Added a pdf with orientation decoding notebook

PopulationSampling.ipynb

@@ -84,18 +84,6 @@
     "N = 40 # number of cells"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [],
-   "source": []
-  },
   {
    "cell_type": "code",
    "execution_count": 3,
@@ -410,60 +398,6 @@
     "plt.imshow(res_reshaped[:, :, 0], cmap='viridis')"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%% md\n"
-    }
-   },
-   "source": [
-    "## Persistence for different dimensions"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 17,
-   "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "# persistence.persistence(res, 1)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 18,
-   "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "# persistence.persistence(res, 2)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 19,
-   "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "# persistence.persistence(res, 3)"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {
@@ -834,6 +768,13 @@
     "plt.scatter(phi_deg[::step], param_1)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Orientation is decoded:"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 42,
@@ -983,90 +924,6 @@
     "plt.title(\"Parameter 2 of CP vs. phase\")\n",
     "plt.scatter(phi_deg[::step], param_2)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 36,
-   "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "is_executing": true,
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [
-    {
-     "ename": "IndexError",
-     "evalue": "index 288 is out of bounds for axis 0 with size 260",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mIndexError\u001b[0m                                Traceback (most recent call last)",
-      "\u001b[1;32m/home/ennucore/dev/amgen/PopulationSampling.ipynb Cell 46\u001b[0m in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> <a href='vscode-notebook-cell:/home/ennucore/dev/amgen/PopulationSampling.ipynb#ch0000042?line=0'>1</a>\u001b[0m plt\u001b[39m.\u001b[39mscatter([phi_deg[i] \u001b[39m*\u001b[39m \u001b[39m180\u001b[39m \u001b[39m/\u001b[39m np\u001b[39m.\u001b[39mpi \u001b[39mfor\u001b[39;00m i \u001b[39min\u001b[39;00m phi_reorder], [param_2[i] \u001b[39mfor\u001b[39;00m i \u001b[39min\u001b[39;00m phi_reorder])\n",
-      "\u001b[1;32m/home/ennucore/dev/amgen/PopulationSampling.ipynb Cell 46\u001b[0m in \u001b[0;36m<listcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[0;32m----> <a href='vscode-notebook-cell:/home/ennucore/dev/amgen/PopulationSampling.ipynb#ch0000042?line=0'>1</a>\u001b[0m plt\u001b[39m.\u001b[39mscatter([phi_deg[i] \u001b[39m*\u001b[39m \u001b[39m180\u001b[39m \u001b[39m/\u001b[39m np\u001b[39m.\u001b[39mpi \u001b[39mfor\u001b[39;00m i \u001b[39min\u001b[39;00m phi_reorder], [param_2[i] \u001b[39mfor\u001b[39;00m i \u001b[39min\u001b[39;00m phi_reorder])\n",
-      "\u001b[0;31mIndexError\u001b[0m: index 288 is out of bounds for axis 0 with size 260"
-     ]
-    }
-   ],
-   "source": [
-    "plt.scatter([phi_deg[i] * 180 / np.pi for i in phi_reorder], [param_2[i] for i in phi_reorder])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "is_executing": true,
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "plt.scatter([theta_deg[i] for i in theta_reorder], [param_2[i] for i in theta_reorder])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "is_executing": true,
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [],
-   "source": [
-    "phi_reorder[:10]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "is_executing": true,
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [],
-   "source": []
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "is_executing": true,
-     "name": "#%%\n"
-    }
-   },
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {