def test_select(self):
d = Dataset(tempfile.mktemp(), 'w')
tb = TargetBuffer(tags=['WI001'], name='White Island main vent',
position=(177.2, -37.5, 50),
position_error=(0.2, 0.2, 20),
description='Main vent in January 2017')
d.register_tags(['WI001', 'MD01', 'measurement'])
t = d.new(tb)
ib = InstrumentBuffer(tags=['MD01'], sensor_id='F00975',
location='West rim',
no_bits=16, type='DOAS',
description='GeoNet permanent instrument')
i = d.new(ib)
rdtb = RawDataTypeBuffer(tags=['measurement'],
name='1st round measurements',
acquisition='stationary')
rdt = d.new(rdtb)
rb = RawDataBuffer(target=t, instrument=i, type=rdt,
d_var=np.zeros((1, 2048)), ind_var=np.arange(2048),
datetime=['2017-01-10T15:23:00'])
r = d.new(rb)
e = d.select("tags == 'MD01'")
self.assertEqual(e['Target'][0], t)
self.assertEqual(e['Instrument'][0], i)
e = d.select("type.acquisition == 'stationary'", etype='RawData')
self.assertEqual(e['RawData'][0], r)
def test_read(self):
"""
Test reading of HDF5 files.
"""
fn = tempfile.mktemp()
d = Dataset(fn, 'w')
tb = TargetBuffer(tags=['WI001'], name='White Island main vent',
position=(177.2, -37.5, 50),
position_error=(0.2, 0.2, 20),
description='Main vent in January 2017')
d.register_tags(['WI001', 'MD01', 'measurement'])
t = d.new(tb)
ib = InstrumentBuffer(tags=['MD01'], sensor_id='F00975',
location='West rim',
no_bits=16, type='DOAS',
description='GeoNet permanent instrument')
i = d.new(ib)
rdtb = RawDataTypeBuffer(tags=['measurement'],
name='1st round measurements',
acquisition='stationary')
rdt = d.new(rdtb)
rb = RawDataBuffer(target=t, instrument=i, type=rdt,
d_var=np.zeros((1, 2048)), ind_var=np.arange(2048),
datetime=['2017-01-10T15:23:00'])
d.new(rb)
d.close()
d1 = Dataset.open(fn)
r1 = d1.elements['RawData'][0]
self.assertEqual(r1.target.name, 'White Island main vent')
self.assertEqual(list(r1.instrument.tags)[0], 'MD01')
def test_pedantic(self):
d = Dataset(tempfile.mktemp(), 'w')
rb = RawDataBuffer()
with self.assertRaises(ValueError):
d.new(rb, pedantic=True)
d.register_tags(['WI001'])
tb = TargetBuffer(tags=['WI001'], name='White Island main vent',
position=(177.2, -37.5, 50),
position_error=(0.2, 0.2, 20),
description='Main vent in January 2017')
d.new(tb)
with self.assertRaises(ValueError):
d.new(tb, pedantic=True)
def test_tagging(self):
"""
Test the tagging of data elements.
"""
d = Dataset(tempfile.mktemp(), 'w')
d.register_tags(['measurement'])
with self.assertRaises(ValueError):
d.register_tags(['measurement'])
tb = TargetBuffer(tags=['WI001', 'Eruption16'])
with self.assertRaises(ValueError):
t = d.new(tb)
d.register_tags(['WI001', 'Eruption16'])
t = d.new(tb)
d.register_tags(['SomethingElse'])
t.tags.append('SomethingElse')
t.tags.remove('WI001')
with warnings.catch_warnings():
warnings.simplefilter('ignore')
d.remove_tags(['Eruption16', 'blub'])
self.assertEqual(list(t.tags), ['SomethingElse'])
# Ensure the same tag is only added once
t.tags.append('SomethingElse')
self.assertEqual(list(t.tags), ['SomethingElse'])
self.assertEqual(len(d._f.root.tags._v_children['SomethingElse'][:]),
1)
def test_append(self):
d = Dataset(tempfile.mktemp(), 'w')
d.register_tags(['WI001', 'MD01', 'measurement'])
tb = TargetBuffer(tags=['WI001'], name='White Island main vent',
position=(177.2, -37.5, 50),
position_error=(0.2, 0.2, 20),
description='Main vent in January 2017')
t = d.new(tb)
ib = InstrumentBuffer(tags=['MD01'], sensor_id='F00975',
location='West rim',
no_bits=16, type='DOAS',
description='GeoNet permanent instrument')
i = d.new(ib)
rdtb = RawDataTypeBuffer(tags=['measurement'],
name='1st round measurements',
acquisition='stationary')
rdt = d.new(rdtb)
rb = RawDataBuffer(target=t, instrument=i, type=rdt,
d_var=np.zeros((1, 2048)), ind_var=np.arange(2048),
datetime=['2017-01-10T15:23:00'])
r = d.new(rb)
rb1 = RawDataBuffer(target=t, instrument=i, type=rdt,
d_var=np.ones((1, 2048)), ind_var=np.arange(2048),
datetime=['2017-01-10T15:23:01'])
r.append(rb1)
self.assertEqual(len(r.ind_var[:]), 4096)
self.assertEqual(np.array(r.ind_var[:]).size, 4096)
self.assertTrue(np.alltrue(np.array(r.d_var[:]) < 2))
np.testing.assert_array_equal(np.array(r.datetime[:]).flatten(),
np.array(['2017-01-10T15:23:00',
'2017-01-10T15:23:01'],
dtype='datetime64[ms]'))
with self.assertRaises(ValueError):
r.append(rb1, pedantic=True)
with self.assertRaises(ValueError):
r.append(rb, pedantic=True)
with self.assertRaises(AttributeError):
t.append(tb)
d.register_tags(['WI002'])
tb1 = TargetBuffer(tags=['WI002'], name='Donald Duck',
position=(177.1, -37.4, 50),
position_error=(0.2, 0.2, 20),
description='Donald Duck vent in January 2010')
t1 = d.new(tb1)
rb2 = RawDataBuffer(target=t1, instrument=i, type=rdt,
d_var=np.ones((1, 2048)), ind_var=np.arange(2048),
datetime=['2017-01-10T15:23:02'])
with self.assertRaises(AttributeError):
rb.append(rb2)
def test_dtbuffer(self):
"""
Testing the behaviour of buffer elements.
"""
d = Dataset(tempfile.mktemp(), 'w')
tb = TargetBuffer(tags=['WI001'], name='White Island main vent',
position=(177.2, -37.5, 50),
position_error=(0.2, 0.2, 20),
description='Main vent in January 2017')
with self.assertRaises(ValueError):
t = d.new(tb)
d.register_tags(['WI001', 'MD01', 'measurement'])
t = d.new(tb)
ib = InstrumentBuffer(tags=['MD01'], sensor_id='F00975',
location='West rim',
no_bits=16, type='DOAS',
description='GeoNet permanent instrument')
i = d.new(ib)
rdtb = RawDataTypeBuffer(tags=['measurement'],
name='1st round measurements',
acquisition='stationary')
rdt = d.new(rdtb)
rb = RawDataBuffer(target=t, instrument=i, type=rdt,
d_var=np.zeros((1, 2048)), ind_var=np.arange(2048),
datetime=['2017-01-10T15:23:00'])
r = d.new(rb)
self.assertTrue(r.target == t)
self.assertTrue(r.instrument == i)
self.assertTrue(r.type == rdt)
rb1 = RawDataBuffer()
rb1.d_var = np.zeros((1, 2048))
rb1.ind_var = np.arange(2048),
rb1.datetime = ['2017-01-10T15:23:00']
rb1.target = t
rb1.instrument = i
rb1.type = rdt
d.new(rb1)