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Updates #87

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Apr 23, 2024
Merged

Updates #87

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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ output/*
*.swp
build/*
dist/*
resources/
*.egg-info*
.cache
docs/api
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5 changes: 5 additions & 0 deletions docs/development.rst
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Expand Up @@ -13,4 +13,9 @@ Running tests

.. code-block:: bash

# download test datasets
cd pocean/tests
python download_test_data.py
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# run test suite
pytest
8 changes: 7 additions & 1 deletion pocean/dsg/trajectory/im.py
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Expand Up @@ -136,7 +136,13 @@ def from_dataframe(cls, df, output, **kwargs):
def ts(t_index, size):
return np.s_[0:size]
default_dimensions = (daxes.sample,)
trajectory = nc.createVariable(axes.trajectory, get_dtype(df[axes.trajectory]))
# To support the IOOS netCDF specification, if traj_strlen is specified
# use a char array for the trajectory variable with a dimension traj_strlen.
if 'traj_strlen' in kwargs:
nc.createDimension('traj_strlen', kwargs['traj_strlen'])
trajectory = nc.createVariable(axes.trajectory, 'S1', ('traj_strlen',))
else:
trajectory = nc.createVariable(axes.trajectory, get_dtype(df[axes.trajectory]))
else:
def ts(t_index, size):
return np.s_[t_index, 0:size]
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4 changes: 2 additions & 2 deletions pocean/dsg/utils.py
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Expand Up @@ -175,8 +175,8 @@ def get_temporal_attributes(df, axes=None):
'attributes': {
'time_coverage_start': mint.strftime('%Y-%m-%dT%H:%M:%SZ'),
'time_coverage_end': maxt.strftime('%Y-%m-%dT%H:%M:%SZ'),
'time_coverage_duration': (maxt - mint).round('1S').isoformat(),
'time_coverage_resolution': mode_value.round('1S').isoformat()
'time_coverage_duration': (maxt - mint).round('1s').isoformat(),
'time_coverage_resolution': mode_value.round('1s').isoformat()
}
}

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16 changes: 8 additions & 8 deletions pocean/tests/dsg/trajectory/test_trajectory_im.py
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Expand Up @@ -158,13 +158,13 @@ def test_imt_calculated_metadata_single(self):

with IncompleteMultidimensionalTrajectory(filepath) as ncd:
s = ncd.calculated_metadata()
assert s.min_t.round('S') == dtparse('1990-01-01 00:00:00')
assert s.max_t.round('S') == dtparse('1990-01-05 03:00:00')
assert s.min_t.round('s') == dtparse('1990-01-01 00:00:00')
assert s.max_t.round('s') == dtparse('1990-01-05 03:00:00')
traj1 = s.trajectories["Trajectory1"]
assert traj1.min_z == 0
assert traj1.max_z == 99
assert traj1.min_t.round('S') == dtparse('1990-01-01 00:00:00')
assert traj1.max_t.round('S') == dtparse('1990-01-05 03:00:00')
assert traj1.min_t.round('s') == dtparse('1990-01-01 00:00:00')
assert traj1.max_t.round('s') == dtparse('1990-01-05 03:00:00')
first_loc = traj1.geometry.coords[0]
assert np.isclose(first_loc[0], -7.9336)
assert np.isclose(first_loc[1], 42.00339)
Expand All @@ -180,17 +180,17 @@ def test_imt_calculated_metadata_multi(self):
traj0 = m.trajectories["Trajectory0"]
assert traj0.min_z == 0
assert traj0.max_z == 35
assert traj0.min_t.round('S') == dtparse('1990-01-01 00:00:00')
assert traj0.max_t.round('S') == dtparse('1990-01-02 11:00:00')
assert traj0.min_t.round('s') == dtparse('1990-01-01 00:00:00')
assert traj0.max_t.round('s') == dtparse('1990-01-02 11:00:00')
first_loc = traj0.geometry.coords[0]
assert np.isclose(first_loc[0], -35.07884)
assert np.isclose(first_loc[1], 2.15286)

traj3 = m.trajectories["Trajectory3"]
assert traj3.min_z == 0
assert traj3.max_z == 36
assert traj3.min_t.round('S') == dtparse('1990-01-01 00:00:00')
assert traj3.max_t.round('S') == dtparse('1990-01-02 12:00:00')
assert traj3.min_t.round('s') == dtparse('1990-01-01 00:00:00')
assert traj3.max_t.round('s') == dtparse('1990-01-02 12:00:00')
first_loc = traj3.geometry.coords[0]
assert np.isclose(first_loc[0], -73.3026)
assert np.isclose(first_loc[1], 1.95761)
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24 changes: 12 additions & 12 deletions pocean/tests/dsg/trajectoryProfile/test_trajectoryProfile_cr.py
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Expand Up @@ -107,14 +107,14 @@ def test_crtp_calculated_metadata_single(self):

with ContiguousRaggedTrajectoryProfile(self.single) as st:
s = st.calculated_metadata(axes=axes)
assert s.min_t.round('S') == dtparse('2014-11-25 18:57:30')
assert s.max_t.round('S') == dtparse('2014-11-27 07:10:30')
assert s.min_t.round('s') == dtparse('2014-11-25 18:57:30')
assert s.max_t.round('s') == dtparse('2014-11-27 07:10:30')
assert len(s.trajectories) == 1
traj = s.trajectories["sp025-20141125T1730"]
assert traj.min_z == 0
assert np.isclose(traj.max_z, 504.37827)
assert traj.min_t.round('S') == dtparse('2014-11-25 18:57:30')
assert traj.max_t.round('S') == dtparse('2014-11-27 07:10:30')
assert traj.min_t.round('s') == dtparse('2014-11-25 18:57:30')
assert traj.max_t.round('s') == dtparse('2014-11-27 07:10:30')

first_loc = traj.geometry.coords[0]
assert np.isclose(first_loc[0], -119.79025)
Expand All @@ -131,34 +131,34 @@ def test_crtp_calculated_metadata_multi(self):

with ContiguousRaggedTrajectoryProfile(self.multi) as mt:
m = mt.calculated_metadata(axes=axes)
assert m.min_t.round('S') == dtparse('1990-01-01 00:00:00')
assert m.max_t.round('S') == dtparse('1990-01-03 02:00:00')
assert m.min_t.round('s') == dtparse('1990-01-01 00:00:00')
assert m.max_t.round('s') == dtparse('1990-01-03 02:00:00')
assert len(m.trajectories) == 5
# First trajectory
traj0 = m.trajectories[0]
assert traj0.min_z == 0
assert traj0.max_z == 43
assert traj0.min_t.round('S') == dtparse('1990-01-02 05:00:00')
assert traj0.max_t.round('S') == dtparse('1990-01-03 01:00:00')
assert traj0.min_t.round('s') == dtparse('1990-01-02 05:00:00')
assert traj0.max_t.round('s') == dtparse('1990-01-03 01:00:00')
first_loc = traj0.geometry.coords[0]
assert first_loc[0] == -60
assert first_loc[1] == 53
assert len(traj0.profiles) == 4
assert traj0.profiles[0].t.round('S') == dtparse('1990-01-03 01:00:00')
assert traj0.profiles[0].t.round('s') == dtparse('1990-01-03 01:00:00')
assert traj0.profiles[0].x == -60
assert traj0.profiles[0].y == 49

# Last trajectory
traj4 = m.trajectories[4]
assert traj4.min_z == 0
assert traj4.max_z == 38
assert traj4.min_t.round('S') == dtparse('1990-01-02 14:00:00')
assert traj4.max_t.round('S') == dtparse('1990-01-02 15:00:00')
assert traj4.min_t.round('s') == dtparse('1990-01-02 14:00:00')
assert traj4.max_t.round('s') == dtparse('1990-01-02 15:00:00')
first_loc = traj4.geometry.coords[0]
assert first_loc[0] == -67
assert first_loc[1] == 47
assert len(traj4.profiles) == 4
assert traj4.profiles[19].t.round('S') == dtparse('1990-01-02 14:00:00')
assert traj4.profiles[19].t.round('s') == dtparse('1990-01-02 14:00:00')
assert traj4.profiles[19].x == -44
assert traj4.profiles[19].y == 47

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