def multi_call_test():
cmor.setup(inpath='Tables',netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_jamie_2.json")
table='CMIP6_Amon.json'
cmor.load_table(table)
axes = [ {'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids)
cmor.write(varid, [275], time_vals = [15], time_bnds = [ [0,30] ])
print 'First write worked as expected'
try:
cmor.write(varid, [275], time_vals = [15], time_bnds = [ [0], [30] ])
raise Exception,"We shouldn't be getting in here"
except:
print 'Second write that should have failed did fail, good!'
pass
cmor.close(varid)
print 'Success'
def test_yr(self):
table = 'Tables/CMIP6_Eyr.json'
cmor.load_table(table)
axes = [
{'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
'coord_vals': np.array([182.5, 547.5]),
'cell_bounds': [[0, 365], [365, 730]]},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]}
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('baresoilFrac', '%', axis_ids)
cmor.write(varid, [40, 60])
self.path = cmor.close(varid, file_name=True)
self.assertEqual(os.path.basename(self.path),
'baresoilFrac_Eyr_PCMDI-test-1-0_piControl-withism_'
'r11i1p1f1_gr_2000-2001.nc')
def test_mon(self):
table = 'Tables/CMIP6_Amon.json'
cmor.load_table(table)
axes = [
{'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
'coord_vals': np.array([15, 45]),
'cell_bounds': [[0, 30], [30, 60]]},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]}
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids)
cmor.write(varid, [273, 274])
self.path = cmor.close(varid, file_name=True)
self.assertEqual(os.path.basename(self.path),
'ts_Amon_PCMDI-test-1-0_piControl-withism_'
'r11i1p1f1_gr_200001-200002.nc')
def test_monclim_rounding_end_time(self):
"""
60 days since 2000-01-01 is 2000-03-01 00:00:00 and so this test makes
sure that an end date at the start of the month is displayed as the
previous month.
"""
table = 'Tables/CMIP6_Oclim.json'
cmor.load_table(table)
axes = [
{'table_entry': 'time2',
'units': 'days since 2000-01-01 00:00:00',
'coord_vals': np.array([15, 45]),
'cell_bounds': [[0, 31], [31, 60]]},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]}
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('difmxybo2d', 'm4 s-1', axis_ids)
cmor.write(varid, [273, 274])
self.path = cmor.close(varid, file_name=True)
self.assertEqual(os.path.basename(self.path),
'difmxybo_Oclim_PCMDI-test-1-0_piControl-withism_'
'r11i1p1f1_gr_200001-200002-clim.nc')
def test_fx(self):
table = 'Tables/CMIP6_fx.json'
cmor.load_table(table)
axes = [
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]}
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('orog', 'm', axis_ids)
cmor.write(varid, [273, 274])
self.path = cmor.close(varid, file_name=True)
self.assertEqual(os.path.basename(self.path),
'orog_fx_PCMDI-test-1-0_piControl-withism_'
'r11i1p1f1_gr.nc')
def test_hour_rounds_minutes(self):
table = 'Tables/CMIP6_E1hr.json'
cmor.load_table(table)
axes = [
{'table_entry': 'time1',
'units': 'minutes since 2000-01-01 00:00:00',
'coord_vals': np.array([12.6, 37.4])},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]}
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('psl', 'Pa', axis_ids)
cmor.write(varid, [99300, 100000])
self.path = cmor.close(varid, file_name=True)
self.assertEqual(os.path.basename(self.path),
'psl_E1hr_PCMDI-test-1-0_piControl-withism_'
'r11i1p1f1_gr_200001010013-200001010037.nc')
def test_subhr_rounds_seconds(self):
table = 'Tables/CMIP6_Esubhr.json'
cmor.load_table(table)
axes = [
{'table_entry': 'time1',
'units': 'seconds since 2000-01-01 00:00:00',
'coord_vals': np.array([750.4, 2250.6])},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]}
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('pr', 'kg m-2 s-1', axis_ids)
cmor.write(varid, [0.000005, 0.000006])
self.path = cmor.close(varid, file_name=True)
self.assertEqual(os.path.basename(self.path),
'pr_Esubhr_PCMDI-test-1-0_piControl-withism_'
'r11i1p1f1_gr_20000101001230-20000101003731.nc')
def test_hour_rounds_midnight(self):
table = 'Tables/CMIP6_6hrLev.json'
cmor.load_table(table)
axes = [
{'table_entry': 'time1',
'units': 'hours since 2000-01-01 00:00:00',
'coord_vals': np.array([23.99999, 30]),
'cell_bounds': [[20.99999, 27], [27, 33]]},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]}
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ps', 'Pa', axis_ids)
cmor.write(varid, [99300, 100000])
self.path = cmor.close(varid, file_name=True)
self.assertEqual(os.path.basename(self.path),
'ps_6hrLev_PCMDI-test-1-0_piControl-withism_'
'r11i1p1f1_gr_200001020000-200001020600.nc')
def test_day_rounds(self):
table = 'Tables/CMIP6_Eday.json'
cmor.load_table(table)
axes = [
{'table_entry': 'time',
'units': 'days since 1960-01-01 00:00:00',
'coord_vals': np.array([0.9999999, 1.9999999]),
'cell_bounds': [[0.9999999 - 0.5, 0.9999999 + 0.5],
[0.9999999 + 0.5, 0.9999999 + 1.5]]},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]}
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids)
cmor.write(varid, [303, 305])
self.path = cmor.close(varid, file_name=True)
self.assertEqual(os.path.basename(self.path),
'ts_Eday_PCMDI-test-1-0_piControl-withism_'
'r11i1p1f1_gr_19600102-19600103.nc')
def test_1hrclimmon(self):
table = 'Tables/CMIP6_E1hrClimMon.json'
cmor.load_table(table)
axes = [
{'table_entry': 'time3',
'units': 'minutes since 2000-01-01 00:00:00',
'coord_vals': np.array([12.5, 37.5]),
'cell_bounds': [[0., 25.], [25., 50.]]},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]}
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('rlut', 'W m-2', axis_ids, positive='up')
cmor.write(varid, [186, 190])
self.path = cmor.close(varid, file_name=True)
self.assertEqual(os.path.basename(self.path),
'rlut_E1hrClimMon_PCMDI-test-1-0_piControl-withism_'
'r11i1p1f1_gr_200001010000-200001010050-clim.nc')
def testCMIP6(self):
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/common_user_input_hier.json")
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010', coord_vals=numpy.array(
[0, 1, 2, 3, 4.]), cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
# ,time_vals=numpy.array([i,]),time_bnds=numpy.array([i,i+1]))
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
f = cdms2.open(cmor.get_final_filename() , 'r')
self.assertEqual(f.coder, "Denis Nadeau")
self.assertEqual(f.hierarchical_attr_setting, "information")
self.assertEqual(f.creator, "PCMDI")
self.assertEqual(f.model, "Ocean Model")
self.assertEqual(f.country, "USA")
f.close()
def testCMIP6(self):
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
filen = cmor.close()
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("tracking_id").split('/')[0]
self.assertNotIn("hdl:21.14100/", a)
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(
inpath='Tables',
netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_CMIP6_CV_badgridlabel.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
except:
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
testOK = self.getAssertTest()
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
# ------------------------------------------
# Check error after signal handler is back
# ------------------------------------------
self.assertIn("\"gs1n\"", testOK)
def path_test():
cmor.setup(inpath='Test',netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset('mytest2010030812', 'ukmo', 'HadCM3', '360_day',
institute_id="PCMDI",
model_id='HadCM3',forcing='co2')
table='CMIP5_Amon_YYYYMMDDHH'
cmor.load_table(table)
axes = [ {'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
'coord_vals': [15],
'cell_bounds': [0, 30]
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids)
cmor.write(varid, [273])
path=cmor.close(varid, file_name=True)
print "Saved file: ",path
def test_mode(mode):
cmor.setup(inpath="Tables", netcdf_file_action=mode)
cmor.dataset(
"pre-industrial control",
"ukmo",
"HadCM3",
"360_day",
institute_id="ukmo",
model_id="HadCM3",
forcing="TO",
contact="Derek Jeter",
history="some global history",
parent_experiment_id="lgm",
parent_experiment_rip="r1i1p1",
branch_time=0,
)
table = "CMIP5_fx"
cmor.load_table(table)
axes = [
{"table_entry": "latitude", "units": "degrees_north", "coord_vals": [0], "cell_bounds": [-1, 1]},
{"table_entry": "longitude", "units": "degrees_east", "coord_vals": [90], "cell_bounds": [89, 91]},
]
values = numpy.array([5000], numpy.float32)
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
for var, units in (("deptho", "m"),):
varid = cmor.variable(var, units, axis_ids, history="variable history")
cmor.write(varid, values)
fnm = cmor.close(varid, file_name=True)
cmor.close()
return fnm
def main():
cmor.setup(inpath='Tables',
netcdf_file_action = cmor.CMOR_REPLACE)
cmor.dataset('pre-industrial control', 'mohc', 'HadGEM2: source',
'360_day',
institute_id = 'ukmo',
model_id = 'HadGEM2',
history = 'some global history',
forcing = 'N/A',
parent_experiment_id = 'N/A',
parent_experiment_rip = 'N/A',
branch_time = 0.,
contact = 'bob')
table = 'CMIP5_6hrLev'
cmor.load_table(table)
axes = [ {'table_entry': 'time1',
'units': 'days since 2000-01-01 00:00:00',
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
{'table_entry': 'hybrid_height',
'coord_vals': [0, 1],
'cell_bounds': [[0., 0.5], [0.5, 1.]],
'units': 'm',
},
]
values = numpy.array([1.2,1.2], numpy.float32)
numpy.reshape(values, (2,1,1,1))
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
print 'cmor.axis calls complete'
cmor.zfactor(axis_ids[3], 'b', '', axis_ids[3:4], 'd', [0., 0.5], [[0., 0.25], [0.25, 1.]])
cmor.zfactor(axis_ids[3], 'orog', 'm', axis_ids[1:3], 'd', [[0.]])
print 'cmor.zfactor calls complete'
varid = cmor.variable('ua',
'm s-1',
axis_ids,
missing_value = -99
)
print 'cmor.variable call complete'
cmor.write(varid, values, time_vals = [6.0])
print 'cmor.write call complete'
cmor.close()
def testCMIP6(self):
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2000',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("further_info_url")
self.assertEqual(
"https://furtherinfo.es-doc.org/CMIP6.PCMDI.PCMDI-test-1-0.piControl-withism.none.r3i1p1f1",
a)
def TestCase(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_CMIP6_CV_badsourcetypeCHEMAER.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
except:
raise
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
def main():
missing = -99.
cmor.setup(inpath='Tables',
netcdf_file_action = cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_jamie_3.json")
table = 'CMIP6_Amon.json'
cmor.load_table(table)
axes = [ {'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
]
values = numpy.array([missing], numpy.float32)
myma = numpy.ma.masked_values(values, missing)
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids, missing_value = myma.fill_value)
cmor.write(varid, myma, time_vals = [15], time_bnds = [ [0,30] ])
cmor.close(varid)
def path_test():
cmor.setup(inpath='Test',netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_YYYMMDDHH_exp_fmt.json")
table='Tables/CMIP6_Amon.json'
cmor.load_table(table)
axes = [ {'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
'coord_vals': [15],
'cell_bounds': [0, 30]
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids)
cmor.write(varid, [273])
path=cmor.close(varid, file_name=True)
print "Saved file: ",path
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
global testOK
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.set_cur_dataset_attribute("source_id", "invalid")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
cmor.close()
except BaseException:
pass
self.assertCV("invalid")
def test():
cmor.setup(inpath='Tables',netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_obs4MIPs.json")
table='CMIP6_Amon.json'
cmor.load_table(table)
axes = [ {'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids)
cmor.write(varid, [275], time_vals = [15], time_bnds = [ [0,30] ])
cmor.close(varid)
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
global testOK
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_CMIP6_CV_trackingNoprefix.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
filen = cmor.close()
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("tracking_id").split('/')[0]
self.assertNotIn("hdl:21.14100/", a)
except:
raise
def testCMIP6(self):
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
try:
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.set_cur_dataset_attribute("grid_label", "gr-0")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
except BaseException:
pass
# ------------------------------------------
# Check error after signal handler is back
# ------------------------------------------
self.assertCV("\"gr-0\"")
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json(
"Test/test_python_CMIP6_CV_badsourcetypeCHEMAER.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
except BaseException:
pass
self.assertCV("invalid source")
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
global testOK
cmor.setup(inpath="Tables", netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_CMIP6_CV_furtherinfourl.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(
table_entry="time",
units="months since 2010",
coord_vals=numpy.array([0, 1, 2, 3, 4.0]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.0]),
)
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units="kg")
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
cmor.close()
except:
raise
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, "w", 0)
sys.stderr = os.fdopen(self.newstderr, "w", 0)
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("further_info_url")
self.assertEqual("http://furtherinfo.es-doc.org/CMIP6.NCC.MIROC-ESM.piControl-withism.none.r1i1p1f1", a)
def cmor_define_and_write(values, axes):
table = 'CMIP5_cfSites'
cmor.load_table(table)
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
igrid = cmor.grid([axis_ids[1]], [0.], [0.])
cmor.zfactor(axis_ids[2], 'b', axis_ids = [axis_ids[2]],
zfactor_values = range(2),
zfactor_bounds = [[x-0.5, x+0.5] for x in range(2)])
cmor.zfactor(axis_ids[2], 'orog', 'm', axis_ids = [igrid],
zfactor_values = [0])
ids_for_var = [axis_ids[0], igrid, axis_ids[2]]
varid = cmor.variable('tnhus',
's-1',
ids_for_var,
history = 'variable history',
missing_value = -99,
)
for time in [x * 1800./ 86400 for x in range(48)]:
time += 1./3600./24.
tr = cdtime.reltime(time,axes[0]["units"])
print "Writing: %.03f" % time,"|",tr.tocomp(cdtime.Calendar360),"|",tr.tocomp()
cmor.write(varid, values, time_vals = [time])
return varid
def cmor_define_and_write(values, axes):
table = 'CMIP6_cfSites.json'
cmor.load_table(table)
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
igrid = cmor.grid([axis_ids[1]], [0.], [0.])
cmor.zfactor(axis_ids[2], 'b', axis_ids = [axis_ids[2]],
zfactor_values = range(2),
zfactor_bounds = [[x-0.5, x+0.5] for x in range(2)])
cmor.zfactor(axis_ids[2], 'orog', 'm', axis_ids = [igrid],
zfactor_values = [0])
ids_for_var = [axis_ids[0], igrid, axis_ids[2]]
varid = cmor.variable('tnhus',
's-1',
ids_for_var,
history = 'variable history',
missing_value = -99,
)
for time in [x * 1800./ 86400 for x in range(48)]:
cmor.write(varid, values, time_vals = [time])
return varid
def cmor_define_and_write(values, axes):
table = 'CMIP5_day'
cmor.load_table(table)
axis_ids = list()
for axis in axes:
axis_ids.append(cmor.axis(**axis))
varid = cmor.variable('rlut',
'W m-2',
axis_ids,
history='variable history',
missing_value=-99,
positive='up'
)
for time in (15, 16, 17):
cmor.write(
varid,
values,
time_vals=[time],
time_bnds=[
time -
0.45,
time +
0.45])
def testCMIP6(self):
try:
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.set_cur_dataset_attribute("experiment_id", "piControlbad")
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010', coord_vals=numpy.array(
[0, 1, 2, 3, 4.]), cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
# ,time_vals=numpy.array([i,]),time_bnds=numpy.array([i,i+1]))
cmor.write(ivar, data[i:i])
cmor.close()
except BaseException:
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
testOK = self.getAssertTest()
self.assertIn('piControlbad', testOK)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
clisccp = FISCCP1_COSP with plev7c, and tau
"""
cmor.write(varid,
data['FISCCP1_COSP'][index, :],
time_vals=timeval,
time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
mmrbc = bc_a1 + bc_a4 + bc_c1 + bc_c4
"""
outdata = data['bc_a1'][index, :] + data['bc_a4'][index, :] + \
data['bc_c1'][index, :] + data['bc_c4'][index, :]
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
drybc = bc_a1DDF + bc_c1DDF + bc_a4DDF + bc_c4DDF
"""
outdata = data['bc_a1DDF'][index, :] + data['bc_c1DDF'][index, :] + \
data['bc_a4DDF'][index, :] + data['bc_c4DDF'][index, :]
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
tauv = -TAUY
"""
cmor.write(varid,
-1 * data[RAW_VARIABLES[0]][index, :],
time_vals=timeval,
time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
tran = QSOIL + QVEGT
"""
outdata = data['QVEGT'][index, :] + data['QSOIL'][index, :]
if kwargs.get('simple'):
return outdata
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
so4_a1 = so4_a1
"""
cmor.write(varid,
data['so4_a1'][index, :],
time_vals=timeval,
time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
rsuscs = FSDSC - FSNSC
"""
outdata = data['FSDSC'][index, :] - data['FSNSC'][index, :]
if kwargs.get('simple'):
return outdata
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
rsus = FSDS - FSNS
"""
outdata = data['FSDS'][index, :].values - data['FSNS'][index, :].values
if kwargs.get('simple'):
return outdata
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
va = V
"""
cmor.write(varid,
data['V'][index, :],
time_vals=timeval,
time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
drydust = dst_a1DDF + dst_a3DDF + dst_c1DDF + dst_c3DDF
"""
outdata = data['dst_a1DDF'][index, :] + data['dst_a3DDF'][index, :] + \
data['dst_c1DDF'][index, :] + data['dst_c3DDF'][index, :]
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
lai = LAISHA + LAISUN
"""
outdata = data['LAISHA'][index, :] + data['LAISUN'][index, :]
if kwargs.get('simple'):
return outdata
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def define_write_var(axis_ids, entry, unit, values):
varid = cmor.variable(entry, unit, axis_ids, missing_value=-99)
print 'cmor.variable call complete'
cmor.write(varid, values, time_vals=[15.0], time_bnds=[0., 30.0])
print 'cmor.write call complete'
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
prsn = (PRECSC + PRECSL) * 1000.0
"""
outdata = (data['PRECSC'][index, :] + data['PRECSL'][index, :]) * 1000.0
if kwargs.get('simple'):
return outdata
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
o3 = O3
"""
outdata = data[RAW_VARIABLES[0]][index, :]
if kwargs.get('simple'):
return outdata
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
rlus = FLDS + FLNS
"""
cmor.write(varid,
data['FLDS'][index, :] + data['FLNS'][index, :],
time_vals=timeval,
time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
rlus = FLDS + FLNS
"""
outdata = data['FLDS'][index, :] + data['FLNS'][index, :]
if kwargs.get('simple'):
return outdata
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
clt = CLDTOT * 100.0
"""
cmor.write(varid,
data['CLDTOT'][index, :] * 100.0,
time_vals=timeval,
time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
wetbc = bc_a1SFWET + bc_a4SFWET + bc_c1SFWET + bc_c4SFWET
"""
outdata = data['bc_a1SFWET'][index, :] + data['bc_a4SFWET'][index, :] + \
data['bc_c1SFWET'][index, :] + data['bc_c4SFWET'][index, :]
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
mmrdust = dst_a1 + dst_a3 + dst_c1 + dst_c4
"""
outdata = data['dst_a1'][index, :] + data['dst_a3'][index, :] + \
data['dst_c1'][index, :] + data['dst_c4'][index, :]
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
SO2 --> so2
"""
cmor.write(varid,
data['SO2'][index, :],
time_vals=timeval,
time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
rsus = FSDS - FSNS
"""
cmor.write(varid,
data['FSDS'][index, :] - data['FSNS'][index, :],
time_vals=timeval,
time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
clcalipso = CLD_CAL with alt40 levels
"""
cmor.write(varid,
data[RAW_VARIABLES[0]][index, :],
time_vals=timeval,
time_bnds=timebnds)
def main():
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE_3)
cmor.dataset('pre-industrial control',
'ukmo',
'HadCM3',
'360_day',
institute_id='ukmo',
model_id='HadCM3',
history='some global history',
forcing='N/A',
parent_experiment_id='N/A',
parent_experiment_rip='N/A',
branch_time=0.,
contact='bob')
table = 'CMIP5_Amon'
cmor.load_table(table)
axes = [
{
'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
},
{
'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]
},
{
'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]
},
]
values = numpy.array([1.], numpy.float32) + 200
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
for var, units, positive in (
('ts', 'K', ''),
('rsut', 'W m-2', 'up'),
('rlut', 'W m-2', 'down'),
):
varid = cmor.variable(var,
units,
axis_ids,
history='variable history',
missing_value=-99,
positive=positive)
cmor.write(varid, values, time_vals=[15], time_bnds=[[0, 30]])
cmor.close()
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
mmrso4 = so4_a1 + so4_a2 + so4_a3 + so4_c1 + so4_c2 + so4_c3
"""
outdata = data['so4_a1'][index, :] + data['so4_a2'][index, :] + \
data['so4_a3'][index, :] + data['so4_c1'][index, :] + \
data['so4_c2'][index, :] + data['so4_c3'][index, :]
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
outdata = data["FLUT"][index, :].values
if kwargs.get('simple'):
return outdata
cmor.write(
varid,
outdata,
time_vals=timeval,
time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
cLitter = (TOTLITC + CWDC)/1000.0
"""
outdata = (data['TOTLITC'][index, :] + data['CWDC'][index, :]) / 1000.0
if kwargs.get('simple'):
return outdata
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
return outdata
def path_test():
cmor.setup(inpath='TestTables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/CMOR_input_example.json")
table = 'CMIP6_Amon.json'
cmor.load_table(table)
axes = [
{
'table_entry': 'time2',
'units': 'months since 2000-01-01 00:00:00',
# 'coord_vals': times,
# 'cell_bounds': times_bnds,
},
{
'table_entry':
'plev19',
'units':
'Pa',
'coord_vals': [
100000., 92500., 85000., 70000., 60000., 50000., 40000.,
30000., 25000., 20000., 15000., 10000., 7000., 5000., 3000.,
2000., 1000., 500, 100
]
},
{
'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]
},
{
'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]
},
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('co2Clim', '1.e-6', axis_ids)
import numpy
data = numpy.array([3, 4, 5])
data.resize((3, 19, 1, 1))
# cmor.write(varid, data)
# for i in range(len(data)):
# cmor.write(varid, data[i], time_vals=times[i], time_bnds=times_bnds[i])
cmor.write(varid,
data,
time_vals=[12, 15, 18],
time_bnds=[[10, 1234], [12, 1125], [15, 1128]])
path = cmor.close(varid, file_name=True)
print(path)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
rldscs = FLDS + FLNS - FLNSC
"""
outdata = data['FLDS'][index, :].values + \
data['FLNS'][index, :].values - data['FLNSC'][index, :].values
if kwargs.get('simple'):
return outdata
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
dryso4 = so4_a1DDF + so4_c1DDF + so4_a2DDF + so4_c2DDF + so4_a3DDF + so4_c3DDF
"""
outdata = data['so4_a1DDF'][index, :] + data['so4_c1DDF'][index, :] + \
data['so4_a2DDF'][index, :] + data['so4_c2DDF'][index, :] + \
data['so4_a3DDF'][index, :] + data['so4_c3DDF'][index, :]
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)
def write_data(varid, data, timeval, timebnds, index, **kwargs):
"""
rlut = FSNTOA - FSNT + FLNT
"""
outdata = data['FSNTOA'][index, :].values - \
data['FSNT'][index, :].values + data['FLNT'][index, :].values
if kwargs.get('simple'):
return outdata
cmor.write(varid, outdata, time_vals=timeval, time_bnds=timebnds)