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    "# running automatic fitting in ROD\n",
    "\n",
    "before running the cells below make sure you have done the following:\n",
    "- have a version of RODautofitting.py in the same directory as where you have saved this notebook\n",
    "- made a copy of rod_init.mac in the ROD directory saved as rod_init_template.mac\n",
    "- saved a copy of fitlogloop5.mac and fitlogloop5run.mac in the ROD directory. Use the text below, replacing 'path\\to\\fitting\\folder'  with you own chosen folder. This will save the output of 5 fitting runs to fitting_#.par files\n",
    "\n",
    "fitlogloop5.mac - carries out 5 ASA fitting loops and saves output\n",
    "```\n",
    "li par \"path\\to\\fitting\\folder\\fitting_0.par\" start_parameters\n",
    "fit control open \"path\\to\\fitting\\folder\\\\fitrun.log\" return return\n",
    "fit asa pl allbo\n",
    "li par \"path\\to\\fitting\\folder\\\\fitting_1.par\" results_from_loop_1\n",
    "fit asa pl allbo\n",
    "li par \"path\\to\\fitting\\folder\\\\fitting_2.par\" results_from_loop_2\n",
    "fit asa pl allbo\n",
    "li par \"path\\to\\fitting\\folder\\\\fitting_3.par\" results_from_loop_3\n",
    "fit asa pl allbo\n",
    "li par \"path\\to\\fitting\\folder\\\\fitting_4.par\" results_from_loop_4\n",
    "fit asa pl allbo\n",
    "li par \"path\\to\\fitting\\folder\\\\fitting_5.par\" results_from_loop_5\n",
    "fit control close return return\n",
    "mac modelout\n",
    "```\n",
    "\n",
    "fitlogloop5run.mac - carries out 5 run fitting loops and saves output\n",
    "```\n",
    "li par \"path\\to\\fitting\\folder\\fitting_0.par\" start_parameters\n",
    "fit control open \"path\\to\\fitting\\folder\\\\fitrun.log\" return return\n",
    "fit run pl allbo\n",
    "li par \"path\\to\\fitting\\folder\\\\fitting_1.par\" results_from_loop_1\n",
    "fit run pl allbo\n",
    "li par \"path\\to\\fitting\\folder\\\\fitting_2.par\" results_from_loop_2\n",
    "fit run pl allbo\n",
    "li par \"path\\to\\fitting\\folder\\\\fitting_3.par\" results_from_loop_3\n",
    "fit run pl allbo\n",
    "li par \"path\\to\\fitting\\folder\\\\fitting_4.par\" results_from_loop_4\n",
    "fit run pl allbo\n",
    "li par \"path\\to\\fitting\\folder\\\\fitting_5.par\" results_from_loop_5\n",
    "fit control close return return\n",
    "mac modelout\n",
    "```"
   ]
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    "## Define all file paths\n",
    "run cell below to load in the path information for where to find and/or save all the important files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5e1b4dc0",
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   "source": [
    "from RODautofitting import * \n",
    "import os\n",
    "\n",
    "# give the path to where the final 5th fitting run is saved for each loop of 5\n",
    "fit5path=fr\"\\path\\to\\fitting\\folder\\fitting_5.par\"\n",
    "folderpath='define path here'\n",
    "# define the files to load into ROD using a dictionary\n",
    "files={}\n",
    "files['fit']= fr\"{folderpath}\\path\\to\\fit\\file\"\n",
    "files['dat']= fr\"{folderpath}path\\to\\dat\\file\"\n",
    "files['bul']= fr\"{folderpath}\\path\\to\\bulk\\file\"\n",
    "files['loadmac']= fr\"{folderpath}\\path\\to\\macro\\file\"  # e.g. for loading matrices\n",
    "files['par']= fr\"{folderpath}\\path\\to\\par\\file\"  #used as starting values\n",
    "files['fitmac']=fr\"{folderpath}\\path\\to\\fittingmacro\\file\"\n",
    "\n",
    "# create model name based on fitfile\n",
    "modname = files['fit'].split(r\"\\\\\")[-1]\n",
    "\n",
    "# set computer specific location for rod program and its init.mac file\n",
    "rodexe=fr\"\\path\\to\\anarod_standard_1-7_mingw\\rod.exe\"\n",
    "initfile=fr\"\\path\\to\\\\anarod_standard_1-7_mingw\\rod_init.mac\"\n",
    "\n",
    "#make a copy of initial rod_init.mac before any edits saved as rod_init_template.mac\n",
    "templateinitfile=fr\"\\path\\to\\anarod_standard_1-7_mingw\\rod_init_template.mac\"\n",
    "\n",
    "# set where to save dummy file used to flag when fitting loop is done\n",
    "donefile=fr\"\\path\\to\\to\\done\\file\"\n",
    "\n",
    "# set path where fitting results are saved as defined in macro fitlogloop5.mac\n",
    "fit5path=fr\"\\path\\to\\path\\to\\fitting\\folder\\fitting_5.par\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b8d02686",
   "metadata": {},
   "source": [
    "## start the fitting routine\n",
    "Running the cell below starts the fitting cycles which does a series of ASA fits and then run fits until the chi squared values have stabilised"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a4b842cd",
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   "source": [
    "#create a ASA loop macro based on files dictionary\n",
    "createmacro(modname,files,files['par'],donefile,'ASA')\n",
    "\n",
    "#do an initial ASA fitting round\n",
    "domacrofits(donefile,rodexe)\n",
    "\n",
    "#define where the outputs are being save for each loop macro\n",
    "run = os.path.dirname(fit5path)+rf\"\\fitting\"\n",
    "\n",
    "#calculate chi-squared information for first fit\n",
    "fitlist, fitted, ranges, fitdf=calcfitlist(run, 5)\n",
    "asacount = 1\n",
    "print(f\"asa loop {asacount}\")\n",
    "\n",
    "#enter a loop that continues running rounds of 5 ASA fits until the final three chi squared values are within 0.01 of each other\n",
    "endasachi,asacount=fitloop(\n",
    "    modname, fitlist, files, fit5path, donefile, rodexe, asacount, run,'ASA'\n",
    "    )\n",
    "\n",
    "# once the ASA fitting gave a stable answer copy the parameters to  a set location\n",
    "shutil.copy(\n",
    "    f\"{fit5path}\",fr\"{folderpath}\\path\\to\\saving\\location\\asafit_{modname.replace('.fit','')}.par\"\n",
    "    )\n",
    "\n",
    "# set starting parameters to the last of the ASA fits\n",
    "startvals = fit5path\n",
    "\n",
    "# create a run loop macro\n",
    "createmacro(modname, files, startvals, donefile,'RUN')\n",
    "\n",
    "# do an initial run fitting round\n",
    "domacrofits(donefile, rodexe)\n",
    "\n",
    "#calculate chi-squared information for first fit\n",
    "fitlist, fitted, ranges, fitdf = calcfitlist(run,5)\n",
    "runcount = 1\n",
    "print(f'run loop {runcount}')\n",
    "\n",
    "#enter a loop that continues running rounds of 5 run fits until the final three chi squared values are within 0.005 of each other\n",
    "endrunchi,runcount=fitloop(\n",
    "    modname,fitlist,files,fit5path,donefile,rodexe,runcount,run,'RUN'\n",
    "    )\n",
    "\n",
    "#once the run fitting gave a stable answer copy the parameters to  a set location\n",
    "shutil.copy(f\"{fit5path}\",fr\"{folderpath}\\path\\to\\saving\\location\\runfit_{modname.replace('.fit','')}.par\")"
   ]
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