Add 'probabilistic_assessment.py'
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# Performs probabilstic assessment on *.yaml files,
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# and saves output shoreline chainages to csv
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import os
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import yaml
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import argparse
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import numpy as np
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import pandas as pd
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import matplotlib
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import matplotlib.patheffects
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import matplotlib.pyplot as plt
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import matplotlib.gridspec as gridspec
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from scipy.optimize import curve_fit
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from scipy import interpolate
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from tqdm import tqdm
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# Suppress pandas SettingWithCopy warnings
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# pd.options.mode.chained_assignment = None
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import __main__
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if not hasattr(__main__, '__file__'):
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get_ipython().magic('matplotlib inline')
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get_ipython().magic('config InlineBackend.figure_format = "svg"')
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def choose(options):
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"""
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Get the user to select one (or all) items from a list of options.
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Args:
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x (list): list of options
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Returns:
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the selected option(s) in a list
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"""
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options.append('All')
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for i, option in enumerate(options):
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print('{:3d}) {:s}'.format(i + 1, option))
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while True:
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try:
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val = input("Choose> ")
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if int(val) == len(options):
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selected = options[:-1]
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else:
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selected = [options[int(val) - 1]]
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return selected
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break
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except (ValueError, IndexError):
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print("Invalid input, please try again")
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def parse_args():
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"""
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Check if a parameter file was provided at the command prompt
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Returns:
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the parsed input arguments in a dict
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"""
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parser = argparse.ArgumentParser(usage=__doc__)
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parser.add_argument(
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'-f', '--file', help='name of parameter file', default=None)
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parser.add_argument(
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'-a',
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'--all',
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help='process all *.yaml files in folder',
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action='store_true')
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return parser.parse_args()
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def read_parameter_file(fname):
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"""
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Read yaml file
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Args:
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fname (str): name of yaml file
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Returns:
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the file contents in a dict
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"""
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with open(fname, 'r') as stream:
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try:
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params = yaml.load(stream)
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except yaml.YAMLError as exc:
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print(exc, "\nCheck the formatting of the yaml file.")
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return params
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def ari_to_aep(x):
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"""
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Convert annual recurrance interval to annual exceedance probability.
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Args:
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x (array_like): input array
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Returns:
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the calculated AEP
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"""
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return 1 - np.exp(-1 / x)
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def aep_to_ari(x):
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"""
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Convert annual exceedance probability to annual recurrance interval.
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Args:
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x (array_like): input array
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Returns:
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the calculated ARI
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"""
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return -1 / np.log(1 - x)
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def get_value_from_ep(x, p):
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"""
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Calculate percentile value from array based on exceedance probability.
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Args:
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x (array_like): input array
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p (float): probability (e.g. p=0.05 for 5% exceedance)
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Returns:
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the calculated percentile value
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"""
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return np.percentile(x, (1 - p) * 100)
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def get_cumulative_distribution(x, min_ep=1e-5, num=1000):
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"""
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Calculate cumulative distrubution function of a random variable.
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Args:
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x (array_like): input array
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min_ep (float): minimum exceedance probability
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num (int): number of points to calculate distribution over
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Returns:
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the cumulative distribution for plotting, e.g.
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plt.plot(exceedance_probability, value)
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"""
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exceedance_probability = np.logspace(np.log10(min_ep), 0, num)
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value = get_value_from_ep(x, exceedance_probability)
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return exceedance_probability, value
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def constrained_log_fit(x, p1, p2):
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"""
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Fit log curve based on AEP values. Gordon (1987) provides two cases:
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1. Low demand, open beaches:
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p1 = 5
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p2 = 30
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2. High demand, rip heads
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p1 = 40
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p2 = 40
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Args:
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x (array_like): input array of AEP values
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p1 (float): parameter 1
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p2 (float): parameter 2
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Returns:
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the fitted values for the given AEPs
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"""
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ari = aep_to_ari(x)
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return p1 + p2 * np.log(ari)
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def get_ongoing_recession(n_runs, start_year, end_year, sea_level_rise,
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bruun_factor, underlying_recession):
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"""
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Use Monte Carlo simulation to calculate ongoing shoreline recession.
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Args:
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n_runs (int): number of runs
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start_year (int): first year of model
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end_year (int): last year of model
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sea_level_rise (dict):
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'year' (array_like): years
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'min' (array_like): minimum value
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'mode' (array_like): most likely value
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'max' (array_like): maximum value
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bruun_factor (dict):
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'min' (float): minimum value
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'mode' (float): most likely value
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'max' (float): maximum value
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underlying_recession (dict):
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'min' (float): minimum value
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'mode' (float): most likely value
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'max' (float): maximum value
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Returns:
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the simulated recession distance (m)
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"""
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# Get time interval from input file
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years = np.arange(start_year, end_year + 1)
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n_years = len(years)
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# Interpolate sea level rise projections (m)
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slr_mode = np.interp(
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years, xp=sea_level_rise['year'],
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fp=sea_level_rise['mode'])[:, np.newaxis]
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try:
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slr_min = np.interp(
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years, xp=sea_level_rise['year'],
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fp=sea_level_rise['min'])[:, np.newaxis]
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except ValueError:
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# Use mode for deterministic beaches
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slr_min = slr_mode
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try:
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slr_max = np.interp(
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years, xp=sea_level_rise['year'],
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fp=sea_level_rise['max'])[:, np.newaxis]
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except ValueError:
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# Use mode for deterministic beaches
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slr_max = slr_mode
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# Initialise sea level rise array
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slr = np.zeros([n_years, n_runs])
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for i in range(n_years):
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# Use triangular distribution for SLR in each year (m)
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try:
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slr[i, :] = np.random.triangular(
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left=slr_min[i],
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mode=slr_mode[i],
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right=slr_max[i],
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size=n_runs)
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except ValueError:
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# Use constant value if slr_min == slr_max
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slr[i, :] = np.ones([1, n_runs]) * slr_mode[i]
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# Sort each row, so SLR follows a smooth trajectory for each model run
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slr.sort(axis=1) # FIXME: re-assign variable?
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# Shuffle columns, so the order of model runs is randomised
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np.random.shuffle(slr.T) # FIXME: re-assign variable?
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# Shift sea level so it is zero in the start year
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slr -= slr[0, :].mean(axis=0)
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# Simulate probabilistic Bruun factors (-)
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if (bruun_factor['min'] < bruun_factor['mode'] < bruun_factor['max']):
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# Use probabilistic method if min and max are provided
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bruun_factor = np.random.triangular(
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left=bruun_factor['min'],
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mode=bruun_factor['mode'],
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right=bruun_factor['max'],
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size=n_runs)
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else:
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# Ensure values were not given in reverse order
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if bruun_factor['min'] > bruun_factor['mode']:
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raise ValueError(
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"bruun_factor['min'] must be less than bruun_factor['mode']")
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if bruun_factor['mode'] > bruun_factor['max']:
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raise ValueError(
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"bruun_factor['mode'] must be less than bruun_factor['max']")
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# Use deterministic method if only mode is provided
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bruun_factor = np.ones([1, n_runs]) * bruun_factor['mode']
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# Simulate probabilistic underlying recession rate (m/y)
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if (underlying_recession['min'] < underlying_recession['mode'] <
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underlying_recession['max']):
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# Use probabilistic method if min and max are provided
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underlying_recession_rate = np.random.triangular(
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left=underlying_recession['min'],
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mode=underlying_recession['mode'],
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right=underlying_recession['max'],
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size=n_runs)
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else:
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# Ensure values were not given in reverse order
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if underlying_recession['min'] > underlying_recession['mode']:
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raise ValueError(("underlying_recession['min'] must be "
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"less than underlying_recession['mode']"))
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if underlying_recession['mode'] > underlying_recession['max']:
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raise ValueError(("underlying_recession['mode'] must be "
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"less than underlying_recession['max']"))
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# Use deterministic method if only mode is provided
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underlying_recession_rate = np.ones([1, n_runs
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]) * underlying_recession['mode']
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# Repeat Bruun factors for each year
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bruun_factor = np.tile(bruun_factor, [n_years, 1])
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# Calculate total underlying recession
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year_factor = np.arange(1, n_years + 1)[:, np.newaxis]
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underlying_recession = underlying_recession_rate * year_factor
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# Remove probabilistic component from start year
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slr[0, :] = slr[0, :].mean()
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underlying_recession[0, :] = underlying_recession[0, :].mean()
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bruun_factor[0, :] = bruun_factor[0, :].mean()
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# Calculate total ongoing recession (m)
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ongoing_recession = slr * bruun_factor + underlying_recession
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return ongoing_recession, slr, bruun_factor, underlying_recession
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def get_storm_demand_volume(ref_aep, ref_vol, n, mode='fit'):
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"""
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Calculate storm demand volume, either by fitting a log curve to the
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supplied values (mode='fit'), or by simulating storm events with a
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poisson distribution (mode='simulate').
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Note: 'simulate' mode tends to overestimate storm demand for high ARIs
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to account for storm clustering.
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Args:
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ref_aep (array_like): input AEP values
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ref_vol (array_like): input volumes (m3)
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n (int): number of model runs
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mode (str): 'fit' (default) or 'simulate'
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Returns:
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the storm demand volume (m3/m)
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"""
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if mode == 'fit':
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# Fit curve based on reference storm demand volumes
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p, _ = curve_fit(constrained_log_fit, ref_aep, ref_vol, p0=(5., 30.))
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rand_aep = np.random.rand(n)
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volume = constrained_log_fit(rand_aep, *p)
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volume[volume < 0] = 0
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elif mode == 'simulate':
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# Simulate number of storms of each ARI magnitude
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lam = np.tile(ref_aep[:, np.newaxis], [1, n])
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n_storms = np.random.poisson(lam)
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# Calculate storm demand volume (m3/m)
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vol_storms = ref_vol[:, np.newaxis] * n_storms
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volume = vol_storms.sum(axis=0)
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else:
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raise ValueError("mode must be 'fit' or 'simulate'")
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return volume
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def process(beach_name, beach_scenario, n_runs, start_year, end_year,
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output_years, output_ep, zsa_profile_file, zfc_profile_file,
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output_folder, figure_folder, sea_level_rise, bruun_factor,
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underlying_recession, storm_demand, plot_stats, omit_from_shp,
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min_chainage, segment_gaps, insert_points, append_points):
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"""
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Calculate probabilistic shorelines using Monte Carlo simulation
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Args:
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beach_name (str): name of beach in photogrammetry database
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beach_scenario (str): name for saved csv profile chainage file
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n_runs (int): number of runs
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start_year (int): first year of model
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end_year (int): last year of model
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output_years (list): years to save profiles
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output_ep (list): EP values for saved profiles
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zsa_profile_file (str): path to storm demand vs chainge data (ZSA)
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zfc_profile_file (str): path to storm demand vs chainge data (ZFC)
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output_folder (str): where to save profiles
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sea_level_rise (dict):
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'year' (list): years
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'min' (list): minimum value
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'mode' (list): most likely value
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'max' (list): maximum value
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bruun_factor (dict):
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'min' (float): minimum value
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'mode' (float): most likely value
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'max' (float): maximum value
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underlying_recession (dict):
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'min' (float): minimum value
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'mode' (float): most likely value
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'max' (float): maximum value
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plot_stats (dict):
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'block' (list): block id for plotting stats
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'profile' (list): profile id for plotting stats
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omit_from_shp (dict):
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'block' (list): block id for plotting stats
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'profile' (list): profile id for plotting stats
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min_chainage (dict):
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'block' (list): block id for trimming chainage
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'profile' (list): profile id for trimming chainage
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'chainage' (list): minimum chainage, at non-erodable barrier
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segment_gaps (dict):
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'block' (list): block id for breaking segment
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'profile' (list): profile id for breaking segments
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insert_points (dict):
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'before' (dict): points to add to (south/west) end of hazard lines
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'x' (list): eastings
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'y' (list): northings
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append_points (dict): points to add to (north/east) end of lines
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'x' (list): eastings
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'y' (list): nortings
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"""
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|
||||||
|
# Get reference storm demand (m3/m)
|
||||||
|
ref_ari = np.asarray(storm_demand['ari'])
|
||||||
|
ref_aep = ari_to_aep(ref_ari)
|
||||||
|
ref_vol = storm_demand['vol']
|
||||||
|
|
||||||
|
# Get year index
|
||||||
|
years = np.arange(start_year, end_year + 1)
|
||||||
|
|
||||||
|
# Check if beach is probabilistic
|
||||||
|
if n_runs == 1:
|
||||||
|
probabilistic = False
|
||||||
|
else:
|
||||||
|
probabilistic = True
|
||||||
|
|
||||||
|
# Simulate ongoing shoreline recession
|
||||||
|
r, slr, bf, ur = get_ongoing_recession(n_runs, start_year, end_year,
|
||||||
|
sea_level_rise, bruun_factor,
|
||||||
|
underlying_recession)
|
||||||
|
ongoing_recession = r.copy()
|
||||||
|
|
||||||
|
# Pre-allocate storm demand volume for each year (m3/m)
|
||||||
|
storm_demand_volume = np.zeros([len(years), n_runs])
|
||||||
|
|
||||||
|
if probabilistic:
|
||||||
|
for i in range(len(years)):
|
||||||
|
# Generate synthetic storm demands for each year
|
||||||
|
storm_demand_volume[i, :] = get_storm_demand_volume(
|
||||||
|
ref_aep, ref_vol, n=n_runs, mode='fit')
|
||||||
|
else:
|
||||||
|
# Get storm demand for 1% AEP event
|
||||||
|
sort_idx = np.argsort(ref_aep)
|
||||||
|
storm_demand_volume[:] = np.interp(output_ep,
|
||||||
|
np.array(ref_aep)[sort_idx],
|
||||||
|
np.array(ref_vol)[sort_idx])
|
||||||
|
|
||||||
|
# Load profile data for current beach
|
||||||
|
pbar_profiles = tqdm(['ZSA', 'ZFC'])
|
||||||
|
for profile_type in pbar_profiles:
|
||||||
|
pbar_profiles.set_description('{}'.format(profile_type))
|
||||||
|
|
||||||
|
if profile_type == 'ZSA':
|
||||||
|
df_in = pd.read_csv(zsa_profile_file)
|
||||||
|
if profile_type == 'ZFC':
|
||||||
|
df_in = pd.read_csv(zfc_profile_file)
|
||||||
|
|
||||||
|
col_names = [c for c in df_in.columns if c.isdigit()]
|
||||||
|
|
||||||
|
# Loop through profiles
|
||||||
|
pbar_profile = tqdm(
|
||||||
|
df_in[df_in['beach'] == beach_name].iterrows(),
|
||||||
|
total=df_in[df_in['beach'] == beach_name].shape[0])
|
||||||
|
for i, prof in pbar_profile:
|
||||||
|
|
||||||
|
pbar_profile.set_description(('Block: {}, profile: {}'.format(
|
||||||
|
prof['block'], prof['profile'])))
|
||||||
|
|
||||||
|
# Convert storm demand volume to a profile chainage (m)
|
||||||
|
profile_volume = np.array([int(c) for c in col_names])
|
||||||
|
profile_chainage = np.array(prof[col_names], dtype=float)
|
||||||
|
valid_idx = np.isfinite(profile_chainage)
|
||||||
|
storm_demand_chainage = np.interp(
|
||||||
|
storm_demand_volume,
|
||||||
|
xp=profile_volume[valid_idx],
|
||||||
|
fp=profile_chainage[valid_idx])
|
||||||
|
|
||||||
|
# Loop through years
|
||||||
|
pbar_year = tqdm(output_years)
|
||||||
|
for year in pbar_year:
|
||||||
|
|
||||||
|
pbar_year.set_description('Year: {}'.format(year))
|
||||||
|
|
||||||
|
# Create output dataframe
|
||||||
|
df_out = df_in[['beach', 'block', 'profile']]
|
||||||
|
|
||||||
|
# Add info on non-erodable sections
|
||||||
|
df_out = df_out.assign(min_chainage=np.nan)
|
||||||
|
for b, p, ch in zip(min_chainage['block'],
|
||||||
|
min_chainage['profile'],
|
||||||
|
min_chainage['chainage']):
|
||||||
|
idx = (df_out['block'] == str(b)) & (
|
||||||
|
df_out['profile'] == p)
|
||||||
|
df_out.loc[idx, 'min_chainage'] = ch
|
||||||
|
|
||||||
|
# Specify which segments to break
|
||||||
|
df_out = df_out.assign(segment_gaps=False)
|
||||||
|
for b, p, in zip(segment_gaps['block'],
|
||||||
|
segment_gaps['profile']):
|
||||||
|
idx = (df_out['block'] == str(b)) & (
|
||||||
|
df_out['profile'] == p)
|
||||||
|
df_out.loc[idx, 'segment_gaps'] = True
|
||||||
|
|
||||||
|
# Specify which profiles to plot
|
||||||
|
df_out = df_out.assign(plot_stats=False)
|
||||||
|
for b, p in zip(plot_stats['block'], plot_stats['profile']):
|
||||||
|
idx = (df_out['block'] == str(b)) & (
|
||||||
|
df_out['profile'] == p)
|
||||||
|
df_out.loc[idx, 'plot_stats'] = True
|
||||||
|
|
||||||
|
# Specify which profiles to omit from shapefiles
|
||||||
|
df_out = df_out.assign(omit_from_shp=False)
|
||||||
|
for b, p in zip(omit_from_shp['block'],
|
||||||
|
omit_from_shp['profile']):
|
||||||
|
idx = (df_out['block'] == str(b)) & (
|
||||||
|
df_out['profile'] == p)
|
||||||
|
df_out.loc[idx, 'omit_from_shp'] = True
|
||||||
|
|
||||||
|
# Specify additional points to be included in shapefiles
|
||||||
|
df_out = df_out.assign(insert_points='').astype('object')
|
||||||
|
for b, p, x, y in zip(insert_points['block'],
|
||||||
|
insert_points['profile'],
|
||||||
|
insert_points['x'], insert_points['y']):
|
||||||
|
idx = np.where((df_out['block'] == str(b)) & (
|
||||||
|
df_out['profile'] == p) & (
|
||||||
|
df_out['beach'] == beach_name))[0][0]
|
||||||
|
if not df_out.loc[idx, 'insert_points']:
|
||||||
|
df_out.loc[idx, 'insert_points'] = []
|
||||||
|
|
||||||
|
df_out.loc[idx, 'insert_points'].append((x, y))
|
||||||
|
|
||||||
|
df_out = df_out.assign(append_points='').astype('object')
|
||||||
|
for b, p, x, y in zip(append_points['block'],
|
||||||
|
append_points['profile'],
|
||||||
|
append_points['x'], append_points['y']):
|
||||||
|
idx = np.where((df_out['block'] == str(b)) & (
|
||||||
|
df_out['profile'] == p) & (
|
||||||
|
df_out['beach'] == beach_name))[0][0]
|
||||||
|
if not df_out.loc[idx, 'append_points']:
|
||||||
|
df_out.loc[idx, 'append_points'] = []
|
||||||
|
|
||||||
|
df_out.loc[idx, 'append_points'].append((x, y))
|
||||||
|
|
||||||
|
# Exit if no profiles found
|
||||||
|
if (df_in['beach'] == beach_name).sum() == 0:
|
||||||
|
raise KeyError('"{}" not found in {}'.format(
|
||||||
|
beach_name, zsa_profile_file))
|
||||||
|
|
||||||
|
# Loop through EP values
|
||||||
|
ep_cols = []
|
||||||
|
for ep in output_ep:
|
||||||
|
# Add column for current EP
|
||||||
|
ep_col_name = 'ep_{}'.format(ep)
|
||||||
|
df_out.loc[:, ep_col_name] = 0
|
||||||
|
ep_cols.append(ep_col_name)
|
||||||
|
|
||||||
|
# Combine recession and storm demand chainage
|
||||||
|
# Subtract because chainages decrease landward
|
||||||
|
chainage_with_recession = (
|
||||||
|
storm_demand_chainage[year >= years, :] -
|
||||||
|
ongoing_recession[year >= years, :])
|
||||||
|
|
||||||
|
# Calculate maximum recession that has occured so far
|
||||||
|
most_receeded_chainage = chainage_with_recession.min(axis=0)
|
||||||
|
|
||||||
|
# Apply recession to current chainage (m)
|
||||||
|
# Use negative exceedance probability,
|
||||||
|
# because chainages increase seaward
|
||||||
|
ch_out = get_value_from_ep(most_receeded_chainage,
|
||||||
|
1 - np.array(output_ep))
|
||||||
|
df_out.loc[i, ep_cols] = ch_out
|
||||||
|
|
||||||
|
# Check if profile is non-erodable
|
||||||
|
ch_min = df_out.loc[i, 'min_chainage']
|
||||||
|
if np.isfinite(ch_min):
|
||||||
|
ch_out[ch_out < ch_min] = ch_min
|
||||||
|
# Stop erosion past maximum limit
|
||||||
|
df_out.loc[i, ep_cols] = ch_out
|
||||||
|
|
||||||
|
# Calculate chainage for zero storm demand
|
||||||
|
zero_chainage = interpolate.interp1d(
|
||||||
|
profile_volume[valid_idx],
|
||||||
|
profile_chainage[valid_idx],
|
||||||
|
fill_value='extrapolate')(0)
|
||||||
|
|
||||||
|
storm_demand_dist = zero_chainage - storm_demand_chainage
|
||||||
|
|
||||||
|
# Plot statistics once for each profile
|
||||||
|
year_idx = year == years
|
||||||
|
|
||||||
|
# Include additional points for shapefile
|
||||||
|
df_csv = df_out[df_out['beach'] == beach_name]
|
||||||
|
|
||||||
|
# Save values for current beach
|
||||||
|
csv_name = os.path.join(output_folder, '{} {} {}.csv'.format(
|
||||||
|
beach_scenario, year, profile_type))
|
||||||
|
|
||||||
|
# Write header for csv file on first iteration
|
||||||
|
if df_out[df_out['beach'] == beach_name].index[0] == i:
|
||||||
|
df_csv.loc[[], :].to_csv(csv_name, index=False)
|
||||||
|
|
||||||
|
# Append data for current profile
|
||||||
|
df_csv[df_csv.index == i].to_csv(
|
||||||
|
csv_name,
|
||||||
|
mode='a',
|
||||||
|
index=False,
|
||||||
|
header=False,
|
||||||
|
float_format='%g')
|
||||||
|
|
||||||
|
|
||||||
|
def main():
|
||||||
|
|
||||||
|
# Choose yaml file, if not already specified
|
||||||
|
args = parse_args()
|
||||||
|
if args.file is not None:
|
||||||
|
param_files = [args.file]
|
||||||
|
else:
|
||||||
|
yaml_files = [f for f in os.listdir('.') if f.endswith('.yaml')]
|
||||||
|
|
||||||
|
# Choose file, unless 'all' option specified
|
||||||
|
if not args.all:
|
||||||
|
param_files = choose(yaml_files)
|
||||||
|
else:
|
||||||
|
param_files = yaml_files
|
||||||
|
|
||||||
|
# Loop through beaches
|
||||||
|
pbar_beach = tqdm(param_files)
|
||||||
|
for p in pbar_beach:
|
||||||
|
|
||||||
|
params = read_parameter_file(p)
|
||||||
|
pbar_beach.set_description('Beach: {}'.format(params['beach_name']))
|
||||||
|
|
||||||
|
process(**params)
|
||||||
|
|
||||||
|
print('\n')
|
||||||
|
|
||||||
|
|
||||||
|
if __name__ == '__main__':
|
||||||
|
main()
|
||||||
Loading…
Reference in New Issue