def from_string(urn_string):
complete = urn_string.split('#')
extras = ''
if len(complete) > 1:
extras = '#{0}'.format(complete[1])
parts = complete[0].split(':')
if len(parts) < 5:
return IoosUrn()
urn = IoosUrn()
urn.asset_type = parts[2]
urn.authority = parts[3]
urn.label = parts[4]
if len(parts) > 5:
if urn.asset_type == 'station':
urn.version = parts[5]
elif len(parts) > 6:
# Also a verion specified, so this has to be the component
urn.component = parts[5] + extras
else:
logger.debug("Assuming that {0} is the 'component' piece of the URN (not the 'version')".format(parts[5] + extras))
urn.component = parts[5] + extras
if len(parts) > 6:
urn.version = parts[6]
if len(parts) > 7:
pass
logger.warning("The URN is too long stripping off '{}'".format(':'.join(parts[7:])))
return urn
def from_string(urn_string):
complete = urn_string.split('#')
extras = ''
if len(complete) > 1:
extras = '#{0}'.format(complete[1])
parts = complete[0].split(':')
if len(parts) < 5:
return IoosUrn()
urn = IoosUrn()
urn.asset_type = parts[2]
urn.authority = parts[3]
urn.label = parts[4]
if len(parts) > 5:
if urn.asset_type == 'station':
urn.version = parts[5]
elif len(parts) > 6:
# Also a verion specified, so this has to be the component
urn.component = parts[5] + extras
else:
logger.debug(
"Assuming that {0} is the 'component' piece of the URN (not the 'version')"
.format(parts[5] + extras))
urn.component = parts[5] + extras
if len(parts) > 6:
urn.version = parts[6]
if len(parts) > 7:
pass
logger.warning("The URN is too long stripping off '{}'".format(
':'.join(parts[7:])))
return urn
def get_dataframe_from_variable(nc, data_var):
""" Returns a Pandas DataFrame of the data.
This always returns positive down depths
"""
time_var = nc.get_variables_by_attributes(standard_name='time')[0]
depth_vars = nc.get_variables_by_attributes(axis=lambda v: v is not None and v.lower() == 'z')
depth_vars += nc.get_variables_by_attributes(standard_name=lambda v: v in ['height', 'depth' 'surface_altitude'], positive=lambda x: x is not None)
# Find the correct depth variable
depth_var = None
for d in depth_vars:
try:
if d._name in data_var.coordinates.split(" ") or d._name in data_var.dimensions:
depth_var = d
break
except AttributeError:
continue
times = netCDF4.num2date(time_var[:], units=time_var.units, calendar=getattr(time_var, 'calendar', 'standard'))
original_times_size = times.size
if depth_var is None and hasattr(data_var, 'sensor_depth'):
depth_type = get_type(data_var.sensor_depth)
depths = np.asarray([data_var.sensor_depth] * len(times)).flatten()
values = data_var[:].flatten()
elif depth_var is None:
depths = np.asarray([np.nan] * len(times)).flatten()
depth_type = get_type(depths)
values = data_var[:].flatten()
else:
depths = depth_var[:]
depth_type = get_type(depths)
if len(data_var.shape) > 1:
times = np.repeat(times, depths.size)
depths = np.tile(depths, original_times_size)
values = data_var[:, :].flatten()
else:
values = data_var[:].flatten()
if getattr(depth_var, 'positive', 'down').lower() == 'up':
logger.warning("Converting depths to positive down before returning the DataFrame")
depths = depths * -1
# https://github.com/numpy/numpy/issues/4595
# We can't call astype on a MaskedConstant
if (
isinstance(depths, np.ma.core.MaskedConstant) or
(hasattr(depths, 'mask') and depths.mask.all())
):
depths = np.asarray([np.nan] * len(times)).flatten()
df = pd.DataFrame({ 'time': times,
'value': values.astype(data_var.dtype),
'unit': data_var.units if hasattr(data_var, 'units') else np.nan,
'depth': depths.astype(depth_type) })
df.set_index([pd.DatetimeIndex(df['time']), pd.Float64Index(df['depth'])], inplace=True)
return df
def global_attributes(self, gas):
# These are set by this script, we don't someone to be able to set them manually
global_skips = ["time_coverage_start", "time_coverage_end", "time_coverage_duration", "time_coverage_resolution",
"featureType", "geospatial_vertical_positive", "geospatial_vertical_min", "geospatial_vertical_max",
"geospatial_lat_min", "geospatial_lon_min", "geospatial_lat_max", "geospatial_lon_max",
"Conventions", "date_created", "cdm_data_type"]
for i in set(global_skips) & gas.keys():
logger.warning("Ignoring global attribute {} because it is calculated or set automatically".format(i))
self._global_attributes = { k: v for k, v in gas.items() if k not in global_skips }
def export(self, output_file):
super(IncompleteProfile, self).export(output_file)
with netCDF4.Dataset(output_file, 'w', clobber=True) as nc:
gas = self.global_attributes
nc.setncatts(gas)
profiles = self.df.profile.unique().size
profile_group = self.df.groupby('profile')
max_z = profile_group.size().max()
nc.createDimension('profile', profiles)
nc.createDimension('z', max_z)
profile = nc.createVariable('profile', self.df.profile.dtype, ('profile',))
_, unique_profile_rows = np.unique(self.df.profile.values, return_index=True)
profile[:] = list(range(profiles))
time = nc.createVariable('time', int, ('profile',))
time[:] = netCDF4.date2num([datetime.utcfromtimestamp(t) for t in self.df.time.unique().astype('<M8[s]').astype(int)], units=self.base_time)
latitude = nc.createVariable('latitude', self.df.latitude.dtype, ('profile',))
latitude[:] = self.df.latitude.values[unique_profile_rows]
longitude = nc.createVariable('longitude', self.df.longitude.dtype, ('profile',))
longitude[:] = self.df.longitude.values[unique_profile_rows]
# Metadata variables
nc.createVariable("crs", 'i4')
nc.createVariable("platform", "i4")
nc.setncattr('platform', 'platform')
# Data vars
reserved_columns = ['profile', 'time', 'latitude', 'longitude']
for i, (name, p) in enumerate(profile_group):
for c in [d for d in self.df.columns if d not in reserved_columns]:
var_name = c.split(' ')[0].lower()
fill = p[c].dtype.type(self.fill_value)
if var_name not in nc.variables:
v = nc.createVariable(var_name, self.df[c].dtype, ('profile', 'z'), fill_value=fill)
else:
v = nc.variables[var_name]
assignable_values = p[c].fillna(fill).values
v[i, :len(assignable_values)] = assignable_values
for k, v in self.variable_attributes.items():
if k in nc.variables:
for n, z in v.items():
try:
nc.variables[k].setncattr(n, z)
except BaseException:
logger.warning('Could not set attribute {} on {}'.format(n, k))
def from_dataframe(df, output_directory, output_filename, latitude, longitude, station_name, global_attributes, variable_name, variable_attributes, sensor_vertical_datum=None, fillvalue=None, data_column=None, vertical_axis_name=None, vertical_positive=None, create_instrument_variable=False, attempts=None):
# Attempts is how many files to try to build a NetCDF files from a
# dataframe. For backwards compatibility purposes, we always try
# everything (even manual matching which takes forever and is a memory
# hog).
attempts = attempts or 5
if fillvalue is None:
fillvalue = -9999.9
if data_column is None:
data_column = 'value'
data_fillvalue = df[data_column].values.dtype.type(fillvalue)
vertical_fillvalue = df['depth'].values.dtype.type(fillvalue)
df[data_column] = df[data_column].fillna(data_fillvalue)
times = np.asarray([ calendar.timegm(x.utctimetuple()) for x in df['time'] ])
df['depth'] = df['depth'].fillna(vertical_fillvalue)
depths = df['depth'].values
try:
ts = TimeSeries(output_directory, latitude, longitude, station_name, global_attributes, times=times, verticals=depths, output_filename=output_filename, vertical_fill=vertical_fillvalue, vertical_axis_name=vertical_axis_name, vertical_positive=vertical_positive)
ts.add_variable(variable_name, df[data_column].values, attributes=variable_attributes, sensor_vertical_datum=sensor_vertical_datum, raise_on_error=True, fillvalue=data_fillvalue, create_instrument_variable=create_instrument_variable)
except ValueError:
if attempts < 2:
raise
logger.warning("Attempt 2: using unique times")
try:
# Try uniquing time
newtimes = np.unique(times)
ts = TimeSeries(output_directory, latitude, longitude, station_name, global_attributes, times=newtimes, verticals=depths, output_filename=output_filename, vertical_fill=vertical_fillvalue, vertical_axis_name=vertical_axis_name, vertical_positive=vertical_positive)
ts.add_variable(variable_name, df[data_column].values, attributes=variable_attributes, sensor_vertical_datum=sensor_vertical_datum, raise_on_error=True, fillvalue=data_fillvalue, create_instrument_variable=create_instrument_variable)
except ValueError:
if attempts < 3:
raise
logger.warning("Attempt 3: using unique depths")
try:
# Try uniquing depths
newdepths = np.unique(df['depth'].values)
ts = TimeSeries(output_directory, latitude, longitude, station_name, global_attributes, times=times, verticals=newdepths, output_filename=output_filename, vertical_fill=vertical_fillvalue, vertical_axis_name=vertical_axis_name, vertical_positive=vertical_positive)
ts.add_variable(variable_name, df[data_column].values, attributes=variable_attributes, sensor_vertical_datum=sensor_vertical_datum, raise_on_error=True, fillvalue=data_fillvalue, create_instrument_variable=create_instrument_variable)
except ValueError:
if attempts < 4:
raise
logger.warning("Attempt 4: using unique time and depth")
try:
# Unique both time and depth
newdepths = np.unique(df['depth'].values)
ts = TimeSeries(output_directory, latitude, longitude, station_name, global_attributes, times=newtimes, verticals=newdepths, output_filename=output_filename, vertical_fill=vertical_fillvalue, vertical_axis_name=vertical_axis_name, vertical_positive=vertical_positive)
ts.add_variable(variable_name, df[data_column].values, attributes=variable_attributes, sensor_vertical_datum=sensor_vertical_datum, raise_on_error=True, fillvalue=data_fillvalue, create_instrument_variable=create_instrument_variable)
except ValueError:
if attempts < 5:
raise
logger.warning("Attempt 5: manually matching (this is SLOW)")
# Manually match
ts = TimeSeries(output_directory, latitude, longitude, station_name, global_attributes, times=times, verticals=depths, output_filename=output_filename, vertical_fill=vertical_fillvalue, vertical_axis_name=vertical_axis_name, vertical_positive=vertical_positive)
ts.add_variable(variable_name, df[data_column].values, attributes=variable_attributes, times=times, verticals=depths, sensor_vertical_datum=sensor_vertical_datum, raise_on_error=False, fillvalue=data_fillvalue, create_instrument_variable=create_instrument_variable)
return ts
def update_attributes(self, attributes):
for k, v in attributes.pop('global', {}).items():
try:
self.setncattr(k, v)
except BaseException:
logger.warning('Could not set global attribute {}: {}'.format(
k, v))
for k, v in attributes.items():
if k in self.variables:
for n, z in v.items():
try:
self.variables[k].setncattr(n, z)
except BaseException:
logger.warning(
'Could not set attribute {} on {}'.format(n, k))
self.sync()
def from_dataframe(df, output_directory, output_filename, latitude, longitude, station_name, global_attributes, variable_name, variable_attributes, sensor_vertical_datum=None, fillvalue=None, data_column=None, vertical_axis_name=None, vertical_positive=None):
if fillvalue is None:
fillvalue = -9999.9
if data_column is None:
data_column = 'value'
df[data_column] = df[data_column].fillna(fillvalue)
times = np.asarray([ calendar.timegm(x.utctimetuple()) for x in df['time'] ])
df['depth'] = df['depth'].fillna(fillvalue)
depths = df['depth'].values
try:
ts = TimeSeries(output_directory, latitude, longitude, station_name, global_attributes, times=times, verticals=depths, output_filename=output_filename, vertical_fill=fillvalue, vertical_axis_name=vertical_axis_name, vertical_positive=vertical_positive)
ts.add_variable(variable_name, df[data_column].values, attributes=variable_attributes, sensor_vertical_datum=sensor_vertical_datum, raise_on_error=True)
except ValueError:
logger.warning("Failed first attempt, trying again with unique times.")
try:
# Try uniquing time
newtimes = np.unique(times)
ts = TimeSeries(output_directory, latitude, longitude, station_name, global_attributes, times=newtimes, verticals=depths, output_filename=output_filename, vertical_fill=fillvalue, vertical_axis_name=vertical_axis_name, vertical_positive=vertical_positive)
ts.add_variable(variable_name, df[data_column].values, attributes=variable_attributes, sensor_vertical_datum=sensor_vertical_datum, raise_on_error=True)
except ValueError:
logger.warning("Failed second attempt, trying again with unique depths.")
try:
# Try uniquing depths
newdepths = np.unique(df['depth'].values)
ts = TimeSeries(output_directory, latitude, longitude, station_name, global_attributes, times=times, verticals=newdepths, output_filename=output_filename, vertical_fill=fillvalue, vertical_axis_name=vertical_axis_name, vertical_positive=vertical_positive)
ts.add_variable(variable_name, df[data_column].values, attributes=variable_attributes, sensor_vertical_datum=sensor_vertical_datum, raise_on_error=True)
except ValueError:
logger.warning("Failed third attempt, uniquing time and depth.")
try:
# Unique both time and depth
newdepths = np.unique(df['depth'].values)
ts = TimeSeries(output_directory, latitude, longitude, station_name, global_attributes, times=newtimes, verticals=newdepths, output_filename=output_filename, vertical_fill=fillvalue, vertical_axis_name=vertical_axis_name, vertical_positive=vertical_positive)
ts.add_variable(variable_name, df[data_column].values, attributes=variable_attributes, sensor_vertical_datum=sensor_vertical_datum, raise_on_error=True)
except ValueError:
logger.warning("Failed fourth attempt, manually matching indexes (this is slow).")
# Manually match
ts = TimeSeries(output_directory, latitude, longitude, station_name, global_attributes, times=times, verticals=depths, output_filename=output_filename, vertical_fill=fillvalue, vertical_axis_name=vertical_axis_name, vertical_positive=vertical_positive)
ts.add_variable(variable_name, df[data_column].values, attributes=variable_attributes, times=times, verticals=depths, sensor_vertical_datum=sensor_vertical_datum, raise_on_error=False)
return ts
def to_dataframe(self, clean_cols=True, clean_rows=True):
# The index variable (trajectory_index) is identified by having an
# attribute with name of instance_dimension whose value is the instance
# dimension name (trajectory in this example). The index variable must
# have the profile dimension as its sole dimension, and must be type
# integer. Each value in the index variable is the zero-based trajectory
# index that the profile belongs to i.e. profile p belongs to trajectory
# i=trajectory_index(p), as in section H.2.5.
r_index_var = self.get_variables_by_attributes(
instance_dimension=lambda x: x is not None)[0]
p_dim = self.dimensions[r_index_var.dimensions[0]] # Profile dimension
r_dim = self.dimensions[
r_index_var.instance_dimension] # Trajectory dimension
# The count variable (row_size) contains the number of elements for
# each profile, which must be written contiguously. The count variable
# is identified by having an attribute with name sample_dimension whose
# value is the sample dimension (obs in this example) being counted. It
# must have the profile dimension as its sole dimension, and must be
# type integer
o_index_var = self.get_variables_by_attributes(
sample_dimension=lambda x: x is not None)[0]
o_dim = self.dimensions[
o_index_var.sample_dimension] # Sample dimension
try:
rvar = self.get_variables_by_attributes(cf_role='trajectory_id')[0]
traj_indexes = normalize_array(rvar)
assert traj_indexes.size == r_dim.size
except BaseException:
logger.warning(
'Could not pull trajectory values a variable with "cf_role=trajectory_id", using a computed range.'
)
traj_indexes = np.arange(r_dim.size)
try:
pvar = self.get_variables_by_attributes(cf_role='profile_id')[0]
profile_indexes = normalize_array(pvar)
assert profile_indexes.size == p_dim.size
except BaseException:
logger.warning(
'Could not pull profile values from a variable with "cf_role=profile_id", using a computed range.'
)
profile_indexes = np.arange(p_dim.size)
# Profile dimension
tvars = self.t_axes()
if len(tvars) > 1:
tvar = [
v for v in self.t_axes() if v.dimensions == (
p_dim.name, ) and getattr(v, 'axis', '').lower() == 't'
][0]
else:
tvar = tvars[0]
xvars = self.x_axes()
if len(xvars) > 1:
xvar = [
v for v in self.x_axes() if v.dimensions == (
p_dim.name, ) and getattr(v, 'axis', '').lower() == 'x'
][0]
else:
xvar = xvars[0]
yvars = self.y_axes()
if len(yvars) > 1:
yvar = [
v for v in self.y_axes() if v.dimensions == (
p_dim.name, ) and getattr(v, 'axis', '').lower() == 'y'
][0]
else:
yvar = yvars[0]
zvars = self.z_axes()
if len(zvars) > 1:
zvar = [
v for v in self.z_axes() if v.dimensions == (
o_dim.name, ) and getattr(v, 'axis', '').lower() == 'z'
][0]
else:
zvar = zvars[0]
p = np.ma.masked_all(o_dim.size, dtype=profile_indexes.dtype)
r = np.ma.masked_all(o_dim.size, dtype=traj_indexes.dtype)
t = np.ma.masked_all(o_dim.size, dtype=tvar.dtype)
x = np.ma.masked_all(o_dim.size, dtype=xvar.dtype)
y = np.ma.masked_all(o_dim.size, dtype=yvar.dtype)
si = 0
for i in np.arange(profile_indexes.size):
ei = si + o_index_var[i]
p[si:ei] = profile_indexes[i]
r[si:ei] = traj_indexes[r_index_var[i]]
t[si:ei] = tvar[i]
x[si:ei] = xvar[i]
y[si:ei] = yvar[i]
si = ei
t_mask = False
tfill = get_fill_value(tvar)
if tfill is not None:
t_mask = np.copy(np.ma.getmaskarray(t))
t[t_mask] = 1
t = np.ma.MaskedArray(
nc4.num2date(t, tvar.units, getattr(tvar, 'calendar', 'standard')))
# Patch the time variable back to its original mask, since num2date
# breaks any missing/fill values
t[t_mask] = np.ma.masked
# X and Y
x = generic_masked(x, minv=-180, maxv=180).round(5)
y = generic_masked(y, minv=-90, maxv=90).round(5)
# Distance
d = np.ma.zeros(o_dim.size, dtype=np.float64)
d[1:] = great_distance(start_latitude=y[0:-1],
end_latitude=y[1:],
start_longitude=x[0:-1],
end_longitude=x[1:])['distance']
d = generic_masked(np.cumsum(d), minv=0).round(2)
# Sample dimension
z = generic_masked(zvar[:].flatten(),
attrs=self.vatts(zvar.name)).round(5)
df_data = {
't': t,
'x': x,
'y': y,
'z': z,
'trajectory': r,
'profile': p,
'distance': d
}
building_index_to_drop = np.ones(o_dim.size, dtype=bool)
extract_vars = list(set(self.data_vars() + self.ancillary_vars()))
for i, dvar in enumerate(extract_vars):
# Profile dimensions
if dvar.dimensions == (p_dim.name, ):
vdata = np.ma.masked_all(o_dim.size, dtype=dvar.dtype)
si = 0
for j in np.arange(profile_indexes.size):
ei = si + o_index_var[j]
vdata[si:ei] = dvar[j]
si = ei
# Sample dimensions
elif dvar.dimensions == (o_dim.name, ):
vdata = generic_masked(dvar[:].flatten(),
attrs=self.vatts(dvar.name)).round(3)
else:
logger.warning(
"Skipping variable {}... it didn't seem like a data variable"
.format(dvar))
building_index_to_drop = (building_index_to_drop == True) & (
vdata.mask == True) # noqa
df_data[dvar.name] = vdata
df = pd.DataFrame(df_data)
# Drop all data columns with no data
if clean_cols:
df = df.dropna(axis=1, how='all')
# Drop all data rows with no data variable data
if clean_rows:
df = df.iloc[~building_index_to_drop]
return df
def urnify_from_dict(naming_authority, station_identifier, data_dict):
def clean_value(v):
return v.replace('(', '').replace(')', '').strip().replace(' ', '_')
extras = []
intervals = [] # Because it can be part of cell_methods and its own dict key
if 'cell_methods' in data_dict and data_dict['cell_methods']:
cm = data_dict['cell_methods']
keys = []
values = []
sofar = ''
for i, c in enumerate(cm):
if c == ":":
if len(keys) == len(values):
keys.append(clean_value(sofar))
else:
for j in reversed(range(0, i)):
if cm[j] == " ":
key = clean_value(cm[j+1:i])
values.append(clean_value(sofar.replace(key, '')))
keys.append(key)
break
sofar = ''
else:
sofar += c
# The last value needs appending
values.append(clean_value(sofar))
pairs = zip(keys, values)
mems = []
cell_intervals = []
pairs = sorted(pairs)
for group, members in itertools.groupby(pairs, lambda x: x[0]):
if group == 'interval':
cell_intervals = [m[1] for m in members]
elif group in ['time', 'area']: # Ignore 'comments'. May need to add more things here...
member_strings = []
for m in members:
member_strings.append('{}:{}'.format(group, m[1]))
mems.append(','.join(member_strings))
if mems:
extras.append('cell_methods={}'.format(','.join(mems)))
if cell_intervals:
intervals += cell_intervals
if 'bounds' in data_dict and data_dict['bounds']:
extras.append('bounds={0}'.format(data_dict['bounds']))
if 'vertical_datum' in data_dict and data_dict['vertical_datum']:
extras.append('vertical_datum={0}'.format(data_dict['vertical_datum']))
if 'interval' in data_dict and data_dict['interval']:
if isinstance(data_dict['interval'], (list, tuple,)):
intervals += data_dict['interval']
elif isinstance(data_dict['interval'], str):
intervals += [data_dict['interval']]
if 'standard_name' in data_dict and data_dict['standard_name']:
variable_name = data_dict['standard_name']
elif 'name' in data_dict and data_dict['name']:
variable_name = data_dict['name']
else:
variable_name = ''.join(random.choice(string.ascii_uppercase) for _ in range(8)).lower()
logger.warning("Had to randomly generate a variable name: {0}".format(variable_name))
if 'discriminant' in data_dict and data_dict['discriminant']:
variable_name = '{}-{}'.format(variable_name, data_dict['discriminant'])
if intervals:
intervals = list(set(intervals)) # Unique them
extras.append('interval={}'.format(','.join(intervals)))
if extras:
variable_name = '{0}#{1}'.format(variable_name, ';'.join(extras))
u = IoosUrn(asset_type='sensor',
authority=naming_authority,
label=station_identifier,
component=variable_name,
version=None)
return u.urn
def safe_attribute_typing(zdtype, value):
try:
return zdtype.type(value)
except ValueError:
logger.warning("Could not convert {} to type {}".format(value, zdtype))
return None
def urnify_from_dict(naming_authority, station_identifier, data_dict):
def clean_value(v):
return v.replace('(', '').replace(')', '').strip().replace(' ', '_')
extras = []
intervals = [] # Because it can be part of cell_methods and its own dict key
if 'cell_methods' in data_dict and data_dict['cell_methods']:
cm = data_dict['cell_methods']
keys = []
values = []
sofar = ''
for i, c in enumerate(cm):
if c == ":":
if len(keys) == len(values):
keys.append(clean_value(sofar))
else:
for j in reversed(range(0, i)):
if cm[j] == " ":
key = clean_value(cm[j+1:i])
values.append(clean_value(sofar.replace(key, '')))
keys.append(key)
break
sofar = ''
else:
sofar += c
# The last value needs appending
values.append(clean_value(sofar))
pairs = zip(keys, values)
mems = []
cell_intervals = []
pairs = sorted(pairs)
for group, members in itertools.groupby(pairs, lambda x: x[0]):
if group == 'interval':
cell_intervals = [m[1] for m in members]
elif group in ['time', 'area']: # Ignore 'comments'. May need to add more things here...
member_strings = []
for m in members:
member_strings.append('{}:{}'.format(group, m[1]))
mems.append(','.join(member_strings))
if mems:
extras.append('cell_methods={}'.format(','.join(mems)))
if cell_intervals:
intervals += cell_intervals
if 'bounds' in data_dict and data_dict['bounds']:
extras.append('bounds={0}'.format(data_dict['bounds']))
if 'vertical_datum' in data_dict and data_dict['vertical_datum']:
extras.append('vertical_datum={0}'.format(data_dict['vertical_datum']))
if 'interval' in data_dict and data_dict['interval']:
if isinstance(data_dict['interval'], (list, tuple,)):
intervals += data_dict['interval']
elif isinstance(data_dict['interval'], str):
intervals += [data_dict['interval']]
if 'standard_name' in data_dict and data_dict['standard_name']:
variable_name = data_dict['standard_name']
elif 'name' in data_dict and data_dict['name']:
variable_name = data_dict['name']
else:
variable_name = ''.join(random.choice(string.ascii_uppercase) for _ in range(8)).lower()
logger.warning("Had to randomly generate a variable name: {0}".format(variable_name))
if 'discriminant' in data_dict and data_dict['discriminant']:
variable_name = '{}-{}'.format(variable_name, data_dict['discriminant'])
if intervals:
intervals = list(set(intervals)) # Unique them
extras.append('interval={}'.format(','.join(intervals)))
if extras:
variable_name = '{0}#{1}'.format(variable_name, ';'.join(extras))
u = IoosUrn(asset_type='sensor',
authority=naming_authority,
label=station_identifier,
component=variable_name,
version=None)
return u.urn
def add_variable(self,
variable_name,
values,
times=None,
verticals=None,
sensor_vertical_datum=None,
attributes=None,
unlink_from_profile=None,
fillvalue=None,
raise_on_error=False):
if isinstance(values, (
list,
tuple,
)) and values:
values = np.asarray(values)
if isinstance(times, (
list,
tuple,
)) and times:
times = np.asarray(times)
if isinstance(verticals, (
list,
tuple,
)) and verticals:
verticals = np.asarray(verticals)
# Set vertical datum on the CRS variable
if sensor_vertical_datum is not None:
try:
self.crs.geoid_name = sensor_vertical_datum
self.crs.vertical_datum = sensor_vertical_datum
self.crs.water_surface_reference_datum = sensor_vertical_datum
except AttributeError:
pass
# Set default fillvalue for new variables
if fillvalue is None:
fillvalue = -9999.9
used_values = None
try:
if unlink_from_profile is True:
used_values = np.ma.reshape(values, (self.time.size, ))
used_values = used_values[self.time_indexes]
# These next two cases should work for all but a few cases, which are caught below
elif self.z.size == 1:
used_values = np.ma.reshape(values, (self.time.size, ))
used_values = used_values[self.time_indexes]
else:
used_values = np.ma.reshape(values, (
self.time.size,
self.z.size,
))
used_values = used_values[self.time_indexes]
try:
used_values = used_values[:, self.vertical_indexes]
except IndexError:
# The vertical values most likely had duplicates. Ignore the
# falty index here and try to save the values as is.
pass
except ValueError:
if raise_on_error is True:
raise
else:
logger.warning(
"Could not do a simple reshape of data, trying to match manually! Time:{!s}, Heights:{!s}, Values:{!s}"
.format(self.time.size, self.z.size, values.size))
if self.z.size > 1:
if times is not None and verticals is not None:
# Hmmm, we have two actual height values for this station.
# Not cool man, not cool.
# Reindex the entire values array. This is slow.
indexed = ((bisect.bisect_left(self.time[:], times[i]),
bisect.bisect_left(self.z[:],
verticals[i]), values[i])
for i in range(values.size))
used_values = np.ndarray((
self.time.size,
self.z.size,
),
dtype=values.dtype)
used_values.fill(float(fillvalue))
for (tzi, zzi, vz) in indexed:
if zzi < self.z.size and tzi < self.time.size:
used_values[tzi, zzi] = vz
else:
raise ValueError(
"You need to pass in both 'times' and 'verticals' parameters that matches the size of the 'values' parameter."
)
else:
if times is not None:
# Ugh, find the time indexes manually
indexed = ((bisect.bisect_left(self.time[:],
times[i]), values[i])
for i in range(values.size))
used_values = np.ndarray((self.time.size, ),
dtype=values.dtype)
used_values.fill(float(fillvalue))
for (tzi, vz) in indexed:
if tzi < self.time.size:
used_values[tzi] = vz
else:
raise ValueError(
"You need to pass in a 'times' parameter that matches the size of the 'values' parameter."
)
with EnhancedDataset(self.out_file, 'a') as nc:
logger.info("Setting values for {}...".format(variable_name))
if len(used_values.shape) == 1:
var = nc.createVariable(variable_name,
used_values.dtype, ("time", ),
fill_value=fillvalue,
chunksizes=(1000, ),
zlib=True)
if self.z.size == 1:
var.coordinates = "{} {} latitude longitude".format(
self.time_axis_name, self.vertical_axis_name)
else:
# This is probably a bottom sensor on an ADCP or something, don't add the height coordinate
var.coordinates = "{} latitude longitude".format(
self.time_axis_name)
if unlink_from_profile is True:
# Create metadata variable for the sensor_depth
if nc.variables.get('sensor_depth') is None:
logger.info(
"Setting the special case 'sensor_depth' metadata variable"
)
inst_depth = nc.createVariable(
'sensor_depth', 'f4')
inst_depth.units = 'm'
inst_depth.standard_name = 'surface_altitude'
inst_depth.positive = self.vertical_positive
if self.vertical_positive.lower() == 'down':
inst_depth.long_name = 'sensor depth below datum'
elif self.vertical_positive.lower() == 'up':
inst_depth.long_name = 'sensor height above datum'
inst_depth.datum = sensor_vertical_datum or 'Unknown'
if verticals and verticals.size > 0:
inst_depth[:] = verticals[0]
else:
inst_depth[:] = self.vertical_fill
elif len(used_values.shape) == 2:
var = nc.createVariable(variable_name,
used_values.dtype, (
"time",
"z",
),
fill_value=fillvalue,
chunksizes=(
1000,
self.z.size,
),
zlib=True)
var.coordinates = "{} {} latitude longitude".format(
self.time_axis_name, self.vertical_axis_name)
else:
raise ValueError(
"Could not create variable. Shape of data is {!s}. Expected a dimension of 1 or 2, not {!s}."
.format(used_values.shape, len(used_values.shape)))
# Set the variable attributes as passed in
if attributes:
for k, v in attributes.items():
if k == 'vertical_datum' and sensor_vertical_datum is None and v is not None:
# Use this as the vertical datum if it is specified and we didn't already have one
try:
self.crs.geoid_name = v
self.crs.vertical_datum = v
self.crs.water_surface_reference_datum = v
except AttributeError:
pass
if k not in ['name', 'coordinates', '_FillValue'
] and v is not None:
try:
var.setncattr(k, v)
except BaseException:
logger.info(
'Could not add attribute {}: {}, skipping.'.
format(k, v))
var.grid_mapping = 'crs'
var[:] = used_values
return var
import pytz
try:
import pyncml
except ImportError:
raise ImportError("You must install the 'pyncml' library to use this functionality.")
import netCDF4
import numpy as np
from pyaxiom.utils import DotDict
from pyaxiom import logger
try:
from nco import Nco
except ImportError:
logger.warning("NCO not found. The NCO python bindings are required to use 'Collection.combine'.")
class Collection(object):
@classmethod
def from_ncml_file(cls, ncml_path, apply_to_members=None):
try:
with open(ncml_path) as f:
return cls(pyncml.scan(f.read(), apply_to_members=apply_to_members))
except BaseException:
logger.exception("Could not load Collection from NcML. Please check the NcML.")
@classmethod
def from_directory(cls, directory, suffix=".nc", subdirs=True, dimName='time', apply_to_members=None):
def add_variable(self, variable_name, values, times=None, verticals=None, sensor_vertical_datum=None, attributes=None, unlink_from_profile=None, fillvalue=None, raise_on_error=False, create_instrument_variable=False):
if isinstance(values, (list, tuple,)) and values:
values = np.asarray(values)
if get_type(values) == np.int64:
# Create values as int32 because DAP does not support int64 until DAP4.
values = values.astype(np.int32)
if isinstance(times, (list, tuple,)) and times:
times = np.asarray(times)
if get_type(times) == np.int64:
# Create time as int32 because DAP does not support int64 until DAP4.
times = times.astype(np.int32)
if isinstance(verticals, (list, tuple,)) and verticals:
verticals = np.asarray(verticals)
if get_type(verticals) == np.int64:
# Create verticals as int32 because DAP does not support int64 until DAP4.
verticals = verticals.astype(np.int32)
# Set vertical datum on the CRS variable
if sensor_vertical_datum is not None:
try:
self.crs.geoid_name = sensor_vertical_datum
self.crs.vertical_datum = sensor_vertical_datum
self.crs.water_surface_reference_datum = sensor_vertical_datum
if not hasattr(self._nc, "geospatial_bounds_vertical_crs"):
self._nc.setncattr("geospatial_bounds_vertical_crs", sensor_vertical_datum)
except AttributeError:
pass
# Set default fillvalue for new variables
if fillvalue is None:
fillvalue = -9999.9
fillvalue = values.dtype.type(fillvalue)
used_values = None
vertical_axis = self._nc.variables.get(self.vertical_axis_name)
try:
if unlink_from_profile is True:
used_values = np.ma.reshape(values, (self.time.size, ))
used_values = used_values[self.time_indexes]
# These next two cases should work for all but a few cases, which are caught below
elif vertical_axis.size == 1:
used_values = np.ma.reshape(values, (self.time.size, ))
used_values = used_values[self.time_indexes]
else:
used_values = np.ma.reshape(values, (self.time.size, vertical_axis.size, ))
used_values = used_values[self.time_indexes]
try:
used_values = used_values[:, self.vertical_indexes]
except IndexError:
# The vertical values most likely had duplicates. Ignore the
# falty index here and try to save the values as is.
pass
except ValueError:
if raise_on_error is True:
raise
else:
logger.warning("Could not do a simple reshape of data, trying to match manually! Time:{!s}, Heights:{!s}, Values:{!s}".format(self.time.size, vertical_axis.size, values.size))
if vertical_axis.size > 1:
if times is not None and verticals is not None:
# Hmmm, we have two actual height values for this station.
# Not cool man, not cool.
# Reindex the entire values array. This is slow.
indexed = ((bisect.bisect_left(self.time[:], times[i]), bisect.bisect_left(vertical_axis[:], verticals[i]), values[i]) for i in range(values.size))
used_values = np.ndarray((self.time.size, vertical_axis.size, ), dtype=get_type(values))
used_values.fill(fillvalue)
for (tzi, zzi, vz) in indexed:
if zzi < vertical_axis.size and tzi < self.time.size:
used_values[tzi, zzi] = vz
del indexed
else:
raise ValueError("You need to pass in both 'times' and 'verticals' parameters that matches the size of the 'values' parameter.")
else:
if times is not None:
# Ugh, find the time indexes manually
indexed = ((bisect.bisect_left(self.time[:], times[i]), values[i]) for i in range(values.size))
used_values = np.ndarray((self.time.size, ), dtype=get_type(values))
used_values.fill(fillvalue)
for (tzi, vz) in indexed:
if tzi < self.time.size:
used_values[tzi] = vz
del indexed
else:
raise ValueError("You need to pass in a 'times' parameter that matches the size of the 'values' parameter.")
logger.info("Setting values for {}...".format(variable_name))
if len(used_values.shape) == 1:
var = self._nc.createVariable(variable_name, get_type(used_values), ("time",), fill_value=fillvalue, chunksizes=(self.time_chunk,), zlib=True)
self._nc.setncattr('ncei_template_version', 'NCEI_NetCDF_TimeSeries_Orthogonal_Template_v2.0')
if vertical_axis.size == 1:
var.coordinates = "{} {} latitude longitude".format(self.time_axis_name, self.vertical_axis_name)
else:
# This is probably a bottom sensor on an ADCP or something, don't add the height coordinate
var.coordinates = "{} latitude longitude".format(self.time_axis_name)
if unlink_from_profile is True:
# Create metadata variable for the sensor_depth
if verticals is not None and self._nc.variables.get('sensor_depth') is None:
logger.info("Setting the special case 'sensor_depth' metadata variable")
inst_depth = self._nc.createVariable('sensor_depth', get_type(verticals))
inst_depth.units = 'm'
inst_depth.standard_name = 'surface_altitude'
inst_depth.positive = self.vertical_positive
if self.vertical_positive.lower() == 'down':
inst_depth.long_name = 'sensor depth below datum'
elif self.vertical_positive.lower() == 'up':
inst_depth.long_name = 'sensor height above datum'
inst_depth.datum = sensor_vertical_datum or 'Unknown'
if verticals and verticals.size > 0:
inst_depth[:] = verticals[0]
else:
inst_depth[:] = self.vertical_fill
elif len(used_values.shape) == 2:
var = self._nc.createVariable(variable_name, get_type(used_values), ("time", "z",), fill_value=fillvalue, chunksizes=(self.time_chunk, vertical_axis.size,), zlib=True)
var.coordinates = "{} {} latitude longitude".format(self.time_axis_name, self.vertical_axis_name)
self._nc.setncattr('ncei_template_version', 'NCEI_NetCDF_TimeSeriesProfile_Orthogonal_Template_v2.0')
else:
raise ValueError("Could not create variable. Shape of data is {!s}. Expected a dimension of 1 or 2, not {!s}.".format(used_values.shape, len(used_values.shape)))
# Set missing_value as well
attributes = attributes or {}
attributes['missing_value'] = fillvalue
# Set the variable attributes as passed in
if attributes:
for k, v in attributes.items():
if k == 'vertical_datum' and sensor_vertical_datum is None and v is not None:
# Use this as the vertical datum if it is specified and we didn't already have one
try:
self.crs.geoid_name = v
self.crs.vertical_datum = v
self.crs.water_surface_reference_datum = v
if not hasattr(self._nc, "geospatial_bounds_vertical_crs"):
self._nc.setncattr("geospatial_bounds_vertical_crs", v)
except AttributeError:
pass
if k not in ['name', 'coordinates', '_FillValue'] and v is not None:
try:
var.setncattr(k, v)
except BaseException:
logger.info('Could not add attribute {}: {}, skipping.'.format(k, v))
# Add a long name if it doesn't exist
if not hasattr(var, 'long_name'):
varunits = getattr(var, 'units', None)
vartitle = getattr(var, 'standard_name', getattr(var, 'name'))
vartitle = vartitle.title().replace('_', ' ')
if varunits is not None:
vartitle = '{} ({})'.format(vartitle, varunits)
var.long_name = vartitle
var.grid_mapping = 'crs'
var.platform = 'platform'
var.ancillary_variables = 'platform'
var.coverage_content_type = 'physicalMeasurement'
var[:] = used_values
if create_instrument_variable is True:
self.add_instrument_variable(variable_name)
self._nc.sync()
del used_values
return var
def add_variable(self, variable_name, values, times=None, verticals=None, sensor_vertical_datum=None, attributes=None, unlink_from_profile=None, fillvalue=None, raise_on_error=False):
if isinstance(values, (list, tuple,)) and values:
values = np.asarray(values)
if isinstance(times, (list, tuple,)) and times:
times = np.asarray(times)
if isinstance(verticals, (list, tuple,)) and verticals:
verticals = np.asarray(verticals)
# Set vertical datum on the CRS variable
if sensor_vertical_datum is not None:
try:
self.crs.geoid_name = sensor_vertical_datum
self.crs.vertical_datum = sensor_vertical_datum
self.crs.water_surface_reference_datum = sensor_vertical_datum
except AttributeError:
pass
# Set default fillvalue for new variables
if fillvalue is None:
fillvalue = -9999.9
used_values = None
try:
if unlink_from_profile is True:
used_values = np.ma.reshape(values, (self.time.size, ))
used_values = used_values[self.time_indexes]
# These next two cases should work for all but a few cases, which are caught below
elif self.z.size == 1:
used_values = np.ma.reshape(values, (self.time.size, ))
used_values = used_values[self.time_indexes]
else:
used_values = np.ma.reshape(values, (self.time.size, self.z.size, ))
used_values = used_values[self.time_indexes]
try:
used_values = used_values[:, self.vertical_indexes]
except IndexError:
# The vertical values most likely had duplicates. Ignore the
# falty index here and try to save the values as is.
pass
except ValueError:
if raise_on_error is True:
raise
else:
logger.warning("Could not do a simple reshape of data, trying to match manually! Time:{!s}, Heights:{!s}, Values:{!s}".format(self.time.size, self.z.size, values.size))
if self.z.size > 1:
if times is not None and verticals is not None:
# Hmmm, we have two actual height values for this station.
# Not cool man, not cool.
# Reindex the entire values array. This is slow.
indexed = ((bisect.bisect_left(self.time[:], times[i]), bisect.bisect_left(self.z[:], verticals[i]), values[i]) for i in range(values.size))
used_values = np.ndarray((self.time.size, self.z.size, ), dtype=values.dtype)
used_values.fill(float(fillvalue))
for (tzi, zzi, vz) in indexed:
if zzi < self.z.size and tzi < self.time.size:
used_values[tzi, zzi] = vz
else:
raise ValueError("You need to pass in both 'times' and 'verticals' parameters that matches the size of the 'values' parameter.")
else:
if times is not None:
# Ugh, find the time indexes manually
indexed = ((bisect.bisect_left(self.time[:], times[i]), values[i]) for i in range(values.size))
used_values = np.ndarray((self.time.size, ), dtype=values.dtype)
used_values.fill(float(fillvalue))
for (tzi, vz) in indexed:
if tzi < self.time.size:
used_values[tzi] = vz
else:
raise ValueError("You need to pass in a 'times' parameter that matches the size of the 'values' parameter.")
with EnhancedDataset(self.out_file, 'a') as nc:
logger.info("Setting values for {}...".format(variable_name))
if len(used_values.shape) == 1:
var = nc.createVariable(variable_name, used_values.dtype, ("time",), fill_value=fillvalue, chunksizes=(1000,), zlib=True)
if self.z.size == 1:
var.coordinates = "{} {} latitude longitude".format(self.time_axis_name, self.vertical_axis_name)
else:
# This is probably a bottom sensor on an ADCP or something, don't add the height coordinate
var.coordinates = "{} latitude longitude".format(self.time_axis_name)
if unlink_from_profile is True:
# Create metadata variable for the sensor_depth
if nc.variables.get('sensor_depth') is None:
logger.info("Setting the special case 'sensor_depth' metadata variable")
inst_depth = nc.createVariable('sensor_depth', 'f4')
inst_depth.units = 'm'
inst_depth.standard_name = 'surface_altitude'
inst_depth.positive = self.vertical_positive
if self.vertical_positive.lower() == 'down':
inst_depth.long_name = 'sensor depth below datum'
elif self.vertical_positive.lower() == 'up':
inst_depth.long_name = 'sensor height above datum'
inst_depth.datum = sensor_vertical_datum or 'Unknown'
if verticals and verticals.size > 0:
inst_depth[:] = verticals[0]
else:
inst_depth[:] = self.vertical_fill
elif len(used_values.shape) == 2:
var = nc.createVariable(variable_name, used_values.dtype, ("time", "z",), fill_value=fillvalue, chunksizes=(1000, self.z.size,), zlib=True)
var.coordinates = "{} {} latitude longitude".format(self.time_axis_name, self.vertical_axis_name)
else:
raise ValueError("Could not create variable. Shape of data is {!s}. Expected a dimension of 1 or 2, not {!s}.".format(used_values.shape, len(used_values.shape)))
# Set the variable attributes as passed in
if attributes:
for k, v in attributes.items():
if k == 'vertical_datum' and sensor_vertical_datum is None and v is not None:
# Use this as the vertical datum if it is specified and we didn't already have one
try:
self.crs.geoid_name = v
self.crs.vertical_datum = v
self.crs.water_surface_reference_datum = v
except AttributeError:
pass
if k not in ['name', 'coordinates', '_FillValue'] and v is not None:
try:
var.setncattr(k, v)
except BaseException:
logger.info('Could not add attribute {}: {}, skipping.'.format(k, v))
var.grid_mapping = 'crs'
var[:] = used_values
return var
import pytz
try:
import pyncml
except ImportError:
raise ImportError("You must install the 'pyncml' library to use this functionality.")
import netCDF4
import numpy as np
from pyaxiom.utils import DotDict
from pyaxiom import logger
try:
from nco import Nco
except ImportError:
logger.warning("NCO not found. The NCO python bindings are required to use 'Collection.combine'.")
class Collection(object):
@classmethod
def from_ncml_file(cls, ncml_path, apply_to_members=None):
try:
with open(ncml_path) as f:
return cls(pyncml.scan(f.read(), apply_to_members=apply_to_members))
except BaseException:
logger.exception("Could not load Collection from NcML. Please check the NcML.")
@classmethod
def from_directory(cls, directory, suffix=".nc", subdirs=True, dimName='time', apply_to_members=None):
def from_dataframe(df,
output_directory,
output_filename,
latitude,
longitude,
station_name,
global_attributes,
variable_name,
variable_attributes,
sensor_vertical_datum=None,
fillvalue=None,
data_column=None,
vertical_axis_name=None,
vertical_positive=None):
if fillvalue is None:
fillvalue = -9999.9
if data_column is None:
data_column = 'value'
df[data_column] = df[data_column].fillna(fillvalue)
times = np.asarray(
[calendar.timegm(x.utctimetuple()) for x in df['time']])
df['depth'] = df['depth'].fillna(fillvalue)
depths = df['depth'].values
try:
ts = TimeSeries(output_directory,
latitude,
longitude,
station_name,
global_attributes,
times=times,
verticals=depths,
output_filename=output_filename,
vertical_fill=fillvalue,
vertical_axis_name=vertical_axis_name,
vertical_positive=vertical_positive)
ts.add_variable(variable_name,
df[data_column].values,
attributes=variable_attributes,
sensor_vertical_datum=sensor_vertical_datum,
raise_on_error=True)
except ValueError:
logger.warning(
"Failed first attempt, trying again with unique times.")
try:
# Try uniquing time
newtimes = np.unique(times)
ts = TimeSeries(output_directory,
latitude,
longitude,
station_name,
global_attributes,
times=newtimes,
verticals=depths,
output_filename=output_filename,
vertical_fill=fillvalue,
vertical_axis_name=vertical_axis_name,
vertical_positive=vertical_positive)
ts.add_variable(variable_name,
df[data_column].values,
attributes=variable_attributes,
sensor_vertical_datum=sensor_vertical_datum,
raise_on_error=True)
except ValueError:
logger.warning(
"Failed second attempt, trying again with unique depths.")
try:
# Try uniquing depths
newdepths = np.unique(df['depth'].values)
ts = TimeSeries(output_directory,
latitude,
longitude,
station_name,
global_attributes,
times=times,
verticals=newdepths,
output_filename=output_filename,
vertical_fill=fillvalue,
vertical_axis_name=vertical_axis_name,
vertical_positive=vertical_positive)
ts.add_variable(
variable_name,
df[data_column].values,
attributes=variable_attributes,
sensor_vertical_datum=sensor_vertical_datum,
raise_on_error=True)
except ValueError:
logger.warning(
"Failed third attempt, uniquing time and depth.")
try:
# Unique both time and depth
newdepths = np.unique(df['depth'].values)
ts = TimeSeries(output_directory,
latitude,
longitude,
station_name,
global_attributes,
times=newtimes,
verticals=newdepths,
output_filename=output_filename,
vertical_fill=fillvalue,
vertical_axis_name=vertical_axis_name,
vertical_positive=vertical_positive)
ts.add_variable(
variable_name,
df[data_column].values,
attributes=variable_attributes,
sensor_vertical_datum=sensor_vertical_datum,
raise_on_error=True)
except ValueError:
logger.warning(
"Failed fourth attempt, manually matching indexes (this is slow)."
)
# Manually match
ts = TimeSeries(output_directory,
latitude,
longitude,
station_name,
global_attributes,
times=times,
verticals=depths,
output_filename=output_filename,
vertical_fill=fillvalue,
vertical_axis_name=vertical_axis_name,
vertical_positive=vertical_positive)
ts.add_variable(
variable_name,
df[data_column].values,
attributes=variable_attributes,
times=times,
verticals=depths,
sensor_vertical_datum=sensor_vertical_datum,
raise_on_error=False)
return ts
