From 9bbd538ef5267b941c17a0e6385173f2c7e52ffc Mon Sep 17 00:00:00 2001
From: Toma Susi <toma.susi@iki.fi>
Date: Sun, 28 Jul 2024 18:08:30 -0400
Subject: [PATCH] Fixed post-processing widget.

---
 notebooks/STEM_post_processing.ipynb          | 12 ++--
 .../STEM_post_processing_calculation.ipynb    | 57 +++++--------------
 2 files changed, 21 insertions(+), 48 deletions(-)

diff --git a/notebooks/STEM_post_processing.ipynb b/notebooks/STEM_post_processing.ipynb
index 3e42936..515784a 100644
--- a/notebooks/STEM_post_processing.ipynb
+++ b/notebooks/STEM_post_processing.ipynb
@@ -14,7 +14,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 540,
+   "execution_count": 549,
    "id": "744695c6-083f-486e-a6fb-7cb959c49637",
    "metadata": {},
    "outputs": [
@@ -22,13 +22,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[########################################] | 100% Completed | 104.34 ms\n"
+      "[########################################] | 100% Completed | 106.18 ms\n"
      ]
     },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "873e219d1106426a9c3c5bc5ed1771cb",
+       "model_id": "5fda696e7e374bdc857be1744791e0fb",
        "version_major": 2,
        "version_minor": 0
       },
@@ -42,10 +42,10 @@
     {
      "data": {
       "text/plain": [
-       "<abtem.visualize.visualizations.Visualization at 0x30a3a1430>"
+       "<abtem.visualize.visualizations.Visualization at 0x30eabe060>"
       ]
      },
-     "execution_count": 540,
+     "execution_count": 549,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -62,7 +62,7 @@
     "\n",
     "all_measurements = abtem.from_zarr(\"data/processed_STEM.zarr\")\n",
     "\n",
-    "all_measurements.show(interact=True, cbar=True)"
+    "all_measurements.show(interact=True, explode=(1,))"
    ]
   },
   {
diff --git a/notebooks/STEM_post_processing_calculation.ipynb b/notebooks/STEM_post_processing_calculation.ipynb
index 529cd16..2dfe85b 100644
--- a/notebooks/STEM_post_processing_calculation.ipynb
+++ b/notebooks/STEM_post_processing_calculation.ipynb
@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 44,
    "id": "744695c6-083f-486e-a6fb-7cb959c49637",
    "metadata": {},
    "outputs": [],
@@ -36,10 +36,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": 45,
    "id": "79901d04-645e-45c3-a9f8-f48a0d9a3c98",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/tomasusi/miniforge3/envs/guide-tem-simulation/lib/python3.12/site-packages/ase/io/cif.py:834: UserWarning: Occupancies present but no occupancy info for \"{symbol}\"\n",
+      "  warnings.warn(str(err))\n"
+     ]
+    }
+   ],
    "source": [
     "sto_lto = repeated_srtio3.copy()\n",
     "\n",
@@ -54,14 +63,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 36,
+   "execution_count": 46,
    "id": "0782c824-d93f-413d-885b-d755ecc45b6c",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a3e2b09fad854dddbbccaa480054137f",
+       "model_id": "e2adf023b6b644c6a2a8f317856091eb",
        "version_major": 2,
        "version_minor": 0
       },
@@ -109,7 +118,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 47,
    "id": "921d92bb-7f8d-45a9-8db8-b1a1f2c12804",
    "metadata": {},
    "outputs": [],
@@ -497,42 +506,6 @@
     "all_measurements.to_zarr(\"data/processed_STEM.zarr\")"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 21,
-   "id": "6b07457c-8120-41ba-8cf8-d9cb8ac1507b",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "8ee1d27841a848fa8f3786d7a60b8b14",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "ImageGUI(children=(VBox(children=(SelectionSlider(continuous_update=False, options=('Nyquist-sampled', 'Interp…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "<abtem.visualize.visualizations.Visualization at 0x1479e8b60>"
-      ]
-     },
-     "execution_count": 21,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "%matplotlib ipympl\n",
-    "all_measurements.show(interact=True, cbar=True)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,