class PCR(GBmi):
"""CSDMS-compliant BMI implementation for GLOFRIM.
Arguments:
GBmi {class} -- Interface (abstract base class) for a model that implements the CSDMS BMI (Basic Model Interface).
Raises:
Warning -- Warning is raised if two-step model initialization is not correctly executed
Warning -- Warning is raised if two-step model initialization is not correctly executed
Exception -- Raised if specified time is smaller than time step or later than model end time
ValueError -- Raised if model time step is not whole number of update interval
Exception -- Raised if end time is already reached as no further update is possible
IOError -- function requires LDD file; if not found, IOerror is raised
IOError -- function requires landsmask file; if not found, IOerror is raised
ValueError -- start time must be yyyy-mm-dd; if not, ValueError is raised
ValueError -- end time must be yyyy-mm-dd; if not, ValueError is raised
"""
_name = 'PCR'
_long_name = 'PCR-GLOBWB'
_version = '2.0.3'
_var_units = {'runoff': 'm/day', 'discharge': 'm3/s', 'cellArea': 'm2'}
_input_var_names = ['cellArea']
_output_var_names = ['runoff', 'discharge']
_area_var_name = 'cellArea'
_timeunit = 'days'
_dt = timedelta(days=1) # NOTE: this is fixed in PCR
def __init__(self, loglevel=logging.INFO, logger=None):
# import PCR-GLOBWB with BMI functions
from pcrglobwb_bmi_v203 import pcrglobwb_bmi as _bmi
self._bmi = _bmi.pcrglobwbBMI()
if logger:
self.logger = logger.getChild(self._name)
else:
self.logger = setlogger(None, self._name, thelevel=loglevel)
self._loglevel = loglevel
self.initialized = False
self.grid = None
###
### Model Control Functions
###
def initialize_config(self, config_fn):
"""Initializing the model configuration file. Aligning GLOFRIM specs for coupled runs
to be consistent with overall run settings.
Arguments:
config_fn {str} -- path to model configuration file (for PCR-GLOBWB: ini-file)
Raises:
Warning -- Warning is raised if two-step model initialization is not correctly executed
"""
# config settings
if self.initialized:
raise Warning(
"model already initialized, it's therefore not longer possible to initialize the config"
)
self._config_fn = abspath(config_fn)
self._config = glib.configread(
self._config_fn,
encoding='utf-8',
cf=ConfigParser(inline_comment_prefixes=('#')))
self._datefmt = "%Y-%m-%d"
# model time
self._startTime = self.get_start_time()
self._endTime = self.get_end_time()
self._t = self._startTime
# model files
self._outdir = abspath(
self.get_attribute_value('globalOptions:outputDir'))
self.logger.info('Config initialized')
def initialize_model(self, **kwargs):
"""Initializes the model, i.e. loading all files and checking for consistency;
can only be executed after the model-specific config-file was initialized. This is essential
for a successful two-step model initialization and aligned model data.
Raises:
Warning -- Warning is raised if two-step model initialization is not correctly executed
"""
if not hasattr(self, '_config_fn'):
raise Warning('run initialize_config before initialize_model')
self.write_config(
) # write updated config to file as bmi does not allow direct access
self._bmi.initialize(self._config_fn)
# stop pcr double logging.
pcr_log = logging.getLogger()
# pcr_log.setLevel(self._loglevel)
self.logger.info("remove PCR logger because it's making to much noise")
pcr_log.handlers = pcr_log.handlers[1:]
self.initialized = True
self.logger.info('Model initialized')
# reset model time to make sure it is consistent with the model
self._startTime = self.get_start_time()
self._endTime = self.get_end_time()
self._t = self._startTime
def initialize(self, config_fn):
"""Initializes the model following a two-step initialization procedure.
First, the config-file is initialized and where necessary aligned with
overall model settings (e.g. output-dir, start and end time).
Second, the model is actually initialized.
Arguments:
config_fn {str} -- path to model configuration file (for PCR-GLOBWB: ini-file)
"""
self.initialize_config(config_fn)
self.initialize_model()
def update(self, dt=None):
"""Updating model for a certain time step interval (default: None).
Checks whether model end time is already reached.
Requires that model-specific time step is a whole number of update time step.
Keyword Arguments:
dt {int} -- update time step interval [s] at which information is exchanged between models (default: {None})
Raises:
ValueError -- Raised if model time step is not whole number of update interval
Exception -- Raised if end time is already reached as no further update is possible
"""
# dt in seconds. if not given model timestep is used
if self._t >= self._endTime:
raise Exception("endTime already reached, model not updated")
if (dt is not None) and (dt != self._dt.total_seconds()):
_dt = timedelta(seconds=dt)
if not glib.check_dts_divmod(_dt, self._dt):
msg = "Invalid value for dt in comparison to model dt. Make sure a whole number of model timesteps ({}) fit in the given dt ({})"
raise ValueError(msg.format(self._dt, _dt))
self._bmi.update(_dt.days)
self._t += _dt
else:
self._bmi.update(self._dt.days)
self._t += self._dt
self.logger.info('updated model to datetime {}'.format(
self._t.strftime("%Y-%m-%d %H:%M")))
def update_until(self, t, dt=None):
"""Updates the model until a certain time t is reached with an update time step dt.
Arguments:
t {int} -- Model time until which the model is updated
Keyword Arguments:
dt {int} -- update time step interval [s] at which information is exchanged between models (default: {None})
Raises:
Exception -- Raised if specified time is smaller than time step or later than model end time
"""
if (t < self._t) or t > self._endTime:
raise Exception(
"wrong time input: smaller than model time or larger than endTime"
)
while self._t < t:
self.update(dt=dt)
def spinup(self):
"""PCR-GLOBWB specific function.
Runs the in ini-file specified number of spin-up years.
"""
self._bmi.spinup()
def finalize(self):
"""Finalizes the model, i.e. shuts down all operations and closes output files.
"""
self.logger.info('finalize bmi. Close logger.')
self._bmi.finalize()
closelogger(self.logger)
###
### Variable Information Functions
###
def get_start_time(self):
"""Provides start time of PCR-GLOBWB
Returns:
date -- start time of PCR-GLOBWB
"""
if self.initialized:
# date to datetime object
startTime = datetime.combine(self._bmi.get_start_time(),
datetime.min.time())
else:
startTime = self.get_attribute_value('globalOptions:startTime')
startTime = datetime.strptime(startTime, self._datefmt)
self._startTime = startTime
return self._startTime
def get_current_time(self):
"""Provides current model time of PCR-GLOBWB
Returns:
[date] -- current model time of PCR-GLOBWB
"""
if self.initialized:
return self._t
else:
return self.get_start_time()
def get_end_time(self):
"""Provides end time of PCR-GLOBWB
Returns:
date -- end time of PCR-GLOBWB
"""
if self.initialized:
# date to datetime object
endTime = datetime.combine(self._bmi.get_end_time(),
datetime.min.time())
else:
endTime = self.get_attribute_value('globalOptions:endTime')
endTime = datetime.strptime(endTime, self._datefmt)
self._endTime = endTime
return self._endTime
def get_time_step(self):
"""Provides time step of PCR-GLOBWB
Returns:
date -- time step of PCR-GLOBWB
"""
return self._dt
def get_time_units(self):
"""Provides time unit of PCR-GLOBWB.
Returns:
str -- time unit of model of PCR-GLOBWB
"""
return self._timeunit
###
### Variable Getter and Setter Functions
###
def get_value(self, long_var_name, fill_value=-999, **kwargs):
"""Retrieval of all values of a certain exposed variable;
entries with fill_value are replaced with NaN values
Arguments:
long_var_name {str} -- name of exposed PCR-GLOBWB variable
Keyword Arguments:
fill_value {int} -- fill_value used in PCR-GLOBWB (default: {-999})
Returns:
array -- array with all entries of retrieved variable
"""
# additional fill_value argument required to translate pcr maps to numpy arrays
var = np.asarray(
self._bmi.get_var(long_var_name,
missingValues=fill_value,
**kwargs))
var = np.where(var == fill_value, np.nan, var)
return var
def get_value_at_indices(self,
long_var_name,
inds,
fill_value=-999,
**kwargs):
"""Retrieval of value at a specific index of a certain exposed variable;
entries with fill_value are replaced with NaN values
Arguments:
long_var_name {str} -- name of exposed PCR-GLOBWB variable
inds {int} -- Index pointing to entry within entire array of variable values
Keyword Arguments:
fill_value {int} -- fill_value used in PCR-GLOBWB (default: {-999})
Returns:
float -- value at specific index of retrieved variable
"""
return self.get_value(long_var_name, fill_value=fill_value,
**kwargs).flat[inds]
def set_value(self, long_var_name, src, fill_value=-999, **kwargs):
"""Overwriting of all values of a certain exposed variable with provided new values;
entries with NaN value are replaced with fill_value;
provided new values must match shape of aim variable
Arguments:
long_var_name {str} -- name of exposed PCR-GLOBWB variable
src {array} -- array with new values
Keyword Arguments:
fill_value {int} -- fill_value used in PCR-GLOBWB (default: {-999})
"""
src = np.where(np.isnan(src), fill_value,
src).astype(self.get_var_type(long_var_name))
self._bmi.set_var(long_var_name,
src,
missingValues=fill_value,
**kwargs)
def set_value_at_indices(self,
long_var_name,
inds,
src,
fill_value=-999,
**kwargs):
"""Overwriting of value at specific entry of a certain exposed variable with provided new values;
entries with NaN value are replaced with fill_value
Arguments:
long_var_name {str} -- name of exposed PCR-GLOBWB variable
inds {int} -- Index pointing to entry within entire array of variable values
src {array} -- array with new values
Keyword Arguments:
fill_value {int} -- fill_value used in PCR-GLOBWB (default: {-999})
"""
val = self.get_value(long_var_name, fill_value=fill_value, **kwargs)
val.flat[inds] = src
self.set_value(long_var_name, val, **kwargs)
def _get_tot_volume_in(self):
# precipitation [m]
P = np.nansum(
self.get_value('precipitation') * self.get_value('cellArea'))
return P
def _get_tot_volume_out(self):
# discharge [m3/s]
Qout = np.nansum(self.get_value_at_indices(
'discharge', self.grid.pits)) * self._dt.total_seconds()
# ET [m] ??
ET = np.nansum(self.get_value('actualET') * self.get_value('cellArea'))
return Qout + ET
###
### Grid Information Functions
###
def get_grid(self):
"""Retreving spatial information about model domain from PCR-GLOBWB landmask file using rasterio
operations;
also retrieving PCR-GLOBWB drainage direction (LDD) information
Raises:
IOError -- function requires LDD file; if not found, IOerror is raised
IOError -- function requires landsmask file; if not found, IOerror is raised
Returns:
grid -- rasterio grid object
"""
if not hasattr(self, 'grid') or (self.grid is None):
# ldd is used for coupling to routing / flood model
_indir = abspath(
self.get_attribute_value('globalOptions:inputDir'))
_ldd_fn = glib.getabspath(
self.get_attribute_value('routingOptions:lddMap'), _indir)
if not isfile(_ldd_fn):
raise IOError('ldd file not found {}'.format(_ldd_fn))
# landmask used for masking out coordinates outside mask if provided
_lm_fn = glib.getabspath(
self.get_attribute_value('globalOptions:landmask'), _indir)
if isfile(_lm_fn):
with rasterio.open(_lm_fn, 'r') as ds:
mask = ds.read(1) == 1
mask_name = basename(_lm_fn)
# use ldd for masking
else:
mask = None
mask_name = basename(_ldd_fn)
self.logger.info(
'Getting rgrid info based on {}; mask based on {}'.format(
basename(_ldd_fn), mask_name))
with rasterio.open(_ldd_fn, 'r') as ds:
if mask is None:
mask = ds.read(1) != ds.nodata
self.grid = RGrid(ds.transform,
ds.height,
ds.width,
crs=ds.crs,
mask=mask)
# read file with pcr readmap
self.logger.info('Getting drainage direction from {}'.format(
basename(_ldd_fn)))
self.grid.set_dd(_ldd_fn, ddtype='ldd')
self.grid.get_pits()
return self.grid
###
### set and get attribute / config
###
def set_start_time(self, start_time):
"""Overwriting default model start time with user-specified start time;
format of provided start time must be yyyy-mm-dd
Arguments:
start_time {date} -- user-specified start time
Raises:
ValueError -- start time must be yyyy-mm-dd; if not, ValueError is raised
"""
if isinstance(start_time, datetime):
start_time = start_time.strftime(self._datefmt)
try:
self._startTime = datetime.strptime(start_time, self._datefmt)
self._t = self._startTime
except ValueError:
raise ValueError('wrong date format, use "yyyy-mm-dd"')
self.set_attribute_value('globalOptions:startTime', start_time)
def set_end_time(self, end_time):
"""Overwriting default model end time with user-specified end time;
format of provided end time must be yyyy-mm-dd
Arguments:
end_time {date} -- user-specified end time
Raises:
ValueError -- end time must be yyyy-mm-dd; if not, ValueError is raised
"""
if isinstance(end_time, datetime):
end_time = end_time.strftime(self._datefmt)
try:
self._endTime = datetime.strptime(end_time, self._datefmt)
except ValueError:
raise ValueError('wrong date format, use "yyyy-mm-dd"')
self.set_attribute_value('globalOptions:endTime', end_time)
def set_out_dir(self, out_dir):
"""Setting output directory of PCR-GLOBWB;
overwrites the default output directory
Arguments:
out_dir {str} -- path to output directory
"""
self.set_attribute_value('globalOptions:outputDir', abspath(out_dir))
def get_attribute_names(self):
"""Provides list with all model attribute names from model config file
Returns:
list -- list with model attribute names
"""
glib.configcheck(self, self.logger)
return glib.configattr(self._config)
def get_attribute_value(self, attribute_name):
"""Gets attribute value in in underlying model;
attribute_name should use the following convention model_name.section_name:attribute_name
Arguments:
attribute_name {str} -- Name of BMI attribute
Returns:
float -- value of attribute
"""
glib.configcheck(self, self.logger)
self.logger.debug("get_attribute_value: " + attribute_name)
return glib.configget(self._config, attribute_name)
def set_attribute_value(self, attribute_name, attribute_value):
"""sets attribute value in in underlying model;
attribute_name should use the following convention model_name.section_name:attribute_name
Arguments:
attribute_name {str} -- Name of BMI attribute
attribute_value {float} -- value to be est
Returns:
[str] -- [no clue]
"""
glib.configcheck(self, self.logger)
self.logger.debug("set_attribute_value: " + attribute_value)
return glib.configset(self._config, attribute_name, attribute_value)
def write_config(self):
"""Write adapted config to file; just before initializing;
only for models which do not allow for direct access to model config via bmi
"""
self._config_fn = glib.write_config(self, self._config,
self._config_fn, self.logger)
class WFL(GBmi):
"""
csdms BMI implementation of the WFLOW BMI adaptor for GLOFRIM.
"""
_name = 'WFL'
_long_name = 'wflow'
_version = ''
_var_units = {}
_input_var_names = []
_output_var_names = []
_area_var_name = 'csize'
_timeunit = 'seconds'
def __init__(self, loglevel=logging.INFO, logger=None):
# import original PCR bmi
import wflow.wflow_bmi as _bmi
self._bmi = _bmi.wflowbmi_csdms()
if logger:
self.logger = logger.getChild(self._name)
else:
self.logger = setlogger(None, self._name, thelevel=loglevel)
self._loglevel = loglevel
self.initialized = False
self.grid = None
"""
Model Control Functions
"""
def initialize_config(self, config_fn):
# config settings
if self.initialized:
raise Warning(
"model already initialized, it's therefore not longer possible to initialize the config"
)
self._config_fn = abspath(config_fn)
self.logger.info('Read ini at {}'.format(self._config_fn))
self._bmi.initialize_config(str(self._config_fn),
loglevel=self._loglevel)
self._config = self._bmi.config
self._datefmt = "%Y-%m-%d %H:%M:%S"
if self.get_attribute_value('run:runlengthdetermination') == 'steps':
raise Warning(
'set WFLOW run:runlengthdetermination to "intervals" in order to use the same time convention as in GLOFRIM'
)
# model time
self._dt = self.get_time_step()
self._startTime = self.get_start_time()
self._endTime = self.get_end_time()
self._t = self._startTime
# model files
self.logger.info('Config initialized')
namesroles = self._bmi.dynModel.wf_supplyVariableNamesAndRoles()
for n, r, u in namesroles:
if r == 0 or r == 3: #input or parameter
self._input_var_names.append(n)
elif r == 1 or r == 2: # output or state
self._output_var_names.append(n)
self._var_units[n] = u
def initialize_model(self, **kwargs):
if not hasattr(self, '_config_fn'):
raise Warning('run initialize_config before initialize_model')
self._bmi.initialize_model()
self.initialized = True
self.logger.info('Model initialized')
# reset model time to make sure it is consistent with the model
self._dt = self.get_time_step()
self._startTime = self.get_start_time()
self._endTime = self.get_end_time()
self._t = self._startTime
def initialize(self, config_fn):
self.initialize_config(config_fn)
self.initialize_model()
def update(self, dt=None):
# dt in seconds. if not given model timestep is used
if self._t >= self._endTime:
raise Exception("endTime already reached, model not updated")
if (dt is not None) and (dt != self._dt.total_seconds()):
dt = timedelta(seconds=dt)
if not glib.check_dts_divmod(dt, self._dt):
msg = "Invalid value for dt in comparison to model dt. Make sure a whole number of model timesteps ({}) fit in the given dt ({})"
raise ValueError(msg.format(self._dt, dt))
tt = timedelta(0)
while tt < dt: # loop required ad self._bmi.update(dt) does not work
self._bmi.update()
tt += self._dt
else:
self._bmi.update()
self._t = self.get_current_time()
self.logger.info('updated model to datetime {}'.format(
self._t.strftime("%Y-%m-%d %H:%M")))
def update_until(self, t, dt=None):
if (t < self._t) or t > self._endTime:
raise Exception(
"wrong time input: smaller than model time or larger than endTime"
)
while self._t < t:
self.update(dt=dt)
def spinup(self):
"""PCR specific spinup function"""
raise NotImplementedError()
def finalize(self):
self.logger.info('finalize bmi. Close logger.')
self._bmi.finalize()
closelogger(self.logger)
"""
Variable Information Functions
"""
def get_start_time(self):
# if self.initialized:
# startTime = datetime.utcfromtimestamp(self._bmi.get_start_time())
# else:
# startTime = self.get_attribute_value('run:starttime')
# startTime = datetime.strptime(startTime, self._datefmt)
startTime = datetime.utcfromtimestamp(self._bmi.get_start_time())
self._startTime = startTime
return self._startTime
def get_current_time(self):
if self.initialized:
#
return datetime.utcfromtimestamp(self._bmi.get_current_time())
else:
return self.get_start_time()
def get_end_time(self):
# if self.initialized:
# endTime = datetime.utcfromtimestamp(self._bmi.get_end_time())
# else:
# endTime = self.get_attribute_value('run:endtime')
# endTime = datetime.strptime(endTime, self._datefmt)
endTime = datetime.utcfromtimestamp(self._bmi.get_end_time())
self._endTime = endTime
return self._endTime
def get_time_step(self):
if not hasattr(self, '_dt'):
self._dt = timedelta(
**{self.get_time_units(): self._bmi.get_time_step()})
return self._dt
def get_time_units(self):
return self._timeunit
"""
Variable Getter and Setter Functions
"""
def get_value(self, long_var_name, fill_value=-999, **kwargs):
# additional fill_value argument required to translate pcr maps to numpy arrays
# NOTE that wflow flips the arrays upside down in the 'wf_supplyMapAsNumpy' function that is called by the bmi.
# TODO: check if we can improve the wflow_bmi and change this
var = np.asarray(self._bmi.get_value(
long_var_name))[::-1, :] # flip array back to N->S
var = np.where(var == fill_value, np.nan, var)
return var
def get_value_at_indices(self,
long_var_name,
inds,
fill_value=-999,
**kwargs):
return self.get_value(long_var_name, fill_value=fill_value,
**kwargs).flat[inds]
def set_value(self, long_var_name, src, fill_value=-999):
src = np.where(np.isnan(src), fill_value,
src).astype(self.get_var_type(long_var_name))
# we need to flip the data again! see note in get_value command
self._bmi.set_value(long_var_name, src[::-1, :])
def set_value_at_indices(self, long_var_name, inds, src, fill_value=-999):
val = self.get_value(long_var_name, fill_value=fill_value)
val.flat[inds] = src
self.set_value(long_var_name, val)
"""
Grid Information Functions
"""
def get_grid(self, mapdir=None):
if not hasattr(self, 'grid') or (self.grid is None):
if mapdir is None:
mapdir = join(dirname(self._config_fn), 'staticmaps')
# ldd is used for coupling to routing / flood model
_ldd_fn = join(mapdir, 'wflow_ldd.map')
if not isfile(_ldd_fn): raise IOError('ldd file not found')
# landmask used for masking out coordinates outside mask
_lm_fn = join(mapdir, 'wflow_subcatch.map')
if not isfile(_lm_fn): raise IOError('subcatch file not found')
self.logger.info('Getting rgrid info based on {}'.format(
basename(_lm_fn)))
with rasterio.open(_lm_fn, 'r') as ds:
# TODO: change transform instead of flipping the grid every time ..
self.grid = RGrid(ds.transform,
ds.height,
ds.width,
crs=ds.crs,
mask=ds.read(1) >= 1)
# river is used for the 1D cells
_riv_fn = join(mapdir, 'wflow_river.map')
if isfile(_riv_fn):
with rasterio.open(_riv_fn, 'r') as ds:
row, col = np.where(ds.read(1) == 1)
x, y = self.grid.xy(row=row, col=col)
inds = self.grid.ravel_multi_index(row, col)
self.grid.set_1d(nodes=np.array(zip(x, y)),
links=None,
inds=inds)
# read file with pcr readmap
self.logger.info('Getting drainage direction from {}'.format(
basename(_ldd_fn)))
self.grid.set_dd(_ldd_fn, ddtype='ldd')
return self.grid
"""
set and get attribute / config
"""
def set_start_time(self, start_time):
if isinstance(start_time, str):
start_time = datetime.strptime(start_time, self._datefmt)
t = (start_time - datetime.utcfromtimestamp(0))
self._startTime = start_time
self._t = start_time
self._bmi.set_start_time(t.days * 86400 + t.seconds)
def set_end_time(self, end_time):
if isinstance(end_time, str):
end_time = datetime.strptime(end_time, self._datefmt)
t = (end_time - datetime.utcfromtimestamp(0))
self._endTime = end_time
self._bmi.set_end_time(t.days * 86400 + t.seconds)
def set_out_dir(self, out_dir):
# NOTE this needs te be set somewhere pre initialize config
# the file setup is hardcoded in wflow
pass
def get_attribute_names(self):
glib.configcheck(self, self.logger)
return glib.configattr(self._config)
def get_attribute_value(self, attribute_name):
glib.configcheck(self, self.logger)
self.logger.debug("get_attribute_value: " + attribute_name)
return self._bmi.get_attribute_value(attribute_name)
def set_attribute_value(self, attribute_name, attribute_value):
glib.configcheck(self, self.logger)
self.logger.info("set_attribute_value {} -> {} ".format(
attribute_name, attribute_value))
# update config
glib.configset(self._config, attribute_name, attribute_value)
# set wfl config
return self._bmi.set_attribute_value(attribute_name, attribute_value)
def write_config(self):
"""write adapted config to file. just before initializing
only for models which do not allow for direct access to model config via bmi"""
glib.write_config(self, self._config, self._config_fn, self.logger)