Created an examples folder to do testing on real data

examples/README.md

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+# SFODA Examples

examples/get_example_data.sh

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+# Download example data
+DATADIR=tmpdata
+IWAVEATLASURL="https://cloudstor.aarnet.edu.au/plus/s/DnOYpT3ZPnqjNsS/download"
+IWAVEATLASFILE=NWS_2km_GLORYS_hex_2013_2014_SSHBC_Harmonics.nc
+
+# IWAVE atlas from a cloudstor public repo
+cd $DATADIR
+echo "Downloading internal wave atlas netcdf data ~160 GB"
+echo $IWAVEATLASURL $IWAVEATLASFILE
+curl $IWAVEATLASURL -o $IWAVEATLASFILE

examples/load_suntans_nc.py

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+"""
+Load an example suntans netcdf file
+"""
+
+import matplotlib.pyplot as plt
+from sfoda.suntans import sunxray
+
+# get the sfoda path
+import os
+import sfoda
+_path = os.path.abspath(sfoda.__file__)
+_dirpath = os.path.dirname(_path)
+
+
+ncfile = "{}/../tmpdata/NWS_2km_GLORYS_hex_2013_2014_SSHBC_Harmonics.nc".format(_dirpath)
+print('Loading suntans data from:\n\t{}'.format(ncfile))
+
+sun = sunxray.Sunxray(ncfile)
+print(sun)
+
+# Xarray object is stored in the ._ds attribute
+# To interface with the data
+data = sun._ds['SSH_BC_var']
+# Plot some data
+print(data)
+plt.figure()
+sun.plotcelldata(data)
+plt.show()
+
+

examples/run_sfoda_cloudstor.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Shows how to install and run [SFODA](https://github.com/mrayson/sfoda.git) in a cloudstor SWAN session\n",
+    "\n",
+    "To install this notebook run:\n",
+    "\n",
+    "    `!curl <insert_git_url> -o run_sfoda_cloudstor.ipynb` \n",
+    "    \n",
+    "in a SWAN notebook"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Install SFODA and dependencies via pip\n",
+    "!pip install git+https://github.com/mrayson/sfoda.git --user"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Download some test netcdf data (~160 GB)\n",
+    "!curl https://cloudstor.aarnet.edu.au/plus/s/DnOYpT3ZPnqjNsS/download -o NWS_2km_GLORYS_hex_2013_2014_SSHBC_Harmonics.nc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "from sfoda.suntans.sunxray import Sunxray\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load the suntans object\n",
+    "basedir = './'\n",
+    "ncfile = 'NWS_2km_GLORYS_hex_2013_2014_SSHBC_Harmonics.nc'.format(basedir)\n",
+    "\n",
+    "sun = Sunxray(ncfile)\n",
+    "sun\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# The xarray obect is stored in the ._ds attribute\n",
+    "# data can be referenced directly via e.g.\n",
+    "data = sun._ds['SSH_BC_var']\n",
+    "data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Use inbuilt plotting methods for quick plotting\n",
+    "plt.figure(figsize=(12,6))\n",
+    "sun.plotcelldata(data, vmax=5e-3, cmap='Reds')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}