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Merge pull request #125 from scipp/tof-workflow
Use time-of-flight workflow in Dream data reduction
2 parents eca4561 + 5c4b3f8 commit bcd4e48

23 files changed

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‎.copier-answers.yml

+1-1
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@@ -5,7 +5,7 @@ description: Diffraction data reduction for the European Spallation Source
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max_python: '3.13'
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min_python: '3.10'
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namespace_package: ess
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nightly_deps: scipp,scippnexus,sciline,plopp,scippneutron,essreduce
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nightly_deps: scipp,scippnexus,sciline,plopp,scippneutron,essreduce,tof
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orgname: scipp
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prettyname: ESSdiffraction
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projectname: essdiffraction

‎docs/user-guide/dream/dream-data-reduction.ipynb

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@@ -20,7 +20,6 @@
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"outputs": [],
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"source": [
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"import scipp as sc\n",
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"\n",
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"from ess import dream, powder\n",
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"import ess.dream.data # noqa: F401\n",
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"from ess.powder.types import *"
@@ -71,22 +70,22 @@
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"workflow[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop\n",
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"# Edges for binning in d-spacing\n",
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"workflow[DspacingBins] = sc.linspace(\"dspacing\", 0.0, 2.3434, 201, unit=\"angstrom\")\n",
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"# Mask in time-of-flight to crop to valid range\n",
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"workflow[TofMask] = lambda x: (x < sc.scalar(0.0, unit=\"ns\")) | (\n",
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" x > sc.scalar(86e6, unit=\"ns\")\n",
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")\n",
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"# Empty masks by default\n",
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"workflow[TofMask] = None\n",
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"workflow[TwoThetaMask] = None\n",
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"workflow[WavelengthMask] = None\n",
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"# No pixel masks\n",
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"workflow = powder.with_pixel_mask_filenames(workflow, [])"
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"workflow = powder.with_pixel_mask_filenames(workflow, [])\n",
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"# Time-of-flight lookup table\n",
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"workflow[TimeOfFlightLookupTableFilename] = dream.data.tof_lookup_table_high_flux()"
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]
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},
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{
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"cell_type": "markdown",
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"id": "6",
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"metadata": {},
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"source": [
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"## Use the workflow\n",
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"## Use the reduction workflow\n",
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"\n",
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"We can visualize the graph for computing the final normalized result for intensity as a function of time-of-flight:"
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]
@@ -152,7 +151,7 @@
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"in the documentation of ESSdiffraction.\n",
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"See https://scipp.github.io/essdiffraction/\n",
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"\"\"\"\n",
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"cif_data.save('reduced.cif')"
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"cif_data.save(\"reduced.cif\")"
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]
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},
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{
@@ -192,9 +191,9 @@
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"outputs": [],
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"source": [
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"two_theta = sc.linspace(\"two_theta\", 0.8, 2.4, 301, unit=\"rad\")\n",
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"intermediates[MaskedData[SampleRun]].hist(two_theta=two_theta, wavelength=300).plot(\n",
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" norm=\"log\"\n",
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")"
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"intermediates[MaskedData[SampleRun]].hist(\n",
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" two_theta=two_theta, wavelength=300\n",
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").plot(norm=\"log\")"
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]
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},
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{
@@ -216,7 +215,7 @@
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"outputs": [],
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"source": [
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"workflow[TwoThetaBins] = sc.linspace(\n",
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" dim=\"two_theta\", unit=\"rad\", start=0.8, stop=2.4, num=17\n",
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" dim=\"two_theta\", unit=\"rad\", start=0.8, stop=2.4, num=201\n",
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")"
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]
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},
@@ -237,31 +236,13 @@
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"id": "19",
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"metadata": {},
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"outputs": [],
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"source": [
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"angle = sc.midpoints(grouped_dspacing.coords[\"two_theta\"])\n",
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"sc.plot(\n",
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" {\n",
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" f\"{angle[group].value:.3f} {angle[group].unit}\": grouped_dspacing[\n",
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" \"two_theta\", group\n",
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" ].hist()\n",
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" for group in range(2, 6)\n",
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" }\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "20",
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"metadata": {},
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"outputs": [],
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"source": [
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"grouped_dspacing.hist().plot(norm=\"log\")"
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]
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},
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{
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"cell_type": "markdown",
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"id": "21",
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"id": "20",
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"metadata": {},
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"source": [
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"## Normalizing by monitor\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "22",
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"id": "21",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "23",
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"id": "22",
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"metadata": {},
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"source": [
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"In addition to the parameters used before, we also need to provide filenames for monitor data and a position of the monitor as that is not saved in the simulation files:"
@@ -301,14 +282,14 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "24",
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"id": "23",
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"metadata": {},
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"outputs": [],
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"source": [
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"workflow[MonitorFilename[SampleRun]] = dream.data.simulated_monitor_diamond_sample()\n",
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"workflow[MonitorFilename[VanadiumRun]] = dream.data.simulated_monitor_vanadium_sample()\n",
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"workflow[MonitorFilename[BackgroundRun]] = dream.data.simulated_monitor_empty_can()\n",
311-
"workflow[CaveMonitorPosition] = sc.vector([0.0, 0.0, -4220.0], unit='mm')\n",
292+
"workflow[CaveMonitorPosition] = sc.vector([0.0, 0.0, -4220.0], unit=\"mm\")\n",
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"\n",
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"# These are the same as at the top of the notebook:\n",
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"workflow[Filename[SampleRun]] = dream.data.simulated_diamond_sample()\n",
@@ -318,18 +299,17 @@
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"workflow[NeXusDetectorName] = \"mantle\"\n",
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"workflow[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop\n",
320301
"workflow[DspacingBins] = sc.linspace(\"dspacing\", 0.0, 2.3434, 201, unit=\"angstrom\")\n",
321-
"workflow[TofMask] = lambda x: (x < sc.scalar(0.0, unit=\"ns\")) | (\n",
322-
" x > sc.scalar(86e6, unit=\"ns\")\n",
323-
")\n",
302+
"workflow[TofMask] = None\n",
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"workflow[TwoThetaMask] = None\n",
325304
"workflow[WavelengthMask] = None\n",
326-
"workflow = powder.with_pixel_mask_filenames(workflow, [])"
305+
"workflow = powder.with_pixel_mask_filenames(workflow, [])\n",
306+
"workflow[TimeOfFlightLookupTableFilename] = dream.data.tof_lookup_table_high_flux()"
327307
]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "25",
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"id": "24",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "26",
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"id": "25",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "27",
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"id": "26",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "28",
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"id": "27",
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"metadata": {},
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"source": [
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"Comparing the final, normalized result shows that it agrees with the data that was normalized by proton-charge:"
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "29",
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"id": "28",
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"metadata": {},
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"outputs": [],
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"source": [
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"sc.plot({\n",
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" 'By proton charge': histogram,\n",
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" 'By monitor': normalized_by_monitor.hist()\n",
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"})"
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"sc.plot({\"By proton charge\": histogram, \"By monitor\": normalized_by_monitor.hist()})"
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]
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}
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],
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.14"
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,

‎docs/user-guide/dream/workflow-widget-dream.ipynb

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@@ -47,7 +47,7 @@
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},
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"outputs": [],
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"source": [
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"from ess.powder.types import DspacingBins, Filename, SampleRun, VanadiumRun\n",
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"from ess.powder.types import DspacingBins, Filename, SampleRun, TimeOfFlightLookupTableFilename, VanadiumRun\n",
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"import ess.dream.data # noqa: F401\n",
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"\n",
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"select = widget.children[0].children[0]\n",
@@ -66,6 +66,7 @@
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"# Set parameters\n",
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"pbox._input_widgets[Filename[SampleRun]].children[0].value = dream.data.simulated_diamond_sample()\n",
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"pbox._input_widgets[Filename[VanadiumRun]].children[0].value = dream.data.simulated_vanadium_sample()\n",
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"pbox._input_widgets[TimeOfFlightLookupTableFilename].children[0].value = dream.data.tof_lookup_table_high_flux()\n",
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"pbox._input_widgets[DspacingBins].fields[\"stop\"].value = 2.3434\n",
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"# Run the workflow\n",
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"rbox = wfw.result_box\n",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.14"
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,

‎docs/user-guide/sns-instruments/POWGEN_data_reduction.ipynb

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"source": [
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"results = workflow.compute(\n",
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" (\n",
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" DetectorData[SampleRun],\n",
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" TofData[SampleRun],\n",
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" MaskedData[SampleRun],\n",
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" FilteredData[SampleRun],\n",
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" FilteredData[VanadiumRun],\n",
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"metadata": {},
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"outputs": [],
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"source": [
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"results[DetectorData[SampleRun]]"
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"results[TofData[SampleRun]]"
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]
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},
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{
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.10.14"
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,

‎pyproject.toml

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"scipp>=24.09.1",
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"scippneutron>=25.02.0",
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"scippnexus>=23.12.0",
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"tof>=25.01.2",
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]
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dynamic = ["version"]

‎requirements/base.in

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scipp>=24.09.1
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scippneutron>=25.02.0
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scippnexus>=23.12.0
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tof>=25.01.2

‎requirements/base.txt

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# SHA1:4b779f60b811ecde0982bc9dc5df5ed5b296b876
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# SHA1:bd57e2addebc398f9de7064eb2a5c993a359ba46
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#
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# This file is autogenerated by pip-compile-multi
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# To update, run:
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# scippnexus
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idna==3.10
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# via email-validator
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importlib-resources==6.5.2
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# via tof
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ipydatawidgets==4.3.5
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# via pythreejs
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ipython==8.32.0
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# via
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# -r base.in
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# scippneutron
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# tof
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prompt-toolkit==3.0.50
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# via ipython
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ptyprocess==0.7.0
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# essreduce
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# scippneutron
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# scippnexus
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# tof
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scippneutron==25.2.0
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# via
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# -r base.in
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# via
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# scippneutron
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# scippnexus
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# tof
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six==1.17.0
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# via python-dateutil
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stack-data==0.6.3
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# via ipython
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tof==25.2.0
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# via -r base.in
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toolz==1.0.0
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# via
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# dask

‎requirements/nightly.in

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plopp @ git+https://github.com/scipp/plopp@main
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scippneutron @ git+https://github.com/scipp/scippneutron@main
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essreduce @ git+https://github.com/scipp/essreduce@main
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tof @ git+https://github.com/scipp/tof@main

‎requirements/nightly.txt

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# SHA1:b20670ae7cbdca0a2dae7facc845a0a636ee537c
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# SHA1:366263fa92dc0eb9f81d46f056e0c80a931f671e
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#
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# This file is autogenerated by pip-compile-multi
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# To update, run:
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# via
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# email-validator
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# requests
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importlib-resources==6.5.2
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# via tof
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iniconfig==2.0.0
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# via pytest
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ipydatawidgets==4.3.5
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# via
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# -r nightly.in
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# scippneutron
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# tof
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pluggy==1.5.0
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# via pytest
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pooch==1.8.2
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# essreduce
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# scippneutron
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# scippnexus
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# tof
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scippneutron @ git+https://github.com/scipp/scippneutron@main
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# via
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# -r nightly.in
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# via
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# scippneutron
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# scippnexus
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# tof
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six==1.17.0
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# via python-dateutil
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stack-data==0.6.3
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# via ipython
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tof @ git+https://github.com/scipp/tof@main
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# via -r nightly.in
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toolz==1.0.0
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# via
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# dask

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