prepare_datasets.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "b65be37b",
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import os\n",
    "from func.ultis import save_obj, load_obj"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a0926776",
   "metadata": {},
   "source": [
    "### HMS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "9216b22a",
   "metadata": {},
   "outputs": [],
   "source": [
    "# please change if needed\n",
    "source_path_raw_img = \"/data/CellSeg_dataset/HMS/raw\"\n",
    "source_path_seg_img = \"/data/CellSeg_dataset/HMS/segmentation\"\n",
    "processed_path_raw_img = \"/data/CellSeg_dataset/HMS_processed/raw\"\n",
    "processed_path_seg_img = \"/data/CellSeg_dataset/HMS_processed/segmentation\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "2eaf35b6",
   "metadata": {},
   "outputs": [],
   "source": [
    "# # step 1\n",
    "# run_py_script = \"python prepare_dataset/prepare_HMS_dataset.py \"+\\\n",
    "# \"--raw_img_file_path \"+source_path_raw_img+\" \"+\\\n",
    "# \"--seg_img_file_path \"+source_path_seg_img+\" \"+\\\n",
    "# \"--processed_raw_img_output_file_path \"+processed_path_raw_img+\" \"+\\\n",
    "# \"--processed_seg_img_output_file_path \"+processed_path_seg_img\n",
    "# print(\"run \"+run_py_script)\n",
    "# os.system(run_py_script)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "41094921",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "run python prepare_dataset/get_the_dataset_info_of_HMS.py --processed_raw_img_file_path /data/CellSeg_dataset/HMS_processed/raw --processed_seg_img_file_path /data/CellSeg_dataset/HMS_processed/segmentation\n",
      "['/home/v-andongwang/Projects/CellSeg_github/prepare_dataset', '/home/v-andongwang/anaconda3/envs/clip/lib/python38.zip', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/lib-dynload', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages/wheel-0.37.1-py3.8.egg', '/home/v-andongwang/Projects/Learning/Dassl.pytorch', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages/locket-0.2.1-py3.8.egg', '/home/v-andongwang/Projects/CellSeg_github']\n",
      "test: ['120', '135', '65', '90']\n",
      "train: ['210' '185' '130' '165' '50' '170' '70' '125' '145' '105' '195' '115'\n",
      " '60' '200' '205' '180' '175' '75' '140' '85' '215' '225' '150' '155'\n",
      " '160' '80' '95' '110' '220' '190' '55' '100']\n",
      "{'train': {'210': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/210.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/210/210_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/210/210_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/210/210_foreground_3d_mask.npy'}, '185': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/185.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/185/185_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/185/185_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/185/185_foreground_3d_mask.npy'}, '130': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/130.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/130/130_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/130/130_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/130/130_foreground_3d_mask.npy'}, '165': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/165.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/165/165_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/165/165_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/165/165_foreground_3d_mask.npy'}, '50': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/50.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/50/50_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/50/50_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/50/50_foreground_3d_mask.npy'}, '170': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/170.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/170/170_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/170/170_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/170/170_foreground_3d_mask.npy'}, '70': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/70.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/70/70_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/70/70_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/70/70_foreground_3d_mask.npy'}, '125': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/125.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/125/125_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/125/125_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/125/125_foreground_3d_mask.npy'}, '145': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/145.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/145/145_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/145/145_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/145/145_foreground_3d_mask.npy'}, '105': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/105.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/105/105_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/105/105_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/105/105_foreground_3d_mask.npy'}, '195': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/195.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/195/195_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/195/195_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/195/195_foreground_3d_mask.npy'}, '115': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/115.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/115/115_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/115/115_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/115/115_foreground_3d_mask.npy'}, '60': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/60.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/60/60_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/60/60_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/60/60_foreground_3d_mask.npy'}, '200': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/200.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/200/200_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/200/200_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/200/200_foreground_3d_mask.npy'}, '205': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/205.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/205/205_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/205/205_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/205/205_foreground_3d_mask.npy'}, '180': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/180.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/180/180_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/180/180_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/180/180_foreground_3d_mask.npy'}, '175': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/175.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/175/175_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/175/175_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/175/175_foreground_3d_mask.npy'}, '75': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/75.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/75/75_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/75/75_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/75/75_foreground_3d_mask.npy'}, '140': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/140.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/140/140_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/140/140_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/140/140_foreground_3d_mask.npy'}, '85': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/85.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/85/85_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/85/85_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/85/85_foreground_3d_mask.npy'}, '215': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/215.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/215/215_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/215/215_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/215/215_foreground_3d_mask.npy'}, '225': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/225.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/225/225_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/225/225_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/225/225_foreground_3d_mask.npy'}, '150': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/150.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/150/150_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/150/150_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/150/150_foreground_3d_mask.npy'}, '155': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/155.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/155/155_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/155/155_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/155/155_foreground_3d_mask.npy'}, '160': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/160.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/160/160_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/160/160_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/160/160_foreground_3d_mask.npy'}, '80': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/80.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/80/80_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/80/80_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/80/80_foreground_3d_mask.npy'}, '95': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/95.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/95/95_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/95/95_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/95/95_foreground_3d_mask.npy'}, '110': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/110.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/110/110_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/110/110_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/110/110_foreground_3d_mask.npy'}, '220': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/220.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/220/220_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/220/220_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/220/220_foreground_3d_mask.npy'}, '190': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/190.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/190/190_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/190/190_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/190/190_foreground_3d_mask.npy'}, '55': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/55.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/55/55_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/55/55_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/55/55_foreground_3d_mask.npy'}, '100': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/100.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/100/100_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/100/100_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/100/100_foreground_3d_mask.npy'}}, 'test': {'90': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/90.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/90/90_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/90/90_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/90/90_foreground_3d_mask.npy', 'ins': '/data/CellSeg_dataset/HMS_processed/segmentation/90/90_ins.npy'}, '120': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/120.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/120/120_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/120/120_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/120/120_foreground_3d_mask.npy', 'ins': '/data/CellSeg_dataset/HMS_processed/segmentation/120/120_ins.npy'}, '135': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/135.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/135/135_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/135/135_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/135/135_foreground_3d_mask.npy', 'ins': '/data/CellSeg_dataset/HMS_processed/segmentation/135/135_ins.npy'}, '65': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/65.npy', 'background': '/data/CellSeg_dataset/HMS_processed/segmentation/65/65_background_3d_mask.npy', 'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/65/65_boundary_3d_mask.npy', 'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/65/65_foreground_3d_mask.npy', 'ins': '/data/CellSeg_dataset/HMS_processed/segmentation/65/65_ins.npy'}}}\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# step2\n",
    "run_py_script = \"python prepare_dataset/get_the_dataset_info_of_HMS.py \"+\\\n",
    "\"--processed_raw_img_file_path \"+processed_path_raw_img+\" \"+\\\n",
    "\"--processed_seg_img_file_path \"+processed_path_seg_img\n",
    "print(\"run \"+run_py_script)\n",
    "os.system(run_py_script)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "5b09f9a9",
   "metadata": {},
   "outputs": [],
   "source": [
    "HMS_data_dict = load_obj(\"dataset_info/HMS_dataset_info\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "02cdd6bc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'train': {'210': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/210.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/210/210_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/210/210_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/210/210_foreground_3d_mask.npy'},\n",
       "  '185': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/185.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/185/185_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/185/185_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/185/185_foreground_3d_mask.npy'},\n",
       "  '130': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/130.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/130/130_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/130/130_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/130/130_foreground_3d_mask.npy'},\n",
       "  '165': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/165.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/165/165_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/165/165_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/165/165_foreground_3d_mask.npy'},\n",
       "  '50': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/50.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/50/50_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/50/50_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/50/50_foreground_3d_mask.npy'},\n",
       "  '170': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/170.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/170/170_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/170/170_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/170/170_foreground_3d_mask.npy'},\n",
       "  '70': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/70.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/70/70_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/70/70_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/70/70_foreground_3d_mask.npy'},\n",
       "  '125': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/125.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/125/125_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/125/125_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/125/125_foreground_3d_mask.npy'},\n",
       "  '145': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/145.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/145/145_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/145/145_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/145/145_foreground_3d_mask.npy'},\n",
       "  '105': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/105.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/105/105_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/105/105_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/105/105_foreground_3d_mask.npy'},\n",
       "  '195': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/195.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/195/195_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/195/195_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/195/195_foreground_3d_mask.npy'},\n",
       "  '115': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/115.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/115/115_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/115/115_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/115/115_foreground_3d_mask.npy'},\n",
       "  '60': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/60.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/60/60_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/60/60_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/60/60_foreground_3d_mask.npy'},\n",
       "  '200': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/200.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/200/200_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/200/200_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/200/200_foreground_3d_mask.npy'},\n",
       "  '205': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/205.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/205/205_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/205/205_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/205/205_foreground_3d_mask.npy'},\n",
       "  '180': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/180.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/180/180_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/180/180_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/180/180_foreground_3d_mask.npy'},\n",
       "  '175': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/175.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/175/175_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/175/175_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/175/175_foreground_3d_mask.npy'},\n",
       "  '75': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/75.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/75/75_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/75/75_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/75/75_foreground_3d_mask.npy'},\n",
       "  '140': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/140.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/140/140_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/140/140_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/140/140_foreground_3d_mask.npy'},\n",
       "  '85': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/85.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/85/85_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/85/85_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/85/85_foreground_3d_mask.npy'},\n",
       "  '215': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/215.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/215/215_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/215/215_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/215/215_foreground_3d_mask.npy'},\n",
       "  '225': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/225.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/225/225_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/225/225_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/225/225_foreground_3d_mask.npy'},\n",
       "  '150': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/150.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/150/150_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/150/150_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/150/150_foreground_3d_mask.npy'},\n",
       "  '155': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/155.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/155/155_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/155/155_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/155/155_foreground_3d_mask.npy'},\n",
       "  '160': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/160.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/160/160_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/160/160_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/160/160_foreground_3d_mask.npy'},\n",
       "  '80': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/80.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/80/80_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/80/80_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/80/80_foreground_3d_mask.npy'},\n",
       "  '95': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/95.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/95/95_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/95/95_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/95/95_foreground_3d_mask.npy'},\n",
       "  '110': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/110.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/110/110_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/110/110_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/110/110_foreground_3d_mask.npy'},\n",
       "  '220': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/220.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/220/220_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/220/220_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/220/220_foreground_3d_mask.npy'},\n",
       "  '190': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/190.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/190/190_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/190/190_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/190/190_foreground_3d_mask.npy'},\n",
       "  '55': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/55.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/55/55_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/55/55_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/55/55_foreground_3d_mask.npy'},\n",
       "  '100': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/100.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/100/100_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/100/100_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/100/100_foreground_3d_mask.npy'}},\n",
       " 'test': {'90': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/90.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/90/90_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/90/90_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/90/90_foreground_3d_mask.npy',\n",
       "   'ins': '/data/CellSeg_dataset/HMS_processed/segmentation/90/90_ins.npy'},\n",
       "  '120': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/120.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/120/120_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/120/120_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/120/120_foreground_3d_mask.npy',\n",
       "   'ins': '/data/CellSeg_dataset/HMS_processed/segmentation/120/120_ins.npy'},\n",
       "  '135': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/135.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/135/135_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/135/135_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/135/135_foreground_3d_mask.npy',\n",
       "   'ins': '/data/CellSeg_dataset/HMS_processed/segmentation/135/135_ins.npy'},\n",
       "  '65': {'raw': '/data/CellSeg_dataset/HMS_processed/raw/65.npy',\n",
       "   'background': '/data/CellSeg_dataset/HMS_processed/segmentation/65/65_background_3d_mask.npy',\n",
       "   'boundary': '/data/CellSeg_dataset/HMS_processed/segmentation/65/65_boundary_3d_mask.npy',\n",
       "   'foreground': '/data/CellSeg_dataset/HMS_processed/segmentation/65/65_foreground_3d_mask.npy',\n",
       "   'ins': '/data/CellSeg_dataset/HMS_processed/segmentation/65/65_ins.npy'}}}"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "HMS_data_dict"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fc6f4450",
   "metadata": {},
   "source": [
    "### ATAS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "a11a01df",
   "metadata": {},
   "outputs": [],
   "source": [
    "# please change if needed\n",
    "source_path = \"/data/CellSeg_dataset/ATAS\"\n",
    "processed_path = \"/data/CellSeg_dataset/ATAS_processed\"\n",
    "pre_cropped_path = \"/data/CellSeg_dataset/ATAS_processed_pre_croped\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "59309adc",
   "metadata": {},
   "outputs": [],
   "source": [
    "# # step 1\n",
    "# run_py_script = \"python prepare_dataset/prepare_ATAS_dataset.py \"+\\\n",
    "# \"--source_file_path \"+source_path+\" \"+\\\n",
    "# \"--output_file_path \"+processed_path+\" \"+\\\n",
    "# \"--width_of_membrane 1.5\"\n",
    "# print(\"run \"+run_py_script)\n",
    "# os.system(run_py_script)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "203ef780",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "run python prepare_dataset/get_the_dataset_info_of_ATAS.py --path /data/CellSeg_dataset/ATAS_processed --test_name 'plant15' \n",
      "['/home/v-andongwang/Projects/CellSeg_github/prepare_dataset', '/home/v-andongwang/anaconda3/envs/clip/lib/python38.zip', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/lib-dynload', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages/wheel-0.37.1-py3.8.egg', '/home/v-andongwang/Projects/Learning/Dassl.pytorch', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages/locket-0.2.1-py3.8.egg', '/home/v-andongwang/Projects/CellSeg_github']\n",
      "{'train': {'plant2_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_68hrs.h5', 'plant2_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_56hrs.h5', 'plant1_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_16hrs.h5', 'plant4_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_64hrs.h5', 'plant18_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_28hrs.h5', 'plant4_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_8hrs.h5', 'plant2_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_76hrs.h5', 'plant1_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_12hrs.h5', 'plant2_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_20hrs.h5', 'plant1_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_0hrs.h5', 'plant2_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_16hrs.h5', 'plant4_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_48hrs.h5', 'plant1_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_68hrs.h5', 'plant4_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_60hrs.h5', 'plant4_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_36hrs.h5', 'plant4_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_68hrs.h5', 'plant18_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_12hrs.h5', 'plant1_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_76hrs.h5', 'plant4_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_12hrs.h5', 'plant13_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_8hrs.h5', 'plant4_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_52hrs.h5', 'plant4_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_4hrs.h5', 'plant1_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_8hrs.h5', 'plant2_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_72hrs.h5', 'plant4_40hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_40hrs.h5', 'plant18_80hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_80hrs.h5', 'plant13_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_36hrs.h5', 'plant13_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_60hrs.h5', 'plant2_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_8hrs.h5', 'plant2_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_44hrs.h5', 'plant2_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_36hrs.h5', 'plant13_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_32hrs.h5', 'plant2_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_52hrs.h5', 'plant13_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_76hrs.h5', 'plant18_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_24hrs.h5', 'plant4_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_24hrs.h5', 'plant1_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_28hrs.h5', 'plant4_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_0hrs.h5', 'plant2_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_60hrs.h5', 'plant13_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_68hrs.h5', 'plant1_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_48hrs.h5', 'plant4_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_16hrs.h5', 'plant4_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_32hrs.h5', 'plant18_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_76hrs.h5', 'plant4_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_72hrs.h5', 'plant13_80hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_80hrs.h5', 'plant13_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_12hrs.h5', 'plant18_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_16hrs.h5', 'plant13_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_48hrs.h5', 'plant18_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_72hrs.h5', 'plant18_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_36hrs.h5', 'plant4_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_44hrs.h5', 'plant4_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_56hrs.h5', 'plant13_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_52hrs.h5', 'plant18_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_52hrs.h5', 'plant4_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_76hrs.h5', 'plant13_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_4hrs.h5', 'plant2_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_28hrs.h5', 'plant13_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_16hrs.h5', 'plant18_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_44hrs.h5', 'plant18_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_32hrs.h5', 'plant2_40hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_40hrs.h5', 'plant2_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_24hrs.h5', 'plant1_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_32hrs.h5', 'plant13_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_20hrs.h5', 'plant13_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_28hrs.h5', 'plant1_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_44hrs.h5', 'plant4_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_28hrs.h5', 'plant1_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_64hrs.h5', 'plant2_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_32hrs.h5', 'plant18_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_60hrs.h5', 'plant13_40hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_40hrs.h5', 'plant1_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_56hrs.h5', 'plant13_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_24hrs.h5', 'plant18_84hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_84hrs.h5', 'plant1_40hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_40hrs.h5', 'plant1_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_52hrs.h5', 'plant18_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_0hrs.h5', 'plant1_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_4hrs.h5', 'plant18_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_48hrs.h5', 'plant4_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_20hrs.h5', 'plant1_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_36hrs.h5', 'plant2_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_48hrs.h5', 'plant18_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_64hrs.h5', 'plant18_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_68hrs.h5', 'plant1_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_20hrs.h5', 'plant18_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_4hrs.h5', 'plant2_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_12hrs.h5', 'plant13_84hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_84hrs.h5', 'plant2_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_0hrs.h5', 'plant1_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_24hrs.h5', 'plant13_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_72hrs.h5', 'plant2_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_64hrs.h5', 'plant13_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_56hrs.h5', 'plant13_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_44hrs.h5', 'plant1_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_60hrs.h5', 'plant13_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_0hrs.h5', 'plant18_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_8hrs.h5', 'plant18_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_56hrs.h5', 'plant2_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_4hrs.h5', 'plant13_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_64hrs.h5', 'plant18_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_20hrs.h5', 'plant1_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_72hrs.h5'}, 'test': {'plant15_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_72hrs.h5', 'plant15_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_0hrs.h5', 'plant15_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_68hrs.h5', 'plant15_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_28hrs.h5', 'plant15_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_64hrs.h5', 'plant15_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_44hrs.h5', 'plant15_80hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_80hrs.h5', 'plant15_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_56hrs.h5', 'plant15_84hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_84hrs.h5', 'plant15_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_12hrs.h5', 'plant15_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_76hrs.h5', 'plant15_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_32hrs.h5', 'plant15_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_20hrs.h5', 'plant15_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_48hrs.h5', 'plant15_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_24hrs.h5', 'plant15_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_4hrs.h5', 'plant15_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_16hrs.h5', 'plant15_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_36hrs.h5', 'plant15_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_60hrs.h5', 'plant15_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_8hrs.h5', 'plant15_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_52hrs.h5', 'plant15_40hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_40hrs.h5'}}\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# step 2\n",
    "run_py_script = \"python prepare_dataset/get_the_dataset_info_of_ATAS.py \"+\\\n",
    "\"--path \"+processed_path+\" \"+\\\n",
    "\"--test_name 'plant15' \"\n",
    "print(\"run \"+run_py_script)\n",
    "os.system(run_py_script)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "35885af7",
   "metadata": {},
   "outputs": [],
   "source": [
    "# # step 3\n",
    "# # use the dataset_info generated from get_the_dataset_info_of_ATAS.py\n",
    "# run_py_script = \"python prepare_dataset/pre_crop_ATAS.py \"+\\\n",
    "# \"--output_path \"+pre_cropped_path+\" \"\n",
    "# print(\"run \"+run_py_script)\n",
    "# os.system(run_py_script)\n",
    "\n",
    "# # step 4\n",
    "# run_py_script = \"python prepare_dataset/get_the_dataset_info_of_ATAS_pre_cropped.py \"+\\\n",
    "# \"--path \"+pre_cropped_path\n",
    "# print(\"run \"+run_py_script)\n",
    "# os.system(run_py_script)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "75e4a26f",
   "metadata": {},
   "outputs": [],
   "source": [
    "ATAS_data_dict = load_obj(\"dataset_info/ATAS_dataset_info\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "a964b896",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'train': {'plant2_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_68hrs.h5',\n",
       "  'plant2_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_56hrs.h5',\n",
       "  'plant1_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_16hrs.h5',\n",
       "  'plant4_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_64hrs.h5',\n",
       "  'plant18_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_28hrs.h5',\n",
       "  'plant4_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_8hrs.h5',\n",
       "  'plant2_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_76hrs.h5',\n",
       "  'plant1_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_12hrs.h5',\n",
       "  'plant2_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_20hrs.h5',\n",
       "  'plant1_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_0hrs.h5',\n",
       "  'plant2_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_16hrs.h5',\n",
       "  'plant4_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_48hrs.h5',\n",
       "  'plant1_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_68hrs.h5',\n",
       "  'plant4_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_60hrs.h5',\n",
       "  'plant4_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_36hrs.h5',\n",
       "  'plant4_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_68hrs.h5',\n",
       "  'plant18_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_12hrs.h5',\n",
       "  'plant1_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_76hrs.h5',\n",
       "  'plant4_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_12hrs.h5',\n",
       "  'plant13_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_8hrs.h5',\n",
       "  'plant4_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_52hrs.h5',\n",
       "  'plant4_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_4hrs.h5',\n",
       "  'plant1_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_8hrs.h5',\n",
       "  'plant2_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_72hrs.h5',\n",
       "  'plant4_40hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_40hrs.h5',\n",
       "  'plant18_80hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_80hrs.h5',\n",
       "  'plant13_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_36hrs.h5',\n",
       "  'plant13_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_60hrs.h5',\n",
       "  'plant2_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_8hrs.h5',\n",
       "  'plant2_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_44hrs.h5',\n",
       "  'plant2_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_36hrs.h5',\n",
       "  'plant13_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_32hrs.h5',\n",
       "  'plant2_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_52hrs.h5',\n",
       "  'plant13_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_76hrs.h5',\n",
       "  'plant18_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_24hrs.h5',\n",
       "  'plant4_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_24hrs.h5',\n",
       "  'plant1_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_28hrs.h5',\n",
       "  'plant4_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_0hrs.h5',\n",
       "  'plant2_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_60hrs.h5',\n",
       "  'plant13_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_68hrs.h5',\n",
       "  'plant1_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_48hrs.h5',\n",
       "  'plant4_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_16hrs.h5',\n",
       "  'plant4_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_32hrs.h5',\n",
       "  'plant18_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_76hrs.h5',\n",
       "  'plant4_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_72hrs.h5',\n",
       "  'plant13_80hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_80hrs.h5',\n",
       "  'plant13_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_12hrs.h5',\n",
       "  'plant18_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_16hrs.h5',\n",
       "  'plant13_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_48hrs.h5',\n",
       "  'plant18_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_72hrs.h5',\n",
       "  'plant18_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_36hrs.h5',\n",
       "  'plant4_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_44hrs.h5',\n",
       "  'plant4_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_56hrs.h5',\n",
       "  'plant13_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_52hrs.h5',\n",
       "  'plant18_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_52hrs.h5',\n",
       "  'plant4_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_76hrs.h5',\n",
       "  'plant13_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_4hrs.h5',\n",
       "  'plant2_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_28hrs.h5',\n",
       "  'plant13_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_16hrs.h5',\n",
       "  'plant18_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_44hrs.h5',\n",
       "  'plant18_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_32hrs.h5',\n",
       "  'plant2_40hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_40hrs.h5',\n",
       "  'plant2_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_24hrs.h5',\n",
       "  'plant1_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_32hrs.h5',\n",
       "  'plant13_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_20hrs.h5',\n",
       "  'plant13_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_28hrs.h5',\n",
       "  'plant1_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_44hrs.h5',\n",
       "  'plant4_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_28hrs.h5',\n",
       "  'plant1_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_64hrs.h5',\n",
       "  'plant2_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_32hrs.h5',\n",
       "  'plant18_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_60hrs.h5',\n",
       "  'plant13_40hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_40hrs.h5',\n",
       "  'plant1_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_56hrs.h5',\n",
       "  'plant13_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_24hrs.h5',\n",
       "  'plant18_84hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_84hrs.h5',\n",
       "  'plant1_40hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_40hrs.h5',\n",
       "  'plant1_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_52hrs.h5',\n",
       "  'plant18_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_0hrs.h5',\n",
       "  'plant1_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_4hrs.h5',\n",
       "  'plant18_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_48hrs.h5',\n",
       "  'plant4_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant4_20hrs.h5',\n",
       "  'plant1_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_36hrs.h5',\n",
       "  'plant2_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_48hrs.h5',\n",
       "  'plant18_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_64hrs.h5',\n",
       "  'plant18_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_68hrs.h5',\n",
       "  'plant1_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_20hrs.h5',\n",
       "  'plant18_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_4hrs.h5',\n",
       "  'plant2_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_12hrs.h5',\n",
       "  'plant13_84hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_84hrs.h5',\n",
       "  'plant2_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_0hrs.h5',\n",
       "  'plant1_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_24hrs.h5',\n",
       "  'plant13_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_72hrs.h5',\n",
       "  'plant2_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_64hrs.h5',\n",
       "  'plant13_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_56hrs.h5',\n",
       "  'plant13_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_44hrs.h5',\n",
       "  'plant1_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_60hrs.h5',\n",
       "  'plant13_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_0hrs.h5',\n",
       "  'plant18_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_8hrs.h5',\n",
       "  'plant18_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_56hrs.h5',\n",
       "  'plant2_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant2_4hrs.h5',\n",
       "  'plant13_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant13_64hrs.h5',\n",
       "  'plant18_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant18_20hrs.h5',\n",
       "  'plant1_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant1_72hrs.h5'},\n",
       " 'test': {'plant15_72hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_72hrs.h5',\n",
       "  'plant15_0hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_0hrs.h5',\n",
       "  'plant15_68hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_68hrs.h5',\n",
       "  'plant15_28hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_28hrs.h5',\n",
       "  'plant15_64hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_64hrs.h5',\n",
       "  'plant15_44hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_44hrs.h5',\n",
       "  'plant15_80hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_80hrs.h5',\n",
       "  'plant15_56hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_56hrs.h5',\n",
       "  'plant15_84hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_84hrs.h5',\n",
       "  'plant15_12hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_12hrs.h5',\n",
       "  'plant15_76hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_76hrs.h5',\n",
       "  'plant15_32hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_32hrs.h5',\n",
       "  'plant15_20hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_20hrs.h5',\n",
       "  'plant15_48hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_48hrs.h5',\n",
       "  'plant15_24hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_24hrs.h5',\n",
       "  'plant15_4hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_4hrs.h5',\n",
       "  'plant15_16hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_16hrs.h5',\n",
       "  'plant15_36hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_36hrs.h5',\n",
       "  'plant15_60hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_60hrs.h5',\n",
       "  'plant15_8hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_8hrs.h5',\n",
       "  'plant15_52hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_52hrs.h5',\n",
       "  'plant15_40hrs.h5': '/data/CellSeg_dataset/ATAS_processed/plant15_40hrs.h5'}}"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ATAS_data_dict"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "db69fd78",
   "metadata": {},
   "source": [
    "### LRP"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "7dbeb97b",
   "metadata": {},
   "outputs": [],
   "source": [
    "source_file_path = \"/data/CellSeg_dataset/LateralRootPrimordia\"\n",
    "output_file_path = \"/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary\"\n",
    "output_file_path_II = \"/data/CellSeg_dataset/LateralRootPrimordia_pre_croped\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "4fb1020b",
   "metadata": {},
   "outputs": [],
   "source": [
    "# # step 1\n",
    "# run_py_script = \"python prepare_dataset/prepare_LateralRootPrimordia_dataset.py \"+\\\n",
    "# \"--source_file_path \"+source_file_path+\" \"+\\\n",
    "# \"--output_file_path \"+output_file_path+\" \"+\\\n",
    "# \"--img_size_scale_factor 0.5 \"+\\\n",
    "# \"--width_of_membrane 2.5\"\n",
    "# print(\"run \"+run_py_script)\n",
    "# os.system(run_py_script)\n",
    "\n",
    "# # # or you can precrop the dataset\n",
    "# # # run_py_script = \"python prepare_dataset/pre_crop_LateralRootPrimordia.py \"+\\\n",
    "# # # \"--source_file_path \"+source_file_path+\" \"+\\\n",
    "# # # \"--output_file_path \"+output_file_path_II\n",
    "# # # print(\"run \"+run_py_script)\n",
    "# # # os.system(run_py_script)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "3fd34ae2",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "run python prepare_dataset/get_the_dataset_info_of_LateralRootPrimordia.py --path /data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary\n",
      "['/home/v-andongwang/Projects/CellSeg_github/prepare_dataset', '/home/v-andongwang/anaconda3/envs/clip/lib/python38.zip', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/lib-dynload', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages/wheel-0.37.1-py3.8.egg', '/home/v-andongwang/Projects/Learning/Dassl.pytorch', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages/locket-0.2.1-py3.8.egg', '/home/v-andongwang/Projects/CellSeg_github']\n",
      "{'train': {'Movie1_t00014_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00014_crop_gt.h5', 'Movie3_T00004_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie3_T00004_crop_gt.h5', 'Movie2_T00010_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00010_crop_gt.h5', 'Movie1_t00012_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00012_crop_gt.h5', 'Movie2_T00016_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00016_crop_gt.h5', 'Movie1_t00045_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00045_crop_gt.h5', 'Movie2_T00012_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00012_crop_gt.h5', 'Movie1_t00003_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00003_crop_gt.h5', 'Movie1_t00010_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00010_crop_gt.h5', 'Movie3_T00002_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie3_T00002_crop_gt.h5', 'Movie1_t00009_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00009_crop_gt.h5', 'Movie1_t00016_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00016_crop_gt.h5', 'Movie2_T00014_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00014_crop_gt.h5', 'Movie1_t00040_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00040_crop_gt.h5', 'Movie1_t00049_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00049_crop_gt.h5', 'Movie2_T00002_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00002_crop_gt.h5', 'Movie2_T00006_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00006_crop_gt.h5', 'Movie1_t00018_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00018_crop_gt.h5', 'Movie1_t00035_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00035_crop_gt.h5', 'Movie1_t00020_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00020_crop_gt.h5', 'Movie2_T00000_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00000_crop_gt.h5', 'Movie2_T00008_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00008_crop_gt.h5', 'Movie1_t00030_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/val/Movie1_t00030_crop_gt.h5', 'Movie1_t00004_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/val/Movie1_t00004_crop_gt.h5'}, 'test': {'Movie2_T00010_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/test/Movie2_T00010_crop_gt.h5', 'Movie1_t00045_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/test/Movie1_t00045_crop_gt.h5', 'Movie1_t00006_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/test/Movie1_t00006_crop_gt.h5', 'Movie2_T00020_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/test/Movie2_T00020_crop_gt.h5'}}\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# step 2\n",
    "run_py_script = \"python prepare_dataset/get_the_dataset_info_of_LateralRootPrimordia.py \"+\\\n",
    "\"--path \"+output_file_path\n",
    "print(\"run \"+run_py_script)\n",
    "os.system(run_py_script)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "6b62f4bd",
   "metadata": {},
   "outputs": [],
   "source": [
    "LRP_data_dict = load_obj(\"dataset_info/LRP_dataset_info\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "e6777b3e",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'train': {'Movie1_t00014_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00014_crop_gt.h5',\n",
       "  'Movie3_T00004_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie3_T00004_crop_gt.h5',\n",
       "  'Movie2_T00010_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00010_crop_gt.h5',\n",
       "  'Movie1_t00012_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00012_crop_gt.h5',\n",
       "  'Movie2_T00016_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00016_crop_gt.h5',\n",
       "  'Movie1_t00045_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00045_crop_gt.h5',\n",
       "  'Movie2_T00012_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00012_crop_gt.h5',\n",
       "  'Movie1_t00003_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00003_crop_gt.h5',\n",
       "  'Movie1_t00010_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00010_crop_gt.h5',\n",
       "  'Movie3_T00002_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie3_T00002_crop_gt.h5',\n",
       "  'Movie1_t00009_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00009_crop_gt.h5',\n",
       "  'Movie1_t00016_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00016_crop_gt.h5',\n",
       "  'Movie2_T00014_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00014_crop_gt.h5',\n",
       "  'Movie1_t00040_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00040_crop_gt.h5',\n",
       "  'Movie1_t00049_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00049_crop_gt.h5',\n",
       "  'Movie2_T00002_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00002_crop_gt.h5',\n",
       "  'Movie2_T00006_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00006_crop_gt.h5',\n",
       "  'Movie1_t00018_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00018_crop_gt.h5',\n",
       "  'Movie1_t00035_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00035_crop_gt.h5',\n",
       "  'Movie1_t00020_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie1_t00020_crop_gt.h5',\n",
       "  'Movie2_T00000_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00000_crop_gt.h5',\n",
       "  'Movie2_T00008_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/train/Movie2_T00008_crop_gt.h5',\n",
       "  'Movie1_t00030_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/val/Movie1_t00030_crop_gt.h5',\n",
       "  'Movie1_t00004_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/val/Movie1_t00004_crop_gt.h5'},\n",
       " 'test': {'Movie2_T00010_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/test/Movie2_T00010_crop_gt.h5',\n",
       "  'Movie1_t00045_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/test/Movie1_t00045_crop_gt.h5',\n",
       "  'Movie1_t00006_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/test/Movie1_t00006_crop_gt.h5',\n",
       "  'Movie2_T00020_crop_gt.h5': '/data/CellSeg_dataset/LateralRootPrimordia_processed_wide_boundary/test/Movie2_T00020_crop_gt.h5'}}"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "LRP_data_dict"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4bba7a20",
   "metadata": {},
   "source": [
    "### Ovules"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "1819a317",
   "metadata": {},
   "outputs": [],
   "source": [
    "source_file_path = \"/data/CellSeg_dataset/Ovules\"\n",
    "output_file_path = \"/data/CellSeg_dataset/Ovules_processed_thin_boundary\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "d1d26d0c",
   "metadata": {},
   "outputs": [],
   "source": [
    "# # step 1\n",
    "# run_py_script = \"python prepare_dataset/prepare_Ovules_dataset.py \"+\\\n",
    "# \"--source_file_path \"+source_file_path+\" \"+\\\n",
    "# \"--output_file_path \"+output_file_path+\" \"+\\\n",
    "# \"--img_size_scale_factor 0.5 \"+\\\n",
    "# \"--width_of_membrane 1\"\n",
    "# print(\"run \"+run_py_script)\n",
    "# os.system(run_py_script)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "1f6239dc",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "run python prepare_dataset/get_the_dataset_info_of_Ovules.py --path /data/CellSeg_dataset/Ovules_processed_thin_boundary\n",
      "['/home/v-andongwang/Projects/CellSeg_github/prepare_dataset', '/home/v-andongwang/anaconda3/envs/clip/lib/python38.zip', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/lib-dynload', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages/wheel-0.37.1-py3.8.egg', '/home/v-andongwang/Projects/Learning/Dassl.pytorch', '/home/v-andongwang/anaconda3/envs/clip/lib/python3.8/site-packages/locket-0.2.1-py3.8.egg', '/home/v-andongwang/Projects/CellSeg_github']\n",
      "{'train': {'N_404_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_404_ds2x.npz', 'N_422_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_422_ds2x.npz', 'N_509_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_509_ds2x.npz', 'N_454_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_454_ds2x.npz', 'N_405_B_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_405_B_ds2x.npz', 'N_536_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_536_ds2x.npz', 'N_512_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_512_ds2x.npz', 'N_449_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_449_ds2x.npz', 'N_405_A_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_405_A_ds2x.npz', 'N_451_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_451_ds2x.npz', 'N_534_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_534_ds2x.npz', 'N_517_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_517_ds2x.npz', 'N_445_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_445_ds2x.npz', 'N_428_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_428_ds2x.npz', 'N_440_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_440_ds2x.npz', 'N_487_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_487_ds2x.npz', 'N_457_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_457_ds2x.npz', 'N_425_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_425_ds2x.npz', 'N_535_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_535_ds2x.npz', 'N_458_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_458_ds2x.npz', 'N_450_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_450_ds2x.npz', 'N_416_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_416_ds2x.npz', 'N_464_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/val/N_464_ds2x.npz', 'N_420_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/val/N_420_ds2x.npz'}, 'test': {'N_441_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_441_final_crop_ds2.npz', 'N_590_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_590_final_crop_ds2.npz', 'N_294_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_294_final_crop_ds2.npz', 'N_593_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_593_final_crop_ds2.npz', 'N_435_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_435_final_crop_ds2.npz', 'N_511_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_511_final_crop_ds2.npz', 'N_522_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_522_final_crop_ds2.npz'}}\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# step 2\n",
    "run_py_script = \"python prepare_dataset/get_the_dataset_info_of_Ovules.py \"+\\\n",
    "\"--path \"+output_file_path\n",
    "print(\"run \"+run_py_script)\n",
    "os.system(run_py_script)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "1bb54355",
   "metadata": {},
   "outputs": [],
   "source": [
    "Ovules_data_dict = load_obj(\"dataset_info/Ovules_dataset_info\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "0194e7c3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'train': {'N_404_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_404_ds2x.npz',\n",
       "  'N_422_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_422_ds2x.npz',\n",
       "  'N_509_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_509_ds2x.npz',\n",
       "  'N_454_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_454_ds2x.npz',\n",
       "  'N_405_B_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_405_B_ds2x.npz',\n",
       "  'N_536_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_536_ds2x.npz',\n",
       "  'N_512_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_512_ds2x.npz',\n",
       "  'N_449_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_449_ds2x.npz',\n",
       "  'N_405_A_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_405_A_ds2x.npz',\n",
       "  'N_451_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_451_ds2x.npz',\n",
       "  'N_534_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_534_ds2x.npz',\n",
       "  'N_517_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_517_ds2x.npz',\n",
       "  'N_445_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_445_ds2x.npz',\n",
       "  'N_428_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_428_ds2x.npz',\n",
       "  'N_440_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_440_ds2x.npz',\n",
       "  'N_487_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_487_ds2x.npz',\n",
       "  'N_457_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_457_ds2x.npz',\n",
       "  'N_425_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_425_ds2x.npz',\n",
       "  'N_535_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_535_ds2x.npz',\n",
       "  'N_458_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_458_ds2x.npz',\n",
       "  'N_450_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_450_ds2x.npz',\n",
       "  'N_416_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/train/N_416_ds2x.npz',\n",
       "  'N_464_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/val/N_464_ds2x.npz',\n",
       "  'N_420_ds2x.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/val/N_420_ds2x.npz'},\n",
       " 'test': {'N_441_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_441_final_crop_ds2.npz',\n",
       "  'N_590_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_590_final_crop_ds2.npz',\n",
       "  'N_294_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_294_final_crop_ds2.npz',\n",
       "  'N_593_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_593_final_crop_ds2.npz',\n",
       "  'N_435_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_435_final_crop_ds2.npz',\n",
       "  'N_511_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_511_final_crop_ds2.npz',\n",
       "  'N_522_final_crop_ds2.npz': '/data/CellSeg_dataset/Ovules_processed_thin_boundary/test/N_522_final_crop_ds2.npz'}}"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Ovules_data_dict"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "148810a4",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "raw torch.Size([1, 39, 45, 61])\n",
      "background torch.Size([1, 39, 45, 61])\n",
      "boundary torch.Size([1, 39, 45, 61])\n",
      "foreground torch.Size([1, 39, 45, 61])\n",
      "weights_background torch.Size([1, 39, 45, 61])\n",
      "weights_boundary torch.Size([1, 39, 45, 61])\n",
      "weights_foreground torch.Size([1, 39, 45, 61])\n"
     ]
    },
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    },
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    },
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    },
    {
     "data": {
      "image/png": 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gSlIjA1OSGq35QZ9RGnxVz2gtHDQZNLAy6sGWln3uPdQ/ECQdaTzClKRGBqYkNTIwJalRc2B2E6F9Mckt3fKmJLcn2d09DpwETZLWiuUM+rwLeAB4Sbd8JXBHVV2d5Mpu+ddf6A0O1uG+wYNRDmAMGpRZOLc4wN6Dm/ratq5/fMn3H3RVz9YXH9dY3XiN8vfYelu4QQNBXv2jtax1mt2twE8DH5rXfCmwo3u+A3jTSCuTpCnT+pH8A8AVwHPz2jZX1T6A7vGUQRvOn5f88cefG7SKJM2Ellkj3wAcqKp7V7KD+fOSb9rkGJOk2dVyDvM84I1JLgGOBl6S5CPA/iRbqmpfN+XugXEWKkmT1jJr5FXAVQBJzgf+dVX9fJL/CGwHru4eb1rqvZ7lRX3zxYxyrphBgzInrHu6v21jf9sgg7Zdba0DMIM4ACON1jCfka8GLkqyG7ioW5akNWtZx3dVdSdwZ/f8G8CFoy9JkqaTozCS1GhV71Z0qF7Eo4ePX9D6zFj32Xoe8onDx/S1rfTuRNN8nnCl5zU9lyp5hClJzQxMSWpkYEpSIwNTkho5RUVn0ODQwi/CT8udiaZF68BN6+CQNO08wpSkRgamJDUyMCWpkYEpSY3W/KDPoKt1+q82WptX9QzSMq3EqPs0a78jaTEeYUpSIwNTkhoZmJLUyMCUpEapqtXbWfIo8FXgJOCxVdvxeMx6H6x/8ma9D2up/pdV1clLbbCqgfndnSb3VNU5q77jEZr1Plj/5M16H47E+v1ILkmNDExJajSpwLxuQvsdpVnvg/VP3qz34YirfyLnMCVpFvmRXJIaGZiS1GjVAzPJxUm+nOQrSa5c7f0vV5IbkhxIsmte26YktyfZ3T2eOMkaX0iS05J8NskDSe5P8q6ufZb6cHSSv0zypa4P7+3aZ6YPAEnWJfliklu65ZmpP8meJH+VZGeSe7q2makfIMkJST6e5MHu38OPLbcPqxqYSdYBHwR+Cngl8NYkr1zNGlbgw8DFC9quBO6oqjOAO7rlaXUIeHdVvQJ4DfDO7nc+S314Brigqs4CtgEXJ3kNs9UHgHcBD8xbnrX6X1dV2+Z9d3HW6v9d4FNV9cPAWfT+LJbXh6patR/gx4Db5i1fBVy1mjWssO7TgV3zlr8MbOmebwG+POkal9GXm4CLZrUPwDHAF4BXz1IfgK3dP8gLgFtm7e8RsAc4aUHbLNX/EuD/0g10r7QPq/2R/FTg4XnLe7u2WbO5qvYBdI+nTLieJklOB84G7mbG+tB9nN0JHABur6pZ68MHgCuA5+a1zVL9BXw6yb1J3t61zVL9PwA8Cvx+d1rkQ0mOZZl9WO3AzIA2v9e0CpIcB/wx8GtV9a1J17NcVXW4qrbRO1I7N8mrJlxSsyRvAA5U1b2TrmUI51XVj9I7nfbOJP9w0gUt04uBHwWuraqzgW+zglMIqx2Ye4HT5i1vBR5Z5RpGYX+SLQDd44EJ1/OCkhxFLyw/WlWf6Jpnqg9zquoJ4E5655VnpQ/nAW9Msgf4GHBBko8wO/VTVY90jweATwLnMkP108uevd0nE4CP0wvQZfVhtQPz88AZSb4/yXrg54CbV7mGUbgZ2N49307vvOBUShLg94AHqup35r00S304OckJ3fONwOuBB5mRPlTVVVW1tapOp/d3/jNV9fPMSP1Jjk1y/Nxz4CeAXcxI/QBV9bfAw0nO7JouBP6a5fZhAidfLwH+D/A3wL+d9Mnghnr/CNgHPEvvf6nLgO+ldwJ/d/e4adJ1vkD9r6V32uM+YGf3c8mM9eFHgC92fdgF/EbXPjN9mNeX8/n/gz4zUT+9839f6n7un/t3Oyv1z+vHNuCe7u/R/wROXG4fvDRSkhp5pY8kNTIwJamRgSlJjQxMSWpkYEpSIwNTkhoZmJLU6P8BYDDTnE52k9YAAAAASUVORK5CYII=",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    },
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    },
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    },
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "from func.load_dataset import Cell_Seg_3D_Dataset\n",
    "import pickle\n",
    "import matplotlib.pyplot as plt\n",
    "def load_obj(name):\n",
    "    with open(name + '.pkl', 'rb') as f:\n",
    "        return pickle.load(f)\n",
    "HMS_dataset_info = load_obj(\"dataset_info/HMS_dataset_info\")\n",
    "dataset = Cell_Seg_3D_Dataset(HMS_dataset_info['train'])\n",
    "idx = 0\n",
    "crop_size = dataset.set_random_crop_size()\n",
    "output = dataset.get(idx, file_format='.npy', crop_size = crop_size, \\\n",
    "    boundary_importance = 1, need_tensor_output = True, need_transform = True)\n",
    "for item in output.keys():\n",
    "    print(item, output[item].shape)\n",
    "    plt.figure()\n",
    "    plt.imshow(output[item][0,0])\n",
    "    plt.title(item)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "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": "3.8.12"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}