From 2100aa04be6aac58e052fe2ee94637e7643bdbee Mon Sep 17 00:00:00 2001
From: gvarnavi <gvarnavi@mit.edu>
Date: Mon, 29 Jul 2024 11:59:26 -0700
Subject: [PATCH] fix post processing widget

---
 notebooks/10_STEM_post_processing.ipynb | 96 +++++++++++++++++++++++++
 1 file changed, 96 insertions(+)
 create mode 100644 notebooks/10_STEM_post_processing.ipynb

diff --git a/notebooks/10_STEM_post_processing.ipynb b/notebooks/10_STEM_post_processing.ipynb
new file mode 100644
index 0000000..de1cb0c
--- /dev/null
+++ b/notebooks/10_STEM_post_processing.ipynb
@@ -0,0 +1,96 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "4e05c48d-a101-4670-bd06-aa261a12532f",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "title: STEM post processing\n",
+    "authors: [Toma Susi]\n",
+    "date: 2024/07/24\n",
+    "---"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "744695c6-083f-486e-a6fb-7cb959c49637",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib ipympl\n",
+    "import abtem\n",
+    "\n",
+    "\n",
+    "abtem.config.set({\"visualize.cmap\": \"viridis\"})\n",
+    "abtem.config.set({\"visualize.continuous_update\": True})\n",
+    "abtem.config.set({\"visualize.autoscale\": True})\n",
+    "\n",
+    "all_measurements = abtem.from_zarr(\"data/processed_STEM.zarr\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "3e3d8994-459e-49d8-ab1e-c8ca2efab8f2",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[########################################] | 100% Completed | 103.55 ms\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "aebe6b1c6e0c4bf2afe222d85edb8b16",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "ImageGUI(children=(VBox(children=(SelectionSlider(options=('Nyquist-sampled', 'Interpolated', 'Blurred', 'Nois…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "#| label: app:stem_processing\n",
+    "viz = all_measurements.show(interact=True, explode=(1,), figsize=(5,5))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "44381286-90b4-4570-9144-01ca47d653b8",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "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": "3.11.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}