fix filename bug in csn data gen v5

xing-lab-pitt · Jan 9, 2023 · 6a66eb2 · 6a66eb2
1 parent 4115e94
commit 6a66eb2
Showing 1 changed file with 5 additions and 4 deletions.
diff --git a/notebooks/correct_seg_data_prep_v5.ipynb b/notebooks/correct_seg_data_prep_v5.ipynb
@@ -1231,14 +1231,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 93,
+   "execution_count": 99,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "100%|██████████| 294/294 [00:25<00:00, 11.61it/s]\n"
+      "100%|██████████| 294/294 [00:25<00:00, 11.42it/s]\n"
      ]
     }
    ],
@@ -1261,6 +1261,7 @@
     "os.makedirs(augmented_diff_seg_dir, exist_ok=True)\n",
     "\n",
     "for sc in tqdm(single_cells):\n",
+    "    img_id = sc.timeframe\n",
     "    for overseg_datarow in sc.uns[overseg_uns_key]:\n",
     "        params = overseg_datarow[1]\n",
     "        img_crop = sc.get_contour_img()\n",
@@ -1280,8 +1281,8 @@
     "            train_path_tuples=train_path_tuples,\n",
     "            augmented_data=augmented_data,\n",
     "            img_id=img_id,\n",
-    "            seg_label=seg_label,\n",
-    "            gt_label=None,\n",
+    "            seg_label=0,\n",
+    "            gt_label=sc.timeframe,\n",
     "            raw_img_path=raw_img_path,\n",
     "            seg_img_path=seg_img_path,\n",
     "            gt_img_path=gt_img_path,\n",