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nsw-2016-storm-impact
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Update QGIS and notebooks

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Chris Leaman 6 years ago
parent ecd1d66dd2
commit 708606391f
3 changed files with 262 additions and 19 deletions
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73
notebooks/07_evaluate_model_performance.ipynb
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@ -58,7 +58,7 @@
"from ipywidgets import widgets, Output\n",
"from IPython.display import display, clear_output, Image, HTML\n",
"from scipy import stats\n",
"from sklearn.metrics import confusion_matrix\n",
"from sklearn.metrics import confusion_matrix, matthews_corrcoef\n",
"import matplotlib.pyplot as plt\n",
"from matplotlib.ticker import MultipleLocator\n",
"from matplotlib.lines import Line2D\n",
@ -116,6 +116,7 @@
"df_tides = df_from_csv('tides.csv', index_col=[0, 1])\n",
"df_profiles = df_from_csv('profiles.csv', index_col=[0, 1, 2])\n",
"df_sites = df_from_csv('sites.csv', index_col=[0])\n",
"df_sites_waves = df_from_csv('sites_waves.csv', index_col=[0])\n",
"df_profile_features_crest_toes = df_from_csv('profile_features_crest_toes.csv', index_col=[0,1])\n",
"\n",
"# Note that the forecasted data sets should be in the same order for impacts and twls\n",
@ -204,12 +205,12 @@
" \n",
" # Determine the height of the figure, based on the number of sites.\n",
" fig_height = max(6, 0.18 * len(n_sites))\n",
" f, (ax1, ax2, ax3, ax4, ax5, ax6, ax7, ax8) = plt.subplots(\n",
" f, (ax1, ax2, ax3, ax4, ax5, ax6, ax7, ax8, ax9) = plt.subplots(\n",
" 1,\n",
" 8,\n",
" 9,\n",
" sharey=True,\n",
" figsize=(18, fig_height),\n",
" gridspec_kw={'width_ratios': [4, 4, 2, 2, 2, 2, 2, 2]})\n",
" gridspec_kw={'width_ratios': [4, 4, 2, 2, 2, 2, 2, 2,2]})\n",
"\n",
" # ax1: Impacts\n",
"\n",
@ -442,7 +443,7 @@
" ax6.plot(df_beach.Hs0, n, color='#999999')\n",
" ax6.set_title('$H_{s0}$')\n",
" ax6.set_xlabel('Sig. wave height (m)')\n",
" ax6.set_xlim([3, 5])\n",
" ax6.set_xlim([2, 6])\n",
"\n",
" ax7.plot(df_beach.Tp, n, color='#999999')\n",
" ax7.set_title('$T_{p}$')\n",
@ -452,7 +453,11 @@
" ax8.plot(df_beach.tide, n, color='#999999')\n",
" ax8.set_title('Tide \\& surge')\n",
" ax8.set_xlabel('Elevation (m AHD)')\n",
" ax8.set_xlim([0, 2])\n",
" ax8.set_xlim([1, 3])\n",
"\n",
" \n",
" # TODO Cumulative wave energy\n",
" # df_sites_waves\n",
" \n",
" plt.tight_layout()\n",
" f.subplots_adjust(top=0.88)\n",
@ -472,12 +477,28 @@
" # # Print to figure\n",
" plt.savefig('07_{}.png'.format(beach), dpi=600, bbox_inches='tight')\n",
"\n",
"# plt.show()\n",
" plt.show()\n",
" plt.close()\n",
" print('Done: {}'.format(beach))\n",
" \n",
" break\n",
"print('Done!')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
@ -523,6 +544,44 @@
" print()\n",
" "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Check matthews coefficient\n",
"# https://scikit-learn.org/stable/modules/generated/sklearn.metrics.matthews_corrcoef.html\n",
"\n",
"for model in impacts['forecasted']:\n",
" df_for = impacts['forecasted'][model]\n",
" df_for.storm_regime = df_for.storm_regime.astype(cat_type)\n",
"\n",
" m = matthews_corrcoef(\n",
" df_obs.storm_regime.astype(cat_type).cat.codes.values,\n",
" df_for.storm_regime.astype(cat_type).cat.codes.values)\n",
" print('{}: {:.2f}'.format(model,m))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Check accuracy\n",
"# https://scikit-learn.org/stable/modules/generated/sklearn.metrics.matthews_corrcoef.html\n",
"\n",
"for model in impacts['forecasted']:\n",
" df_for = impacts['forecasted'][model]\n",
" df_for.storm_regime = df_for.storm_regime.astype(cat_type)\n",
"\n",
" m = sklearn.metrics.accuracy_score(\n",
" df_obs.storm_regime.astype(cat_type).cat.codes.values,\n",
" df_for.storm_regime.astype(cat_type).cat.codes.values)\n",
" print('{}: {:.2f}'.format(model,m))"
]
}
],
"metadata": {

208
notebooks/11_investigate.ipynb
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@ -63,7 +63,9 @@
"from matplotlib.lines import Line2D\n",
"from cycler import cycler\n",
"from scipy.interpolate import interp1d\n",
"from pandas.api.types import CategoricalDtype"
"from pandas.api.types import CategoricalDtype\n",
"import seaborn as sns\n",
"sns.set(style=\"white\")"
]
},
{
@ -144,7 +146,8 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"# Sec1"
"# Gather data into one dataframe\n",
"For plotting, gather all our data into one dataframe."
]
},
{
@ -153,9 +156,43 @@
"metadata": {},
"outputs": [],
"source": [
"# Which forecasted impacts dataframe should we use to assess prediction performance?\n",
"df_selected_forecast = impacts['forecasted']['postintertidal_slope_sto06']\n",
"\n",
"# Create df with all our data\n",
"df = impacts['observed'].merge(df_sites_waves,left_index=True,right_index=True)\n",
"df.columns"
"df = impacts['observed'].merge(\n",
" df_sites_waves, left_index=True, right_index=True)\n",
"\n",
"# Join observed/forecasted regimes\n",
"df_forecasted = df_selected_forecast.rename(\n",
" {'storm_regime': 'forecasted_regime'\n",
" }, axis='columns').forecasted_regime\n",
"df = pd.concat([df, df_forecasted], axis=1)\n",
"\n",
"# Create new accuracy column which categorises each prediction\n",
"df.loc[(df.storm_regime == 'swash') & (df.forecasted_regime == 'swash'), 'accuracy'] = 'correct swash'\n",
"df.loc[(df.storm_regime == 'collision') & (df.forecasted_regime == 'collision'), 'accuracy'] = 'correct collision'\n",
"df.loc[(df.storm_regime == 'swash') & (df.forecasted_regime == 'collision'), 'accuracy'] = 'overpredicted swash'\n",
"df.loc[(df.storm_regime == 'collision') & (df.forecasted_regime == 'swash'), 'accuracy'] = 'underpredicted collision'\n",
"\n",
"print('df columns:\\n===')\n",
"for col in sorted(df.columns):\n",
" print(col)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Create plots"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Variable pairplot, by observed storm impact\n",
"Create pairplot of selected variables and look for relationships between each. Colors represent the different observed storm impact regimes."
]
},
{
@ -164,8 +201,6 @@
"metadata": {},
"outputs": [],
"source": [
"import seaborn as sns\n",
"sns.set(style=\"white\")\n",
"g = sns.pairplot(\n",
" data=df,\n",
" hue='storm_regime',\n",
@ -175,13 +210,23 @@
" 'collision': 'orange',\n",
" 'overwash': 'red'\n",
" },\n",
" plot_kws=dict(s=20, edgecolor=\"white\", linewidth=0.1, alpha=0.1),\n",
" vars=['beta_prestorm_mean',\n",
" 'beta_poststorm_mean',\n",
" 'beta_diff_mean',\n",
" 'swash_pct_change',\n",
" 'df_width_msl_change_m',\n",
" 'df_width_msl_change_pct',\n",
" 'Exscum'])"
" 'width_msl_change_m',\n",
" 'width_msl_change_pct',\n",
" 'Exscum'])\n",
"g.savefig('11_pairplot_observed_impacts.png')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Variable pairplot, by observed/prediction class\n",
"Create pairplot of selected variables and look for relationships between each. Colors represent the different observed/prediction classes."
]
},
{
@ -190,8 +235,142 @@
"metadata": {},
"outputs": [],
"source": [
"g.savefig('11_pairplot.png')"
"g = sns.pairplot(\n",
" data=df,\n",
" hue='accuracy',\n",
" dropna=True,\n",
" palette={\n",
" 'correct swash': 'blue',\n",
" 'correct collision': 'green',\n",
" 'overpredicted swash': 'orange',\n",
" 'underpredicted collision': 'red',\n",
" },\n",
" plot_kws=dict(s=20, edgecolor=\"white\", linewidth=0.1, alpha=0.1),\n",
" vars=['beta_prestorm_mean',\n",
" 'beta_poststorm_mean',\n",
" 'beta_diff_mean',\n",
" 'swash_pct_change',\n",
" 'width_msl_change_m',\n",
" 'width_msl_change_pct',\n",
" 'Exscum'])\n",
"g.savefig('11_pairplot_accuracy_classes.png')\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Pre/post storm slope by observed/predicted class"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# First create a melted dataframe since our coulmn's aren't exactly as they should be for plotting\n",
"df_temp = df.copy()\n",
"df_temp = df_temp.reset_index()\n",
"\n",
"df_melt = pd.melt(\n",
" df_temp,\n",
" id_vars=['site_id', 'accuracy'],\n",
" value_vars=['beta_prestorm_mean', 'beta_poststorm_mean'],\n",
" var_name='profile_type',\n",
" value_name='beta_mean')\n",
"\n",
"df_melt.loc[df_melt.profile_type == 'beta_prestorm_mean','profile_type'] = 'prestorm'\n",
"df_melt.loc[df_melt.profile_type == 'beta_poststorm_mean','profile_type'] = 'poststorm'\n",
"df_melt.head()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"f, ax = plt.subplots(figsize=(6,5))\n",
"\n",
"cats = ['correct swash', 'overpredicted swash','underpredicted collision','correct collision']\n",
"\n",
"# Plot the orbital period with horizontal boxes\n",
"sns.boxplot(\n",
" data=df_melt,\n",
" x=\"accuracy\",\n",
" y=\"beta_mean\",\n",
" hue=\"profile_type\",\n",
" order=cats\n",
")\n",
"\n",
"group_labels = [x.replace(' ','\\n') for x in cats]\n",
"ax.set_xticklabels(group_labels)\n",
"\n",
"# Setup ticks and grid\n",
"ax.xaxis.grid(True)\n",
"major_ticks = np.arange(-1, 1, 0.05)\n",
"minor_ticks = np.arange(-1, 1, 0.01)\n",
"ax.set_yticks(major_ticks)\n",
"ax.set_yticks(minor_ticks, minor=True)\n",
"ax.grid(which='both')\n",
"ax.grid(which='minor', alpha=0.3,linestyle='--')\n",
"ax.grid(which='major', alpha=0.8,linestyle='-')\n",
"\n",
"ax.set_ylim([-0.02,0.3])\n",
"\n",
"f.savefig('11_prepost_slopes_accuracy_classes.png',dpi=600)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Change in slope by observed/predicted class"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"f, ax = plt.subplots(figsize=(6,5))\n",
"\n",
"cats = ['correct swash', 'overpredicted swash','underpredicted collision','correct collision']\n",
"\n",
"# Plot the orbital period with horizontal boxes\n",
"sns.boxplot(\n",
" data=df,\n",
" x=\"accuracy\",\n",
" y=\"beta_diff_mean\",\n",
" order=cats\n",
")\n",
"\n",
"group_labels = [x.replace(' ','\\n') for x in cats]\n",
"ax.set_xticklabels(group_labels)\n",
"\n",
"# Setup ticks and grid\n",
"ax.xaxis.grid(True)\n",
"major_ticks = np.arange(-1, 1, 0.05)\n",
"minor_ticks = np.arange(-1, 1, 0.01)\n",
"ax.set_yticks(major_ticks)\n",
"ax.set_yticks(minor_ticks, minor=True)\n",
"ax.grid(which='both')\n",
"ax.grid(which='minor', alpha=0.3,linestyle='--')\n",
"ax.grid(which='major', alpha=0.8,linestyle='-')\n",
"\n",
"ax.set_ylim([-0.2,0.2])\n",
"\n",
"f.savefig('11_change_in_slopes_accuracy_classes.png',dpi=600)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
@ -222,9 +401,14 @@
"title_cell": "Table of Contents",
"title_sidebar": "Contents",
"toc_cell": false,
"toc_position": {},
"toc_position": {
"height": "calc(100% - 180px)",
"left": "10px",
"top": "150px",
"width": "223.594px"
},
"toc_section_display": true,
"toc_window_display": false
"toc_window_display": true
},
"varInspector": {
"cols": {

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