Update IO tutorial

cardiacvision · May 10, 2024 · f2fe773 · f2fe773
1 parent 1859a67
commit f2fe773
Showing 1 changed file with 118 additions and 12 deletions.
diff --git a/docs/tutorials/io.ipynb b/docs/tutorials/io.ipynb
@@ -380,33 +380,72 @@
    "execution_count": null,
    "metadata": {
     "tags": [
-     "skip-execution"
+     "remove-input",
+     "remove-output"
     ]
    },
    "outputs": [],
+   "source": [
+    "import optimap as om\n",
+    "from IPython.display import Video\n",
+    "video = om.load_video(om.download_example_data(\"Sinus_Rabbit_1.npy\", silent=True))\n",
+    "video = om.video.rotate_left(video)\n",
+    "om.video.set_ffmpeg_defaults('libx264', {'-c:v': 'libx264', '-crf': '20', '-preset': 'fast', \"-pix_fmt\": \"yuv420p\"})"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
    "source": [
     "om.export_video('video.mp4', video)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "Video(filename='video.mp4', embed=True, html_attributes=\"controls autoplay loop\")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "This will generate a .mp4 video file containing the entire video data at the original resolution with a display framerate of 60fps (default). See {func}`video.export_video` for more options, e.g.:"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "om.export_video(\"video.mp4\", video, fps=15, cmap=\"magma\", vmin=0.5, vmax=0.9)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
     "tags": [
-     "skip-execution"
+     "remove-input"
     ]
    },
    "outputs": [],
    "source": [
-    "om.export_video(\"video.mp4\", video[100:500], fps=30, skip_frames=2,\n",
-    "                cmap=\"viridis\", vmin=0.1, vmax=0.9)"
+    "Video(filename='video.mp4', html_attributes=\"controls autoplay loop\", embed=True)"
    ]
   },
   {
@@ -428,8 +467,80 @@
    },
    "outputs": [],
    "source": [
-    "video_waves = om.video.normalize_pixelwise(video)\n",
-    "om.video.export_video_with_overlay(\"video.mp4\", video, video_waves)"
+    "overlay = om.video.normalize_pixelwise(video)\n",
+    "om.video.export_video_with_overlay(\"video.mp4\", video, overlay=overlay, fps=15)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "# video_warped = om.motion_compensate(video, contrast_kernel=5, ref_frame=40)\n",
+    "# video_waves = om.video.temporal_difference(video_warped, 3)\n",
+    "# video_waves[video_waves > 0] = 0\n",
+    "# video_waves = om.video.normalize_pixelwise(video_waves)\n",
+    "# overlay = 1-video_waves.copy()\n",
+    "# overlay[overlay < 0.5] = 0\n",
+    "# overlay[:, om.background_mask(video_warped[0], show=False)] = 0\n",
+    "# om.video.export_video_with_overlay(\"video.mp4\", video_warped, overlay, vmin_overlay=0, vmax_overlay=0.9, fps=15)\n",
+    "# Video(filename=\"video.mp4\", html_attributes=\"controls autoplay loop\", embed=True)\n",
+    "\n",
+    "video_warped = om.motion_compensate(video, contrast_kernel=5, ref_frame=40)\n",
+    "overlay = om.video.temporal_difference(video_warped, 3)\n",
+    "# normalize to range [1, -1], note that we invert we are interested in negative values\n",
+    "overlay = om.video.normalize_pixelwise(overlay, ymin=1, ymax=-1)\n",
+    "# set background to zero\n",
+    "background = om.background_mask(video_warped[0], show=False)\n",
+    "overlay[:, background] = 0\n",
+    "alpha = overlay.copy()\n",
+    "alpha[alpha < 0.5] = 0\n",
+    "\n",
+    "overlay_motion = om.video.temporal_difference(video, 3)\n",
+    "overlay_motion = om.video.normalize_pixelwise(overlay_motion, ymin=1, ymax=-1)\n",
+    "\n",
+    "om.video.export_video_with_overlay(\"video.mp4\", video_warped, overlay=overlay, alpha=alpha, fps=15)\n",
+    "Video(filename=\"video.mp4\", html_attributes=\"controls autoplay loop\", embed=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "To export videos side-by-side, use {func}`om.video.export_videos`:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "om.video.export_videos(\"video.mp4\", [video, overlay_motion, video_warped, overlay], ncols=2, fps=15,\n",
+    "                       cmaps=['gray', 'Purples', 'gray', 'Purples'],\n",
+    "                       vmins=0,\n",
+    "                       vmaxs=1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "remove-input"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    " # , padding=26, padding_color=\"white\",\n",
+    "Video(filename='video.mp4', embed=True, html_attributes=\"controls autoplay loop\")"
    ]
   },
   {
@@ -479,11 +590,6 @@
     "om.save_mask(\"mask.png\", mask)\n",
     "```"
    ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": []
   }
  ],
  "metadata": {
@@ -502,7 +608,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.9"
+   "version": "3.12.2"
   },
   "test_name": "notebook1"
  },