update classify_mitosis_data_prep.ipynb: fix test column mitosis_type…

… missing issue
xing-lab-pitt · Nov 1, 2023 · 4986c21 · 4986c21
1 parent 55e4897
commit 4986c21
Showing 1 changed file with 36 additions and 15 deletions.
diff --git a/notebooks/classify_mitosis_data_prep.ipynb b/notebooks/classify_mitosis_data_prep.ipynb
@@ -446,6 +446,17 @@
     "    test_class2sample_extra_info[key] = np.array(all_class2sample_extra_info[key], dtype=object)[_test_indices]\n",
     "    train_class2sample_extra_info[key] = list(train_class2sample_extra_info[key])\n",
     "    test_class2sample_extra_info[key] = list(test_class2sample_extra_info[key])\n",
+    "\n",
+    "\n",
+    "# # for debug\n",
+    "if DEBUG:\n",
+    "    test_sample_num = 3\n",
+    "    padding_pixels = [1, 20]\n",
+    "    train_class2samples = {key: value[:test_sample_num] for key, value in all_class2samples.items()}\n",
+    "    test_class2samples = {key: value[:test_sample_num] for key, value in all_class2samples.items()}\n",
+    "    train_class2sample_extra_info = {key: value[:test_sample_num] for key, value in all_class2sample_extra_info.items()}\n",
+    "    test_class2sample_extra_info = {key: value[:test_sample_num] for key, value in all_class2sample_extra_info.items()}\n",
+    "\n",
     "\n"
    ]
   },
@@ -473,7 +484,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "video_frames_and_masks_from_sample(train_class2samples[\"normal\"][6])[0][0].shape\n",
+    "video_frames_and_masks_from_sample(train_class2samples[\"normal\"][0])[0][0].shape\n",
     "# train_class2samples[\"normal\"][6][1].show_panel()"
    ]
   },
@@ -488,13 +499,20 @@
     "importlib.reload(livecellx.track.classify_utils)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Check some sample generation"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "idx_to_check = 6\n",
+    "idx_to_check = 0\n",
     "video_frames, video_frame_masks = video_frames_and_masks_from_sample(train_class2samples[\"normal\"][idx_to_check], padding_pixels=0)\n",
     "print(\"video frames dtype:\", video_frames[0].dtype)\n",
     "print(\"video frames shape:\", video_frames[0].shape)\n",
@@ -612,20 +630,32 @@
     "Include original, drop-div and st"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "train_class2sample_extra_info"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import copy\n",
+    "from copy import deepcopy\n",
     "\n",
-    "def modify_class2sample_extra_info(class2sample_extra_info: Dict[str, List[Dict]], mitosis_traj_type, copy_info=True):\n",
+    "def modify_class2sample_extra_info(class2sample_extra_info: Dict[str, List[Dict]], mitosis_traj_type, copy=True):\n",
     "    for cls in class2sample_extra_info:\n",
-    "        for _info in class2sample_extra_info[cls]:\n",
-    "            if copy_info:\n",
-    "                _info = copy_info.deepcopy(_info)\n",
+    "        for i, _info in enumerate(class2sample_extra_info[cls]):\n",
+    "            if copy:\n",
+    "                _info = dict(_info)\n",
     "            _info[\"mitosis_traj_type\"] = mitosis_traj_type\n",
+    "            class2sample_extra_info[cls][i] = _info\n",
+    "    \n",
     "\n",
     "modify_class2sample_extra_info(train_class2sample_extra_info, \"full\")\n",
     "modify_class2sample_extra_info(test_class2sample_extra_info, \"full\")\n",
@@ -712,15 +742,6 @@
     "import livecellx.core.sc_video_utils\n",
     "importlib.reload(livecellx.core.sc_video_utils)\n",
     "\n",
-    "# # for debug\n",
-    "if DEBUG:\n",
-    "    test_sample_num = 3\n",
-    "    padding_pixels = [1, 20]\n",
-    "    train_class2samples = {key: value[:test_sample_num] for key, value in all_class2samples.items()}\n",
-    "    test_class2samples = {key: value[:test_sample_num] for key, value in all_class2samples.items()}\n",
-    "    train_class2sample_extra_info = {key: value[:test_sample_num] for key, value in all_class2sample_extra_info.items()}\n",
-    "    test_class2sample_extra_info = {key: value[:test_sample_num] for key, value in all_class2sample_extra_info.items()}\n",
-    "\n",
     "# padding_pixels = [20]\n",
     "\n",
     "train_sample_info_df = livecellx.core.sc_video_utils.gen_class2sample_samples(\n",