{
 "cells": [
  {
   "cell_type": "code",
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   "source": [
    "import rioxarray\n",
    "import os\n",
    "\n",
    "# <<< INVASIVE SPECIES MAP >>>\n",
    "INVASIVE_BIRDS_PATH = 'Datasets/Machine Learning/1km Rasters/Birds/All_Invasive_Birds_1km.tif'\n",
    "\n",
    "# <<< LAND COVER MAP >>>\n",
    "# Dimensions: 700000x1300000\n",
    "LAND_COVER_MAP_PATH = 'Datasets/Machine Learning/1km Rasters/Features/gb2021lcm1km_percentage_target.tif'\n",
    "\n",
    "# <<< FERTILISER >>>\n",
    "# The dataset consists of maps of the predicted average annual application rates (2010-2015) of three different inorganic \n",
    "# chemical fertilisers – nitrogen (N), phosphorus (P) and potassium (K) – in England across a six-year period, along with \n",
    "# their respective estimates of uncertainty, at a 1 km x 1 km resolution. \n",
    "FERTILISER_K_PATH = 'Datasets/Machine Learning/1km Rasters/Features/fertiliser_k_prediction_uncertainty.tif'\n",
    "FERTILISER_N_PATH = 'Datasets/Machine Learning/1km Rasters/Features/fertiliser_n_prediction_uncertainty.tif'\n",
    "FERTILISER_P_PATH = 'Datasets/Machine Learning/1km Rasters/Features/fertiliser_p_prediction_uncertainty.tif'\n",
    "\n",
    "# <<< PESTICIDE >>>\n",
    "PESTICIDE_FOLDER_PATH = 'Datasets/Machine Learning/1km Rasters/Features/Pesticides/'\n",
    "\n",
    "# <<< INTEGRATED HYDROLOGICAL DIGITAL TERRAIN MODEL >>>\n",
    "# Dimensions: 700000x1300000\n",
    "# These datasets all only have one band\n",
    "ELEVATION_PATH = 'Datasets/Machine Learning/1km Rasters/Features/HGHT_1km.tif'\n",
    "CUMULATIVE_CATCHMENT_AREA_PATH = 'Datasets/Machine Learning/1km Rasters/Features/CCAR_1km.tif'\n",
    "SURFACE_TYPE_PATH = 'Datasets/Machine Learning/1km Rasters/Features/SURF_1km.tif'\n",
    "OUTFLOWING_DRAINAGE_DIRECTION_PATH = 'Datasets/Machine Learning/1km Rasters/Features/OUTF_1km.tif'\n",
    "INFLOWING_DRAINAGE_PATTERN_PATH = 'Datasets/Machine Learning/1km Rasters/Features/INFL_1km.tif'\n",
    "\n",
    "IHDTM = {\n",
    "    'Elevation': ELEVATION_PATH, \n",
    "    'Cumulative catchment area': CUMULATIVE_CATCHMENT_AREA_PATH, \n",
    "    'Surface type': SURFACE_TYPE_PATH, \n",
    "    'Outflowing drainage direction': OUTFLOWING_DRAINAGE_DIRECTION_PATH, \n",
    "    'Inflowing drainage direction': INFLOWING_DRAINAGE_PATTERN_PATH\n",
    "}\n",
    "\n",
    "\n",
    "# <<< Opening in rasterio >>>\n",
    "# dataset = rasterio.open(FERTILISER_P_PATH)\n",
    "# data = dataset.read()\n",
    "# np.max(data)\n",
    "\n",
    "# <<< Opening in rioxarray >>>\n",
    "# dataset = rioxarray.open_rasterio(ELEVATION_PATH)\n",
    "# dataset.name = 'data'\n",
    "# df = dataset.to_dataframe()\n"
   ]
  },
  {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>band</th>\n",
       "      <th>Deciduous woodland</th>\n",
       "      <th>Coniferous woodland</th>\n",
       "      <th>Arable</th>\n",
       "      <th>Improve grassland</th>\n",
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       "      <th>Heather grassland</th>\n",
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       "      <th>Supralittoral sediment</th>\n",
       "      <th>Littoral rock</th>\n",
       "      <th>Littoral sediment</th>\n",
       "      <th>Saltmarsh</th>\n",
       "      <th>Urban</th>\n",
       "      <th>Suburban</th>\n",
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      ],
      "text/plain": [
       "band                Deciduous woodland  Coniferous woodland  Arable  \\\n",
       "y         x                                                           \n",
       "1299500.0 500.0                      0                    0       0   \n",
       "          1500.0                     0                    0       0   \n",
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       "\n",
       "band                Improve grassland  Neutral grassland  \\\n",
       "y         x                                                \n",
       "1299500.0 500.0                     0                  0   \n",
       "          1500.0                    0                  0   \n",
       "          2500.0                    0                  0   \n",
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       "\n",
       "band                Calcareous grassland  Acid grassland  Fen  Heather  \\\n",
       "y         x                                                              \n",
       "1299500.0 500.0                        0               0    0        0   \n",
       "          1500.0                       0               0    0        0   \n",
       "          2500.0                       0               0    0        0   \n",
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       "...                                  ...             ...  ...      ...   \n",
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       "\n",
       "band                Heather grassland  ...  Inland rock  Saltwater  \\\n",
       "y         x                            ...                           \n",
       "1299500.0 500.0                     0  ...            0          0   \n",
       "          1500.0                    0  ...            0          0   \n",
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       "...                               ...  ...          ...        ...   \n",
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       "          699500.0                  0  ...            0          0   \n",
       "\n",
       "band                Freshwater  Supralittoral rock  Supralittoral sediment  \\\n",
       "y         x                                                                  \n",
       "1299500.0 500.0              0                   0                       0   \n",
       "          1500.0             0                   0                       0   \n",
       "          2500.0             0                   0                       0   \n",
       "          3500.0             0                   0                       0   \n",
       "          4500.0             0                   0                       0   \n",
       "...                        ...                 ...                     ...   \n",
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       "          699500.0           0                   0                       0   \n",
       "\n",
       "band                Littoral rock  Littoral sediment  Saltmarsh  Urban  \\\n",
       "y         x                                                              \n",
       "1299500.0 500.0                 0                  0          0      0   \n",
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       "...                           ...                ...        ...    ...   \n",
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       "\n",
       "band                Suburban  \n",
       "y         x                   \n",
       "1299500.0 500.0            0  \n",
       "          1500.0           0  \n",
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       "          4500.0           0  \n",
       "...                      ...  \n",
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       "\n",
       "[910000 rows x 21 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Open the land cover map raster file, transform its bands into feature columns and use this as the base \n",
    "# for the main dataframe as this has the widest extent out of all the files and is arguably one of the \n",
    "# most important dataframes\n",
    "\n",
    "lcm = rioxarray.open_rasterio(LAND_COVER_MAP_PATH)\n",
    "lcm.name = 'data'\n",
    "main_df = lcm.to_dataframe().drop(columns='spatial_ref')\n",
    "# print(main_df.value_counts()) \n",
    "main_df = main_df.unstack(level='band')\n",
    "\n",
    "LCM_CLASSES = [\n",
    "    'Deciduous woodland', \n",
    "    'Coniferous woodland', \n",
    "    'Arable', \n",
    "    'Improve grassland', \n",
    "    'Neutral grassland', \n",
    "    'Calcareous grassland', \n",
    "    'Acid grassland',  \n",
    "    'Fen', \n",
    "    'Heather', \n",
    "    'Heather grassland', \n",
    "    'Bog',\n",
    "    'Inland rock', \n",
    "    'Saltwater',\n",
    "    'Freshwater',\n",
    "    'Supralittoral rock',\n",
    "    'Supralittoral sediment',\n",
    "    'Littoral rock',\n",
    "    'Littoral sediment',\n",
    "    'Saltmarsh',\n",
    "    'Urban',\n",
    "    'Suburban'\n",
    "    ]\n",
    "\n",
    "main_df = main_df['data'].rename(columns={i+1: j for i, j in enumerate(LCM_CLASSES)})\n",
    "main_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
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       "</table>\n",
       "<p>910000 rows × 26 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    Deciduous woodland  Coniferous woodland  Arable  \\\n",
       "y         x                                                           \n",
       "1299500.0 500.0                      0                    0       0   \n",
       "          1500.0                     0                    0       0   \n",
       "          2500.0                     0                    0       0   \n",
       "          3500.0                     0                    0       0   \n",
       "          4500.0                     0                    0       0   \n",
       "...                                ...                  ...     ...   \n",
       "500.0     695500.0                   0                    0       0   \n",
       "          696500.0                   0                    0       0   \n",
       "          697500.0                   0                    0       0   \n",
       "          698500.0                   0                    0       0   \n",
       "          699500.0                   0                    0       0   \n",
       "\n",
       "                    Improve grassland  Neutral grassland  \\\n",
       "y         x                                                \n",
       "1299500.0 500.0                     0                  0   \n",
       "          1500.0                    0                  0   \n",
       "          2500.0                    0                  0   \n",
       "          3500.0                    0                  0   \n",
       "          4500.0                    0                  0   \n",
       "...                               ...                ...   \n",
       "500.0     695500.0                  0                  0   \n",
       "          696500.0                  0                  0   \n",
       "          697500.0                  0                  0   \n",
       "          698500.0                  0                  0   \n",
       "          699500.0                  0                  0   \n",
       "\n",
       "                    Calcareous grassland  Acid grassland  Fen  Heather  \\\n",
       "y         x                                                              \n",
       "1299500.0 500.0                        0               0    0        0   \n",
       "          1500.0                       0               0    0        0   \n",
       "          2500.0                       0               0    0        0   \n",
       "          3500.0                       0               0    0        0   \n",
       "          4500.0                       0               0    0        0   \n",
       "...                                  ...             ...  ...      ...   \n",
       "500.0     695500.0                     0               0    0        0   \n",
       "          696500.0                     0               0    0        0   \n",
       "          697500.0                     0               0    0        0   \n",
       "          698500.0                     0               0    0        0   \n",
       "          699500.0                     0               0    0        0   \n",
       "\n",
       "                    Heather grassland  ...  Littoral rock  Littoral sediment  \\\n",
       "y         x                            ...                                     \n",
       "1299500.0 500.0                     0  ...              0                  0   \n",
       "          1500.0                    0  ...              0                  0   \n",
       "          2500.0                    0  ...              0                  0   \n",
       "          3500.0                    0  ...              0                  0   \n",
       "          4500.0                    0  ...              0                  0   \n",
       "...                               ...  ...            ...                ...   \n",
       "500.0     695500.0                  0  ...              0                  0   \n",
       "          696500.0                  0  ...              0                  0   \n",
       "          697500.0                  0  ...              0                  0   \n",
       "          698500.0                  0  ...              0                  0   \n",
       "          699500.0                  0  ...              0                  0   \n",
       "\n",
       "                    Saltmarsh  Urban  Suburban  Elevation  \\\n",
       "y         x                                                 \n",
       "1299500.0 500.0             0      0         0      -9999   \n",
       "          1500.0            0      0         0      -9999   \n",
       "          2500.0            0      0         0      -9999   \n",
       "          3500.0            0      0         0      -9999   \n",
       "          4500.0            0      0         0      -9999   \n",
       "...                       ...    ...       ...        ...   \n",
       "500.0     695500.0          0      0         0      -9999   \n",
       "          696500.0          0      0         0      -9999   \n",
       "          697500.0          0      0         0      -9999   \n",
       "          698500.0          0      0         0      -9999   \n",
       "          699500.0          0      0         0      -9999   \n",
       "\n",
       "                    Cumulative catchment area  Surface type  \\\n",
       "y         x                                                   \n",
       "1299500.0 500.0                         -9999            -1   \n",
       "          1500.0                        -9999            -1   \n",
       "          2500.0                        -9999            -1   \n",
       "          3500.0                        -9999            -1   \n",
       "          4500.0                        -9999            -1   \n",
       "...                                       ...           ...   \n",
       "500.0     695500.0                      -9999            -1   \n",
       "          696500.0                      -9999            -1   \n",
       "          697500.0                      -9999            -1   \n",
       "          698500.0                      -9999            -1   \n",
       "          699500.0                      -9999            -1   \n",
       "\n",
       "                    Outflowing drainage direction  \\\n",
       "y         x                                         \n",
       "1299500.0 500.0                                -1   \n",
       "          1500.0                               -1   \n",
       "          2500.0                               -1   \n",
       "          3500.0                               -1   \n",
       "          4500.0                               -1   \n",
       "...                                           ...   \n",
       "500.0     695500.0                             -1   \n",
       "          696500.0                             -1   \n",
       "          697500.0                             -1   \n",
       "          698500.0                             -1   \n",
       "          699500.0                             -1   \n",
       "\n",
       "                    Inflowing drainage direction  \n",
       "y         x                                       \n",
       "1299500.0 500.0                              255  \n",
       "          1500.0                             255  \n",
       "          2500.0                             255  \n",
       "          3500.0                             255  \n",
       "          4500.0                             255  \n",
       "...                                          ...  \n",
       "500.0     695500.0                           255  \n",
       "          696500.0                           255  \n",
       "          697500.0                           255  \n",
       "          698500.0                           255  \n",
       "          699500.0                           255  \n",
       "\n",
       "[910000 rows x 26 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# For each IHDTM file, append its raster data to the main dataframe\n",
    "for key in IHDTM:\n",
    "    ihdtm_data = rioxarray.open_rasterio(IHDTM[key])\n",
    "    ihdtm_data = ihdtm_data.squeeze().drop(\"spatial_ref\").drop(\"band\")\n",
    "    ihdtm_data.name = key\n",
    "    ihdtm_df = ihdtm_data.to_dataframe()\n",
    "\n",
    "    # Adding 25 to x and y coordinates to match index of other datasets\n",
    "    ihdtm_df.index = ihdtm_df.index.set_levels(ihdtm_df.index.levels[0]+25, level=0)\n",
    "    ihdtm_df.index = ihdtm_df.index.set_levels(ihdtm_df.index.levels[1]+25, level=1)\n",
    "    main_df = main_df.join(ihdtm_df)\n",
    "main_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
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       "      <th></th>\n",
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       "      <th>Deciduous woodland</th>\n",
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       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th rowspan=\"5\" valign=\"top\">1299500.0</th>\n",
       "      <th>500.0</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>-9999</td>\n",
       "      <td>-9999</td>\n",
       "      <td>-1</td>\n",
       "      <td>-1</td>\n",
       "      <td>255</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1500.0</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>-9999</td>\n",
       "      <td>-9999</td>\n",
       "      <td>-1</td>\n",
       "      <td>-1</td>\n",
       "      <td>255</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2500.0</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>-9999</td>\n",
       "      <td>-9999</td>\n",
       "      <td>-1</td>\n",
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       "      <td>255</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
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       "      <td>0</td>\n",
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       "      <td>NaN</td>\n",
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       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <th rowspan=\"5\" valign=\"top\">500.0</th>\n",
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       "      <th>697500.0</th>\n",
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       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>910000 rows × 29 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    Deciduous woodland  Coniferous woodland  Arable  \\\n",
       "y         x                                                           \n",
       "1299500.0 500.0                      0                    0       0   \n",
       "          1500.0                     0                    0       0   \n",
       "          2500.0                     0                    0       0   \n",
       "          3500.0                     0                    0       0   \n",
       "          4500.0                     0                    0       0   \n",
       "...                                ...                  ...     ...   \n",
       "500.0     695500.0                   0                    0       0   \n",
       "          696500.0                   0                    0       0   \n",
       "          697500.0                   0                    0       0   \n",
       "          698500.0                   0                    0       0   \n",
       "          699500.0                   0                    0       0   \n",
       "\n",
       "                    Improve grassland  Neutral grassland  \\\n",
       "y         x                                                \n",
       "1299500.0 500.0                     0                  0   \n",
       "          1500.0                    0                  0   \n",
       "          2500.0                    0                  0   \n",
       "          3500.0                    0                  0   \n",
       "          4500.0                    0                  0   \n",
       "...                               ...                ...   \n",
       "500.0     695500.0                  0                  0   \n",
       "          696500.0                  0                  0   \n",
       "          697500.0                  0                  0   \n",
       "          698500.0                  0                  0   \n",
       "          699500.0                  0                  0   \n",
       "\n",
       "                    Calcareous grassland  Acid grassland  Fen  Heather  \\\n",
       "y         x                                                              \n",
       "1299500.0 500.0                        0               0    0        0   \n",
       "          1500.0                       0               0    0        0   \n",
       "          2500.0                       0               0    0        0   \n",
       "          3500.0                       0               0    0        0   \n",
       "          4500.0                       0               0    0        0   \n",
       "...                                  ...             ...  ...      ...   \n",
       "500.0     695500.0                     0               0    0        0   \n",
       "          696500.0                     0               0    0        0   \n",
       "          697500.0                     0               0    0        0   \n",
       "          698500.0                     0               0    0        0   \n",
       "          699500.0                     0               0    0        0   \n",
       "\n",
       "                    Heather grassland  ...  Urban  Suburban  Elevation  \\\n",
       "y         x                            ...                               \n",
       "1299500.0 500.0                     0  ...      0         0      -9999   \n",
       "          1500.0                    0  ...      0         0      -9999   \n",
       "          2500.0                    0  ...      0         0      -9999   \n",
       "          3500.0                    0  ...      0         0      -9999   \n",
       "          4500.0                    0  ...      0         0      -9999   \n",
       "...                               ...  ...    ...       ...        ...   \n",
       "500.0     695500.0                  0  ...      0         0      -9999   \n",
       "          696500.0                  0  ...      0         0      -9999   \n",
       "          697500.0                  0  ...      0         0      -9999   \n",
       "          698500.0                  0  ...      0         0      -9999   \n",
       "          699500.0                  0  ...      0         0      -9999   \n",
       "\n",
       "                    Cumulative catchment area  Surface type  \\\n",
       "y         x                                                   \n",
       "1299500.0 500.0                         -9999            -1   \n",
       "          1500.0                        -9999            -1   \n",
       "          2500.0                        -9999            -1   \n",
       "          3500.0                        -9999            -1   \n",
       "          4500.0                        -9999            -1   \n",
       "...                                       ...           ...   \n",
       "500.0     695500.0                      -9999            -1   \n",
       "          696500.0                      -9999            -1   \n",
       "          697500.0                      -9999            -1   \n",
       "          698500.0                      -9999            -1   \n",
       "          699500.0                      -9999            -1   \n",
       "\n",
       "                    Outflowing drainage direction  \\\n",
       "y         x                                         \n",
       "1299500.0 500.0                                -1   \n",
       "          1500.0                               -1   \n",
       "          2500.0                               -1   \n",
       "          3500.0                               -1   \n",
       "          4500.0                               -1   \n",
       "...                                           ...   \n",
       "500.0     695500.0                             -1   \n",
       "          696500.0                             -1   \n",
       "          697500.0                             -1   \n",
       "          698500.0                             -1   \n",
       "          699500.0                             -1   \n",
       "\n",
       "                    Inflowing drainage direction  Fertiliser K  Fertiliser N  \\\n",
       "y         x                                                                    \n",
       "1299500.0 500.0                              255           NaN           NaN   \n",
       "          1500.0                             255           NaN           NaN   \n",
       "          2500.0                             255           NaN           NaN   \n",
       "          3500.0                             255           NaN           NaN   \n",
       "          4500.0                             255           NaN           NaN   \n",
       "...                                          ...           ...           ...   \n",
       "500.0     695500.0                           255           NaN           NaN   \n",
       "          696500.0                           255           NaN           NaN   \n",
       "          697500.0                           255           NaN           NaN   \n",
       "          698500.0                           255           NaN           NaN   \n",
       "          699500.0                           255           NaN           NaN   \n",
       "\n",
       "                    Fertiliser P  \n",
       "y         x                       \n",
       "1299500.0 500.0              NaN  \n",
       "          1500.0             NaN  \n",
       "          2500.0             NaN  \n",
       "          3500.0             NaN  \n",
       "          4500.0             NaN  \n",
       "...                          ...  \n",
       "500.0     695500.0           NaN  \n",
       "          696500.0           NaN  \n",
       "          697500.0           NaN  \n",
       "          698500.0           NaN  \n",
       "          699500.0           NaN  \n",
       "\n",
       "[910000 rows x 29 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# For each fertiliser, append its raster data to the main dataframe\n",
    "fertiliser = {'Fertiliser K' : FERTILISER_K_PATH, 'Fertiliser N' : FERTILISER_N_PATH, 'Fertiliser P' : FERTILISER_P_PATH}\n",
    "\n",
    "for key in fertiliser:\n",
    "    fert_dataset = rioxarray.open_rasterio(fertiliser[key])\n",
    "    fert_dataset.name = key\n",
    "    fert_df = fert_dataset.to_dataframe().drop(columns='spatial_ref')\n",
    "    fert_df = fert_df.drop(index=2).droplevel('band')\n",
    "    main_df = main_df.join(fert_df)\n",
    "main_df\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>Deciduous woodland</th>\n",
       "      <th>Coniferous woodland</th>\n",
       "      <th>Arable</th>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
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       "      <th>...</th>\n",
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       "      <td>...</td>\n",
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       "      <th rowspan=\"5\" valign=\"top\">500.0</th>\n",
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       "    <tr>\n",
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       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>910000 rows × 39 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    Deciduous woodland  Coniferous woodland  Arable  \\\n",
       "y         x                                                           \n",
       "1299500.0 500.0                      0                    0       0   \n",
       "          1500.0                     0                    0       0   \n",
       "          2500.0                     0                    0       0   \n",
       "          3500.0                     0                    0       0   \n",
       "          4500.0                     0                    0       0   \n",
       "...                                ...                  ...     ...   \n",
       "500.0     695500.0                   0                    0       0   \n",
       "          696500.0                   0                    0       0   \n",
       "          697500.0                   0                    0       0   \n",
       "          698500.0                   0                    0       0   \n",
       "          699500.0                   0                    0       0   \n",
       "\n",
       "                    Improve grassland  Neutral grassland  \\\n",
       "y         x                                                \n",
       "1299500.0 500.0                     0                  0   \n",
       "          1500.0                    0                  0   \n",
       "          2500.0                    0                  0   \n",
       "          3500.0                    0                  0   \n",
       "          4500.0                    0                  0   \n",
       "...                               ...                ...   \n",
       "500.0     695500.0                  0                  0   \n",
       "          696500.0                  0                  0   \n",
       "          697500.0                  0                  0   \n",
       "          698500.0                  0                  0   \n",
       "          699500.0                  0                  0   \n",
       "\n",
       "                    Calcareous grassland  Acid grassland  Fen  Heather  \\\n",
       "y         x                                                              \n",
       "1299500.0 500.0                        0               0    0        0   \n",
       "          1500.0                       0               0    0        0   \n",
       "          2500.0                       0               0    0        0   \n",
       "          3500.0                       0               0    0        0   \n",
       "          4500.0                       0               0    0        0   \n",
       "...                                  ...             ...  ...      ...   \n",
       "500.0     695500.0                     0               0    0        0   \n",
       "          696500.0                     0               0    0        0   \n",
       "          697500.0                     0               0    0        0   \n",
       "          698500.0                     0               0    0        0   \n",
       "          699500.0                     0               0    0        0   \n",
       "\n",
       "                    Heather grassland  ...  Chlorothalonil  Glyphosate  \\\n",
       "y         x                            ...                               \n",
       "1299500.0 500.0                     0  ...             NaN         NaN   \n",
       "          1500.0                    0  ...             NaN         NaN   \n",
       "          2500.0                    0  ...             NaN         NaN   \n",
       "          3500.0                    0  ...             NaN         NaN   \n",
       "          4500.0                    0  ...             NaN         NaN   \n",
       "...                               ...  ...             ...         ...   \n",
       "500.0     695500.0                  0  ...             NaN         NaN   \n",
       "          696500.0                  0  ...             NaN         NaN   \n",
       "          697500.0                  0  ...             NaN         NaN   \n",
       "          698500.0                  0  ...             NaN         NaN   \n",
       "          699500.0                  0  ...             NaN         NaN   \n",
       "\n",
       "                    Mancozeb  Mecoprop-P  Metamitron  Pendimethalin  \\\n",
       "y         x                                                           \n",
       "1299500.0 500.0          NaN         NaN         NaN            NaN   \n",
       "          1500.0         NaN         NaN         NaN            NaN   \n",
       "          2500.0         NaN         NaN         NaN            NaN   \n",
       "          3500.0         NaN         NaN         NaN            NaN   \n",
       "          4500.0         NaN         NaN         NaN            NaN   \n",
       "...                      ...         ...         ...            ...   \n",
       "500.0     695500.0       NaN         NaN         NaN            NaN   \n",
       "          696500.0       NaN         NaN         NaN            NaN   \n",
       "          697500.0       NaN         NaN         NaN            NaN   \n",
       "          698500.0       NaN         NaN         NaN            NaN   \n",
       "          699500.0       NaN         NaN         NaN            NaN   \n",
       "\n",
       "                    PropamocarbHydrochloride  Prosulfocarb  Sulphur  \\\n",
       "y         x                                                           \n",
       "1299500.0 500.0                          NaN           NaN      NaN   \n",
       "          1500.0                         NaN           NaN      NaN   \n",
       "          2500.0                         NaN           NaN      NaN   \n",
       "          3500.0                         NaN           NaN      NaN   \n",
       "          4500.0                         NaN           NaN      NaN   \n",
       "...                                      ...           ...      ...   \n",
       "500.0     695500.0                       NaN           NaN      NaN   \n",
       "          696500.0                       NaN           NaN      NaN   \n",
       "          697500.0                       NaN           NaN      NaN   \n",
       "          698500.0                       NaN           NaN      NaN   \n",
       "          699500.0                       NaN           NaN      NaN   \n",
       "\n",
       "                    Tri-allate  \n",
       "y         x                     \n",
       "1299500.0 500.0            NaN  \n",
       "          1500.0           NaN  \n",
       "          2500.0           NaN  \n",
       "          3500.0           NaN  \n",
       "          4500.0           NaN  \n",
       "...                        ...  \n",
       "500.0     695500.0         NaN  \n",
       "          696500.0         NaN  \n",
       "          697500.0         NaN  \n",
       "          698500.0         NaN  \n",
       "          699500.0         NaN  \n",
       "\n",
       "[910000 rows x 39 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# For each file in pesticide folder, append its raster data to the main dataframe\n",
    "for file in os.listdir(PESTICIDE_FOLDER_PATH):\n",
    "    filename = os.fsdecode(file)\n",
    "    if not filename.endswith('.tif'):\n",
    "         continue\n",
    "    \n",
    "    pest_dataset = rioxarray.open_rasterio(PESTICIDE_FOLDER_PATH+filename)\n",
    "    pest_dataset.name = filename[:-4]\n",
    "    pest_df = pest_dataset.to_dataframe().drop(columns='spatial_ref')\n",
    "    pest_df = pest_df.drop(index=2).droplevel('band')\n",
    "    main_df = main_df.join(pest_df)\n",
    "main_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th>Deciduous woodland</th>\n",
       "      <th>Coniferous woodland</th>\n",
       "      <th>Arable</th>\n",
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       "      <th>Neutral grassland</th>\n",
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       "      <th>Prosulfocarb</th>\n",
       "      <th>Sulphur</th>\n",
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       "    </tr>\n",
       "    <tr>\n",
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       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>910000 rows × 40 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    Deciduous woodland  Coniferous woodland  Arable  \\\n",
       "y         x                                                           \n",
       "1299500.0 500.0                      0                    0       0   \n",
       "          1500.0                     0                    0       0   \n",
       "          2500.0                     0                    0       0   \n",
       "          3500.0                     0                    0       0   \n",
       "          4500.0                     0                    0       0   \n",
       "...                                ...                  ...     ...   \n",
       "500.0     695500.0                   0                    0       0   \n",
       "          696500.0                   0                    0       0   \n",
       "          697500.0                   0                    0       0   \n",
       "          698500.0                   0                    0       0   \n",
       "          699500.0                   0                    0       0   \n",
       "\n",
       "                    Improve grassland  Neutral grassland  \\\n",
       "y         x                                                \n",
       "1299500.0 500.0                     0                  0   \n",
       "          1500.0                    0                  0   \n",
       "          2500.0                    0                  0   \n",
       "          3500.0                    0                  0   \n",
       "          4500.0                    0                  0   \n",
       "...                               ...                ...   \n",
       "500.0     695500.0                  0                  0   \n",
       "          696500.0                  0                  0   \n",
       "          697500.0                  0                  0   \n",
       "          698500.0                  0                  0   \n",
       "          699500.0                  0                  0   \n",
       "\n",
       "                    Calcareous grassland  Acid grassland  Fen  Heather  \\\n",
       "y         x                                                              \n",
       "1299500.0 500.0                        0               0    0        0   \n",
       "          1500.0                       0               0    0        0   \n",
       "          2500.0                       0               0    0        0   \n",
       "          3500.0                       0               0    0        0   \n",
       "          4500.0                       0               0    0        0   \n",
       "...                                  ...             ...  ...      ...   \n",
       "500.0     695500.0                     0               0    0        0   \n",
       "          696500.0                     0               0    0        0   \n",
       "          697500.0                     0               0    0        0   \n",
       "          698500.0                     0               0    0        0   \n",
       "          699500.0                     0               0    0        0   \n",
       "\n",
       "                    Heather grassland  ...  Glyphosate  Mancozeb  Mecoprop-P  \\\n",
       "y         x                            ...                                     \n",
       "1299500.0 500.0                     0  ...         NaN       NaN         NaN   \n",
       "          1500.0                    0  ...         NaN       NaN         NaN   \n",
       "          2500.0                    0  ...         NaN       NaN         NaN   \n",
       "          3500.0                    0  ...         NaN       NaN         NaN   \n",
       "          4500.0                    0  ...         NaN       NaN         NaN   \n",
       "...                               ...  ...         ...       ...         ...   \n",
       "500.0     695500.0                  0  ...         NaN       NaN         NaN   \n",
       "          696500.0                  0  ...         NaN       NaN         NaN   \n",
       "          697500.0                  0  ...         NaN       NaN         NaN   \n",
       "          698500.0                  0  ...         NaN       NaN         NaN   \n",
       "          699500.0                  0  ...         NaN       NaN         NaN   \n",
       "\n",
       "                    Metamitron  Pendimethalin  PropamocarbHydrochloride  \\\n",
       "y         x                                                               \n",
       "1299500.0 500.0            NaN            NaN                       NaN   \n",
       "          1500.0           NaN            NaN                       NaN   \n",
       "          2500.0           NaN            NaN                       NaN   \n",
       "          3500.0           NaN            NaN                       NaN   \n",
       "          4500.0           NaN            NaN                       NaN   \n",
       "...                        ...            ...                       ...   \n",
       "500.0     695500.0         NaN            NaN                       NaN   \n",
       "          696500.0         NaN            NaN                       NaN   \n",
       "          697500.0         NaN            NaN                       NaN   \n",
       "          698500.0         NaN            NaN                       NaN   \n",
       "          699500.0         NaN            NaN                       NaN   \n",
       "\n",
       "                    Prosulfocarb  Sulphur  Tri-allate  Occurrence  \n",
       "y         x                                                        \n",
       "1299500.0 500.0              NaN      NaN         NaN           0  \n",
       "          1500.0             NaN      NaN         NaN           0  \n",
       "          2500.0             NaN      NaN         NaN           0  \n",
       "          3500.0             NaN      NaN         NaN           0  \n",
       "          4500.0             NaN      NaN         NaN           0  \n",
       "...                          ...      ...         ...         ...  \n",
       "500.0     695500.0           NaN      NaN         NaN           0  \n",
       "          696500.0           NaN      NaN         NaN           0  \n",
       "          697500.0           NaN      NaN         NaN           0  \n",
       "          698500.0           NaN      NaN         NaN           0  \n",
       "          699500.0           NaN      NaN         NaN           0  \n",
       "\n",
       "[910000 rows x 40 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Label data with entire bird dataset\n",
    "# -> Convert every non-null value into 1s and every null value into 0\n",
    "\n",
    "bird_dataset = rioxarray.open_rasterio(INVASIVE_BIRDS_PATH)\n",
    "bird_dataset.name = 'data'\n",
    "bird_df = bird_dataset.squeeze().drop(\"spatial_ref\").drop(\"band\").to_dataframe()\n",
    "\n",
    "bird_df['Occurrence'] = [0 if x == -1 else 1 for x in bird_df['data']]\n",
    "main_df = main_df.join(bird_df.drop(columns='data'))\n",
    "main_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Occurrence\n",
       "0    876916\n",
       "1     33084\n",
       "dtype: int64"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Checking to see values\n",
    "main_df.value_counts('Occurrence')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Cleaning data\n",
    "# main_df = main_df.loc[main_df['Deciduous woodland']\n",
    "#                         + main_df['Coniferous woodland']\n",
    "#                         + main_df['Arable']\n",
    "#                         + main_df['Improve grassland']\n",
    "#                         + main_df['Neutral grassland']\n",
    "#                         + main_df['Calcareous grassland']\n",
    "#                         + main_df['Acid grassland']\n",
    "#                         + main_df['Fen']\n",
    "#                         + main_df['Heather']\n",
    "#                         + main_df['Heather grassland']\n",
    "#                         + main_df['Bog']\n",
    "#                         + main_df['Inland rock']\n",
    "#                         + main_df['Saltwater']\n",
    "#                         + main_df['Freshwater']\n",
    "#                         + main_df['Supralittoral rock']\n",
    "#                         + main_df['Supralittoral sediment']\n",
    "#                         + main_df['Littoral rock']\n",
    "#                         + main_df['Littoral sediment']\n",
    "#                         + main_df['Saltmarsh']\n",
    "#                         + main_df['Urban']\n",
    "#                         + main_df['Suburban'] != 0\n",
    "#                     ]\n",
    "# main_df.value_counts('Occurrence')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['Fertiliser K', 'Fertiliser N', 'Fertiliser P', 'Chlorothalonil', 'Glyphosate', 'Mancozeb', 'Mecoprop-P', 'Metamitron', 'Pendimethalin', 'PropamocarbHydrochloride', 'Prosulfocarb', 'Sulphur', 'Tri-allate']\n"
     ]
    }
   ],
   "source": [
    "# Show columns with null values\n",
    "nan_columns = []\n",
    "for column in main_df:\n",
    "    if main_df[column].isnull().values.any():\n",
    "        nan_columns.append(column)\n",
    "print(nan_columns)\n",
    "\n",
    "# Only the pesticides have null values"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Replace null values with the minimum float value\n",
    "main_df = main_df.fillna(main_df.min())\n",
    "# old value: -3.4e+38"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
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       "    }\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></th>\n",
       "      <th>Deciduous woodland</th>\n",
       "      <th>Coniferous woodland</th>\n",
       "      <th>Arable</th>\n",
       "      <th>Improve grassland</th>\n",
       "      <th>Neutral grassland</th>\n",
       "      <th>Calcareous grassland</th>\n",
       "      <th>Acid grassland</th>\n",
       "      <th>Fen</th>\n",
       "      <th>Heather</th>\n",
       "      <th>Heather grassland</th>\n",
       "      <th>...</th>\n",
       "      <th>Glyphosate</th>\n",
       "      <th>Mancozeb</th>\n",
       "      <th>Mecoprop-P</th>\n",
       "      <th>Metamitron</th>\n",
       "      <th>Pendimethalin</th>\n",
       "      <th>PropamocarbHydrochloride</th>\n",
       "      <th>Prosulfocarb</th>\n",
       "      <th>Sulphur</th>\n",
       "      <th>Tri-allate</th>\n",
       "      <th>Occurrence</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>y</th>\n",
       "      <th>x</th>\n",
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       "    <tr>\n",
       "      <th rowspan=\"5\" valign=\"top\">500.0</th>\n",
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       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
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       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
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       "      <td>-3.400000e+38</td>\n",
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       "      <td>-3.400000e+38</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
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       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
       "      <td>-3.400000e+38</td>\n",
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       "    </tr>\n",
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       "      <th>699500.0</th>\n",
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       "      <td>-3.400000e+38</td>\n",
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       "      <td>-3.400000e+38</td>\n",
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       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>910000 rows × 40 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    Deciduous woodland  Coniferous woodland  Arable  \\\n",
       "y         x                                                           \n",
       "1299500.0 500.0                      0                    0       0   \n",
       "          1500.0                     0                    0       0   \n",
       "          2500.0                     0                    0       0   \n",
       "          3500.0                     0                    0       0   \n",
       "          4500.0                     0                    0       0   \n",
       "...                                ...                  ...     ...   \n",
       "500.0     695500.0                   0                    0       0   \n",
       "          696500.0                   0                    0       0   \n",
       "          697500.0                   0                    0       0   \n",
       "          698500.0                   0                    0       0   \n",
       "          699500.0                   0                    0       0   \n",
       "\n",
       "                    Improve grassland  Neutral grassland  \\\n",
       "y         x                                                \n",
       "1299500.0 500.0                     0                  0   \n",
       "          1500.0                    0                  0   \n",
       "          2500.0                    0                  0   \n",
       "          3500.0                    0                  0   \n",
       "          4500.0                    0                  0   \n",
       "...                               ...                ...   \n",
       "500.0     695500.0                  0                  0   \n",
       "          696500.0                  0                  0   \n",
       "          697500.0                  0                  0   \n",
       "          698500.0                  0                  0   \n",
       "          699500.0                  0                  0   \n",
       "\n",
       "                    Calcareous grassland  Acid grassland  Fen  Heather  \\\n",
       "y         x                                                              \n",
       "1299500.0 500.0                        0               0    0        0   \n",
       "          1500.0                       0               0    0        0   \n",
       "          2500.0                       0               0    0        0   \n",
       "          3500.0                       0               0    0        0   \n",
       "          4500.0                       0               0    0        0   \n",
       "...                                  ...             ...  ...      ...   \n",
       "500.0     695500.0                     0               0    0        0   \n",
       "          696500.0                     0               0    0        0   \n",
       "          697500.0                     0               0    0        0   \n",
       "          698500.0                     0               0    0        0   \n",
       "          699500.0                     0               0    0        0   \n",
       "\n",
       "                    Heather grassland  ...    Glyphosate      Mancozeb  \\\n",
       "y         x                            ...                               \n",
       "1299500.0 500.0                     0  ... -3.400000e+38 -3.400000e+38   \n",
       "          1500.0                    0  ... -3.400000e+38 -3.400000e+38   \n",
       "          2500.0                    0  ... -3.400000e+38 -3.400000e+38   \n",
       "          3500.0                    0  ... -3.400000e+38 -3.400000e+38   \n",
       "          4500.0                    0  ... -3.400000e+38 -3.400000e+38   \n",
       "...                               ...  ...           ...           ...   \n",
       "500.0     695500.0                  0  ... -3.400000e+38 -3.400000e+38   \n",
       "          696500.0                  0  ... -3.400000e+38 -3.400000e+38   \n",
       "          697500.0                  0  ... -3.400000e+38 -3.400000e+38   \n",
       "          698500.0                  0  ... -3.400000e+38 -3.400000e+38   \n",
       "          699500.0                  0  ... -3.400000e+38 -3.400000e+38   \n",
       "\n",
       "                      Mecoprop-P    Metamitron  Pendimethalin  \\\n",
       "y         x                                                     \n",
       "1299500.0 500.0    -3.400000e+38 -3.400000e+38  -3.400000e+38   \n",
       "          1500.0   -3.400000e+38 -3.400000e+38  -3.400000e+38   \n",
       "          2500.0   -3.400000e+38 -3.400000e+38  -3.400000e+38   \n",
       "          3500.0   -3.400000e+38 -3.400000e+38  -3.400000e+38   \n",
       "          4500.0   -3.400000e+38 -3.400000e+38  -3.400000e+38   \n",
       "...                          ...           ...            ...   \n",
       "500.0     695500.0 -3.400000e+38 -3.400000e+38  -3.400000e+38   \n",
       "          696500.0 -3.400000e+38 -3.400000e+38  -3.400000e+38   \n",
       "          697500.0 -3.400000e+38 -3.400000e+38  -3.400000e+38   \n",
       "          698500.0 -3.400000e+38 -3.400000e+38  -3.400000e+38   \n",
       "          699500.0 -3.400000e+38 -3.400000e+38  -3.400000e+38   \n",
       "\n",
       "                    PropamocarbHydrochloride  Prosulfocarb       Sulphur  \\\n",
       "y         x                                                                \n",
       "1299500.0 500.0                -3.400000e+38 -3.400000e+38 -3.400000e+38   \n",
       "          1500.0               -3.400000e+38 -3.400000e+38 -3.400000e+38   \n",
       "          2500.0               -3.400000e+38 -3.400000e+38 -3.400000e+38   \n",
       "          3500.0               -3.400000e+38 -3.400000e+38 -3.400000e+38   \n",
       "          4500.0               -3.400000e+38 -3.400000e+38 -3.400000e+38   \n",
       "...                                      ...           ...           ...   \n",
       "500.0     695500.0             -3.400000e+38 -3.400000e+38 -3.400000e+38   \n",
       "          696500.0             -3.400000e+38 -3.400000e+38 -3.400000e+38   \n",
       "          697500.0             -3.400000e+38 -3.400000e+38 -3.400000e+38   \n",
       "          698500.0             -3.400000e+38 -3.400000e+38 -3.400000e+38   \n",
       "          699500.0             -3.400000e+38 -3.400000e+38 -3.400000e+38   \n",
       "\n",
       "                      Tri-allate  Occurrence  \n",
       "y         x                                   \n",
       "1299500.0 500.0    -3.400000e+38           0  \n",
       "          1500.0   -3.400000e+38           0  \n",
       "          2500.0   -3.400000e+38           0  \n",
       "          3500.0   -3.400000e+38           0  \n",
       "          4500.0   -3.400000e+38           0  \n",
       "...                          ...         ...  \n",
       "500.0     695500.0 -3.400000e+38           0  \n",
       "          696500.0 -3.400000e+38           0  \n",
       "          697500.0 -3.400000e+38           0  \n",
       "          698500.0 -3.400000e+38           0  \n",
       "          699500.0 -3.400000e+38           0  \n",
       "\n",
       "[910000 rows x 40 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "main_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Output dataframe as csv\n",
    "main_df.to_csv('Datasets/Machine Learning/Dataframes/1km_All_Birds_DF.csv')"
   ]
  }
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