file_sorting_subsampling.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "fab29458",
   "metadata": {},
   "source": [
    "## Copy a subset of .tif files from a massive unsorted folder into individual folders per sample, as determined by the R##### in part of the file name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "0d4f6677",
   "metadata": {},
   "outputs": [],
   "source": [
    "import shutil\n",
    "import glob\n",
    "import os\n",
    "from pathlib import Path"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9d928dc6",
   "metadata": {},
   "source": [
    "Make sure to change the target folder. It should be the folder with all of the .tif MIPs in it."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "e8df02b1",
   "metadata": {},
   "outputs": [],
   "source": [
    "targetFolder = \"G:/20220518_160557_051822h2bgfp6hpfish Mips/\"\n",
    "fileList = glob.glob(targetFolder+'S000_t000000_V000_R*.tif')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "1f8ea690",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0000_X000_Y000_C02_I0_D0_P00503_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0001_X000_Y000_C02_I0_D0_P00522_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0002_X000_Y000_C02_I0_D0_P00486_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0003_X000_Y000_C02_I0_D0_P00487_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0004_X000_Y000_C02_I0_D0_P00506_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0005_X000_Y000_C02_I0_D0_P00490_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0006_X000_Y000_C02_I0_D0_P00507_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0007_X000_Y000_C02_I0_D0_P00485_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0008_X000_Y000_C02_I0_D0_P00503_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0009_X000_Y000_C02_I0_D0_P00468_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0010_X000_Y000_C02_I0_D0_P00486_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0011_X000_Y000_C02_I0_D0_P00518_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0012_X000_Y000_C02_I0_D0_P00468_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0013_X000_Y000_C02_I0_D0_P00505_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0014_X000_Y000_C02_I0_D0_P00489_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0015_X000_Y000_C02_I0_D0_P00468_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0016_X000_Y000_C02_I0_D0_P00466_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0017_X000_Y000_C02_I0_D0_P00468_MP.tif',\n",
       " 'G:/20220518_160557_051822h2bgfp6hpfish Mips\\\\S000_t000000_V000_R0018_X000_Y000_C02_I0_D0_P00486_MP.tif']"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#just to check, should show the files you want to copy\n",
    "fileList"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "20de35ff",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
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    },
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[1;32md:\\pytorch\\file_sorting_subsampling.ipynb Cell 6\u001b[0m in \u001b[0;36m<cell line: 1>\u001b[1;34m()\u001b[0m\n\u001b[0;32m     <a href='vscode-notebook-cell:/d%3A/pytorch/file_sorting_subsampling.ipynb#ch0000003?line=12'>13</a>\u001b[0m \u001b[39mprint\u001b[39m(time_check)\n\u001b[0;32m     <a href='vscode-notebook-cell:/d%3A/pytorch/file_sorting_subsampling.ipynb#ch0000003?line=13'>14</a>\u001b[0m \u001b[39mif\u001b[39;00m (\u001b[39mint\u001b[39m(time_check)\u001b[39m%\u001b[39m\u001b[39m4\u001b[39m\u001b[39m==\u001b[39m\u001b[39m0\u001b[39m):\n\u001b[1;32m---> <a href='vscode-notebook-cell:/d%3A/pytorch/file_sorting_subsampling.ipynb#ch0000003?line=14'>15</a>\u001b[0m     shutil\u001b[39m.\u001b[39;49mcopyfile(Path(temp), outputDirectory\u001b[39m+\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39m/\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39m+\u001b[39;49mPath(temp)\u001b[39m.\u001b[39;49mstem\u001b[39m+\u001b[39;49mPath(temp)\u001b[39m.\u001b[39;49msuffix)\n",
      "File \u001b[1;32md:\\Anaconda\\envs\\fastai2\\lib\\shutil.py:274\u001b[0m, in \u001b[0;36mcopyfile\u001b[1;34m(src, dst, follow_symlinks)\u001b[0m\n\u001b[0;32m    271\u001b[0m \u001b[39m# Windows, see:\u001b[39;00m\n\u001b[0;32m    272\u001b[0m \u001b[39m# https://github.com/python/cpython/pull/7160#discussion_r195405230\u001b[39;00m\n\u001b[0;32m    273\u001b[0m \u001b[39melif\u001b[39;00m _WINDOWS \u001b[39mand\u001b[39;00m file_size \u001b[39m>\u001b[39m \u001b[39m0\u001b[39m:\n\u001b[1;32m--> 274\u001b[0m     _copyfileobj_readinto(fsrc, fdst, \u001b[39mmin\u001b[39;49m(file_size, COPY_BUFSIZE))\n\u001b[0;32m    275\u001b[0m     \u001b[39mreturn\u001b[39;00m dst\n\u001b[0;32m    277\u001b[0m copyfileobj(fsrc, fdst)\n",
      "File \u001b[1;32md:\\Anaconda\\envs\\fastai2\\lib\\shutil.py:185\u001b[0m, in \u001b[0;36m_copyfileobj_readinto\u001b[1;34m(fsrc, fdst, length)\u001b[0m\n\u001b[0;32m    183\u001b[0m         fdst\u001b[39m.\u001b[39mwrite(smv)\n\u001b[0;32m    184\u001b[0m \u001b[39melse\u001b[39;00m:\n\u001b[1;32m--> 185\u001b[0m     fdst_write(mv)\n",
      "\u001b[1;31mKeyboardInterrupt\u001b[0m: "
     ]
    }
   ],
   "source": [
    "for file in fileList:\n",
    "    file = Path(file)\n",
    "    name = file.stem\n",
    "    current_position = name.split('_')[3]\n",
    "    outputDirectory = targetFolder+\"/\"+current_position\n",
    "    outputDirectoryExistsCheck = os.path.exists(outputDirectory)\n",
    "    if not outputDirectoryExistsCheck:\n",
    "        os.mkdir(outputDirectory)\n",
    "    files_to_move = glob.glob(targetFolder+'*'+current_position+'*.*')\n",
    "    #print(files_to_move)\n",
    "    for temp in files_to_move:\n",
    "        time_check = Path(temp).stem.split('_')[1][1:]\n",
    "        #print(time_check)\n",
    "        if (int(time_check)%4==0):\n",
    "            shutil.copyfile(Path(temp), outputDirectory+\"/\"+Path(temp).stem+Path(temp).suffix)\n",
    "\n",
    "        #print(Path(temp).stem+Path(temp).suffix)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "cadfed2c",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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