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Update HDF5 to avoid scipp.DataArray.attrs deprecation warnings #25

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Oct 26, 2023
Merged

Update HDF5 to avoid scipp.DataArray.attrs deprecation warnings #25

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5e69671
Update HDF5 to avoid scipp.DataArray.attrs deprecation warnings
SimonHeybrock Oct 24, 2023
e88abde
Apply offsets to fix instrument info from file
SimonHeybrock Oct 26, 2023
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8 changes: 4 additions & 4 deletions src/esssans/data.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# SPDX-License-Identifier: BSD-3-Clause
# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
_version = '1'
_version = '2'

__all__ = ['get_path']

Expand All @@ -15,9 +15,9 @@ def _make_pooch():
version=_version,
registry={
'DIRECT_SANS2D_REAR_34327_4m_8mm_16Feb16.hdf5': 'md5:43f4188301d709aa49df0631d03a67cb', # noqa: E501
'SANS2D00063091.hdf5': 'md5:c212f1c8c68db69eae88eca90a19e7e6',
'SANS2D00063114.hdf5': 'md5:806a5780ff02676afcea1c3d8777ee21',
'SANS2D00063159.hdf5': 'md5:7be098bcc1f4ca73394584076a99146d',
'SANS2D00063091.hdf5': 'md5:1fdbe36a496e914336f2f9b5cad9f00e',
'SANS2D00063114.hdf5': 'md5:536303077b9f55286af5ef6ec5124e1c',
'SANS2D00063159.hdf5': 'md5:e2f2aea3ed9251e579210718de568203',
},
)

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38 changes: 28 additions & 10 deletions src/esssans/sans2d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,10 +28,26 @@
def pooch_load(filename: Filename[RunType]) -> RawData[RunType]:
from .data import get_path

da = sc.io.load_hdf5(filename=get_path(filename))
if 'gravity' not in da.coords:
da.coords["gravity"] = gravity_vector()
return RawData[RunType](da)
dg = sc.io.load_hdf5(filename=get_path(filename))
data = dg['data']
if 'gravity' not in data.coords:
data.coords["gravity"] = gravity_vector()
data.coords['pixel_width'] = sc.scalar(0.002033984375, unit='m')
data.coords['pixel_height'] = sc.scalar(0.0035, unit='m')

# Some fixes specific for these Sans2d runs
sample_pos_z_offset = 0.053 * sc.units.m
# There is some uncertainty here
monitor4_pos_z_offset = -6.719 * sc.units.m

data.coords['sample_position'].fields.z += sample_pos_z_offset
# Results are actually slightly better at high-Q if we do not apply a bench offset
# bench_pos_y_offset = 0.001 * sc.units.m
# data.coords['position'].fields.y += bench_pos_y_offset
dg['monitors']['monitor4']['data'].coords[
'position'
].fields.z += monitor4_pos_z_offset
return RawData[RunType](dg)


def pooch_load_direct_beam(filename: DirectBeamFilename) -> DirectBeam:
Expand All @@ -41,21 +57,23 @@ def pooch_load_direct_beam(filename: DirectBeamFilename) -> DirectBeam:


def get_monitor(
da: RawData[RunType], nexus_name: NeXusMonitorName[MonitorType]
dg: RawData[RunType], nexus_name: NeXusMonitorName[MonitorType]
) -> RawMonitor[RunType, MonitorType]:
# See https://github.com/scipp/sciline/issues/52 why copy needed
mon = da.attrs[nexus_name].value.copy()
mon = dg['monitors'][nexus_name]['data'].copy()
return RawMonitor[RunType, MonitorType](mon)


def detector_edge_mask(sample: RawData[SampleRun]) -> DetectorEdgeMask:
def detector_edge_mask(raw: RawData[SampleRun]) -> DetectorEdgeMask:
sample = raw['data']
mask_edges = (
sc.abs(sample.coords['position'].fields.x) > sc.scalar(0.48, unit='m')
) | (sc.abs(sample.coords['position'].fields.y) > sc.scalar(0.45, unit='m'))
return DetectorEdgeMask(mask_edges)


def sample_holder_mask(sample: RawData[SampleRun]) -> SampleHolderMask:
def sample_holder_mask(raw: RawData[SampleRun]) -> SampleHolderMask:
sample = raw['data']
summed = sample.sum('tof')
holder_mask = (
(summed.data < sc.scalar(100, unit='counts'))
Expand All @@ -68,7 +86,7 @@ def sample_holder_mask(sample: RawData[SampleRun]) -> SampleHolderMask:


def mask_detectors(
da: RawData[RunType],
dg: RawData[RunType],
edge_mask: Optional[DetectorEdgeMask],
holder_mask: Optional[SampleHolderMask],
) -> MaskedData[RunType]:
Expand All @@ -83,7 +101,7 @@ def mask_detectors(
holder_mask:
Mask for sample holder.
"""
da = da.copy(deep=False)
da = dg['data'].copy(deep=False)
if edge_mask is not None:
da.masks['edges'] = edge_mask
if holder_mask is not None:
Expand Down