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 _shift(var, dim, forward, out_of_bounds):
fill = var[dim, 0:1].copy()
fill.values = np.full_like(fill.values, out_of_bounds)
if forward:
return sc.concat([fill, var[dim, :-1]], dim)
else:
return sc.concat([var[dim, 1:], fill], dim)
def to_bin_edges(x: sc.Variable, dim: str) -> sc.Variable:
"""
Convert array centers to edges
"""
idim = x.dims.index(dim)
if x.shape[idim] < 2:
one = 1.0 * x.unit
return sc.concat([x[dim, 0:1] - one, x[dim, 0:1] + one], dim)
else:
center = to_bin_centers(x, dim)
# Note: use range of 0:1 to keep dimension dim in the slice to avoid
# switching round dimension order in concatenate step.
left = center[dim, 0:1] - (x[dim, 1] - x[dim, 0])
right = center[dim, -1] + (x[dim, -1] - x[dim, -2])
return sc.concat([left, center, right], dim)
def make_unphysical_tof(t0, da):
# 0 < t < t0, t < 0, t > t0
tof = sc.concat([t0 - t0 / 2, sc.full_like(t0, -2), 2 * t0], 'tof')
is_unphysical = sc.array(dims=['energy_transfer'],
values=[True, True, False]).broadcast(
['energy_transfer', 'spectrum'],
[3, da.sizes['spectrum']])
return tof, is_unphysical
def test_simple_case_any_naming():
ds = _make_simple_dataset(u=2, v=10, w=10)
grouped = groupby2D(ds, nx_target=5, ny_target=5, x='w', y='v', z='u')
assert grouped['a'].shape == [2, 5, 5]
projection = sc.array(dims=['v', 'w'], values=np.ones((5, 5))) * 4
expected_data = sc.concat([projection, projection], dim='u')
assert sc.all(
sc.isclose(grouped['a'].data, expected_data,
atol=1e-14 * sc.units.one)).value
def test_linlogspace_log_linear():
q_loglin = tools.linlogspace(dim='qz',
edges=[0.008, 0.03, 0.08],
unit='1/angstrom',
scale=['log', 'linear'],
num=[16, 20])
exp_log = sc.geomspace(dim='qz', start=0.008, stop=0.03, num=16, unit='1/angstrom')
exp_lin = sc.linspace(dim='qz', start=0.03, stop=0.08, num=21, unit='1/angstrom')
expected = sc.concat([exp_log, exp_lin['qz', 1:]], 'qz')
assert sc.allclose(q_loglin, expected)
def _interpolate_transform(transform, xnew):
# scipy can't interpolate with a single value
if transform.sizes["time"] == 1:
transform = sc.concat([transform, transform], dim="time")
transform = sc.interpolate.interp1d(transform,
"time",
kind="previous",
fill_value="extrapolate")(xnew=xnew)
return transform
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 linlogspace(dim: str,
edges: Union[list, np.ndarray],
scale: Union[list, str],
num: Union[list, int],
unit: str = None) -> sc.Variable:
"""
Generate a 1d array of bin edges with a mixture of linear and/or logarithmic
spacings.
Examples:
- Create linearly spaced edges (equivalent to `sc.linspace`):
linlogspace(dim='x', edges=[0.008, 0.08], scale='linear', num=50, unit='m')
- Create logarithmically spaced edges (equivalent to `sc.geomspace`):
linlogspace(dim='x', edges=[0.008, 0.08], scale='log', num=50, unit='m')
- Create edges with a linear and a logarithmic part:
linlogspace(dim='x', edges=[1, 3, 8], scale=['linear', 'log'], num=[16, 20])
:param dim: The dimension of the ouptut Variable.
:param edges: The edges for the different parts of the mesh.
:param scale: A string or list of strings specifying the scaling for the different
parts of the mesh. Possible values for the scaling are `"linear"` and `"log"`.
If a list is supplied, the length of the list must be one less than the length
of the `edges` parameter.
:param num: An integer or a list of integers specifying the number of points to use
in each part of the mesh. If a list is supplied, the length of the list must be
one less than the length of the `edges` parameter.
:param unit: The unit of the ouptut Variable.
"""
if not isinstance(scale, list):
scale = [scale]
if not isinstance(num, list):
num = [num]
if len(scale) != len(edges) - 1:
raise ValueError(
"Sizes do not match. The length of edges should be one "
"greater than scale.")
funcs = {"linear": sc.linspace, "log": sc.geomspace}
grids = []
for i in range(len(edges) - 1):
# Skip the leading edge in the piece when concatenating
start = int(i > 0)
mesh = funcs[scale[i]](dim=dim,
start=edges[i],
stop=edges[i + 1],
num=num[i] + start,
unit=unit)
grids.append(mesh[dim, start:])
return sc.concat(grids, dim)
def get_full_transformation_matrix(group: Group,
nexus: LoadFromNexus) -> sc.DataArray:
"""
Get the 4x4 transformation matrix for a component, resulting
from the full chain of transformations linked by "depends_on"
attributes
:param group: The HDF5 group of the component, containing depends_on
:param nexus: wrap data access to hdf file or objects from json
:return: 4x4 passive transformation matrix as a data array
"""
transformations = []
try:
depends_on = nexus.load_scalar_string(group, "depends_on")
except MissingDataset:
depends_on = '.'
_get_transformations(depends_on, transformations, group,
nexus.get_name(group), nexus)
total_transform = sc.spatial.affine_transform(value=np.identity(4),
unit=sc.units.m)
for transform in transformations:
if isinstance(total_transform, sc.DataArray) and isinstance(
transform, sc.DataArray):
xnew = sc.datetimes(values=np.unique(
sc.concat([
total_transform.coords["time"].to(unit=sc.units.ns,
copy=True),
transform.coords["time"].to(unit=sc.units.ns, copy=True),
],
dim="time").values),
dims=["time"],
unit=sc.units.ns)
total_transform = _interpolate_transform(
transform, xnew) * _interpolate_transform(
total_transform, xnew)
else:
total_transform = transform * total_transform
return total_transform
def reduce_to_q(data, *, q_bins, reducer, wavelength_bands=None):
"""
Example:
>>> reduced = reduce_to_q(data, q_bins=q_bins, reducer=simple_reducer('spectrum')) # noqa: E501
"""
# TODO Backup of the coord is necessary until `convert` can keep original
wavelength = data.coords['wavelength']
data = scn.convert(data, 'wavelength', 'Q', scatter=True)
if wavelength_bands is None:
data = sc.histogram(data, q_bins)
return reducer(data)
data.coords['wavelength'] = wavelength
bands = None
for i in range(wavelength_bands.sizes['wavelength'] - 1):
low = wavelength_bands['wavelength', i]
high = wavelength_bands['wavelength', i + 1]
band = sc.histogram(data['wavelength', low:high], q_bins)
band = reducer(band)
bands = sc.concat([bands, band],
'wavelength') if bands is not None else band
bands.coords['wavelength'] = wavelength_bands
return bands
def load_detector_data(event_data_groups: List[Group],
detector_groups: List[Group], nexus: LoadFromNexus,
quiet: bool,
bin_by_pixel: bool) -> Optional[sc.DataArray]:
detectors = _load_data_from_each_nx_detector(detector_groups, nexus)
detectors = _load_data_from_each_nx_event_data(detectors,
event_data_groups, nexus,
quiet)
if not detectors:
# If there were no data to load we are done
return
def get_detector_id(data: DetectorData):
# Assume different detector banks do not have
# intersecting ranges of detector ids
if data.detector_ids is None:
return 0
return data.detector_ids.values[0]
detectors.sort(key=get_detector_id)
_create_empty_event_data(detectors)
pixel_positions_loaded = all(
[data.pixel_positions is not None for data in detectors])
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
_dim = _detector_dimension if bin_by_pixel else _bank_dimension
events = sc.concat([_bin_events(item) for item in detectors], _dim)
if bin_by_pixel:
_min_tof = events.bins.coords[_time_of_flight].min()
_max_tof = events.bins.coords[_time_of_flight].max()
# This can happen if there were no events in the file at all as sc.min will
# return double_max and sc.max will return double_min
if _min_tof.value >= _max_tof.value:
_min_tof, _max_tof = _max_tof, _min_tof
if np.issubdtype(type(_max_tof.value), np.integer):
if _max_tof.value != np.iinfo(type(_max_tof.value)).max:
_max_tof += sc.ones_like(_max_tof)
else:
if _max_tof.value != np.finfo(type(_max_tof.value)).max:
_max_tof.value = np.nextafter(_max_tof.value, float("inf"))
events.coords[_time_of_flight] = sc.concat([_min_tof, _max_tof],
_time_of_flight)
return events
def convert_EventWorkspace_to_data_array(ws,
load_pulse_times=True,
advanced_geometry=False,
load_run_logs=True,
**ignored):
dim, unit = validate_and_get_unit(ws.getAxis(0).getUnit())
spec_dim, spec_coord = init_spec_axis(ws)
nHist = ws.getNumberHistograms()
_, data_unit = validate_and_get_unit(ws.YUnit(), allow_empty=True)
n_event = ws.getNumberEvents()
coord = sc.zeros(dims=['event'],
shape=[n_event],
unit=unit,
dtype=sc.DType.float64)
weights = sc.ones(dims=['event'],
shape=[n_event],
unit=data_unit,
dtype=sc.DType.float32,
with_variances=True)
pulse_times = sc.empty(dims=['event'],
shape=[n_event],
dtype=sc.DType.datetime64,
unit=sc.units.ns) if load_pulse_times else None
begins = sc.zeros(dims=[spec_dim, dim],
shape=[nHist, 1],
dtype=sc.DType.int64)
ends = begins.copy()
current = 0
for i in range(nHist):
sp = ws.getSpectrum(i)
size = sp.getNumberEvents()
coord['event', current:current + size].values = sp.getTofs()
if load_pulse_times:
pulse_times['event', current:current +
size].values = sp.getPulseTimesAsNumpy()
if _contains_weighted_events(sp):
weights['event', current:current + size].values = sp.getWeights()
weights['event',
current:current + size].variances = sp.getWeightErrors()
begins.values[i] = current
ends.values[i] = current + size
current += size
proto_events = {'data': weights, 'coords': {dim: coord}}
if load_pulse_times:
proto_events["coords"]["pulse_time"] = pulse_times
events = sc.DataArray(**proto_events)
coords_labs_data = _convert_MatrixWorkspace_info(
ws, advanced_geometry=advanced_geometry, load_run_logs=load_run_logs)
# For now we ignore potential finer bin edges to avoid creating too many
# bins. Use just a single bin along dim and use extents given by workspace
# edges.
# TODO If there are events outside edges this might create bins with
# events that are not within bin bounds. Consider using `bin` instead
# of `bins`?
edges = coords_labs_data['coords'][dim]
# Using range slice of thickness 1 to avoid transposing 2-D coords
coords_labs_data['coords'][dim] = sc.concat(
[edges[dim, :1], edges[dim, -1:]], dim)
coords_labs_data["data"] = sc.bins(begin=begins,
end=ends,
dim='event',
data=events)
return sc.DataArray(**coords_labs_data)
