Histogram_for_brochure.ipynb

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     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "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()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "ename": "FileNotFoundError",
     "evalue": "File b'C:\\\\Users\\\\aquiles\\\\Data\\\\run10\\\\tracking\\\\20-06-18\\\\run4/particleDiameters4.csv' does not exist",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mFileNotFoundError\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-2-4ff0319a5197>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0mfile_dir\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'C:\\\\Users\\\\aquiles\\\\Data\\\\run10\\\\tracking\\\\20-06-18\\\\run4'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0mfilename\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'particleDiameters4.csv'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread_csv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfile_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfilename\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mheader\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m~/.virtualenvs/UTrack/lib/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36mparser_f\u001b[0;34m(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, escapechar, comment, encoding, dialect, tupleize_cols, error_bad_lines, warn_bad_lines, skipfooter, doublequote, delim_whitespace, low_memory, memory_map, float_precision)\u001b[0m\n\u001b[1;32m    676\u001b[0m                     skip_blank_lines=skip_blank_lines)\n\u001b[1;32m    677\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 678\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0m_read\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilepath_or_buffer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    679\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    680\u001b[0m     \u001b[0mparser_f\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__name__\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.virtualenvs/UTrack/lib/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36m_read\u001b[0;34m(filepath_or_buffer, kwds)\u001b[0m\n\u001b[1;32m    438\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    439\u001b[0m     \u001b[0;31m# Create the parser.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 440\u001b[0;31m     \u001b[0mparser\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mTextFileReader\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilepath_or_buffer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    441\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    442\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mchunksize\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0miterator\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.virtualenvs/UTrack/lib/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, f, engine, **kwds)\u001b[0m\n\u001b[1;32m    785\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moptions\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'has_index_names'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mkwds\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'has_index_names'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    786\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 787\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_make_engine\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mengine\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    788\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    789\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mclose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.virtualenvs/UTrack/lib/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36m_make_engine\u001b[0;34m(self, engine)\u001b[0m\n\u001b[1;32m   1012\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m_make_engine\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mengine\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'c'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1013\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mengine\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'c'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1014\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_engine\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCParserWrapper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0moptions\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1015\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1016\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mengine\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'python'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/.virtualenvs/UTrack/lib/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, src, **kwds)\u001b[0m\n\u001b[1;32m   1706\u001b[0m         \u001b[0mkwds\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'usecols'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0musecols\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1707\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1708\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_reader\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mparsers\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mTextReader\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msrc\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1709\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1710\u001b[0m         \u001b[0mpassed_names\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnames\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader.__cinit__\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._setup_parser_source\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;31mFileNotFoundError\u001b[0m: File b'C:\\\\Users\\\\aquiles\\\\Data\\\\run10\\\\tracking\\\\20-06-18\\\\run4/particleDiameters4.csv' does not exist"
     ]
    }
   ],
   "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)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'data' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-3-e3dc6d1e828d>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0mp1\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfigure\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtitle\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"Histogram particle diameter\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbackground_fill_color\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"#E8DDCB\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mhist\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0medges\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhistogram\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdensity\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbins\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m50\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      3\u001b[0m \u001b[0mbin_centres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0medges\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0medges\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m/\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mgauss\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0mp\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m     \u001b[0mA\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmu\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msigma\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mNameError\u001b[0m: name 'data' is not defined"
     ]
    }
   ],
   "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)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "data = np.random.normal(loc=30,scale=5,size=300)\n",
    "data2 = np.random.normal(loc=45,scale=5, size=200)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
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\",\"dtype\":\"float64\",\"shape\":[500]}},\"selected\":{\"id\":\"01f3221b-3246-40cc-8aa8-1d93a74d28dd\",\"type\":\"Selection\"},\"selection_policy\":{\"id\":\"1d529537-0942-4b63-942f-95bed479a537\",\"type\":\"UnionRenderers\"}},\"id\":\"e2f1a64b-c19c-4cda-be32-983846f30368\",\"type\":\"ColumnDataSource\"},{\"attributes\":{},\"id\":\"a5bd500f-2a3d-44ba-9a6c-624483b759cc\",\"type\":\"UnionRenderers\"},{\"attributes\":{\"dimension\":1,\"plot\":{\"id\":\"af17990c-cf4a-47a1-be5f-d1e9e3701eaa\",\"subtype\":\"Figure\",\"type\":\"Plot\"},\"ticker\":{\"id\":\"5291a79a-2428-4d54-a71c-5d81acf01441\",\"type\":\"BasicTicker\"}},\"id\":\"bf4c457e-db2e-4a15-8fe4-50c3a9f99ea3\",\"type\":\"Grid\"},{\"attributes\":{\"data_source\":{\"id\":\"30d866b7-b786-4989-b39f-fd5efd0369ec\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"c223944d-8a8d-46a1-b1ab-751077db297a\",\"type\":\"Quad\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"9e2b6963-89a7-491c-9710-a7da0b7cf4e6\",\"type\":\"Quad\"},\"selection_glyph\":null,\"view\":{\"id\":\"df3ae6e6-f0d4-4a09-a525-e25dba0d3a4a\",\"type\":\"CDSView\"}},\"id\":\"ce791739-ef8a-4a2a-96e3-77ed91864597\",\"type\":\"GlyphRenderer\"},{\"attributes\":{},\"id\":\"d20044c1-36cf-4ce5-ba72-006888544cef\",\"type\":\"Selection\"},{\"attributes\":{},\"id\":\"ef5e7ed7-8360-47f3-9c57-e3164699daf9\",\"type\":\"BasicTicker\"},{\"attributes\":{},\"id\":\"56b6a97f-c56d-417c-998e-5d60f0ae14c7\",\"type\":\"UnionRenderers\"},{\"attributes\":{\"plot\":{\"id\":\"af17990c-cf4a-47a1-be5f-d1e9e3701eaa\",\"subtype\":\"Figure\",\"type\":\"Plot\"},\"ticker\":{\"id\":\"ef5e7ed7-8360-47f3-9c57-e3164699daf9\",\"type\":\"BasicTicker\"}},\"id\":\"d93284a8-756a-4d6e-b55f-48ccc6c5eee7\",\"type\":\"Grid\"},{\"attributes\":{},\"id\":\"01f3221b-3246-40cc-8aa8-1d93a74d28dd\",\"type\":\"Selection\"},{\"attributes\":{},\"id\":\"e84f35df-c8b1-4c33-83f7-6ef8957d5ca5\",\"type\":\"LinearScale\"},{\"attributes\":{},\"id\":\"1d529537-0942-4b63-942f-95bed479a537\",\"type\":\"UnionRenderers\"},{\"attributes\":{\"callback\":null},\"id\":\"1fba7558-6114-4ba0-819a-3bafa668922d\",\"type\":\"DataRange1d\"},{\"attributes\":{},\"id\":\"7a1d0cb8-58d3-470b-8b3d-86e427c750c9\",\"type\":\"Selection\"},{\"attributes\":{\"axis_label\":\"Particle Count\",\"axis_label_text_font_size\":{\"value\":\"18pt\"},\"formatter\":{\"id\":\"1668f0f8-eaf4-46c8-b7b0-664a34d2e52c\",\"type\":\"BasicTickFormatter\"},\"major_label_text_font_size\":{\"value\":\"16pt\"},\"plot\":{\"id\":\"af17990c-cf4a-47a1-be5f-d1e9e3701eaa\",\"subtype\":\"Figure\",\"type\":\"Plot\"},\"ticker\":{\"id\":\"5291a79a-2428-4d54-a71c-5d81acf01441\",\"type\":\"BasicTicker\"}},\"id\":\"c8a5168c-b05d-4e54-a562-674434c66855\",\"type\":\"LinearAxis\"},{\"attributes\":{},\"id\":\"06778671-d662-42ec-b574-8f3e4d15eac1\",\"type\":\"UnionRenderers\"},{\"attributes\":{},\"id\":\"4775fe31-3a6c-4c49-987d-d1c8ada13759\",\"type\":\"LinearScale\"},{\"attributes\":{\"bottom\":{\"value\":0},\"fill_alpha\":{\"value\":0.1},\"fill_color\":{\"value\":\"#1f77b4\"},\"left\":{\"field\":\"left\"},\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1f77b4\"},\"right\":{\"field\":\"right\"},\"top\":{\"field\":\"top\"}},\"id\":\"9e2b6963-89a7-491c-9710-a7da0b7cf4e6\",\"type\":\"Quad\"},{\"attributes\":{\"callback\":null},\"id\":\"e7e4e671-2479-4a14-a291-0f3330ffc4f6\",\"type\":\"DataRange1d\"},{\"attributes\":{},\"id\":\"5291a79a-2428-4d54-a71c-5d81acf01441\",\"type\":\"BasicTicker\"},{\"attributes\":{},\"id\":\"616fe8d4-59c1-4e70-b891-77720474f96b\",\"type\":\"PanTool\"}],\"root_ids\":[\"af17990c-cf4a-47a1-be5f-d1e9e3701eaa\"]},\"title\":\"Bokeh Application\",\"version\":\"0.13.0\"}};\n",
       "  var render_items = [{\"docid\":\"943e8e02-c2d2-4b8c-b944-3c44d3a07ec9\",\"roots\":{\"af17990c-cf4a-47a1-be5f-d1e9e3701eaa\":\"52ebabe6-0e73-426f-8c34-508368986ea5\"}}];\n",
       "  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n",
       "\n",
       "  }\n",
       "  if (root.Bokeh !== undefined) {\n",
       "    embed_document(root);\n",
       "  } else {\n",
       "    var attempts = 0;\n",
       "    var timer = setInterval(function(root) {\n",
       "      if (root.Bokeh !== undefined) {\n",
       "        embed_document(root);\n",
       "        clearInterval(timer);\n",
       "      }\n",
       "      attempts++;\n",
       "      if (attempts > 100) {\n",
       "        console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\")\n",
       "        clearInterval(timer);\n",
       "      }\n",
       "    }, 10, root)\n",
       "  }\n",
       "})(window);"
      ],
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "af17990c-cf4a-47a1-be5f-d1e9e3701eaa"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "p1 = figure(title=\"Histogram particle diameter\", background_fill_color=\"#E8DDCB\")\n",
    "hist, edges = np.histogram(data, density=True, bins=20)\n",
    "hist2, edges2 = np.histogram(data2, density=True, bins=20)\n",
    "bin_centres = (edges[:-1] + edges[1:])/2\n",
    "bin_centres2 = (edges2[:-1]+edges2[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*300, p0=p0)\n",
    "coeff2, var_matrix2 = curve_fit(gauss, bin_centres2, hist2*200, p0=p0)\n",
    "x_hist = np.linspace(10, 60, 500)\n",
    "hist_fit = gauss(x_hist, *coeff)\n",
    "hist_fit2 = gauss(x_hist, *coeff2)\n",
    "\n",
    "p1.quad(top=hist*300, bottom=0, left=edges[:-1], right=edges[1:],\n",
    "        fill_color=\"#036564\", line_color=\"#033649\")\n",
    "p1.quad(top=hist2*200, bottom=0, left=edges2[:-1], right=edges2[1:],\n",
    "        fill_color=\"#032364\", line_color=\"#033649\")\n",
    "p1.line(x_hist, hist_fit, line_color='#ff8821', line_width=5)\n",
    "p1.line(x_hist, hist_fit2, line_color='#ffaa21', line_width=5)\n",
    "p1.xaxis.axis_label = 'Particle diameter (nm)'\n",
    "p1.yaxis.axis_label = 'Particle Count'\n",
    "p1.xaxis.axis_label_text_font_size = '18pt'\n",
    "p1.yaxis.axis_label_text_font_size = '18pt'\n",
    "p1.xaxis.major_label_text_font_size = '16pt'\n",
    "p1.yaxis.major_label_text_font_size = '16pt'\n",
    "p1.title.text_font_size = '22pt'\n",
    "show(p1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 72,
   "metadata": {},
   "outputs": [],
   "source": [
    "ep_1 = np.random.normal(loc=-3, scale=0.5, size=200)\n",
    "ep_2 = np.random.normal(loc=-1.5, scale=0.5, size=200)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 99,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "\n",
       "\n",
       "\n",
       "\n",
       "\n",
       "  <div class=\"bk-root\" id=\"59a39fdd-9063-4b3d-9296-79b6069cca15\"></div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": [
       "(function(root) {\n",
       "  function embed_document(root) {\n",
       "    \n",
       "  var docs_json = {\"242fb296-e8c5-4e67-96b0-25f6f42a0ca2\":{\"roots\":{\"references\":[{\"attributes\":{},\"id\":\"1f56a3d8-78cc-49eb-a6e3-0aad937bd1e5\",\"type\":\"BasicTicker\"},{\"attributes\":{\"axis_label\":\"Electrophoretic Mobility (\\u03bcm 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\":\"4176ff4b-be84-4e27-ba81-cb8431c9b66d\",\"type\":\"SaveTool\"},{\"id\":\"5d974625-791c-4def-b5f8-146bd0c6ad1b\",\"type\":\"ResetTool\"},{\"id\":\"8f58eb45-0e63-4059-8897-496897d60dc3\",\"type\":\"HelpTool\"}]},\"id\":\"8ed4a182-41da-408f-8240-2fcd3cd86fce\",\"type\":\"Toolbar\"},{\"attributes\":{},\"id\":\"0731e0c7-6a6a-4d38-adc4-5e0ebfece8b1\",\"type\":\"PanTool\"},{\"attributes\":{\"bottom\":{\"value\":0},\"fill_alpha\":{\"value\":0.1},\"fill_color\":{\"value\":\"#1f77b4\"},\"left\":{\"field\":\"left\"},\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1f77b4\"},\"right\":{\"field\":\"right\"},\"top\":{\"field\":\"top\"}},\"id\":\"aa2e29b8-efe1-4008-bc62-52b531f3c8bf\",\"type\":\"Quad\"},{\"attributes\":{\"overlay\":{\"id\":\"1cdc7933-3a5e-4e3f-9c76-66153aba5ca1\",\"type\":\"BoxAnnotation\"}},\"id\":\"250d6263-2110-4d79-9642-1ae1bf2177f3\",\"type\":\"BoxZoomTool\"},{\"attributes\":{\"data_source\":{\"id\":\"0f594aaa-f8c9-4a64-a17e-c7dd1dc06df4\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"19467b4d-1322-4a82-9ee5-758ed06e6ec3\",\"type\":\"Quad\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"9902f97c-cd6d-4903-b98a-96240d2c309a\",\"type\":\"Quad\"},\"selection_glyph\":null,\"view\":{\"id\":\"fac345ba-e446-4e61-bac1-905d0b260d86\",\"type\":\"CDSView\"}},\"id\":\"1503775a-8548-4fc4-abfc-988cce9f4e5b\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"bottom\":{\"value\":0},\"fill_alpha\":{\"value\":0.1},\"fill_color\":{\"value\":\"#1f77b4\"},\"left\":{\"field\":\"left\"},\"line_alpha\":{\"value\":0.1},\"line_color\":{\"value\":\"#1f77b4\"},\"right\":{\"field\":\"right\"},\"top\":{\"field\":\"top\"}},\"id\":\"9902f97c-cd6d-4903-b98a-96240d2c309a\",\"type\":\"Quad\"},{\"attributes\":{},\"id\":\"db2fc98b-ff3a-4c5d-b7da-f1fcd1376b90\",\"type\":\"BasicTicker\"},{\"attributes\":{},\"id\":\"e466edc0-78b2-4d6a-b603-5933a766ba62\",\"type\":\"LinearScale\"},{\"attributes\":{\"source\":{\"id\":\"361d9dd3-9b3e-41cb-b3ee-078e9ee257c8\",\"type\":\"ColumnDataSource\"}},\"id\":\"79d13837-7ab1-4935-b857-b5360449e51f\",\"type\":\"CDSView\"},{\"attributes\":{},\"id\":\"a538c485-1a63-4274-8bc3-c2b647ac0712\",\"type\":\"LinearScale\"},{\"attributes\":{\"data_source\":{\"id\":\"361d9dd3-9b3e-41cb-b3ee-078e9ee257c8\",\"type\":\"ColumnDataSource\"},\"glyph\":{\"id\":\"f941903b-4cb1-4639-802e-ec80028e67df\",\"type\":\"Quad\"},\"hover_glyph\":null,\"muted_glyph\":null,\"nonselection_glyph\":{\"id\":\"aa2e29b8-efe1-4008-bc62-52b531f3c8bf\",\"type\":\"Quad\"},\"selection_glyph\":null,\"view\":{\"id\":\"79d13837-7ab1-4935-b857-b5360449e51f\",\"type\":\"CDSView\"}},\"id\":\"fb358ce5-dbc4-4e6a-906d-309d390202fe\",\"type\":\"GlyphRenderer\"},{\"attributes\":{\"plot\":null,\"text\":\"Electrophoretic 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Count\",\"axis_label_text_font_size\":{\"value\":\"18pt\"},\"formatter\":{\"id\":\"f390a090-1b0c-4b1c-8621-5adcc0f3ee9f\",\"type\":\"BasicTickFormatter\"},\"major_label_text_font_size\":{\"value\":\"16pt\"},\"plot\":{\"id\":\"d0a98231-cbac-42d5-b00b-4d3c6dd25b29\",\"subtype\":\"Figure\",\"type\":\"Plot\"},\"ticker\":{\"id\":\"1f56a3d8-78cc-49eb-a6e3-0aad937bd1e5\",\"type\":\"BasicTicker\"}},\"id\":\"0c4d5c1a-b0e1-48f7-a274-55bd3e901d83\",\"type\":\"LinearAxis\"},{\"attributes\":{},\"id\":\"097afb69-ac3f-4a9b-94d4-e24c95868285\",\"type\":\"BasicTickFormatter\"},{\"attributes\":{},\"id\":\"14dd4fcc-b9a1-48ff-b768-00bdf661a9b2\",\"type\":\"WheelZoomTool\"},{\"attributes\":{\"background_fill_color\":{\"value\":\"#E8DDCB\"},\"below\":[{\"id\":\"0ab26fec-8012-45de-b627-ec4662fdfed6\",\"type\":\"LinearAxis\"}],\"left\":[{\"id\":\"0c4d5c1a-b0e1-48f7-a274-55bd3e901d83\",\"type\":\"LinearAxis\"}],\"renderers\":[{\"id\":\"0ab26fec-8012-45de-b627-ec4662fdfed6\",\"type\":\"LinearAxis\"},{\"id\":\"44e7ebad-9fc3-4003-b666-0c24599445f2\",\"type\":\"Grid\"},{\"id\":\"0c4d5c1a-b0e1-48f7-a274-55bd3e901d83\",\"type\":\"LinearAxis\"},{\"id\":\"45c81ae8-32a0-43d3-be85-e8476bc2973d\",\"type\":\"Grid\"},{\"id\":\"1cdc7933-3a5e-4e3f-9c76-66153aba5ca1\",\"type\":\"BoxAnnotation\"},{\"id\":\"fb358ce5-dbc4-4e6a-906d-309d390202fe\",\"type\":\"GlyphRenderer\"},{\"id\":\"1503775a-8548-4fc4-abfc-988cce9f4e5b\",\"type\":\"GlyphRenderer\"}],\"title\":{\"id\":\"625f1f10-cf87-4eb4-8b9d-e498b12f7efc\",\"type\":\"Title\"},\"toolbar\":{\"id\":\"8ed4a182-41da-408f-8240-2fcd3cd86fce\",\"type\":\"Toolbar\"},\"x_range\":{\"id\":\"ebe3adda-2069-44de-a350-45fe3b301d10\",\"type\":\"Range1d\"},\"x_scale\":{\"id\":\"a538c485-1a63-4274-8bc3-c2b647ac0712\",\"type\":\"LinearScale\"},\"y_range\":{\"id\":\"b48c66d7-931f-48e3-a007-fa643afaf197\",\"type\":\"DataRange1d\"},\"y_scale\":{\"id\":\"e466edc0-78b2-4d6a-b603-5933a766ba62\",\"type\":\"LinearScale\"}},\"id\":\"d0a98231-cbac-42d5-b00b-4d3c6dd25b29\",\"subtype\":\"Figure\",\"type\":\"Plot\"},{\"attributes\":{},\"id\":\"8f58eb45-0e63-4059-8897-496897d60dc3\",\"type\":\"HelpTool\"},{\"attributes\":{\"bottom\":{\"value\":0},\"fill_color\":{\"value\":\"#032364\"},\"left\":{\"field\":\"left\"},\"line_color\":{\"value\":\"#033649\"},\"right\":{\"field\":\"right\"},\"top\":{\"field\":\"top\"}},\"id\":\"19467b4d-1322-4a82-9ee5-758ed06e6ec3\",\"type\":\"Quad\"}],\"root_ids\":[\"d0a98231-cbac-42d5-b00b-4d3c6dd25b29\"]},\"title\":\"Bokeh Application\",\"version\":\"0.13.0\"}};\n",
       "  var render_items = [{\"docid\":\"242fb296-e8c5-4e67-96b0-25f6f42a0ca2\",\"roots\":{\"d0a98231-cbac-42d5-b00b-4d3c6dd25b29\":\"59a39fdd-9063-4b3d-9296-79b6069cca15\"}}];\n",
       "  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n",
       "\n",
       "  }\n",
       "  if (root.Bokeh !== undefined) {\n",
       "    embed_document(root);\n",
       "  } else {\n",
       "    var attempts = 0;\n",
       "    var timer = setInterval(function(root) {\n",
       "      if (root.Bokeh !== undefined) {\n",
       "        embed_document(root);\n",
       "        clearInterval(timer);\n",
       "      }\n",
       "      attempts++;\n",
       "      if (attempts > 100) {\n",
       "        console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\")\n",
       "        clearInterval(timer);\n",
       "      }\n",
       "    }, 10, root)\n",
       "  }\n",
       "})(window);"
      ],
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "d0a98231-cbac-42d5-b00b-4d3c6dd25b29"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "p1 = figure(title='Electrophoretic Mobility', background_fill_color=\"#E8DDCB\", plot_height=600, plot_width=600, x_range=(-5, 0))\n",
    "# p2 = figure(title=None, background_fill_color=\"#E8DDCB\", plot_height=300, x_range=(-5, 0))\n",
    "hist, edges = np.histogram(ep_1, density=False, bins=20)\n",
    "hist2, edges2 = np.histogram(ep_2, density=False, bins=20)\n",
    "# bin_centres = (edges[:-1] + edges[1:])/2\n",
    "# bin_centres2 = (edges2[:-1]+edges2[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*300, p0=p0)\n",
    "# coeff2, var_matrix2 = curve_fit(gauss, bin_centres2, hist2*200, p0=p0)\n",
    "# x_hist = np.linspace(10, 60, 500)\n",
    "# hist_fit = gauss(x_hist, *coeff)\n",
    "# hist_fit2 = gauss(x_hist, *coeff2)\n",
    "\n",
    "p1.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:],\n",
    "        fill_color=\"#036564\", line_color=\"#033649\")\n",
    "p1.quad(top=hist2, bottom=0, left=edges2[:-1], right=edges2[1:],\n",
    "        fill_color=\"#032364\", line_color=\"#033649\")\n",
    "# p1.line(x_hist, hist_fit, line_color='#ff8821', line_width=5)\n",
    "# p1.line(x_hist, hist_fit2, line_color='#ffaa21', line_width=5)\n",
    "# p1.xaxis.visible = False\n",
    "# p1.yaxis.major_label_text_font_size = '16pt'\n",
    "p1.title.text_font_size = '22pt'\n",
    "p1.xaxis.axis_label = 'Electrophoretic Mobility (μm cm/Vs)'\n",
    "p1.xaxis.axis_label_text_font_size = '18pt'\n",
    "p1.yaxis.axis_label_text_font_size = '18pt'\n",
    "p1.xaxis.major_label_text_font_size = '16pt'\n",
    "p1.yaxis.major_label_text_font_size = '16pt'\n",
    "p1.yaxis.axis_label = 'Particle Count'\n",
    "show(p1)\n",
    "# show(column(p1, p2))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 117,
   "metadata": {},
   "outputs": [],
   "source": [
    "intensity = np.random.normal(loc=4000, scale=350, size=200)\n",
    "intensity2 = np.random.normal(loc=3000, scale=350, size=300)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 118,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "\n",
       "\n",
       "\n",
       "\n",
       "\n",
       "  <div class=\"bk-root\" id=\"fffa0118-1a8c-4688-8bfb-b03766f40b85\"></div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
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    {
     "data": {
      "application/javascript": [
       "(function(root) {\n",
       "  function embed_document(root) {\n",
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       "  var render_items = [{\"docid\":\"0f8b6839-573d-4674-a008-c984c0692e77\",\"roots\":{\"2458d776-f4c3-4c2b-9b71-6c0e2903d57a\":\"fffa0118-1a8c-4688-8bfb-b03766f40b85\"}}];\n",
       "  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n",
       "\n",
       "  }\n",
       "  if (root.Bokeh !== undefined) {\n",
       "    embed_document(root);\n",
       "  } else {\n",
       "    var attempts = 0;\n",
       "    var timer = setInterval(function(root) {\n",
       "      if (root.Bokeh !== undefined) {\n",
       "        embed_document(root);\n",
       "        clearInterval(timer);\n",
       "      }\n",
       "      attempts++;\n",
       "      if (attempts > 100) {\n",
       "        console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\")\n",
       "        clearInterval(timer);\n",
       "      }\n",
       "    }, 10, root)\n",
       "  }\n",
       "})(window);"
      ],
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "2458d776-f4c3-4c2b-9b71-6c0e2903d57a"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "f1 = figure(title=\"Intensity and diameter\", background_fill_color=\"#E8DDCB\")\n",
    "f1.circle(data, intensity2, fill_alpha=0.3, radius=.3, color=\"#036564\")\n",
    "f1.circle(data2, intensity, fill_alpha=0.3, radius=.3, color=\"#032364\")\n",
    "f1.title.text_font_size = '22pt'\n",
    "f1.xaxis.axis_label = 'Particle diameter (nm)'\n",
    "f1.xaxis.axis_label_text_font_size = '18pt'\n",
    "f1.yaxis.axis_label_text_font_size = '18pt'\n",
    "f1.xaxis.major_label_text_font_size = '16pt'\n",
    "f1.yaxis.major_label_text_font_size = '16pt'\n",
    "f1.yaxis.axis_label = 'Average intensity (counts)'\n",
    "show(f1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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