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# coding=utf-8
import glob
import shutil
import uuid
import netCDF4
import os
from datetime import datetime
import pygrib
from autosubmit.config.log import Log
from autosubmit.date.chunk_date_lib import parse_date, chunk_end_date, previous_day, date2str, add_months
from earthdiagnostics.variable import Variable
from earthdiagnostics.utils import TempFile, Utils
class Cmorizer(object):
"""
Class to manage CMORization
:param data_manager: experiment's data manager
:type data_manager: DataManager
:param startdate: startdate to cmorize
:type startdate: str
:param member: member to cmorize
:type member: int
"""
def __init__(self, data_manager, startdate, member):
self.data_manager = data_manager
self.startdate = startdate
self.member = member
self.config = data_manager.config
self.experiment = self.config.experiment
self.cmor = self.config.cmor
self.member_str = self.experiment.get_member_str(member)
self.original_files_path = os.path.join(self.config.data_dir, self.experiment.expid, 'original_files',
self.startdate, self.member_str, 'outputs')
def cmorize_ocean(self):
"""
CMORizes ocean files from MMO files
:return:
"""
if not self.cmor.ocean:
return
self._unpack_ocean_files('MMO')
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self._unpack_ocean_files('PPO')
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self._unpack_ocean_files('diags')
def _unpack_ocean_files(self, prefix):
tar_folder = os.path.join(self.original_files_path, '{0}*'.format(prefix))
tar_files = glob.glob(tar_folder)
tar_files.sort()
errors = list()
count = 1
for tarfile in tar_files:
Log.info('Unpacking oceanic file {0}/{1}'.format(count, len(tar_files)))
self._unpack_tar(tarfile)
Log.result('Oceanic file {0}/{1} finished'.format(count, len(tar_files)))
count += 1
return errors
def _unpack_tar(self, tarfile):
Log.info('Unpacking {0}', tarfile)
scratch_dir = os.path.join(self.config.scratch_dir, 'CMOR')
if os.path.exists(scratch_dir):
shutil.rmtree(scratch_dir)
os.makedirs(scratch_dir)
Utils.untar((tarfile,), scratch_dir)
errors = Utils.unzip(glob.glob(os.path.join(scratch_dir, '*.gz')))
if os.path.basename(tarfile).startswith('MMA'):
temp = TempFile.get()
for filename in glob.glob(os.path.join(scratch_dir, 'MMA_*_SH_*.nc')):
Utils.cdo.sp2gpl(options='-O', input=filename, output=temp)
shutil.move(temp, filename)
sh_files = glob.glob(os.path.join(scratch_dir, 'MMA_*_SH_*.nc'))
Utils.cdo.mergetime(input=sh_files, output=os.path.join(scratch_dir, 'sh.nc'))
gg_files = glob.glob(os.path.join(scratch_dir, 'MMA_*_GG_*.nc'))
Utils.cdo.mergetime(input=gg_files, output=os.path.join(scratch_dir, 'gg.nc'))
for filename in sh_files + gg_files:
os.remove(filename)
Utils.nco.ncks(input=os.path.join(scratch_dir, 'sh.nc'),
output=os.path.join(scratch_dir, 'gg.nc'), options='-A')
os.remove(os.path.join(scratch_dir, 'sh.nc'))
tar_startdate = tarfile[0:-4].split('_')[5].split('-')
new_name = 'MMA_1m_{0[0]}_{0[1]}.nc'.format(tar_startdate)
shutil.move(os.path.join(scratch_dir, 'gg.nc'), os.path.join(scratch_dir, new_name))
for filename in glob.glob(os.path.join(scratch_dir, '*.nc')):
self._cmorize_nc_file(filename)
return errors
def cmorize_atmos(self):
"""
CMORizes atmospheric data, from grib or MMA files
:return:
"""
if not self.cmor.atmosphere:
return
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if self.cmor.use_grib:
grb_path = os.path.join(self.original_files_path, '*.grb')
gribfiles = glob.glob(grb_path)
else:
gribfiles = tuple()
if len(gribfiles) == 0:
tar_files = glob.glob(
os.path.join(self.original_files_path, 'MMA*'))
tar_files.sort()
count = 1
for tarfile in tar_files:
Log.info('Unpacking atmospheric file {0}/{1}'.format(count, len(tar_files)))
self._unpack_tar(tarfile)
Log.result('Atmospheric file {0}/{1} finished'.format(count, len(tar_files)))
count += 1
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self._cmorize_grib()
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def _cmorize_grib(self):
count = 1
atmos_timestep = None
chunk_start = parse_date(self.startdate)
while os.path.exists(os.path.join(self.original_files_path, self._get_grib_filename('GG', chunk_start))) or \
os.path.exists(os.path.join(self.original_files_path, self._get_grib_filename('SH', chunk_start))):
chunk_end = chunk_end_date(chunk_start, self.experiment.chunk_size, 'month', 'standard')
chunk_end = previous_day(chunk_end, 'standard')
Log.info('CMORizing chunk {0}-{1}', date2str(chunk_start), date2str(chunk_end))
for grid in ('SH', 'GG'):
Log.info('Processing {0} variables', grid)
if not os.path.exists(os.path.join(self.original_files_path,
self._get_grib_filename(grid, chunk_start))):
continue
for month in range(0, self.experiment.chunk_size):
current_month = add_months(chunk_start, month, 'standard')
original_gribfile = os.path.join(self.original_files_path,
self._get_grib_filename(grid, current_month))
Log.info('Processing month {1}', grid, date2str(current_month))
gribfile = os.path.join(self.config.scratch_dir, os.path.basename(original_gribfile))
if not os.path.isfile(gribfile):
Log.info('Copying file...', grid, date2str(current_month))
shutil.copy(original_gribfile, gribfile)
if atmos_timestep is None:
atmos_timestep = self._get_atmos_timestep(gribfile)
prev_gribfile = os.path.join(self.config.scratch_dir,
self._get_grib_filename(grid,
add_months(current_month, -1, 'standard')))
if os.path.exists(prev_gribfile):
self._merge_grib_files(current_month, prev_gribfile, gribfile)
full_file = 'ICM'
else:
full_file = gribfile
Log.info('Unpacking... ')
# remap on regular Gauss grid
if grid == 'SH':
Utils.cdo.splitparam(input='-sp2gpl {0}'.format(full_file), output=gribfile + '_',
options='-f nc4')
else:
Utils.cdo.splitparam(input=full_file, output=gribfile + '_', options='-R -f nc4')
# total precipitation (remove negative values)
Utils.cdo.setcode(228, input='-setmisstoc,0 -setvrange,0,Inf -add '
'{0}_{{142,143}}.128.nc'.format(gribfile),
output='{0}_228.128.nc'.format(gribfile))
Utils.remove_file('ICM')
next_gribfile = os.path.join(self.original_files_path,
self._get_grib_filename(grid,
add_months(current_month, 1, 'standard')))
if not os.path.exists(next_gribfile):
os.remove(gribfile)
cdo_reftime = parse_date(self.startdate).strftime('%Y-%m-%d,00:00')
self._ungrib_vars(cdo_reftime, gribfile, current_month.month, '{0}hr'.format(atmos_timestep))
self._ungrib_vars(cdo_reftime, gribfile, current_month.month, '1d')
self._ungrib_vars(cdo_reftime, gribfile, current_month.month, '1m')
for splited_file in glob.glob('{0}_*.128.nc'.format(gribfile)):
os.remove(splited_file)
Log.result('Month {0}, {1} variables finished', date2str(current_month), grid)
count += 1
self._merge_and_cmorize_atmos(chunk_start, chunk_end, grid, '1m')
self._merge_and_cmorize_atmos(chunk_start, chunk_end, grid, '1d')
self._merge_and_cmorize_atmos(chunk_start, chunk_end, grid,
'{0}hr'.format(atmos_timestep))
chunk_start = chunk_end_date(chunk_start, self.experiment.chunk_size, 'month', 'standard')
def _get_grib_filename(self, grid, month):
return 'ICM{0}{1}+{2}.grb'.format(grid, self.experiment.expid, date2str(month)[:-2])
def _get_atmos_timestep(self, gribfile):
Log.info('Getting timestep...')
grib_handler = pygrib.open(gribfile)
mes1 = grib_handler.message(1)
mes2 = grib_handler.readline()
while mes2.analDate == mes1.analDate:
mes2 = grib_handler.readline()
atmos_timestep = mes2.analDate - mes1.analDate
atmos_timestep = int(atmos_timestep.total_seconds() / 3600)
self.experiment.atmos_timestep = atmos_timestep
grib_handler.close()
return atmos_timestep
def _cmorize_nc_file(self, filename):
Log.info('Processing file {0}', filename)
temp = TempFile.get()
handler = Utils.openCdf(filename)
variables = handler.variables.keys()
handler.close()
if not self.cmor.any_required(variables):
os.remove(filename)
return
Utils.execute_shell_command(["nccopy", "-4", "-d4", "-s", filename, temp])
shutil.move(temp, filename)
file_parts = os.path.basename(filename).split('_')
if self.experiment.expid in [file_parts[1], file_parts[2]]:
frequency = 'm'
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elif self.experiment.expid == file_parts[0]:
try:
parse_date(file_parts[1])
frequency = 'm'
except ValueError:
frequency = file_parts[1][1].lower()
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else:
frequency = file_parts[1][1].lower()
variables = dict()
variables['time_counter'] = 'time'
variables['time_counter_bnds'] = 'time_bnds'
variables['tbnds'] = 'bnds'
variables['nav_lat'] = 'lat'
variables['nav_lon'] = 'lon'
variables['x'] = 'i'
variables['y'] = 'j'
Utils.rename_variables(filename, variables, False, True)
handler = Utils.openCdf(filename)
self._add_common_attributes(frequency, handler)
self._update_time_variables(handler)
handler.sync()
temp = TempFile.get()
Log.info('Splitting file {0}', filename)
for variable in handler.variables.keys():
if variable in ('lon', 'lat', 'time', 'time_bnds', 'leadtime', 'lev', 'icethi',
'deptht', 'depthu', 'depthw', 'depthv', 'time_centered', 'time_centered_bounds',
'deptht_bounds', 'depthu_bounds', 'depthv_bounds', 'depthw_bounds',
'time_counter_bounds', 'ncatice',
'nav_lat_grid_V', 'nav_lat_grid_U', 'nav_lat_grid_T',
'nav_lon_grid_V', 'nav_lon_grid_U', 'nav_lon_grid_T',
'depth', 'depth_2', 'depth_3', 'depth_4',
'mlev', 'hyai', 'hybi', 'hyam', 'hybm'):
continue
self.extract_variable(filename, handler, frequency, temp, variable)
Log.result('File {0} cmorized!', filename)
handler.close()
os.remove(filename)
def extract_variable(self, file_path, handler, frequency, temp, variable):
"""
Extracts a variable from a file and creates the CMOR file
:param file_path: path to the file
:type file_path: str
:param handler: netCDF4 handler for the file
:type handler: netCDF$.Dataset
:param frequency: variable's frequency
:type frequency: str
:param temp: temporal file to use
:type temp: str
:param variable: variable's name
:type variable: str
"""
file_parts = os.path.basename(file_path).split('_')
var_cmor = Variable.get_variable(variable)
if var_cmor is None:
return
if not self.cmor.cmorize(var_cmor):
return
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if frequency == 'd':
frequency = 'day'
elif frequency == 'm':
frequency = 'mon'
elif frequency == 'h':
frequency = '6hr'
else:
raise Exception('Frequency {0} not supported'.format(frequency))
Utils.nco.ncks(input=file_path, output=temp, options='-v {0}'.format(variable))
if var_cmor.domain == 'ocean':
Utils.rename_variables(temp, {'deptht': 'lev', 'depthu': 'lev', 'depthw': 'lev', 'depthv': 'lev',
'depth': 'lev'}, False, True)
elif var_cmor.domain in ('land', 'landIce'):
Utils.rename_variables(temp, {'depth': 'sdepth', 'depth_2': 'sdepth', 'depth_3': 'sdepth',
'depth_4': 'sdepth'}, False, True)
elif var_cmor.domain == 'atmos':
Utils.rename_variables(temp, {'depth': 'plev'}, False, True)
handler_cmor = Utils.openCdf(temp)
Utils.copy_variable(handler, handler_cmor, 'lon', False)
Utils.copy_variable(handler, handler_cmor, 'lat', False)
if 'time' in handler_cmor.dimensions.keys():
Utils.copy_variable(handler, handler_cmor, 'leadtime', False)
handler_cmor.close()
if var_cmor.basin is None:
region = None
else:
region = var_cmor.basin.fullname
if file_parts[0] == self.experiment.expid or file_parts[0].startswith('ORCA') or \
file_parts[0] in ('MMA', 'MMO'):
# Model output
date_str = '{0}-{1}'.format(file_parts[2][0:6], file_parts[3][0:6])
elif file_parts[1] == self.experiment.expid:
# Files generated by the old version of the diagnostics
date_str = '{0}-{1}'.format(file_parts[4][0:6], file_parts[5][0:6])
else:
Log.error('Variable {0} can not be cmorized. Original filename does not match a recognized pattern',
var_cmor.short_name)
return
self.data_manager.send_file(temp, var_cmor.domain, var_cmor.short_name, self.startdate, self.member,
frequency=frequency, rename_var=variable, date_str=date_str, region=region,
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move_old=True, grid=var_cmor.grid)
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@staticmethod
def _merge_grib_files(current_month, prev_gribfile, gribfile):
Log.info('Merging data from different files...')
fd = open('rules_files', 'w')
fd.write('if (dataDate >= {0.year}{0.month:02}01) {{ write ; }}\n'.format(current_month))
fd.close()
# get first timestep for each month from previous file (if possible)
if os.path.exists('ICM'):
os.remove('ICM')
Utils.execute_shell_command('grib_filter -o ICM rules_files '
'{0} {1}'.format(os.path.basename(prev_gribfile),
os.path.basename(gribfile)))
os.remove('rules_files')
Utils.remove_file(prev_gribfile)
def _ungrib_vars(self, cdo_reftime, gribfile, month, frequency):
Log.info('Preparing {0} variables'.format(frequency))
var_codes = self.config.cmor.get_variables(frequency)
for var_code in var_codes:
if not os.path.exists('{0}_{1}.128.nc'.format(gribfile, var_code)):
continue
new_units = None
cdo_operator = '-selmon,{0}'.format(month)
if frequency in ('month', 'monthly', 'mon', '1m'):
if var_code == 201:
cdo_operator = "-monmean -daymax {0}".format(cdo_operator)
elif var_code == 202:
cdo_operator = "-monmean -daymax {0}".format(cdo_operator)
else:
cdo_operator = "-monmean {0} ".format(cdo_operator)
elif frequency in ('day', 'daily', '1d'):
if var_code == 201:
cdo_operator = "-daymax {0} ".format(cdo_operator)
elif var_code == 202:
cdo_operator = "-daymin {0} ".format(cdo_operator)
else:
cdo_operator = "-daymean {0} ".format(cdo_operator)
if var_code in (144, 146, 147, 169, 175, 176, 177, 179, 180, 181, 182, 201, 202, 205, 212, 228):
cdo_operator = '{0} -shifttime,-{1}hours'.format(cdo_operator, self.experiment.atmos_timestep)
if var_code == 129:
# geopotential
new_units = "m"
cdo_operator = "-divc,9.81 {0}".format(cdo_operator)
elif var_code in (146, 147, 169, 175, 176, 177, 179, 212):
# radiation
new_units = "W m-2"
cdo_operator = "-divc,{0} {1}".format(self.experiment.atmos_timestep * 3600, cdo_operator)
elif var_code in (180, 181):
# momentum flux
new_units = "N m-2"
cdo_operator = "-divc,{0} {1}".format(self.experiment.atmos_timestep * 3600, cdo_operator)
elif var_code in (144, 182, 205, 228):
# precipitation/evaporation/runoff
new_units = "kg m-2 s-1"
cdo_operator = "-mulc,1000 -divc,{0}".format(self.experiment.atmos_timestep * 3600)
levels = self.config.cmor.get_levels(frequency, var_code)
if levels:
cdo_operator = "{0} -sellevel,{1}".format(cdo_operator, levels)
Utils.execute_shell_command('cdo -t ecmwf setreftime,{0} '
'{1} {2}_{3}.128.nc '
'{2}_{3}_{4}.nc'.format(cdo_reftime, cdo_operator,
gribfile, var_code, frequency))
h_var_file = '{0}_{1}_{2}.nc'.format(gribfile, var_code, frequency)
handler = Utils.openCdf(h_var_file)
if new_units:
for var in handler.variables.values():
if 'code' in var.ncattrs() and var.code == var_code:
var.units = new_units
break
var_name = None
for key in handler.variables.keys():
if key + '_2' in handler.variables and key not in handler.dimensions:
var_name = key
handler.close()
if var_name is not None:
Utils.nco.ncks(input='{0}_{1}_1m.nc'.format(gribfile, var_code),
output='{0}_{1}_1m.nc'.format(gribfile, var_code),
options='-O -v {0}'.format(var_name))
def _merge_and_cmorize_atmos(self, chunk_start, chunk_end, grid, frequency):
merged_file = 'MMA_{0}_{1}_{2}_{3}.nc'.format(frequency, date2str(chunk_start), date2str(chunk_end), grid)
files = glob.glob(os.path.join(self.config.scratch_dir,
'{0}_*_{1}.nc'.format(self._get_grib_filename(grid, chunk_start), frequency)))
for first_file in files:
shutil.move(first_file, merged_file)
current_month = add_months(chunk_start, 1, 'standard')
while current_month < chunk_end:
month_file = first_file.replace('+{0}.grb'.format(date2str(chunk_start)[:-2]),
'+{0}.grb'.format(date2str(current_month)[:-2]))
Utils.concat_variables(month_file, merged_file, True)
current_month = add_months(current_month, 1, 'standard')
self._cmorize_nc_file(merged_file)
def _update_time_variables(self, handler):
time_var = handler.variables['time']
times = Utils.get_datetime_from_netcdf(handler)
if type(times[0]) is not datetime:
for x in range(0, times.shape[0]):
# noinspection PyProtectedMember
times[x] = times[x]._to_real_datetime()
time_var[:] = netCDF4.date2num(times, 'days since 1850-01-01', 'standard')
if 'axis_nbounds' in handler.dimensions:
handler.renameDimension('axis_nbounds', 'bnds')
if 'time_counter_bounds' in handler.variables:
handler.renameVariable('time_counter_bounds', 'time_bnds')
handler.sync()
if 'time_bnds' in handler.variables:
time_bounds_var = handler.variables['time_bnds']
time_var.bounds = "time_bnds"
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try:
units = time_bounds_var.units
except AttributeError:
# we suppose that if not units are present, they match the ones in the time variable
units = time_var.units
time_bounds_var.units = units
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time_bounds = Utils.get_datetime_from_netcdf(handler, 'time_bnds')
if type(time_bounds[0, 0]) is not datetime:
for x in range(0, time_bounds.shape[0]):
for y in range(0, time_bounds.shape[1]):
# noinspection PyProtectedMember
time_bounds[x, y] = time_bounds[x, y]._to_real_datetime()
time_bounds_var[:] = netCDF4.date2num(time_bounds, 'days since 1850-01-01', 'standard')
time_var.units = 'days since 1850-01-01'
time_var.time_origin = "1850-01-01"
time_var.calendar = 'standard'
time_var.long_name = "Verification time of the forecast"
time_var.standard_name = "time"
time_var.axis = "T"
if 'leadtime' in handler.variables:
var = handler.variables['leadtime']
else:
var = handler.createVariable('leadtime', float, 'time')
var.units = "days"
var.long_name = "Time elapsed since the start of the forecast"
var.standard_name = "forecast_period"
leadtime = (Utils.get_datetime_from_netcdf(handler) - parse_date(self.startdate))
for lt in range(0, leadtime.shape[0]):
var[lt] = leadtime[lt].days
def _add_common_attributes(self, frequency, handler):
cmor = self.config.cmor
experiment = self.config.experiment
handler.associated_experiment = cmor.associated_experiment
handler.batch = '{0}{1}'.format(experiment.institute, datetime.now().strftime('%Y-%m-%d(T%H:%M:%SZ)'))
handler.contact = 'Pierre-Antoine Bretonnière, pierre-antoine.bretonniere@bsc.es , ' \
'Javier Vegas-Regidor, javier.vegas@bsc.es '
handler.Conventions = 'CF-1.6'
handler.creation_date = datetime.now().strftime('%Y-%m-%d(T%H:%M:%SZ)')
handler.experiment_id = experiment.experiment_name
handler.forecast_reference_time = parse_date(self.startdate).strftime('%Y-%m-%d(T%H:%M:%SZ)')
if frequency == 'd':
handler.frequency = 'day'
elif frequency == 'm':
handler.frequency = 'mon'
handler.institute_id = experiment.institute
handler.institution = experiment.institute
handler.initialization_method = cmor.initialization_method
handler.initialization_description = cmor.initialization_description
handler.physics_version = cmor.physics_version
handler.physics_description = cmor.physics_description
handler.model_id = experiment.model
handler.associated_model = cmor.associated_model
handler.project_id = 'SPECS'
handler.realization = str(self.member + 1)
handler.source = cmor.source
handler.startdate = 'S{0}'.format(self.startdate)
handler.tracking_id = str(uuid.uuid1())
handler.title = "{0} model output prepared for SPECS {1}".format(experiment.model, experiment.experiment_name)