Quick_Histogram_Plot.ipynb

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   "source": [
    "import os\n",
    "import h5py\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "import matplotlib as mpl\n",
    "import pandas as pd\n",
    "from bokeh.plotting import figure, show, output_file\n",
    "from bokeh.io import output_notebook, push_notebook\n",
    "from bokeh.models import HoverTool, CustomJS, Slider, ColumnDataSource\n",
    "from bokeh.layouts import row, column, gridplot\n",
    "import trackpy as tp\n",
    "from scipy.ndimage.filters import gaussian_filter\n",
    "from scipy.ndimage import label\n",
    "from scipy.optimize import curve_fit\n",
    "output_notebook()"
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   "source": [
    "file_dir = 'C:\\\\Users\\\\aquiles\\\\Data\\\\run10\\\\tracking\\\\20-06-18\\\\run4'\n",
    "filename = 'particleDiameters4.csv'\n",
    "data = pd.read_csv(os.path.join(file_dir, filename), header=None)"
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   "source": [
    "p1 = figure(title=\"Histogram particle diameter\", background_fill_color=\"#E8DDCB\")\n",
    "hist, edges = np.histogram(data[1], density=True, bins=50)\n",
    "bin_centres = (edges[:-1] + edges[1:])/2\n",
    "def gauss(x, *p):\n",
    "    A, mu, sigma = p\n",
    "    return A*np.exp(-(x-mu)**2/(2.*sigma**2))\n",
    "p0 = [0.035, 20., 10.]\n",
    "coeff, var_matrix = curve_fit(gauss, bin_centres, hist, p0=p0)\n",
    "x_hist = np.linspace(0, 160, 500)\n",
    "hist_fit = gauss(x_hist, *coeff)\n",
    "\n",
    "p1.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:],\n",
    "        fill_color=\"#036564\", line_color=\"#033649\")\n",
    "p1.line(x_hist, hist_fit, line_color='#ff8821', line_width=5)\n",
    "p1.xaxis.axis_label = 'Particle diameter (nm)'\n",
    "p1.yaxis.axis_label = 'Frequency'\n",
    "p1.xaxis.axis_label_text_font_size = '14pt'\n",
    "p1.yaxis.axis_label_text_font_size = '14pt'\n",
    "p1.xaxis.major_label_text_font_size = '12pt'\n",
    "p1.yaxis.major_label_text_font_size = '12pt'\n",
    "show(p1)"
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