{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Command line executable to fix marthe fmt\n",
    "\n",
    "In some older versions of MARTHE, grid attributes were miswritten.\n",
    "A fix script is included in `gridmarthe` if users need to read such file.\n",
    "This example show how to use this script, called `cleanmgrid`. All kind of gridfiles may not be included. Please make an issue if you appear to lack a treatment.\n",
    "\n",
    "\n",
    "*nb: the next commands are shell commands, the '!' mark is only here for the python notebook version.*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "vscode": {
     "languageId": "shellscript"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Marthe_Grid Version=9.0\n",
      "Title=Bidon                                                                  H_SUBSTRAT     1\n",
      "[Infos]\n",
      "Field=\n",
      "Type=\n",
      "Elem_Number=0\n",
      "Name=\n",
      "Time_Step=-9999\n",
      "Time=0\n",
      "Layer=0\n",
      "Max_Layer=0\n",
      "Nest_grid=0\n",
      "Max_NestG=0\n",
      "[Structure]\n",
      "X_Left_Corner=528\n",
      "Y_Lower_Corner=2503\n",
      "Ncolumn=320\n",
      "Nrows=189\n",
      "[Data_Descript]\n",
      "! Line 1       :   0   ,     0          , <   1 , 2 , 3 , Ncolumn   >\n",
      "! Line 2       :   0   ,     0          , < X_Center_of_all_Columns >\n",
      "! Line 2+1     :   1   , Y_of_Row_1     , < Field_Values_of_all_Columns > , Dy_of_Row_1\n",
      "! Line 2+2     :   2   , Y_of_Row_2     , < Field_Values_of_all_Columns > , Dy_of_Row_2\n",
      "! Line 2+Nrows : Nrows , Y_of_Row_Nrows , < Field_Values_of_all_Columns > , Dy_of_Row_2\n",
      "! Line 3+Nrows :   0   ,     0          , <     Dx_of_all_Colums    >\n",
      "[Data]\n",
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      "1\t2597.25\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t.5\t\n",
      "2\t2596.75\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t-24.81\t-24.93\t-23\t-25.13\t-23\t-24.04\t-20\t-21.98\t-20.87\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t9999\t.5\t\n"
     ]
    }
   ],
   "source": [
    "# how to use: print help message\n",
    "!head -30 ./data/grid_wrong_attrs.hsubs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Clean one grid, with arguments\n",
    "\n",
    "In the above results, we can see that `Layer`, `Max_Layer`, `Nest_grid`, `Max_Nestg` are all set to 0.\n",
    "This is an error which prevent successfull Marthe IO operations with `gridmarthe` or `pymarthe`.\n",
    "The script `cleanmgrid` is going to fix it."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "vscode": {
     "languageId": "shellscript"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "usage: cleanmgrid [-h] [--layer LAYER] [--grid GRID] [--output OUTPUT]\n",
      "                  [--no_overwrite]\n",
      "                  PATH_TO_FILE\n",
      "\n",
      "Clean marthe grid file for miswritten attributes. Only works for marthe grid v9.0 (a check is performed and <v9 are skipped)\n",
      "\n",
      "positional arguments:\n",
      "  PATH_TO_FILE          PATH_TO_FILE can be a relative path, if it ends with\n",
      "                        \".rma\" all grid file in rma project will be processed.\n",
      "\n",
      "options:\n",
      "  -h, --help            show this help message and exit\n",
      "  --layer LAYER, -l LAYER\n",
      "                        Number of layer. Only if PATH_TO_FILE is *NOT* a rma\n",
      "                        file. Otherwise, it will be parsed from Marthe's\n",
      "                        files.\n",
      "  --grid GRID, -g GRID  Number of nested grid. Only if PATH_TO_FILE is *NOT* a\n",
      "                        rma file. Otherwise, it will be parsed from Marthe's\n",
      "                        files.\n",
      "  --output OUTPUT, -o OUTPUT\n",
      "                        Output file. Only if PATH_TO_FILE is a single grid\n",
      "                        file and *NOT* a rma file. Otherwise, all files will\n",
      "                        be bakup and clean\n",
      "  --no_overwrite, -n    Do no overwrite file, add `.fix` extension. By default\n",
      "                        file is bakup and then overwrite.\n",
      "\n",
      "gridmarthe  Copyright (C) 2024  BRGM.\n",
      "This program comes with ABSOLUTELY NO WARRANTY.\n",
      "This is free software, see GNU General Public Lisence v3 for copying.\n"
     ]
    }
   ],
   "source": [
    "# print help to check for accepted args\n",
    "!cleanmgrid -h"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`cleanmgrid` is designed to work with single grid files or rma (Marthe Projects) files.\n",
    "In the first case, you need to give to the program the value to fix (number of layer,\n",
    "number of nested grids) before the argument (file to clean).\n",
    "In the second case (rma mode), you only need to give the rma file as argument. All\n",
    "values will be parsed from marthe files."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "vscode": {
     "languageId": "shellscript"
    }
   },
   "outputs": [],
   "source": [
    "# let's try for a simple case, with only one grid file\n",
    "!cleanmgrid ./data/grid_wrong_attrs.hsubs -l 1 -g 3 -o grid_clean.hsubs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "vscode": {
     "languageId": "shellscript"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Marthe_Grid Version=9.0\n",
      "Title=Bidon                                                                  H_SUBSTRAT     1\n",
      "[Infos]\n",
      "Field=H_SUBSTRAT\n",
      "Type=\n",
      "Elem_Number=0\n",
      "Name=\n",
      "Time_Step=-9999\n",
      "Time=0\n",
      "Layer=1\n",
      "Max_Layer=1\n",
      "Nest_grid=0\n",
      "Max_NestG=3\n",
      "[Structure]\n",
      "X_Left_Corner=528\n",
      "Y_Lower_Corner=2503\n",
      "Ncolumn=320\n",
      "Nrows=189\n",
      "[Data_Descript]\n",
      "! Line 1       :   0   ,     0          , <   1 , 2 , 3 , Ncolumn   >\n",
      "! Line 2       :   0   ,     0          , < X_Center_of_all_Columns >\n",
      "! Line 2+1     :   1   , Y_of_Row_1     , < Field_Values_of_all_Columns > , Dy_of_Row_1\n",
      "! Line 2+2     :   2   , Y_of_Row_2     , < Field_Values_of_all_Columns > , Dy_of_Row_2\n",
      "! Line 2+Nrows : Nrows , Y_of_Row_Nrows , < Field_Values_of_all_Columns > , Dy_of_Row_2\n",
      "! Line 3+Nrows :   0   ,     0          , <     Dx_of_all_Colums    >\n",
      "[Data]\n",
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     ]
    }
   ],
   "source": [
    "# print variables headers and dimensions with nco tools\n",
    "!head -30 ./data/grid_clean.hsubs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Process all grid of a Marthe Project\n",
    "\n",
    "`cleanmgrid` also work if you specified a `*.rma` file (Marthe Project). In such case, the program will try to fix all grid files of the project !"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "shellscript"
    }
   },
   "outputs": [],
   "source": [
    "## juste do:\n",
    "# cleanmgrid MyModel.rma"
   ]
  }
 ],
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