Update tutorial notebook to document worm lighter than background feature

Author: iteal

examples/check_dataset.ipynb

@@ -90,10 +90,14 @@
     "# for Tierpsy tracker data this will be the root path of a folder containing subfolders for each videos\n",
     "dataset_path = \"wormpose_data/datasets/sample_data\"\n",
     "\n",
+    "# Set if the worm is lighter than the background in the image\n",
+    "# In the sample data, the worm is darker so we set this variable to False\n",
+    "worm_is_lighter = False\n",
+    "\n",
     "# This function loads the dataset\n",
     "# optional fields: there is an optional resize parameter to resize the images\n",
     "# also you can select specific videos from the dataset instead of loading them all\n",
-    "dataset = load_dataset(dataset_loader, dataset_path)"
+    "dataset = load_dataset(dataset_loader, dataset_path, worm_is_lighter=worm_is_lighter)"
    ]
   },
   {
@@ -310,9 +314,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.8.6"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}

examples/tutorial_sample_data.ipynb

@@ -97,10 +97,14 @@
     "dataset_root_name = os.path.basename(os.path.normpath(dataset_path))\n",
     "project_dir = os.path.join(default_paths.WORK_DIR, dataset_root_name)\n",
     "\n",
+    "# Set if the worm is lighter than the background in the image\n",
+    "# in the sample data, the worm is darker so we set this variable to False\n",
+    "worm_is_lighter = False\n",
+    "\n",
     "# This function loads the dataset\n",
     "# optional fields: there is an optional resize parameter to resize the images\n",
     "# also you can select specific videos from the dataset instead of loading them all\n",
-    "dataset = load_dataset(dataset_loader, dataset_path)"
+    "dataset = load_dataset(dataset_loader, dataset_path, worm_is_lighter=worm_is_lighter)"
    ]
   },
   {
@@ -153,7 +157,9 @@
     "from wormpose.demo.synthetic_simple_visualizer import SyntheticSimpleVisualizer\n",
     "from ipython_utils import ImagesViewer, display_as_slider\n",
     "\n",
-    "synth_viz = SyntheticSimpleVisualizer(dataset_loader, dataset_path).generate()\n",
+    "synth_viz = SyntheticSimpleVisualizer(dataset_loader,\n",
+    "                                      dataset_path, \n",
+    "                                      worm_is_lighter=worm_is_lighter).generate()\n",
     "img_viewer, img_viewer_plot = ImagesViewer(), ImagesViewer()\n",
     "num_images = 50\n",
     "\n",
@@ -194,7 +200,9 @@
     "from wormpose.demo.real_simple_visualizer import RealSimpleVisualizer\n",
     "from ipython_utils import ImagesViewer, display_as_slider\n",
     "\n",
-    "viz = RealSimpleVisualizer(dataset_loader, dataset_path).generate()\n",
+    "viz = RealSimpleVisualizer(dataset_loader, \n",
+    "                           dataset_path, \n",
+    "                           worm_is_lighter=worm_is_lighter).generate()\n",
     "orig_img_viewer, processed_img_viewer = ImagesViewer(), ImagesViewer()\n",
     "\n",
     "max_viz = 100\n",
@@ -234,7 +242,10 @@
     "from wormpose.commands import calibrate\n",
     "from ipython_utils import ImagesViewer\n",
     "\n",
-    "video_name, result_file = next(calibrate(dataset_loader, dataset_path, save_images=True))\n",
+    "video_name, result_file = next(calibrate(dataset_loader, \n",
+    "                                         dataset_path, \n",
+    "                                         worm_is_lighter=worm_is_lighter,\n",
+    "                                         save_images=True))\n",
     "\n",
     "VIEW_SCORES = 5\n",
     "\n",
@@ -285,7 +296,8 @@
     "display(fp)\n",
     "\n",
     "gen_progress = generate(dataset_loader,\n",
-    "                        dataset_path, \n",
+    "                        dataset_path,\n",
+    "                        worm_is_lighter=worm_is_lighter,\n",
     "                        num_train_samples=1000)\n",
     "for progress_value in gen_progress:\n",
     "    fp.value = progress_value"
@@ -447,9 +459,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.8.6"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}