{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "0fc479ca-6750-4092-a7c0-60d77c6293d3",
   "metadata": {},
   "source": [
    "# JOnes vector"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "0e08d6e9",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[[0.71751273-0.58897687j 0.        +0.j        ]\n",
      " [0.66100408+0.40190631j 0.        +0.j        ]]\n",
      "\n",
      "with Pi analyzer\n",
      "[[0.71751273-0.58897687j 0.        +0.j        ]\n",
      " [0.        +0.j         0.        +0.j        ]\n",
      " [0.        +0.j         0.        +0.j        ]]\n"
     ]
    }
   ],
   "source": [
    "import nexus as nx\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "iron = nx.Material.Template(nx.lib.material.Fe)\n",
    "\n",
    "layer_Fe = nx.Layer(id = \"Fe layer\",\n",
    "                    material = iron,\n",
    "                    thickness = 3000)\n",
    "\n",
    "sample1 = nx.Sample(layers = [layer_Fe])\n",
    "\n",
    "layer_Pt = nx.Layer(id = \"Pt layer\",\n",
    "                    material = nx.Material.Template(nx.lib.material.Pt),\n",
    "                    thickness = 1000)\n",
    "\n",
    "sample2 = nx.Sample(layers=[layer_Pt])\n",
    "\n",
    "beam = nx.Beam()\n",
    "beam.LinearSigma()\n",
    "\n",
    "exp = nx.Experiment(beam = beam,\n",
    "                    objects = [sample1, sample2],\n",
    "                    isotope = nx.lib.moessbauer.Fe57)\n",
    "\n",
    "jones_vectors = nx.JonesVectors(experiment = exp,\n",
    "                                energy = 14400)\n",
    "\n",
    "print(jones_vectors())\n",
    "\n",
    "# now we add an analyzer\n",
    "print(\"\\nwith Pi analyzer\")\n",
    "\n",
    "analyzer  = nx.Analyzer()\n",
    "analyzer.LinearPi()\n",
    "\n",
    "exp.objects = [sample1, analyzer, sample2]\n",
    "\n",
    "print(jones_vectors())"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.12.0"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}