Untitled1.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import tifffile\n",
    "\n",
    "vol = tifffile.imread(\"../../data/Mauricio/hsprasmkate_par3gfp_ath5rfpline_17102017_Subset_cell1_average2x-1.tif\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(21, 51, 2, 332, 165)"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vol.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "ch1 = vol[:,:,0,:,:]\n",
    "tifffile.imsave(\"../../data/Mauricio/ch1.tif\",ch1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "ch2 = vol[:,:,1,:,:]\n",
    "tifffile.imsave(\"../../data/Mauricio/ch2.tif\", ch2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "ename": "FileExistsError",
     "evalue": "[Errno 17] File exists: '../../data/Mauricio/ch1'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mFileExistsError\u001b[0m                           Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-9-c881df7433e0>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0mch1Dir\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"../../data/Mauricio/ch1\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0mch2Dir\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"../../data/Mauricio/ch2\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmakedirs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mch1Dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      5\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmakedirs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mch2Dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/os.py\u001b[0m in \u001b[0;36mmakedirs\u001b[0;34m(name, mode, exist_ok)\u001b[0m\n\u001b[1;32m    239\u001b[0m             \u001b[0;32mreturn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    240\u001b[0m     \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 241\u001b[0;31m         \u001b[0mmkdir\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmode\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    242\u001b[0m     \u001b[0;32mexcept\u001b[0m \u001b[0mOSError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    243\u001b[0m         \u001b[0;31m# Cannot rely on checking for EEXIST, since the operating system\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mFileExistsError\u001b[0m: [Errno 17] File exists: '../../data/Mauricio/ch1'"
     ]
    }
   ],
   "source": [
    "import os\n",
    "ch1Dir = \"../../data/Mauricio/ch1\"\n",
    "ch2Dir = \"../../data/Mauricio/ch2\"\n",
    "os.makedirs(ch1Dir)\n",
    "os.makedirs(ch2Dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "for i in range(vol.shape[0]):\n",
    "    suff=''\n",
    "    if (i<10):\n",
    "        suff='0'\n",
    "    tifffile.imsave(ch1Dir+\"/t_\"+suff+str(i)+\".tif\", ch1[i])\n",
    "    tifffile.imsave(ch2Dir+\"/t_\"+suff+str(i)+\".tif\", ch2[i])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "ename": "FileExistsError",
     "evalue": "[Errno 17] File exists: '../../data/Mauricio/crop_ch1'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mFileExistsError\u001b[0m                           Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-18-77dea13c5a01>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0mch1Dir\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"../../data/Mauricio/crop_ch1\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0mch2Dir\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"../../data/Mauricio/crop_ch2\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmakedirs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mch1Dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      7\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmakedirs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mch2Dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/os.py\u001b[0m in \u001b[0;36mmakedirs\u001b[0;34m(name, mode, exist_ok)\u001b[0m\n\u001b[1;32m    239\u001b[0m             \u001b[0;32mreturn\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    240\u001b[0m     \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 241\u001b[0;31m         \u001b[0mmkdir\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmode\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    242\u001b[0m     \u001b[0;32mexcept\u001b[0m \u001b[0mOSError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    243\u001b[0m         \u001b[0;31m# Cannot rely on checking for EEXIST, since the operating system\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mFileExistsError\u001b[0m: [Errno 17] File exists: '../../data/Mauricio/crop_ch1'"
     ]
    }
   ],
   "source": [
    "import os\n",
    "\n",
    "vol_crop = tifffile.imread(\"../../data/Mauricio/crop.tif\")\n",
    "ch1Dir = \"../../data/Mauricio/crop_ch1\"\n",
    "ch2Dir = \"../../data/Mauricio/crop_ch2\"\n",
    "os.makedirs(ch1Dir)\n",
    "os.makedirs(ch2Dir)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "for i in range(vol.shape[0]):\n",
    "    suff=''\n",
    "    if (i<10):\n",
    "        suff='0'\n",
    "    tifffile.imsave(ch1Dir+\"/t_\"+suff+str(i)+\".tif\", vol_crop[i,:,0,:,:])\n",
    "    tifffile.imsave(ch2Dir+\"/t_\"+suff+str(i)+\".tif\", vol_crop[i,:,1,:,:])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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