},
]
axisIds = list()
# Create list of axes
for axis in axes:
axisId = cmor.axis(**axis)
axisIds.append(axisId)
#pdb.set_trace() ; # Debug statement
# Setup units and create variable to write using cmor - see https://cmor.llnl.gov/mydoc_cmor3_api/#cmor_set_variable_attribute
d1.units = outputUnits[fi]
varid = cmor.variable(outputVarName[fi],
d1.units,
axisIds,
missing_value=d1.missing)
values = np.array(d1[:], np.float32)
# Append valid_min and valid_max to variable before writing using cmor - see https://cmor.llnl.gov/mydoc_cmor3_api/#cmor_set_variable_attribute
#cmor.set_variable_attribute(varid,'valid_min','f',2.0)
#cmor.set_variable_attribute(varid,'valid_max','f',3.0)
# Prepare variable for writing, then write and close file - see https://cmor.llnl.gov/mydoc_cmor3_api/#cmor_set_variable_attribute
cmor.set_deflate(varid, 1, 1, 1)
# shuffle=1,deflate=1,deflate_level=1 - Deflate options compress file data
cmor.write(varid, values, time_vals=time[:], time_bnds=time.getBounds())
# Write variable with time axis
f.close()
cmor.close()
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': lat[:],
'cell_bounds': lat.getBounds()},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': lon[:],
'cell_bounds': lon.getBounds()},
]
axisIds = list() ; # Create list of axes
for axis in axes:
axisId = cmor.axis(**axis)
axisIds.append(axisId)
#pdb.set_trace() ; # Debug statement
# Setup units and create variable to write using cmor - see https://cmor.llnl.gov/mydoc_cmor3_api/#cmor_set_variable_attribute
d.units = outputUnits
varid = cmor.variable(outputVarName,d.units,axisIds,missing_value=d.missing)
values = np.array(d[:],np.float32)
# Append valid_min and valid_max to variable before writing using cmor - see https://cmor.llnl.gov/mydoc_cmor3_api/#cmor_set_variable_attribute
cmor.set_variable_attribute(varid,'valid_min','f',2.0)
cmor.set_variable_attribute(varid,'valid_max','f',3.0)
# Prepare variable for writing, then write and close file - see https://cmor.llnl.gov/mydoc_cmor3_api/#cmor_set_variable_attribute
cmor.set_deflate(varid,1,1,1) ; # shuffle=1,deflate=1,deflate_level=1 - Deflate options compress file data
cmor.write(varid,values,time_vals=time[:],time_bnds=time.getBounds()) ; # Write variable with time axis
f.close()
cmor.close()
myaxes[2] = cmor.axis(table_entry = 'time',
units = s.getTime().units,
coord_vals = s.getTime()[:],cell_bounds=s.getTime().getBounds())
pass_axes = [myaxes[2],myaxes[0],myaxes[1]]
myvars[0] = cmor.variable( table_entry = varout,
units = s.units,
axis_ids = pass_axes,
original_name = s.id,
history = 'no history',
comment = 'testing speed'
)
cmor.set_deflate(myvars[0], shuffle, 1, level)
import time,MV2
st = time.time()
totcmor=0
totcdms=0
maxcmor=0
mincmor=1000
maxcdms=0
mincdms=1000
c0=st
f=cdms2.open("Test/crap.nc","w")
#print 'Time:',i
print s.filled().shape
cmor.write(myvars[0],s.filled(),ntimes_passed=ntimes)
c=time.time()
#pdb.set_trace() ; # Debug statement
# Setup units and create variable to write using cmor - see https://cmor.llnl.gov/mydoc_cmor3_api/#cmor_set_variable_attribute
d.units = outputUnits
if inputDict[key][var]['positive'] == 'down':
varid = cmor.variable(outputVarName,d.units,axisIds,missing_value=d.missing,positive='down')
else:
varid = cmor.variable(outputVarName,d.units,axisIds,missing_value=d.missing) ; # This is not trapping the correct missing_value
values = np.array(d[:],np.float32)
# Append valid_min and valid_max to variable before writing - see https://cmor.llnl.gov/mydoc_cmor3_api/#cmor_set_variable_attribute
#cmor.set_variable_attribute(varid,'valid_min','f',2.0)
#cmor.set_variable_attribute(varid,'valid_max','f',3.0)
# Prepare variable for writing, then write and close file - see https://cmor.llnl.gov/mydoc_cmor3_api/#cmor_set_variable_attribute
cmor.set_deflate(varid,1,1,1) ; # shuffle=1,deflate=1,deflate_level=1 - Deflate options compress file data
print 'Start CMOR write..'
if key == 'OmonC':
cmor.write(varid,values) ; # Write variable with time axis
elif key == 'OyrC':
cmor.write(varid,values) ; # Write variable with time axis
elif key == 'LIyrC':
cmor.write(varid,values) ; # Write variable with time axis
elif key == 'Ofx':
cmor.write(varid,values) ; # Write variable without time axis
elif key == 'LIfx':
cmor.write(varid,values) ; # Write variable without time axis
else:
cmor.write(varid,values,time_vals=time,time_bnds=time.getBounds()) ; # Write variable with time axis
print 'End CMOR write..'
# Alteratively write in append mode
def main(args, opts):
print args
print opts
print 'python ./cmor4alma.gswp3.py ALAM_VarName'
print '----------------------------------------' + '\n'
almavn = args[0]
alma = ALMA(almavn)
# read json file &
# Update frequency based on variable and write output to CMOR input file
prjJson = json.load(open('./gswp3-do-input.json'))
prjJson['frequency'] = alma.cmorjson('variable_entry')['frequency']
json.dump(prjJson,
open('tmp.json', 'w'),
ensure_ascii=True,
encoding='utf-8',
sort_keys=True)
print '=' * 80
print 'CMOR Table Path:', alma.tblpath
for srcpath in alma.fileList:
print srcpath
f = cdm.open(srcpath)
d = f(alma.varname)
# Or use temporal subset for testing below
# Reset missing value
d.setMissing(1e20)
# This should also set fill_value, and suppress CMOR variable history being written
# Get axes
lat = d.getLatitude()
lon = d.getLongitude()
time = d.getTime()
# Assumes variable is named 'time', for the demo file this is named 'months'
#%% Initialize and run CMOR
print 'Start CMORizing..'
# For more information see https://cmor.llnl.gov/mydoc_cmor3_api/
cmor.setup(
inpath='./',
netcdf_file_action=cmor.CMOR_REPLACE_4) #,logfile='cmorLog.txt')
cmor.dataset_json('tmp.json')
cmor.load_table(alma.tblpath)
if hasattr(alma, 'heightEntry'):
axisIds = [
cmor.axis(**CMORAxes.get_timeAx(alma, time)),
cmor.axis(**CMORAxes.get_heightAx(alma, cdm)),
cmor.axis(**CMORAxes.get_latitudalAx(lat)),
cmor.axis(**CMORAxes.get_longitudalAx(lon)),
]
else:
axisIds = [
cmor.axis(**CMORAxes.get_timeAx(alma, time)),
cmor.axis(**CMORAxes.get_latitudalAx(lat)),
cmor.axis(**CMORAxes.get_longitudalAx(lon)),
]
print axisIds
# Setup units and create variable to write using cmor - see https://cmor.llnl.gov/mydoc_cmor3_api/#cmor_set_variable_attribute
d.units = alma.outputUnits
varid = cmor.variable(alma.outputVarName,
d.units,
axisIds,
missing_value=d.missing,
positive=alma.positive)
values = np.array(d[:], np.float32)
cmor.set_deflate(varid, 1, 1, 1)
# shuffle=1,deflate=1,deflate_level=1 - Deflate options compress file data
# Write variable with time axis
cmor.write(varid, values, time_vals=time, time_bnds=time.getBounds())
f.close()
cmor.close()
os.remove('tmp.json')
return
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': lat[:],
'cell_bounds': lat.getBounds()},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': lon[:],
'cell_bounds': lon.getBounds()},
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable(var.id,var.units,axis_ids)
values = np.array(d[:],np.float32)
cmor.set_deflate(varid,1,1,1) ; # shuffle=1,deflate=1,deflate_level=1 ; CMOR 3.0.6+
cmor.write(varid,values,time_vals=time[:],time_bnds=time.getBounds())
f.close()
cmor.close()
# Cleanup
del(outFile,var,f,d,lat,lon,time) ; gc.collect()
# Write obs variables
if 'amipobs' in filePath:
cmor.setup(inpath='CMOR/input4MIPs-cmor-tables/Tables',netcdf_file_action=cmor.CMOR_REPLACE_4)
cmor.dataset_json("CMOR/drive_input4MIPs_obs.json")
f = cdm.open(outFile)
d = f[var.id]
lat = d.getLatitude()
lon = d.getLongitude()
time = d.getTime()