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  {
   "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": [
      "[[0.71709362-0.58944207j 0.        +0.j        ]\n",
      " [0.66125439+0.40144845j 0.        +0.j        ]]\n",
      "\n",
      "with Pi analyzer\n",
      "[[7.17093622e-01-5.89442071e-01j 0.00000000e+00+0.00000000e+00j]\n",
      " [2.68867044e-33-2.21005378e-33j 4.39093204e-17-3.60929173e-17j]\n",
      " [2.47930684e-33+1.50519060e-33j 4.04901534e-17+2.45816279e-17j]]\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())"
   ]
  }
 ],
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