{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Temporal Resampling and gapfilling"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "> The package `otbApplication` is not installed in SISE environment. You must activate SISE-3.7 environnment by launching the following command in Anaconda Prompt : `conda activate sise-3.7`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "All libraries successfully imported!\n"
     ]
    }
   ],
   "source": [
    "import glob, os, subprocess\n",
    "import pandas as pd\n",
    "import otbApplication as otb\n",
    "from pathlib import Path\n",
    "import datetime\n",
    "import rasterio\n",
    "import numpy as np\n",
    "\n",
    "print('All libraries successfully imported!')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Set directory**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "computer_path = '/export/miro/ndeffense/LBRAT2104/'\n",
    "grp_nb        = '99'\n",
    "\n",
    "# Directory for all work files\n",
    "work_path = f'{computer_path}STUDENTS/GROUP_{grp_nb}/TP/'\n",
    "\n",
    "clipped_path   = f'{work_path}2_L2A_CLIPPED/'\n",
    "gapfilled_path = f'{work_path}4_L2A_GAPFILLED/'\n",
    "\n",
    "Path(gapfilled_path).mkdir(parents=True, exist_ok=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Parameters**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "band_list = ['B02','B03']\n",
    "\n",
    "format     = '%Y%m%d' # format : YYYYMMDD\n",
    "begin_date = 7\n",
    "\n",
    "# Distance between interpolated dates\n",
    "frequency = '1m'\n",
    "\n",
    "# Interpolation type\n",
    "interp_type = 'linear'  # 'spline'\n",
    "\n",
    "flag_otbAPI = False\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Prepare data\n",
    "### Get dataframe with all inputs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "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>date</th>\n",
       "      <th>date_str</th>\n",
       "      <th>SCL</th>\n",
       "      <th>B02</th>\n",
       "      <th>B03</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2020-01-16</td>\n",
       "      <td>20200116</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2020-02-12</td>\n",
       "      <td>20200212</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2020-03-16</td>\n",
       "      <td>20200316</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2020-04-17</td>\n",
       "      <td>20200417</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>2020-05-20</td>\n",
       "      <td>20200520</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>2020-06-21</td>\n",
       "      <td>20200621</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>2020-07-19</td>\n",
       "      <td>20200719</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>2020-08-13</td>\n",
       "      <td>20200813</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>2020-09-14</td>\n",
       "      <td>20200914</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>2020-10-19</td>\n",
       "      <td>20201019</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>2020-11-18</td>\n",
       "      <td>20201118</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>2020-12-18</td>\n",
       "      <td>20201218</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "      <td>/export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          date  date_str                                                SCL  \\\n",
       "0   2020-01-16  20200116  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "1   2020-02-12  20200212  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "2   2020-03-16  20200316  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "3   2020-04-17  20200417  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "4   2020-05-20  20200520  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "5   2020-06-21  20200621  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "6   2020-07-19  20200719  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "7   2020-08-13  20200813  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "8   2020-09-14  20200914  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "9   2020-10-19  20201019  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "10  2020-11-18  20201118  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "11  2020-12-18  20201218  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "\n",
       "                                                  B02  \\\n",
       "0   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "1   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "2   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "3   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "4   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "5   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "6   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "7   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "8   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "9   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "10  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "11  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...   \n",
       "\n",
       "                                                  B03  \n",
       "0   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  \n",
       "1   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  \n",
       "2   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  \n",
       "3   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  \n",
       "4   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  \n",
       "5   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  \n",
       "6   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  \n",
       "7   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  \n",
       "8   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  \n",
       "9   /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  \n",
       "10  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  \n",
       "11  /export/miro/ndeffense/LBRAT2104/STUDENTS/GROU...  "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "dict_list = []\n",
    "\n",
    "for im in glob.glob(f'{clipped_path}*SCL*10m*.tif'):\n",
    "    \n",
    "    date_str = os.path.basename(im)[begin_date:begin_date+8]\n",
    "\n",
    "    date_im = datetime.datetime.strptime(date_str, format).date()\n",
    "    dict_list.append({'date': date_im,\n",
    "                      'date_str': date_str,\n",
    "                      'SCL': im})\n",
    "\n",
    "df = pd.DataFrame.from_dict(dict_list).sort_values('date')\n",
    "\n",
    "\n",
    "for band in band_list:\n",
    "\n",
    "    df[band] = \"\"  # Create empty column in dataframe\n",
    "\n",
    "    for im in glob.glob(f'{clipped_path}*{band}*.tif'):\n",
    "        \n",
    "        date_str = os.path.basename(im)[begin_date:begin_date+8]\n",
    "\n",
    "        date_im = datetime.datetime.strptime(date_str, format).date()\n",
    "\n",
    "        df.loc[df.date == date_im, band] = im\n",
    "\n",
    "display(df)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Modify and concatenate masks "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(570, 986, 12)\n",
      "There are 12 masks\n"
     ]
    }
   ],
   "source": [
    "mask_concat_file = f'{gapfilled_path}SCL_timeserie.tif'\n",
    "    \n",
    "list_src_arr = []\n",
    "\n",
    "for i, row in df.iterrows():\n",
    "\n",
    "    im_file    = row['SCL']\n",
    "\n",
    "    src = rasterio.open(im_file, \"r\")\n",
    "\n",
    "    out_meta = src.meta\n",
    "    out_meta.update(count=len(df))\n",
    "\n",
    "    # Read file as numpy array\n",
    "    SCL = src.read(1)\n",
    "    src.close()\n",
    "\n",
    "    SCL[SCL == 0] = 1    # No data\n",
    "    SCL[SCL == 1] = 1    # Saturated or defective\n",
    "    SCL[SCL == 2] = 1    # Dark area pixels\n",
    "    SCL[SCL == 3] = 1    # Cloud shadows\n",
    "    SCL[SCL == 4] = 0    # Vegetation\n",
    "    SCL[SCL == 5] = 0    # Not vegetated\n",
    "    SCL[SCL == 6] = 0    # Water\n",
    "    SCL[SCL == 7] = 0    # Unclassified\n",
    "    SCL[SCL == 8] = 1    # Cloud medium probability\n",
    "    SCL[SCL == 9] = 1    # Cloud high probability\n",
    "    SCL[SCL == 10] = 1   # Thin cirrus\n",
    "    SCL[SCL == 11] = 1   # Snow\n",
    "\n",
    "    list_src_arr.append(SCL)\n",
    "\n",
    "mask_arr_stack = np.dstack(list_src_arr)#.astype(np.float32)\n",
    "\n",
    "print(mask_arr_stack.shape)\n",
    "print(f'There are {mask_arr_stack.shape[2]} masks')\n",
    "\n",
    "with rasterio.open(mask_concat_file, \"w\", **out_meta) as dest:\n",
    "    for band_nr, src in enumerate(list_src_arr, start=1):\n",
    "        dest.write(src, band_nr)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get input dates"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "input_dates_txt = f'{gapfilled_path}input_dates.txt'\n",
    "\n",
    "input_dates_list = df['date_str'].to_list()\n",
    "\n",
    "with open(input_dates_txt, 'w') as f:\n",
    "    for i in range(0,len(input_dates_list)):\n",
    "        f.write(input_dates_list[i] + '\\n')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get output dates"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "20200131\n",
      "20200229\n",
      "20200331\n",
      "20200430\n",
      "20200531\n",
      "20200630\n",
      "20200731\n",
      "20200831\n",
      "20200930\n",
      "20201031\n",
      "20201130\n"
     ]
    }
   ],
   "source": [
    "output_dates_txt = f'{gapfilled_path}output_dates.txt'\n",
    "\n",
    "start_date = df['date'].iloc[0]\n",
    "end_date  = df['date'].iloc[-1]\n",
    "\n",
    "output_dates_list = pd.date_range(start_date,end_date,freq=frequency).strftime('%Y%m%d').to_list()\n",
    "\n",
    "with open(output_dates_txt, 'w') as f:\n",
    "    for i in range(0,len(output_dates_list)):\n",
    "        print(output_dates_list[i])\n",
    "        f.write(output_dates_list[i] + '\\n')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Concatenate reflectance timeseries"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "otbcli_ConcatenateImages -il /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200116T105309_B02_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200212T104049_B02_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200316T104709_B02_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200417T104021_B02_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200520T105031_B02_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200621T103629_B02_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200719T105031_B02_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200813T104629_B02_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200914T104031_B02_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20201019T103959_B02_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20201118T104329_B02_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20201218T104349_B02_10m_ROI.tif -out /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/B02_timeserie.tif\n",
      "-------------------------------------------\n",
      "otbcli_ConcatenateImages -il /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200116T105309_B03_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200212T104049_B03_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200316T104709_B03_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200417T104021_B03_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200520T105031_B03_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200621T103629_B03_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200719T105031_B03_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200813T104629_B03_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20200914T104031_B03_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20201019T103959_B03_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20201118T104329_B03_10m_ROI.tif /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/2_L2A_CLIPPED/T31UFS_20201218T104349_B03_10m_ROI.tif -out /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/B03_timeserie.tif\n",
      "-------------------------------------------\n"
     ]
    }
   ],
   "source": [
    "for band in band_list:\n",
    "\n",
    "    im_concat_file = f'{gapfilled_path}{band}_timeserie.tif'\n",
    "    \n",
    "    im_path_list = df[band].tolist()\n",
    "    \n",
    "    if flag_otbAPI:\n",
    "        app = otb.Registry.CreateApplication(\"ConcatenateImages\")\n",
    "\n",
    "        app.SetParameterStringList(\"il\", im_path_list)\n",
    "        app.SetParameterString(\"out\", im_concat_file)\n",
    "\n",
    "        app.ExecuteAndWriteOutput()\n",
    "\n",
    "    else:\n",
    "        cmd = 'otbcli_ConcatenateImages'\n",
    "        cmd += f' -il {\" \".join(im_path_list)}'\n",
    "        cmd += f' -out {im_concat_file}'\n",
    "\n",
    "        print(cmd)\n",
    "        subprocess.call(cmd, shell=True)\n",
    "        print('-------------------------------------------')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Temporal Resampling and Gapfilling"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "otbcli_ImageTimeSeriesGapFilling -in /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/B02_timeserie.tif -mask /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/SCL_timeserie.tif -out /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/B02_timeserie_gapfilled_1m.tif -comp 1 -it linear -id /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/input_dates.txt -od /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/output_dates.txt\n",
      "-------------------------------------------\n",
      "otbcli_ImageTimeSeriesGapFilling -in /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/B03_timeserie.tif -mask /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/SCL_timeserie.tif -out /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/B03_timeserie_gapfilled_1m.tif -comp 1 -it linear -id /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/input_dates.txt -od /export/miro/ndeffense/LBRAT2104/STUDENTS/GROUP_99/TP/4_L2A_GAPFILLED/output_dates.txt\n",
      "-------------------------------------------\n"
     ]
    }
   ],
   "source": [
    "for band in band_list:\n",
    "\n",
    "    im_concat_file = f'{gapfilled_path}{band}_timeserie.tif'\n",
    "\n",
    "    gapfilled_file = f'{gapfilled_path}{band}_timeserie_gapfilled_{frequency}.tif'\n",
    "\n",
    "    if flag_otbAPI:\n",
    "        app = otb.Registry.CreateApplication(\"ImageTimeSeriesGapFilling\")\n",
    "\n",
    "        app.SetParameterString(\"in\", im_concat_file)\n",
    "        app.SetParameterString(\"mask\", mask_concat_file)\n",
    "        app.SetParameterString(\"out\", gapfilled_file)\n",
    "        app.SetParameterInt(\"comp\", 1)\n",
    "        app.SetParameterString(\"it\", interp_type)\n",
    "        app.SetParameterString(\"id\", input_dates_txt)\n",
    "        app.SetParameterString(\"od\", output_dates_txt)\n",
    "\n",
    "        app.ExecuteAndWriteOutput()\n",
    "    \n",
    "    else:\n",
    "        cmd = 'otbcli_ImageTimeSeriesGapFilling'\n",
    "        cmd += f' -in {im_concat_file}'\n",
    "        cmd += f' -mask {mask_concat_file}'\n",
    "        cmd += f' -out {gapfilled_file}'\n",
    "        cmd += f' -comp 1'\n",
    "        cmd += f' -it {interp_type}'\n",
    "        cmd += f' -id {input_dates_txt}'\n",
    "        cmd += f' -od {output_dates_txt}'\n",
    "\n",
    "        print(cmd)\n",
    "        subprocess.call(cmd, shell=True)\n",
    "        print('-------------------------------------------')"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Display gapfilled timeserie\n",
    "\n",
    "**TO DO**"
   ]
  }
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