add slides, small changes

clewis7 · clewis7 · commit 83d0bdd5f6ad · 2024-11-06T19:39:40.000-05:00
diff --git a/Duke fpl talk.pdf b/Duke fpl talk.pdf
diff --git a/neuro.ipynb b/neuro.ipynb
@@ -726,7 +726,7 @@
    "outputs": [],
    "source": [
     "from sklearn.decomposition import PCA\n",
-    "from scipy.stats import zscore"
+    "from sklearn.preprocessing import RobustScaler"
    ]
   },
   {
@@ -746,8 +746,9 @@
    "source": [
     "pca = PCA(n_components=3)\n",
     "\n",
-    "zscored = zscore(np.sqrt(temporal_data.to_numpy()), axis=1)\n",
-    "calcium_pca = pca.fit_transform(gaussian_filter1d(zscored, sigma=3))"
+    "rs = RobustScaler()\n",
+    "scaled = rs.fit_transform(gaussian_filter1d(temporal_data.to_numpy(), sigma=5))\n",
+    "calcium_pca = pca.fit_transform(scaled)"
    ]
   },
   {
@@ -803,7 +804,7 @@
     "    controller_types=\"orbit\",\n",
     ")\n",
     "fig_pca[0, 0].add_scatter(calcium_pca, cmap=\"hsv\", cmap_transform=ry_transform, sizes=4, alpha=0.4)\n",
-    "marker_graphic = fig_pca[0, 0].add_scatter(calcium_pca[0], sizes=10)\n",
+    "marker_graphic = fig_pca[0, 0].add_scatter(calcium_pca[0], sizes=20)\n",
     "\n",
     "fig_pca.show()"
    ]
@@ -847,16 +848,6 @@
     "fig_pca[0, 0].controller = \"fly\""
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "bb0df1db-126e-430a-842b-9448649f7de9",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "nap_figure[\"behavior\"].graphics[1].thickness = 0.1"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
diff --git a/overview.ipynb b/overview.ipynb
@@ -388,17 +388,6 @@
     "cosine_graphic.colors[:30:2] = \"cyan\""
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "f6c1907f-f2a6-48dd-a86c-414bece50a09",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# more complex slicing, set the blue value directly from an array\n",
-    "cosine_graphic.colors[65:90, 0] = np.linspace(0, 1, 90-65)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "ff17474b-775e-4970-82d5-390d31f28020",
@@ -687,6 +676,14 @@
    "metadata": {},
    "outputs": [],
    "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "06cde66b-b6de-44a7-86cf-788b49b020ae",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
