Update basics tutorial

cardiacvision · Sep 21, 2023 · 224b991 · 224b991
1 parent abeee96
commit 224b991
Showing 1 changed file with 105 additions and 4 deletions.
diff --git a/docs/tutorials/basics.ipynb b/docs/tutorials/basics.ipynb
@@ -392,6 +392,12 @@
    "source": [
     "## Fluorescence wave isolation\n",
     "\n",
+    "```{note}\n",
+    "The rest of this tutorial is currently work in progress. We will add more information soon.\n",
+    "```\n",
+    "\n",
+    "### Sliding window normalization\n",
+    "\n",
     "To better visualize the action potential propagation we can compute a pixel-wise normalization to [0, 1] using a sliding/rolling window. This is done using the {func}`video.normalize_pixelwise_slidingwindow` function. The `window_size` parameter controls the size of the sliding window, here we use a window size of 60 frames (120 ms)."
    ]
   },
@@ -420,29 +426,124 @@
    },
    "outputs": [],
    "source": [
+    "norm_raw = om.video.normalize_pixelwise_slidingwindow(video, window_size=60)\n",
+    "norm_warped = om.video.normalize_pixelwise_slidingwindow(warped, window_size=60)\n",
     "def f():\n",
-    "    norm_raw = om.video.normalize_pixelwise_slidingwindow(video, window_size=60)\n",
-    "    norm_warped = om.video.normalize_pixelwise_slidingwindow(warped, window_size=60)\n",
     "    return om.video.play2(norm_raw[:500], norm_warped[:500], title1=\"with motion\", title2=\"without motion\", interval=20)\n",
     "render_ani_func(f)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The dark waves is the fluorescent signal, they correspond to the action potential propagation."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "mask = om.background_mask(warped[0])\n",
-    "norm_warped[:, mask] = 0"
+    "norm_warped[:, mask] = 1.0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "skip-execution"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "om.video.play(norm_warped, interval=20);"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "render_ani_func(lambda: om.video.play(norm_warped, interval=40))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "skip-execution"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "alpha = np.clip(-(2*norm_warped - 1), 0, 1)\n",
+    "om.video.play_with_overlay(warped, 1-norm_warped, alpha=alpha);"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "alpha = np.clip(-(2*norm_warped - 1), 0, 1)\n",
+    "render_ani_func(lambda: om.video.play_with_overlay(warped, 1-norm_warped, alpha=alpha), interval=20)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
    "metadata": {},
+   "source": [
+    "### Temporal difference"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "skip-execution"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "diff = om.video.temporal_difference(warped, 10)\n",
+    "diff[diff > 0] = 0\n",
+    "diff[:, mask] = 0\n",
+    "diff = om.video.normalize_pixelwise_slidingwindow(-diff, window_size=60)\n",
+    "om.video.play_with_overlay(warped, diff, vmin_overlay=-1, vmax_overlay=1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-input"
+    ]
+   },
    "outputs": [],
-   "source": []
+   "source": [
+    "diff = om.video.temporal_difference(warped, 10)\n",
+    "diff[diff > 0] = 0\n",
+    "diff[:, mask] = 0\n",
+    "diff = om.video.normalize_pixelwise_slidingwindow(-diff, window_size=60)\n",
+    "render_ani_func(lambda: om.video.play_with_overlay(warped, diff, vmin_overlay=-1, vmax_overlay=1))"
+   ]
   }
  ],
  "metadata": {