Estia

docs/api-reference/index.md

@@ -34,6 +34,7 @@
    types
    tools
    workflow
+   figures
 ```
 
 ## Amor
@@ -48,11 +49,33 @@
 
    conversions
    data
-   instrument_view
    load
    orso
    resolution
    types
    utils
-   figures
+   normalization
+   workflow
+```
+
+## Estia
+
+```{eval-rst}
+.. currentmodule:: ess.estia
+
+.. autosummary::
+   :toctree: ../generated/modules
+   :template: module-template.rst
+   :recursive:
+
+   conversions
+   maskings
+   corrections
+   data
+   mcstas
+   load
+   resolution
+   types
+   normalization
+   workflow
 ```

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

@@ -299,7 +299,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ess.amor.figures import wavelength_theta_figure\n",
+    "from ess.reflectometry.figures import wavelength_theta_figure\n",
     "\n",
     "wavelength_theta_figure(\n",
     "    [result[ReflectivityOverZW] for result in diagnostics.values()],\n",
@@ -329,7 +329,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ess.amor.figures import q_theta_figure\n",
+    "from ess.reflectometry.figures import q_theta_figure\n",
     "\n",
     "q_theta_figure(\n",
     "    [res[ReflectivityOverZW] for res in diagnostics.values()],\n",
@@ -355,7 +355,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ess.amor.figures import wavelength_z_figure\n",
+    "from ess.reflectometry.figures import wavelength_z_figure\n",
     "\n",
     "workflow[Filename[SampleRun]] = runs['608'][Filename[SampleRun]]\n",
     "workflow[SampleRotation[SampleRun]] = runs['608'][SampleRotation[SampleRun]]\n",

docs/user-guide/estia/estia-mcstas-reduction.ipynb

@@ -0,0 +1,328 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# Reduction of ESTIA McStas data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1",
+   "metadata": {},
+   "source": [
+    "This notebook demonstrates how to run the data reduction on the output of McStas simulations of the instrument.\n",
+    "\n",
+    "Essentially this looks very similar to how one would do data reduction on real data files from the physical instrument,\n",
+    "but we replace the default loader with the `load_mcstas_events` provider."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#%matplotlib widget\n",
+    "import scipp as sc\n",
+    "\n",
+    "from ess.estia.load import load_mcstas_events\n",
+    "from ess.estia.data import estia_mcstas_example, estia_mcstas_groundtruth\n",
+    "from ess.estia import EstiaWorkflow\n",
+    "from ess.reflectometry.types import *\n",
+    "from ess.reflectometry.figures import wavelength_z_figure, wavelength_theta_figure, q_theta_figure"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3",
+   "metadata": {},
+   "source": [
+    "The Estia reduction workflow is created and we set parameters such as region of interest, wavelengthbins, and q-bins."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "wf = EstiaWorkflow()\n",
+    "wf.insert(load_mcstas_events)\n",
+    "wf[Filename[ReferenceRun]] = estia_mcstas_example('reference')\n",
+    "\n",
+    "wf[YIndexLimits]  = sc.scalar(35), sc.scalar(64)\n",
+    "wf[ZIndexLimits] = sc.scalar(0), sc.scalar(14 * 32)\n",
+    "wf[BeamDivergenceLimits] = sc.scalar(-0.75, unit='deg'), sc.scalar(0.75, unit='deg')\n",
+    "wf[WavelengthBins] = sc.geomspace('wavelength', 3.5, 12, 2001, unit='angstrom')\n",
+    "wf[QBins] = 1000\n",
+    "\n",
+    "# There is no proton current data in the McStas files, here we just add some fake proton current\n",
+    "# data to make the workflow run.\n",
+    "wf[ProtonCurrent[SampleRun]] = sc.DataArray(\n",
+    "    sc.array(dims=('time',), values=[]),\n",
+    "    coords={'time': sc.array(dims=('time',), values=[], unit='s')})\n",
+    "wf[ProtonCurrent[ReferenceRun]] = sc.DataArray(\n",
+    "    sc.array(dims=('time',), values=[]),\n",
+    "    coords={'time': sc.array(dims=('time',), values=[], unit='s')})\n",
+    "\n",
+    "\n",
+    "def compute_reflectivity_curve_for_mcstas_data(wf, results):\n",
+    "    R, ref, da = w.compute((ReflectivityOverQ, Reference, ReducibleData[SampleRun])).values()\n",
+    "    # In the McStas simulation the reference has quite low intensity.\n",
+    "    # To make the reflectivity curve a bit more clean\n",
+    "    # we filter out the Q-points where the reference has too large uncertainties.\n",
+    "    ref = ref.hist(Q=R.coords['Q'])\n",
+    "    too_large_uncertainty_in_reference = sc.stddevs(ref).data > 0.3 * ref.data\n",
+    "    R = R.hist()\n",
+    "    R.data = sc.where(too_large_uncertainty_in_reference, sc.scalar(float('nan'), unit=R.unit), R.data)\n",
+    "    results[f\"{da.coords['sample_rotation'].value} {da.coords['sample_rotation'].unit}\"] = R\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5",
+   "metadata": {},
+   "source": [
+    "## Ni/Ti multilayer sample\n",
+    "\n",
+    "Below is a comparison between the reflectivity curve obtained using the reduction workflow and the ground truth reflectivity curve that was used in the McStas simulation.\n",
+    "The sample was simulated at different sample rotation settings, each settings produces a separate reflectivity curve covering a higher Q-range, and that is the angle in the legend of the figure."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results = {}\n",
+    "for path in estia_mcstas_example('Ni/Ti-multilayer'):\n",
+    "    w = wf.copy()\n",
+    "    w[Filename[SampleRun]] = path\n",
+    "    compute_reflectivity_curve_for_mcstas_data(w, results)\n",
+    "\n",
+    "ground_truth = estia_mcstas_groundtruth('Ni/Ti-multilayer')\n",
+    "\n",
+    "sc.plot({'ground_truth': ground_truth} | results, norm='log', vmin=1e-8)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7",
+   "metadata": {},
+   "source": [
+    "Below are a number of figures displaying different projections of the measured intensity distribution."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results = []\n",
+    "for path in estia_mcstas_example('Ni/Ti-multilayer'):\n",
+    "    w = wf.copy()\n",
+    "    w[Filename[SampleRun]] = path\n",
+    "    results.append(w.compute(Sample))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wavelength_z_figure(results[3], wavelength_bins=400)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "10",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wavelength_theta_figure(results, wavelength_bins=400, theta_bins=200, q_edges_to_display=[sc.scalar(0.016, unit='1/angstrom'), sc.scalar(0.19, unit='1/angstrom')])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "11",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "q_theta_figure(results, q_bins=300, theta_bins=200)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "12",
+   "metadata": {},
+   "source": [
+    "## Ni on Silicon"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "13",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results = {}\n",
+    "for path in estia_mcstas_example('Ni-film on silicon'):\n",
+    "    w = wf.copy()\n",
+    "    w[Filename[SampleRun]] = path\n",
+    "    compute_reflectivity_curve_for_mcstas_data(w, results)\n",
+    "\n",
+    "ground_truth = estia_mcstas_groundtruth('Ni-film on silicon')\n",
+    "sc.plot({'ground_truth': ground_truth} | results, norm='log', vmin=1e-9)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "14",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results = []\n",
+    "for path in estia_mcstas_example('Ni-film on silicon'):\n",
+    "    w = wf.copy()\n",
+    "    w[Filename[SampleRun]] = path\n",
+    "    results.append(w.compute(ReducibleData[SampleRun]))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "15",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wavelength_z_figure(results[3], wavelength_bins=400)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "16",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wavelength_theta_figure(results, wavelength_bins=400, theta_bins=200, q_edges_to_display=[sc.scalar(0.016, unit='1/angstrom'), sc.scalar(0.19, unit='1/angstrom')])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "17",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "q_theta_figure(results, q_bins=300, theta_bins=200)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "18",
+   "metadata": {},
+   "source": [
+    "## SiO2 on Silicon"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "19",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results = {}\n",
+    "for path in estia_mcstas_example('Natural SiO2 on silicon'):\n",
+    "    w = wf.copy()\n",
+    "    w[Filename[SampleRun]] = path\n",
+    "    compute_reflectivity_curve_for_mcstas_data(w, results)\n",
+    "\n",
+    "ground_truth = estia_mcstas_groundtruth('Natural SiO2 on silicon')\n",
+    "sc.plot({'ground_truth': ground_truth} | results, norm='log', vmin=1e-9)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "20",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "results = []\n",
+    "for path in estia_mcstas_example('Natural SiO2 on silicon'):\n",
+    "    w = wf.copy()\n",
+    "    w[Filename[SampleRun]] = path\n",
+    "    results.append(w.compute(ReducibleData[SampleRun]))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "21",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wavelength_z_figure(results[3], wavelength_bins=400)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "22",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "wavelength_theta_figure(results, wavelength_bins=400, theta_bins=200, q_edges_to_display=[sc.scalar(0.016, unit='1/angstrom')])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "23",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "q_theta_figure(results, q_bins=300, theta_bins=200)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.14"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}