dan_nexus_example.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "sys.path.append('/dls_sw/i16/software/python')\n",
    "from dlstools.pdnx import *\n",
    "from matplotlib.pyplot import *\n",
    "%matplotlib notebook \n",
    "p='/dls/i16/data/2019/cm22970-1/%i.nxs'\n",
    "\n",
    "n=pdnx(p % 734847)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>TimeFromEpoch</th>\n",
       "      <th>TimeSec</th>\n",
       "      <th>count_time</th>\n",
       "      <th>delta_axis_offset</th>\n",
       "      <th>eta</th>\n",
       "      <th>ic1monitor</th>\n",
       "      <th>kap</th>\n",
       "      <th>kdelta</th>\n",
       "      <th>kgam</th>\n",
       "      <th>kmu</th>\n",
       "      <th>kphi</th>\n",
       "      <th>kth</th>\n",
       "      <th>maxval</th>\n",
       "      <th>maxx</th>\n",
       "      <th>maxy</th>\n",
       "      <th>path</th>\n",
       "      <th>rc</th>\n",
       "      <th>sum</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1.548867e+09</td>\n",
       "      <td>708863.688522</td>\n",
       "      <td>0.5</td>\n",
       "      <td>8.8</td>\n",
       "      <td>30.039944</td>\n",
       "      <td>740.786415</td>\n",
       "      <td>-10.793954</td>\n",
       "      <td>60.119889</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>224.109267</td>\n",
       "      <td>33.515083</td>\n",
       "      <td>2856.0</td>\n",
       "      <td>239.0</td>\n",
       "      <td>99.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>298.672729</td>\n",
       "      <td>25646.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1.548867e+09</td>\n",
       "      <td>708864.928955</td>\n",
       "      <td>0.5</td>\n",
       "      <td>8.8</td>\n",
       "      <td>30.040944</td>\n",
       "      <td>740.780312</td>\n",
       "      <td>-10.793954</td>\n",
       "      <td>60.119889</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>224.109267</td>\n",
       "      <td>33.516083</td>\n",
       "      <td>3276.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>99.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>298.665222</td>\n",
       "      <td>28076.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1.548867e+09</td>\n",
       "      <td>708865.914431</td>\n",
       "      <td>0.5</td>\n",
       "      <td>8.8</td>\n",
       "      <td>30.041944</td>\n",
       "      <td>740.819995</td>\n",
       "      <td>-10.793954</td>\n",
       "      <td>60.119889</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>224.109267</td>\n",
       "      <td>33.517083</td>\n",
       "      <td>3588.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>99.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>298.660828</td>\n",
       "      <td>30048.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1.548867e+09</td>\n",
       "      <td>708867.025306</td>\n",
       "      <td>0.5</td>\n",
       "      <td>8.8</td>\n",
       "      <td>30.042944</td>\n",
       "      <td>740.621561</td>\n",
       "      <td>-10.793954</td>\n",
       "      <td>60.119889</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>224.109267</td>\n",
       "      <td>33.518083</td>\n",
       "      <td>4063.0</td>\n",
       "      <td>240.0</td>\n",
       "      <td>99.0</td>\n",
       "      <td>4.0</td>\n",
       "      <td>298.650146</td>\n",
       "      <td>33255.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>37</th>\n",
       "      <td>1.548867e+09</td>\n",
       "      <td>708906.822007</td>\n",
       "      <td>0.5</td>\n",
       "      <td>8.8</td>\n",
       "      <td>30.076944</td>\n",
       "      <td>739.998775</td>\n",
       "      <td>-10.793954</td>\n",
       "      <td>60.119889</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>224.109267</td>\n",
       "      <td>33.552083</td>\n",
       "      <td>1039.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>96.0</td>\n",
       "      <td>38.0</td>\n",
       "      <td>298.383942</td>\n",
       "      <td>15212.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>38</th>\n",
       "      <td>1.548867e+09</td>\n",
       "      <td>708907.922379</td>\n",
       "      <td>0.5</td>\n",
       "      <td>8.8</td>\n",
       "      <td>30.077944</td>\n",
       "      <td>739.992667</td>\n",
       "      <td>-10.793954</td>\n",
       "      <td>60.119889</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>224.109267</td>\n",
       "      <td>33.553083</td>\n",
       "      <td>930.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>96.0</td>\n",
       "      <td>39.0</td>\n",
       "      <td>298.378723</td>\n",
       "      <td>14045.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>39</th>\n",
       "      <td>1.548867e+09</td>\n",
       "      <td>708908.924138</td>\n",
       "      <td>0.5</td>\n",
       "      <td>8.8</td>\n",
       "      <td>30.078944</td>\n",
       "      <td>740.130049</td>\n",
       "      <td>-10.793954</td>\n",
       "      <td>60.119889</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>224.109267</td>\n",
       "      <td>33.554083</td>\n",
       "      <td>750.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>96.0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>298.369507</td>\n",
       "      <td>12197.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>40</th>\n",
       "      <td>1.548867e+09</td>\n",
       "      <td>708910.139862</td>\n",
       "      <td>0.5</td>\n",
       "      <td>8.8</td>\n",
       "      <td>30.079944</td>\n",
       "      <td>739.974349</td>\n",
       "      <td>-10.793954</td>\n",
       "      <td>60.119889</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>224.109267</td>\n",
       "      <td>33.555083</td>\n",
       "      <td>650.0</td>\n",
       "      <td>242.0</td>\n",
       "      <td>96.0</td>\n",
       "      <td>41.0</td>\n",
       "      <td>298.362854</td>\n",
       "      <td>10926.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>41 rows × 18 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    TimeFromEpoch        TimeSec  count_time  delta_axis_offset        eta  ic1monitor        kap     kdelta  kgam  kmu        kphi        kth  maxval   maxx  maxy  path          rc      sum\n",
       "0    1.548867e+09  708863.688522         0.5                8.8  30.039944  740.786415 -10.793954  60.119889   0.0  0.0  224.109267  33.515083  2856.0  239.0  99.0   1.0  298.672729  25646.0\n",
       "1    1.548867e+09  708864.928955         0.5                8.8  30.040944  740.780312 -10.793954  60.119889   0.0  0.0  224.109267  33.516083  3276.0  240.0  99.0   2.0  298.665222  28076.0\n",
       "2    1.548867e+09  708865.914431         0.5                8.8  30.041944  740.819995 -10.793954  60.119889   0.0  0.0  224.109267  33.517083  3588.0  240.0  99.0   3.0  298.660828  30048.0\n",
       "3    1.548867e+09  708867.025306         0.5                8.8  30.042944  740.621561 -10.793954  60.119889   0.0  0.0  224.109267  33.518083  4063.0  240.0  99.0   4.0  298.650146  33255.0\n",
       "..            ...            ...         ...                ...        ...         ...        ...        ...   ...  ...         ...        ...     ...    ...   ...   ...         ...      ...\n",
       "37   1.548867e+09  708906.822007         0.5                8.8  30.076944  739.998775 -10.793954  60.119889   0.0  0.0  224.109267  33.552083  1039.0  242.0  96.0  38.0  298.383942  15212.0\n",
       "38   1.548867e+09  708907.922379         0.5                8.8  30.077944  739.992667 -10.793954  60.119889   0.0  0.0  224.109267  33.553083   930.0  242.0  96.0  39.0  298.378723  14045.0\n",
       "39   1.548867e+09  708908.924138         0.5                8.8  30.078944  740.130049 -10.793954  60.119889   0.0  0.0  224.109267  33.554083   750.0  242.0  96.0  40.0  298.369507  12197.0\n",
       "40   1.548867e+09  708910.139862         0.5                8.8  30.079944  739.974349 -10.793954  60.119889   0.0  0.0  224.109267  33.555083   650.0  242.0  96.0  41.0  298.362854  10926.0\n",
       "\n",
       "[41 rows x 18 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      ".nx.entry1.before_scan : \tbefore_scan\n"
     ]
    }
   ],
   "source": [
    "n.find('before_scan')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "ename": "NeXusError",
     "evalue": "No plotting signal defined",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mNeXusError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-11-98590cfed531>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mn\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnx\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplot\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/dls_sw/apps/python/anaconda/1.7.0/64/envs/cctbx/lib/python2.7/site-packages/nexusformat/nexus/tree.pyc\u001b[0m in \u001b[0;36mplot\u001b[0;34m(self, **opts)\u001b[0m\n\u001b[1;32m   3820\u001b[0m         \u001b[0mplotdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplottable_data\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3821\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mplotdata\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 3822\u001b[0;31m             \u001b[0mplotdata\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplot\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mopts\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   3823\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3824\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mNeXusError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"There is no plottable data\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/dls_sw/apps/python/anaconda/1.7.0/64/envs/cctbx/lib/python2.7/site-packages/nexusformat/nexus/tree.pyc\u001b[0m in \u001b[0;36mplot\u001b[0;34m(self, fmt, xmin, xmax, ymin, ymax, vmin, vmax, **opts)\u001b[0m\n\u001b[1;32m   4962\u001b[0m         \u001b[0msignal\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnxsignal\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   4963\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0msignal\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 4964\u001b[0;31m             \u001b[0;32mraise\u001b[0m \u001b[0mNeXusError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"No plotting signal defined\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   4965\u001b[0m         \u001b[0;32melif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0msignal\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexists\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   4966\u001b[0m             \u001b[0;32mraise\u001b[0m \u001b[0mNeXusError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Data for '%s' does not exist\"\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0msignal\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnxpath\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mNeXusError\u001b[0m: No plotting signal defined"
     ]
    }
   ],
   "source": [
    "n.nx.plot()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[u'mirrors',\n",
       " u'gains_atten',\n",
       " u's7xtrans',\n",
       " u'pp',\n",
       " u'source',\n",
       " u'offsets',\n",
       " u'beamline_slits',\n",
       " u'pa',\n",
       " u'mono',\n",
       " u'lakeshore',\n",
       " u'psi',\n",
       " u's7ytrans',\n",
       " u'dettrans',\n",
       " u'beta',\n",
       " u'alpha',\n",
       " u'mrwolf',\n",
       " u's7xgap',\n",
       " u'diffractometer_sample',\n",
       " u's7ygap',\n",
       " u'positions',\n",
       " u'jjslits',\n",
       " u'delta_offset',\n",
       " u'dummypd']"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "n.nx.entry1.before_scan.keys()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[u'kdelta',\n",
       " u'maxx',\n",
       " u'maxy',\n",
       " u'maxval',\n",
       " u'count_time',\n",
       " u'sum',\n",
       " u'eta',\n",
       " u'kgam',\n",
       " u'kmu',\n",
       " u'TimeFromEpoch',\n",
       " u'kth',\n",
       " u'TimeSec',\n",
       " u'rc',\n",
       " u'path',\n",
       " u'ic1monitor',\n",
       " u'kphi',\n",
       " u'delta_axis_offset',\n",
       " u'kap']"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "n.nx.entry1.measurement.keys()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
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  "language_info": {
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