nii2ndarray.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import cv2\n",
    "import SimpleITK as sitk\n",
    "import os\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['0038.nii', '0005.nii', '0048.nii', '0058.nii', '0046.nii']"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "file_names = [name[-8:] for name in os.listdir('../pancreas/images/')]\n",
    "file_names[:5]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "82"
      ]
     },
     "execution_count": 43,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(file_names)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "deleting... Done!\n",
      "****************************patient: 0, start: 89, end:171\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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    {
     "name": "stdout",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 4, start: 59, end:139\n",
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      "--------------------------------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "****************************patient: 5, start: 99, end:169\n",
      "patient: 5, seq: 99, img_index: 472\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 6, start: 90, end:169\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 7, start: 113, end:192\n",
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      "--------------------------------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "****************************patient: 8, start: 85, end:157\n",
      "patient: 8, seq: 85, img_index: 703\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 9, start: 82, end:161\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 10, start: 106, end:212\n",
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      "--------------------------------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "****************************patient: 11, start: 64, end:131\n",
      "patient: 11, seq: 64, img_index: 963\n",
      "patient: 11, seq: 65, img_index: 964\n",
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      "patient: 11, seq: 131, img_index: 1030\n",
      "--------------------------------------------------------\n",
      "****************************patient: 12, start: 118, end:193\n",
      "patient: 12, seq: 118, img_index: 1031\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 13, start: 148, end:199\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 14, start: 78, end:172\n",
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      "patient: 14, seq: 135, img_index: 1216\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 14, seq: 136, img_index: 1217\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 15, start: 71, end:174\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 16, start: 186, end:330\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 16, seq: 302, img_index: 1474\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 17, start: 81, end:151\n",
      "patient: 17, seq: 81, img_index: 1503\n",
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      "patient: 17, seq: 151, img_index: 1573\n",
      "--------------------------------------------------------\n",
      "****************************patient: 18, start: 133, end:210\n",
      "patient: 18, seq: 133, img_index: 1574\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 19, start: 102, end:213\n",
      "patient: 19, seq: 102, img_index: 1652\n",
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      "patient: 19, seq: 159, img_index: 1709\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 19, seq: 160, img_index: 1710\n",
      "patient: 19, seq: 161, img_index: 1711\n",
      "patient: 19, seq: 162, img_index: 1712\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 20, start: 77, end:167\n",
      "patient: 20, seq: 77, img_index: 1764\n",
      "patient: 20, seq: 78, img_index: 1765\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 21, start: 95, end:164\n",
      "patient: 21, seq: 95, img_index: 1855\n",
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      "patient: 21, seq: 141, img_index: 1901\n",
      "patient: 21, seq: 142, img_index: 1902\n",
      "patient: 21, seq: 143, img_index: 1903\n",
      "patient: 21, seq: 144, img_index: 1904\n",
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      "patient: 21, seq: 146, img_index: 1906\n",
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      "patient: 21, seq: 150, img_index: 1910\n",
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      "patient: 21, seq: 152, img_index: 1912\n",
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      "patient: 21, seq: 158, img_index: 1918\n",
      "patient: 21, seq: 159, img_index: 1919\n",
      "patient: 21, seq: 160, img_index: 1920\n",
      "patient: 21, seq: 161, img_index: 1921\n",
      "patient: 21, seq: 162, img_index: 1922\n",
      "patient: 21, seq: 163, img_index: 1923\n",
      "patient: 21, seq: 164, img_index: 1924\n",
      "--------------------------------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "****************************patient: 22, start: 73, end:153\n",
      "patient: 22, seq: 73, img_index: 1925\n",
      "patient: 22, seq: 74, img_index: 1926\n",
      "patient: 22, seq: 75, img_index: 1927\n",
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      "patient: 22, seq: 94, img_index: 1946\n",
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      "patient: 22, seq: 96, img_index: 1948\n",
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      "patient: 22, seq: 98, img_index: 1950\n",
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      "patient: 22, seq: 102, img_index: 1954\n",
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      "patient: 22, seq: 113, img_index: 1965\n",
      "patient: 22, seq: 114, img_index: 1966\n",
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      "patient: 22, seq: 116, img_index: 1968\n",
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      "patient: 22, seq: 118, img_index: 1970\n",
      "patient: 22, seq: 119, img_index: 1971\n",
      "patient: 22, seq: 120, img_index: 1972\n",
      "patient: 22, seq: 121, img_index: 1973\n",
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      "patient: 22, seq: 128, img_index: 1980\n",
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      "patient: 22, seq: 132, img_index: 1984\n",
      "patient: 22, seq: 133, img_index: 1985\n",
      "patient: 22, seq: 134, img_index: 1986\n",
      "patient: 22, seq: 135, img_index: 1987\n",
      "patient: 22, seq: 136, img_index: 1988\n",
      "patient: 22, seq: 137, img_index: 1989\n",
      "patient: 22, seq: 138, img_index: 1990\n",
      "patient: 22, seq: 139, img_index: 1991\n",
      "patient: 22, seq: 140, img_index: 1992\n",
      "patient: 22, seq: 141, img_index: 1993\n",
      "patient: 22, seq: 142, img_index: 1994\n",
      "patient: 22, seq: 143, img_index: 1995\n",
      "patient: 22, seq: 144, img_index: 1996\n",
      "patient: 22, seq: 145, img_index: 1997\n",
      "patient: 22, seq: 146, img_index: 1998\n",
      "patient: 22, seq: 147, img_index: 1999\n",
      "patient: 22, seq: 148, img_index: 2000\n",
      "patient: 22, seq: 149, img_index: 2001\n",
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      "patient: 22, seq: 151, img_index: 2003\n",
      "patient: 22, seq: 152, img_index: 2004\n",
      "patient: 22, seq: 153, img_index: 2005\n",
      "--------------------------------------------------------\n",
      "****************************patient: 23, start: 67, end:150\n",
      "patient: 23, seq: 67, img_index: 2006\n",
      "patient: 23, seq: 68, img_index: 2007\n",
      "patient: 23, seq: 69, img_index: 2008\n",
      "patient: 23, seq: 70, img_index: 2009\n",
      "patient: 23, seq: 71, img_index: 2010\n",
      "patient: 23, seq: 72, img_index: 2011\n",
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      "patient: 23, seq: 74, img_index: 2013\n",
      "patient: 23, seq: 75, img_index: 2014\n",
      "patient: 23, seq: 76, img_index: 2015\n",
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      "patient: 23, seq: 78, img_index: 2017\n",
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      "patient: 23, seq: 80, img_index: 2019\n",
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      "patient: 23, seq: 82, img_index: 2021\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 24, start: 84, end:172\n",
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      "patient: 24, seq: 141, img_index: 2147\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 24, seq: 142, img_index: 2148\n",
      "patient: 24, seq: 143, img_index: 2149\n",
      "patient: 24, seq: 144, img_index: 2150\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 25, start: 56, end:142\n",
      "patient: 25, seq: 56, img_index: 2179\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 26, start: 87, end:181\n",
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      "--------------------------------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "****************************patient: 27, start: 80, end:155\n",
      "patient: 27, seq: 80, img_index: 2361\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 28, start: 97, end:184\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 29, start: 86, end:166\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 29, seq: 143, img_index: 2582\n",
      "patient: 29, seq: 144, img_index: 2583\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 30, start: 62, end:140\n",
      "patient: 30, seq: 62, img_index: 2606\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 31, start: 83, end:182\n",
      "patient: 31, seq: 83, img_index: 2685\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 32, start: 80, end:175\n",
      "patient: 32, seq: 80, img_index: 2785\n",
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      "patient: 32, seq: 136, img_index: 2841\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 32, seq: 137, img_index: 2842\n",
      "patient: 32, seq: 138, img_index: 2843\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 33, start: 132, end:208\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 34, start: 153, end:227\n",
      "patient: 34, seq: 153, img_index: 2958\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 35, start: 112, end:201\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 35, seq: 170, img_index: 3091\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 36, start: 74, end:162\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "****************************patient: 38, start: 89, end:214\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 39, start: 63, end:131\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 40, start: 86, end:167\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 40, seq: 143, img_index: 3570\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 41, start: 96, end:177\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 42, start: 80, end:145\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 43, start: 89, end:171\n",
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      "patient: 43, seq: 147, img_index: 3801\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 43, seq: 148, img_index: 3802\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 44, start: 105, end:186\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 45, start: 85, end:164\n",
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      "--------------------------------------------------------\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 46, seq: 103, img_index: 4042\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n"
     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "****************************patient: 49, start: 49, end:161\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "patient: 51, seq: 120, img_index: 4526\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 54, seq: 140, img_index: 4767\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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     ]
    },
    {
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     "output_type": "stream",
     "text": [
      "patient: 57, seq: 128, img_index: 5009\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "****************************patient: 60, start: 112, end:205\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 62, seq: 167, img_index: 5472\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "****************************patient: 66, start: 62, end:159\n",
      "patient: 66, seq: 62, img_index: 5719\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 68, seq: 141, img_index: 5972\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 70, start: 79, end:146\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 71, start: 60, end:173\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 71, seq: 119, img_index: 6199\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n",
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      "--------------------------------------------------------\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "****************************patient: 74, start: 75, end:163\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 75, start: 60, end:142\n",
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      "--------------------------------------------------------\n",
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 76, seq: 136, img_index: 6673\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 77, start: 145, end:217\n",
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      "--------------------------------------------------------\n",
      "****************************patient: 78, start: 82, end:166\n",
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      "patient: 78, seq: 152, img_index: 6831\n",
      "patient: 78, seq: 153, img_index: 6832\n",
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      "patient: 78, seq: 155, img_index: 6834\n",
      "patient: 78, seq: 156, img_index: 6835\n",
      "patient: 78, seq: 157, img_index: 6836\n",
      "patient: 78, seq: 158, img_index: 6837\n",
      "patient: 78, seq: 159, img_index: 6838\n",
      "patient: 78, seq: 160, img_index: 6839\n",
      "patient: 78, seq: 161, img_index: 6840\n",
      "patient: 78, seq: 162, img_index: 6841\n",
      "patient: 78, seq: 163, img_index: 6842\n",
      "patient: 78, seq: 164, img_index: 6843\n",
      "patient: 78, seq: 165, img_index: 6844\n",
      "patient: 78, seq: 166, img_index: 6845\n",
      "--------------------------------------------------------\n",
      "****************************patient: 79, start: 122, end:186\n",
      "patient: 79, seq: 122, img_index: 6846\n",
      "patient: 79, seq: 123, img_index: 6847\n",
      "patient: 79, seq: 124, img_index: 6848\n",
      "patient: 79, seq: 125, img_index: 6849\n",
      "patient: 79, seq: 126, img_index: 6850\n",
      "patient: 79, seq: 127, img_index: 6851\n",
      "patient: 79, seq: 128, img_index: 6852\n",
      "patient: 79, seq: 129, img_index: 6853\n",
      "patient: 79, seq: 130, img_index: 6854\n",
      "patient: 79, seq: 131, img_index: 6855\n",
      "patient: 79, seq: 132, img_index: 6856\n",
      "patient: 79, seq: 133, img_index: 6857\n",
      "patient: 79, seq: 134, img_index: 6858\n",
      "patient: 79, seq: 135, img_index: 6859\n",
      "patient: 79, seq: 136, img_index: 6860\n",
      "patient: 79, seq: 137, img_index: 6861\n",
      "patient: 79, seq: 138, img_index: 6862\n",
      "patient: 79, seq: 139, img_index: 6863\n",
      "patient: 79, seq: 140, img_index: 6864\n",
      "patient: 79, seq: 141, img_index: 6865\n",
      "patient: 79, seq: 142, img_index: 6866\n",
      "patient: 79, seq: 143, img_index: 6867\n",
      "patient: 79, seq: 144, img_index: 6868\n",
      "patient: 79, seq: 145, img_index: 6869\n",
      "patient: 79, seq: 146, img_index: 6870\n",
      "patient: 79, seq: 147, img_index: 6871\n",
      "patient: 79, seq: 148, img_index: 6872\n",
      "patient: 79, seq: 149, img_index: 6873\n",
      "patient: 79, seq: 150, img_index: 6874\n",
      "patient: 79, seq: 151, img_index: 6875\n",
      "patient: 79, seq: 152, img_index: 6876\n",
      "patient: 79, seq: 153, img_index: 6877\n",
      "patient: 79, seq: 154, img_index: 6878\n",
      "patient: 79, seq: 155, img_index: 6879\n",
      "patient: 79, seq: 156, img_index: 6880\n",
      "patient: 79, seq: 157, img_index: 6881\n",
      "patient: 79, seq: 158, img_index: 6882\n",
      "patient: 79, seq: 159, img_index: 6883\n",
      "patient: 79, seq: 160, img_index: 6884\n",
      "patient: 79, seq: 161, img_index: 6885\n",
      "patient: 79, seq: 162, img_index: 6886\n",
      "patient: 79, seq: 163, img_index: 6887\n",
      "patient: 79, seq: 164, img_index: 6888\n",
      "patient: 79, seq: 165, img_index: 6889\n",
      "patient: 79, seq: 166, img_index: 6890\n",
      "patient: 79, seq: 167, img_index: 6891\n",
      "patient: 79, seq: 168, img_index: 6892\n",
      "patient: 79, seq: 169, img_index: 6893\n",
      "patient: 79, seq: 170, img_index: 6894\n",
      "patient: 79, seq: 171, img_index: 6895\n",
      "patient: 79, seq: 172, img_index: 6896\n",
      "patient: 79, seq: 173, img_index: 6897\n",
      "patient: 79, seq: 174, img_index: 6898\n",
      "patient: 79, seq: 175, img_index: 6899\n",
      "patient: 79, seq: 176, img_index: 6900\n",
      "patient: 79, seq: 177, img_index: 6901\n",
      "patient: 79, seq: 178, img_index: 6902\n",
      "patient: 79, seq: 179, img_index: 6903\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "patient: 79, seq: 180, img_index: 6904\n",
      "patient: 79, seq: 181, img_index: 6905\n",
      "patient: 79, seq: 182, img_index: 6906\n",
      "patient: 79, seq: 183, img_index: 6907\n",
      "patient: 79, seq: 184, img_index: 6908\n",
      "patient: 79, seq: 185, img_index: 6909\n",
      "patient: 79, seq: 186, img_index: 6910\n",
      "--------------------------------------------------------\n",
      "****************************patient: 80, start: 91, end:156\n",
      "patient: 80, seq: 91, img_index: 6911\n",
      "patient: 80, seq: 92, img_index: 6912\n",
      "patient: 80, seq: 93, img_index: 6913\n",
      "patient: 80, seq: 94, img_index: 6914\n",
      "patient: 80, seq: 95, img_index: 6915\n",
      "patient: 80, seq: 96, img_index: 6916\n",
      "patient: 80, seq: 97, img_index: 6917\n",
      "patient: 80, seq: 98, img_index: 6918\n",
      "patient: 80, seq: 99, img_index: 6919\n",
      "patient: 80, seq: 100, img_index: 6920\n",
      "patient: 80, seq: 101, img_index: 6921\n",
      "patient: 80, seq: 102, img_index: 6922\n",
      "patient: 80, seq: 103, img_index: 6923\n",
      "patient: 80, seq: 104, img_index: 6924\n",
      "patient: 80, seq: 105, img_index: 6925\n",
      "patient: 80, seq: 106, img_index: 6926\n",
      "patient: 80, seq: 107, img_index: 6927\n",
      "patient: 80, seq: 108, img_index: 6928\n",
      "patient: 80, seq: 109, img_index: 6929\n",
      "patient: 80, seq: 110, img_index: 6930\n",
      "patient: 80, seq: 111, img_index: 6931\n",
      "patient: 80, seq: 112, img_index: 6932\n",
      "patient: 80, seq: 113, img_index: 6933\n",
      "patient: 80, seq: 114, img_index: 6934\n",
      "patient: 80, seq: 115, img_index: 6935\n",
      "patient: 80, seq: 116, img_index: 6936\n",
      "patient: 80, seq: 117, img_index: 6937\n",
      "patient: 80, seq: 118, img_index: 6938\n",
      "patient: 80, seq: 119, img_index: 6939\n",
      "patient: 80, seq: 120, img_index: 6940\n",
      "patient: 80, seq: 121, img_index: 6941\n",
      "patient: 80, seq: 122, img_index: 6942\n",
      "patient: 80, seq: 123, img_index: 6943\n",
      "patient: 80, seq: 124, img_index: 6944\n",
      "patient: 80, seq: 125, img_index: 6945\n",
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      "patient: 80, seq: 127, img_index: 6947\n",
      "patient: 80, seq: 128, img_index: 6948\n",
      "patient: 80, seq: 129, img_index: 6949\n",
      "patient: 80, seq: 130, img_index: 6950\n",
      "patient: 80, seq: 131, img_index: 6951\n",
      "patient: 80, seq: 132, img_index: 6952\n",
      "patient: 80, seq: 133, img_index: 6953\n",
      "patient: 80, seq: 134, img_index: 6954\n",
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      "patient: 80, seq: 136, img_index: 6956\n",
      "patient: 80, seq: 137, img_index: 6957\n",
      "patient: 80, seq: 138, img_index: 6958\n",
      "patient: 80, seq: 139, img_index: 6959\n",
      "patient: 80, seq: 140, img_index: 6960\n",
      "patient: 80, seq: 141, img_index: 6961\n",
      "patient: 80, seq: 142, img_index: 6962\n",
      "patient: 80, seq: 143, img_index: 6963\n",
      "patient: 80, seq: 144, img_index: 6964\n",
      "patient: 80, seq: 145, img_index: 6965\n",
      "patient: 80, seq: 146, img_index: 6966\n",
      "patient: 80, seq: 147, img_index: 6967\n",
      "patient: 80, seq: 148, img_index: 6968\n",
      "patient: 80, seq: 149, img_index: 6969\n",
      "patient: 80, seq: 150, img_index: 6970\n",
      "patient: 80, seq: 151, img_index: 6971\n",
      "patient: 80, seq: 152, img_index: 6972\n",
      "patient: 80, seq: 153, img_index: 6973\n",
      "patient: 80, seq: 154, img_index: 6974\n",
      "patient: 80, seq: 155, img_index: 6975\n",
      "patient: 80, seq: 156, img_index: 6976\n",
      "--------------------------------------------------------\n",
      "****************************patient: 81, start: 70, end:155\n",
      "patient: 81, seq: 70, img_index: 6977\n",
      "patient: 81, seq: 71, img_index: 6978\n",
      "patient: 81, seq: 72, img_index: 6979\n",
      "patient: 81, seq: 73, img_index: 6980\n",
      "patient: 81, seq: 74, img_index: 6981\n",
      "patient: 81, seq: 75, img_index: 6982\n",
      "patient: 81, seq: 76, img_index: 6983\n",
      "patient: 81, seq: 77, img_index: 6984\n",
      "patient: 81, seq: 78, img_index: 6985\n",
      "patient: 81, seq: 79, img_index: 6986\n",
      "patient: 81, seq: 80, img_index: 6987\n",
      "patient: 81, seq: 81, img_index: 6988\n",
      "patient: 81, seq: 82, img_index: 6989\n",
      "patient: 81, seq: 83, img_index: 6990\n",
      "patient: 81, seq: 84, img_index: 6991\n",
      "patient: 81, seq: 85, img_index: 6992\n",
      "patient: 81, seq: 86, img_index: 6993\n",
      "patient: 81, seq: 87, img_index: 6994\n",
      "patient: 81, seq: 88, img_index: 6995\n",
      "patient: 81, seq: 89, img_index: 6996\n",
      "patient: 81, seq: 90, img_index: 6997\n",
      "patient: 81, seq: 91, img_index: 6998\n",
      "patient: 81, seq: 92, img_index: 6999\n",
      "patient: 81, seq: 93, img_index: 7000\n",
      "patient: 81, seq: 94, img_index: 7001\n",
      "patient: 81, seq: 95, img_index: 7002\n",
      "patient: 81, seq: 96, img_index: 7003\n",
      "patient: 81, seq: 97, img_index: 7004\n",
      "patient: 81, seq: 98, img_index: 7005\n",
      "patient: 81, seq: 99, img_index: 7006\n",
      "patient: 81, seq: 100, img_index: 7007\n",
      "patient: 81, seq: 101, img_index: 7008\n",
      "patient: 81, seq: 102, img_index: 7009\n",
      "patient: 81, seq: 103, img_index: 7010\n",
      "patient: 81, seq: 104, img_index: 7011\n",
      "patient: 81, seq: 105, img_index: 7012\n",
      "patient: 81, seq: 106, img_index: 7013\n",
      "patient: 81, seq: 107, img_index: 7014\n",
      "patient: 81, seq: 108, img_index: 7015\n",
      "patient: 81, seq: 109, img_index: 7016\n",
      "patient: 81, seq: 110, img_index: 7017\n",
      "patient: 81, seq: 111, img_index: 7018\n",
      "patient: 81, seq: 112, img_index: 7019\n",
      "patient: 81, seq: 113, img_index: 7020\n",
      "patient: 81, seq: 114, img_index: 7021\n",
      "patient: 81, seq: 115, img_index: 7022\n",
      "patient: 81, seq: 116, img_index: 7023\n",
      "patient: 81, seq: 117, img_index: 7024\n",
      "patient: 81, seq: 118, img_index: 7025\n",
      "patient: 81, seq: 119, img_index: 7026\n",
      "patient: 81, seq: 120, img_index: 7027\n",
      "patient: 81, seq: 121, img_index: 7028\n",
      "patient: 81, seq: 122, img_index: 7029\n",
      "patient: 81, seq: 123, img_index: 7030\n",
      "patient: 81, seq: 124, img_index: 7031\n",
      "patient: 81, seq: 125, img_index: 7032\n",
      "patient: 81, seq: 126, img_index: 7033\n",
      "patient: 81, seq: 127, img_index: 7034\n",
      "patient: 81, seq: 128, img_index: 7035\n",
      "patient: 81, seq: 129, img_index: 7036\n",
      "patient: 81, seq: 130, img_index: 7037\n",
      "patient: 81, seq: 131, img_index: 7038\n",
      "patient: 81, seq: 132, img_index: 7039\n",
      "patient: 81, seq: 133, img_index: 7040\n",
      "patient: 81, seq: 134, img_index: 7041\n",
      "patient: 81, seq: 135, img_index: 7042\n",
      "patient: 81, seq: 136, img_index: 7043\n",
      "patient: 81, seq: 137, img_index: 7044\n",
      "patient: 81, seq: 138, img_index: 7045\n",
      "patient: 81, seq: 139, img_index: 7046\n",
      "patient: 81, seq: 140, img_index: 7047\n",
      "patient: 81, seq: 141, img_index: 7048\n",
      "patient: 81, seq: 142, img_index: 7049\n",
      "patient: 81, seq: 143, img_index: 7050\n",
      "patient: 81, seq: 144, img_index: 7051\n",
      "patient: 81, seq: 145, img_index: 7052\n",
      "patient: 81, seq: 146, img_index: 7053\n",
      "patient: 81, seq: 147, img_index: 7054\n",
      "patient: 81, seq: 148, img_index: 7055\n",
      "patient: 81, seq: 149, img_index: 7056\n",
      "patient: 81, seq: 150, img_index: 7057\n",
      "patient: 81, seq: 151, img_index: 7058\n",
      "patient: 81, seq: 152, img_index: 7059\n",
      "patient: 81, seq: 153, img_index: 7060\n",
      "patient: 81, seq: 154, img_index: 7061\n",
      "patient: 81, seq: 155, img_index: 7062\n",
      "--------------------------------------------------------\n"
     ]
    }
   ],
   "source": [
    "index = 0\n",
    "count = 0\n",
    "zero_index = 100\n",
    "\n",
    "pancreas_dataset_path = '../pancreas/pancreas_dataset'\n",
    "if os.path.exists(pancreas_dataset_path):\n",
    "    import shutil\n",
    "    shutil.rmtree(pancreas_dataset_path, ignore_errors=True)\n",
    "    print(\"deleting... Done!\")\n",
    "    \n",
    "os.mkdir(pancreas_dataset_path)\n",
    "os.mkdir(os.path.join(pancreas_dataset_path,'imgs'))\n",
    "os.mkdir(os.path.join(pancreas_dataset_path,'masks'))\n",
    "\n",
    "#file_names = file_names[:5]\n",
    "for i,name in enumerate(file_names):\n",
    "    cts = sitk.ReadImage(os.path.join('../pancreas/images/','PANCREAS_'+name))\n",
    "    labels = sitk.ReadImage(os.path.join('../pancreas/labels/','label'+name))\n",
    "    \n",
    "    cts_array = sitk.GetArrayFromImage(cts)\n",
    "    labels_array = sitk.GetArrayFromImage(labels)\n",
    "    \n",
    "    start = -1\n",
    "    end = -1\n",
    "    for j in range(cts_array.shape[0]):\n",
    "        img = cts_array[j]\n",
    "        mask = labels_array[j]\n",
    "        if start == -1 and mask.sum() != 0:\n",
    "            start=j\n",
    "            continue\n",
    "        if start != -1 and mask.sum() != 0:\n",
    "            end = j\n",
    "        \n",
    "    print('****************************patient: %d, start: %d, end:%d'%(i,start,end))\n",
    "#     start = start - 20\n",
    "#     end = end + 30\n",
    "    '''\n",
    "        没必要将那些全是背景的图片加入数据集\n",
    "        因为单单是含有pancreas的图片中，背景就足够多了！\n",
    "    '''\n",
    "    for j in range(cts_array.shape[0]):\n",
    "        #print(cts_array.shape)\n",
    "        img = cts_array[j]\n",
    "        mask = labels_array[j]\n",
    "        if j < start or j > end: \n",
    "            #print(j) 根据需要选择是否打印idx\n",
    "            continue\n",
    "            \n",
    "        \n",
    "        \n",
    "        mask = mask*255\n",
    "        \n",
    "        print(\"patient: %d, seq: %d, img_index: %d\" %(i,j,index))\n",
    "        cv2.imwrite(os.path.join(pancreas_dataset_path,'imgs',str(index)+'.jpg'),img)\n",
    "        cv2.imwrite(os.path.join(pancreas_dataset_path,'masks',str(index)+'_mask.jpg'),mask)\n",
    "        #print(img.shape)\n",
    "        #print(mask.sum(),mask.min(),mask.max(),mask.dtype)\n",
    "        #plt.imshow(img,cmap='gray')\n",
    "        #plt.imshow(mask,cmap='gray')\n",
    "        #plt.colorbar()\n",
    "        \n",
    "        index += 1\n",
    "\n",
    "    print('--------------------------------------------------------')"
   ]
  }
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