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Support event-mode I(Q) #65

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merged 13 commits into from
Feb 6, 2024
Merged

Support event-mode I(Q) #65

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c17c64d
Support event-mode I(Q)
SimonHeybrock Feb 1, 2024
be91239
Add "drop" broadcast mode.
SimonHeybrock Feb 1, 2024
c0c105b
Add variances to event data loaded with ScippNexus
SimonHeybrock Feb 1, 2024
54dfa06
Fix direct-beam iteration to work with data that has variances
SimonHeybrock Feb 1, 2024
2f82e33
Add and update tests
SimonHeybrock Feb 1, 2024
0b4880a
Update tests/loki/iofq_test.py
SimonHeybrock Feb 5, 2024
ca4eb37
Update src/esssans/__init__.py
SimonHeybrock Feb 5, 2024
5439933
Merge branch 'main' into event-mode
SimonHeybrock Feb 5, 2024
cb97c6e
Refactor to handle wavelength bands during normalization step
SimonHeybrock Feb 5, 2024
50122c3
Update notebook
SimonHeybrock Feb 5, 2024
6268fbe
Inline helper functions
SimonHeybrock Feb 6, 2024
2a728d7
Move function to related file
SimonHeybrock Feb 6, 2024
146ac86
Merge pull request #68 from scipp/refactor-band-handling
SimonHeybrock Feb 6, 2024
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4 changes: 3 additions & 1 deletion docs/examples/loki-direct-beam.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -92,6 +92,7 @@
"\n",
"params[CorrectForGravity] = True\n",
"params[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound\n",
"params[sans.ReturnEvents] = False\n",
"\n",
"params[QBins] = sc.linspace(dim='Q', start=0.01, stop=0.3, num=101, unit='1/angstrom')"
]
Expand Down Expand Up @@ -391,7 +392,8 @@
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3"
"pygments_lexer": "ipython3",
"version": "3.10.12"
}
},
"nbformat": 4,
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40 changes: 33 additions & 7 deletions docs/examples/sans2d.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,8 @@
" dims=['wavelength'], values=[0.7, 17.1], unit='angstrom'\n",
")\n",
"pipeline[CorrectForGravity] = True\n",
"pipeline[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound"
"pipeline[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound\n",
"pipeline[sans.ReturnEvents] = True"
]
},
{
Expand Down Expand Up @@ -158,7 +159,25 @@
"outputs": [],
"source": [
"result = iofq.compute()\n",
"result.plot()"
"result.hist().plot(scale={'Q': 'log'}, norm='log')"
]
},
{
"cell_type": "markdown",
"id": "28532aa7",
"metadata": {},
"source": [
"As the result was computed in event-mode, we can also use a different $Q$-binning, without re-reducing the data:"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "e0748a1a",
"metadata": {},
"outputs": [],
"source": [
"result.hist(Q=60).plot(scale={'Q': 'log'}, norm='log')"
]
},
{
Expand All @@ -182,7 +201,7 @@
"result_drop = pipeline.compute(BackgroundSubtractedIofQ)\n",
"# Reset the UnsertaintyBroadcastMode to the old value\n",
"pipeline[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound\n",
"sc.DataGroup(upper_bound=result, dropped=result_drop).plot(norm='log')"
"sc.DataGroup(upper_bound=result, dropped=result_drop).hist().plot(norm='log')"
]
},
{
Expand Down Expand Up @@ -246,8 +265,15 @@
"\n",
"display(plot_flat_detector_xy(results[MaskedData[SampleRun]].sum('tof'), norm='log'))\n",
"\n",
"parts = {str(key): results[key] for key in parts}\n",
"parts = {key: val if val.bins is None else val.hist() for key, val in parts.items()}\n",
"wavelength = pipeline.compute(WavelengthBins)\n",
"display(\n",
" results[CleanSummedQ[SampleRun, Numerator]]\n",
" .hist(wavelength=wavelength)\n",
" .transpose()\n",
" .plot(norm='log')\n",
")\n",
"display(results[CleanSummedQ[SampleRun, Denominator]].plot(norm='log'))\n",
"parts = {str(key): results[key].sum('wavelength') for key in parts}\n",
"display(sc.plot(parts, norm='log'))\n",
"\n",
"iofqs = {str(key): results[key] for key in iofqs}\n",
Expand Down Expand Up @@ -291,7 +317,7 @@
")\n",
"pipeline.set_param_table(param_table)\n",
"results = pipeline.compute(sciline.Series[Mode, BackgroundSubtractedIofQ])\n",
"sc.DataGroup(results).plot(norm='log')"
"sc.DataGroup(results).hist().plot(norm='log')"
]
},
{
Expand Down Expand Up @@ -354,7 +380,7 @@
"metadata": {},
"outputs": [],
"source": [
"pp.plot(sc.collapse(result, keep='Q'), norm='log')"
"pp.plot(sc.collapse(result.hist(), keep='Q'), norm='log')"
]
}
],
Expand Down
16 changes: 14 additions & 2 deletions docs/examples/zoom.ipynb
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Expand Up @@ -111,7 +111,8 @@
" dims=['wavelength'], values=[0.7, 17.1], unit='angstrom'\n",
")\n",
"params[CorrectForGravity] = True\n",
"params[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound"
"params[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound\n",
"params[sans.ReturnEvents] = False"
]
},
{
Expand Down Expand Up @@ -246,8 +247,19 @@
" )\n",
")\n",
"\n",
"wavelength = pipeline.compute(WavelengthBins)\n",
"display(\n",
" results[CleanSummedQ[SampleRun, Numerator]]\n",
" .hist(wavelength=wavelength)\n",
" .transpose()\n",
" .plot(norm='log')\n",
")\n",
"display(results[CleanSummedQ[SampleRun, Denominator]].plot(norm='log'))\n",
"parts = {str(key): results[key] for key in parts}\n",
"parts = {key: val if val.bins is None else val.hist() for key, val in parts.items()}\n",
"parts = {\n",
" key: val.sum('wavelength') if val.bins is None else val.hist()\n",
" for key, val in parts.items()\n",
"}\n",
"display(sc.plot(parts, norm='log', scale={'Q': 'log'}))\n",
"\n",
"iofqs = {str(key): results[key] for key in iofqs}\n",
Expand Down
5 changes: 5 additions & 0 deletions src/esssans/__init__.py
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Expand Up @@ -21,6 +21,7 @@
)
from .common import transmission_from_background_run, transmission_from_sample_run
from .direct_beam import direct_beam
from .types import BackgroundSubtractedIofQ, IofQ, ReturnEvents, SampleRun
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Not sure why we are now importing those on the top level? Was it to get away from the from types import *?
If so, should this be reflected in the notebooks?

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Yes. types is meaningless for the user. We should name (and categorize things) in a meaningful way. Yes, there are a lot of things that need updating, I wanted to do that separately, in particular given that there is also other ongoing work that may conflict.

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Should we sit down and discuss what would be the best way to do this, so we're all on the same page?

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Definitely!


providers = (
*conversions.providers,
Expand All @@ -41,6 +42,10 @@
del importlib

__all__ = [
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'BackgroundSubtractedIofQ',
'IofQ',
'SampleRun',
'ReturnEvents',
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Above, you import BackgroundSubtractedIofQ, IofQ, ReturnEvents, SampleRun
Should all of them be listed here?

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Fixed!

'beam_center_finder',
'common',
'conversions',
Expand Down
11 changes: 9 additions & 2 deletions src/esssans/beam_center_finder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,14 @@
mask_wavelength,
to_Q,
)
from .i_of_q import merge_spectra, process_wavelength_bands
from .i_of_q import merge_spectra
from .logging import get_logger
from .normalization import iofq_denominator, normalize, solid_angle
from .normalization import (
iofq_denominator,
normalize,
process_wavelength_bands,
solid_angle,
)
from .types import (
BeamCenter,
DetectorPixelShape,
Expand All @@ -27,6 +32,7 @@
MaskedData,
NormWavelengthTerm,
QBins,
ReturnEvents,
SampleRun,
UncertaintyBroadcastMode,
WavelengthBins,
Expand Down Expand Up @@ -177,6 +183,7 @@ def _iofq_in_quadrants(
]
params = {}
params[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.upper_bound
params[ReturnEvents] = False
params[WavelengthBins] = wavelength_bins
params[QBins] = q_bins
params[DetectorPixelShape[SampleRun]] = pixel_shape
Expand Down
5 changes: 4 additions & 1 deletion src/esssans/conversions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -228,7 +228,10 @@ def to_Q(
"""
Convert a data array from wavelength to Q.
"""
return CleanQ[RunType, IofQPart](data.transform_coords('Q', graph=graph))
# Keep naming of wavelength dim, subsequent steps use a (Q, wavelength) binning.
return CleanQ[RunType, IofQPart](
data.transform_coords('Q', graph=graph, rename_dims=False)
)


providers = (
Expand Down
2 changes: 1 addition & 1 deletion src/esssans/direct_beam.py
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Expand Up @@ -134,7 +134,7 @@ def direct_beam(pipeline: Pipeline, I0: sc.Variable, niter: int = 5) -> List[dic
# parameters, nor given by any providers, so it will be considered flat.
# TODO: Should we have a check that DirectBeam cannot be computed from the
# pipeline?
iofq = pipeline.compute(BackgroundSubtractedIofQ)
iofq = sc.values(pipeline.compute(BackgroundSubtractedIofQ))
iofq_full = iofq['band', -1]
iofq_bands = iofq['band', :-1]

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