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deduplicate timestamps with check #96

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merged 3 commits into from
Jun 22, 2022
Merged

deduplicate timestamps with check #96

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d1ebe36
deduplicate timestamps with check
callumrollo Jun 20, 2022
7764091
check for xarray drop_duplicates
callumrollo Jun 20, 2022
0b00b51
implement rough drop_duplicates
callumrollo Jun 22, 2022
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21 changes: 18 additions & 3 deletions pyglider/seaexplorer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -360,6 +360,24 @@ def raw_to_timeseries(indir, outdir, deploymentyaml, kind='raw',
profile_min_time=profile_min_time)
ds = utils.get_derived_eos_raw(ds)

# somehow this comes out unsorted:
ds = ds.sortby(ds.time)
# Drop duplicate timestamps and check how many are removed this way
if "drop_duplicates" in ds.__dir__():
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I think:

Suggested change
if "drop_duplicates" in ds.__dir__():
if hasattr(ds, "drop_duplicates"):

len_before_drop = len(ds.time)
ds = ds.drop_duplicates(dim="time")
len_after_drop = len(ds.time)
proportion_kept = len_after_drop / len_before_drop
loss_str = f"{100 * (1-proportion_kept)} % samples removed by timestamp deduplication."
if proportion_kept < 0.5:
raise ValueError(f"{loss_str} Check input data for duplicate timestamps")
elif proportion_kept < 0.999:
_log.warning(loss_str)
else:
_log.info(loss_str)
else:
_log.warning("drop_duplicates not found in xarray. Install xarray>=2022.3.0 for deduplication functionality")

# Correct oxygen if present:
if 'oxygen_concentration' in ncvar.keys():
if 'correct_oxygen' in ncvar['oxygen_concentration'].keys():
Expand All @@ -374,9 +392,6 @@ def raw_to_timeseries(indir, outdir, deploymentyaml, kind='raw',

ds = utils.fill_metadata(ds, deployment['metadata'], device_data)

# somehow this comes out unsorted:
ds = ds.sortby(ds.time)

start = ds['time'].values[0]
end = ds['time'].values[-1]

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