fit_Bifrost_data_old.ipynb

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   "id": "6c956100-a914-45b2-beba-3cdfbd26ca25",
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   "source": [
    "# from sim_bfr_240611.config import RAW_DATA_DIR\n",
    "RAW_DATA_DIR = 'Greg_simulation'\n",
    "import scipp as sc\n",
    "import plopp as pp\n",
    "import scippneutron as scn\n",
    "import scippnexus as snx\n",
    "import numpy as np\n",
    "from easyscience.Objects.new_variable import Parameter\n",
    "from easyscience.Objects.ObjectClasses import BaseObj\n",
    "from easyscience.fitting import Fitter\n",
    "import matplotlib.pyplot as plt\n",
    "from scipy.interpolate import interp1d\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "f727e359-8e89-463b-afe3-2a27cbc60e05",
   "metadata": {},
   "outputs": [],
   "source": [
    "filename=RAW_DATA_DIR +\"/BIFROST_20240610T151842.h5\"\n",
    "dg = snx.File(filename)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "2fbcabca",
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   ],
   "source": [
    "# example_data=dg['/entry/instrument/110_frame_3']['data']['time',1]\n",
    "example_data=dg['/entry/instrument/090_frame_1']['data']['time',1]\n",
    "# example_data=dg['/entry/instrument/007_frame_0']['data']['time',1]\n",
    "\n",
    "example_data.coords['t']=sc.midpoints(example_data.coords['t']) # convert from bin edges to bin centers\n",
    "\n",
    "# Plotting the data is very simple. You can pass more arguments to the plot function if you want.\n",
    "example_data.plot()\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "3d082b0d",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Define a fit function. In this simple example the fit parameters are global variables.\n",
    "def Gaussian(x: np.ndarray) -> np.ndarray:\n",
    "    \"\"\"\n",
    "    Mathematical model for a Gaussian function.\n",
    "    \n",
    "    :x: values to calculate the model over. \n",
    "    :A: amplitude of the Gaussian.\n",
    "    :mu: mean (center) of the Gaussian.\n",
    "    :sigma: standard deviation of the Gaussian.\n",
    "    :BG: background.\n",
    "    \n",
    "    :return: model values.\n",
    "    \"\"\"\n",
    "    return A.value * np.exp(-0.5 * ((x - mu.value) / sigma.value) ** 2)+BG.value\n",
    "\n",
    "\n",
    "# The easyscience workflow is to create a function, then define the relevant Parameters. The Parameters are collected in a BaseObj, which is then passed to the Fitter along with the fit function.\n",
    "# To fit the data, we pass x, y and weights to the fitter.\n",
    "\n",
    "#Create easyscience Parameters with starting values and optional constraints\n",
    "A=Parameter(name='A', value=2e9, fixed=False,min=0)\n",
    "mu=Parameter(name='mu', value=30000, fixed=False)\n",
    "# mu=Parameter(name='mu', value=9000, fixed=False)\n",
    "sigma=Parameter(name='sigma', value=1500, fixed=False,min=0)\n",
    "BG=Parameter(name='BG', value=0.1, fixed=False,min=0)\n",
    "\n",
    "#Create easyscience BaseObj with the Gaussian model and the Parameters\n",
    "Gaussian_Obj = BaseObj(name='Gaussian_Obj', A=A, mu=mu, sigma=sigma,BG=BG)\n",
    "f = Fitter(Gaussian_Obj, Gaussian )\n",
    "# You can do more things here, such as changing the fit method. Let's stick with the default for now.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "b665bfe3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(<Parameter 'A': 2432216160.1011 ± 206036987.9111, bounds=[0.0:inf]>,\n",
       " <Parameter 'mu': 35361.9572 ± 134.2069, bounds=[-inf:inf]>,\n",
       " <Parameter 'sigma': 1647.8314 ± 48.2259, bounds=[0.0:inf]>,\n",
       " <Parameter 'BG': 5.1748 ± 20754.6410, bounds=[0.0:inf]>)"
      ]
     },
     "execution_count": 13,
     "metadata": {},
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   "source": [
    "# Extract x, y and errors to pass to the fitter.\n",
    "x=example_data.coords['t'].values\n",
    "y=example_data.values\n",
    "yerr=np.sqrt(example_data.variances+1e7) # adding a constant to the variance to avoid problems at the tails\n",
    "\n",
    "# Carry out the fitting,.\n",
    "res=f.fit(x=x, y=y, weights=1/yerr)\n",
    "# res=f.fit(x=x, y=y, weights=np.sqrt(y))\n",
    "A,mu,sigma,BG\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "0e3cb99e",
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      "text/plain": [
       "Figure(600x400, 2 artists)"
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     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\n",
    "\n",
    "# Calculate the fit values for the x values of the data\n",
    "xx=np.linspace(0,70000,5000) # Plot the fit on a smoother curve by using more points\n",
    "fit_values=sc.array(values=Gaussian(xx),dims='t',unit='counts')\n",
    "\n",
    "# Put the fit into a DataArray for plotting. We need to tell scipp what the units are.\n",
    "Fit=sc.DataArray(data=fit_values,coords={'t': sc.array(values=xx,dims='t',unit='micro*s')})\n",
    "\n",
    "data_and_fit=sc.DataGroup({'Data': example_data,\n",
    "                          'Fit': Fit})\n",
    "\n",
    "# We use plopp to plot the data and the fit\n",
    "pp.plot(data_and_fit,\n",
    "        linestyle=         {'Data': 'none',    'Fit': '-'},\n",
    "        marker=            {'Data': 'o',       'Fit':'none'},\n",
    "        markerfacecolor=   {'Data': 'none',    'Fit':'red'},\n",
    "        color=             {'Data': 'black',   'Fit':'red'})\n",
    "\n",
    "\n"
   ]
  }
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