add notes to demo nbs

nel-lab · Nov 5, 2023 · fdf8aba · fdf8aba
1 parent a175d04
commit fdf8aba
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Showing 2 changed files with 66 additions and 12 deletions.
diff --git a/notebooks/cnmfe.ipynb b/notebooks/cnmfe.ipynb
@@ -1,5 +1,15 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "3f25bdda-7790-454c-aafb-bbee6f9ab9cd",
+   "metadata": {},
+   "source": [
+    "# Running this notebook\n",
+    "\n",
+    "**The visualizations in this notebook will run in [jupyter lab](https://github.com/jupyterlab/jupyterlab#installation), not jupyter notebook. Google colab is not supported either. VS Code notebooks _might_ work but that has not been tested.** See the fastplotlib supported frameworks for more info: https://github.com/fastplotlib/fastplotlib/#supported-frameworks "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -28,6 +38,46 @@
     "from mesmerize_viz import *"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2e1fb091-b86c-45c3-a59d-995a7ef28cc1",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "from mesmerize_core.caiman_extensions.cnmf import cnmf_cache"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e174dd7d-a1ed-43ec-a0c0-cda1e1ee81b3",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "if os.name == \"nt\":\n",
+    "    # disable the cache on windows, this will be automatic in a future version\n",
+    "    cnmf_cache.set_maxsize(0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1ff12d10-980d-454a-a023-e593243a0709",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Mac users!\n",
+    "# temporary patch for Mac, won't be necessary in next release\n",
+    "# Thanks Ryan Ly for the PR! :D I need to dig into it more before merging\n",
+    "# conda_prefix_1_str = os.environ['CONDA_PREFIX'].replace(os.path.join(' ', 'envs', 'mescore')[1:], '')\n",
+    "# os.environ['CONDA_PREFIX_1'] = conda_prefix_1_str"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -37,6 +87,7 @@
    },
    "outputs": [],
    "source": [
+    "# This is just a pandas table display formatting option\n",
     "pd.options.display.max_colwidth = 120"
    ]
   },
@@ -1231,7 +1282,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.3"
+   "version": "3.11.2"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/mcorr_cnmf.ipynb b/notebooks/mcorr_cnmf.ipynb
@@ -1,5 +1,15 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "3f221a4a-8930-4fbf-85a1-aaa6b959bf54",
+   "metadata": {},
+   "source": [
+    "# Running this notebook\n",
+    "\n",
+    "**The visualizations in this notebook will run in [jupyter lab](https://github.com/jupyterlab/jupyterlab#installation), not jupyter notebook. Google colab is not supported either. VS Code notebooks _might_ work but that has not been tested.** See the fastplotlib supported frameworks for more info: https://github.com/fastplotlib/fastplotlib/#supported-frameworks "
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -18,10 +28,10 @@
     "import numpy as np\n",
     "import pandas as pd\n",
     "from matplotlib import pyplot as plt\n",
+    "import fastplotlib as fpl\n",
     "\n",
     "import mesmerize_core as mc\n",
-    "import mesmerize_viz\n",
-    "import fastplotlib as fpl"
+    "import mesmerize_viz"
    ]
   },
   {
@@ -64,21 +74,14 @@
     "# os.environ['CONDA_PREFIX_1'] = conda_prefix_1_str"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "c646c333-1306-4043-b5aa-3cb63fd9966f",
-   "metadata": {},
-   "source": [
-    "**You will need `mesmerize-viz` installed for the visualizations**"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "d8e11779-e36d-42d6-a885-8a527742195b",
    "metadata": {},
    "outputs": [],
    "source": [
+    "# This is just a pandas table display formatting option\n",
     "pd.options.display.max_colwidth = 120"
    ]
   },
@@ -1837,7 +1840,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.3"
+   "version": "3.11.2"
   }
  },
  "nbformat": 4,