def main(output_path, delta, ncml_file=None, glob_string=None, apply_to_members=None, hard_start=None, hard_end=None):
if glob_string is not None:
collection = Collection.from_glob(glob_string, ncml=ncml_file)
elif ncml_file is not None:
collection = Collection.from_ncml_file(ncml_file, apply_to_members=apply_to_members)
if delta.years > 0:
starting = collection.aggregation.starting.replace(microsecond=0, second=0, minute=0, hour=0, day=1, month=1)
elif delta.months > 0:
starting = collection.aggregation.starting.replace(microsecond=0, second=0, minute=0, hour=0, day=1)
elif delta.days > 0:
starting = collection.aggregation.starting.replace(microsecond=0, second=0, minute=0, hour=0)
windows = collection.bins(delta=delta, starting=starting, hard_start=hard_start, hard_end=hard_end)
# Create output directory
if not os.path.exists(output_path):
os.makedirs(output_path)
for i, window in enumerate(windows):
# Create a file name
starting = window.starting.strftime("%Y%m%dT%H%M")
ending = window.ending.strftime("%Y%m%dT%H%M")
if starting == ending:
file_name = "{0}.nc".format(starting)
else:
file_name = "{0}_TO_{1}.nc".format(starting, ending)
output_file = os.path.join(output_path, file_name)
pyaxiomlogger.info("Combining ({0}/{1}) - {2} files into {3}".format(i+1, len(windows), len(window.members), output_file))
Collection.combine(members=window.members, output_file=output_file)
return 0
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.info("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 main(output_path,
delta,
ncml_file=None,
glob_string=None,
apply_to_members=None,
hard_start=None,
hard_end=None):
if glob_string is not None:
collection = Collection.from_glob(glob_string, ncml=ncml_file)
elif ncml_file is not None:
collection = Collection.from_ncml_file(
ncml_file, apply_to_members=apply_to_members)
if delta.years > 0:
starting = collection.aggregation.starting.replace(microsecond=0,
second=0,
minute=0,
hour=0,
day=1,
month=1)
elif delta.months > 0:
starting = collection.aggregation.starting.replace(microsecond=0,
second=0,
minute=0,
hour=0,
day=1)
elif delta.days > 0:
starting = collection.aggregation.starting.replace(microsecond=0,
second=0,
minute=0,
hour=0)
windows = collection.bins(delta=delta,
starting=starting,
hard_start=hard_start,
hard_end=hard_end)
# Create output directory
if not os.path.exists(output_path):
os.makedirs(output_path)
for i, window in enumerate(windows):
# Create a file name
starting = window.starting.strftime("%Y%m%dT%H%M")
ending = window.ending.strftime("%Y%m%dT%H%M")
if starting == ending:
file_name = "{0}.nc".format(starting)
else:
file_name = "{0}_TO_{1}.nc".format(starting, ending)
output_file = os.path.join(output_path, file_name)
pyaxiomlogger.info("Combining ({0}/{1}) - {2} files into {3}".format(
i + 1, len(windows), len(window.members), output_file))
Collection.combine(members=window.members, output_file=output_file)
return 0
def test_is_mine(klass, fp):
dsg = CFDataset.load(fp)
assert dsg.__class__ == klass
allsubs = list(all_subclasses(CFDataset))
subs = [s for s in allsubs if s != klass]
dsg = CFDataset(fp)
logger.info('\nTesting {}'.format(klass.__name__))
assert klass.is_mine(dsg) is True
for s in subs:
if hasattr(s, 'is_mine'):
logger.info(' * Trying {}...'.format(s.__name__))
assert s.is_mine(dsg) is False
dsg.close()
def from_glob(cls, glob_string, timevar_name='time', ncml=None):
dataset_name = None
dataset_starting = None
dataset_ending = None
dataset_variables = []
dataset_members = []
files = glob(glob_string)
logger.info("Processing aggregation containing {!s} files".format(len(files)))
for i, filepath in enumerate(files):
logger.info("Processing member ({0}/{1}) - {2} ".format(i+1, len(files), filepath))
nc = None
try:
if ncml is not None:
# Apply NcML
tmp_f, tmp_fp = tempfile.mkstemp(prefix="nc")
os.close(tmp_f)
nc = pyncml.apply(filepath, ncml, output_file=tmp_fp)
else:
nc = netCDF4.Dataset(filepath)
if dataset_name is None:
if hasattr(nc, 'name'):
dataset_name = nc.name
elif hasattr(nc, 'title'):
dataset_name = nc.title
else:
dataset_name = "Pyaxiom Glob Dataset"
timevar = nc.variables.get(timevar_name)
if timevar is None:
logger.error("Time variable '{0}' was not found in file '{1}'. Skipping.".format(timevar_name, filepath))
continue
# Start/Stop of NetCDF file
starting = netCDF4.num2date(np.min(timevar[:]), units=timevar.units)
ending = netCDF4.num2date(np.max(timevar[:]), units=timevar.units)
variables = filter(None, [ nc.variables[v].standard_name if hasattr(nc.variables[v], 'standard_name') else None for v in nc.variables.keys() ])
dataset_variables = list(set(dataset_variables + variables))
if starting.tzinfo is None:
starting = starting.replace(tzinfo=pytz.utc)
if ending.tzinfo is None:
ending = ending.replace(tzinfo=pytz.utc)
if dataset_starting is None or starting < dataset_starting:
dataset_starting = starting
if dataset_ending is None or ending > dataset_ending:
dataset_ending = ending
member = DotDict(path=filepath, standard_names=variables, starting=starting, ending=ending)
dataset_members.append(member)
except BaseException:
logger.exception("Something went wrong with {0}".format(filepath))
continue
finally:
nc.close()
try:
os.remove(tmp_fp)
except (OSError, UnboundLocalError):
pass
dataset_members = sorted(dataset_members, key=operator.attrgetter('starting'))
return cls(DotDict(name=dataset_name,
timevar_name=timevar_name,
starting=dataset_starting,
ending=dataset_ending,
standard_names=dataset_variables,
members=dataset_members))
def from_glob(cls, glob_string, timevar_name='time', ncml=None):
dataset_name = None
dataset_starting = None
dataset_ending = None
dataset_variables = []
dataset_members = []
files = glob(glob_string)
logger.info("Processing aggregation containing {!s} files".format(len(files)))
for i, filepath in enumerate(files):
logger.info("Processing member ({0}/{1}) - {2} ".format(i+1, len(files), filepath))
nc = None
try:
if ncml is not None:
# Apply NcML
tmp_f, tmp_fp = tempfile.mkstemp(prefix="nc")
os.close(tmp_f)
nc = pyncml.apply(filepath, ncml, output_file=tmp_fp)
else:
nc = netCDF4.Dataset(filepath)
if dataset_name is None:
if 'name' in nc.ncattrs():
dataset_name = nc.name
elif 'title' in nc.ncattrs():
dataset_name = nc.title
else:
dataset_name = "Pyaxiom Glob Dataset"
timevar = nc.variables.get(timevar_name)
if timevar is None:
logger.error("Time variable '{0}' was not found in file '{1}'. Skipping.".format(timevar_name, filepath))
continue
# Start/Stop of NetCDF file
starting = netCDF4.num2date(np.min(timevar[:]), units=timevar.units)
ending = netCDF4.num2date(np.max(timevar[:]), units=timevar.units)
variables = list([_f for _f in [ nc.variables[v].standard_name if hasattr(nc.variables[v], 'standard_name') else None for v in list(nc.variables.keys()) ] if _f])
dataset_variables = list(set(dataset_variables + variables))
if starting.tzinfo is None:
starting = starting.replace(tzinfo=pytz.utc)
if ending.tzinfo is None:
ending = ending.replace(tzinfo=pytz.utc)
if dataset_starting is None or starting < dataset_starting:
dataset_starting = starting
if dataset_ending is None or ending > dataset_ending:
dataset_ending = ending
member = DotDict(path=filepath, standard_names=variables, starting=starting, ending=ending)
dataset_members.append(member)
except BaseException:
logger.exception("Something went wrong with {0}".format(filepath))
continue
finally:
nc.close()
try:
os.remove(tmp_fp)
except (OSError, UnboundLocalError):
pass
dataset_members = sorted(dataset_members, key=operator.attrgetter('starting'))
return cls(DotDict(name=dataset_name,
timevar_name=timevar_name,
starting=dataset_starting,
ending=dataset_ending,
standard_names=dataset_variables,
members=dataset_members))
def __init__(self, output_directory, latitude, longitude, station_name, global_attributes, times=None, verticals=None, vertical_fill=None, output_filename=None, vertical_axis_name=None, vertical_positive=None):
if output_filename is None:
output_filename = '{}_{}.nc'.format(station_name, int(random.random() * 100000))
logger.info("No output filename specified, saving as {}".format(output_filename))
self.vertical_positive = vertical_positive or 'down'
self.vertical_axis_name = vertical_axis_name or 'z'
self.time_axis_name = 'time'
# Make directory
if not os.path.exists(output_directory):
os.makedirs(output_directory)
self.time = None
self.out_file = os.path.abspath(os.path.join(output_directory, output_filename))
if os.path.isfile(self.out_file):
os.remove(self.out_file)
with EnhancedDataset(self.out_file, 'w') as nc:
# Global attributes
# 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", "geospatial_bounds"
"geospatial_vertical_resolution", "geospatial_lat_resolution", "geospatial_lon_resolution",
"Conventions", "date_created", "date_modified", "date_issued"]
for k, v in global_attributes.items():
if v is None:
v = "None"
if k not in global_skips:
nc.setncattr(k, v)
now_date = datetime.utcnow().strftime("%Y-%m-%dT%H:%M:00Z")
nc.setncattr("Conventions", "CF-1.6,ACDD-1.3")
nc.setncattr("date_created", now_date)
nc.setncattr("date_modified", now_date)
nc.setncattr("date_issued", now_date)
if not hasattr(nc, "date_metadata_modified"):
nc.setncattr("date_metadata_modified", now_date)
# Allow the customization of this attribute
if 'cdm_data_type' not in global_attributes:
nc.setncattr('cdm_data_type', 'Station')
old_history = getattr(nc, 'history', '')
new_history = '{} - {} - {}'.format(now_date, 'pyaxiom', 'File created using pyaxiom')
if old_history:
nc.setncattr('history', '{}\n{}'.format(old_history, new_history))
else:
nc.setncattr('history', new_history)
# Station name
nc.createDimension("feature_type_instance", len(station_name))
name = nc.createVariable("feature_type_instance", "S1", ("feature_type_instance",))
name.cf_role = "timeseries_id"
name.long_name = "Identifier for each feature type instance"
name[:] = list(station_name)
# Location
lat = nc.createVariable("latitude", get_type(latitude))
lat.units = "degrees_north"
lat.standard_name = "latitude"
lat.long_name = "sensor latitude"
lat.axis = "Y"
lat.valid_min = latitude
lat.valid_max = latitude
lat[:] = latitude
nc.setncattr("geospatial_lat_min", latitude)
nc.setncattr("geospatial_lat_max", latitude)
nc.setncattr("geospatial_lat_resolution", 0)
nc.setncattr("geospatial_lat_units", "degrees_north")
lon = nc.createVariable("longitude", get_type(longitude))
lon.units = "degrees_east"
lon.standard_name = "longitude"
lon.long_name = "sensor longitude"
lon.axis = "X"
lon.valid_min = longitude
lon.valid_max = longitude
lon[:] = longitude
nc.setncattr("geospatial_lon_min", longitude)
nc.setncattr("geospatial_lon_max", longitude)
nc.setncattr("geospatial_lon_resolution", 0)
nc.setncattr("geospatial_lon_units", "degrees_east")
nc.setncattr("geospatial_bounds", "POINT({} {})".format(longitude, latitude))
if not hasattr(nc, "geospatial_bounds_crs"):
nc.setncattr("geospatial_bounds_crs", "EPSG:4326")
# Metadata variables
self.crs = nc.createVariable("crs", "i4")
self.crs.long_name = "http://www.opengis.net/def/crs/EPSG/0/4326"
self.crs.grid_mapping_name = "latitude_longitude"
self.crs.epsg_code = "EPSG:4326"
self.crs.semi_major_axis = float(6378137.0)
self.crs.inverse_flattening = float(298.257223563)
platform = nc.createVariable("platform", "i4")
platform.definition = "http://mmisw.org/ont/ioos/definition/stationID"
urn = IoosUrn.from_string(station_name)
if urn.valid() is True:
platform.short_name = global_attributes.get("title", urn.label)
platform.long_name = global_attributes.get('summary', 'Station {}'.format(urn.label))
platform.ioos_code = urn.urn
else:
platform.short_name = global_attributes.get("title", station_name)
platform.long_name = global_attributes.get("summary", station_name)
platform.ioos_code = station_name
if vertical_fill is None:
vertical_fill = -9999.9
self.vertical_fill = vertical_fill
self._nc = EnhancedDataset(self.out_file, 'a')
self.setup_times_and_verticals(times, verticals)
logger.info("Created file at '{}'".format(self.out_file))
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 __init__(self, output_directory, latitude, longitude, station_name, global_attributes, times=None, verticals=None, vertical_fill=None, output_filename=None, vertical_axis_name=None, vertical_positive=None):
if output_filename is None:
output_filename = '{}_{}.nc'.format(station_name, int(random.random()*100000))
logger.info("No output filename specified, saving as {}".format(output_filename))
self.vertical_positive = vertical_positive or 'down'
self.vertical_axis_name = vertical_axis_name or 'z'
self.time_axis_name = 'time'
# Make directory
if not os.path.exists(output_directory):
os.makedirs(output_directory)
out_file = os.path.abspath(os.path.join(output_directory, output_filename))
self.nc = netCDF4.Dataset(out_file, 'w')
self.time = None
# Global attributes
# 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",
"geospatial_vertical_resolution", "Conventions", "date_created"]
for k, v in global_attributes.iteritems():
if v is None:
v = "None"
if k not in global_skips:
self.nc.setncattr(k, v)
self.nc.setncattr("Conventions", "CF-1.6")
self.nc.setncattr("date_created", datetime.utcnow().strftime("%Y-%m-%dT%H:%M:00Z"))
# Station name
self.nc.createDimension("feature_type_instance", len(station_name))
name = self.nc.createVariable("feature_type_instance", "S1", ("feature_type_instance",))
name.cf_role = "timeseries_id"
name.long_name = "Identifier for each feature type instance"
name[:] = list(station_name)
# Location
lat = self.nc.createVariable("latitude", "f8")
lat.units = "degrees_north"
lat.standard_name = "latitude"
lat.long_name = "sensor latitude"
lat[:] = latitude
self.nc.setncattr("geospatial_lat_min", latitude)
self.nc.setncattr("geospatial_lat_max", latitude)
lon = self.nc.createVariable("longitude", "f8")
lon.units = "degrees_east"
lon.standard_name = "longitude"
lon.long_name = "sensor longitude"
lon[:] = longitude
self.nc.setncattr("geospatial_lon_min", longitude)
self.nc.setncattr("geospatial_lon_max", longitude)
# Metadata variables
self.crs = self.nc.createVariable("crs", "i4")
self.crs.long_name = "http://www.opengis.net/def/crs/EPSG/0/4326"
self.crs.grid_mapping_name = "latitude_longitude"
self.crs.epsg_code = "EPSG:4326"
self.crs.semi_major_axis = float(6378137.0)
self.crs.inverse_flattening = float(298.257223563)
platform = self.nc.createVariable("platform", "i4")
platform.ioos_code = station_name
platform.short_name = global_attributes.get("title", station_name)
platform.long_name = global_attributes.get("description", station_name)
platform.definition = "http://mmisw.org/ont/ioos/definition/stationID"
if vertical_fill is None:
vertical_fill = -9999.9
self.vertical_fill = vertical_fill
self.setup_times_and_verticals(times, verticals)
logger.info("Created file at '{}'".format(out_file))
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:
self.close()
raise
else:
logger.exception("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 xrange(values.size))
used_values = np.ndarray((self.time.size, self.z.size, ), dtype=np.float64)
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:
self.close()
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 xrange(values.size))
used_values = np.ndarray((self.time.size, ), dtype=np.float64)
used_values.fill(float(fillvalue))
for (tzi, vz) in indexed:
if tzi < self.time.size:
used_values[tzi] = vz
else:
self.close()
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, "f8", ("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 = "time latitude longitude"
if unlink_from_profile is True:
# Create metadata variable for the sensor_depth
if 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', 'f4')
inst_depth.units = 'm'
inst_depth.standard_name = 'surface_altitude'
inst_depth.long_name = 'sensor depth below datum'
inst_depth.positive = self.vertical_positive
inst_depth.datum = sensor_vertical_datum or 'Unknown'
inst_depth[:] = verticals[0] * -1
elif len(used_values.shape) == 2:
var = self.nc.createVariable(variable_name, "f8", ("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.iteritems():
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 != '_FillValue' and v is not None:
try:
setattr(var, k, v)
except BaseException:
logger.info('Could not add attribute {}: {}, skipping.'.format(k, v))
var.grid_mapping = 'crs'
var[:] = 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
def __init__(self,
output_directory,
latitude,
longitude,
station_name,
global_attributes,
times=None,
verticals=None,
vertical_fill=None,
output_filename=None,
vertical_axis_name=None,
vertical_positive=None):
if output_filename is None:
output_filename = '{}_{}.nc'.format(station_name,
int(random.random() * 100000))
logger.info("No output filename specified, saving as {}".format(
output_filename))
self.vertical_positive = vertical_positive or 'down'
self.vertical_axis_name = vertical_axis_name or 'z'
self.time_axis_name = 'time'
# Make directory
if not os.path.exists(output_directory):
os.makedirs(output_directory)
self.time = None
self.out_file = os.path.abspath(
os.path.join(output_directory, output_filename))
if os.path.isfile(self.out_file):
os.remove(self.out_file)
with EnhancedDataset(self.out_file, 'w') as nc:
# Global attributes
# 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",
"geospatial_vertical_resolution", "Conventions", "date_created"
]
for k, v in global_attributes.items():
if v is None:
v = "None"
if k not in global_skips:
nc.setncattr(k, v)
nc.setncattr("Conventions", "CF-1.6")
nc.setncattr("date_created",
datetime.utcnow().strftime("%Y-%m-%dT%H:%M:00Z"))
nc.setncattr("date_issued",
datetime.utcnow().strftime("%Y-%m-%dT%H:%M:00Z"))
nc.setncattr('cdm_data_type', 'Station')
# Station name
nc.createDimension("feature_type_instance", len(station_name))
name = nc.createVariable("feature_type_instance", "S1",
("feature_type_instance", ))
name.cf_role = "timeseries_id"
name.long_name = "Identifier for each feature type instance"
name[:] = list(station_name)
# Location
lat = nc.createVariable("latitude", "f8")
lat.units = "degrees_north"
lat.standard_name = "latitude"
lat.long_name = "sensor latitude"
lat[:] = latitude
nc.setncattr("geospatial_lat_min", latitude)
nc.setncattr("geospatial_lat_max", latitude)
nc.setncattr("geospatial_lat_units", "degrees_north")
lon = nc.createVariable("longitude", "f8")
lon.units = "degrees_east"
lon.standard_name = "longitude"
lon.long_name = "sensor longitude"
lon[:] = longitude
nc.setncattr("geospatial_lon_min", longitude)
nc.setncattr("geospatial_lon_max", longitude)
nc.setncattr("geospatial_lon_units", "degrees_east")
# Metadata variables
self.crs = nc.createVariable("crs", "i4")
self.crs.long_name = "http://www.opengis.net/def/crs/EPSG/0/4326"
self.crs.grid_mapping_name = "latitude_longitude"
self.crs.epsg_code = "EPSG:4326"
self.crs.semi_major_axis = float(6378137.0)
self.crs.inverse_flattening = float(298.257223563)
platform = nc.createVariable("platform", "i4")
platform.ioos_code = station_name
platform.short_name = global_attributes.get("title", station_name)
platform.long_name = global_attributes.get("description",
station_name)
platform.definition = "http://mmisw.org/ont/ioos/definition/stationID"
nc.setncattr('platform', 'platform')
if vertical_fill is None:
vertical_fill = -9999.9
self.vertical_fill = vertical_fill
self.setup_times_and_verticals(times, verticals)
logger.info("Created file at '{}'".format(self.out_file))
