Add illustration of inhomogeneity from absorption

docs/user-guide/dream/dream-visualize-absorption.ipynb

@@ -0,0 +1,140 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "0",
+   "metadata": {},
+   "source": [
+    "# DREAM instrument view\n",
+    "\n",
+    "This notebook is a simple example of how to use the instrument view for the DREAM instrument.\n",
+    "\n",
+    "- The DREAM-specific instrument view is capable of slicing the data with a slider widget along a dimension (e.g. `tof`) by using the `dim` argument.\n",
+    "- There are also checkboxes to hide/show the different elements that make up the DREAM detectors.\n",
+    "\n",
+    "We begin with relevant imports.\n",
+    "We will be using tutorial data downloaded with `pooch`.\n",
+    "If you get an error about a missing module `pooch`, you can install it with `!pip install pooch`:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import scipp as sc\n",
+    "from ess import dream\n",
+    "import ess.dream.data  # noqa: F401"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2",
+   "metadata": {},
+   "source": [
+    "## Load the data\n",
+    "\n",
+    "We load a dataset from a Geant4 simulation (stored as a `.csv` file).\n",
+    "In each detector bank, the data is organised by `wire`, `strip`, `module`, `segment`, and `counter`.\n",
+    "The high resolution detector also has an additional `sector` dimension."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dg = dream.io.load_geant4_csv(dream.data.get_path(\"data_dream0_new_hkl_Si_pwd.csv.zip\"))\n",
+    "dg = dg[\"instrument\"]  # Extract the instrument data\n",
+    "\n",
+    "# Extract the events from nested data groups\n",
+    "dg = sc.DataGroup({key: detector[\"events\"] for key, detector in dg.items()})\n",
+    "dg"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4",
+   "metadata": {},
+   "source": [
+    "## Display inhomogeneity from absorption\n",
+    "\n",
+    "If the sample absorbs or scatters a large fraction of the incoming neutrons the intensity in the detector will vary even if the scattering is inhomogeneous.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import scipp as sc\n",
+    "\n",
+    "from scippneutron.absorption import compute_transmission_map\n",
+    "from scippneutron.absorption.cylinder import Cylinder\n",
+    "from scippneutron.absorption.material import Material\n",
+    "from scippneutron.atoms import ScatteringParams\n",
+    "\n",
+    "\n",
+    "material =  Material(\n",
+    "    scattering_params=ScatteringParams.for_isotope('V'),\n",
+    "    effective_sample_number_density=sc.scalar(0.07192, unit='1/angstrom**3')\n",
+    ")\n",
+    "sample_shape = Cylinder(\n",
+    "    symmetry_line=sc.vector([0, 1, 0]),\n",
+    "    center_of_base=sc.vector([0, -2.5, 0], unit='cm'),\n",
+    "    radius=sc.scalar(1, unit='cm'),\n",
+    "    height=sc.scalar(5., unit='cm')\n",
+    ")\n",
+    "\n",
+    "transmission_fraction = compute_transmission_map(\n",
+    "    sample_shape,\n",
+    "    material,\n",
+    "    beam_direction=sc.vector([0, 0, 1]),\n",
+    "    wavelength=sc.linspace('wavelength', 4, 8, 20, unit='angstrom'),\n",
+    "    detector_position=dg['mantle'].coords['position']['strip', ::4]['wire', ::2].copy(),\n",
+    "    quadrature_kind='cheap',\n",
+    ")\n",
+    "\n",
+    "transmission_fraction.coords['position'] = transmission_fraction.coords.pop('detector_position')\n",
+    "dream.instrument_view(transmission_fraction.transpose((*set(transmission_fraction.dims) - {'wavelength'}, 'wavelength')), dim='wavelength')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "transmission_fraction"
+   ]
+  }
+ ],
+ "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
+}