Feat/ascii to netcdf

notebooks/create_netcdf_mesh_description_file.ipynb

@@ -0,0 +1,193 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Create netCDF mesh description file"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "This notebook gives an example of how to:\n",
+    "a) read the ASCII files that make up a FESOM mesh \n",
+    "b) compute a number of mesh caracteristics. \n",
+    "c) save the mesh as a [CDO](https://code.mpimet.mpg.de/projects/cdo) readable netCDF file for further use."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pyfesom2 as pf"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "griddir='/work/ab0246/a270092/input/fesom2/core2/'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "reading node (grid point) coordinates and coast information ...\n",
+      "... done. grid contains 126858 nodes of which 9311.0 are coastal (according to info in nod2d.out).\n",
+      "... execution Time: 0.47 seconds\n",
+      "reading neighbourhood (triangular elements) information ...\n",
+      "... done. grid contains 244659 triangular elements.\n",
+      "... execution Time: 0.65 seconds\n",
+      "reordering clockwise triangular elements counterclockwise ...\n",
+      "... done. 5 of 244659 elements reordered.\n",
+      "... execution Time: 5.81 seconds\n",
+      "reading 3D information ...\n",
+      "... done. Grid over all levels contains 3705887 elements.\n",
+      "... execution Time: 0.21 seconds\n",
+      "searching all neighbors of each node based on the triangular elements ...\n",
+      "... done. number of neighbors ranges from 3 to 9 nodes and is 5.8592 on average.\n",
+      "... execution Time: 12.8 seconds\n",
+      "determining which elements include coastal nodes ...\n",
+      "... done. grid features 9365 elements that contain coastal nodes.\n",
+      "... execution Time: 1.04 seconds\n",
+      "computing barycenters (centroids) for all triangular elements ...\n",
+      "... done.\n",
+      "... execution Time: 7.19 seconds\n",
+      "generate 'stamp polygons' around each node ...\n",
+      "... done. number of 'stamp polygon' vertices per node ranges from 6 (before padding) to 18 and is 11.7184 on average (before padding).\n",
+      "... execution Time: 24.23 seconds\n",
+      "computing element and 'stamp polygon' areas ...\n",
+      "... done.\n",
+      "... execution Time: 57.43 seconds\n"
+     ]
+    }
+   ],
+   "source": [
+    "grid = pf.read_fesom_ascii_grid(griddir=griddir)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "the grid has 3140 nodes (grid points) with up to 16 stamp polygon vertices per node.\n",
+      "the grid has 48 vertical levels.\n",
+      "Horizontal grid description file complete.\n",
+      "You can use this file to set the horizontal grid of a corresponding NetCDF file with 'cdo setgrid,/work/ab0246/a270092/input/fesom2/pi_mesh/mesh.nc ifile.nc ofile.nc'.\n"
+     ]
+    }
+   ],
+   "source": [
+    "pf.write_mesh_to_netcdf(grid, ofile=griddir+'mesh.nc',overwrite=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Lets check the grid we crated"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Dimensions:\n",
+      "ncells: 3140\n",
+      "vertices: 16\n",
+      "nlinks_max: 8\n",
+      "ntriags: 5839\n",
+      "Three: 3\n",
+      "nlev: 48\n",
+      "nlev_bnds: 49\n",
+      "\n",
+      "Variables:\n",
+      "lon: (3140,) \n",
+      "lon_bnds: (16, 3140) \n",
+      "lat: (3140,) \n",
+      "lat_bnds: (16, 3140) \n",
+      "cell_area: (3140,) \n",
+      "node_node_links: (8, 3140) \n",
+      "triag_nodes: (3, 5839) \n",
+      "coast: (3140,) \n",
+      "depth: (48,) \n",
+      "depth_bnds: (49,) \n",
+      "depth_lev: (3140,) \n",
+      "\n",
+      "Global attributes:\n",
+      "Conventions: CF-1.4\n",
+      "History: 2023-08-03 15:20:22 GMT; Grid description file generated with pyfesom2 version :0.2.0.; Grid written with: writeCDO(grid, ofile='/work/ab0246/a270092/input/fesom2/pi_mesh/mesh.nc', netcdf=True, netcdf_prec='double', ascii_digits=inf, overwrite=True, verbose=True, cell_area=True, node_node_links=True, triag_nodes=True, coast=True, depth=True, ofile_ZAXIS=None, fesom2velocities=False, conventions='original')\n"
+     ]
+    }
+   ],
+   "source": [
+    "import netCDF4 as nc\n",
+    "\n",
+    "# Replace 'your_file.nc' with the path to your actual NetCDF file\n",
+    "file_path = griddir+'mesh.nc'\n",
+    "\n",
+    "# Open the NetCDF file in read mode\n",
+    "nc_file = nc.Dataset(file_path, 'r')\n",
+    "\n",
+    "# Get information about the dimensions, variables, and global attributes\n",
+    "print(\"Dimensions:\")\n",
+    "for dimname, dim in nc_file.dimensions.items():\n",
+    "    print(f\"{dimname}: {len(dim)}\")\n",
+    "\n",
+    "print(\"\\nVariables:\")\n",
+    "for varname, var in nc_file.variables.items():\n",
+    "    print(f\"{varname}: {var.shape} {var.units if 'units' in var.ncattrs() else ''}\")\n",
+    "\n",
+    "print(\"\\nGlobal attributes:\")\n",
+    "for attrname in nc_file.ncattrs():\n",
+    "    print(f\"{attrname}: {getattr(nc_file, attrname)}\")\n",
+    "\n",
+    "# Close the NetCDF file after reading\n",
+    "nc_file.close()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

pyfesom2/__init__.py

@@ -21,3 +21,4 @@
 from .datasets import open_dataset
 from .accessor import FESOMDataArray as _FESOMDataArray
 from .transport import cross_section_transport
+from .ascii_to_netcdf import read_fesom_ascii_grid, write_mesh_to_netcdf