disdrodb 0.0.21__py3-none-any.whl → 0.1.0__py3-none-any.whl

disdrodb/utils/time.py

@@ -0,0 +1,657 @@
+# -----------------------------------------------------------------------------.
+# Copyright (c) 2021-2023 DISDRODB developers
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# -----------------------------------------------------------------------------.
+"""This module contains utilities related to the processing of temporal dataset."""
+import logging
+import numbers
+import re
+from typing import Optional
+
+import numpy as np
+import pandas as pd
+import xarray as xr
+
+from disdrodb.utils.logger import log_info, log_warning
+from disdrodb.utils.xarray import define_fill_value_dictionary
+
+logger = logging.getLogger(__name__)
+
+####------------------------------------------------------------------------------------.
+#### Sampling Interval Acronyms
+
+
+def seconds_to_acronym(seconds):
+    """
+    Convert a duration in seconds to a readable string format (e.g., "1H30", "1D2H").
+
+    Parameters
+    ----------
+    - seconds (int): The time duration in seconds.
+
+    Returns
+    -------
+    - str: The duration as a string in a format like "30S", "1MIN30S", "1H30MIN", or "1D2H".
+    """
+    timedelta = pd.Timedelta(seconds=seconds)
+    components = timedelta.components
+
+    parts = []
+    if components.days > 0:
+        parts.append(f"{components.days}D")
+    if components.hours > 0:
+        parts.append(f"{components.hours}H")
+    if components.minutes > 0:
+        parts.append(f"{components.minutes}MIN")
+    if components.seconds > 0:
+        parts.append(f"{components.seconds}S")
+    acronym = "".join(parts)
+    return acronym
+
+
+def get_resampling_information(sample_interval_acronym):
+    """
+    Extract resampling information from the sample interval acronym.
+
+    Parameters
+    ----------
+    sample_interval_acronym: str
+      A string representing the sample interval: e.g., "1H30MIN", "ROLL1H30MIN".
+
+    Returns
+    -------
+    sample_interval_seconds, rolling: tuple
+        Sample_interval in seconds and whether rolling is enabled.
+    """
+    rolling = sample_interval_acronym.startswith("ROLL")
+    if rolling:
+        sample_interval_acronym = sample_interval_acronym[4:]  # Remove "ROLL"
+
+    # Allowed pattern: one or more occurrences of "<number><unit>"
+    # where unit is exactly one of D, H, MIN, or S.
+    # Examples: 1H, 30MIN, 2D, 45S, and any concatenation like 1H30MIN.
+    pattern = r"^(\d+(?:D|H|MIN|S))+$"
+
+    # Check if the entire string matches the pattern
+    if not re.match(pattern, sample_interval_acronym):
+        raise ValueError(
+            f"Invalid sample interval acronym '{sample_interval_acronym}'. "
+            "Must be composed of one or more <number><unit> groups, where unit is D, H, MIN, or S.",
+        )
+
+    # Regular expression to match duration components and extract all (value, unit) pairs
+    pattern = r"(\d+)(D|H|MIN|S)"
+    matches = re.findall(pattern, sample_interval_acronym)
+
+    # Conversion factors for each unit
+    unit_to_seconds = {
+        "D": 86400,  # Seconds in a day
+        "H": 3600,  # Seconds in an hour
+        "MIN": 60,  # Seconds in a minute
+        "S": 1,  # Seconds in a second
+    }
+
+    # Parse matches and calculate total seconds
+    sample_interval = 0
+    for value, unit in matches:
+        value = int(value)
+        if unit in unit_to_seconds:
+            sample_interval += value * unit_to_seconds[unit]
+    return sample_interval, rolling
+
+
+def acronym_to_seconds(acronym):
+    """
+    Extract the interval in seconds from the duration acronym.
+
+    Parameters
+    ----------
+    acronym: str
+      A string representing a duration: e.g., "1H30MIN", "ROLL1H30MIN".
+
+    Returns
+    -------
+    seconds
+        Duration in seconds.
+    """
+    seconds, _ = get_resampling_information(acronym)
+    return seconds
+
+
+####----------------------------------------------------------------------------.
+#### File start and end time utilities
+def get_dataframe_start_end_time(df: pd.DataFrame, time_column="time"):
+    """Retrieves dataframe starting and ending time.
+
+    Parameters
+    ----------
+    df : pandas.DataFrame
+        Input dataframe
+    time_column: str
+        Name of the time column.
+        The default is "time".
+        The column must be of type datetime.
+
+    Returns
+    -------
+    (start_time, end_time): tuple
+        File start and end time of type pandas.Timestamp.
+
+    """
+    starting_time = pd.to_datetime(df[time_column].iloc[0])
+    ending_time = pd.to_datetime(df[time_column].iloc[-1])
+    return (starting_time, ending_time)
+
+
+def get_dataset_start_end_time(ds: xr.Dataset, time_dim="time"):
+    """Retrieves dataset starting and ending time.
+
+    Parameters
+    ----------
+    ds : xarray.Dataset
+        Input dataset
+    time_dim: str
+        Name of the time dimension.
+        The default is "time".
+
+    Returns
+    -------
+    (start_time, end_time): tuple
+        File start and end time of type pandas.Timestamp.
+
+    """
+    starting_time = pd.to_datetime(ds[time_dim].to_numpy()[0])
+    ending_time = pd.to_datetime(ds[time_dim].to_numpy()[-1])
+    return (starting_time, ending_time)
+
+
+def get_file_start_end_time(obj, time="time"):
+    """Retrieves object starting and ending time.
+
+    Parameters
+    ----------
+    obj : xarray.Dataset or pandas.DataFrame
+        Input object with time dimension or column respectively.
+    time: str
+        Name of the time dimension or column.
+        The default is "time".
+
+    Returns
+    -------
+    (start_time, end_time): tuple
+        File start and end time of type pandas.Timestamp.
+
+    """
+    if isinstance(obj, xr.Dataset):
+        return get_dataset_start_end_time(obj, time_dim=time)
+    if isinstance(obj, pd.DataFrame):
+        return get_dataframe_start_end_time(obj, time_column=time)
+    raise TypeError("Expecting a xarray Dataset or a pandas Dataframe object.")
+
+
+####------------------------------------------------------------------------------------.
+#### Xarray utilities
+
+
+def ensure_sorted_by_time(obj, time="time"):
+    """Ensure a xarray object or pandas Dataframe is sorted by time."""
+    # Check sorted by time and sort if necessary
+    is_sorted = np.all(np.diff(obj[time].to_numpy().astype(int)) > 0)
+    if not is_sorted:
+        if isinstance(obj, pd.DataFrame):
+            return obj.sort_values(by="time")
+        # Else xarray DataArray or Dataset
+        obj = obj.sortby("time")
+    return obj
+
+
+def _check_time_sorted(ds, time_dim):
+    """Ensure the xarray.Dataset is sorted."""
+    time_diff = np.diff(ds[time_dim].to_numpy().astype(int))
+    if np.any(time_diff == 0):
+        raise ValueError(f"In the {time_dim} dimension there are duplicated timesteps !")
+    if not np.all(time_diff > 0):
+        print(f"The {time_dim} dimension was not sorted. Sorting it now !")
+        ds = ds.sortby(time_dim)
+    return ds
+
+
+def regularize_dataset(
+    xr_obj,
+    freq: str,
+    time_dim: str = "time",
+    method: Optional[str] = None,
+    fill_value=None,
+):
+    """Regularize a dataset across time dimension with uniform resolution.
+
+    Parameters
+    ----------
+    xr_obj : xarray.Dataset or xr.DataArray
+        xarray object with time dimension.
+    time_dim : str, optional
+        The time dimension in the xarray object. The default value is ``"time"``.
+    freq : str
+        The ``freq`` string to pass to `pd.date_range()` to define the new time coordinates.
+        Examples: ``freq="2min"``.
+    method : str, optional
+        Method to use for filling missing timesteps.
+        If ``None``, fill with ``fill_value``. The default value is ``None``.
+        For other possible methods, see xarray.Dataset.reindex()`.
+    fill_value : (float, dict), optional
+        Fill value to fill missing timesteps.
+        If not specified, for float variables it uses ``dtypes.NA`` while for
+        for integers variables it uses the maximum allowed integer value or,
+        in case of undecoded variables, the ``_FillValue`` DataArray attribute..
+
+    Returns
+    -------
+    ds_reindexed : xarray.Dataset
+        Regularized dataset.
+
+    """
+    xr_obj = _check_time_sorted(xr_obj, time_dim=time_dim)
+    start_time, end_time = get_dataset_start_end_time(xr_obj, time_dim=time_dim)
+
+    # Define new time index
+    new_time_index = pd.date_range(
+        start=start_time,
+        end=end_time,
+        freq=freq,
+    )
+    # Check all existing timesteps are within the new time index
+    # - Otherwise raise error because it means that the desired frequency is not compatible
+    idx_missing = np.where(~np.isin(xr_obj[time_dim].data, new_time_index))[0]
+    if len(idx_missing) > 0:
+        not_included_timesteps = xr_obj[time_dim].data[idx_missing].astype("M8[s]")
+        raise ValueError(f"With freq='{freq}', the following timesteps would be dropped: {not_included_timesteps}")
+
+    # Define fill_value dictionary
+    if fill_value is None:
+        fill_value = define_fill_value_dictionary(xr_obj)
+
+    # Regularize dataset and fill with NA values
+    xr_obj = xr_obj.reindex(
+        {time_dim: new_time_index},
+        method=method,  # do not fill gaps
+        # tolerance=tolerance,  # mismatch in seconds
+        fill_value=fill_value,
+    )
+    return xr_obj
+
+
+####------------------------------------------
+#### Sampling interval utilities
+
+
+def ensure_sample_interval_in_seconds(sample_interval):  # noqa: PLR0911
+    """
+    Ensure the sample interval is in seconds.
+
+    Parameters
+    ----------
+    sample_interval : int, numpy.ndarray, xarray.DataArray, or numpy.timedelta64
+        The sample interval to be converted to seconds.
+        It can be:
+        - An integer representing the interval in seconds.
+        - A numpy array or xarray DataArray of integers representing intervals in seconds.
+        - A numpy.timedelta64 object representing the interval.
+        - A numpy array or xarray DataArray of numpy.timedelta64 objects representing intervals.
+
+    Returns
+    -------
+    int, numpy.ndarray, or xarray.DataArray
+        The sample interval converted to seconds. The return type matches the input type:
+        - If the input is an integer, the output is an integer.
+        - If the input is a numpy array, the output is a numpy array of integers (unless NaN is present)
+        - If the input is an xarray DataArray, the output is an xarray DataArray of integers (unless NaN is present).
+
+    """
+    # Deal with timedelta objects
+    if isinstance(sample_interval, np.timedelta64):
+        return (sample_interval.astype("m8[s]") / np.timedelta64(1, "s")).astype(int)
+        # return sample_interval.astype("m8[s]").astype(int)
+
+    # Deal with scalar pure integer types (Python int or numpy int32/int64/etc.)
+    # --> ATTENTION: this also include np.timedelta64 objects !
+    if isinstance(sample_interval, numbers.Integral):
+        return sample_interval
+
+    # Deal with numpy or xarray arrays of integer types
+    if isinstance(sample_interval, (np.ndarray, xr.DataArray)) and np.issubdtype(sample_interval.dtype, int):
+        return sample_interval
+
+    # Deal with scalar floats that are actually integers (e.g. 1.0, np.float64(3.0))
+    if isinstance(sample_interval, numbers.Real):
+        if float(sample_interval).is_integer():
+            # Cast back to int seconds
+            return int(sample_interval)
+        raise TypeError(f"sample_interval floats must be whole numbers of seconds, got {sample_interval}")
+
+    # Deal with timedelta64 numpy arrays
+    if isinstance(sample_interval, np.ndarray) and np.issubdtype(sample_interval.dtype, np.timedelta64):
+        is_nat = np.isnat(sample_interval)
+        if np.any(is_nat):
+            sample_interval = sample_interval.astype("timedelta64[s]").astype(float)
+            sample_interval[is_nat] = np.nan
+            return sample_interval
+        return sample_interval.astype("timedelta64[s]").astype(int)
+    # Deal with timedelta64 xarray arrays
+    if isinstance(sample_interval, xr.DataArray) and np.issubdtype(sample_interval.dtype, np.timedelta64):
+        sample_interval = sample_interval.copy()
+        is_nat = np.isnat(sample_interval)
+        if np.any(is_nat):
+            sample_interval_array = sample_interval.data.astype("timedelta64[s]").astype(float)
+            sample_interval_array[is_nat] = np.nan
+            sample_interval.data = sample_interval_array
+            return sample_interval
+        sample_interval_array = sample_interval.data.astype("timedelta64[s]").astype(int)
+        sample_interval.data = sample_interval_array
+        return sample_interval
+
+    # Deal with numpy array of floats that are all integer-valued (with optionally some NaN)
+    if isinstance(sample_interval, np.ndarray) and np.issubdtype(sample_interval.dtype, np.floating):
+        mask_nan = np.isnan(sample_interval)
+        if mask_nan.any():
+            # Check non-NaN entries are whole numbers
+            nonnan = sample_interval[~mask_nan]
+            if not np.allclose(nonnan, np.rint(nonnan)):
+                raise TypeError("Float array sample_interval must contain only whole numbers or NaN.")
+            # Leave as float array so NaNs are preserved
+            return sample_interval
+        # No NaNs: can safely cast to integer dtype
+        if not np.allclose(sample_interval, np.rint(sample_interval)):
+            raise TypeError("Float array sample_interval must contain only whole numbers.")
+        return sample_interval.astype(int)
+
+    # Deal with xarray.DataArrayy of floats that are all integer-valued (with optionally some NaN)
+    if isinstance(sample_interval, xr.DataArray) and np.issubdtype(sample_interval.dtype, np.floating):
+        arr = sample_interval.copy()
+        data = arr.data
+        mask_nan = np.isnan(data)
+        if mask_nan.any():
+            nonnan = data[~mask_nan]
+            if not np.allclose(nonnan, np.rint(nonnan)):
+                raise TypeError("Float DataArray sample_interval must contain only whole numbers or NaN.")
+            # return as float DataArray so NaNs stay
+            return arr
+        if not np.allclose(data, np.rint(data)):
+            raise TypeError("Float DataArray sample_interval must contain only whole numbers.")
+        arr.data = data.astype(int)
+        return arr
+
+    raise TypeError(
+        "sample_interval must be an integer value or array, or numpy.ndarray / xarray.DataArray with type timedelta64.",
+    )
+
+
+def infer_sample_interval(ds, robust=False, verbose=False, logger=None):
+    """Infer the sample interval of a dataset.
+
+    Duplicated timesteps are removed before inferring the sample interval.
+
+    NOTE: This function is used only for the reader preparation.
+    """
+    # Check sorted by time and sort if necessary
+    ds = ensure_sorted_by_time(ds)
+
+    # Retrieve timesteps
+    # - Remove duplicate timesteps
+    timesteps = np.unique(ds["time"].data)
+
+    # Calculate number of timesteps
+    n_timesteps = len(timesteps)
+
+    # Calculate time differences in seconds
+    deltadt = np.diff(timesteps).astype("timedelta64[s]").astype(int)
+
+    # Round each delta to the nearest multiple of 5 (because the smallest possible sample interval is 10 s)
+    # Example: for sample_interval = 10, deltat values like 8, 9, 11, 12 become 10 ...
+    # Example: for sample_interval = 10, deltat values like 6, 7 or 13, 14 become respectively 5 and 15 ...
+    # Example: for sample_interval = 30, deltat values like 28,29,30,31,32 deltat  become 30 ...
+    # Example: for sample_interval = 30, deltat values like 26, 27 or 33, 34 become respectively 25 and 35 ...
+    # --> Need other rounding after having identified the most frequent sample interval to coerce such values to 30
+    min_sample_interval = 10
+    min_half_sample_interval = min_sample_interval / 2
+    deltadt = np.round(deltadt / min_half_sample_interval) * min_half_sample_interval
+
+    # Identify unique time intervals and their occurrences
+    unique_deltas, counts = np.unique(deltadt, return_counts=True)
+
+    # Determine the most frequent time interval (mode)
+    most_frequent_delta_idx = np.argmax(counts)
+    sample_interval = unique_deltas[most_frequent_delta_idx]
+
+    # Reround deltadt once knowing the sample interval
+    # - If sample interval is 10: all values between 6 and 14 are rounded to 10, below 6 to 0, above 14 to 20
+    # - If sample interval is 30: all values between 16 and 44 are rounded to 30, below 16 to 0, above 44 to 20
+    deltadt = np.round(deltadt / min_sample_interval) * min_sample_interval
+
+    # Identify unique time intervals and their occurrences
+    unique_deltas, counts = np.unique(deltadt, return_counts=True)
+    fractions = np.round(counts / len(deltadt) * 100, 2)
+
+    # Determine the most frequent time interval (mode)
+    most_frequent_delta_idx = np.argmax(counts)
+    sample_interval = unique_deltas[most_frequent_delta_idx]
+    sample_interval_fraction = fractions[most_frequent_delta_idx]
+
+    # Inform about irregular sampling
+    unexpected_intervals = unique_deltas[unique_deltas != sample_interval]
+    unexpected_intervals_counts = counts[unique_deltas != sample_interval]
+    unexpected_intervals_fractions = fractions[unique_deltas != sample_interval]
+    if verbose and len(unexpected_intervals) > 0:
+        msg = "Non-unique interval detected."
+        log_info(logger=logger, msg=msg, verbose=verbose)
+        for interval, count, fraction in zip(
+            unexpected_intervals,
+            unexpected_intervals_counts,
+            unexpected_intervals_fractions,
+        ):
+            msg = f"--> Interval: {interval} seconds, Occurrence: {count}, Frequency: {fraction} %"
+            log_info(logger=logger, msg=msg, verbose=verbose)
+
+    # Perform checks
+    # - Raise error if negative or zero time intervals are presents
+    # - If robust = False, still return the estimated sample_interval
+    if robust and np.any(deltadt == 0):
+        raise ValueError("Likely presence of duplicated timesteps.")
+
+    if robust and len(unexpected_intervals) > 0:
+        raise ValueError("Not unique sampling interval.")
+
+    ###-------------------------------------------------------------------------.
+    ### Display informative messages
+    # - Log a warning if estimated sample interval has frequency less than 60 %
+    sample_interval_fraction_threshold = 60
+    msg = (
+        f"The most frequent sampling interval ({sample_interval} s) "
+        + f"has a frequency lower than {sample_interval_fraction_threshold}%: {sample_interval_fraction} %. "
+        + f"(Total number of timesteps: {n_timesteps})"
+    )
+    if sample_interval_fraction < sample_interval_fraction_threshold:
+        log_warning(logger=logger, msg=msg, verbose=verbose)
+
+    # - Log a warning if an unexpected interval has frequency larger than 20 percent
+    frequent_unexpected_intervals = unexpected_intervals[unexpected_intervals_fractions > 20]
+    if len(frequent_unexpected_intervals) != 0:
+        frequent_unexpected_intervals_str = ", ".join(
+            f"{interval} seconds" for interval in frequent_unexpected_intervals
+        )
+        msg = (
+            "The following unexpected intervals have a frequency "
+            + f"greater than 20%: {frequent_unexpected_intervals_str}. "
+            + f"(Total number of timesteps: {n_timesteps})"
+        )
+        log_warning(logger=logger, msg=msg, verbose=verbose)
+    return int(sample_interval)
+
+
+####---------------------------------------------------------------------------------
+#### Timesteps regularization
+
+
+def get_problematic_timestep_indices(timesteps, sample_interval):
+    """Identify timesteps with missing previous or following timesteps."""
+    previous_time = timesteps - pd.Timedelta(seconds=sample_interval)
+    next_time = timesteps + pd.Timedelta(seconds=sample_interval)
+    idx_previous_missing = np.where(~np.isin(previous_time, timesteps))[0][1:]
+    idx_next_missing = np.where(~np.isin(next_time, timesteps))[0][:-1]
+    idx_isolated_missing = np.intersect1d(idx_previous_missing, idx_next_missing)
+    idx_previous_missing = idx_previous_missing[np.isin(idx_previous_missing, idx_isolated_missing, invert=True)]
+    idx_next_missing = idx_next_missing[np.isin(idx_next_missing, idx_isolated_missing, invert=True)]
+    return idx_previous_missing, idx_next_missing, idx_isolated_missing
+
+
+def regularize_timesteps(ds, sample_interval, robust=False, add_quality_flag=True, logger=None, verbose=True):
+    """Ensure timesteps match with the sample_interval.
+
+    This function:
+    - drop dataset indices with duplicated timesteps,
+    - but does not add missing timesteps to the dataset.
+    """
+    # Check sorted by time and sort if necessary
+    ds = ensure_sorted_by_time(ds)
+
+    # Convert time to pandas.DatetimeIndex for easier manipulation
+    times = pd.to_datetime(ds["time"].to_numpy())
+
+    # Determine the start and end times
+    start_time = times[0].floor(f"{sample_interval}s")
+    end_time = times[-1].ceil(f"{sample_interval}s")
+
+    # Create the expected time grid
+    expected_times = pd.date_range(start=start_time, end=end_time, freq=f"{sample_interval}s")
+
+    # Convert to numpy arrays
+    times = times.to_numpy(dtype="M8[s]")
+    expected_times = expected_times.to_numpy(dtype="M8[s]")
+
+    # Map original times to the nearest expected times
+    # Calculate the difference between original times and expected times
+    time_deltas = np.abs(times - expected_times[:, None]).astype(int)
+
+    # Find the index of the closest expected time for each original time
+    nearest_indices = np.argmin(time_deltas, axis=0)
+    adjusted_times = expected_times[nearest_indices]
+
+    # Check for duplicates in adjusted times
+    unique_times, counts = np.unique(adjusted_times, return_counts=True)
+    duplicates = unique_times[counts > 1]
+
+    # Initialize time quality flag
+    # - 0 when ok or just rounded to closest 00
+    # - 1 if previous timestep is missing
+    # - 2 if next timestep is missing
+    # - 3 if previous and next timestep is missing
+    # - 4 if solved duplicated timesteps
+    # - 5 if needed to drop duplicated timesteps and select the last
+    flag_previous_missing = 1
+    flag_next_missing = 2
+    flag_isolated_timestep = 3
+    flag_solved_duplicated_timestep = 4
+    flag_dropped_duplicated_timestep = 5
+    qc_flag = np.zeros(adjusted_times.shape)
+
+    # Initialize list with the duplicated timesteps index to drop
+    # - We drop the first occurrence because is likely the shortest interval
+    idx_to_drop = []
+
+    # Attempt to resolve for duplicates
+    if duplicates.size > 0:
+        # Handle duplicates
+        for dup_time in duplicates:
+            # Indices of duplicates
+            dup_indices = np.where(adjusted_times == dup_time)[0]
+            n_duplicates = len(dup_indices)
+            # Define previous and following timestep
+            prev_time = dup_time - pd.Timedelta(seconds=sample_interval)
+            next_time = dup_time + pd.Timedelta(seconds=sample_interval)
+            # Try to find missing slots before and after
+            # - If more than 3 duplicates, impossible to solve !
+            count_solved = 0
+            # If the previous timestep is available, set that one
+            if n_duplicates == 2:
+                if prev_time not in adjusted_times:
+                    adjusted_times[dup_indices[0]] = prev_time
+                    qc_flag[dup_indices[0]] = flag_solved_duplicated_timestep
+                    count_solved += 1
+                elif next_time not in adjusted_times:
+                    adjusted_times[dup_indices[-1]] = next_time
+                    qc_flag[dup_indices[-1]] = flag_solved_duplicated_timestep
+                    count_solved += 1
+                else:
+                    pass
+            elif n_duplicates == 3:
+                if prev_time not in adjusted_times:
+                    adjusted_times[dup_indices[0]] = prev_time
+                    qc_flag[dup_indices[0]] = flag_solved_duplicated_timestep
+                    count_solved += 1
+                if next_time not in adjusted_times:
+                    adjusted_times[dup_indices[-1]] = next_time
+                    qc_flag[dup_indices[-1]] = flag_solved_duplicated_timestep
+                    count_solved += 1
+            if count_solved != n_duplicates - 1:
+                idx_to_drop = np.append(idx_to_drop, dup_indices[0:-1])
+                qc_flag[dup_indices[-1]] = flag_dropped_duplicated_timestep
+                msg = (
+                    f"Cannot resolve {n_duplicates} duplicated timesteps "
+                    f"(after trailing seconds correction) around {dup_time}."
+                )
+                log_warning(logger=logger, msg=msg, verbose=verbose)
+                if robust:
+                    raise ValueError(msg)
+
+    # Update the time coordinate (Convert to ns for xarray compatibility)
+    ds = ds.assign_coords({"time": adjusted_times.astype("datetime64[ns]")})
+
+    # Update quality flag values for next and previous timestep is missing
+    if add_quality_flag:
+        idx_previous_missing, idx_next_missing, idx_isolated_missing = get_problematic_timestep_indices(
+            adjusted_times,
+            sample_interval,
+        )
+        qc_flag[idx_previous_missing] = np.maximum(qc_flag[idx_previous_missing], flag_previous_missing)
+        qc_flag[idx_next_missing] = np.maximum(qc_flag[idx_next_missing], flag_next_missing)
+        qc_flag[idx_isolated_missing] = np.maximum(qc_flag[idx_isolated_missing], flag_isolated_timestep)
+
+        # If the first timestep is at 00:00 and currently flagged as previous missing (1), reset to 0
+        # first_time = pd.to_datetime(adjusted_times[0]).time()
+        # first_expected_time = pd.Timestamp("00:00:00").time()
+        # if first_time == first_expected_time and qc_flag[0] == flag_previous_missing:
+        #     qc_flag[0] = 0
+
+        # # If the last timestep is flagged and currently flagged as next missing (2), reset it to 0
+        # last_time = pd.to_datetime(adjusted_times[-1]).time()
+        # last_time_expected = (pd.Timestamp("00:00:00") - pd.Timedelta(30, unit="seconds")).time()
+        # # Check if adding one interval would go beyond the end_time
+        # if last_time == last_time_expected and qc_flag[-1] == flag_next_missing:
+        #     qc_flag[-1] = 0
+
+        # Assign time quality flag coordinate
+        ds["time_qc"] = xr.DataArray(qc_flag, dims="time")
+        ds = ds.set_coords("time_qc")
+
+    # Drop duplicated timesteps
+    # - Using ds =  ds.drop_isel({"time": idx_to_drop.astype(int)}) raise:
+    #   --> pandas.errors.InvalidIndexError: Reindexing only valid with uniquely valued Index objects
+    #   --> https://github.com/pydata/xarray/issues/6605
+    if len(idx_to_drop) > 0:
+        idx_to_drop = idx_to_drop.astype(int)
+        idx_valid_timesteps = np.arange(0, ds["time"].size)
+        idx_valid_timesteps = np.delete(idx_valid_timesteps, idx_to_drop)
+        ds = ds.isel(time=idx_valid_timesteps)
+    # Return dataset
+    return ds

disdrodb/utils/warnings.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python3
+
+# -----------------------------------------------------------------------------.
+# Copyright (c) 2021-2023 DISDRODB developers
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+# -----------------------------------------------------------------------------.
+"""Warning utilities."""
+import warnings
+from contextlib import contextmanager
+
+
+@contextmanager
+def suppress_warnings():
+    """Context manager suppressing RuntimeWarnings and UserWarnings."""
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore", RuntimeWarning)
+        warnings.simplefilter("ignore", UserWarning)
+        yield