examples/Notebooks/flopy3_export.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# FloPy\n",
    "\n",
    "### Demo of netCDF and shapefile export capabilities within the flopy export module. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "flopy is installed in /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/flopy\n",
      "3.7.3 | packaged by conda-forge | (default, Jul  1 2019, 14:38:56) \n",
      "[Clang 4.0.1 (tags/RELEASE_401/final)]\n",
      "flopy version: 3.3.1\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "import sys\n",
    "import datetime\n",
    "\n",
    "# run installed version of flopy or add local path\n",
    "try:\n",
    "    import flopy\n",
    "except:\n",
    "    fpth = os.path.abspath(os.path.join('..', '..'))\n",
    "    sys.path.append(fpth)\n",
    "    import flopy\n",
    "\n",
    "print(sys.version)\n",
    "print('flopy version: {}'.format(flopy.__version__))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Load our old friend...the Freyberg model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "nam_file = \"freyberg.nam\"\n",
    "model_ws = os.path.join(\"..\", \"data\", \"freyberg_multilayer_transient\")\n",
    "ml = flopy.modflow.Modflow.load(nam_file, model_ws=model_ws, check=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can see the ``Modelgrid`` instance has generic entries, as does ``start_datetime``"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "xll:622241.1904510253; yll:3343617.741737109; rotation:15.0; proj4_str:+proj=utm +zone=14 +ellps=WGS84 +datum=WGS84 +units=m +no_defs; units:meters; lenuni:2"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ml.modelgrid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'1/1/2015'"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ml.modeltime.start_datetime"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Setting the attributes of the ``ml.modelgrid`` is easy:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "proj4_str = \"+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\"\n",
    "ml.modelgrid.set_coord_info(xoff=123456.7, yoff=765432.1, angrot=15.0, proj4=proj4_str)\n",
    "ml.dis.start_datetime = '7/4/1776'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'7/4/1776'"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ml.modeltime.start_datetime"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Some netCDF export capabilities:\n",
    "\n",
    "#### Export the whole model (inputs and outputs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "# make directory\n",
    "pth = os.path.join('data', 'netCDF_export')\n",
    "if not os.path.exists(pth):\n",
    "    os.makedirs(pth)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
      "initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
      "initialize_geometry::nc_crs = epsg:4326\n",
      "transforming coordinates using = proj=noop ellps=GRS80\n",
      "initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
      "initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
      "initialize_geometry::nc_crs = epsg:4326\n",
      "transforming coordinates using = proj=noop ellps=GRS80\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<flopy.export.netcdf.NetCdf at 0x11e6accc0>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fnc = ml.export(os.path.join(pth, ml.name+'.in.nc'))\n",
    "hds = flopy.utils.HeadFile(os.path.join(model_ws,\"freyberg.hds\"))\n",
    "flopy.export.utils.output_helper(os.path.join(pth, ml.name+'.out.nc'), ml, {\"hds\":hds})"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### export a single array to netcdf or shapefile"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
      "initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
      "initialize_geometry::nc_crs = epsg:4326\n",
      "transforming coordinates using = proj=noop ellps=GRS80\n",
      "wrote data/netCDF_export/top.shp\n"
     ]
    }
   ],
   "source": [
    "# export a 2d array\n",
    "ml.dis.top.export(os.path.join(pth, 'top.nc'))\n",
    "ml.dis.top.export(os.path.join(pth, 'top.shp'))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### sparse export of stress period data for a boundary condition package  \n",
    "* excludes cells that aren't in the package (aren't in `package.stress_period_data`)  \n",
    "* by default, stress periods with duplicate parameter values (e.g., stage, conductance, etc.) are omitted\n",
    "(`squeeze=True`); only stress periods with different values are exported  \n",
    "* argue `squeeze=False` to export all stress periods"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "wrote data/netCDF_export/drn.shp\n"
     ]
    }
   ],
   "source": [
    "ml.drn.stress_period_data.export(os.path.join(pth, 'drn.shp'), sparse=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Export a 3d array"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
      "initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
      "initialize_geometry::nc_crs = epsg:4326\n",
      "transforming coordinates using = proj=noop ellps=GRS80\n",
      "wrote data/netCDF_export/hk.shp\n"
     ]
    }
   ],
   "source": [
    "#export a 3d array\n",
    "ml.upw.hk.export(os.path.join(pth, 'hk.nc'))\n",
    "ml.upw.hk.export(os.path.join(pth, 'hk.shp'))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Export a number of things to the same netCDF file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
      "initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
      "initialize_geometry::nc_crs = epsg:4326\n",
      "transforming coordinates using = proj=noop ellps=GRS80\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<flopy.export.netcdf.NetCdf at 0x11e3255c0>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# export lots of things to the same nc file\n",
    "fnc = ml.dis.botm.export(os.path.join(pth, 'test.nc'))\n",
    "ml.upw.hk.export(fnc)\n",
    "ml.dis.top.export(fnc)\n",
    "\n",
    "# export transient 2d\n",
    "ml.rch.rech.export(fnc)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Export whole packages to a netCDF file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
      "initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
      "initialize_geometry::nc_crs = epsg:4326\n",
      "transforming coordinates using = proj=noop ellps=GRS80\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<class 'netCDF4._netCDF4.Dataset'>\n",
       "root group (NETCDF4 data model, file format HDF5):\n",
       "    Conventions: CF-1.6, ACDD-1.3, flopy 3.3.1\n",
       "    date_created: 2020-06-26T13:32:00Z\n",
       "    geospatial_vertical_positive: up\n",
       "    geospatial_vertical_min: -25.0\n",
       "    geospatial_vertical_max: 4.832500457763672\n",
       "    geospatial_vertical_resolution: variable\n",
       "    featureType: Grid\n",
       "    namefile: freyberg.nam\n",
       "    model_ws: ../data/freyberg_multilayer_transient\n",
       "    exe_name: mf2005.exe\n",
       "    modflow_version: mfnwt\n",
       "    create_hostname: IGSAAAHMLT40179\n",
       "    create_platform: Darwin\n",
       "    create_directory: /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/examples/Notebooks\n",
       "    solver_head_tolerance: -999\n",
       "    solver_flux_tolerance: -999\n",
       "    flopy_sr_xll: 123456.7\n",
       "    flopy_sr_yll: 765432.1\n",
       "    flopy_sr_rotation: 15.0\n",
       "    flopy_sr_proj4_str: +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
       "    start_datetime: 7/4/1776\n",
       "    dimensions(sizes): time(1097), layer(3), y(40), x(20)\n",
       "    variables(dimensions): int32 crs(), float64 time(time), float64 elevation(layer,y,x), float64 longitude(y,x), float64 latitude(y,x), float64 x_proj(y,x), float64 y_proj(y,x), float32 layer(layer), float32 delc(y), float32 delr(x), |S1 VerticalTransform(), float32 wel_flux(time,layer,y,x), float32 hani(layer,y,x), float32 hk(layer,y,x), float32 ss(layer,y,x), float32 sy(layer,y,x), float32 vka(layer,y,x), float32 vkcb(layer,y,x)\n",
       "    groups: "
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# export mflist\n",
    "fnc = ml.wel.export(os.path.join(pth, 'packages.nc'))\n",
    "ml.upw.export(fnc)\n",
    "fnc.nc"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Export the whole model to a netCDF"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
      "initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
      "initialize_geometry::nc_crs = epsg:4326\n",
      "transforming coordinates using = proj=noop ellps=GRS80\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<class 'netCDF4._netCDF4.Dataset'>\n",
       "root group (NETCDF4 data model, file format HDF5):\n",
       "    Conventions: CF-1.6, ACDD-1.3, flopy 3.3.1\n",
       "    date_created: 2020-06-26T13:32:00Z\n",
       "    geospatial_vertical_positive: up\n",
       "    geospatial_vertical_min: -25.0\n",
       "    geospatial_vertical_max: 4.832500457763672\n",
       "    geospatial_vertical_resolution: variable\n",
       "    featureType: Grid\n",
       "    namefile: freyberg.nam\n",
       "    model_ws: ../data/freyberg_multilayer_transient\n",
       "    exe_name: mf2005.exe\n",
       "    modflow_version: mfnwt\n",
       "    create_hostname: IGSAAAHMLT40179\n",
       "    create_platform: Darwin\n",
       "    create_directory: /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/examples/Notebooks\n",
       "    solver_head_tolerance: -999\n",
       "    solver_flux_tolerance: -999\n",
       "    flopy_sr_xll: 123456.7\n",
       "    flopy_sr_yll: 765432.1\n",
       "    flopy_sr_rotation: 15.0\n",
       "    flopy_sr_proj4_str: +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
       "    start_datetime: 7/4/1776\n",
       "    dimensions(sizes): time(1097), layer(3), y(40), x(20)\n",
       "    variables(dimensions): int32 crs(), float64 time(time), float64 elevation(layer,y,x), float64 longitude(y,x), float64 latitude(y,x), float64 x_proj(y,x), float64 y_proj(y,x), float32 layer(layer), float32 delc(y), float32 delr(x), |S1 VerticalTransform(), float32 botm(layer,y,x), float32 thickness(layer,y,x), float32 model_top(y,x), int32 ibound(layer,y,x), float32 strt(layer,y,x), float32 rech(time,layer,y,x), float32 wel_flux(time,layer,y,x), float32 hani(layer,y,x), float32 hk(layer,y,x), float32 ss(layer,y,x), float32 sy(layer,y,x), float32 vka(layer,y,x), float32 vkcb(layer,y,x), float32 drn_elev(time,layer,y,x), float32 drn_cond(time,layer,y,x)\n",
       "    groups: "
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "fnc = ml.export(os.path.join(pth, 'model.nc'))\n",
    "fnc.nc"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Export output to netcdf\n",
    "\n",
    "FloPy has utilities to export model outputs to a netcdf file. Valid output types for export are MODFLOW binary head files, formatted head files, cell budget files, seawat concentration files, and zonebudget output.\n",
    "\n",
    "Let's use output from the Freyberg model as an example of these functions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
      "initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
      "initialize_geometry::nc_crs = epsg:4326\n",
      "transforming coordinates using = proj=noop ellps=GRS80\n",
      "error getting data for cell_by_cell_flowstorage at time 1.0:list index out of range\n",
      "error getting data for cell_by_cell_flowstorage at time 1097.0:list index out of range\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<class 'netCDF4._netCDF4.Dataset'>\n",
       "root group (NETCDF4 data model, file format HDF5):\n",
       "    Conventions: CF-1.6, ACDD-1.3, flopy 3.3.1\n",
       "    date_created: 2020-06-26T13:33:00Z\n",
       "    geospatial_vertical_positive: up\n",
       "    geospatial_vertical_min: -25.0\n",
       "    geospatial_vertical_max: 4.832500457763672\n",
       "    geospatial_vertical_resolution: variable\n",
       "    featureType: Grid\n",
       "    namefile: freyberg.nam\n",
       "    model_ws: ../data/freyberg_multilayer_transient\n",
       "    exe_name: mf2005.exe\n",
       "    modflow_version: mfnwt\n",
       "    create_hostname: IGSAAAHMLT40179\n",
       "    create_platform: Darwin\n",
       "    create_directory: /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/examples/Notebooks\n",
       "    solver_head_tolerance: -999\n",
       "    solver_flux_tolerance: -999\n",
       "    flopy_sr_xll: 123456.7\n",
       "    flopy_sr_yll: 765432.1\n",
       "    flopy_sr_rotation: 15.0\n",
       "    flopy_sr_proj4_str: +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
       "    start_datetime: 7/4/1776\n",
       "    dimensions(sizes): time(1097), layer(3), y(40), x(20)\n",
       "    variables(dimensions): int32 crs(), float64 time(time), float64 elevation(layer,y,x), float64 longitude(y,x), float64 latitude(y,x), float64 x_proj(y,x), float64 y_proj(y,x), float32 layer(layer), float32 delc(y), float32 delr(x), |S1 VerticalTransform(), float32 head(time,layer,y,x), float32 constant_head(time,layer,y,x), float32 flow_right_face(time,layer,y,x), float32 flow_front_face(time,layer,y,x), float32 flow_lower_face(time,layer,y,x), float32 storage(time,layer,y,x)\n",
       "    groups: "
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# load binary head and cell budget files\n",
    "fhead = os.path.join(model_ws, 'freyberg.hds')\n",
    "fcbc = os.path.join(model_ws, 'freyberg.cbc')\n",
    "\n",
    "hds = flopy.utils.HeadFile(fhead)\n",
    "cbc = flopy.utils.CellBudgetFile(fcbc)\n",
    "\n",
    "export_dict = {\"hds\": hds,\n",
    "               \"cbc\": cbc}\n",
    "\n",
    "# export head and cell budget outputs to netcdf\n",
    "fnc = flopy.export.utils.output_helper(os.path.join(pth, \"output.nc\"), ml, export_dict)\n",
    "fnc.nc"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Exporting zonebudget output\n",
    "\n",
    "zonebudget output can be exported with other modflow outputs, and is placed in a seperate group which allows the user to post-process the zonebudget output before exporting.\n",
    "\n",
    "Here are two examples on how to export zonebudget output with a binary head and cell budget file\n",
    "\n",
    "__Example 1__: No postprocessing of the zonebudget output"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ZoneBudgetOutput Class\n",
       "----------------------\n",
       "\n",
       "Number of zones: 4\n",
       "Unique zones: 0, 1, 2, 3\n",
       "Number of buget records: 3291"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# load the zonebudget output file\n",
    "zonbud_ws = os.path.join(\"..\", \"data\", \"zonbud_examples\")\n",
    "fzonbud = os.path.join(zonbud_ws, \"freyberg_mlt.2.csv\")\n",
    "zon_arrays = flopy.utils.zonbud.read_zbarray(os.path.join(zonbud_ws, \"zonef_mlt.zbr\"))\n",
    "\n",
    "zbout = flopy.utils.ZoneBudgetOutput(fzonbud, ml.dis, zon_arrays)\n",
    "zbout"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
      "initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
      "initialize_geometry::nc_crs = epsg:4326\n",
      "transforming coordinates using = proj=noop ellps=GRS80\n",
      "error getting data for cell_by_cell_flowstorage at time 1.0:list index out of range\n",
      "error getting data for cell_by_cell_flowstorage at time 1097.0:list index out of range\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<class 'netCDF4._netCDF4.Dataset'>\n",
       "root group (NETCDF4 data model, file format HDF5):\n",
       "    Conventions: CF-1.6, ACDD-1.3, flopy 3.3.1\n",
       "    date_created: 2020-06-26T13:33:00Z\n",
       "    geospatial_vertical_positive: up\n",
       "    geospatial_vertical_min: -25.0\n",
       "    geospatial_vertical_max: 4.832500457763672\n",
       "    geospatial_vertical_resolution: variable\n",
       "    featureType: Grid\n",
       "    namefile: freyberg.nam\n",
       "    model_ws: ../data/freyberg_multilayer_transient\n",
       "    exe_name: mf2005.exe\n",
       "    modflow_version: mfnwt\n",
       "    create_hostname: IGSAAAHMLT40179\n",
       "    create_platform: Darwin\n",
       "    create_directory: /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/examples/Notebooks\n",
       "    solver_head_tolerance: -999\n",
       "    solver_flux_tolerance: -999\n",
       "    flopy_sr_xll: 123456.7\n",
       "    flopy_sr_yll: 765432.1\n",
       "    flopy_sr_rotation: 15.0\n",
       "    flopy_sr_proj4_str: +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
       "    start_datetime: 7/4/1776\n",
       "    dimensions(sizes): time(1097), layer(3), y(40), x(20)\n",
       "    variables(dimensions): int32 crs(), float64 time(time), float64 elevation(layer,y,x), float64 longitude(y,x), float64 latitude(y,x), float64 x_proj(y,x), float64 y_proj(y,x), float32 layer(layer), float32 delc(y), float32 delr(x), |S1 VerticalTransform(), float32 head(time,layer,y,x), float32 constant_head(time,layer,y,x), float32 flow_right_face(time,layer,y,x), float32 flow_front_face(time,layer,y,x), float32 flow_lower_face(time,layer,y,x), float32 storage(time,layer,y,x), float32 budget_zones(time,layer,y,x)\n",
       "    groups: zonebudget"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "export_dict = {'hds': hds,\n",
    "               'cbc': cbc}\n",
    "\n",
    "fnc = flopy.export.utils.output_helper(os.path.join(pth, \"output_with_zonebudget.nc\"),\n",
    "                                       ml, export_dict)\n",
    "\n",
    "fnc = zbout.export(fnc, ml)\n",
    "fnc.nc"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "A budget_zones variable has been added to the root group and a new zonebudget group has been added to the netcdf file which hosts all of the budget data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "__Example 2__: postprocessing zonebudget output then exporting"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>kper</th>\n",
       "      <th>kstp</th>\n",
       "      <th>zone</th>\n",
       "      <th>storage</th>\n",
       "      <th>constant head</th>\n",
       "      <th>other zones</th>\n",
       "      <th>total</th>\n",
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       "      <th>zone 1</th>\n",
       "      <th>zone 2</th>\n",
       "      <th>zone 3</th>\n",
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       "      <th>2</th>\n",
       "      <td>0</td>\n",
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       "      <th>3</th>\n",
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       "      <td>-18.493</td>\n",
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       "      <td>2489.4040</td>\n",
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       "      <td>0.0</td>\n",
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       "    <tr>\n",
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       "      <td>0.0</td>\n",
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       "      <td>236.617</td>\n",
       "      <td>0.0000</td>\n",
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       "      <td>1097.0</td>\n",
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       "</table>\n",
       "<p>3291 rows × 13 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      kper  kstp  zone     storage  constant head  other zones     total  \\\n",
       "0        0     0     1    0.000000    -821.281900    -1570.821 -2392.103   \n",
       "1        0     0     2    0.000000    -648.804700      630.730   -18.075   \n",
       "2        0     0     3    0.000000    -976.232200      940.092   -36.140   \n",
       "3        1     0     1  218.568500    -816.347300    -1173.221 -1770.999   \n",
       "4        1     0     2  191.816342    -643.938700      433.628   -18.493   \n",
       "...    ...   ...   ...         ...            ...          ...       ...   \n",
       "3286  1095     0     2 -626.408120    -505.116270     1113.766   -17.758   \n",
       "3287  1095     0     3 -627.235750    -801.732376     1393.454   -35.514   \n",
       "3288  1096     0     1    0.000000    -230.548300     -152.236  -382.784   \n",
       "3289  1096     0     2    0.000000      15.864900      -30.796   -14.931   \n",
       "3290  1096     0     3    0.000000    -212.896600      183.031   -29.865   \n",
       "\n",
       "      zone 0     zone 1    zone 2     zone 3  tslen   totim  \n",
       "0        0.0     0.0000 -1530.422   -40.3993    1.0     1.0  \n",
       "1        0.0  1530.4220     0.000  -899.6920    1.0     1.0  \n",
       "2        0.0    40.3993   899.692     0.0000    1.0     1.0  \n",
       "3        0.0     0.0000 -1134.937   -38.2835    1.0     2.0  \n",
       "4        0.0  1134.9370     0.000  -701.3090    1.0     2.0  \n",
       "...      ...        ...       ...        ...    ...     ...  \n",
       "3286     0.0  2489.4040     0.000 -1375.6380    1.0  1096.0  \n",
       "3287     0.0    17.8163  1375.638     0.0000    1.0  1096.0  \n",
       "3288     0.0     0.0000  -205.822    53.5856    1.0  1097.0  \n",
       "3289     0.0   205.8220     0.000  -236.6170    1.0  1097.0  \n",
       "3290     0.0   -53.5856   236.617     0.0000    1.0  1097.0  \n",
       "\n",
       "[3291 rows x 13 columns]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# load the zonebudget output and get the budget information\n",
    "zbout = flopy.utils.ZoneBudgetOutput(fzonbud, ml.dis, zon_arrays)\n",
    "df = zbout.dataframe\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's calculate a yearly volumetric budget from the zonebudget data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "data": {
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       "      <th>2</th>\n",
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       "      <td>37296.183058</td>\n",
       "      <td>-158237.438437</td>\n",
       "      <td>114408.0385</td>\n",
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       "      <td>91777.777222</td>\n",
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       "      <td>0.0000</td>\n",
       "      <td>-398769.3120</td>\n",
       "      <td>-8512.4548</td>\n",
       "      <td>546.0</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1777</td>\n",
       "      <td>2</td>\n",
       "      <td>42820.852999</td>\n",
       "      <td>-200142.961123</td>\n",
       "      <td>150829.2320</td>\n",
       "      <td>398769.3120</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>-247940.0845</td>\n",
       "      <td>546.0</td>\n",
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       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>1777</td>\n",
       "      <td>3</td>\n",
       "      <td>42818.153555</td>\n",
       "      <td>-312276.958409</td>\n",
       "      <td>256452.5519</td>\n",
       "      <td>8512.4548</td>\n",
       "      <td>247940.0845</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>546.0</td>\n",
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       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>1778</td>\n",
       "      <td>1</td>\n",
       "      <td>108226.799462</td>\n",
       "      <td>-255186.105500</td>\n",
       "      <td>-378440.1290</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>-371720.4820</td>\n",
       "      <td>-6719.6672</td>\n",
       "      <td>911.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>1778</td>\n",
       "      <td>2</td>\n",
       "      <td>44930.564942</td>\n",
       "      <td>-188836.557151</td>\n",
       "      <td>137315.0100</td>\n",
       "      <td>371720.4820</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>-234405.4742</td>\n",
       "      <td>911.0</td>\n",
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       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>1778</td>\n",
       "      <td>3</td>\n",
       "      <td>44936.970500</td>\n",
       "      <td>-299267.807443</td>\n",
       "      <td>241125.1428</td>\n",
       "      <td>6719.6672</td>\n",
       "      <td>234405.4742</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>911.0</td>\n",
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       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>1779</td>\n",
       "      <td>1</td>\n",
       "      <td>5348.709896</td>\n",
       "      <td>-129448.085100</td>\n",
       "      <td>-231291.1680</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>-227734.8190</td>\n",
       "      <td>-3556.3570</td>\n",
       "      <td>1097.0</td>\n",
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       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>1779</td>\n",
       "      <td>2</td>\n",
       "      <td>3241.895778</td>\n",
       "      <td>-95653.391040</td>\n",
       "      <td>88972.3010</td>\n",
       "      <td>227734.8190</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>-138762.5241</td>\n",
       "      <td>1097.0</td>\n",
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       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>1779</td>\n",
       "      <td>3</td>\n",
       "      <td>3233.272516</td>\n",
       "      <td>-152427.866886</td>\n",
       "      <td>142318.8767</td>\n",
       "      <td>3556.3570</td>\n",
       "      <td>138762.5241</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>1097.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    year  zone        storage  constant head  other zones       zone 1  \\\n",
       "0   1776     1   81203.267170 -134930.451200 -176631.7910       0.0000   \n",
       "1   1776     2   37268.485533 -102758.917473   62223.7540  172310.4031   \n",
       "2   1776     3   37296.183058 -158237.438437  114408.0385    4321.3803   \n",
       "3   1777     1   91777.777222 -265545.355300 -407281.7640       0.0000   \n",
       "4   1777     2   42820.852999 -200142.961123  150829.2320  398769.3120   \n",
       "5   1777     3   42818.153555 -312276.958409  256452.5519    8512.4548   \n",
       "6   1778     1  108226.799462 -255186.105500 -378440.1290       0.0000   \n",
       "7   1778     2   44930.564942 -188836.557151  137315.0100  371720.4820   \n",
       "8   1778     3   44936.970500 -299267.807443  241125.1428    6719.6672   \n",
       "9   1779     1    5348.709896 -129448.085100 -231291.1680       0.0000   \n",
       "10  1779     2    3241.895778  -95653.391040   88972.3010  227734.8190   \n",
       "11  1779     3    3233.272516 -152427.866886  142318.8767    3556.3570   \n",
       "\n",
       "         zone 2       zone 3   totim  \n",
       "0  -172310.4031   -4321.3803   181.0  \n",
       "1        0.0000 -110086.6556   181.0  \n",
       "2   110086.6556       0.0000   181.0  \n",
       "3  -398769.3120   -8512.4548   546.0  \n",
       "4        0.0000 -247940.0845   546.0  \n",
       "5   247940.0845       0.0000   546.0  \n",
       "6  -371720.4820   -6719.6672   911.0  \n",
       "7        0.0000 -234405.4742   911.0  \n",
       "8   234405.4742       0.0000   911.0  \n",
       "9  -227734.8190   -3556.3570  1097.0  \n",
       "10       0.0000 -138762.5241  1097.0  \n",
       "11  138762.5241       0.0000  1097.0  "
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# get a dataframe of volumetric budget information\n",
    "vol_df = zbout.volumetric_flux()\n",
    "\n",
    "# add a year field to the dataframe using datetime\n",
    "start_date = ml.modeltime.start_datetime\n",
    "start_date = datetime.datetime.strptime(start_date, \"%m/%d/%Y\")\n",
    "nzones = len(zbout.zones) - 1\n",
    "\n",
    "year = [start_date.year] * nzones\n",
    "for totim in vol_df.totim.values[:-nzones]:\n",
    "    t = start_date + datetime.timedelta(days=totim)\n",
    "    year.append(t.year)\n",
    "\n",
    "vol_df['year'] = year\n",
    "    \n",
    "# calculate yearly volumetric change using pandas\n",
    "totim_df = vol_df.groupby(['year', 'zone'], as_index=False)['totim'].max()\n",
    "yearly = vol_df.groupby(['year', 'zone'], as_index=False)[['storage', 'constant head', 'other zones',\n",
    "                                                           'zone 1', 'zone 2', 'zone 3']].sum()\n",
    "yearly['totim'] = totim_df['totim']\n",
    "yearly"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And finally, export the pandas dataframe to netcdf"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "initialize_geometry::proj4_str = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
      "initialize_geometry::self.grid_crs = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +type=crs\n",
      "initialize_geometry::nc_crs = epsg:4326\n",
      "transforming coordinates using = proj=noop ellps=GRS80\n",
      "error getting data for cell_by_cell_flowstorage at time 1.0:list index out of range\n",
      "error getting data for cell_by_cell_flowstorage at time 1097.0:list index out of range\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "<class 'netCDF4._netCDF4.Dataset'>\n",
       "root group (NETCDF4 data model, file format HDF5):\n",
       "    Conventions: CF-1.6, ACDD-1.3, flopy 3.3.1\n",
       "    date_created: 2020-06-26T13:33:00Z\n",
       "    geospatial_vertical_positive: up\n",
       "    geospatial_vertical_min: -25.0\n",
       "    geospatial_vertical_max: 4.832500457763672\n",
       "    geospatial_vertical_resolution: variable\n",
       "    featureType: Grid\n",
       "    namefile: freyberg.nam\n",
       "    model_ws: ../data/freyberg_multilayer_transient\n",
       "    exe_name: mf2005.exe\n",
       "    modflow_version: mfnwt\n",
       "    create_hostname: IGSAAAHMLT40179\n",
       "    create_platform: Darwin\n",
       "    create_directory: /Users/jdhughes/Documents/Development/flopy_git/flopy_fork/examples/Notebooks\n",
       "    solver_head_tolerance: -999\n",
       "    solver_flux_tolerance: -999\n",
       "    flopy_sr_xll: 123456.7\n",
       "    flopy_sr_yll: 765432.1\n",
       "    flopy_sr_rotation: 15.0\n",
       "    flopy_sr_proj4_str: +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs\n",
       "    start_datetime: 7/4/1776\n",
       "    dimensions(sizes): time(1097), layer(3), y(40), x(20)\n",
       "    variables(dimensions): int32 crs(), float64 time(time), float64 elevation(layer,y,x), float64 longitude(y,x), float64 latitude(y,x), float64 x_proj(y,x), float64 y_proj(y,x), float32 layer(layer), float32 delc(y), float32 delr(x), |S1 VerticalTransform(), float32 head(time,layer,y,x), float32 constant_head(time,layer,y,x), float32 flow_right_face(time,layer,y,x), float32 flow_front_face(time,layer,y,x), float32 flow_lower_face(time,layer,y,x), float32 storage(time,layer,y,x), float32 budget_zones(time,layer,y,x)\n",
       "    groups: zonebudget"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# process the new dataframe into a format that is compatible with netcdf exporting\n",
    "zbncf = zbout.dataframe_to_netcdf_fmt(yearly, flux=False)\n",
    "\n",
    "# export to netcdf\n",
    "export_dict = {\"hds\": hds,\n",
    "               \"cbc\": cbc,\n",
    "               \"zbud\": zbncf}\n",
    "\n",
    "fnc = flopy.export.utils.output_helper(os.path.join(pth, \"output_with_zonebudget.2.nc\"),\n",
    "                                       ml, export_dict)\n",
    "fnc.nc"
   ]
  }
 ],
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