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731 lines
28 KiB
Python
731 lines
28 KiB
Python
# 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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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('-f',
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'--file',
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help='name of parameter file',
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default=None)
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parser.add_argument('-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.safe_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(years,
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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(years,
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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(years,
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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(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)
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# Shuffle columns, so the order of model runs is randomised
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np.random.shuffle(slr.T)
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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(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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underlying_recession_rate = np.tile(underlying_recession_rate,
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[n_years, 1])
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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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underlying_recession_rate[0, :] = underlying_recession_rate[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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underlying_recession_rate)
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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, zrfc_profile_file,
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output_folder, figure_folder, sea_level_rise, bruun_factor,
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underlying_recession, storm_demand, diagnostics, omit,
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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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zrfc_profile_file (str): path to storm demand vs chainge data (ZRFC)
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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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diagnostics (dict):
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'block' (list): block IDs for outputting diagnostics
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'profile' (list): profile IDs for outputting diagnostics
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omit (dict):
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'block' (list): block IDs to omit from analysis
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'profile' (list): profile IDs to omit from analysis
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min_chainage (dict):
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'block' (list): block IDs for trimming chainage
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'profile' (list): profile IDs 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 IDs for breaking segment
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'profile' (list): profile IDs 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)
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ref_ari = np.asarray(storm_demand['ari'])
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ref_aep = ari_to_aep(ref_ari)
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ref_vol = storm_demand['vol']
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# Get year index
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years = np.arange(start_year, end_year + 1)
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# Check if beach is probabilistic
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if n_runs == 1:
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probabilistic = False
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else:
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probabilistic = True
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# Simulate ongoing shoreline recession
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r, slr, bf, ur, ur_rate = get_ongoing_recession(n_runs, start_year,
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end_year, sea_level_rise,
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bruun_factor,
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underlying_recession)
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ongoing_recession = r.copy()
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# Pre-allocate storm demand volume for each year (m3/m)
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storm_demand_volume = np.zeros([len(years), n_runs])
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if probabilistic:
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for i in range(len(years)):
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# Generate synthetic storm demands for each year
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storm_demand_volume[i, :] = get_storm_demand_volume(ref_aep,
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ref_vol,
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n=n_runs,
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mode='fit')
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else:
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# Get storm demand for 1% AEP event
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sort_idx = np.argsort(ref_aep)
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storm_demand_volume[:] = np.interp(output_ep,
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np.array(ref_aep)[sort_idx],
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np.array(ref_vol)[sort_idx])
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# Load profile data for current beach
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pbar_profiles = tqdm(['ZSA', 'ZRFC'], leave=False)
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for profile_type in pbar_profiles:
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pbar_profiles.set_description('{}'.format(profile_type))
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if profile_type == 'ZSA':
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df_in = pd.read_csv(zsa_profile_file)
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if profile_type == 'ZRFC':
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df_in = pd.read_csv(zrfc_profile_file)
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col_names = [c for c in df_in.columns if c.isdigit()]
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# Loop through profiles
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dff = df_in[df_in['beach'] == beach_name]
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# Remove omitted profiles
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dff = pd.merge(
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pd.DataFrame(omit), dff, how='outer',
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indicator='source').query('source!="both"').drop(columns='source')
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pbar_profile = tqdm(dff.iterrows(), total=dff.shape[0], leave=False)
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for i, prof in pbar_profile:
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pbar_profile.set_description(
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('Block: {}, profile: {}'.format(prof['block'],
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prof['profile'])))
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# Convert storm demand volume to a profile chainage (m)
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profile_volume = np.array([int(c) for c in col_names])
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profile_chainage = np.array(prof[col_names], dtype=float)
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valid_idx = np.isfinite(profile_chainage)
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storm_demand_chainage = np.interp(storm_demand_volume,
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xp=profile_volume[valid_idx],
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fp=profile_chainage[valid_idx])
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fig, ax = plt.subplots(9,
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len(output_years),
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figsize=(16, 24),
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sharey='row')
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# Check whether to save probabilistic diagnostics
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for _, bp in pd.DataFrame(diagnostics).iterrows():
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if ((str(prof['block']) == str(bp['block']))
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and (prof['profile'] == bp['profile'])):
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output_diagnostics = True
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# Loop through years
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pbar_year = tqdm(output_years, leave=False)
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for j, year in enumerate(pbar_year):
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pbar_year.set_description('Year: {}'.format(year))
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# Create output dataframe
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df_out = df_in[['beach', 'block', 'profile']].copy()
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df_out['block'] = df_out['block'].astype(str)
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# Add info on non-erodable sections
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df_out = df_out.assign(min_chainage=np.nan)
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for b, p, ch in zip(min_chainage['block'],
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min_chainage['profile'],
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min_chainage['chainage']):
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idx = (df_out['block'] == str(b)) & (df_out['profile']
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== p)
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df_out.loc[idx, 'min_chainage'] = ch
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# Specify which segments to break
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df_out = df_out.assign(segment_gaps=False)
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for b, p, in zip(segment_gaps['block'],
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segment_gaps['profile']):
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idx = (df_out['block'] == str(b)) & (df_out['profile']
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== p)
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df_out.loc[idx, 'segment_gaps'] = True
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# Specify which profiles to plot
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|
df_out = df_out.assign(diagnostics=False)
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for b, p in zip(diagnostics['block'], diagnostics['profile']):
|
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idx = (df_out['block'] == str(b)) & (df_out['profile']
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== p)
|
|
df_out.loc[idx, 'diagnostics'] = True
|
|
|
|
# Specify which profiles to omit from shapefiles
|
|
df_out = df_out.assign(omit=False)
|
|
for b, p in zip(omit['block'], omit['profile']):
|
|
idx = (df_out['block'] == b) & (df_out['profile'] == p)
|
|
df_out.loc[idx, 'omit'] = 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
|
|
|
|
# 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)
|
|
|
|
# Only save points if they are going into shapefile
|
|
df_csv = df_csv[~df_csv['omit'].astype(bool)]
|
|
|
|
# Append data for current profile
|
|
df_csv[df_csv.index == i].to_csv(csv_name,
|
|
mode='a',
|
|
index=False,
|
|
header=False,
|
|
float_format='%g')
|
|
|
|
if output_diagnostics:
|
|
# Save probabilistic diagnostics
|
|
year_idx = year == years
|
|
|
|
# Find index where most extreme event occurred
|
|
event_year_idx = chainage_with_recession.argmin(axis=0)
|
|
|
|
# define dummy index
|
|
ix = np.arange(n_runs)
|
|
dump_data = {
|
|
'Sea level rise (m)':
|
|
slr[event_year_idx, ix].ravel(),
|
|
'Bruun factor (-)':
|
|
bf[event_year_idx, ix].ravel(),
|
|
'Bruun factor x SLR (m)':
|
|
slr[event_year_idx, ix].ravel() *
|
|
bf[event_year_idx, ix].ravel(),
|
|
'Underlying trend rate (m/yr)':
|
|
ur_rate[year_idx, :].ravel(),
|
|
'Underlying trend (m)':
|
|
ur[event_year_idx, ix].ravel(),
|
|
'Underlying + SLR (m)':
|
|
r[event_year_idx, ix].ravel(),
|
|
'Total movement (m)':
|
|
(storm_demand_dist + r)[event_year_idx, ix].ravel(),
|
|
'Storm demand distance (m)':
|
|
storm_demand_dist[event_year_idx, ix].ravel(),
|
|
'Storm demand volume (m3/m)':
|
|
storm_demand_volume[event_year_idx, ix].ravel(),
|
|
}
|
|
|
|
dump_df = pd.DataFrame(dump_data)
|
|
dump_df['Run ID'] = np.arange(len(event_year_idx)) + 1
|
|
dump_df['Event year'] = years[event_year_idx]
|
|
dump_df['Years elapsed'] = event_year_idx + 1
|
|
|
|
# Reorder columns
|
|
dump_df = dump_df[[
|
|
'Run ID',
|
|
'Event year',
|
|
'Years elapsed',
|
|
'Sea level rise (m)',
|
|
'Bruun factor (-)',
|
|
'Bruun factor x SLR (m)',
|
|
'Underlying trend rate (m/yr)',
|
|
'Underlying trend (m)',
|
|
'Underlying + SLR (m)',
|
|
'Total movement (m)',
|
|
'Storm demand distance (m)',
|
|
'Storm demand volume (m3/m)',
|
|
]]
|
|
|
|
# Sort based on maximum movement
|
|
dump_df = dump_df.sort_values('Total movement (m)',
|
|
ascending=False)
|
|
|
|
# Add encounter probabilities
|
|
dump_df['Encounter probability (%)'] = np.linspace(
|
|
0, 100, num=n_runs + 2)[1:-1]
|
|
dump_df = dump_df.set_index('Encounter probability (%)')
|
|
|
|
csv_name = os.path.join(
|
|
'diagnostics',
|
|
'{} {} {}.csv'.format(beach_scenario, year,
|
|
profile_type))
|
|
dump_df.to_csv(csv_name, float_format='%g')
|
|
|
|
for i, c in enumerate(dump_df.columns[3:]):
|
|
ax[i, j].plot(dump_df.index,
|
|
dump_df[c],
|
|
'.',
|
|
color='#666666',
|
|
markersize=2)
|
|
ax[i, j].spines['right'].set_visible(False)
|
|
ax[i, j].spines['top'].set_visible(False)
|
|
if j == 0:
|
|
ax[i, 0].yaxis.set_label_coords(-0.4, 0.5)
|
|
label = c.replace('(', '\n(')
|
|
ax[i, 0].set_ylabel(label,
|
|
va='top',
|
|
linespacing=1.5)
|
|
|
|
ax[i, j].set_xlabel('Encounter probability (%)',
|
|
labelpad=10)
|
|
ax[0, j].set_title(year)
|
|
|
|
fig.suptitle('{}, block {}, profile {}'.format(
|
|
beach_scenario, prof['block'], prof['profile']),
|
|
y=0.92)
|
|
|
|
if output_diagnostics:
|
|
figname = os.path.join(
|
|
'diagnostics',
|
|
f'{beach_scenario} {profile_type} scatter.png')
|
|
plt.savefig(figname, bbox_inches='tight', dpi=300)
|
|
plt.close(fig)
|
|
|
|
|
|
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()
|