def test_calculate_internal_single_deployment(self):
ctd_ds = xr.open_dataset(os.path.join(DATA_DIR, self.ctdpf_fn),
decode_times=False)
ctd_ds = ctd_ds[[
'obs', 'time', 'deployment', 'temperature', 'pressure',
'pressure_temp', 'conductivity', 'ext_volt0'
]]
ctd_stream_dataset = StreamDataset(self.ctdpf_sk, {}, [], 'UNIT')
ctd_stream_dataset.events = self.ctd_events
ctd_stream_dataset._insert_dataset(ctd_ds)
ctd_stream_dataset.calculate_all()
for deployment in ctd_stream_dataset.datasets:
ds = ctd_stream_dataset.datasets[deployment]
tempwat = ctd_sbe16plus_tempwat(
ds.temperature,
ctd_stream_dataset.events.get_cal('CC_a0', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a1', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a2', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a3', deployment)[0][2])
np.testing.assert_array_equal(ds.seawater_temperature, tempwat)
pracsal = ctd_pracsal(ds.seawater_conductivity,
ds.seawater_temperature,
ds.seawater_pressure)
np.testing.assert_array_equal(ds.practical_salinity, pracsal)
def test_calculate_internal_multiple_deployments(self):
ctd_ds = xr.open_dataset(os.path.join(DATA_DIR, self.ctdpf_fn),
decode_times=False)
ctd_ds = ctd_ds[[
'obs', 'time', 'deployment', 'temperature', 'pressure',
'pressure_temp', 'conductivity', 'ext_volt0'
]]
# remap times to make this two separate deployments
dep1_start = self.ctd_events.deps[1].ntp_start
dep2_stop = self.ctd_events.deps[2].ntp_start + 864000
ctd_ds.time.values = np.linspace(dep1_start + 1,
dep2_stop - 1,
num=ctd_ds.time.shape[0])
ctd_stream_dataset = StreamDataset(self.ctdpf_sk, {}, [], 'UNIT')
ctd_stream_dataset.events = self.ctd_events
ctd_stream_dataset._insert_dataset(ctd_ds)
ctd_stream_dataset.calculate_all()
for deployment in ctd_stream_dataset.datasets:
ds = ctd_stream_dataset.datasets[deployment]
tempwat = ctd_sbe16plus_tempwat(
ds.temperature,
ctd_stream_dataset.events.get_cal('CC_a0', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a1', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a2', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a3', deployment)[0][2])
np.testing.assert_array_equal(ds.seawater_temperature, tempwat)
pracsal = ctd_pracsal(ds.seawater_conductivity,
ds.seawater_temperature,
ds.seawater_pressure)
np.testing.assert_array_equal(ds.practical_salinity, pracsal)
def test_calculate_internal_multiple_deployments(self):
ctd_ds = xr.open_dataset(os.path.join(DATA_DIR, self.ctdpf_fn), decode_times=False)
ctd_ds = ctd_ds[['obs', 'time', 'deployment', 'temperature', 'pressure',
'pressure_temp', 'conductivity', 'ext_volt0']]
# remap times to make this two separate deployments
dep1_start = self.ctd_events.deps[1].ntp_start
dep2_stop = self.ctd_events.deps[2].ntp_start + 864000
ctd_ds.time.values = np.linspace(dep1_start+1, dep2_stop-1, num=ctd_ds.time.shape[0])
ctd_stream_dataset = StreamDataset(self.ctdpf_sk, {}, [], 'UNIT')
ctd_stream_dataset.events = self.ctd_events
ctd_stream_dataset._insert_dataset(ctd_ds)
ctd_stream_dataset.calculate_all()
for deployment in ctd_stream_dataset.datasets:
ds = ctd_stream_dataset.datasets[deployment]
tempwat = ctd_sbe16plus_tempwat(ds.temperature,
ctd_stream_dataset.events.get_cal('CC_a0', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a1', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a2', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a3', deployment)[0][2])
np.testing.assert_array_equal(ds.seawater_temperature, tempwat)
pracsal = ctd_pracsal(ds.seawater_conductivity,
ds.seawater_temperature,
ds.seawater_pressure)
np.testing.assert_array_equal(ds.practical_salinity, pracsal)
def test_calculate_internal_multiple_deployments(self):
tr = TimeRange(3.65342400e+09, 3.65351040e+09)
coefficients = {k: [{'start': tr.start-1, 'stop': tr.stop+1, 'value': v, 'deployment': 1},
{'start': tr.start-1, 'stop': tr.stop+1, 'value': v, 'deployment': 2}]
for k, v in self.ctd_nutnr_cals.iteritems()}
coefficients = CalibrationCoefficientStore(coefficients, 'UNIT')
ctd_ds = xr.open_dataset(os.path.join(DATA_DIR, self.ctdpf_fn), decode_times=False)
ctd_ds = ctd_ds[['obs', 'time', 'deployment', 'temperature', 'pressure',
'pressure_temp', 'conductivity', 'ext_volt0']]
ctd_ds.deployment.values[:100000] = 1
ctd_ds.deployment.values[100000:] = 2
ctd_stream_dataset = StreamDataset(self.ctdpf_sk, coefficients, {}, [], 'UNIT')
ctd_stream_dataset._insert_dataset(ctd_ds)
ctd_stream_dataset.calculate_internal()
for ds in ctd_stream_dataset.datasets.itervalues():
tempwat = ctd_sbe16plus_tempwat(ds.temperature,
self.ctd_nutnr_cals['CC_a0'], self.ctd_nutnr_cals['CC_a1'],
self.ctd_nutnr_cals['CC_a2'], self.ctd_nutnr_cals['CC_a3'])
np.testing.assert_array_equal(ds.seawater_temperature, tempwat)
pracsal = ctd_pracsal(ds.seawater_conductivity,
ds.seawater_temperature,
ds.seawater_pressure)
np.testing.assert_array_equal(ds.practical_salinity, pracsal)
def test_calculate(self):
nutnr_sk = StreamKey('CE04OSPS', 'SF01B', '4A-NUTNRA102', 'streamed',
'nutnr_a_sample')
ctdpf_sk = StreamKey('CE04OSPS', 'SF01B', '2A-CTDPFA107', 'streamed',
'ctdpf_sbe43_sample')
nutnr_fn = 'nutnr_a_sample.nc'
ctdpf_fn = 'ctdpf_sbe43_sample.nc'
cals = json.load(open(os.path.join(DATA_DIR, 'cals.json')))
tr = TimeRange(3.65342400e+09, 3.65351040e+09)
coefficients = {
k: [{
'start': tr.start - 1,
'stop': tr.stop + 1,
'value': cals[k],
'deployment': 1
}]
for k in cals
}
sr = StreamRequest(nutnr_sk, [2443],
coefficients,
tr, {},
request_id='UNIT')
nutnr_ds = xr.open_dataset(os.path.join(DATA_DIR, nutnr_fn),
decode_times=False)
ctdpf_ds = xr.open_dataset(os.path.join(DATA_DIR, ctdpf_fn),
decode_times=False)
nutnr_ds = nutnr_ds[self.base_params +
[p.name for p in sr.stream_parameters[nutnr_sk]]]
ctdpf_ds = ctdpf_ds[self.base_params +
[p.name for p in sr.stream_parameters[ctdpf_sk]]]
sr.datasets[ctdpf_sk] = StreamDataset(ctdpf_sk, sr.coefficients,
sr.uflags, [nutnr_sk],
sr.request_id)
sr.datasets[nutnr_sk] = StreamDataset(nutnr_sk, sr.coefficients,
sr.uflags, [ctdpf_sk],
sr.request_id)
sr.datasets[ctdpf_sk]._insert_dataset(ctdpf_ds)
sr.datasets[nutnr_sk]._insert_dataset(nutnr_ds)
sr.calculate_derived_products()
ds = sr.datasets[ctdpf_sk]
tempwat = ctd_sbe16plus_tempwat(ds.datasets[0].temperature,
cals['CC_a0'], cals['CC_a1'],
cals['CC_a2'], cals['CC_a3'])
np.testing.assert_array_equal(ds.datasets[0].seawater_temperature,
tempwat)
pracsal = ctd_pracsal(ds.datasets[0].seawater_conductivity,
ds.datasets[0].seawater_temperature,
ds.datasets[0].seawater_pressure)
np.testing.assert_array_equal(ds.datasets[0].practical_salinity,
pracsal)
response = json.loads(JsonResponse(sr).json())
self.assertEqual(len(response), len(nutnr_ds.time.values))
def test_ctd_sbe16plus_tempwat(self):
"""
Test ctd_sbe16plus_tempwat function.
Values based on those described in DPS as available on Alfresco:
OOI (2012). Data Product Specification for Water Temperature. Document
Control Number 1341-00010. https://alfresco.oceanobservatories.org/
(See: Company Home >> OOI >> Controlled >> 1000 System Level >>
1341-00010_Data_Product_SPEC_TEMPWAT_OOI.pdf)
Implemented by Christopher Wingard, April 2013
"""
# test inputs
t0 = 248471
a0 = 1.281651e-3
a1 = 2.706002e-4
a2 = -1.027561e-6
a3 = 1.749446e-7
tout = ctdfunc.ctd_sbe16plus_tempwat(t0, a0, a1, a2, a3)
np.testing.assert_allclose(tout, 22.544681, rtol=1e-6, atol=0)
def test_ctd_sbe16plus_tempwat(self):
"""
Test ctd_sbe16plus_tempwat function.
Values based on those described in DPS as available on Alfresco:
OOI (2012). Data Product Specification for Water Temperature. Document
Control Number 1341-00010. https://alfresco.oceanobservatories.org/
(See: Company Home >> OOI >> Controlled >> 1000 System Level >>
1341-00010_Data_Product_SPEC_TEMPWAT_OOI.pdf)
Implemented by Christopher Wingard, April 2013
"""
# test inputs
t0 = 248471
a0 = 1.281651e-3
a1 = 2.706002e-4
a2 = -1.027561e-6
a3 = 1.749446e-7
tout = ctdfunc.ctd_sbe16plus_tempwat(t0, a0, a1, a2, a3)
np.testing.assert_allclose(tout, 22.544681, rtol=1e-6, atol=0)
def test_calculate_internal_single_deployment(self):
ctd_ds = xr.open_dataset(os.path.join(DATA_DIR, self.ctdpf_fn), decode_times=False)
ctd_ds = ctd_ds[['obs', 'time', 'deployment', 'temperature', 'pressure',
'pressure_temp', 'conductivity', 'ext_volt0']]
ctd_stream_dataset = StreamDataset(self.ctdpf_sk, {}, [], 'UNIT')
ctd_stream_dataset.events = self.ctd_events
ctd_stream_dataset._insert_dataset(ctd_ds)
ctd_stream_dataset.calculate_all()
for deployment in ctd_stream_dataset.datasets:
ds = ctd_stream_dataset.datasets[deployment]
tempwat = ctd_sbe16plus_tempwat(ds.temperature,
ctd_stream_dataset.events.get_cal('CC_a0', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a1', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a2', deployment)[0][2],
ctd_stream_dataset.events.get_cal('CC_a3', deployment)[0][2])
np.testing.assert_array_equal(ds.seawater_temperature, tempwat)
pracsal = ctd_pracsal(ds.seawater_conductivity,
ds.seawater_temperature,
ds.seawater_pressure)
np.testing.assert_array_equal(ds.practical_salinity, pracsal)
def test_calculate(self):
nutnr_sk = StreamKey('CE04OSPS', 'SF01B', '4A-NUTNRA102', 'streamed', 'nutnr_a_sample')
ctdpf_sk = StreamKey('CE04OSPS', 'SF01B', '2A-CTDPFA107', 'streamed', 'ctdpf_sbe43_sample')
nutnr_fn = 'nutnr_a_sample.nc'
ctdpf_fn = 'ctdpf_sbe43_sample.nc'
cals = json.load(open(os.path.join(DATA_DIR, 'cals.json')))
tr = TimeRange(3.65342400e+09, 3.65351040e+09)
coefficients = {k: [{'start': tr.start-1, 'stop': tr.stop+1, 'value': cals[k], 'deployment': 1}] for k in cals}
sr = StreamRequest(nutnr_sk, [2443], coefficients, tr, {}, request_id='UNIT')
nutnr_ds = xr.open_dataset(os.path.join(DATA_DIR, nutnr_fn), decode_times=False)
ctdpf_ds = xr.open_dataset(os.path.join(DATA_DIR, ctdpf_fn), decode_times=False)
nutnr_ds = nutnr_ds[self.base_params + [p.name for p in sr.stream_parameters[nutnr_sk]]]
ctdpf_ds = ctdpf_ds[self.base_params + [p.name for p in sr.stream_parameters[ctdpf_sk]]]
sr.datasets[ctdpf_sk] = StreamDataset(ctdpf_sk, sr.coefficients, sr.uflags, [nutnr_sk], sr.request_id)
sr.datasets[nutnr_sk] = StreamDataset(nutnr_sk, sr.coefficients, sr.uflags, [ctdpf_sk], sr.request_id)
sr.datasets[ctdpf_sk]._insert_dataset(ctdpf_ds)
sr.datasets[nutnr_sk]._insert_dataset(nutnr_ds)
sr.calculate_derived_products()
ds = sr.datasets[ctdpf_sk]
tempwat = ctd_sbe16plus_tempwat(ds.datasets[0].temperature,
cals['CC_a0'], cals['CC_a1'],
cals['CC_a2'], cals['CC_a3'])
np.testing.assert_array_equal(ds.datasets[0].seawater_temperature, tempwat)
pracsal = ctd_pracsal(ds.datasets[0].seawater_conductivity,
ds.datasets[0].seawater_temperature,
ds.datasets[0].seawater_pressure)
np.testing.assert_array_equal(ds.datasets[0].practical_salinity, pracsal)
response = json.loads(JsonResponse(sr).json())
self.assertEqual(len(response), len(nutnr_ds.time.values))