event_mode=False):
# Make beamline parameters for 6 frames
coords = wfm.make_fake_beamline(nframes=6)
# They are all created half-way through the pulse.
# Compute their arrival time at the detector.
alpha = sc.to_unit(constants.m_n / constants.h, 's/m/angstrom')
dz = sc.norm(coords['position'] - coords['source_position'])
arrival_times = sc.to_unit(alpha * dz * wavelengths,
'us') + coords['source_pulse_t_0'] + (
0.5 * coords['source_pulse_length'])
coords[dim] = arrival_times
# Make a data array that contains the beamline and the time coordinate
tmin = sc.min(arrival_times)
tmax = sc.max(arrival_times)
dt = 0.1 * (tmax - tmin)
if event_mode:
num = 2
else:
num = 2001
time_binning = sc.linspace(dim=dim,
start=(tmin - dt).value,
stop=(tmax + dt).value,
num=num,
unit=dt.unit)
events = sc.DataArray(data=sc.ones(dims=['event'],
shape=arrival_times.shape,
unit=sc.units.counts,
with_variances=True),
coords=coords)
if event_mode:
da = sc.bin(events, edges=[time_binning])
else:
da = sc.histogram(events, bins=time_binning)
# Find location of frames
frames = wfm.get_frames(da)
stitched = wfm.stitch(frames=frames, data=da, dim=dim, bins=2001)
wav = scn.convert(stitched,
origin='tof',
target='wavelength',
scatter=False)
if event_mode:
out = wav
else:
out = sc.rebin(wav,
dim='wavelength',
bins=sc.linspace(dim='wavelength',
start=1.0,
stop=10.0,
num=1001,
unit='angstrom'))
choppers = {key: da.meta[key].value for key in ch.find_chopper_keys(da)}
# Distance between WFM choppers
dz_wfm = sc.norm(choppers["chopper_wfm_2"]["position"].data -
choppers["chopper_wfm_1"]["position"].data)
# Delta_lambda / lambda
dlambda_over_lambda = dz_wfm / sc.norm(
coords['position'] - frames['wfm_chopper_mid_point'].data)
return out, dlambda_over_lambda