Simulation.ipynb

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   "source": [
    "from tkinter import Tk, filedialog   # input the QA.nii.gz data \n",
    "from scipy.ndimage import uniform_filter  # 用于均值滤波\n",
    "from matplotlib.patches import Rectangle  # Draw ROI area\n",
    "import numpy as np\n",
    "import nibabel as nib\n",
    "import re\n",
    "from skimage.filters import threshold_otsu\n",
    "from skimage.morphology import binary_dilation\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "from sklearn.linear_model import LinearRegression   # detrend\n",
    "import math\n",
    "from scipy.stats import norm  # for normal distribution regression of the time course\n",
    "import cv2\n",
    "from reportlab.pdfgen import canvas\n",
    "from PyPDF2 import PdfMerger\n",
    "import os\n",
    "import time\n",
    "\n",
    "%config InlineBackend.figure_format = 'retina'\n",
    "%matplotlib inline  \n",
    "%config InlineBackend.figure_format = 'svg'\n",
    "\n",
    "plt.rcParams['font.sans-serif'] = ['Arial']\n",
    "plt.rcParams['font.size'] = 20\n",
    "plt.style.use(['seaborn-bright', 'seaborn-paper'])"
   ]
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   "cell_type": "code",
   "execution_count": 71,
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      "text/plain": [
       "<Figure size 500x300 with 1 Axes>"
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     "metadata": {},
     "output_type": "display_data"
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   ],
   "source": [
    "rf_duration = 100 # us\n",
    "rf_delay = 200 # us\n",
    "fs = 0.1 # 1/us\n",
    "N_unit = 30\n",
    "\n",
    "N_rf_dur = int(rf_duration*fs)\n",
    "N_rf_delay = int(rf_delay*fs)\n",
    "\n",
    "rf_p05 = [0.5]*N_rf_dur\n",
    "rf_m05 = [-0.5]*N_rf_dur\n",
    "rf_p = [1]*N_rf_dur\n",
    "rf_m = [-1]*N_rf_dur\n",
    "delay = [0]*N_rf_delay\n",
    "\n",
    "mt_unit = rf_p+delay+rf_m+delay\n",
    "\n",
    "#mt_pulse_train = np.array([0]+mt_unit*N_unit)\n",
    "#mt_pulse_train = np.array(mt_unit*N_unit)\n",
    "#mt_pulse_train = np.array(rf_m05+delay+mt_unit*N_unit+rf_p05+delay)\n",
    "mt_pulse_train = np.array([0]+rf_m05+delay+mt_unit*N_unit+rf_p05+delay)\n",
    "time_train = np.arange(len(mt_pulse_train))/fs\n",
    "\n",
    "\n",
    "# Plot\n",
    "fig, ax = plt.subplots(figsize=(5, 3))\n",
    "ax.plot(time_train,mt_pulse_train)\n",
    "ax.set_xlabel(\"$t$ (us)\")\n",
    "ax.set_ylabel(\"Normalized $B_1$\")\n",
    "ax.set_title('MT Pulse-train')\n",
    "\n",
    "plt.tight_layout()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [
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      "text/plain": [
       "<Figure size 500x300 with 1 Axes>"
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     },
     "metadata": {},
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   "source": [
    "# FFT\n",
    "spec = np.abs(np.fft.fft(mt_pulse_train))\n",
    "freq = np.fft.fftfreq(len(spec), 1/fs)*1000000  # Hz\n",
    "\n",
    "spec_shifted = np.fft.fftshift(spec)\n",
    "freq_shifted = np.fft.fftshift(freq)\n",
    "\n",
    "# Plot\n",
    "fig, ax = plt.subplots(figsize=(5, 3))\n",
    "\n",
    "ax.plot(freq_shifted,spec_shifted)\n",
    "ax.set_xlim(-10000, 10000)\n",
    "ax.set_xlabel(\"Off-resonance Frequency (Hz)\")\n",
    "ax.set_ylabel(\"Magnitude\")\n",
    "ax.set_title('Spectrum of MT Pulse-train')\n",
    "\n",
    "plt.tight_layout()\n"
   ]
  }
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