Simplify AMOR/reflectometry workflow (#107)

* simplify the amor workflow


---------

Co-authored-by: Jan-Lukas Wynen <[email protected]>

Author: jokasimr

docs/user-guide/amor/amor-reduction.ipynb

@@ -44,23 +44,7 @@
     "## Create and configure the workflow\n",
     "\n",
     "We begin by creating the Amor workflow object which is a skeleton for reducing Amor data,\n",
-    "with pre-configured steps."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "workflow = amor.AmorWorkflow()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "We then need to set the missing parameters which are specific to each experiment:"
+    "with pre-configured steps, and then set the missing parameters which are specific to each experiment:"
    ]
   },
   {
@@ -69,20 +53,22 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "workflow = amor.AmorWorkflow()\n",
     "workflow[SampleSize[SampleRun]] = sc.scalar(10.0, unit='mm')\n",
     "workflow[SampleSize[ReferenceRun]] = sc.scalar(10.0, unit='mm')\n",
     "\n",
     "workflow[ChopperPhase[ReferenceRun]] = sc.scalar(-7.5, unit='deg')\n",
     "workflow[ChopperPhase[SampleRun]] = sc.scalar(-7.5, unit='deg')\n",
     "\n",
     "workflow[QBins] = sc.geomspace(dim='Q', start=0.005, stop=0.3, num=391, unit='1/angstrom')\n",
-    "workflow[WavelengthBins] = sc.geomspace('wavelength', 2.8, 12, 301, unit='angstrom')\n",
+    "workflow[WavelengthBins] = sc.geomspace('wavelength', 2.8, 12.5, 2001, unit='angstrom')\n",
     "\n",
     "# The YIndexLimits and ZIndexLimits define ranges on the detector where\n",
     "# data is considered to be valid signal.\n",
     "# They represent the lower and upper boundaries of a range of pixel indices.\n",
-    "workflow[YIndexLimits] = sc.scalar(11, unit=None), sc.scalar(41, unit=None)\n",
-    "workflow[ZIndexLimits] = sc.scalar(80, unit=None), sc.scalar(370, unit=None)"
+    "workflow[YIndexLimits] = sc.scalar(11), sc.scalar(41)\n",
+    "workflow[ZIndexLimits] = sc.scalar(80), sc.scalar(370)\n",
+    "workflow[BeamDivergenceLimits] = sc.scalar(-0.75, unit='deg'), sc.scalar(0.75, unit='deg')"
    ]
   },
   {
@@ -116,9 +102,9 @@
     "# The sample rotation value in the file is slightly off, so we set it manually\n",
     "workflow[SampleRotation[ReferenceRun]] = sc.scalar(0.65, unit='deg')\n",
     "\n",
-    "reference_result = workflow.compute(IdealReferenceIntensity)\n",
+    "reference_result = workflow.compute(ReducedReference)\n",
     "# Set the result back onto the pipeline to cache it\n",
-    "workflow[IdealReferenceIntensity] = reference_result"
+    "workflow[ReducedReference] = reference_result"
    ]
   },
   {
@@ -198,6 +184,7 @@
     "    },\n",
     "}\n",
     "\n",
+    "\n",
     "reflectivity = {}\n",
     "for run_number, params in runs.items():\n",
     "    workflow[Filename[SampleRun]] = params[Filename[SampleRun]]\n",
@@ -282,11 +269,20 @@
     "for run_number, params in runs.items():\n",
     "    workflow[Filename[SampleRun]] = params[Filename[SampleRun]]\n",
     "    workflow[SampleRotation[SampleRun]] = params[SampleRotation[SampleRun]]\n",
-    "    diagnostics[run_number] = workflow.compute((ReflectivityData, ThetaBins[SampleRun]))\n",
+    "    diagnostics[run_number] = workflow.compute((ReflectivityOverZW, ThetaBins[SampleRun]))\n",
     "\n",
     "# Scale the results using the scale factors computed earlier\n",
     "for run_number, scale_factor in zip(reflectivity.keys(), scale_factors, strict=True):\n",
-    "    diagnostics[run_number][ReflectivityData] *= scale_factor"
+    "    diagnostics[run_number][ReflectivityOverZW] *= scale_factor"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "diagnostics['608'][ReflectivityOverZW].hist().flatten(('blade', 'wire'), to='z').plot(norm='log')"
    ]
   },
   {
@@ -306,7 +302,7 @@
     "from ess.amor.figures import wavelength_theta_figure\n",
     "\n",
     "wavelength_theta_figure(\n",
-    "    [result[ReflectivityData] for result in diagnostics.values()],\n",
+    "    [result[ReflectivityOverZW] for result in diagnostics.values()],\n",
     "    theta_bins=[result[ThetaBins[SampleRun]] for result in diagnostics.values()],\n",
     "    q_edges_to_display=(sc.scalar(0.018, unit='1/angstrom'), sc.scalar(0.113, unit='1/angstrom'))\n",
     ")"
@@ -336,7 +332,7 @@
     "from ess.amor.figures import q_theta_figure\n",
     "\n",
     "q_theta_figure(\n",
-    "    [res[ReflectivityData] for res in diagnostics.values()],\n",
+    "    [res[ReflectivityOverZW] for res in diagnostics.values()],\n",
     "    theta_bins=[res[ThetaBins[SampleRun]] for res in diagnostics.values()],\n",
     "    q_bins=workflow.compute(QBins)\n",
     ")"
@@ -364,11 +360,11 @@
     "workflow[Filename[SampleRun]] = runs['608'][Filename[SampleRun]]\n",
     "workflow[SampleRotation[SampleRun]] = runs['608'][SampleRotation[SampleRun]]\n",
     "wavelength_z_figure(\n",
-    "    workflow.compute(FootprintCorrectedData[SampleRun]),\n",
+    "    workflow.compute(Sample),\n",
     "    wavelength_bins=workflow.compute(WavelengthBins),\n",
     "    grid=False\n",
     ") + wavelength_z_figure(\n",
-    "    reference_result,\n",
+    "     workflow.compute(Reference),\n",
     "    grid=False\n",
     ")"
    ]
@@ -455,24 +451,6 @@
     ")"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "To support tracking provenance, we also list the corrections that were done by the workflow and store them in the dataset:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "iofq_dataset.info.reduction.corrections = orso.find_corrections(\n",
-    "    workflow.get(orso.OrsoIofQDataset)\n",
-    ")"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

docs/user-guide/amor/compare-to-eos.ipynb

@@ -85,25 +85,22 @@
     "workflow[SampleSize[ReferenceRun]] = sc.scalar(10.0, unit='mm')\n",
     "workflow[ChopperPhase[SampleRun]] = sc.scalar(-7.5, unit='deg')\n",
     "\n",
-    "# In Jochens workflow:\n",
-    "#    * divergence mask: [-0.7, 0.7]\n",
-    "#    * note, divergence relative to beam center\n",
     "workflow[WavelengthBins] = sc.geomspace('wavelength', 2.8, 12.5, 301, unit='angstrom')\n",
     "workflow[QBins] = sc.geomspace(\n",
     "    dim='Q', start=0.00505, stop=2.93164766e-01, num=391, unit='1/angstrom'\n",
     ")\n",
-    "workflow[YIndexLimits] = sc.scalar(11, unit=None), sc.scalar(41, unit=None)\n",
-    "workflow[ZIndexLimits] = sc.scalar(80, unit=None), sc.scalar(370, unit=None)\n",
+    "workflow[YIndexLimits] = sc.scalar(11), sc.scalar(41)\n",
+    "workflow[ZIndexLimits] = sc.scalar(80), sc.scalar(370)\n",
     "\n",
     "# Chopper phase value in the file is wrong, so we set it manually\n",
     "workflow[ChopperPhase[ReferenceRun]] = sc.scalar(-7.5, unit='deg')\n",
     "# The sample rotation value in the file is slightly off, so we set it manually\n",
     "workflow[SampleRotation[ReferenceRun]] = sc.scalar(0.65, unit='deg')\n",
     "workflow[Filename[ReferenceRun]] = amor.data.amor_reference_run()\n",
     "\n",
-    "reference_result = workflow.compute(IdealReferenceIntensity)\n",
+    "reference_result = workflow.compute(ReducedReference)\n",
     "# Set the result back onto the pipeline to cache it\n",
-    "workflow[IdealReferenceIntensity] = reference_result"
+    "workflow[ReducedReference] = reference_result"
    ]
   },
   {

src/ess/amor/__init__.py

@@ -5,23 +5,30 @@
 import sciline
 import scipp as sc
 
+
 from ..reflectometry import providers as reflectometry_providers
 from ..reflectometry import supermirror
 from ..reflectometry.types import (
     BeamSize,
     DetectorSpatialResolution,
-    Gravity,
     NeXusDetectorName,
     RunType,
     SamplePosition,
     BeamDivergenceLimits,
 )
-from . import conversions, load, orso, resolution, utils, figures
+from . import (
+    conversions,
+    load,
+    orso,
+    resolution,
+    utils,
+    figures,
+    normalization,
+    workflow,
+)
 from .instrument_view import instrument_view
 from .types import (
     AngularResolution,
-    Chopper1Position,
-    Chopper2Position,
     ChopperFrequency,
     ChopperPhase,
     QThetaFigure,
@@ -42,10 +49,11 @@
     *reflectometry_providers,
     *load.providers,
     *conversions.providers,
-    *resolution.providers,
+    *normalization.providers,
     *utils.providers,
     *figures.providers,
     *orso.providers,
+    *workflow.providers,
 )
 """
 List of providers for setting up a Sciline pipeline.
@@ -61,12 +69,14 @@ def default_parameters() -> dict:
         supermirror.Alpha: sc.scalar(0.25 / 0.088, unit=sc.units.angstrom),
         BeamSize[RunType]: 2.0 * sc.units.mm,
         DetectorSpatialResolution[RunType]: 0.0025 * sc.units.m,
-        Gravity: sc.vector(value=[0, -1, 0]) * sc.constants.g,
         SamplePosition[RunType]: sc.vector([0, 0, 0], unit="m"),
         NeXusDetectorName[RunType]: "detector",
         ChopperPhase[RunType]: sc.scalar(7.0, unit="deg"),
         ChopperFrequency[RunType]: sc.scalar(8.333, unit="Hz"),
-        BeamDivergenceLimits: (sc.scalar(-0.7, unit='deg'), sc.scalar(0.7, unit='deg')),
+        BeamDivergenceLimits: (
+            sc.scalar(-0.75, unit='deg'),
+            sc.scalar(0.75, unit='deg'),
+        ),
     }