OSEM算法实现——Jupyter笔记（1）

最新推荐文章于 2024-09-18 15:38:19 发布
hxq_晴天
最新推荐文章于 2024-09-18 15:38:19 发布
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分类专栏： PET图像重建文章标签： python
本文链接：https://blog.csdn.net/weixin_51870331/article/details/142335150
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  "language_info": {
   "name": "python",
   "codemirror_mode": {
    "name": "ipython",
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 },
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import cv2\n",
    "import matplotlib.pyplot as plt # plt 用于显示图片\n",
    "import matplotlib.image as mpimg # mpimg 用于读取图片\n",
    "import pandas as pd\n",
    "from tqdm import tqdm\n",
    "from scipy.fftpack import fft,ifft\n",
    "import PIL\n",
    "import matlab\n",
    "import matlab.engine\n",
    "import math\n",
    "from tqdm import tqdm\n",
    "#engine = matlab.engine.start_matlab() # Start MATLAB process"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "imgData = np.fromfile('whole_bone.raw', dtype=\"float32\")\n",
    "#imgData = imgData.reshape(width, height, channels)\n",
    "df=pd.read_excel('angle_r.xlsx')\n",
    "angle_r = df.values\n",
    "a_r = np.zeros((2,60))\n",
    "a_r[0] = angle_r[[0,2,4,6],:].reshape(1,60)\n",
    "a_r[1] = angle_r[[1,3,5,7],:].reshape(1,60)\n",
    "np.max(a_r[1])\n",
    "pi_d = 4.0625#mm\n",
    "fir = np.zeros((60,128))\n",
    "base = 128*128\n",
    "# for i in range(0,60):\n",
    "#     ip = i*base\n",
    "#     ip1 = ip +128\n",
    "#     fir[i] = imgData[ip:ip1]\n",
    "# plt.imshow(fir)\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "outputs": [],
   "source": [
    "### OSEM FOR SPECT"
   ]
  },
  {
   "cell_type": "code",
   "metadata": {},
   "outputs": [],
   "source": [
    "#creat transform matrix\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": "100%|██████████| 60/60 [03:54<00:00,  3.83s/it]\n"
    }
   ],
   "source": [
    "pro = imgData.reshape(60,128,128)\n",
    "end = 128*128\n",
    "im1 = imgData[0:end]\n",
    "p1 = pro[:,70,:]\n",
    "#plt.imshow(p1,cmap=\"gray\")\n",
    "fft_p = np.zeros((60,128))\n",
    "#engine.imshow(engine.iradon(matlab.double(list_p),0:59),[])\n",
    "def return_x(a,c):\n",
    "    x_m = y_m=np.linspace(-64,64,129,dtype=\"float32\")\n",
    "    y_i = a*x_m+c\n",
    "    x_i = (y_m-c)/a\n",
    "    x_i = x_i[(x_i>=-64) & (x_i<=64)]\n",
    "    y_i = y_i[(y_i>=-64) & (y_i<=64)]\n",
    "    return x_i,y_i\n",
    "\n",
    "\n",
    "def get_spect_tran_m(theta):\n",
    "    #rotate detector theta from initial ang\n",
    "    c = np.zeros((end,128),dtype=\"float32\")\n",
    "    for i in np.linspace(-63.5,63.5,128):\n",
    "        ang = math.pi-theta*math.pi/180\n",
    "        a = math.tan(ang)\n",
    "        b = i/math.cos(theta*math.pi/180+1e-6)\n",
    "        c_y = int(i+63.5)\n",
    "        if a<=0:\n",
    "            for x in range(-63,65):\n",
    "                for y in range(-63,65):\n",
    "                    x2 = x-1\n",
    "                    y2 = y-1\n",
    "                    # if (i==0.5) & (theta==6) & (x==1) & (y==2):\n",
    "                        \n",
    "                    #     print(a)\n",
    "                    #     print(b)\n",
    "                    #     print(a*x+b-y)\n",
    "                    #     print(a*x2+b-y2)\n",
    "                    if (a*x+b-y)*(a*x2+b-y2) <=0:\n",
    "                        pos = (x+63)*128+y+63\n",
    "                        c[pos,c_y] = 1\n",
    "        else:\n",
    "            for x in range(-63,65):\n",
    "                for y in range(-63,65):\n",
    "                    x1 = x-1\n",
    "                    y1 = y\n",
    "                    x2 = x\n",
    "                    y2 = y-2\n",
    "                    if (a*x1+b-y1)*(a*x2+b-y2) <=0:\n",
    "                        pos = (x+63)*128+y+63\n",
    "                        c[pos,c_y] = 1\n",
    "\n",
    "\n",
    "\n",
    "    return c\n",
    "theta_range = np.arange(0,60,dtype=\"float32\")*6\n",
    "bias = 1e-6\n",
    "theta_range[np.linspace(0,45,4,dtype = \"int\")] = theta_range[np.linspace(0,45,4,dtype=\"int\")] + bias\n",
    "dic_c = {}\n",
    "i = 0\n",
    "\n",
    "for n in tqdm(range(0,60)):\n",
    "    num = str(i)\n",
    "    dic_c[num] = get_spect_tran_m(theta_range[i])\n",
    "    i = i + 1\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": "(16384, 7680)\n"
    }
   ],
   "source": [
    "total_c = np.zeros((128*128,128*60),dtype=\"float32\")\n",
    "total_p = np.zeros((1,128*60),dtype=\"float32\").squeeze(0)\n",
    "for i in range(0,59):\n",
    "    range1 = 128*i\n",
    "    range2 = 128*(i+1) \n",
    "    total_c[:,range1:range2] = dic_c[str(i)]\n",
    "    total_p[range1:range2] = p1[i]\n",
    "\n",
    "print(total_c.shape)\n",
    "#np.savetxt(\"total_c.csv\", total_c, delimiter=\",\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-8-e21345ae4e5e>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[1;32m----> 1\u001b[1;33m \u001b[0mb\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mloadtxt\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;34m\"total_c.csv\"\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mdelimiter\u001b[0m\u001b[1;33m=\u001b[0m\u001b[1;34m\",\"\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m      2\u001b[0m \u001b[0mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mmax\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mb\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mreshape\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m-\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m  \u001b[1;31m#打印b数组中的最大值\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      3\u001b[0m \u001b[0mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mmin\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mb\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mreshape\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m-\u001b[0m\u001b[1;36m1\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m  \u001b[1;31m#打印b数组中的最小值\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mD:\\anacondaspace\\lib\\site-packages\\numpy\\lib\\npyio.py\u001b[0m in \u001b[0;36mloadtxt\u001b[1;34m(fname, dtype, comments, delimiter, converters, skiprows, usecols, unpack, ndmin, encoding, max_rows)\u001b[0m\n\u001b[0;32m   1132\u001b[0m         \u001b[1;31m# converting the data\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1133\u001b[0m         \u001b[0mX\u001b[0m \u001b[1;33m=\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1134\u001b[1;33m         \u001b[1;32mfor\u001b[0m \u001b[0mx\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mread_data\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0m_loadtxt_chunksize\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1135\u001b[0m             \u001b[1;32mif\u001b[0m \u001b[0mX\u001b[0m \u001b[1;32mis\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1136\u001b[0m                 \u001b[0mX\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0marray\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mx\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mdtype\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;32mD:\\anacondaspace\\lib\\site-packages\\numpy\\lib\\npyio.py\u001b[0m in \u001b[0;36mread_data\u001b[1;34m(chunk_size)\u001b[0m\n\u001b[0;32m   1047\u001b[0m         \u001b[0mline_iter\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mitertools\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mchain\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mfirst_line\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mfh\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1048\u001b[0m         \u001b[0mline_iter\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mitertools\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mislice\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mline_iter\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mmax_rows\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m-> 1049\u001b[1;33m         \u001b[1;32mfor\u001b[0m \u001b[0mi\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mline\u001b[0m \u001b[1;32min\u001b[0m \u001b[0menumerate\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mline_iter\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m   1050\u001b[0m             \u001b[0mvals\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0msplit_line\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mline\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m   1051\u001b[0m             \u001b[1;32mif\u001b[0m \u001b[0mlen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mvals\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;33m==\u001b[0m \u001b[1;36m0\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[1;31mKeyboardInterrupt\u001b[0m: "
     ]
    }
   ],
   "source": [
    "#b = np.loadtxt(\"total_c.csv\", delimiter=\",\")\n",
    "print(max(b.reshape(-1)))  #打印b数组中的最大值\n",
    "print(min(b.reshape(-1)))  #打印b数组中的最小值"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 166,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": "[1.00000000e-06 6.00000000e+00 1.20000000e+01 1.80000000e+01\n 2.40000000e+01 3.00000000e+01 3.60000000e+01 4.20000000e+01\n 4.80000000e+01 5.40000000e+01 6.00000000e+01 6.60000000e+01\n 7.20000000e+01 7.80000000e+01 8.40000000e+01 9.00000010e+01\n 9.60000000e+01 1.02000000e+02 1.08000000e+02 1.14000000e+02\n 1.20000000e+02 1.26000000e+02 1.32000000e+02 1.38000000e+02\n 1.44000000e+02 1.50000000e+02 1.56000000e+02 1.62000000e+02\n 1.68000000e+02 1.74000000e+02 1.80000001e+02 1.86000000e+02\n 1.92000000e+02 1.98000000e+02 2.04000000e+02 2.10000000e+02\n 2.16000000e+02 2.22000000e+02 2.28000000e+02 2.34000000e+02\n 2.40000000e+02 2.46000000e+02 2.52000000e+02 2.58000000e+02\n 2.64000000e+02 2.70000001e+02 2.76000000e+02 2.82000000e+02\n 2.88000000e+02 2.94000000e+02 3.00000000e+02 3.06000000e+02\n 3.12000000e+02 3.18000000e+02 3.24000000e+02 3.30000000e+02\n 3.36000000e+02 3.42000000e+02 3.48000000e+02 3.54000000e+02]\n"
    }
   ],
   "source": [
    "print(theta_range)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": "0.0\nTrue\n"
    }
   ],
   "source": [
    "m = dic_c[\"1\"]\n",
    "print(m[8257,64])\n",
    "mm = theta_range[1]\n",
    "print(mm==6)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": "100%|██████████| 10/10 [00:19<00:00,  1.98s/it]\n"
    },
    {
     "data": {
      "text/plain": "<matplotlib.image.AxesImage at 0x21b625733c8>"
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
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      "text/plain": "<Figure size 432x288 with 1 Axes>"
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "p1 = pro[:,20,:]\n",
    "#plt.imshow(p1,cmap=\"gray\")\n",
    "it = 10\n",
    "f0 = np.ones((1,end),dtype=\"float64\").squeeze(0)\n",
    "def iter_osem_spect(p,f,i):\n",
    "    num = str(i)\n",
    "    c = dic_c[num]\n",
    "    pj = p/(f.dot(c)+bias)\n",
    "    temp =c.dot(pj)*(f/np.sum(c+bias,axis=1))\n",
    "    return temp\n",
    "\n",
    "\n",
    "\n",
    "for i in tqdm(range(0,it)):\n",
    "    for j in range(0,59):\n",
    "        temp = iter_osem_spect(p1[j],f0,j)\n",
    "        f0 = temp\n",
    "plt.imshow(f0.reshape(128,128))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": "(7680,)\n(7680,)\n"
    }
   ],
   "source": [
    "p1 = pro[:,1,:]\n",
    "total_c = np.zeros((128*128,128*60),dtype=\"float64\")\n",
    "total_p = np.zeros((1,128*60),dtype=\"float64\").squeeze(0)\n",
    "for i in range(0,59):\n",
    "    range1 = 128*i\n",
    "    range2 = 128*(i+1) \n",
    "    total_c[:,range1:range2] = dic_c[str(i)]\n",
    "    total_p[range1:range2] = p1[i]\n",
    "\n",
    "print(total_p.shape)\n",
    "a = p1.reshape(128*60,1).squeeze(1)\n",
    "print(a.shape)\n",
    "\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": "(7680,)\n"
    }
   ],
   "source": [
    "pro_splice = pro[:,2,:]\n",
    "total_c = pro_splice.reshape(128*60,1).squeeze(1)\n",
    "print(total_c.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": "  5%|▌         | 5/100 [00:09<03:04,  1.94s/it]"
    },
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[1;32m<ipython-input-24-7dd28f9710c4>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m()\u001b[0m\n\u001b[0;32m      4\u001b[0m \u001b[1;32mfrom\u001b[0m \u001b[0mtqdm\u001b[0m \u001b[1;32mimport\u001b[0m \u001b[0mtqdm\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      5\u001b[0m \u001b[1;32mfor\u001b[0m \u001b[0mi\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mtqdm\u001b[0m\u001b[1;33m(\u001b[0m