feat: create application_EBSS_120hrs_gaohan_data_normalize_conversion…

….ipynb

notebooks/application_EBSS_120hrs_gaohan_data_normalize_conversion.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Create Napari UI for editing SingleCellTrajectoryCollection (SCTC)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Loading sample data and create a sample trajectory collection"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pathlib import Path\n",
+    "from livecellx.sample_data import tutorial_three_image_sys\n",
+    "\n",
+    "from livecellx.core.io_sc import prep_scs_from_mask_dataset\n",
+    "\n",
+    "from livecellx.core.single_cell import (\n",
+    "    SingleCellStatic,\n",
+    "    SingleCellTrajectory,\n",
+    "    SingleCellTrajectoryCollection,\n",
+    ")\n",
+    "\n",
+    "\n",
+    "# scs_path = r\"D:\\LiveCellTracker-dev\\notebooks\\application_results\\5days_notreat_XY03_max_age=3_min_hits=1\\5days_notreat_XY03_max_age=3_min_hits=1.json\"\n",
+    "scs_path = (\n",
+    "    Path(\n",
+    "        r\"D:\\LiveCellTracker-dev\\notebooks\\application_results\\Gaohan_5days_notreat\\pos_scs\"\n",
+    "    )\n",
+    "    / \"XY03_scs.json\"\n",
+    ")\n",
+    "scs_path = scs_path.as_posix()\n",
+    "scs = SingleCellStatic.load_single_cells_json(scs_path)\n",
+    "# sctc = SingleCellTrajectoryCollection.load_from_json_file(scs_path)\n",
+    "\n",
+    "# single_cells = prep_scs_from_mask_dataset(mask_dataset, dic_dataset)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "39340"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(scs)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from typing import List\n",
+    "from livecellx.track.sort_tracker_utils import (\n",
+    "    gen_SORT_detections_input_from_contours,\n",
+    "    update_traj_collection_by_SORT_tracker_detection,\n",
+    "    track_SORT_bbox_from_contours,\n",
+    "    track_SORT_bbox_from_scs,\n",
+    ")\n",
+    "\n",
+    "\n",
+    "dic_dataset = scs[0].img_dataset\n",
+    "mask_dataset = scs[0].mask_dataset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "|-----> Creating output directory E:\\xing-imaging\\tifs_CFP_A549_VIM_120hr_NoTreat_NA_YL_Ti2e_2023-03-22\\tifs_CFP_A549_VIM_120hr_NoTreat_NA_YL_Ti2e_2023-03-22\\XY03\\DIC_8bit\n"
+     ]
+    }
+   ],
+   "source": [
+    "import importlib\n",
+    "import livecellx\n",
+    "from livecellx.preprocess.conversion import (\n",
+    "    convert_livecell_dataset\n",
+    ")\n",
+    "importlib.reload(livecellx.preprocess.conversion)  \n",
+    "out_dir = r\"E:\\xing-imaging\\tifs_CFP_A549_VIM_120hr_NoTreat_NA_YL_Ti2e_2023-03-22\\tifs_CFP_A549_VIM_120hr_NoTreat_NA_YL_Ti2e_2023-03-22\\XY03\\DIC_8bit\"\n",
+    "livecellx.preprocess.conversion.convert_livecell_dataset(dic_dataset, out_dir=out_dir)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "livecell-work",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.16"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}