def test_without_region_pass(self):
"""Append centroids without region id."""
centr1 = Centroids()
centr1.tag = Tag('file_1.mat', 'description 1')
centr1.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr1.id = np.array([5, 7, 9])
centr2 = Centroids()
centr2.tag = Tag('file_2.mat', 'description 2')
centr2.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr2.id = np.array([5, 7, 9])
centr2.region_id = np.array([1, 1, 1])
centr1.append(centr2)
self.assertTrue(np.array_equal(centr1.region_id, np.array([], int)))
centr1 = Centroids()
centr1.tag = Tag('file_1.mat', 'description 1')
centr1.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr1.id = np.array([5, 7, 9])
centr1.region_id = np.array([1, 1, 1])
centr2 = Centroids()
centr2.tag = Tag('file_2.mat', 'description 2')
centr2.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr2.id = np.array([5, 7, 9])
centr1.append(centr2)
self.assertTrue(np.array_equal(centr1.region_id, np.array([1, 1, 1])))
def test_all_new_elem_pass(self):
"""Append a centroids with a new element."""
centr1 = Centroids()
centr1.tag = Tag('file_1.mat', 'description 1')
centr1.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr1.id = np.array([5, 7, 9])
centr2 = Centroids()
centr2.tag = Tag('file_2.mat', 'description 2')
centr2.coord = np.array([[7, 8], [1, 5]])
centr2.id = np.array([5, 7])
centr1.append(centr2)
self.assertEqual(len(centr1.tag.file_name), 2)
self.assertEqual(len(centr1.tag.description), 2)
self.assertEqual(centr1.coord.shape, (5, 2))
self.assertTrue(np.array_equal(centr1.coord[0, :], [1, 2]))
self.assertTrue(np.array_equal(centr1.coord[1, :], [3, 4]))
self.assertTrue(np.array_equal(centr1.coord[2, :], [5, 6]))
self.assertTrue(np.array_equal(centr1.coord[3, :], [7, 8]))
self.assertTrue(np.array_equal(centr1.coord[4, :], [1, 5]))
self.assertEqual(centr1.id.shape, (5, ))
self.assertTrue(np.array_equal(centr1.id, \
np.array([5, 7, 9, 10, 11])))
self.assertTrue(np.array_equal(centr1.region_id, np.array([], int)))
def test_new_elem_pass(self):
"""Append a centroids with a new element."""
centr1 = Centroids()
centr1.tag = Tag('file_1.mat', 'description 1')
centr1.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr1.id = np.array([5, 7, 9])
centr1.region_id = np.array([1, 2, 3])
centr1.dist_coast = np.array([1.5, 2.6, 3.5])
centr2 = Centroids()
centr2.tag = Tag('file_2.mat', 'description 2')
centr2.coord = np.array([[1, 2], [3, 4], [5, 6], [7, 8]])
centr2.id = np.array([6, 7, 9, 1])
centr2.region_id = np.array([3, 4, 5, 6])
centr2.dist_coast = np.array([4.5, 5.6, 6.5, 7.8])
centr1.append(centr2)
self.assertEqual(len(centr1.tag.file_name), 2)
self.assertEqual(len(centr1.tag.description), 2)
self.assertEqual(centr1.coord.shape, (4, 2))
self.assertTrue(np.array_equal(centr1.coord[0, :], [1, 2]))
self.assertTrue(np.array_equal(centr1.coord[1, :], [3, 4]))
self.assertTrue(np.array_equal(centr1.coord[2, :], [5, 6]))
self.assertTrue(np.array_equal(centr1.coord[3, :], [7, 8]))
self.assertEqual(centr1.id.shape, (4, ))
self.assertTrue(np.array_equal(centr1.id, np.array([5, 7, 9, 1])))
self.assertTrue(
np.array_equal(centr1.region_id, np.array([1, 2, 3, 6])))
self.assertTrue(
np.array_equal(centr1.dist_coast, np.array([1.5, 2.6, 3.5, 7.8])))
def test_appended_type(self):
"""Append the same centroids."""
centr1 = Centroids()
centr1.tag = Tag('file_1.mat', 'description 1')
centr1.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr1.id = np.array([5, 7, 9])
centr2 = centr1
centr1.append(centr2)
self.assertEqual(type(centr1.tag.file_name), str)
self.assertEqual(type(centr1.tag.description), str)
self.assertEqual(type(centr1.coord), np.ndarray)
self.assertEqual(type(centr1.id), np.ndarray)
self.assertTrue(type(centr1.region_id), np.ndarray)
def test_append_to_empty_fill(self):
"""Append to empty centroids."""
centr1 = Centroids()
centr2 = Centroids()
centr2.tag = Tag('file_1.mat', 'description 1')
centr2.coord = np.array([[1, 2], [3, 4], [5, 6]])
centr2.id = np.array([5, 7, 9])
centr1.append(centr2)
self.assertEqual(centr1.tag.file_name, 'file_1.mat')
self.assertEqual(centr1.tag.description, 'description 1')
self.assertEqual(centr1.coord.shape, (3, 2))
self.assertTrue(np.array_equal(centr1.coord[0, :], [1, 2]))
self.assertTrue(np.array_equal(centr1.coord[1, :], [3, 4]))
self.assertTrue(np.array_equal(centr1.coord[2, :], [5, 6]))
self.assertEqual(centr1.id.shape, (3, ))
self.assertTrue(np.array_equal(centr1.id, np.array([5, 7, 9])))
self.assertTrue(np.array_equal(centr1.region_id, np.array([], int)))
class Hazard():
"""Contains events of some hazard type defined at centroids. Loads from
files with format defined in FILE_EXT.
Attributes:
tag (TagHazard): information about the source
units (str): units of the intensity
centroids (Centroids): centroids of the events
event_id (np.array): id (>0) of each event
event_name (list(str)): name of each event (default: event_id)
date (np.array): integer date corresponding to the proleptic
Gregorian ordinal, where January 1 of year 1 has ordinal 1
(ordinal format of datetime library)
orig (np.array): flags indicating historical events (True)
or probabilistic (False)
frequency (np.array): frequency of each event in years
intensity (sparse.csr_matrix): intensity of the events at centroids
fraction (sparse.csr_matrix): fraction of affected exposures for each
event at each centroid
"""
intensity_thres = 10
""" Intensity threshold per hazard used to filter lower intensities. To be
set for every hazard type """
vars_oblig = {'tag',
'units',
'centroids',
'event_id',
'frequency',
'intensity',
'fraction'
}
"""Name of the variables needed to compute the impact. Types: scalar, str,
list, 1dim np.array of size num_events, scipy.sparse matrix of shape
num_events x num_centroids, Centroids and Tag."""
vars_def = {'date',
'orig',
'event_name'
}
"""Name of the variables used in impact calculation whose value is
descriptive and can therefore be set with default values. Types: scalar,
string, list, 1dim np.array of size num_events.
"""
vars_opt = set()
"""Name of the variables that aren't need to compute the impact. Types:
scalar, string, list, 1dim np.array of size num_events."""
def __init__(self, haz_type):
"""Initialize values.
Parameters:
haz_type (str, optional): acronym of the hazard type (e.g. 'TC').
Examples:
Fill hazard values by hand:
>>> haz = Hazard('TC')
>>> haz.intensity = sparse.csr_matrix(np.zeros((2, 2)))
>>> ...
Take hazard values from file:
>>> haz = Hazard('TC', HAZ_DEMO_MAT)
>>> haz.read_mat(HAZ_DEMO_MAT, 'demo')
"""
self.tag = TagHazard()
self.tag.haz_type = haz_type
self.units = ''
self.centroids = Centroids()
# following values are defined for each event
self.event_id = np.array([], int)
self.frequency = np.array([], float)
self.event_name = list()
self.date = np.array([], int)
self.orig = np.array([], bool)
# following values are defined for each event and centroid
self.intensity = sparse.csr_matrix(np.empty((0, 0))) # events x centroids
self.fraction = sparse.csr_matrix(np.empty((0, 0))) # events x centroids
def clear(self):
"""Reinitialize attributes."""
for (var_name, var_val) in self.__dict__.items():
if isinstance(var_val, np.ndarray) and var_val.ndim == 1:
setattr(self, var_name, np.array([], dtype=var_val.dtype))
elif isinstance(var_val, sparse.csr_matrix):
setattr(self, var_name, sparse.csr_matrix(np.empty((0, 0))))
else:
setattr(self, var_name, var_val.__class__())
def check(self):
"""Check if the attributes contain consistent data.
Raises:
ValueError
"""
self.centroids.check()
self._check_events()
def read_mat(self, file_name, description='', centroids=None,
var_names=DEF_VAR_MAT):
"""Read climada hazard generate with the MATLAB code.
Parameters:
file_name (str): absolute file name
description (str, optional): description of the data
centroids (Centroids, optional): provide centroids if not contained
in the file
var_names (dict, default): name of the variables in the file,
default: DEF_VAR_MAT constant
Raises:
KeyError
"""
self.clear()
self.tag.file_name = file_name
self.tag.description = description
try:
data = hdf5.read(file_name)
try:
data = data[var_names['field_name']]
except KeyError:
pass
haz_type = hdf5.get_string(data[var_names['var_name']['per_id']])
self.tag.haz_type = haz_type
self._read_centroids(centroids=centroids, var_names=var_names['var_cent'])
self._read_att_mat(data, file_name, var_names)
except KeyError as var_err:
LOGGER.error("Not existing variable: %s", str(var_err))
raise var_err
def read_excel(self, file_name, description='', centroids=None,
var_names=DEF_VAR_EXCEL):
"""Read climada hazard generate with the MATLAB code.
Parameters:
file_name (str): absolute file name
description (str, optional): description of the data
centroids (Centroids, optional): provide centroids if not contained
in the file
var_names (dict, default): name of the variables in the file,
default: DEF_VAR_EXCEL constant
Raises:
KeyError
"""
haz_type = self.tag.haz_type
self.clear()
self.tag.file_name = file_name
self.tag.haz_type = haz_type
self.tag.description = description
try:
self._read_centroids(centroids=centroids, var_names=var_names['col_centroids'])
self._read_att_excel(file_name, var_names)
except KeyError as var_err:
LOGGER.error("Not existing variable: %s", str(var_err))
raise var_err
def select(self, date=None, orig=None, reg_id=None):
"""Select events within provided date and/or historical or synthetical.
Frequency of the events may need to be recomputed!
Parameters:
date (tuple(str or int), optional): (initial date, final date) in
string ISO format or datetime ordinal integer
orig (bool, optional): select only historical (True) or only
synthetic (False)
Returns:
Hazard or children
"""
try:
haz = self.__class__()
except TypeError:
haz = Hazard(self.tag.haz_type)
sel_ev = np.ones(self.event_id.size, bool)
sel_cen = np.ones(self.centroids.size, bool)
# filter events with date
if isinstance(date, tuple):
date_ini, date_end = date[0], date[1]
if isinstance(date_ini, str):
date_ini = u_dt.str_to_date(date[0])
date_end = u_dt.str_to_date(date[1])
sel_ev = np.logical_and(date_ini <= self.date,
self.date <= date_end)
if not np.any(sel_ev):
LOGGER.info('No hazard in date range %s.', date)
return None
# filter events hist/synthetic
if isinstance(orig, bool):
sel_ev = np.logical_and(sel_ev, self.orig.astype(bool) == orig)
if not np.any(sel_ev):
LOGGER.info('No hazard with %s tracks.', str(orig))
return None
# filter centroids
if reg_id is not None:
sel_cen = np.argwhere(self.centroids.region_id == reg_id).reshape(-1)
if not sel_cen.size:
LOGGER.info('No hazard centroids with region %s.', str(reg_id))
return None
sel_ev = np.argwhere(sel_ev).squeeze()
for (var_name, var_val) in self.__dict__.items():
if isinstance(var_val, np.ndarray) and var_val.ndim == 1 and \
var_val.size:
setattr(haz, var_name, var_val[sel_ev])
elif isinstance(var_val, sparse.csr_matrix):
setattr(haz, var_name, var_val[sel_ev, :][:, sel_cen])
elif isinstance(var_val, list) and var_val:
setattr(haz, var_name, [var_val[idx] for idx in sel_ev])
elif var_name == 'centroids':
if reg_id is not None:
setattr(haz, var_name, var_val.select(reg_id))
else:
setattr(haz, var_name, var_val)
else:
setattr(haz, var_name, var_val)
return haz
def local_exceedance_inten(self, return_periods=(25, 50, 100, 250)):
""" Compute exceedance intensity map for given return periods.
Parameters:
return_periods (np.array): return periods to consider
Returns:
np.array
"""
LOGGER.info('Computing exceedance intenstiy map for return periods: %s',
return_periods)
num_cen = self.intensity.shape[1]
inten_stats = np.zeros((len(return_periods), num_cen))
cen_step = int(CONFIG['global']['max_matrix_size']/self.intensity.shape[0])
if not cen_step:
LOGGER.error('Increase max_matrix_size configuration parameter to'\
' > %s', str(self.intensity.shape[0]))
raise ValueError
# separte in chunks
chk = -1
for chk in range(int(num_cen/cen_step)):
self._loc_return_inten(np.array(return_periods), \
self.intensity[:, chk*cen_step:(chk+1)*cen_step].todense(), \
inten_stats[:, chk*cen_step:(chk+1)*cen_step])
self._loc_return_inten(np.array(return_periods), \
self.intensity[:, (chk+1)*cen_step:].todense(), \
inten_stats[:, (chk+1)*cen_step:])
return inten_stats
def plot_rp_intensity(self, return_periods=(25, 50, 100, 250), **kwargs):
"""Compute and plot hazard exceedance intensity maps for different
return periods. Calls local_exceedance_inten.
Parameters:
return_periods (tuple(int), optional): return periods to consider
kwargs (optional): arguments for pcolormesh matplotlib function
used in event plots
Returns:
matplotlib.figure.Figure, matplotlib.axes._subplots.AxesSubplot,
np.ndarray (return_periods.size x num_centroids)
"""
inten_stats = self.local_exceedance_inten(np.array(return_periods))
colbar_name = 'Intensity (' + self.units + ')'
title = list()
for ret in return_periods:
title.append('Return period: ' + str(ret) + ' years')
fig, axis = u_plot.geo_im_from_array(inten_stats, self.centroids.coord,
colbar_name, title, **kwargs)
return fig, axis, inten_stats
def plot_intensity(self, event=None, centr=None, **kwargs):
"""Plot intensity values for a selected event or centroid.
Parameters:
event (int or str, optional): If event > 0, plot intensities of
event with id = event. If event = 0, plot maximum intensity in
each centroid. If event < 0, plot abs(event)-largest event. If
event is string, plot events with that name.
centr (int or tuple, optional): If centr > 0, plot intensity
of all events at centroid with id = centr. If centr = 0,
plot maximum intensity of each event. If centr < 0,
plot abs(centr)-largest centroid where higher intensities
are reached. If tuple with (lat, lon) plot intensity of nearest
centroid.
kwargs (optional): arguments for pcolormesh matplotlib function
used in event plots
Returns:
matplotlib.figure.Figure, matplotlib.axes._subplots.AxesSubplot
Raises:
ValueError
"""
col_label = 'Intensity %s' % self.units
if event is not None:
if isinstance(event, str):
event = self.get_event_id(event)
return self._event_plot(event, self.intensity, col_label, **kwargs)
if centr is not None:
if isinstance(centr, tuple):
centr = self.centroids.get_nearest_id(centr[0], centr[1])
return self._centr_plot(centr, self.intensity, col_label)
LOGGER.error("Provide one event id or one centroid id.")
raise ValueError
def plot_fraction(self, event=None, centr=None, **kwargs):
"""Plot fraction values for a selected event or centroid.
Parameters:
event (int or str, optional): If event > 0, plot fraction of event
with id = event. If event = 0, plot maximum fraction in each
centroid. If event < 0, plot abs(event)-largest event. If event
is string, plot events with that name.
centr (int or tuple, optional): If centr > 0, plot fraction
of all events at centroid with id = centr. If centr = 0,
plot maximum fraction of each event. If centr < 0,
plot abs(centr)-largest centroid where highest fractions
are reached. If tuple with (lat, lon) plot fraction of nearest
centroid.
kwargs (optional): arguments for pcolormesh matplotlib function
used in event plots
Returns:
matplotlib.figure.Figure, matplotlib.axes._subplots.AxesSubplot
Raises:
ValueError
"""
col_label = 'Fraction'
if event is not None:
if isinstance(event, str):
event = self.get_event_id(event)
return self._event_plot(event, self.fraction, col_label, **kwargs)
if centr is not None:
if isinstance(centr, tuple):
centr = self.centroids.get_nearest_id(centr[0], centr[1])
return self._centr_plot(centr, self.fraction, col_label)
LOGGER.error("Provide one event id or one centroid id.")
raise ValueError
def get_event_id(self, event_name):
""""Get an event id from its name. Several events might have the same
name.
Parameters:
event_name (str): Event name
Returns:
np.array(int)
"""
list_id = self.event_id[[i_name for i_name, val_name \
in enumerate(self.event_name) if val_name == event_name]]
if list_id.size == 0:
LOGGER.error("No event with name: %s", event_name)
raise ValueError
return list_id
def get_event_name(self, event_id):
""""Get the name of an event id.
Parameters:
event_id (int): id of the event
Returns:
str
Raises:
ValueError
"""
try:
return self.event_name[np.argwhere(
self.event_id == event_id)[0][0]]
except IndexError:
LOGGER.error("No event with id: %s", event_id)
raise ValueError
def get_event_date(self, event=None):
""" Return list of date strings for given event or for all events,
if no event provided.
Parameters:
event (str or int, optional): event name or id.
Returns:
list(str)
"""
if event is None:
l_dates = [u_dt.date_to_str(date) for date in self.date]
elif isinstance(event, str):
ev_ids = self.get_event_id(event)
l_dates = [u_dt.date_to_str(self.date[ \
np.argwhere(self.event_id == ev_id)[0][0]]) \
for ev_id in ev_ids]
else:
ev_idx = np.argwhere(self.event_id == event)[0][0]
l_dates = [u_dt.date_to_str(self.date[ev_idx])]
return l_dates
def calc_year_set(self):
""" From the dates of the original events, get number yearly events.
Returns:
dict: key are years, values array with event_ids of that year
"""
orig_year = np.array([dt.datetime.fromordinal(date).year
for date in self.date[self.orig]])
orig_yearset = {}
for year in np.unique(orig_year):
orig_yearset[year] = self.event_id[self.orig][orig_year == year]
return orig_yearset
def append(self, hazard, set_uni_id=True):
"""Append events in hazard. Id is perserved if not present in current
hazard. Otherwise, a new id is provided. Calls Centroids.append.
All arrays and lists of the instances are appended.
Parameters:
hazard (Hazard): Hazard instance to append to current
set_uni_id (bool, optional): set event_id and centroids.id to
unique values
Raises:
ValueError
"""
hazard._check_events()
if self.event_id.size == 0:
for key in hazard.__dict__:
try:
self.__dict__[key] = copy.deepcopy(hazard.__dict__[key])
except TypeError:
self.__dict__[key] = copy.copy(hazard.__dict__[key])
return
if (self.units == '') and (hazard.units != ''):
LOGGER.info("Initial hazard does not have units.")
self.units = hazard.units
elif hazard.units == '':
LOGGER.info("Appended hazard does not have units.")
elif self.units != hazard.units:
LOGGER.error("Hazards with different units can't be appended: "
"%s != %s.", self.units, hazard.units)
raise ValueError
self.tag.append(hazard.tag)
n_ini_ev = self.event_id.size
# append all 1-dim variables
for (var_name, var_val), haz_val in zip(self.__dict__.items(),
hazard.__dict__.values()):
if isinstance(var_val, np.ndarray) and var_val.ndim == 1 and \
var_val.size:
setattr(self, var_name, np.append(var_val, haz_val). \
astype(var_val.dtype, copy=False))
elif isinstance(var_val, list) and var_val:
setattr(self, var_name, var_val + haz_val)
# append intensity and fraction:
# if same centroids, just append events
# else, check centroids correct column
if np.array_equal(self.centroids.coord, hazard.centroids.coord):
self.intensity = sparse.vstack([self.intensity, \
hazard.intensity], format='csr')
self.fraction = sparse.vstack([self.fraction, \
hazard.fraction], format='csr')
else:
cen_self, cen_haz = self._append_haz_cent(hazard.centroids, set_uni_id)
self.intensity = sparse.vstack([self.intensity, \
sparse.lil_matrix((hazard.intensity.shape[0], \
self.intensity.shape[1]))], format='lil')
self.fraction = sparse.vstack([self.fraction, \
sparse.lil_matrix((hazard.intensity.shape[0], \
self.intensity.shape[1]))], format='lil')
self.intensity[n_ini_ev:, cen_self] = hazard.intensity[:, cen_haz]
self.fraction[n_ini_ev:, cen_self] = hazard.fraction[:, cen_haz]
self.intensity = self.intensity.tocsr()
self.fraction = self.fraction.tocsr()
# Make event id unique
if set_uni_id:
_, unique_idx = np.unique(self.event_id, return_index=True)
rep_id = [pos for pos in range(self.event_id.size)
if pos not in unique_idx]
sup_id = np.max(self.event_id) + 1
self.event_id[rep_id] = np.arange(sup_id, sup_id+len(rep_id))
def remove_duplicates(self):
"""Remove duplicate events (events with same name and date)."""
dup_pos = list()
set_ev = set()
for ev_pos, (ev_name, ev_date) in enumerate(zip(self.event_name,
self.date)):
if (ev_name, ev_date) in set_ev:
dup_pos.append(ev_pos)
set_ev.add((ev_name, ev_date))
if len(set_ev) == self.event_id.size:
return
for var_name, var_val in self.__dict__.items():
if isinstance(var_val, np.ndarray) and var_val.ndim == 1:
setattr(self, var_name, np.delete(var_val, dup_pos))
elif isinstance(var_val, list):
setattr(self, var_name, np.delete(var_val, dup_pos).tolist())
mask = np.ones(self.intensity.shape, dtype=bool)
mask[dup_pos, :] = False
self.intensity = sparse.csr_matrix(self.intensity[mask].\
reshape(self.event_id.size, self.intensity.shape[1]))
self.fraction = sparse.csr_matrix(self.fraction[mask].\
reshape(self.event_id.size, self.intensity.shape[1]))
@property
def size(self):
""" Returns number of events """
return self.event_id.size
def write_hdf5(self, file_name):
""" Write hazard in hdf5 format.
Parameters:
file_name (str): file name to write, with h5 format
"""
hf_data = h5py.File(file_name, 'w')
str_dt = h5py.special_dtype(vlen=str)
for (var_name, var_val) in self.__dict__.items():
if var_name == 'centroids':
hf_centr = hf_data.create_group(var_name)
hf_centr.create_dataset('latitude', data=var_val.lat)
hf_centr.create_dataset('longitude', data=var_val.lon)
hf_centr.create_dataset('id', data=var_val.id)
elif var_name == 'tag':
hf_str = hf_data.create_dataset('haz_type', (1,), dtype=str_dt)
hf_str[0] = var_val.haz_type
hf_str = hf_data.create_dataset('file_name', (1,), dtype=str_dt)
hf_str[0] = str(var_val.file_name)
hf_str = hf_data.create_dataset('description', (1,), dtype=str_dt)
hf_str[0] = str(var_val.description)
elif isinstance(var_val, sparse.csr_matrix):
hf_csr = hf_data.create_group(var_name)
hf_csr.create_dataset('data', data=var_val.data)
hf_csr.create_dataset('indices', data=var_val.indices)
hf_csr.create_dataset('indptr', data=var_val.indptr)
hf_csr.attrs['shape'] = var_val.shape
elif isinstance(var_val, str):
hf_str = hf_data.create_dataset(var_name, (1,), dtype=str_dt)
hf_str[0] = var_val
elif isinstance(var_val, list) and isinstance(var_val[0], str):
hf_str = hf_data.create_dataset(var_name, (len(var_val),), dtype=str_dt)
for i_ev, var_ev in enumerate(var_val):
hf_str[i_ev] = var_ev
else:
hf_data.create_dataset(var_name, data=var_val)
hf_data.close()
def read_hdf5(self, file_name):
""" Read hazard in hdf5 format.
Parameters:
file_name (str): file name to read, with h5 format
"""
self.clear()
hf_data = h5py.File(file_name, 'r')
for (var_name, var_val) in self.__dict__.items():
if var_name == 'centroids':
hf_centr = hf_data.get(var_name)
self.centroids.coord = np.stack([np.array(hf_centr.get('latitude')),
np.array(hf_centr.get('longitude'))], axis=1)
self.centroids.id = np.array(hf_centr.get('id'))
elif var_name == 'tag':
self.tag.haz_type = hf_data.get('haz_type')[0]
self.tag.file_name = hf_data.get('file_name')[0]
self.tag.description = hf_data.get('description')[0]
elif isinstance(var_val, np.ndarray) and var_val.ndim == 1:
setattr(self, var_name, np.array(hf_data.get(var_name)))
elif isinstance(var_val, sparse.csr_matrix):
hf_csr = hf_data.get(var_name)
setattr(self, var_name, sparse.csr_matrix((hf_csr['data'][:], \
hf_csr['indices'][:], hf_csr['indptr'][:]), hf_csr.attrs['shape']))
elif isinstance(var_val, str):
setattr(self, var_name, hf_data.get(var_name)[0])
elif isinstance(var_val, list):
setattr(self, var_name, hf_data.get(var_name).value.tolist())
else:
setattr(self, var_name, hf_data.get(var_name))
hf_data.close()
def _append_all(self, list_haz_ev):
"""Append event by event with same centroids. Takes centroids and units
of first event.
Parameters:
list_haz_ev (list): Hazard instances with one event and same
centroids
"""
self.clear()
num_ev = len(list_haz_ev)
num_cen = list_haz_ev[0].centroids.size
# check for new variables
for key_new in list_haz_ev[0].__dict__.keys():
if key_new not in self.__dict__:
self.__dict__[key_new] = list_haz_ev[0].__dict__[key_new]
for var_name, var_val in self.__dict__.items():
if isinstance(var_val, np.ndarray) and var_val.ndim == 1:
setattr(self, var_name, np.zeros((num_ev,), dtype=var_val.dtype))
elif isinstance(var_val, sparse.csr.csr_matrix):
setattr(self, var_name, sparse.lil_matrix((num_ev, num_cen)))
for i_ev, haz_ev in enumerate(list_haz_ev):
for (var_name, var_val), ev_val in zip(self.__dict__.items(),
haz_ev.__dict__.values()):
if isinstance(var_val, np.ndarray) and var_val.ndim == 1:
var_val[i_ev] = ev_val[0]
elif isinstance(var_val, list):
var_val.extend(ev_val)
elif isinstance(var_val, sparse.lil_matrix):
var_val[i_ev, :] = ev_val[0, :]
elif isinstance(var_val, TagHazard):
var_val.append(ev_val)
self.centroids = copy.deepcopy(list_haz_ev[0].centroids)
self.units = list_haz_ev[0].units
self.intensity = self.intensity.tocsr()
self.fraction = self.fraction.tocsr()
self.event_id = np.arange(1, num_ev+1)
def _append_haz_cent(self, centroids, set_uni_id=True):
"""Append centroids. Get positions of new centroids.
Parameters:
centroids (Centroids): centroids to append
set_uni_id (bool, optional): set centroids.id to unique values
Returns:
cen_self (np.array): positions in self of new centroids
cen_haz (np.array): corresponding positions in centroids
"""
# append different centroids
n_ini_cen = self.centroids.id.size
new_pos = self.centroids.append(centroids, set_uni_id)
self.intensity = sparse.hstack([self.intensity, \
sparse.lil_matrix((self.intensity.shape[0], \
self.centroids.id.size - n_ini_cen))], format='lil')
self.fraction = sparse.hstack([self.fraction, \
sparse.lil_matrix((self.fraction.shape[0], \
self.centroids.id.size - n_ini_cen))], format='lil')
# compute positions of repeated and different centroids
new_vals = np.argwhere(new_pos).squeeze(axis=1)
rep_vals = np.argwhere(np.logical_not(new_pos)).squeeze(axis=1)
if rep_vals.size:
view_x = self.centroids.coord[:self.centroids.size-new_vals.size].\
astype(float).view(complex).reshape(-1,)
view_y = centroids.coord[rep_vals].\
astype(float).view(complex).reshape(-1,)
index = np.argsort(view_x)
sorted_index = np.searchsorted(view_x[index], view_y)
yindex = np.take(index, sorted_index, mode="clip")
else:
yindex = np.array([])
cen_self = np.zeros(centroids.size, dtype=int)
cen_haz = np.zeros(centroids.size, dtype=int)
cen_self[:rep_vals.size] = yindex
cen_haz[:rep_vals.size] = rep_vals
cen_self[rep_vals.size:] = np.arange(new_vals.size) + n_ini_cen
cen_haz[rep_vals.size:] = new_vals
return cen_self, cen_haz
def _events_set(self):
"""Generate set of tuples with (event_name, event_date) """
ev_set = set()
for ev_name, ev_date in zip(self.event_name, self.date):
ev_set.add((ev_name, ev_date))
return ev_set
def _event_plot(self, event_id, mat_var, col_name, **kwargs):
""""Plot an event of the input matrix.
Parameters:
event_id (int or np.array(int)): If event_id > 0, plot mat_var of
event with id = event_id. If event_id = 0, plot maximum
mat_var in each centroid. If event_id < 0, plot
abs(event_id)-largest event.
mat_var (sparse matrix): Sparse matrix where each row is an event
col_name (sparse matrix): Colorbar label
kwargs (optional): arguments for pcolormesh matplotlib function
Returns:
matplotlib.figure.Figure, matplotlib.axes._subplots.AxesSubplot
"""
if not isinstance(event_id, np.ndarray):
event_id = np.array([event_id])
array_val = list()
l_title = list()
for ev_id in event_id:
if ev_id > 0:
try:
event_pos = np.where(self.event_id == ev_id)[0][0]
except IndexError:
LOGGER.error('Wrong event id: %s.', ev_id)
raise ValueError from IndexError
im_val = mat_var[event_pos, :].todense().transpose()
title = 'Event ID %s: %s' % (str(self.event_id[event_pos]), \
self.event_name[event_pos])
elif ev_id < 0:
max_inten = np.asarray(np.sum(mat_var, axis=1)).reshape(-1)
event_pos = np.argpartition(max_inten, ev_id)[ev_id:]
event_pos = event_pos[np.argsort(max_inten[event_pos])][0]
im_val = mat_var[event_pos, :].todense().transpose()
title = '%s-largest Event. ID %s: %s' % (np.abs(ev_id), \
str(self.event_id[event_pos]), self.event_name[event_pos])
else:
im_val = np.max(mat_var, axis=0).todense().transpose()
title = '%s max intensity at each point' % self.tag.haz_type
array_val.append(im_val)
l_title.append(title)
return u_plot.geo_im_from_array(array_val, self.centroids.coord,
col_name, l_title, **kwargs)
def _centr_plot(self, centr_id, mat_var, col_name):
""""Plot a centroid of the input matrix.
Parameters:
centr_id (int): If centr_id > 0, plot mat_var
of all events at centroid with id = centr_id. If centr_id = 0,
plot maximum mat_var of each event. If centr_id < 0,
plot abs(centr_id)-largest centroid where highest mat_var
are reached.
mat_var (sparse matrix): Sparse matrix where each column represents
a centroid
col_name (sparse matrix): Colorbar label
Returns:
matplotlib.figure.Figure, matplotlib.axes._subplots.AxesSubplot
"""
if centr_id > 0:
try:
centr_pos = np.where(self.centroids.id == centr_id)[0][0]
except IndexError:
LOGGER.error('Wrong centroid id: %s.', centr_id)
raise ValueError from IndexError
array_val = mat_var[:, centr_pos].todense()
title = 'Centroid ID %s: (%s, %s)' % (str(centr_id), \
self.centroids.coord[centr_pos, 0], \
self.centroids.coord[centr_pos, 1])
elif centr_id < 0:
max_inten = np.asarray(np.sum(mat_var, axis=0)).reshape(-1)
centr_pos = np.argpartition(max_inten, centr_id)[centr_id:]
centr_pos = centr_pos[np.argsort(max_inten[centr_pos])][0]
array_val = mat_var[:, centr_pos].todense()
title = '%s-largest Centroid. ID %s: (%s, %s)' % \
(np.abs(centr_id), str(self.centroids.id[centr_pos]), \
self.centroids.coord[centr_pos, 0], \
self.centroids.coord[centr_pos, 1])
else:
array_val = np.max(mat_var, axis=1).todense()
title = '%s max intensity at each event' % self.tag.haz_type
graph = u_plot.Graph2D(title)
graph.add_subplot('Event number', col_name)
graph.add_curve(range(len(array_val)), array_val, 'b')
graph.set_x_lim(range(len(array_val)))
return graph.get_elems()
def _loc_return_inten(self, return_periods, inten, exc_inten):
""" Compute local exceedence intensity for given return period.
Parameters:
return_periods (np.array): return periods to consider
cen_pos (int): centroid position
Returns:
np.array
"""
# sorted intensity
sort_pos = np.argsort(inten, axis=0)[::-1, :]
columns = np.ones(inten.shape, int)
columns *= np.arange(columns.shape[1])
inten_sort = inten[sort_pos, columns]
# cummulative frequency at sorted intensity
freq_sort = self.frequency[sort_pos]
np.cumsum(freq_sort, axis=0, out=freq_sort)
for cen_idx in range(inten.shape[1]):
exc_inten[:, cen_idx] = self._cen_return_inten(
inten_sort[:, cen_idx], freq_sort[:, cen_idx],
self.intensity_thres, return_periods)
def _check_events(self):
""" Check that all attributes but centroids contain consistent data.
Put default date, event_name and orig if not provided. Check not
repeated events (i.e. with same date and name)
Raises:
ValueError
"""
num_ev = len(self.event_id)
num_cen = len(self.centroids.id)
if np.unique(self.event_id).size != num_ev:
LOGGER.error("There are events with the same identifier.")
raise ValueError
check.check_oligatories(self.__dict__, self.vars_oblig, 'Hazard.',
num_ev, num_ev, num_cen)
check.check_optionals(self.__dict__, self.vars_opt, 'Hazard.', num_ev)
self.event_name = check.array_default(num_ev, self.event_name, \
'Hazard.event_name', list(self.event_id))
self.date = check.array_default(num_ev, self.date, 'Hazard.date', \
np.ones(self.event_id.shape, dtype=int))
self.orig = check.array_default(num_ev, self.orig, 'Hazard.orig', \
np.zeros(self.event_id.shape, dtype=bool))
if len(self._events_set()) != num_ev:
LOGGER.error("There are events with same date and name.")
raise ValueError
@staticmethod
def _cen_return_inten(inten, freq, inten_th, return_periods):
"""From ordered intensity and cummulative frequency at centroid, get
exceedance intensity at input return periods.
Parameters:
inten (np.array): sorted intensity at centroid
freq (np.array): cummulative frequency at centroid
inten_th (float): intensity threshold
return_periods (np.array): return periods
Returns:
np.array
"""
inten_th = np.asarray(inten > inten_th).squeeze()
inten_cen = inten[inten_th]
freq_cen = freq[inten_th]
if not inten_cen.size:
return np.zeros((return_periods.size,))
try:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
pol_coef = np.polyfit(np.log(freq_cen), inten_cen, deg=1)
except ValueError:
pol_coef = np.polyfit(np.log(freq_cen), inten_cen, deg=0)
inten_fit = np.polyval(pol_coef, np.log(1/return_periods))
wrong_inten = np.logical_and(return_periods > np.max(1/freq_cen), \
np.isnan(inten_fit))
inten_fit[wrong_inten] = 0.
return inten_fit
def _read_att_mat(self, data, file_name, var_names):
""" Read MATLAB hazard's attributes. """
self.frequency = np.squeeze(data[var_names['var_name']['freq']])
self.orig = np.squeeze(data[var_names['var_name']['orig']]).astype(bool)
self.event_id = np.squeeze(data[var_names['var_name']['even_id']]. \
astype(np.int, copy=False))
try:
self.units = hdf5.get_string(data[var_names['var_name']['unit']])
except KeyError:
pass
n_cen = len(self.centroids.id)
n_event = len(self.event_id)
try:
self.intensity = hdf5.get_sparse_csr_mat( \
data[var_names['var_name']['inten']], (n_event, n_cen))
except ValueError as err:
LOGGER.error('Size missmatch in intensity matrix.')
raise err
try:
self.fraction = hdf5.get_sparse_csr_mat( \
data[var_names['var_name']['frac']], (n_event, n_cen))
except ValueError as err:
LOGGER.error('Size missmatch in fraction matrix.')
raise err
except KeyError:
self.fraction = sparse.csr_matrix(np.ones(self.intensity.shape,
dtype=np.float))
# Event names: set as event_id if no provided
try:
self.event_name = hdf5.get_list_str_from_ref(
file_name, data[var_names['var_name']['ev_name']])
except KeyError:
self.event_name = list(self.event_id)
try:
comment = hdf5.get_string(data[var_names['var_name']['comment']])
self.tag.description += ' ' + comment
except KeyError:
pass
try:
datenum = data[var_names['var_name']['datenum']].squeeze()
self.date = np.array([(dt.datetime.fromordinal(int(date)) + \
dt.timedelta(days=date%1)- \
dt.timedelta(days=366)).toordinal() for date in datenum])
except KeyError:
pass
def _read_centroids(self, centroids, var_names):
"""Read centroids file if no centroids provided"""
if centroids is None:
self.centroids = Centroids()
self.centroids.read(self.tag.file_name, self.tag.description,
var_names)
else:
self.centroids = centroids
def _read_att_excel(self, file_name, var_names):
""" Read Excel hazard's attributes. """
num_cen = self.centroids.id.size
dfr = pd.read_excel(file_name, var_names['sheet_name']['freq'])
num_events = dfr.shape[0]
self.frequency = dfr[var_names['col_name']['freq']].values
self.orig = dfr[var_names['col_name']['orig']].values.astype(bool)
self.event_id = dfr[var_names['col_name']['even_id']].values. \
astype(int, copy=False)
self.date = dfr[var_names['col_name']['even_dt']].values. \
astype(int, copy=False)
self.event_name = dfr[var_names['col_name']['even_name']].values.tolist()
dfr = pd.read_excel(file_name, var_names['sheet_name']['inten'])
# number of events (ignore centroid_ID column)
# check the number of events is the same as the one in the frequency
if dfr.shape[1] - 1 is not num_events:
LOGGER.error('Hazard intensity is given for a number of events ' \
'different from the number of defined in its frequency: ' \
'%s != %s', dfr.shape[1] - 1, num_events)
raise ValueError
# check number of centroids is the same as retrieved before
if dfr.shape[0] is not num_cen:
LOGGER.error('Hazard intensity is given for a number of centroids ' \
'different from the number of centroids defined: %s != %s', \
dfr.shape[0], num_cen)
raise ValueError
# check centroids ids are correct
if not np.array_equal(dfr[var_names['col_name']['cen_id']].values,
self.centroids.id[-num_cen:]):
LOGGER.error('Hazard intensity centroids ids do not match ' \
'previously defined centroids.')
raise ValueError
self.intensity = sparse.csr_matrix(dfr.values[:, 1:num_events+1].transpose())
self.fraction = sparse.csr_matrix(np.ones(self.intensity.shape,
dtype=np.float))