from __future__ import annotations
from dataclasses import dataclass
from typing import Generator
from typing import Tuple
from typing import Union
import h5py
import numpy
from silx.io.nxdata import NXdata
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@dataclass
class AxisInfo:
array: numpy.ndarray
name: str = ""
units: str = ""
[docs]
@dataclass
class AzimuthalPoint:
value: Union[float, int]
name: str
sector_index: int
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@dataclass
class IntegratedPattern:
"""Store one pyFAI integrated pattern"""
point: Union[float, int, None]
radial: numpy.ndarray
radial_name: str
radial_units: str
intensity: numpy.ndarray
intensity_errors: Union[numpy.ndarray, None]
azimuthal_point: Union[AzimuthalPoint, None] = None
def _read_axis_info(nxdata: NXdata, index: int) -> Union[AxisInfo, None]:
axis_dataset = nxdata.axes[index]
if axis_dataset is None:
return None
return AxisInfo(
name=str(nxdata.axes_dataset_names[index]),
array=axis_dataset[()],
units=axis_dataset.attrs.get("units", ""),
)
def _read_nexus_integrated_patterns_1d(
nxdata: NXdata,
) -> Generator[Tuple[int, IntegratedPattern]]:
radial = _read_axis_info(nxdata, index=-1)
if radial is None:
radial = AxisInfo(array=numpy.arange(nxdata.signal.shape[-1]))
if (len(radial.array),) != nxdata.signal.shape:
raise RuntimeError("Shape mismatch between axes and signal")
yield 0, IntegratedPattern(
None, radial.array, radial.name, radial.units, nxdata.signal, nxdata.errors
)
def _read_nexus_integrated_patterns_2d(
nxdata: NXdata,
) -> Generator[Tuple[int, IntegratedPattern]]:
radial = _read_axis_info(nxdata, index=-1)
if radial is None:
radial = AxisInfo(array=numpy.arange(nxdata.signal.shape[-1]))
intensities = nxdata.signal
if nxdata.errors is None:
errors = [None] * intensities.shape[0]
else:
errors = nxdata.errors
if nxdata.axes_dataset_names[0] == "chi": # (azim, radial)
azimuthal = _read_axis_info(nxdata, index=0)
if azimuthal is None:
raise RuntimeError("No azimuthal axis found !")
if (len(azimuthal.array), len(radial.array)) != intensities.shape:
raise RuntimeError("Shape mismatch between axes and signal")
for index, azimuthal_value in enumerate(azimuthal.array):
yield 0, IntegratedPattern(
None,
radial.array,
radial.name,
radial.units,
intensities[index],
errors[index],
AzimuthalPoint(azimuthal_value, azimuthal.name, index),
)
else: # (points, radial)
if nxdata.axes[0] is None:
points = [None] * intensities.shape[0]
else:
points = nxdata.axes[0][()]
if (len(points), len(radial.array)) != intensities.shape:
raise RuntimeError("Shape mismatch between axes and signal")
for index, point in enumerate(points):
yield index, IntegratedPattern(
point,
radial.array,
radial.name,
radial.units,
intensities[index],
errors[index],
)
def _read_nexus_integrated_patterns_3d(nxdata: NXdata):
intensities = nxdata.signal
radial = _read_axis_info(nxdata, index=-1)
if radial is None:
radial = AxisInfo(array=numpy.arange(intensities.shape[-1]))
azimuthal = _read_axis_info(nxdata, index=1)
if azimuthal is None:
raise RuntimeError("No azimuthal axis found !")
if nxdata.axes[0] is None:
points = [None] * intensities.shape[0]
else:
points = nxdata.axes[0][()]
if nxdata.errors is None:
errors = [[None] * intensities.shape[1]] * intensities.shape[0]
else:
errors = nxdata.errors
if (len(points), len(azimuthal.array), len(radial.array)) != intensities.shape:
raise RuntimeError("Shape mismatch between axes and signal")
for index, point in enumerate(points):
for azim_index, azimuthal_value in enumerate(azimuthal.array):
yield index, IntegratedPattern(
point,
radial.array,
radial.name,
radial.units,
intensities[index, azim_index],
errors[index][azim_index],
AzimuthalPoint(azimuthal_value, azimuthal.name, azim_index),
)
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def read_nexus_integrated_patterns(
group: h5py.Group,
) -> Generator[Tuple[int, IntegratedPattern]]:
"""Read integrated patterns from a HDF5 NXdata group.
Reads single 1D pattern, multi 1D patterns (2D signal), single 2D pattern, or multi 2D patterns (3D signal) NXdata.
:return: tuple with frame index and IntegratedPattern
"""
nxdata = NXdata(group)
if not nxdata.is_valid:
raise RuntimeError(
f"Cannot parse NXdata group: {group.file.filename}::{group.name}"
)
if nxdata.signal_is_1d: # (radial,)
return _read_nexus_integrated_patterns_1d(nxdata)
elif nxdata.signal_is_2d: # (points, radial) or (azim, radial)
return _read_nexus_integrated_patterns_2d(nxdata)
elif nxdata.signal_is_3d: # (points, azim, radial)
return _read_nexus_integrated_patterns_3d(nxdata)
else:
raise RuntimeError(
f"Signal is not a 1D, 2D or 3D dataset: {group.file.filename}::{group.name}"
)