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Javier Vegas-Regidor
committed
import shutil
import threading
import uuid
from datetime import datetime
import netCDF4
import numpy as np
import os
from autosubmit.date.chunk_date_lib import parse_date, chunk_start_date, chunk_end_date, previous_day, add_months, \
date2str
def __init__(self, institution, model, expid, datafolder, frequency, chunk_size, experiment_name, num_chunks,
scratch_dir, nfrp, member_digits, calendar='standard'):
"""
:param institution:
:param model:
:param expid:
:param datafolder:
:param frequency:
:param chunk_size:
:param experiment_name:
:param num_chunks:
:param calendar:
"""
self.initialization_method = 'to be filled'
self.initialization_description = 'to be filled'
self.physics_version = 'to be filled'
self.physics_description = 'to be filled'
self.associated_model = 'to be filled'
self.source = 'to be filled'
self.associated_experiment = 'to be filled'
self.institution = institution
self.model = model
self.expid = expid
self.data_dir = datafolder
self.frequency = frequency
self.chunk_size = chunk_size
self.experiment_name = experiment_name
self.add_startdate = True
self.add_name = True
self.num_chunks = num_chunks
self.calendar = calendar
self.scratch_dir = scratch_dir
self.nfrp = nfrp
self.member_digits = member_digits
# noinspection PyPep8Naming
def prepare_CMOR_files(self, startdates, members, force_rebuild, ocean, atmosphere):
"""
Prepares the data to be used by the diagnostic.
If CMOR data is not created, it show a warning and closes. In the future, an automatic cmorization procedure
will be launched
If CMOR data is available but packed, the procedure will unpack it.
:param atmosphere: activates atmosphere files cmorization
:type atmosphere: bool
:param ocean: activates ocean files cmorization
:type ocean: bool
:param force_rebuild: if True, forces the creation of the CMOR files
:type force_rebuild: bool
:param startdates: list of startdates that will be used by the diagnostics
:type startdates: list[str]
:param members: lists of members that will be used by the diagnostics
:type members: list[int]
:return:
"""
for startdate in startdates:
for member in members:
if force_rebuild or not os.path.exists(os.path.join(self.data_dir, self.expid, 'cmorfiles',
startdate, self.get_member_str(member))):
Log.info('CMORizing startdate {0} member {1}', startdate, self.get_member_str(member))
if ocean:
path_MMO = os.path.join(self.data_dir, self.expid, 'original_files', startdate,
self.get_member_str(member), 'outputs', 'MMO*')
for tarfile in glob.glob(path_MMO):
self._unpack_tar(member, startdate, tarfile)
if not atmosphere:
continue
grb_path = os.path.join(self.data_dir, self.expid, 'original_files', startdate,
self.get_member_str(member), 'outputs', '*.grb')
gribfiles = glob.glob(grb_path)
if len(gribfiles) == 0:
for tarfile in glob.glob(os.path.join(self.data_dir, self.expid, 'original_files', startdate,
self.get_member_str(member),
'outputs', 'MMA*')):
self._unpack_tar(member, startdate, tarfile)
self._cmorize_grib(startdate, member, gribfiles)
for startdate in startdates:
for member in members:
Javier Vegas-Regidor
committed
member_path = os.path.join(self.data_dir, self.expid, 'cmorfiles', startdate,
self.get_member_str(member), 'outputs')
Log.info('Preparing CMOR files for startdate {0} and member {1}'.format(startdate, member))
filepaths = glob.glob(os.path.join(member_path, '*.gz'))
if len(filepaths) == 0:
continue
self._unpack_cmorfiles(filepaths, member_path)
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def _cmorize_grib(self, startdate, member, gribfiles):
gribfiles.sort()
copied_gribfiles = list()
for gribfile in gribfiles:
shutil.copy(gribfile, os.path.join(self.scratch_dir, os.path.basename(gribfile)))
copied_gribfiles.append(os.path.join(self.scratch_dir, os.path.basename(gribfile)))
for gribfile in copied_gribfiles:
cdo = Utils.cdo
start = parse_date(gribfile[-10:-4])
month = '{0:02}'.format(start.month)
times = cdo.showtimestamp(input=gribfile)
times = times[0].split()[0:2]
time_diff = datetime.strptime(times[1], '%Y-%m-%dT%H:%M:%S') - datetime.strptime(times[0],
'%Y-%m-%dT%H:%M:%S')
nfrp = (time_diff.seconds // 3600)
param_6hr = (151, 167, 168, 164, 165, 166, 129,)
param_day = (167, 165, 166, 151, 164, 168, 169, 177, 179, 228, 201, 202, 130)
param_mon = (167, 201, 202, 165, 166, 151, 144, 228, 205, 182, 164, 146, 147, 176, 169,
177, 175, 212, 141, 180, 181, 179, 168, 243, 129, 130, 131, 132, 133)
grid = os.path.basename(gribfile)[3:5]
if os.path.exists('ICM{0}{1}+{2.year}{2.month:02}.grb'.format(grid, self.expid,
add_months(start, -1,
'standard'))):
fd = open('rules_files', 'w')
fd.write('if (dataDate >= {0.year}{0.month:02}01) {{ write ; }}\n'.format(start))
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 '
'ICM{0}{1}+{2.year}{2.month:02}.grb '
'{3}'.format(grid, self.expid,
add_months(start, -1, 'standard'),
gribfile))
os.remove('rules_files')
else:
shutil.copy(gribfile, 'ICM')
# remap on regular Gauss grid
if grid == 'SH':
Utils.cdo.splitparam(input='-sp2gpl ICM', output=gribfile + '_')
else:
Utils.cdo.splitparam(input='ICM', output=gribfile + '_', options='-R')
# total precipitation (remove negative values)
Utils.cdo.setcode(228, input='-setmisstoc,0 -setvrange,0,Inf -add '
'{0}_{{142,143}}.128.grb'.format(gribfile),
output='{0}_228.128.grb'.format(gribfile))
os.remove('ICM')
cdo_reftime = parse_date(startdate).strftime('%Y-%m-%d,00:00')
# daily variables
for param in param_day:
if not os.path.exists('{0}_{1}.128.grb'.format(gribfile, param)):
continue
new_units = None
if param in (169, 177, 179):
# radiation
new_units = "W m-2"
cdo_operator = "-divc,{0} -daymean -selmon,{2} " \
"-shifttime,-{1}hours".format(nfrp * 3600, nfrp, month)
elif param == 228:
# precipitation
new_units = "kg m-2 -s"
cdo_operator = "-mulc,1000 -divc,{0} -daymean -selmon,{2} " \
"-shifttime,-{1}hours".format(nfrp * 3600, nfrp, month)
elif param == 201:
# maximum
cdo_operator = "-daymax -selmon,{1} -shifttime,-{0}hours".format(nfrp, month)
elif param == 202:
# minmimum
cdo_operator = "-daymin -selmon,{1} -shifttime,-{0}hours".format(nfrp, month)
elif param == 130:
# 850 hPa
cdo_operator = "-daymean -sellevel,85000 -selmon,{0}".format(month)
else:
# default, plain daily mean
cdo_operator = "-daymean -selmon,{0}".format(month)
Utils.execute_shell_command('cdo -f nc -t ecmwf setreftime,{0} '
'{1} {2}_{3}.128.grb '
'{2}_{3}_day.nc'.format(cdo_reftime, cdo_operator,
gribfile, param))
if new_units:
handler = Utils.openCdf('{0}_{1}_day.nc'.format(gribfile, param))
for var in handler.variables.values():
if 'code' in var.ncattrs() and var.code == param:
var.units = new_units
break
handler.close()
# concat all vars in one file for day
Utils.nco.ncks(input='{0}_{1}_day.nc'.format(gribfile, param),
output='{0}_day.nc'.format(gribfile), options='-A')
os.remove('{0}_{1}_day.nc'.format(gribfile, param))
# monthly variables
for param in param_mon:
if not os.path.exists('{0}_{1}.128.grb'.format(gribfile, param)):
continue
new_units = None
if param in (146, 147, 176, 169, 177, 175, 179, 212):
# radiation/heat
new_units = "W m-2"
cdo_operator = "-divc,{0} -monmean -selmon,{2} " \
"-shifttime,-{1}hours".format(nfrp * 3600, nfrp, month)
elif param in (180, 181):
# momentum flux
new_units = "N m-2"
cdo_operator = "-divc,{0} -monmean -selmon,{2} " \
"-shifttime,-{1}hours".format(nfrp * 3600, nfrp, month)
elif param in (144, 228, 205, 182):
# precipitation/evaporation/runoff
new_units = "kg m-2 s-1"
cdo_operator = "-mulc,1000 -divc,{0} -monmean -selmon,{2} " \
"-shifttime,-{1}hours".format(nfrp * 3600, nfrp, month)
elif param == 201:
# mean daily maximum
cdo_operator = "-monmean -daymax -selmon,{1} " \
"-shifttime,-{0}hours".format(nfrp, month)
elif param == 202:
# mean daily minmimum
cdo_operator = "-monmean -daymin -selmon,{1} " \
"-shifttime,-{0}hours".format(nfrp, month)
elif param in (130, 131, 132, 133):
# upper-air
cdo_operator = "-monmean -sellevel,5000,20000,50000,85000 " \
"-selmon,{0}".format(month)
elif param == 129:
# upper-air geopotential
new_units = "m"
cdo_operator = "-divc,9.81 -timmean -sellevel,5000,20000,50000,85000 " \
"-selmon,{0}".format(month)
else:
# default, plain monthly mean
cdo_operator = "-monmean -selmon,{0}".format(month)
Utils.execute_shell_command('cdo -f nc -t ecmwf setreftime,{0} '
'{1} {2}_{3}.128.grb '
'{2}_{3}_mon.nc'.format(cdo_reftime, cdo_operator,
gribfile, param))
handler = Utils.openCdf('{0}_{1}_mon.nc'.format(gribfile, param))
if new_units:
for var in handler.variables.values():
if 'code' in var.ncattrs() and var.code == param:
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}_mon.nc'.format(gribfile, param),
output='{0}_{1}_mon.nc'.format(gribfile, param),
options='-O -v {0}'.format(var_name))
# concat all vars in one file for mon
Utils.nco.ncks(input='{0}_{1}_mon.nc'.format(gribfile, param),
output='{0}_mon.nc'.format(gribfile), options='-A')
os.remove('{0}_{1}_mon.nc'.format(gribfile, param))
# 6-hourly variables
for param in param_6hr:
if not os.path.exists('{0}_{1}.128.grb'.format(gribfile, param)):
continue
new_units = None
if param == 129:
# geopotential
new_units = "m"
cdo_operator = "-divc,9.81 -sellevel,50000 -selmon,{0}".format(month)
else:
# default, plain monthly mean
cdo_operator = "-selmon,{0}".format(month)
Utils.execute_shell_command('cdo -f nc -t ecmwf setreftime,{0} '
'{1} {2}_{3}.128.grb '
'{2}_{3}_6hr.nc'.format(cdo_reftime, cdo_operator,
gribfile, param))
if new_units:
handler = Utils.openCdf('{0}_{1}_6hr.nc'.format(gribfile, param))
for var in handler.variables.values():
if 'code' in var.ncattrs() and var.code == param:
var.units = new_units
break
handler.close()
# concat all vars in one file for 6hr
Utils.nco.ncks(input='{0}_{1}_6hr.nc'.format(gribfile, param),
output='{0}_6hr.nc'.format(gribfile), options='-A')
os.remove('{0}_{1}_6hr.nc'.format(gribfile, param))
for splited_file in glob.glob('{0}_???.128.grb'.format(gribfile)):
os.remove(splited_file)
chunk_start = parse_date(startdate)
while os.path.exists(os.path.join(self.scratch_dir,
'ICMGG{0}+{1}.grb'.format(self.expid,
date2str(chunk_start)[:-2]))):
chunk_end = chunk_end_date(chunk_start, self.chunk_size, 'month', 'standard')
chunk_end = previous_day(chunk_end, 'standard')
chunk_files_gg_mon = list()
chunk_files_gg_day = list()
chunk_files_gg_6h = list()
chunk_files_sh_mon = list()
chunk_files_sh_day = list()
chunk_files_sh_6h = list()
for month in range(0, self.chunk_size):
chunk_file = 'ICMGG{0}+{1}.grb'.format(self.expid,
date2str(add_months(chunk_start, month,
'standard'))[:-2])
os.remove(chunk_file)
os.remove('ICMSH' + chunk_file[5:])
chunk_files_gg_mon.append(chunk_file + '_mon.nc')
chunk_files_gg_day.append(chunk_file + '_day.nc')
chunk_files_gg_6h.append(chunk_file + '_6hr.nc')
chunk_files_sh_mon.append('ICMSH' + chunk_file[5:] + '_mon.nc')
chunk_files_sh_day.append('ICMSH' + chunk_file[5:] + '_day.nc')
chunk_files_sh_6h.append('ICMSH' + chunk_file[5:] + '_6hr.nc')
self._merge_and_cmorize_atmos(startdate, member, chunk_start, chunk_end, chunk_files_sh_mon,
'SH', '1m')
self._merge_and_cmorize_atmos(startdate, member, chunk_start, chunk_end, chunk_files_sh_day,
'SH', '1d')
self._merge_and_cmorize_atmos(startdate, member, chunk_start, chunk_end, chunk_files_sh_6h,
'SH', '6hr')
self._merge_and_cmorize_atmos(startdate, member, chunk_start, chunk_end, chunk_files_gg_mon,
'GG', '1m')
self._merge_and_cmorize_atmos(startdate, member, chunk_start, chunk_end, chunk_files_gg_day,
'GG', '1d')
self._merge_and_cmorize_atmos(startdate, member, chunk_start, chunk_end, chunk_files_gg_6h,
'GG', '6hr')
chunk_start = chunk_end_date(chunk_start, self.chunk_size, 'month', 'standard')
def _merge_and_cmorize_atmos(self, startdate, member, chunk_start, chunk_end, chunk_files, grid, frequency):
merged_file = 'MMA_{0}_{1}_{2}_{3}.nc'.format(frequency, date2str(chunk_start), date2str(chunk_end), grid)
for x in range(0, len(chunk_files)):
chunk_files[x] = os.path.join(self.scratch_dir, chunk_files[x])
Utils.cdo.mergetime(input=' '.join(chunk_files), output=merged_file, options='-O')
for filepath in chunk_files:
os.remove(filepath)
self._cmorize_nc_file(merged_file, member, startdate)
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def _unpack_cmorfiles(self, filepaths, member_path):
threads = list()
numthreads = Utils.available_cpu_count()
for numthread in range(0, numthreads):
t = threading.Thread(target=DataManager._unzip,
args=([filepaths[numthread::numthreads]]))
threads.append(t)
t.start()
for t in threads:
t.join()
filepaths = glob.glob(os.path.join(member_path, '*.tar'))
for numthread in range(0, numthreads):
t = threading.Thread(target=DataManager._untar,
args=(filepaths[numthread::numthreads], member_path))
threads.append(t)
t.start()
for t in threads:
t.join()
if self.experiment_name != self.model:
bad_path = os.path.join(member_path, 'output', self.institution, self.model, self.model)
for (dirpath, dirnames, filenames) in os.walk(bad_path, False):
for filename in filenames:
filepath = os.path.join(dirpath, filename)
good = filepath.replace('_{0}_output_'.format(self.model),
'_{0}_{1}_'.format(self.model, self.experiment_name))
good = good.replace('/{0}/{0}'.format(self.model),
'/{0}/{1}'.format(self.model,
self.experiment_name))
Utils.move_file(filepath, good)
os.rmdir(dirpath)
good_dir = os.path.join(member_path, 'output', self.institution, self.model, self.experiment_name)
for sdate in os.listdir(good_dir):
for (dirpath, dirnames, filenames) in os.walk(os.path.join(good_dir, sdate), False):
for filename in filenames:
filepath = os.path.join(dirpath, filename)
good = filepath.replace('_{0}_{1}_r'.format(self.model, self.experiment_name, sdate),
'_{0}_{1}_{2}_r'.format(self.model, self.experiment_name, sdate))
if good != filepath:
Log.info('Moving {0} to {1}'.format(filename, good))
Utils.move_file(filepath, good)
def _unpack_tar(self, member, startdate, tarfile):
scratch_dir = os.path.join(self.scratch_dir, 'CMOR')
if os.path.exists(scratch_dir):
shutil.rmtree(scratch_dir)
os.makedirs(scratch_dir)
self._untar((tarfile,), scratch_dir)
self._unzip(glob.glob(os.path.join(scratch_dir, '*.gz')))
if os.path.basename(tarfile).startswith('MMA'):
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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, member, startdate)
def _cmorize_nc_file(self, filename, member, startdate):
Log.info('Processing file {0}', filename)
file_parts = os.path.basename(filename).split('_')
frequency = file_parts[1][1].lower()
variables = dict()
variables['time_counter'] = 'time'
variables['time_counter_bnds'] = 'time_bnds'
# variables['time_counter_bounds'] = 'time_bnds'
variables['tbnds'] = 'bnds'
# variables['axis_nbounds'] = '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, member, startdate)
self._update_time_variables(handler, startdate)
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(file_parts, filename, frequency, handler, member, startdate, temp,
variable)
Log.result('File {0} cmorized!', filename)
handler.close()
os.remove(filename)
def extract_variable(self, file_parts, filename, frequency, handler, member, startdate, temp, variable):
var_cmor = Variable.get_variable(variable)
if var_cmor is None:
return
Utils.nco.ncks(input=filename, 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.modeling_realm = var_cmor.domain
handler_cmor.table_id = 'SPECS_' + self.domain_abbreviation(var_cmor.domain, frequency)
var_handler = handler_cmor.variables[variable]
var_handler.short_name = var_cmor.short_name
var_handler.standard_name = var_cmor.standard_name
var_handler.long_name = var_cmor.long_name
handler_cmor.close()
if frequency == 'd':
frequency = 'day'
elif frequency == 'm':
frequency = 'mon'
elif frequency == 'h':
frequency = '6hr'
else:
raise Exception('Frequency {0} not supported'.format(frequency))
if var_cmor.basin is None:
region = None
else:
region = var_cmor.basin.fullname
self.send_file(temp, var_cmor.domain, var_cmor.short_name, startdate, member,
frequency=frequency, rename_var=variable,
date_str='{0}-{1}'.format(file_parts[2][0:6], file_parts[3][0:6]),
region=region)
@staticmethod
def _update_time_variables(handler, startdate):
time_var = handler.variables['time']
times = netCDF4.num2date(time_var[:], time_var.units, time_var.calendar)
if type(times[0]) is not datetime:
for x in range(0, times.shape[0]):
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# 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:
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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"
time_bounds = netCDF4.num2date(time_bounds_var[:], time_var.units, time_var.calendar)
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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]):
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# 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 = (netCDF4.num2date(time_var[:], time_var.units, time_var.calendar) - parse_date(startdate))
for lt in range(0, leadtime.shape[0]):
var[lt] = leadtime[lt].days
def _add_common_attributes(self, frequency, handler, member, startdate):
handler.associated_experiment = self.associated_experiment
handler.batch = '{0}{1}'.format(self.institution, datetime.now().strftime('%Y-%m-%dT%H:%M:%SZ'))
handler.contact = 'Pierre-Antoine Bretonnire, 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-%dT%H:%M:%SZ')
handler.experiment_id = self.experiment_name
handler.forecast_reference_time = datetime.now().strftime('%Y-%m-%dT%H:%M:%SZ')
if frequency == 'd':
handler.frequency = 'daily'
elif frequency == 'm':
handler.frequency = 'monthly'
handler.institute_id = self.institution
handler.institution = self.institution
handler.initialization_method = self.initialization_method
handler.initialization_description = self.initialization_description
handler.physics_version = self.physics_version
handler.physics_description = self.physics_description
handler.associated_model = self.associated_model
handler.realization = member + 1
handler.source = self.source
handler.startdate = 'S{0}'.format(startdate)
handler.tracking_id = str(uuid.uuid1())
handler.title = "{0} model output prepared for SPECS {1}".format(self.model, self.experiment_name)
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@staticmethod
def _unzip(files):
for filepath in files:
Log.debug('Unzipping {0}', filepath)
Utils.execute_shell_command('gunzip {0}'.format(filepath))
@staticmethod
def _untar(files, member_path):
for filepath in files:
Log.debug('Unpacking {0}', filepath)
Utils.execute_shell_command('tar -xvf {0} -C {1}'.format(filepath, member_path))
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def get_files(self, startdate, member, chunk, domain, variables, grid=None):
"""
Returns a list of filenames for different variables
:param startdate: startdate to retrieve
:type startdate: str
:param member: member to retrieve
:type member: int
:param chunk: chunk to retrieve
:type chunk: int
:param domain: variable's CMOR domain
:type domain:str
:param variables: variables list
:type variables: list[str], tuple[str]
:param grid: specifies if the variable must be in a interpolated grid
:type grid: str
:return:
"""
domain_abreviattion = self.domain_abbreviation(domain, self.frequency)
start = parse_date(startdate)
member_plus = str(member + 1)
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member_path = os.path.join(self.data_dir, self.expid, 'cmorfiles', startdate, self.get_member_str(member),
'outputs', 'output', self.institution, self.model, self.experiment_name,
'S' + startdate, self.frequency, domain)
chunk_start = chunk_start_date(start, chunk, self.chunk_size, 'month', 'standard')
chunk_end = chunk_end_date(chunk_start, self.chunk_size, 'month', 'standard')
chunk_end = previous_day(chunk_end, 'standard')
var_file = list()
for var in variables:
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if grid:
var_path = os.path.join(member_path, var, grid, 'r{0}i1p1'.format(member_plus))
else:
var_path = os.path.join(member_path, var, 'r{0}i1p1'.format(member_plus))
var_file.append(os.path.join(var_path,
'{7}-{8}.nc'.format(var, domain_abreviattion,
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self.frequency, self.model, self.experiment_name,
startdate, member_plus,
"{0:04}{1:02}".format(chunk_start.year,
chunk_start.month),
"{0:04}{1:02}".format(chunk_end.year,
chunk_end.month))))
file_names.append(var_file)
return file_names
def get_file(self, domain, var, startdate, member, chunk, grid=None, box=None, frequency=None):
"""
Copies a given file from the CMOR repository to the scratch folder and returns the path to the scratch's copy
:param domain: CMOR domain
:type domain: str
:param var: variable name
:type var: str
:param startdate: file's startdate
:type startdate: str
:param member: file's member
:type member: int
:param chunk: file's chunk
:type chunk: int
:param grid: file's grid (only needed if it is not the original)
:type grid: str
:param box: file's box (only needed to retrieve sections or averages)
:type box: Box
:param frequency: file's frequency (only needed if it is different from the default)
:type frequency: str
:return: path to the copy created on the scratch folder
:rtype: str
"""
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if not frequency:
frequency = self.frequency
domain_abbreviation = self.domain_abbreviation(domain, frequency)
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start = parse_date(startdate)
member_plus = str(member + 1)
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member_path = os.path.join(self.data_dir, self.expid, 'cmorfiles', startdate, self.get_member_str(member),
'outputs', 'output', self.institution, self.model, self.experiment_name,
'S' + startdate, frequency, domain)
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chunk_start = chunk_start_date(start, chunk, self.chunk_size, 'month', 'standard')
chunk_end = chunk_end_date(chunk_start, self.chunk_size, 'month', 'standard')
chunk_end = previous_day(chunk_end, 'standard')
if box:
var += box.get_lon_str() + box.get_lat_str() + box.get_depth_str()
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if grid:
var_path = os.path.join(member_path, var, grid, 'r{0}i1p1'.format(member_plus))
else:
var_path = os.path.join(member_path, var, 'r{0}i1p1'.format(member_plus))
filepath = os.path.join(var_path, '{0}_{1}_{3}_{4}_S{5}_r{6}i1p1_'
'{7}-{8}.nc'.format(var, domain_abbreviation, frequency, self.model,
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self.experiment_name, startdate, member_plus,
"{0:04}{1:02}".format(chunk_start.year,
chunk_start.month),
"{0:04}{1:02}".format(chunk_end.year,
chunk_end.month)))
temp_path = TempFile.get()
shutil.copyfile(filepath, temp_path)
return temp_path
def send_file(self, filetosend, domain, var, startdate, member, chunk=None, grid=None, region=None, box=None,
rename_var=None, frequency=None, year=None, date_str=None):
"""
Copies a given file to the CMOR repository. It also automatically converts to netCDF 4 if needed and can merge
with already existing ones as needed
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
:param year: if frequency is yearly, this parameter is used to give the corresponding year
:type year: int
:param rename_var: if exists, the given variable will be renamed to the one given by var
:type rename_var: str
:param filetosend: path to the file to send to the CMOR repository
:type filetosend: str
:param region: specifies the region represented by the file. If it is defined, the data will be appended to the
CMOR repository as a new region in the file or will overwrite if region was already present
:type region: str
:param domain: CMOR domain
:type domain: str
:param var: variable name
:type var: str
:param startdate: file's startdate
:type startdate: str
:param member: file's member
:type member: int
:param chunk: file's chunk
:type chunk: int
:param grid: file's grid (only needed if it is not the original)
:type grid: str
:param box: file's box (only needed to retrieve sections or averages)
:type box: Box
:param frequency: file's frequency (only needed if it is different from the default)
:type frequency: str
:return: path to the copy created on the scratch folder
:rtype: str
"""
if box:
var += box.get_lon_str() + box.get_lat_str() + box.get_depth_str()
if rename_var:
Utils.rename_variable(filetosend, rename_var, var)
if not frequency:
frequency = self.frequency
domain_abreviattion = self.domain_abbreviation(domain, frequency)
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start = parse_date(startdate)
member_plus = str(member + 1)
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member_path = os.path.join(self.data_dir, self.expid, 'cmorfiles', startdate, self.get_member_str(member),
'outputs', 'output', self.institution, self.model, self.experiment_name,
'S' + startdate,
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if chunk is not None:
chunk_start = chunk_start_date(start, chunk, self.chunk_size, 'month', 'standard')
chunk_end = chunk_end_date(chunk_start, self.chunk_size, 'month', 'standard')
chunk_end = previous_day(chunk_end, 'standard')
time_bound = "{0:04}{1:02}-{2:04}{3:02}".format(chunk_start.year, chunk_start.month, chunk_end.year,
chunk_end.month)
elif year is not None:
if frequency is not 'yr':
raise ValueError('Year may be provided instead of chunk only if frequency is "yr"')
time_bound = str(year)
elif date_str is not None:
time_bound = date_str
else:
raise ValueError('Chunk and year can not be None at the same time')
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if grid:
var_path = os.path.join(member_path, var, grid, 'r{0}i1p1'.format(member_plus))
else:
var_path = os.path.join(member_path, var, 'r{0}i1p1'.format(member_plus))
filepath = os.path.join(var_path, '{0}_{1}_{2}_{3}_S{4}_r{5}i1p1_'
'{6}.nc'.format(var, domain_abreviattion, self.model,
self.experiment_name, startdate, member_plus, time_bound))
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if region:
Utils.convert2netcdf4(filetosend)
if not os.path.exists(filepath):
handler = Utils.openCdf(filetosend)
handler.createDimension('region')
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var_region = handler.createVariable('region', str, 'region')
var_region[0] = region
original_var = handler.variables[var]
new_var = handler.createVariable('new_var', original_var.datatype,
original_var.dimensions + ('region',))
new_var.setncatts({k: original_var.getncattr(k) for k in original_var.ncattrs()})
value = original_var[:]
new_var[..., 0] = value
handler.close()
Utils.nco.ncks(input=filetosend, output=filetosend, options='-O -x -v {0}'.format(var))
Utils.rename_variable(filetosend, 'new_var', var)
else:
temp = TempFile.get()
shutil.copyfile(filepath, temp)
Utils.nco.ncks(input=temp, output=temp, options='-O --mk_rec_dmn region')
handler = Utils.openCdf(temp)
handler_send = Utils.openCdf(filetosend)
value = handler_send.variables[var][:]
var_region = handler.variables['region']
basin_index = np.where(var_region[:] == region)
if len(basin_index[0]) == 0:
var_region[var_region.shape[0]] = region
basin_index = var_region.shape[0] - 1
else:
basin_index = basin_index[0][0]
handler.variables[var][..., basin_index] = value
handler.close()
handler_send.close()
Utils.move_file(temp, filetosend)
Utils.nco.ncks(input=filetosend, output=filetosend, options='-O --fix_rec_dmn region')
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temp = TempFile.get()
Utils.execute_shell_command(["nccopy", "-4", "-d4", "-s", filetosend, temp])
shutil.move(temp, filetosend)
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Utils.move_file(filetosend, filepath)
if frequency in ('d', 'daily', 'day'):
freq_str = 'daily_mean'
else:
freq_str = 'monthly_mean'
if domain in ['ocean', 'seaIce']:
link_path = os.path.join(self.data_dir, self.expid, freq_str, '{0}_f6h'.format(var))
else:
link_path = os.path.join(self.data_dir, self.expid, freq_str, '{0}_f{1}h'.format(var, self.nfrp))
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if not os.path.exists(link_path):
# This can be a race condition
# noinspection PyBroadException
try:
os.makedirs(link_path)
except Exception:
pass
link_path = os.path.join(link_path, os.path.basename(filepath))
if os.path.lexists(link_path):
os.remove(link_path)
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os.symlink(filepath, link_path)
@staticmethod
def domain_abbreviation(domain, frequency):
"""
Returns the table name for a domain-frequency pair
:param domain: variable's domain
:type domain: str
:param frequency: variable's frequency
:type frequency: str
:return: variable's table name
:rtype: str
"""
if frequency == 'mon':
if domain == 'seaIce':
domain_abreviattion = 'OImon'
elif domain == 'landIce':
domain_abreviattion = 'LImon'
else:
domain_abreviattion = domain[0].upper() + 'mon'
elif frequency == '6hr':
domain_abreviattion = '6hrPlev'
else:
domain_abreviattion = 'day'
return domain_abreviattion
def get_year(self, domain, var, startdate, member, year, grid=None, box=None):
Gets all the data corresponding to a given year from the CMOR repository to the scratch folder as one file and
returns the path to the scratch's copy.
:param year: year to retrieve
:type year: int
:param domain: CMOR domain
:type domain: str
:param var: variable name
:type var: str
:param startdate: file's startdate
:type startdate: str
:param member: file's member
:type member: int
:param grid: file's grid (only needed if it is not the original)
:type grid: str
:param box: file's box (only needed to retrieve sections or averages)
:type box: Box
:return: path to the copy created on the scratch folder
:rtype: str
"""
chunk_files = list()
for chunk in self.get_year_chunks(startdate, year):
chunk_files.append(self.get_file(domain, var, startdate, member, chunk, grid=grid, box=box))
if len(chunk_files) > 1:
temp = TempFile.get()
Utils.nco.ncrcat(input=' '.join(chunk_files), output=temp)
for chunk_file in chunk_files:
os.remove(chunk_file)
else:
temp = chunk_files[0]
temp2 = TempFile.get()
handler = Utils.openCdf(temp)
time = Utils.get_datetime_from_netcdf(handler)
handler.close()
start = None
end = None
for x in range(0, len(time)):
date = time[x]
if date.year == year:
if date.month == 1:
start = x
elif date.month == 12:
end = x
Utils.nco.ncks(input=temp, output=temp2, options='-O -d time,{0},{1}'.format(start, end))
os.remove(temp)
return temp2
def get_year_chunks(self, startdate, year):
"""
Get the list of chunks containing timesteps from the given year
:param startdate: startdate to use
:type startdate: str
:param year: reference year
:type year: int
:return: list of chunks containing data from the given year
:rtype: list[int]
date = parse_date(startdate)
chunks = list()
for chunk in range(1, self.num_chunks + 1):
chunk_start = chunk_start_date(date, chunk, self.chunk_size, 'month', self.calendar)
if chunk_start.year > year:
break
elif chunk_start.year == year or chunk_end_date(chunk_start, self.chunk_size, 'month',
self.calendar).year == year:
return chunks
def get_full_years(self, startdate):
"""
Returns the list of full years that are in the given startdate
:param startdate: startdate to use
:type startdate: str
:return: list of full years
:rtype: list[int]
"""
chunks_per_year = 12 / self.chunk_size
date = parse_date(startdate)
first_january = 0
first_year = date.year
if date.month != 1:
month = date.month
first_year += 1
while month + self.chunk_size < 12:
month += self.chunk_size
first_january += 1
years = list()
for chunk in range(first_january, self.num_chunks - chunks_per_year, chunks_per_year):
years.append(first_year)
first_year += 1
return years
def get_member_str(self, member):
"""
Returns the member name for a given member number.
:param member: member's number
:type member: int