InputPipeline-multi.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np \n",
    "import os\n",
    "import glob\n",
    "import utils "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Convert .avi to .jpg"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Directory of mice index: DG 13\n",
      "Directory of .avi files stored:\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 13/7-12-17/preprocessed_dF.avi\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 13/7-16-17/preprocessed_dF.avi\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 13/8-11-17/preprocessed_dF.avi\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 13/8-16-17/preprocessed_dF.avi\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 13/8-18-17/preprocessed_dF.avi\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 13/8-3-17/preprocessed_dF.avi\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 13/8-8-17/preprocessed_dF.avi\n",
      "\n",
      "Directory of mice index: DG 21\n",
      "Directory of .avi files stored:\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 21/7-12-17/preprocessed_dF.avi\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 21/7-16-17/preprocessed_dF.avi\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 21/8-11-17/preprocessed_dF.avi\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 21/8-3-17/preprocessed_dF.avi\n",
      "\n",
      "For:  /home/kevinteng/Desktop/Students_Preprocessing/DG 21/8-8-17/preprocessed_dF.avi\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "input_path = '/home/kevinteng/Desktop/Students_Preprocessing/'\n",
    "save_path = '/home/kevinteng/Desktop/project/avi_to_jpg/'\n",
    "\n",
    "utils.vid2frames_from_files(input_path, save_path)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Convert .jpg stacks to .npy arrays"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "input_path = '/home/kevinteng/Desktop/project/avi_to_jpg/' \n",
    "save_path = '/home/kevinteng/Desktop/project/jpg_to_npy/' \n",
    "for main_dir in sorted(os.listdir(input_path)):\n",
    "    merge_dir = os.path.join(input_path + main_dir)\n",
    "    utils.imgs_to_arrays(merge_dir, extension='.jpg', RGB=False, \n",
    "                   save_as_npy=True, img_resize = 200, save_path= save_path)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Convert .mat File"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
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      "\n",
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      "/home/kevinteng/Desktop/Students_Preprocessing/DG 13/7-16-17/preprocessedCaSignal.mat\n",
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      "/home/kevinteng/Desktop/Students_Preprocessing/DG 13/7-16-17/preprocessed_ROIvalues.mat\n",
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      "/home/kevinteng/Desktop/Students_Preprocessing/DG 13/8-16-17/preprocessedvidalign.mat\n",
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      "(1, 1)\n",
      "\n",
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      "/home/kevinteng/Desktop/Students_Preprocessing/DG 13/8-8-17/preprocessedvidalign.mat\n",
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      "/home/kevinteng/Desktop/Students_Preprocessing/DG 21/8-8-17/name.mat\n",
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      "\n"
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    }
   ],
   "source": [
    "input_path = '/home/kevinteng/Desktop/Students_Preprocessing/'\n",
    "save_path = '/home/kevinteng/Desktop/project/mat/'\n",
    "\n",
    "utils.mat_2_npy(input_path, save_path)"
   ]
  }
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