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Javier Vegas-Regidor
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import shutil
import threading
import netCDF4
import numpy as np
from autosubmit.config.log import Log
from autosubmit.date.chunk_date_lib import parse_date, chunk_start_date, chunk_end_date, previous_day
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from earthdiagnostics import Utils, TempFile
def __init__(self, institution, model, expid, datafolder, frequency, chunk_size, experiment_name):
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
# noinspection PyPep8Naming
def prepare_CMOR_files(self, startdates, members):
# Check if cmorized and convert if not
if not os.path.exists(os.path.join(self.data_dir, self.expid)):
raise Exception('The experiment {0} is not CMORized. '
'Please, CMORize it and launch again.'.format(self.expid))
for startdate in startdates:
for member in members:
member_path = os.path.join(self.data_dir, self.expid, startdate, 'fc{0}'.format(member), 'outputs')
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Log.info('Preparing CMOR files for startdate {0} and member {1}'.format(startdate, member))
threads = list()
numthreads = Utils.available_cpu_count()
filepaths = glob.glob(os.path.join(member_path, '*.gz'))
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)
@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))
os.remove(filepath)
def get_files(self, startdate, member, chunk, domain, variables, grid=None):
file_names = list()
if domain == 'seaIce':
domain_abreviattion = 'OI'
else:
domain_abreviattion = domain[0].upper()
start = parse_date(startdate)
member_plus = str(member + 1)
member_path = os.path.join(self.data_dir, self.expid, startdate, 'fc' + 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,
'{0}_{1}{2}_{3}_{4}_S{5}_r{6}i1p1_'
'{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
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def get_file(self, domain, var, startdate, member, chunk, grid=None):
if domain == 'seaIce':
domain_abreviattion = 'OI'
else:
domain_abreviattion = domain[0].upper()
start = parse_date(startdate)
member_plus = str(member + 1)
member_path = os.path.join(self.data_dir, self.expid, startdate, 'fc' + 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')
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}_{4}_S{5}_r{6}i1p1_'
'{7}-{8}.nc'.format(var, domain_abreviattion, 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)))
temp_path = TempFile.get()
shutil.copyfile(filepath, temp_path)
return temp_path
def send_file(self, filetosend, domain, var, startdate, member, chunk, grid=None, region=None):
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if domain == 'seaIce':
domain_abreviattion = 'OI'
else:
domain_abreviattion = domain[0].upper()
start = parse_date(startdate)
member_plus = str(member + 1)
member_path = os.path.join(self.data_dir, self.expid, startdate, 'fc' + 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')
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}_{4}_S{5}_r{6}i1p1_'
'{7}-{8}.nc'.format(var, domain_abreviattion, 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)))
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if region:
if not os.path.exists(filepath):
Utils.convert2netcdf4(filetosend)
handler = Utils.cdo.openCdf(filetosend)
handler.createDimension('region')
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)
handler = Utils.cdo.openCdf(temp)
handler_send = Utils.cdo.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_send.variables[var][..., basin_index] = value
handler.close()
handler_send.close()
Utils.move_file(temp, filetosend)
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Utils.move_file(filetosend, filepath)
handler = netCDF4.Dataset('temp.nc', 'w')
handler.createDimension('time')
handler.createDimension('region')
var_time = handler.createVariable('time', float, 'time')
var_time[:] = [0, 1, 2]
var_region = handler.createVariable('region', str, 'region')
var_region[0] = 'region1'
var_content = handler.createVariable('content', float, ('time', 'region'))
var_content[:, 0] = [1, 2, 3]
handler.close()
handler = netCDF4.Dataset('temp.nc', 'a')
var_region = handler.variables['region']
var_region[1] = 'region2'
var_content = handler.variables['content']
var_content[..., 1] = [4, 5, 6]
handler.close()
Utils.execute_shell_command('ncdump temp.nc', Log.INFO)
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#
# set -vx
#
# exp=a034
# dir=/group_workspaces/jasmin2/primavera1/WP2/CPL/EC-EARTH3.1/HIST_T511ORCA025
# res=$( echo $dir | cut -f3 -d"_" )
# model=$(echo $dir | cut -f7 -d"/" )
#
# cd /esnas/exp/ecearth/$exp/
#
# for sd in [1-2]*
# do
# cd /esnas/exp/ecearth/$exp/$sd
# for fc in *
# do
# cd /esnas/exp/ecearth/$exp/$sd/$fc/outputs
# realization=$(( $(echo $fc | cut -c 3-) + 1 ))
# outdir=/esnas/exp/ecearth/$exp/$sd/$fc/outputs/primavera
# mkdir -p $outdir
# for tarfile in MMO*tar
# do
# lt=$(echo $tarfile | cut -f 5-6 -d"_" | cut -f1 -d"." )
# tar kxvf $tarfile -C $outdir
# cd $outdir
# for file in ${exp}_1m_*grid*gz ${exp}_*icemod*gz
# do
# echo $file
# gunzip $file
# for var in $( cdo showvar ${file%???} )
# do
# varnew=""
# case $var in
# votemper) varnew=thetao; realm=Omon ; modeling_realm="ocean" ; units="C";;
# vosaline) varnew=so; realm=Omon ; modeling_realm="ocean" ;;
# sosstsst) varnew=tos; realm=Omon ; modeling_realm="ocean" ; units="C";;
# sosaline) varnew=sos; realm=Omon ; modeling_realm="ocean" ;;
# sossheig) varnew=zos; realm=Omon ; modeling_realm="ocean" ;;
# vozocrtx) varnew=uo; realm=Omon ; modeling_realm="ocean" ;;
# vomecrty) varnew=vo; realm=Omon ; modeling_realm="ocean" ;;
# iiceconc) varnew=sic; realm=OImon ; modeling_realm="seaIce" ;;
# iicethic) varnew=sit; realm=OImon ; modeling_realm="seaIce" ;;
# isnowthi) varnew=snd; realm=OImon ; modeling_realm="seaIce" ;;
# iicesurt) varnew=tsice; realm=OImon ; modeling_realm="seaIce" ; units="C";;
# esac
# outfile=$(echo ${varnew}_${realm}_${model}_${res}_BSC_${realization}_${lt}.nc )
# if [[ ! -z $varnew ]] && [[ ! -f ${outdir}/${outfile} ]]; then #check if var belongs to list
# cdo selvar,$var ${file%???} ${outdir}/$outfile
# ncrename -v .time_counter,time -d time_counter,time -v nav_lon,longitude -v nav_lat,latitude -v .${var},${varnew} ${outdir}/${outfile}
# for att in institution institute_id experiment_id model_id contact experiment frequency creation_date project_id modeling_realm realization
# do
# case $att in
# institution) att_val="Barcelona Supercomputing Center - Centro Nacional de Supercomputacion" ;;
# institute_id) att_val="BSC-CNS" ;;
# experiment_id) att_val=$(echo $dir | cut -f7 -d"/") ;;
# model_id) att_val="$model" ;;
# contact) att_val="pierre-antoine.bretonniere@bsc.es" ;;
# experiment) att_val=$(echo $dir | cut -f7 -d"/") ;;
# frequency) att_val="mon" ;;
# creation_date) att_val="$(echo $(date --rfc-3339=seconds | cut -f1 -d"+" | sed -e 's/ /T/')Z)" ;;
# project_id) att_val="PRIMAVERA" ;;
# modeling_realm) att_val="$modeling_realm" ;;
# realization) att_val="$realization" ;;
# esac
# ncatted -O -h -a ${att},global,c,c,"${att_val}" ${outdir}/$outfile
# if [[ "$units" == "C" ]]; then
# cdo addc,273.25 ${outdir}/$outfile ${outdir}/${outfile}.tmp
# mv ${outdir}/${outfile}.tmp ${outdir}/${outfile}
# ncatted -O -h -a units,${varnew},m,c,"K" ${outdir}/$outfile
# fi #temp from C to K
# done #attributes
# fi
# done #var
# rm ${file%???}
# done #file
# cd /esnas/exp/ecearth/$exp/$sd/$fc/outputs
# done #tarfile
# scp -i ~/.ssh/id_rsa_jasmin ${outdir}/*Omon*nc pabretonniere@jasmin-xfer1.ceda.ac.uk:$dir/.
# scp -i ~/.ssh/id_rsa_jasmin ${outdir}/*OImon*nc pabretonniere@jasmin-xfer1.ceda.ac.uk:$dir/.
# done #fc
# done #sd