01_data_check.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Check whether images contain invalid values"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To read the NETCDF files containing the data we use the MeteoSwiss version of Py-ART that can be found [here](https://github.com/meteoswiss-mdr/pyart). The conda package can be obtained [here](https://anaconda.org/conda-forge/pyart_mch)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "## You are using the Python ARM Radar Toolkit (Py-ART), an open source\n",
      "## library for working with weather radar data. Py-ART is partly\n",
      "## supported by the U.S. Department of Energy as part of the Atmospheric\n",
      "## Radiation Measurement (ARM) Climate Research Facility, an Office of\n",
      "## Science user facility.\n",
      "##\n",
      "## If you use this software to prepare a publication, please cite:\n",
      "##\n",
      "##     JJ Helmus and SM Collis, JORS 2016, doi: 10.5334/jors.119\n",
      "\n"
     ]
    }
   ],
   "source": [
    "import glob\n",
    "import os\n",
    "import pyart\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "from copy import deepcopy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/opt/anaconda3/envs/exts-ml2/lib/python3.7/site-packages/ipykernel/ipkernel.py:287: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.\n",
      "  and should_run_async(code)\n"
     ]
    }
   ],
   "source": [
    "# suppress anoying iypthon warnings. Not ideal since we suppress also potentially relevant warnings\n",
    "import warnings\n",
    "warnings.filterwarnings('ignore')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Auxiliary functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Function to read original dataset\n",
    "# data is stored as (nz, ny, nx), we return (nx, ny)\n",
    "def read_nc(fname):\n",
    "    sat_grid = pyart.io.read_grid(fname)\n",
    "    for field_name in sat_grid.fields.keys():\n",
    "        data = np.transpose(np.squeeze(sat_grid.fields[field_name]['data']))\n",
    "    return data        "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "def check_nans(variables):\n",
    "    for var in variables:\n",
    "        flist = glob.glob(fbasepath+'*/NETCDF/'+var+'/*.nc')\n",
    "        flist.sort()\n",
    "        print(var, len(flist))\n",
    "        nnan = 0\n",
    "        for fname in flist:\n",
    "            # Get time step\n",
    "            bfile = os.path.basename(fname)\n",
    "            dt_str = bfile[0:14]\n",
    "            print(dt_str, end=\"\\r\", flush=True)\n",
    "            \n",
    "            data = read_nc(fname).flatten()\n",
    "            ind = np.where(np.isnan(data))[0]\n",
    "            if ind.size > 0:\n",
    "                print('File '+dt_str+' contains '+str(ind.size)+' NaNs')\n",
    "                nnan += 1\n",
    "        print('Number of files with NaNs:', nnan)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Some global variables"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "fbasepath = '/data/pyrad_products/MSG_ML/'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "jupyter": {
     "outputs_hidden": true
    }
   },
   "source": [
    "## Check variables"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "File 20200616134500 contains 8 NaNs\n",
      "File 20200616164000 contains 3 NaNs\n",
      "File 20200616165000 contains 4 NaNs\n",
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      "File 20200616171500 contains 4 NaNs\n",
      "File 20200616172000 contains 38 NaNs\n",
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      "File 20200616173000 contains 3 NaNs\n",
      "File 20200618154000 contains 7 NaNs\n",
      "File 20200618154500 contains 7 NaNs\n",
      "File 20200618155000 contains 2 NaNs\n",
      "File 20200618160000 contains 7 NaNs\n",
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      "File 20200619124000 contains 7 NaNs\n",
      "File 20200619124500 contains 7 NaNs\n",
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      "File 20200619135000 contains 1 NaNs\n",
      "File 20200619135500 contains 1 NaNs\n",
      "File 20200619140000 contains 9 NaNs\n",
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      "File 20200619145000 contains 16 NaNs\n",
      "File 20200624160500 contains 2 NaNs\n",
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      "File 20200624164000 contains 9 NaNs\n",
      "File 20200624165000 contains 2 NaNs\n",
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      "File 20200624170000 contains 26 NaNs\n",
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      "File 20200624173000 contains 4 NaNs\n",
      "File 20200624173500 contains 28 NaNs\n",
      "File 20200624174000 contains 7 NaNs\n",
      "File 20200624174500 contains 5 NaNs\n",
      "File 20200624175000 contains 6 NaNs\n",
      "File 20200624175500 contains 37 NaNs\n",
      "File 20200626050500 contains 8 NaNs\n",
      "File 20200626051000 contains 9 NaNs\n",
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      "File 20200626053500 contains 25 NaNs\n",
      "File 20200626061000 contains 6 NaNs\n",
      "File 20200626061500 contains 3 NaNs\n",
      "File 20200626071000 contains 12 NaNs\n",
      "File 20200626082000 contains 14 NaNs\n",
      "File 20200626082500 contains 1 NaNs\n",
      "File 20200626112000 contains 1 NaNs\n",
      "File 20200626120000 contains 1 NaNs\n",
      "File 20200626124000 contains 4 NaNs\n",
      "File 20200626125000 contains 12 NaNs\n",
      "File 20200626125500 contains 3 NaNs\n",
      "File 20200626131500 contains 1 NaNs\n",
      "File 20200626133000 contains 1 NaNs\n",
      "File 20200626134500 contains 4 NaNs\n",
      "File 20200626141000 contains 20 NaNs\n",
      "File 20200626141500 contains 12 NaNs\n",
      "File 20200626142000 contains 1 NaNs\n",
      "File 20200626143500 contains 2 NaNs\n",
      "File 20200626144000 contains 12 NaNs\n",
      "File 20200626145500 contains 15 NaNs\n",
      "File 20200626150000 contains 4 NaNs\n",
      "File 20200626150500 contains 4 NaNs\n",
      "File 20200626151000 contains 20 NaNs\n",
      "File 20200626152000 contains 1 NaNs\n",
      "File 20200626152500 contains 1 NaNs\n",
      "File 20200626153000 contains 13 NaNs\n",
      "File 20200626153500 contains 12 NaNs\n",
      "File 20200626154000 contains 7 NaNs\n",
      "File 20200626155000 contains 1 NaNs\n",
      "File 20200626155500 contains 5 NaNs\n",
      "File 20200626160500 contains 3 NaNs\n",
      "File 20200626161500 contains 7 NaNs\n",
      "File 20200626162000 contains 3 NaNs\n",
      "File 20200626162500 contains 28 NaNs\n",
      "File 20200626163000 contains 6 NaNs\n",
      "File 20200626170500 contains 22 NaNs\n",
      "File 20200626171000 contains 14 NaNs\n",
      "File 20200626171500 contains 30 NaNs\n",
      "File 20200626172000 contains 1 NaNs\n",
      "File 20200626172500 contains 4 NaNs\n",
      "File 20200626173000 contains 1 NaNs\n",
      "File 20200626173500 contains 4 NaNs\n",
      "File 20200626174500 contains 3 NaNs\n",
      "File 20200626175000 contains 5 NaNs\n",
      "File 20200627131000 contains 1 NaNs\n",
      "File 20200627142000 contains 2 NaNs\n",
      "File 20200627151000 contains 3 NaNs\n",
      "File 20200627170000 contains 5 NaNs\n",
      "File 20200627173000 contains 4 NaNs\n",
      "File 20200627174000 contains 9 NaNs\n",
      "File 20200701050500 contains 29 NaNs\n",
      "File 20200701051000 contains 25 NaNs\n",
      "File 20200701051500 contains 40 NaNs\n",
      "File 20200701052000 contains 40 NaNs\n",
      "File 20200701052500 contains 97 NaNs\n",
      "File 20200701053500 contains 35 NaNs\n",
      "File 20200701054000 contains 32 NaNs\n",
      "File 20200701054500 contains 50 NaNs\n",
      "File 20200701091500 contains 9 NaNs\n",
      "File 20200701092000 contains 17 NaNs\n",
      "File 20200701092500 contains 3 NaNs\n",
      "File 20200701093500 contains 3 NaNs\n",
      "File 20200701095500 contains 1 NaNs\n",
      "File 20200701100000 contains 3 NaNs\n",
      "File 20200701100500 contains 1 NaNs\n",
      "File 20200701101000 contains 12 NaNs\n",
      "File 20200701102000 contains 4 NaNs\n",
      "File 20200701102500 contains 1 NaNs\n",
      "File 20200701103000 contains 1 NaNs\n",
      "File 20200701104000 contains 1 NaNs\n",
      "File 20200701104500 contains 9 NaNs\n",
      "File 20200701142500 contains 2 NaNs\n",
      "File 20200701144000 contains 2 NaNs\n",
      "File 20200701150000 contains 13 NaNs\n",
      "File 20200701150500 contains 5 NaNs\n",
      "File 20200701151000 contains 4 NaNs\n",
      "File 20200701151500 contains 1 NaNs\n",
      "File 20200701152000 contains 4 NaNs\n",
      "File 20200701152500 contains 13 NaNs\n",
      "File 20200701153000 contains 2 NaNs\n",
      "File 20200701153500 contains 7 NaNs\n",
      "File 20200701154000 contains 20 NaNs\n",
      "File 20200701154500 contains 19 NaNs\n",
      "File 20200701155000 contains 2 NaNs\n",
      "File 20200701160000 contains 9 NaNs\n",
      "File 20200701160500 contains 6 NaNs\n",
      "File 20200701161500 contains 13 NaNs\n",
      "File 20200701162000 contains 2 NaNs\n",
      "File 20200701162500 contains 2 NaNs\n",
      "File 20200701170500 contains 10 NaNs\n",
      "File 20200701171000 contains 3 NaNs\n",
      "File 20200701171500 contains 4 NaNs\n",
      "File 20200701172000 contains 5 NaNs\n",
      "File 20200701172500 contains 8 NaNs\n",
      "File 20200701173000 contains 11 NaNs\n",
      "File 20200701173500 contains 8 NaNs\n",
      "File 20200701174000 contains 6 NaNs\n",
      "File 20200701174500 contains 8 NaNs\n",
      "File 20200701175500 contains 7 NaNs\n",
      "File 20200702161500 contains 7 NaNs\n",
      "File 20200702175000 contains 1 NaNs\n",
      "File 20200702175500 contains 1 NaNs\n",
      "File 20200703110000 contains 20 NaNs\n",
      "File 20200703112000 contains 65 NaNs\n",
      "File 20200703122500 contains 46 NaNs\n",
      "File 20200703123500 contains 64 NaNs\n",
      "File 20200703124000 contains 70 NaNs\n",
      "File 20200703124500 contains 96 NaNs\n",
      "File 20200703125000 contains 51 NaNs\n",
      "File 20200703125500 contains 43 NaNs\n",
      "File 20200703130000 contains 56 NaNs\n",
      "File 20200703130500 contains 11 NaNs\n",
      "File 20200703131000 contains 44 NaNs\n",
      "File 20200703132000 contains 103 NaNs\n",
      "File 20200703132500 contains 53 NaNs\n",
      "File 20200703133000 contains 74 NaNs\n",
      "File 20200703133500 contains 153 NaNs\n",
      "File 20200703134000 contains 92 NaNs\n",
      "File 20200703134500 contains 109 NaNs\n",
      "File 20200703135000 contains 65 NaNs\n",
      "File 20200703135500 contains 191 NaNs\n",
      "File 20200703140000 contains 155 NaNs\n",
      "File 20200703140500 contains 159 NaNs\n",
      "File 20200703141000 contains 242 NaNs\n",
      "File 20200703141500 contains 169 NaNs\n",
      "File 20200703142000 contains 268 NaNs\n",
      "File 20200703142500 contains 220 NaNs\n",
      "File 20200703143000 contains 100 NaNs\n",
      "File 20200703143500 contains 180 NaNs\n",
      "File 20200703144000 contains 214 NaNs\n",
      "File 20200703144500 contains 186 NaNs\n",
      "File 20200703145000 contains 161 NaNs\n",
      "File 20200703145500 contains 338 NaNs\n",
      "File 20200703150000 contains 95 NaNs\n",
      "File 20200703150500 contains 141 NaNs\n",
      "File 20200703151000 contains 275 NaNs\n",
      "File 20200703151500 contains 232 NaNs\n",
      "File 20200703152000 contains 178 NaNs\n",
      "File 20200703152500 contains 185 NaNs\n",
      "File 20200703153000 contains 217 NaNs\n",
      "File 20200703153500 contains 241 NaNs\n",
      "File 20200703154000 contains 101 NaNs\n",
      "File 20200703154500 contains 293 NaNs\n",
      "File 20200703155000 contains 296 NaNs\n",
      "File 20200703155500 contains 289 NaNs\n",
      "File 20200703160000 contains 177 NaNs\n",
      "File 20200703160500 contains 111 NaNs\n",
      "File 20200703161000 contains 137 NaNs\n",
      "File 20200703161500 contains 146 NaNs\n",
      "File 20200703162000 contains 197 NaNs\n",
      "File 20200703163500 contains 136 NaNs\n",
      "File 20200703164000 contains 128 NaNs\n",
      "File 20200703165000 contains 178 NaNs\n",
      "File 20200710135500 contains 1 NaNs\n",
      "File 20200710140000 contains 1 NaNs\n",
      "File 20200710143500 contains 2 NaNs\n",
      "File 20200710144000 contains 5 NaNs\n",
      "File 20200710144500 contains 1 NaNs\n",
      "File 20200710150500 contains 10 NaNs\n",
      "File 20200710151000 contains 20 NaNs\n",
      "File 20200710151500 contains 12 NaNs\n",
      "File 20200710153000 contains 7 NaNs\n",
      "File 20200710153500 contains 6 NaNs\n",
      "File 20200710154500 contains 6 NaNs\n",
      "File 20200710155500 contains 1 NaNs\n",
      "File 20200710160000 contains 14 NaNs\n",
      "File 20200710160500 contains 13 NaNs\n",
      "File 20200710161500 contains 1 NaNs\n",
      "File 20200710162000 contains 13 NaNs\n",
      "File 20200710164500 contains 1 NaNs\n",
      "File 20200710175000 contains 2 NaNs\n",
      "File 20200710175500 contains 2 NaNs\n",
      "File 20200711051000 contains 2 NaNs\n",
      "File 20200711053500 contains 2 NaNs\n",
      "File 20200711054500 contains 4 NaNs\n",
      "File 20200711055000 contains 1 NaNs\n",
      "File 20200711061500 contains 5 NaNs\n",
      "File 20200711062500 contains 17 NaNs\n",
      "File 20200711063500 contains 5 NaNs\n",
      "File 20200711064000 contains 6 NaNs\n",
      "File 20200711071000 contains 7 NaNs\n",
      "File 20200711071500 contains 2 NaNs\n",
      "File 20200711073000 contains 2 NaNs\n",
      "File 20200711073500 contains 6 NaNs\n",
      "File 20200711074000 contains 4 NaNs\n",
      "File 20200711074500 contains 12 NaNs\n",
      "File 20200711081000 contains 6 NaNs\n",
      "File 20200711081500 contains 3 NaNs\n",
      "File 20200711083000 contains 3 NaNs\n",
      "File 20200711083500 contains 1 NaNs\n",
      "File 20200711092500 contains 10 NaNs\n",
      "File 20200711093000 contains 3 NaNs\n",
      "File 20200711114000 contains 5 NaNs\n",
      "File 20200711115500 contains 2 NaNs\n",
      "File 20200711121000 contains 2 NaNs\n",
      "File 20200711122000 contains 11 NaNs\n",
      "File 20200711122500 contains 8 NaNs\n",
      "File 20200711123000 contains 20 NaNs\n",
      "File 20200711124000 contains 39 NaNs\n",
      "File 20200711124500 contains 14 NaNs\n",
      "File 20200711125000 contains 9 NaNs\n",
      "File 20200711125500 contains 10 NaNs\n",
      "File 20200711130000 contains 32 NaNs\n",
      "File 20200711130500 contains 27 NaNs\n",
      "File 20200711131000 contains 29 NaNs\n",
      "File 20200711131500 contains 29 NaNs\n",
      "File 20200711132000 contains 16 NaNs\n",
      "File 20200711132500 contains 56 NaNs\n",
      "File 20200711133000 contains 14 NaNs\n",
      "File 20200711133500 contains 7 NaNs\n",
      "File 20200711134000 contains 12 NaNs\n",
      "File 20200711134500 contains 24 NaNs\n",
      "File 20200711135000 contains 23 NaNs\n",
      "File 20200711135500 contains 21 NaNs\n",
      "File 20200711140000 contains 30 NaNs\n",
      "File 20200711140500 contains 47 NaNs\n",
      "File 20200711141000 contains 4 NaNs\n",
      "File 20200711141500 contains 5 NaNs\n",
      "File 20200711142000 contains 2 NaNs\n",
      "File 20200711142500 contains 13 NaNs\n",
      "File 20200711143000 contains 15 NaNs\n",
      "File 20200711143500 contains 14 NaNs\n",
      "File 20200721123000 contains 3 NaNs\n",
      "File 20200721130500 contains 2 NaNs\n",
      "File 20200721134000 contains 1 NaNs\n",
      "File 20200721150500 contains 5 NaNs\n",
      "File 20200721152000 contains 1 NaNs\n",
      "File 20200721153000 contains 1 NaNs\n",
      "File 20200721155500 contains 3 NaNs\n",
      "File 20200721161500 contains 2 NaNs\n",
      "File 20200721171500 contains 2 NaNs\n",
      "File 20200721173500 contains 3 NaNs\n",
      "File 20200721174000 contains 1 NaNs\n",
      "File 20200721174500 contains 1 NaNs\n",
      "File 20200722135500 contains 34 NaNs\n",
      "File 20200722142000 contains 18 NaNs\n",
      "File 20200722142500 contains 7 NaNs\n",
      "File 20200722143000 contains 13 NaNs\n",
      "File 20200722143500 contains 4 NaNs\n",
      "File 20200722144000 contains 40 NaNs\n",
      "File 20200722144500 contains 40 NaNs\n",
      "File 20200722145500 contains 29 NaNs\n",
      "File 20200722150500 contains 45 NaNs\n",
      "File 20200722151000 contains 92 NaNs\n",
      "File 20200722152000 contains 33 NaNs\n",
      "File 20200722152500 contains 86 NaNs\n",
      "File 20200722153000 contains 99 NaNs\n",
      "File 20200722153500 contains 90 NaNs\n",
      "File 20200722155000 contains 49 NaNs\n",
      "File 20200722155500 contains 17 NaNs\n",
      "File 20200722160000 contains 54 NaNs\n",
      "File 20200722160500 contains 113 NaNs\n",
      "File 20200722161000 contains 10 NaNs\n",
      "File 20200722161500 contains 91 NaNs\n",
      "File 20200722162000 contains 80 NaNs\n",
      "File 20200722162500 contains 52 NaNs\n",
      "File 20200722163000 contains 56 NaNs\n",
      "File 20200722170500 contains 68 NaNs\n",
      "File 20200722171000 contains 21 NaNs\n",
      "File 20200722171500 contains 23 NaNs\n",
      "File 20200722172000 contains 37 NaNs\n",
      "File 20200722172500 contains 21 NaNs\n",
      "File 20200722173000 contains 17 NaNs\n",
      "File 20200722173500 contains 25 NaNs\n",
      "File 20200722174000 contains 12 NaNs\n",
      "File 20200722174500 contains 20 NaNs\n",
      "File 20200724052500 contains 116 NaNs\n",
      "File 20200724053500 contains 145 NaNs\n",
      "File 20200724054000 contains 72 NaNs\n",
      "File 20200724054500 contains 155 NaNs\n",
      "File 20200724055000 contains 105 NaNs\n",
      "File 20200724060000 contains 170 NaNs\n",
      "File 20200724060500 contains 134 NaNs\n",
      "File 20200724061000 contains 153 NaNs\n",
      "File 20200724061500 contains 63 NaNs\n",
      "File 20200724135500 contains 8 NaNs\n",
      "File 20200724140000 contains 11 NaNs\n",
      "File 20200728133500 contains 1 NaNs\n",
      "File 20200728140500 contains 1 NaNs\n",
      "File 20200728142000 contains 4 NaNs\n",
      "File 20200728144500 contains 1 NaNs\n",
      "File 20200728150000 contains 5 NaNs\n",
      "File 20200728152000 contains 1 NaNs\n",
      "File 20200728152500 contains 7 NaNs\n",
      "File 20200728153000 contains 4 NaNs\n",
      "File 20200728153500 contains 4 NaNs\n",
      "File 20200728155000 contains 5 NaNs\n",
      "File 20200728160000 contains 1 NaNs\n",
      "File 20200728160500 contains 12 NaNs\n",
      "File 20200728161000 contains 4 NaNs\n",
      "File 20200728161500 contains 2 NaNs\n",
      "File 20200728162000 contains 2 NaNs\n",
      "File 20200728162500 contains 13 NaNs\n",
      "File 20200728164000 contains 7 NaNs\n",
      "File 20200728164500 contains 27 NaNs\n",
      "File 20200728165000 contains 3 NaNs\n",
      "File 20200728165500 contains 3 NaNs\n",
      "File 20200728170000 contains 3 NaNs\n",
      "File 20200728170500 contains 46 NaNs\n",
      "File 20200728171000 contains 5 NaNs\n",
      "File 20200728171500 contains 16 NaNs\n",
      "File 20200728172000 contains 7 NaNs\n",
      "File 20200728172500 contains 10 NaNs\n",
      "File 20200728173000 contains 1 NaNs\n",
      "File 20200728173500 contains 5 NaNs\n",
      "File 20200728174000 contains 17 NaNs\n",
      "File 20200730133500 contains 2 NaNs\n",
      "File 20200730134000 contains 2 NaNs\n",
      "File 20200730140500 contains 7 NaNs\n",
      "File 20200730142500 contains 3 NaNs\n",
      "File 20200730143000 contains 4 NaNs\n",
      "File 20200730144000 contains 18 NaNs\n",
      "File 20200730144500 contains 3 NaNs\n",
      "File 20200730145000 contains 7 NaNs\n",
      "File 20200730150000 contains 9 NaNs\n",
      "File 20200730150500 contains 1 NaNs\n",
      "File 20200730151500 contains 3 NaNs\n",
      "File 20200730152500 contains 13 NaNs\n",
      "File 20200730153000 contains 5 NaNs\n",
      "File 20200730154000 contains 2 NaNs\n",
      "File 20200730154500 contains 10 NaNs\n",
      "File 20200730155000 contains 7 NaNs\n",
      "File 20200730155500 contains 3 NaNs\n",
      "File 20200730160500 contains 7 NaNs\n",
      "File 20200730161500 contains 10 NaNs\n",
      "File 20200730162000 contains 24 NaNs\n",
      "File 20200730162500 contains 7 NaNs\n",
      "File 20200730163000 contains 10 NaNs\n",
      "File 20200730163500 contains 26 NaNs\n",
      "File 20200730170500 contains 17 NaNs\n",
      "File 20200730171000 contains 32 NaNs\n",
      "File 20200730171500 contains 59 NaNs\n",
      "File 20200730172000 contains 38 NaNs\n",
      "File 20200730172500 contains 27 NaNs\n",
      "File 20200730173000 contains 26 NaNs\n",
      "File 20200730173500 contains 23 NaNs\n",
      "File 20200730174000 contains 32 NaNs\n",
      "File 20200731142500 contains 11 NaNs\n",
      "File 20200731151000 contains 2 NaNs\n",
      "File 20200731151500 contains 4 NaNs\n",
      "File 20200731152000 contains 1 NaNs\n",
      "File 20200731153000 contains 6 NaNs\n",
      "File 20200731153500 contains 1 NaNs\n",
      "File 20200731171500 contains 14 NaNs\n",
      "File 20200731172000 contains 2 NaNs\n",
      "File 20200731172500 contains 10 NaNs\n",
      "File 20200731173000 contains 3 NaNs\n",
      "Number of files with NaNs: 2680\n"
     ]
    }
   ],
   "source": [
    "check_nans(['IR_108_text'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "2680 files contain some invalid values in the IR_108 variable although most of them have very few invalid pixels. This invalid values appear due to limitations in the float precision that cause the local variance to be negative and consequently the standard deviation (the root of the local variance) to become a non-valid number. Invalid numbers could be safely replaced by 0s. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "HRV_norm_text 4353\n",
      "File 20180612155000 contains 9862 NaNs\n",
      "File 20180807125500 contains 13415 NaNs\n",
      "Number of files with NaNs: 2\n"
     ]
    }
   ],
   "source": [
    "check_nans(['HRV_norm_text'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Visual inspection has shown that the two files that contain such a large amount of invalid numbers correspond with files with corrupted HRV values and they will be removed from the dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "WV_062-IR_108_text 4355\n",
      "File 20180429170500 contains 1 NaNs\n",
      "File 20180506170000 contains 1 NaNs\n",
      "File 20180509143500 contains 1 NaNs\n",
      "File 20180509162500 contains 1 NaNs\n",
      "File 20180512144000 contains 1 NaNs\n",
      "File 20180515130000 contains 1 NaNs\n",
      "File 20180515154500 contains 1 NaNs\n",
      "File 20180515160500 contains 2 NaNs\n",
      "File 20180520141000 contains 1 NaNs\n",
      "File 20180526164500 contains 2 NaNs\n",
      "File 20180527173000 contains 3 NaNs\n",
      "File 20180530151500 contains 1 NaNs\n",
      "File 20180530155500 contains 1 NaNs\n",
      "File 20180530165000 contains 3 NaNs\n",
      "File 20180530171500 contains 1 NaNs\n",
      "File 20180531100000 contains 2 NaNs\n",
      "File 20180531134500 contains 1 NaNs\n",
      "File 20180531155000 contains 1 NaNs\n",
      "File 20180604120000 contains 1 NaNs\n",
      "File 20180604145000 contains 1 NaNs\n",
      "File 20180604160500 contains 1 NaNs\n",
      "File 20180604161500 contains 1 NaNs\n",
      "File 20180604164500 contains 5 NaNs\n",
      "File 20180605162500 contains 2 NaNs\n",
      "File 20180611073500 contains 4 NaNs\n",
      "File 20180611105500 contains 2 NaNs\n",
      "File 20180611112000 contains 1 NaNs\n",
      "File 20180612065500 contains 1 NaNs\n",
      "File 20180612075000 contains 5 NaNs\n",
      "File 20180612090500 contains 1 NaNs\n",
      "File 20180612100000 contains 1 NaNs\n",
      "File 20180612154500 contains 1 NaNs\n",
      "File 20180612160000 contains 1 NaNs\n",
      "File 20180612161500 contains 1 NaNs\n",
      "File 20180612165000 contains 4 NaNs\n",
      "File 20180703051500 contains 1 NaNs\n",
      "File 20180703132500 contains 1 NaNs\n",
      "File 20180703161000 contains 1 NaNs\n",
      "File 20180703161500 contains 1 NaNs\n",
      "File 20180703172500 contains 1 NaNs\n",
      "File 20180704111000 contains 1 NaNs\n",
      "File 20180704121000 contains 1 NaNs\n",
      "File 20180704123500 contains 1 NaNs\n",
      "File 20180704155000 contains 2 NaNs\n",
      "File 20180801161500 contains 1 NaNs\n",
      "File 20180801165000 contains 1 NaNs\n",
      "File 20180801170500 contains 2 NaNs\n",
      "File 20180801172500 contains 8 NaNs\n",
      "File 20180805165500 contains 3 NaNs\n",
      "File 20180813125500 contains 2 NaNs\n",
      "File 20180821154500 contains 1 NaNs\n",
      "File 20190426105500 contains 4 NaNs\n",
      "File 20190426114000 contains 1 NaNs\n",
      "File 20190610090000 contains 1 NaNs\n",
      "File 20190622081000 contains 1 NaNs\n",
      "File 20190622083000 contains 2 NaNs\n",
      "File 20190622091500 contains 1 NaNs\n",
      "File 20190622101000 contains 3 NaNs\n",
      "File 20190627164500 contains 1 NaNs\n",
      "File 20190703154000 contains 2 NaNs\n",
      "File 20190802125500 contains 2 NaNs\n",
      "File 20190806164000 contains 12 NaNs\n",
      "File 20190806165500 contains 2 NaNs\n",
      "File 20190806171500 contains 2 NaNs\n",
      "File 20190806172000 contains 3 NaNs\n",
      "File 20190811153500 contains 12 NaNs\n",
      "File 20200612134000 contains 3 NaNs\n",
      "File 20200614175000 contains 1 NaNs\n",
      "File 20200626062000 contains 2 NaNs\n",
      "File 20200721130500 contains 1 NaNs\n",
      "File 20200722172500 contains 1 NaNs\n",
      "File 20200724053500 contains 2 NaNs\n",
      "Number of files with NaNs: 72\n"
     ]
    }
   ],
   "source": [
    "check_nans(['WV_062-IR_108_text'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "72 files contain NaNs. The reasons for the existence of nans are the same as for the IR_108_text variable"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "IR_108 4355\n",
      "Number of files with NaNs: 0\n",
      "HRV 4353\n",
      "Number of files with NaNs: 0\n",
      "HRV_norm 4353\n",
      "Number of files with NaNs: 0\n",
      "WV_062-IR_108 4355\n",
      "Number of files with NaNs: 0\n"
     ]
    }
   ],
   "source": [
    "check_nans(['IR_108', 'HRV', 'HRV_norm', 'WV_062-IR_108'])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The data check has shown that the original variables contain only valid values. NaN values may appears as a result of artifacts in the computation of the texture. These NaN values could be safely considered to be 0s. However they appear mostly in areas that are of no interest for the RF models (since they are thresholded) and there is sufficient data to train the model. Therefore we will simply ignore remove them from the RF model dataset. The data check has also exposed to files containing corrupted HRV values. These files will be removed from the u-net dataset.   "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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