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from parser import Parser
from autosubmit.config.log import Log
from earthdiagnostics.ocean import Salinity
from utils import Utils
from earthdiagnostics import cdftools
from autosubmit.date.chunk_date_lib import *
import shutil
import os
class Diags:
def __init__(self, config_file):
self._read_config(config_file)
Utils.scratch_folder = os.path.join(self.scratch_dir)
cdftools.path = self.cdftools_path
def run(self):
if not os.path.exists(self.scratch_dir):
os.makedirs(self.scratch_dir)
os.chdir(self.scratch_dir)
# Copy mesh files
Log.info('Copying mesh files')
shutil.copy(os.path.join(self.con_files, 'mesh_mask_nemo.{0}.nc'.format(self.nemo_version)), 'mesh_hgr.nc')
shutil.copy(os.path.join(self.con_files, 'mesh_mask_nemo.{0}.nc'.format(self.nemo_version)), 'mesh_zgr.nc')
shutil.copy(os.path.join(self.con_files, 'mesh_mask_nemo.{0}.nc'.format(self.nemo_version)), 'mask.nc')
shutil.copy(os.path.join(self.con_files, 'new_maskglo.{0}.nc'.format(self.nemo_version)), 'new_maskglo.nc')
# dic_variables = dict()
# dic_variables['x'] = 'i'
# dic_variables['y'] = 'j'
# dic_variables['z'] = 'lev'
# dic_variables['nav_lon'] = 'lon'
# dic_variables['nav_lat'] = 'lat'
# dic_variables['nav_lev'] = 'lev'
# dic_variables['time_counter'] = 'time'
# dic_variables['t'] = 'time'
#
# Utils.rename_variables('mesh_hgr.nc', dic_variables, False, True)
# Utils.rename_variables('mesh_zgr.nc', dic_variables, False, True)
# Utils.rename_variables('mask.nc', dic_variables, False, True)
if os.path.exists(os.path.join(self.con_files, 'mask.regions.{0}.nc'.format(self.nemo_version))):
shutil.copy(os.path.join(self.con_files, 'mask.regions.{0}.nc'.format(self.nemo_version)),
'mask_regions.nc')
# Check if cmorized and convert if not
# Run diagnostics
Log.info('Running diagnostics')
for diag in self.diags.split():
if diag == 'vert_mean_sal':
Log.info("Running vert_mean_sal")
min_depth = 0
max_depth = 300
for [input_file, output_file] in self._get_file_names('ocean', 'so',
'vertmeansal'.format(min_depth, max_depth)):
Salinity.vertical_mean(str(input_file), str(output_file), min_depth, max_depth)
Log.result('Finished vert_mean_sal')
Utils.clean()
def _read_config(self, config_file):
self.parser = Parser()
self.parser.optionxform = str
self.parser.read(config_file)
# Read diags config
self.scratch_dir = self.parser.get_option('DIAGNOSTICS', 'SCRATCH_DIR')
self.data_dir = self.parser.get_option('DIAGNOSTICS', 'DATA_DIR')
self.con_files = self.parser.get_option('DIAGNOSTICS', 'CON_FILES')
self.diags = self.parser.get_option('DIAGNOSTICS', 'DIAGS')
self.frequency = self.parser.get_option('DIAGNOSTICS', 'FREQUENCY')
self.cdftools_path = self.parser.get_option('DIAGNOSTICS', 'CDFTOOLS_PATH')
# Read experiment config
self.institute = self.parser.get_option('EXPERIMENT', 'INSTITUTE')
self.expid = self.parser.get_option('EXPERIMENT', 'EXPID')
self.members = self.parser.get_option('EXPERIMENT', 'MEMBERS')
self.startdates = self.parser.get_option('EXPERIMENT', 'STARTDATES')
self.chunk_size = self.parser.get_int_option('EXPERIMENT', 'CHUNK_SIZE')
self.chunks = self.parser.get_int_option('EXPERIMENT', 'CHUNKS')
self.model = self.parser.get_option('EXPERIMENT', 'MODEL')
self.nemo_version = self.parser.get_option('EXPERIMENT', 'NEMO_VERSION')
self.scratch_dir = os.path.join(self.scratch_dir, 'diags', self.expid)
def _get_file_names(self, domain, input_var, output_var):
file_names = list()
for startdate in self.startdates.split():
start = parse_date(startdate)
for member in self.members:
member_plus = str(int(member)+1)
member_path = os.path.join(self.data_dir,self.expid, startdate, 'fc'+member, 'outputs', 'output',
self.institute, self.model, self.model, 'S'+startdate, self.frequency,
domain)
for chunk in range(1, self.chunks + 1):
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')
input_file = os.path.join(member_path, input_var, 'r{0}i1p1'.format(member_plus),
'{0}_{1[0]}{2}_{3}_output_r{4}i1p1_'
'{5}-{6}.nc'.format(input_var, domain.upper(),
self.frequency, self.model, member_plus,
"{0:04}{1:02}".format(chunk_start.year,
chunk_start.month),
"{0:04}{1:02}".format(chunk_end.year,
chunk_end.month)))
output_file = os.path.join(member_path, input_var, 'r{0}i1p1'.format(member_plus),
'{0}_{1[0]}{2}_{3}_output_r{4}i1p1_'
'{5}-{6}.nc'.format(output_var, domain.upper(),
self.frequency, self.model, 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([input_file, output_file])
return file_names
def main():
Log.set_console_level(Log.DEBUG)
diags = Diags('/home/Earth/jvegas/pyCharm/ocean_diagnostics/earthdiagnostics/diags.conf')
diags.run()
# Utils.clean()
if __name__ == "__main__":
main()