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First pass on removing nan values in model from obs with colocate time #755

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First pass on removing nan values in model from obs with colocate time #755

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4 changes: 3 additions & 1 deletion pyaerocom/colocateddata.py
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Expand Up @@ -526,10 +526,12 @@ def resample_time(
colocate_time = self.metadata["colocate_time"]

# if colocate time is activated, remove datapoints from model, where
# there is no observation
# there is no observation, or vice versa
if colocate_time:
mask = np.isnan(col.data[0]).data
mask_model = np.isnan(col.data[1]).data
col.data.data[1][mask] = np.nan
col.data.data[0][mask_model] = np.nan

res = TimeResampler(col.data)
data_arr = res.resample(
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6 changes: 5 additions & 1 deletion pyaerocom/colocation.py
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Expand Up @@ -522,11 +522,13 @@ def _colocate_site_data_helper_timecol(
min_num_obs=min_num_obs,
inplace=True,
)

# Save time indices of the observations and a mask of where it is NaN
obs_idx = stat_data_ref[var_ref].index
obs_isnan = stat_data_ref[var_ref].isnull()

# loc of nan model values
mod_isnan = stat_data[var].isnull()

# now both StationData objects are in the same resolution, but they still
# might have gaps in their time axis, thus concatenate them in a DataFrame,
# which will merge the time index
Expand All @@ -538,7 +540,9 @@ def _colocate_site_data_helper_timecol(
merged = merged.interpolate("index").reindex(obs_idx).loc[obs_idx]
# Set to NaN at times when observations were NaN originally
# (because the interpolation will interpolate the 'ref' column as well)
# Sets to NaN at times where mod were NaN originally
merged.loc[obs_isnan] = np.nan
merged.loc[mod_isnan] = np.nan
# due to interpolation some model values may be NaN, where there is obs
merged.loc[merged.data.isnull()] = np.nan
# Ensure the whole timespan of the model is kept in "merged"
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4 changes: 3 additions & 1 deletion pyaerocom/helpers.py
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Expand Up @@ -1756,7 +1756,9 @@ def make_dummy_cube(

latdim.guess_bounds()
londim.guess_bounds()
dummy = iris.cube.Cube(np.ones((len(times), len(lats), len(lons))), units=unit)

data = np.ones((len(times), len(lats), len(lons)))
dummy = iris.cube.Cube(data, units=unit)

dummy.add_dim_coord(latdim, 1)
dummy.add_dim_coord(londim, 2)
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