From 0ca0f6a9209c93ac00c4033142173cc088ccdc6e Mon Sep 17 00:00:00 2001
From: Johannes Kasimir <johanneskasimir@gmail.com>
Date: Fri, 11 Oct 2024 15:21:29 +0200
Subject: [PATCH] docs: adapt tutorial to new tool

---
 docs/user-guide/amor/amor-reduction.ipynb | 64 ++++++++++++++++-------
 1 file changed, 45 insertions(+), 19 deletions(-)

diff --git a/docs/user-guide/amor/amor-reduction.ipynb b/docs/user-guide/amor/amor-reduction.ipynb
index 3a15367e..33e13c69 100644
--- a/docs/user-guide/amor/amor-reduction.ipynb
+++ b/docs/user-guide/amor/amor-reduction.ipynb
@@ -137,8 +137,32 @@
    "source": [
     "## Computing sample reflectivity\n",
     "\n",
-    "We now compute the sample reflectivity from 3 runs that used different sample rotation angles.\n",
-    "The different rotation angles cover different ranges in $Q$."
+    "We now compute the sample reflectivity from 4 runs that used different sample rotation angles.\n",
+    "The measurements at different rotation angles cover different ranges of $Q$."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "In this tutorial we use some Amor data files we have received.\n",
+    "The file paths to the tutorial files are obtained by calling:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "amor.data.amor_sample_run(608)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "When you encounter `amor.data.amor_sample_run` you should imagining replacing that with a path to your own dataset."
    ]
   },
   {
@@ -148,17 +172,25 @@
    "outputs": [],
    "source": [
     "runs = {\n",
-    "    '608': sc.scalar(0.85, unit='deg'),\n",
-    "    '609': sc.scalar(2.25, unit='deg'),\n",
-    "    '610': sc.scalar(3.65, unit='deg'),\n",
-    "    '611': sc.scalar(5.05, unit='deg'),\n",
+    "    run_number: {\n",
+    "        # The sample rotation values in the files are slightly off, so we replace\n",
+    "        # them with corrected values.\n",
+    "        SampleRotation[SampleRun]: sc.scalar(sample_rotation_angle, unit='deg'),\n",
+    "        Filename[SampleRun]: amor.data.amor_sample_run(run_number),\n",
+    "    }\n",
+    "    for run_number, sample_rotation_angle in (\n",
+    "        ('608', 0.85),\n",
+    "        ('609', 2.25),\n",
+    "        ('610', 3.65),\n",
+    "        ('611', 5.05),\n",
+    "    )\n",
     "}\n",
     "\n",
     "results = {}\n",
-    "for file, angle in runs.items():\n",
-    "    workflow[Filename[SampleRun]] = amor.data.amor_sample_run(file)\n",
-    "    workflow[SampleRotation[SampleRun]] = angle\n",
-    "    results[file] = workflow.compute(ReflectivityOverQ).hist()\n",
+    "for run_number, params in runs.items():\n",
+    "    workflow[Filename[SampleRun]] = params[Filename[SampleRun]]\n",
+    "    workflow[SampleRotation[SampleRun]] = params[SampleRotation[SampleRun]]\n",
+    "    results[run_number] = workflow.compute(ReflectivityOverQ).hist()\n",
     "\n",
     "sc.plot(results, norm='log', vmin=1e-4)"
    ]
@@ -202,8 +234,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow[Filename[SampleRun]] = amor.data.amor_sample_run(608)\n",
-    "workflow[SampleRotation[SampleRun]] = sc.scalar(0.85, unit='deg')\n",
+    "workflow[Filename[SampleRun]] = runs['608'][Filename[SampleRun]]\n",
+    "workflow[SampleRotation[SampleRun]] = runs['608'][SampleRotation[SampleRun]]\n",
     "workflow.compute(ReflectivityDiagnosticsView)"
    ]
   },
@@ -349,13 +381,7 @@
     "\n",
     "datasets = orso_datasets_from_measurements(\n",
     "    workflow,\n",
-    "    # `orso_datasets_from_measurements` expects a dictionary with filenames as keys\n",
-    "    # and a dictionary of parameters as the value.\n",
-    "    # In this case the only file-dependent parameter we want to set is the sample rotation.\n",
-    "    {\n",
-    "        amor.data.amor_sample_run(run): {SampleRotation[SampleRun]: value}\n",
-    "        for run, value in runs.items()\n",
-    "    },\n",
+    "    runs.values(),\n",
     "    # Optionally scale the curves to overlap using `scale_reflectivity_curves_to_overlap`\n",
     "    scale_to_overlap=True\n",
     ")"