Rename mat parsing file and convert to callable CLI commands
Chris Leaman
6 years ago
parent
67b7043ec3
commit
99e036a4cd
@ -1,263 +0,0 @@
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"""
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Converts raw .mat files into a flattened .csv structure which can be imported into python pandas.
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"""
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import logging.config
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from datetime import datetime, timedelta
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import pandas as pd
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from mat4py import loadmat
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import numpy as np
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logging.config.fileConfig('./src/logging.conf', disable_existing_loggers=False)
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logger = logging.getLogger(__name__)
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def parse_orientations(orientations_mat):
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"""
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Parses the raw orientations.mat file and returns a pandas dataframe. Note that orientations are the direction
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towards land measured in degrees anti-clockwise from east.
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:param orientations_mat:
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:return:
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"""
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logger.info('Parsing %s', orientations_mat)
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mat_data = loadmat(orientations_mat)['output']
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rows = []
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for i in range(0, len(mat_data['beach'])):
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rows.append({
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'beach': mat_data['beach'][i],
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'orientation': mat_data['orientation'][i],
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'lat_center': mat_data['lat_center'][i],
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'lon_center': mat_data['lon_center'][i],
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'lat_land': mat_data['lat_land'][i],
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'lon_land': mat_data['lon_land'][i],
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'lat_sea': mat_data['lat_sea'][i],
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'lon_sea': mat_data['lon_sea'][i],
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})
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df = pd.DataFrame(rows)
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return df
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def combine_sites_and_orientaions(df_sites, df_orientations):
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"""
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Replaces beach/lat/lon columns with the unique site_id.
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:param dfs:
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:param df_sites:
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:return:
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"""
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df_merged_sites = df_sites.merge(df_orientations[['beach', 'lat_center', 'lon_center', 'orientation']],
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left_on=['beach', 'lat', 'lon'],
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right_on=['beach', 'lat_center', 'lon_center'])
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# Check that all our records have a unique site identifier
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n_unmatched = len(df_sites) - len(df_merged_sites)
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if n_unmatched > 0:
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logger.warning('Not all records (%d of %d) matched with an orientation', n_unmatched, len(df_sites))
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# Drop extra columns
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df_merged_sites = df_merged_sites.drop(columns = ['lat_center', 'lon_center'])
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return df_merged_sites
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def specify_lat_lon_profile_center(df_sites, x_val=200):
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"""
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Specify which x-coordinate in the beach profile cross section the lat/lon corresponds to
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:param df_sites:
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:return:
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"""
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df_sites['profile_x_lat_lon'] = x_val
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return df_sites
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def parse_waves(waves_mat):
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"""
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Parses the raw waves.mat file and returns a pandas dataframe
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:param waves_mat:
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:return:
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"""
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logger.info('Parsing %s', waves_mat)
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mat_data = loadmat(waves_mat)['data']
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rows = []
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for i in range(0, len(mat_data['site'])):
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for j in range(0, len(mat_data['dates'][i])):
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rows.append({
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'beach': mat_data['site'][i],
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'lon': mat_data['lon'][i],
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'lat': mat_data['lat'][i],
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'datetime': matlab_datenum_to_datetime(mat_data['dates'][i][j][0]),
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'Hs': mat_data['H'][i][j][0],
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'Hs0': mat_data['Ho'][i][j][0],
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'Tp': mat_data['T'][i][j][0],
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'dir': mat_data['D'][i][j][0],
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'E': mat_data['E'][i][j][0],
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'P': mat_data['P'][i][j][0],
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'Exs': mat_data['Exs'][i][j][0],
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'Pxs': mat_data['Pxs'][i][j][0],
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})
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df = pd.DataFrame(rows)
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df['datetime'] = df['datetime'].dt.round('1s')
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return df
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def parse_tides(tides_mat):
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"""
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Parses the raw tides.mat file and returns a pandas dataframe
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:param tides_mat:
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:return:
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"""
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logger.info('Parsing %s', tides_mat)
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mat_data = loadmat(tides_mat)['data']
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rows = []
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for i in range(0, len(mat_data['site'])):
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for j in range(0, len(mat_data['time'])):
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rows.append({
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'beach': mat_data['site'][i][0],
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'lon': mat_data['lons'][i][0],
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'lat': mat_data['lats'][i][0],
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'datetime': matlab_datenum_to_datetime(mat_data['time'][j][0]),
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'tide': mat_data['tide'][i][j]
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})
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df = pd.DataFrame(rows)
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df['datetime'] = df['datetime'].dt.round('1s')
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return df
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def parse_profiles(profiles_mat):
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"""
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Parses the raw profiles.mat file and returns a pandas dataframe
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:param tides_mat:
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:return:
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"""
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logger.info('Parsing %s', profiles_mat)
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mat_data = loadmat(profiles_mat)['data']
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rows = []
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for i in range(0, len(mat_data['site'])):
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for j in range(0, len(mat_data['pfx'][i])):
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for profile_type in ['prestorm', 'poststorm']:
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if profile_type == 'prestorm':
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z = mat_data['pf1'][i][j][0]
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if profile_type == 'poststorm':
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z = mat_data['pf2'][i][j][0]
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rows.append({
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'beach': mat_data['site'][i],
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'lon': mat_data['lon'][i],
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'lat': mat_data['lat'][i],
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'profile_type': profile_type,
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'x': mat_data['pfx'][i][j][0],
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'z': z,
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})
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df = pd.DataFrame(rows)
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return df
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def remove_zeros(df_profiles):
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"""
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When parsing the pre/post storm profiles, the end of some profiles have constant values of zero. Let's change
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these to NaNs for consistancy. Didn't use pandas fillnan because 0 may still be a valid value.
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:param df:
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:return:
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"""
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df_profiles = df_profiles.sort_index()
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groups = df_profiles.groupby(level=['site_id','profile_type'])
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for key, _ in groups:
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logger.debug('Removing zeros from {} profile at {}'.format(key[1], key[0]))
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idx_site = (df_profiles.index.get_level_values('site_id') == key[0]) & \
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(df_profiles.index.get_level_values('profile_type') == key[1])
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df_profile = df_profiles[idx_site]
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x_last_ele = df_profile[df_profile.z!=0].index.get_level_values('x')[-1]
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df_profiles.loc[idx_site & (df_profiles.index.get_level_values('x')>x_last_ele), 'z'] = np.nan
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return df_profiles
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def matlab_datenum_to_datetime(matlab_datenum):
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# https://stackoverflow.com/a/13965852
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return datetime.fromordinal(int(matlab_datenum)) + timedelta(days=matlab_datenum % 1) - timedelta(
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days=366)
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def get_unique_sites(dfs, cols=['beach', 'lat', 'lon']):
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"""
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Generates a dataframe of unique sites based on beach names, lats and lons. Creates a unique site ID for each.
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:param dfs:
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:param cols:
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:return:
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"""
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rows = []
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df_all = pd.concat([df[cols] for df in dfs])
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beach_groups = df_all.groupby(['beach'])
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for beach_name, beach_group in beach_groups:
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site_groups = beach_group.groupby(['lat', 'lon'])
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siteNo = 1
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for site_name, site_group in site_groups:
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site = '{}{:04d}'.format(beach_name, siteNo)
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rows.append({'site_id': site,
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'lat': site_name[0],
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'lon': site_name[1],
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'beach': beach_name})
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siteNo += 1
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df = pd.DataFrame(rows)
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return df
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def replace_unique_sites(df, df_sites, cols=['beach', 'lat', 'lon']):
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"""
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Replaces beach/lat/lon columns with the unique site_id
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:param dfs:
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:param df_sites:
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:return:
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"""
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df_merged = df.merge(df_sites, on=cols)
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# Check that all our records have a unique site identifier
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n_unmatched = len(df) - len(df_merged)
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if n_unmatched > 0:
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logger.warning('Not all records (%d of %d) matched with a unique site', n_unmatched, len(df))
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df_merged = df_merged.drop(columns=cols)
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return df_merged
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def main():
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df_waves = parse_waves(waves_mat='./data/raw/processed_shorelines/waves.mat')
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df_tides = parse_tides(tides_mat='./data/raw/processed_shorelines/tides.mat')
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df_profiles = parse_profiles(profiles_mat='./data/raw/processed_shorelines/profiles.mat')
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df_sites = get_unique_sites(dfs=[df_waves, df_tides, df_profiles])
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df_orientations = parse_orientations(orientations_mat='./data/raw/processed_shorelines/orientations.mat')
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logger.info('Identifying unique sites')
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df_waves = replace_unique_sites(df_waves, df_sites)
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df_tides = replace_unique_sites(df_tides, df_sites)
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df_profiles = replace_unique_sites(df_profiles, df_sites)
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logger.info('Combine orientations into sites')
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df_sites = combine_sites_and_orientaions(df_sites, df_orientations)
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df_sites = specify_lat_lon_profile_center(df_sites)
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logger.info('Setting pandas index')
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df_profiles.set_index(['site_id', 'profile_type', 'x'], inplace=True)
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df_waves.set_index(['site_id', 'datetime'], inplace=True)
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df_tides.set_index(['site_id', 'datetime'], inplace=True)
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df_sites.set_index(['site_id'], inplace=True)
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logger.info('Nanning profile zero elevations')
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df_profiles = remove_zeros(df_profiles)
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logger.info('Outputting .csv files')
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df_profiles.to_csv('./data/interim/profiles.csv')
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df_tides.to_csv('./data/interim/tides.csv')
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df_waves.to_csv('./data/interim/waves.csv')
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df_sites.to_csv('./data/interim/sites.csv')
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logger.info('Done!')
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if __name__ == '__main__':
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main()
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@ -0,0 +1,345 @@
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"""
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Converts raw .mat files into a flattened .csv structure which can be imported into python pandas.
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"""
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import logging.config
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from datetime import datetime, timedelta
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import click
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import pandas as pd
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from mat4py import loadmat
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import numpy as np
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logging.config.fileConfig("./src/logging.conf", disable_existing_loggers=False)
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logger = logging.getLogger(__name__)
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def parse_orientations(orientations_mat):
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"""
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Parses the raw orientations.mat file and returns a pandas dataframe. Note that orientations are the direction
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towards land measured in degrees anti-clockwise from east.
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:param orientations_mat:
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:return:
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"""
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logger.info("Parsing %s", orientations_mat)
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mat_data = loadmat(orientations_mat)["output"]
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rows = []
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for i in range(0, len(mat_data["beach"])):
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rows.append(
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{
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"beach": mat_data["beach"][i],
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"orientation": mat_data["orientation"][i],
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"lat_center": mat_data["lat_center"][i],
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"lon_center": mat_data["lon_center"][i],
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"lat_land": mat_data["lat_land"][i],
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"lon_land": mat_data["lon_land"][i],
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"lat_sea": mat_data["lat_sea"][i],
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"lon_sea": mat_data["lon_sea"][i],
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}
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)
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df = pd.DataFrame(rows)
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return df
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def combine_sites_and_orientaions(df_sites, df_orientations):
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"""
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Replaces beach/lat/lon columns with the unique site_id.
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:param dfs:
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:param df_sites:
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:return:
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"""
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df_merged_sites = df_sites.merge(
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df_orientations[["beach", "lat_center", "lon_center", "orientation"]],
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left_on=["beach", "lat", "lon"],
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right_on=["beach", "lat_center", "lon_center"],
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)
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# Check that all our records have a unique site identifier
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n_unmatched = len(df_sites) - len(df_merged_sites)
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if n_unmatched > 0:
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logger.warning("Not all records (%d of %d) matched with an orientation", n_unmatched, len(df_sites))
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# Drop extra columns
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df_merged_sites = df_merged_sites.drop(columns=["lat_center", "lon_center"])
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return df_merged_sites
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def specify_lat_lon_profile_center(df_sites, x_val=200):
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"""
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Specify which x-coordinate in the beach profile cross section the lat/lon corresponds to
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:param df_sites:
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:return:
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"""
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df_sites["profile_x_lat_lon"] = x_val
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return df_sites
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def parse_waves(waves_mat):
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"""
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Parses the raw waves.mat file and returns a pandas dataframe
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:param waves_mat:
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:return:
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"""
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logger.info("Parsing %s", waves_mat)
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mat_data = loadmat(waves_mat)["data"]
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rows = []
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for i in range(0, len(mat_data["site"])):
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for j in range(0, len(mat_data["dates"][i])):
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rows.append(
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{
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"beach": mat_data["site"][i],
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"lon": mat_data["lon"][i],
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"lat": mat_data["lat"][i],
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"datetime": matlab_datenum_to_datetime(mat_data["dates"][i][j][0]),
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"Hs": mat_data["H"][i][j][0],
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"Hs0": mat_data["Ho"][i][j][0],
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"Tp": mat_data["T"][i][j][0],
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"dir": mat_data["D"][i][j][0],
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"E": mat_data["E"][i][j][0],
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"P": mat_data["P"][i][j][0],
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"Exs": mat_data["Exs"][i][j][0],
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"Pxs": mat_data["Pxs"][i][j][0],
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}
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)
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df = pd.DataFrame(rows)
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df["datetime"] = df["datetime"].dt.round("1s")
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return df
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def parse_tides(tides_mat):
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"""
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Parses the raw tides.mat file and returns a pandas dataframe
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:param tides_mat:
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:return:
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"""
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logger.info("Parsing %s", tides_mat)
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mat_data = loadmat(tides_mat)["data"]
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rows = []
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for i in range(0, len(mat_data["site"])):
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for j in range(0, len(mat_data["time"])):
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rows.append(
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{
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"beach": mat_data["site"][i][0],
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"lon": mat_data["lons"][i][0],
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"lat": mat_data["lats"][i][0],
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"datetime": matlab_datenum_to_datetime(mat_data["time"][j][0]),
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"tide": mat_data["tide"][i][j],
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}
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)
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df = pd.DataFrame(rows)
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df["datetime"] = df["datetime"].dt.round("1s")
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return df
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def parse_profiles(profiles_mat):
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"""
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Parses the raw profiles.mat file and returns a pandas dataframe
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:param tides_mat:
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:return:
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"""
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logger.info("Parsing %s", profiles_mat)
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mat_data = loadmat(profiles_mat)["data"]
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rows = []
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for i in range(0, len(mat_data["site"])):
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for j in range(0, len(mat_data["pfx"][i])):
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for profile_type in ["prestorm", "poststorm"]:
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if profile_type == "prestorm":
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z = mat_data["pf1"][i][j][0]
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if profile_type == "poststorm":
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z = mat_data["pf2"][i][j][0]
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rows.append(
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{
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"beach": mat_data["site"][i],
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"lon": mat_data["lon"][i],
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"lat": mat_data["lat"][i],
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"profile_type": profile_type,
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"x": mat_data["pfx"][i][j][0],
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"z": z,
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}
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)
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df = pd.DataFrame(rows)
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return df
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def remove_zeros(df_profiles):
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"""
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When parsing the pre/post storm profiles, the end of some profiles have constant values of zero. Let's change
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these to NaNs for consistancy. Didn't use pandas fillnan because 0 may still be a valid value.
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:param df:
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:return:
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"""
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df_profiles = df_profiles.sort_index()
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groups = df_profiles.groupby(level=["site_id", "profile_type"])
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for key, _ in groups:
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logger.debug("Removing zeros from {} profile at {}".format(key[1], key[0]))
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idx_site = (df_profiles.index.get_level_values("site_id") == key[0]) & (
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df_profiles.index.get_level_values("profile_type") == key[1]
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)
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df_profile = df_profiles[idx_site]
|
||||
x_last_ele = df_profile[df_profile.z != 0].index.get_level_values("x")[-1]
|
||||
df_profiles.loc[idx_site & (df_profiles.index.get_level_values("x") > x_last_ele), "z"] = np.nan
|
||||
|
||||
return df_profiles
|
||||
|
||||
|
||||
def matlab_datenum_to_datetime(matlab_datenum):
|
||||
"""
|
||||
Adapted from https://stackoverflow.com/a/13965852
|
||||
:param matlab_datenum:
|
||||
:return:
|
||||
"""
|
||||
return datetime.fromordinal(int(matlab_datenum)) + timedelta(days=matlab_datenum % 1) - timedelta(days=366)
|
||||
|
||||
|
||||
def get_unique_sites(dfs, cols=["beach", "lat", "lon"]):
|
||||
"""
|
||||
Generates a dataframe of unique sites based on beach names, lats and lons. Creates a unique site ID for each.
|
||||
:param dfs:
|
||||
:param cols:
|
||||
:return:
|
||||
"""
|
||||
|
||||
rows = []
|
||||
df_all = pd.concat([df[cols] for df in dfs])
|
||||
beach_groups = df_all.groupby(["beach"])
|
||||
for beach_name, beach_group in beach_groups:
|
||||
site_groups = beach_group.groupby(["lat", "lon"])
|
||||
siteNo = 1
|
||||
for site_name, site_group in site_groups:
|
||||
site = "{}{:04d}".format(beach_name, siteNo)
|
||||
rows.append({"site_id": site, "lat": site_name[0], "lon": site_name[1], "beach": beach_name})
|
||||
siteNo += 1
|
||||
|
||||
df = pd.DataFrame(rows)
|
||||
|
||||
return df
|
||||
|
||||
|
||||
def replace_unique_sites(df, df_sites, cols=["lat", "lon"]):
|
||||
"""
|
||||
Replaces beach/lat/lon columns with the unique site_id
|
||||
:param dfs:
|
||||
:param df_sites:
|
||||
:return:
|
||||
"""
|
||||
# Make the sites index a column, so it can be merged into df
|
||||
df_sites["site_id"] = df_sites.index.get_level_values("site_id")
|
||||
|
||||
# Merging on a float can lead to subtle bugs. Lets convert lat/lons to integers and merge on that instead
|
||||
precision = 8
|
||||
df_sites["lat_int"] = np.round(df_sites["lat"] * 10 ** precision).astype(np.int64)
|
||||
df_sites["lon_int"] = np.round(df_sites["lon"] * 10 ** precision).astype(np.int64)
|
||||
df["lat_int"] = np.round(df["lat"] * 10 ** precision).astype(np.int64)
|
||||
df["lon_int"] = np.round(df["lon"] * 10 ** precision).astype(np.int64)
|
||||
|
||||
df_merged = df.merge(df_sites, on=["lat_int", "lon_int"])
|
||||
|
||||
# Check that all our records have a unique site identifier
|
||||
n_unmatched = len(df) - len(df_merged)
|
||||
if n_unmatched > 0:
|
||||
logger.warning("Not all records (%d of %d) matched with a unique site", n_unmatched, len(df))
|
||||
|
||||
df_merged = df_merged.drop(
|
||||
columns=[
|
||||
"lat_x",
|
||||
"lon_x",
|
||||
"lat_int",
|
||||
"lon_int",
|
||||
"beach_y",
|
||||
"beach_x",
|
||||
"lat_y",
|
||||
"lon_y",
|
||||
"orientation",
|
||||
"profile_x_lat_lon",
|
||||
]
|
||||
)
|
||||
|
||||
return df_merged
|
||||
|
||||
|
||||
@click.command(short_help="create sites.csv")
|
||||
@click.option("--waves-mat", required=True, help=".mat file containing wave records")
|
||||
@click.option("--tides-mat", required=True, help=".mat file containing tide records")
|
||||
@click.option("--profiles-mat", required=True, help=".mat file containing beach profiles")
|
||||
@click.option("--orientations-mat", required=True, help=".mat file containing orientation of beach profiles")
|
||||
@click.option("--output-file", required=True, help="where to save sites.csv")
|
||||
def create_sites_csv(waves_mat, tides_mat, profiles_mat, orientations_mat, output_file):
|
||||
logger.info("Creating %s", output_file)
|
||||
df_waves = parse_waves(waves_mat=waves_mat)
|
||||
df_tides = parse_tides(tides_mat=tides_mat)
|
||||
df_profiles = parse_profiles(profiles_mat=profiles_mat)
|
||||
df_orientations = parse_orientations(orientations_mat=orientations_mat)
|
||||
df_sites = get_unique_sites(dfs=[df_waves, df_tides, df_profiles])
|
||||
df_sites = combine_sites_and_orientaions(df_sites, df_orientations)
|
||||
df_sites = specify_lat_lon_profile_center(df_sites)
|
||||
df_sites.set_index(["site_id"], inplace=True)
|
||||
df_sites.to_csv(output_file)
|
||||
logger.info("Created %s", output_file)
|
||||
|
||||
|
||||
@click.command(short_help="create waves.csv")
|
||||
@click.option("--waves-mat", required=True, help=".mat file containing wave records")
|
||||
@click.option("--sites-csv", required=True, help=".csv file description of cross section sites")
|
||||
@click.option("--output-file", required=True, help="where to save waves.csv")
|
||||
def create_waves_csv(waves_mat, sites_csv, output_file):
|
||||
logger.info("Creating %s", output_file)
|
||||
df_waves = parse_waves(waves_mat=waves_mat)
|
||||
df_sites = pd.read_csv(sites_csv, index_col=[0])
|
||||
df_waves = replace_unique_sites(df_waves, df_sites)
|
||||
df_waves.set_index(["site_id", "datetime"], inplace=True)
|
||||
df_waves.sort_index(inplace=True)
|
||||
df_waves.to_csv(output_file)
|
||||
logger.info("Created %s", output_file)
|
||||
|
||||
|
||||
@click.command(short_help="create profiles.csv")
|
||||
@click.option("--profiles-mat", required=True, help=".mat file containing beach profiles")
|
||||
@click.option("--sites-csv", required=True, help=".csv file description of cross section sites")
|
||||
@click.option("--output-file", required=True, help="where to save profiles.csv")
|
||||
def create_profiles_csv(profiles_mat, sites_csv, output_file):
|
||||
logger.info("Creating %s", output_file)
|
||||
df_profiles = parse_profiles(profiles_mat=profiles_mat)
|
||||
df_sites = pd.read_csv(sites_csv, index_col=[0])
|
||||
df_profiles = replace_unique_sites(df_profiles, df_sites)
|
||||
df_profiles.set_index(["site_id", "profile_type", "x"], inplace=True)
|
||||
df_profiles.sort_index(inplace=True)
|
||||
df_profiles.to_csv(output_file)
|
||||
logger.info("Created %s", output_file)
|
||||
|
||||
|
||||
@click.command(short_help="create profiles.csv")
|
||||
@click.option("--tides-mat", required=True, help=".mat file containing tides")
|
||||
@click.option("--sites-csv", required=True, help=".csv file description of cross section sites")
|
||||
@click.option("--output-file", required=True, help="where to save tides.csv")
|
||||
def create_tides_csv(tides_mat, sites_csv, output_file):
|
||||
logger.info("Creating %s", output_file)
|
||||
df_tides = parse_tides(tides_mat=tides_mat)
|
||||
df_sites = pd.read_csv(sites_csv, index_col=[0])
|
||||
df_tides = replace_unique_sites(df_tides, df_sites)
|
||||
df_tides.set_index(["site_id", "datetime"], inplace=True)
|
||||
df_tides.sort_index(inplace=True)
|
||||
df_tides.to_csv(output_file)
|
||||
logger.info("Created %s", output_file)
|
||||
|
||||
|
||||
@click.group()
|
||||
def cli():
|
||||
pass
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
cli.add_command(create_sites_csv)
|
||||
cli.add_command(create_waves_csv)
|
||||
cli.add_command(create_profiles_csv)
|
||||
cli.add_command(create_tides_csv)
|
||||
cli()
|
||||
|
||||
pd.set_option("display.precision", 8)
|
||||
pd.set_option("display.max_columns", None)
|
||||
Loading…
Reference in New Issue