def get_geocoords(infile, lat='lat', lon='lon'):
df = EcoFOCI_netCDF(infile)
nchandle = df._getnchandle_()
data = {}
for j, v in enumerate([lat, lon]):
data[v] = nchandle.variables[v][:]
df.close()
return (data)
def from_netcdf_1dsplice(infile, height_ind, lat_ind, lon_ind):
""" Uses ncreadfile_dic which returns a dictionary of all data from netcdf"""
###nc readin/out
df = EcoFOCI_netCDF(infile)
nchandle = df._getnchandle_()
params = df.get_vars() #gets all of them
print "Parameters available: "
#print params
ncdata = ncreadfile_dic_slice(nchandle, params, height_ind=height_ind, lat_ind=lat_ind, lon_ind=lon_ind)
df.close()
return ncdata
parser.add_argument('sourcefile',
metavar='sourcefile',
type=str,
help='path to .nc files')
parser.add_argument('add_dsg_idvar',
metavar='add_dsg_idvar',
type=str,
help='name of dsg style id variable')
args = parser.parse_args()
"---"
df = EcoFOCI_netCDF(args.sourcefile)
global_atts = df.get_global_atts()
vars_dic = df.get_vars()
nchandle = df._getnchandle_()
data = df.ncreadfile_dic()
try:
nchandle.createDimension('id_strlen', 5)
nchandle.createVariable('profileid',
'S1',
dimensions=('record_number', 'id_strlen'))
nchandle.variables['profileid'].cf_role = args.add_dsg_idvar
nchandle.variables['profileid'].long_name = 'profile_id'
except:
print "{0} - not added".format(args.add_dsg_idvar)
#fill with default values
profileid = args.sourcefile.split('/')[-1].split('.nc')[0].split('_')[1]
def repl_var(nchandle, var_name, val=1e35):
nchandle.variables[var_name][:] = np.ones_like(nchandle.variables[var_name][:]) * float(val)
return
"""------------------------------- MAIN--------------------------------------------"""
parser = argparse.ArgumentParser(description='Replace EPIC Variable with 1e35 for all depths')
parser.add_argument('sourcefile', metavar='sourcefile', type=str,
help='complete path to netcdf file')
parser.add_argument('user_var', metavar='user_var', type=str,
help='EPIC Key Code or variable name')
parser.add_argument('Value', metavar='Value', type=str,
help='replacement value')
args = parser.parse_args()
###nc readin
ncfile = args.sourcefile
df = EcoFOCI_netCDF(ncfile)
global_atts = df.get_global_atts()
vars_dic = df.get_vars()
data = df.ncreadfile_dic()
print ncfile.split('/')[-1]
repl_var(df._getnchandle_(), args.user_var, val=args.Value)
df.close()
#converttime to datetime
data_dati = EPIC2Datetime(ncdata['time'], ncdata['time2'])
data_dati = np.array(data_dati)
time_ind = (data_dati >= datetime.datetime.strptime(args.trim_bounds[0],'%Y-%m-%dT%H:%M:%S')) & \
(data_dati <= datetime.datetime.strptime(args.trim_bounds[1],'%Y-%m-%dT%H:%M:%S'))
#create new netcdf file
ncinstance = NetCDF_Trimmed_2D(savefile=(args.sourcefile).replace('.nc','.trimmed_missing.nc'))
ncinstance.file_create()
ncinstance.sbeglobal_atts(raw_data_file=global_atts['DATA_CMNT'], Station_Name=global_atts['MOORING'],
Water_Depth=global_atts['WATER_DEPTH'], Inst_Type=global_atts['INST_TYPE'],
Water_Mass=global_atts['WATER_MASS'], Experiment=global_atts['EXPERIMENT'],
Project=global_atts['PROJECT'])
ncinstance.dimension_init(time_len=len(ncdata['time'][time_ind]),depth_len=len(ncdata['depth']))
ncinstance.variable_init(df._getnchandle_())
ncinstance.add_coord_data(depth=ncdata['depth'], latitude=ncdata[lat], longitude=ncdata[lon],
time1=ncdata['time'][time_ind], time2=ncdata['time2'][time_ind])
ncinstance.add_data(data=ncdata, trim_index=time_ind)
ncinstance.add_history('Data Trimmed')
ncinstance.close()
elif args.isProfile:
sys.exit("Profiles rarely can be trimmed by date unless prawler or glider - exiting")
else:
df = EcoFOCI_netCDF( args.sourcefile )
global_atts = df.get_global_atts()
