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Merge pull request #93 from scipp/monitor-norm
DREAM monitor normalization
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‎docs/user-guide/dream/dream-data-reduction.ipynb

+149-55
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@@ -20,7 +20,8 @@
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"outputs": [],
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"source": [
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"import scipp as sc\n",
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"from scippneutron.io import cif\n",
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"import scippneutron as scn\n",
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"import scippneutron.io\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",
@@ -44,7 +45,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"workflow = dream.DreamGeant4Workflow()"
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"workflow = dream.DreamGeant4Workflow(run_norm=powder.RunNormalization.proton_charge)"
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]
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},
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{
@@ -74,7 +75,7 @@
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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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" x > sc.scalar(86e6, unit=\"ns\")\n",
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")\n",
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"workflow[TwoThetaMask] = None\n",
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"workflow[WavelengthMask] = None\n",
@@ -86,31 +87,6 @@
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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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"We also need some parameters to configure the output file:"
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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": "7",
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"metadata": {},
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"outputs": [],
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"source": [
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"workflow[CIFAuthors] = CIFAuthors([\n",
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" cif.Author(\n",
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" name=\"Jane Doe\",\n",
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" email=\"[email protected]\",\n",
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" orcid=\"0000-0000-0000-0001\",\n",
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" role=\"measurement\",\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": "markdown",
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"id": "8",
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"metadata": {},
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"source": [
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"## Use the workflow\n",
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"\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "9",
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"id": "7",
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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": "10",
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"id": "8",
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"metadata": {},
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"source": [
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"We then call `compute()` to compute the result:\n",
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"(The `cif` object will later be used to write the result to disk.)"
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"We then call `compute()` to compute the result:"
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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": "11",
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"id": "9",
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"metadata": {},
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"outputs": [],
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"source": [
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"results = workflow.compute([IofDspacing, ReducedDspacingCIF])\n",
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"result = results[IofDspacing]\n",
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"cif_data = results[ReducedDspacingCIF]"
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"result = workflow.compute(IofDspacing)\n",
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"result"
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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": "12",
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"id": "10",
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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": "13",
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"id": "11",
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"metadata": {},
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"source": [
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"We can now save the result to disk:\n",
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"(The comment is optional but helps to identify the file later.)"
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"We can now save the result to disk:"
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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": "14",
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"id": "12",
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"metadata": {},
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"outputs": [],
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"source": [
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"cif_data.comment = \"\"\"This file was generated with the DREAM data reduction user guide\n",
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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('dspacing.cif')"
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"to_save = dspacing_histogram.assign_coords(\n",
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" dspacing=sc.midpoints(\n",
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" dspacing_histogram.coords[\"dspacing\"]\n",
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" ))\n",
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"scn.io.save_xye(\"dspacing.xye\", to_save)"
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]
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},
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{
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"cell_type": "markdown",
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"id": "15",
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"id": "13",
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"metadata": {},
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"source": [
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"## Compute intermediate results\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "16",
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"id": "14",
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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": "17",
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"id": "15",
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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": "18",
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"id": "16",
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"metadata": {},
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"source": [
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"## Grouping by scattering angle\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "19",
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"id": "17",
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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": "20",
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"id": "18",
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"metadata": {},
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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": "21",
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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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{
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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": "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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"metadata": {},
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"source": [
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"## Normalizing by monitor\n",
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"\n",
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"The workflow used above normalizes the detected counts by proton charge.\n",
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"Alternatively, ESSdiffraction can normalize by a monitor.\n",
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"In this example, this is DREAM's cave monitor.\n",
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"\n",
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"There are two options for normalizing by monitor:\n",
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"1. Normalize by a wavelength-histogram of the monitor counts ([normalize_by_monitor_histogram](../../generated/modules/ess.powder.correction.normalize_by_monitor_histogram.rst)).\n",
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"2. Normalized by the integral over all wavelength bins ([normalize_by_monitor_integrated](../../generated/modules/ess.powder.correction.normalize_by_monitor_integrated.rst)).\n",
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"\n",
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"Here, we use option 1.\n",
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"Option 2 can be chosen by constructing a workflow using `run_norm=powder.RunNormalization.monitor_integrated`.\n",
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"\n",
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"Construct a workflow as before but select normalization by monitor histogram:"
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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": "22",
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"metadata": {},
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"outputs": [],
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"source": [
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"workflow = dream.DreamGeant4Workflow(run_norm=powder.RunNormalization.monitor_histogram)"
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]
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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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"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:"
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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": "24",
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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",
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"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",
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"workflow[Filename[VanadiumRun]] = dream.data.simulated_vanadium_sample()\n",
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"workflow[Filename[BackgroundRun]] = dream.data.simulated_empty_can()\n",
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"workflow[CalibrationFilename] = None\n",
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"workflow[NeXusDetectorName] = \"mantle\"\n",
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"workflow[UncertaintyBroadcastMode] = UncertaintyBroadcastMode.drop\n",
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"workflow[DspacingBins] = sc.linspace(\"dspacing\", 0.0, 2.3434, 201, unit=\"angstrom\")\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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"workflow[TwoThetaMask] = None\n",
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"workflow[WavelengthMask] = None\n",
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"workflow = powder.with_pixel_mask_filenames(workflow, [])"
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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": "25",
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"metadata": {},
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"outputs": [],
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"source": [
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"workflow.visualize(IofDspacing, graph_attr={\"rankdir\": \"LR\"})"
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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": "26",
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"metadata": {},
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"outputs": [],
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"source": [
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"results = workflow.compute((IofDspacing, WavelengthMonitor[SampleRun, CaveMonitor]))\n",
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"normalized_by_monitor = results[IofDspacing]\n",
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"monitor = results[WavelengthMonitor[SampleRun, CaveMonitor]]\n",
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"monitor"
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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": "27",
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"metadata": {},
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"outputs": [],
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"source": [
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"monitor.plot()"
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]
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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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"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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},
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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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"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': dspacing_histogram,\n",
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" 'By monitor': normalized_by_monitor.hist()\n",
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"})"
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]
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}
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],
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"metadata": {
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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": "3.10.13"
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"version": "3.10.14"
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}
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},
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"nbformat": 4,

‎src/ess/dream/data.py

+27
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"DREAM_simple_pwd_workflow/data_dream_vana_container_sample_union.csv.zip": "md5:1e22917b2bb68b5cacfb506b72700a4d", # noqa: E501
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"DREAM_simple_pwd_workflow/data_dream_vanadium.csv.zip": "md5:e5addfc06768140c76533946433fa2ec", # noqa: E501
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"DREAM_simple_pwd_workflow/data_dream_vanadium_inc_coh.csv.zip": "md5:39d1a44e248b12966b26f7c2f6c602a2", # noqa: E501
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"DREAM_simple_pwd_workflow/Cave_TOF_Monitor_diam_in_can.dat": "md5:ef24f4a4186c628574046e6629e31611", # noqa: E501
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"DREAM_simple_pwd_workflow/Cave_TOF_Monitor_van_can.dat": "md5:e63456c347fb36a362a0b5ae2556b3cf", # noqa: E501
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"DREAM_simple_pwd_workflow/Cave_TOF_Monitor_vana_inc_coh.dat": "md5:701d66792f20eb283a4ce76bae0c8f8f", # noqa: E501
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},
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)
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return get_path(
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"DREAM_simple_pwd_workflow/data_dream_vana_container_sample_union.csv.zip"
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)
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def simulated_monitor_diamond_sample() -> str:
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"""Path to a Mcstas file for a monitor for the diamond measurement.
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This is the DREAM cave monitor for ``simulated_diamond_sample``.
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"""
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return get_path("DREAM_simple_pwd_workflow/Cave_TOF_Monitor_diam_in_can.dat")
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def simulated_monitor_vanadium_sample() -> str:
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"""Path to a Mcstas file for a monitor for the vanadium measurement.
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This is the DREAM cave monitor for ``simulated_vanadium_sample``.
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"""
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return get_path("DREAM_simple_pwd_workflow/Cave_TOF_Monitor_vana_inc_coh.dat")
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def simulated_monitor_empty_can() -> str:
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"""Path to a Mcstas file for a monitor for the empty can measurement.
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This is the DREAM cave monitor for ``simulated_empty_can``.
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"""
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return get_path("DREAM_simple_pwd_workflow/Cave_TOF_Monitor_van_can.dat")

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