tsp 1.7.7__py3-none-any.whl → 1.8.1__py3-none-any.whl

tsp/core.py

@@ -1,1035 +1,1162 @@
-from __future__ import annotations
-
-import pandas as pd
-import re
-import inspect
-import numpy as np
-import functools
-import warnings
-
-try:
-    import netCDF4 as nc
-
-    try:
-        from pfit.pfnet_standard import make_temperature_base
-    except ModuleNotFoundError:
-        warnings.warn("Missing pfit library. Some functionality will be limited.", stacklevel=2)
-
-except ModuleNotFoundError:
-    warnings.warn("Missing netCDF4 library. Some functionality will be limited.", stacklevel=2)
-
-from typing import Union, Optional
-from datetime import datetime, tzinfo, timezone, timedelta
-
-import tsp
-import tsp.labels as lbl
-import tsp.tspwarnings as tw
-
-from tsp.physics import analytical_fourier
-from tsp.plots.static import trumpet_curve, colour_contour, time_series, profile_evolution
-from tsp.time import format_utc_offset
-from tsp.time import get_utc_offset
-from tsp.misc import completeness
-
-from matplotlib.figure import Figure
-
-
-class TSP:
-    """ A Time Series Profile (a collection of time series data at different depths)
-    
-    A TSP can also be:
-    Thermal State of Permafrost
-    Temperature du Sol en Profondeur
-    Temperatures, Secondes, Profondeurs
-
-    Parameters
-    ----------
-    times : pandas.DatetimeIndex
-        DatetimeIndex with optional UTC offset. List-like array of datetime objects can also be passed, 
-        but will be converted to a DatetimeIndex with no UTC offset.
-    depths : list-like
-        d-length array of depths
-    values : numpy.ndarray
-        array with shape (t,d) containing values at (t)emperatures and (d)epths
-    longitude : float, optional
-        Longitude at which data were collected
-    latitude : float, optional
-        Latitude at which data were collected
-    site_id : str, optional
-        Name of location at which data were collected
-    metadata : dict
-        Additional metadata
-
-    Attributes
-    ----------
-    values
-    latitude : float
-        Latitude at which data were collected
-    longitude : float  
-        Longitude at which data were collected
-    metadata : dict
-        Additional metadata provided at instantiation or by other methods
-    """
-
-    def __repr__(self) -> str:
-        return repr(self.wide)
-
-    def __str__(self) -> str:
-        return str(self.wide)
-
-    def __init__(self, times, depths, values, 
-                 latitude: Optional[float]=None, 
-                 longitude: Optional[float]=None,
-                 site_id: Optional[str]=None,
-                 metadata: dict={}):
-
-        self._times = handle_incoming_times(times)
-        if self._times.duplicated().any():
-            warnings.warn(tw.DuplicateTimesWarning(self._times), stacklevel=2)
-        
-        if self.utc_offset:
-            self._output_utc_offset = self.utc_offset
-        else:
-            self._output_utc_offset = None
-        
-        self._depths = np.atleast_1d(depths)
-        self._values = np.atleast_2d(values)
-        self.__number_of_observations = np.ones_like(values, dtype=int)
-        self.__number_of_observations[np.isnan(values)] = 0
-        self.metadata = metadata
-        self.latitude = latitude
-        self.longitude = longitude
-        self.site_id = site_id
-        self._freq = None
-        self._completeness = None
-
-    @property
-    def freq(self) -> Optional[int]:
-        """ Measurement frequency [s] """
-        return self._freq
-    
-    @freq.setter
-    def freq(self, value: int):
-        if not isinstance(value, int):
-            raise TypeError("Must be string, e.g. '1D', '3600s'")
-        self._freq = value
-
-    @property
-    def completeness(self) -> Optional[pd.DataFrame]:
-        """ Data completeness """
-        return self._completeness
-    
-    @completeness.setter
-    def completeness(self, value):
-        raise ValueError("You can't assign this variable.")
-
-    @classmethod
-    def from_tidy_format(cls, times, depths, values,
-                        number_of_observations=None,
-                        latitude: Optional[float]=None, 
-                        longitude: Optional[float]=None,
-                        site_id: Optional[str]=None,
-                        metadata:dict={}):
-        """ Create a TSP from data in a 'tidy' or 'long' format 
-
-        Parameters
-        ----------
-        times : list-like
-            n-length array of datetime objects
-        depths : list-like
-            n-length array of depths
-        values : numpy.ndarray
-            n-length array of (temperaure) values at associated time and depth
-        number_of_observations : numpy.ndarray, optional
-            n-length array of number of observations at associated time and 
-            depth for aggregated values (default: 1)
-        longitude : float, optional
-            Longitude at which data were collected
-        latitude : float, optional
-            Latitude at which data were collected
-        site_id : str, optional
-            Name of location at which data were collected
-        metadata : dict
-            Additional metadata
-        """
-        times = np.atleast_1d(times)
-        depths = np.atleast_1d(depths)
-        values = np.atleast_1d(values)
-        
-        number_of_observations = number_of_observations if number_of_observations else np.ones_like(values)
-        df = pd.DataFrame({"times": times, "depths": depths, "temperature_in_ground": values, "number_of_observations": number_of_observations})
-        df.set_index(["times", "depths"], inplace=True)
-
-        try:
-            unstacked = df.unstack()
-        except ValueError as e:
-            if np.any(df.index.duplicated()):
-                print(f"Duplicate data found at {df.iloc[np.where(df.index.duplicated())[0], :].index.get_level_values(0).unique()}")
-            raise e
-
-        temps = unstacked.get('temperature_in_ground') 
-        
-        this = cls(times=temps.index.values,
-                   depths=temps.columns.values,
-                   values=temps.values,
-                   latitude=latitude, 
-                   longitude=longitude,
-                   site_id=site_id,
-                   metadata=metadata)
-        
-        number_of_observations = unstacked.get('number_of_observations').values
-
-        number_of_observations[np.isnan(number_of_observations)] = 0
-        this.__number_of_observations = number_of_observations
-        return this
-
-    @classmethod
-    def __from_tsp(cls, t:TSP, **kwargs) -> "TSP":
-        """ Use an existing TSP object as a template, """
-        kw = {}
-        for arg in inspect.getfullargspec(TSP).args[1:]:
-            if kwargs.get(arg) is not None:
-                kw[arg] = kwargs.get(arg)
-            else:
-                kw[arg] = getattr(t, arg)
-        
-        t = TSP(**kw)
-
-        return t
-
-    @classmethod
-    def from_json(cls, json_file) -> "TSP":
-        """ Read data from a json file 
-
-        Parameters
-        ----------
-        json_file : str
-            Path to a json file from which to read
-        """
-        df = pd.read_json(json_file)
-        depth_pattern = r"^(-?[0-9\.]+)$"
-
-        times = pd.to_datetime(df['time']).values
-        depths = [re.search(depth_pattern, c).group(1) for c in df.columns if tsp._is_depth_column(c, depth_pattern)]
-        values = df.loc[:, depths].to_numpy()
-        
-        t = cls(times=times, depths=depths, values=values)
-        
-        return t
-
-    @classmethod
-    def synthetic(cls, depths: "np.ndarray", start="2000-01-01", end="2003-01-01",
-                  Q:"Optional[float]"=0.2, 
-                  c:"Optional[float]"=1.6e6,
-                  k:"Optional[float]"=2.5,
-                  A:"Optional[float]"=6,
-                  MAGST:"Optional[float]"=-0.5) -> "TSP":
-        """
-        Create a 'synthetic' temperature time series using the analytical solution to the heat conduction equation.
-        Suitable for testing 
-        
-        Parameters
-        ----------   
-        depths : np.ndarray
-            array of depths in m
-        start : str
-            array of times in seconds
-        Q : Optional[float], optional
-            Ground heat flux [W m-2], by default 0.2
-        c : Optional[float], optional
-            heat capacity [J m-3 K-1], by default 1.6e6
-        k : Optional[float], optional
-            thermal conductivity [W m-1 K-1], by default 2.5
-        A : Optional[float], optional
-            Amplitude of temperature fluctuation [C], by default 6
-        MAGST : Optional[float], optional
-            Mean annual ground surface temperature [C], by default -0.5
-        
-        Returns 
-        -------
-        TSP 
-            A timeseries profile (TSP) object
-        """
-        times = pd.date_range(start=start, end=end).to_pydatetime()
-        t_sec = np.array([(t-times[0]).total_seconds() for t in times])
-        
-        values = analytical_fourier(depths=depths, times=t_sec, Q=Q, c=c, k=k, A=A, MAGST=MAGST)
-        
-        this = cls(depths=depths, times=times, values=values)
-        
-        return this
-
-    @property
-    @functools.lru_cache()
-    def long(self) -> "pd.DataFrame":
-        """ Return the data in a 'long' or 'tidy' format (one row per observation, one column per variable)
-
-        Returns
-        -------
-        pandas.DataFrame
-            Time series profile data with columns:
-                - **time**: time
-                - **depth**: depth 
-                - **temperature_in_ground**: temperature
-                - **number_of_observations**: If data are aggregated, how many observations are used in the aggregation
-        """
-        values = self.wide.melt(id_vars='time',
-                                var_name="depth",
-                                value_name="temperature_in_ground")
-
-        number_of_observations = self.number_of_observations.melt(id_vars='time',
-                                  var_name="depth",
-                                  value_name="number_of_observations")
-                              
-        values['number_of_observations'] = number_of_observations['number_of_observations']
-
-        return values
-
-    @property
-    @functools.lru_cache()
-    def wide(self) -> "pd.DataFrame":
-        """ Return the data in a 'wide' format (one column per depth)
-
-        Returns
-        -------
-        pandas.DataFrame
-            Time series profile data
-        """
-        tabular = pd.DataFrame(self._values)
-        tabular.columns = self._depths
-        tabular.index = self.times
-        tabular.insert(0, "time", self.times)
-
-        return tabular
-
-    @property
-    @functools.lru_cache()
-    def number_of_observations(self) -> "pd.DataFrame":
-        """ The number of observations for an average at a particular depth or time.
-
-        For pure observational data, the number of observations will always be '1'. When data are aggregated, 
-        (e.g. using :py:meth:`~tsp.core.TSP.monthly` or :py:meth:`~tsp.core.TSP.daily`) these numbers
-        will be greater than 1.
-
-        Returns
-        -------
-        DataFrame
-            Number of observations 
-        """
-        tabular = pd.DataFrame(self.__number_of_observations, dtype=int)
-        tabular.columns = self._depths
-        tabular.index = self._times
-        tabular.insert(0, "time", self._times)
-
-        return tabular
-
-    @number_of_observations.setter
-    def number_of_observations(self, value):
-        raise ValueError(f"You can't assign {value} to this variable (no assignment allowed).")
-
-    def reset_counts(self):
-        """ Set observation count to 1 if data exists, 0 otherwise """
-        self.__number_of_observations = (~self.wide.isna()).astype('boolean')
-
-    def set_utc_offset(self, offset:"Union[int,str]") -> None:
-        """ Set the time zone of the data by providing a UTC offset 
-
-        Parameters
-        ----------
-        offset : int, str
-            If int, the number of seconds. If str, a string in the format "+HH:MM" or "-HH:MM"
-        """
-        if self.utc_offset is not None:
-            raise ValueError("You can only set the UTC offset once.")
-
-        utc_offset = get_utc_offset(offset)
-
-        tz = timezone(timedelta(seconds = utc_offset)) 
-        self._times = self._times.tz_localize(tz)
-        self._output_utc_offset = timezone(timedelta(seconds = utc_offset)) 
-
-        TSP.wide.fget.cache_clear()
-        TSP.long.fget.cache_clear()
-
-    @property
-    def utc_offset(self) -> "Optional[tzinfo]":
-        """ Get the time zone of the data by providing a UTC offset
-
-        Returns
-        -------
-        datetime.tzinfo
-            A timezone object
-        """
-        if self._times.tz is None:
-            return None
-        else:
-            return self._times.tz
-    
-    @utc_offset.setter
-    def utc_offset(self, value):
-        self.set_utc_offset(value)
-    
-    @property
-    def output_utc_offset(self) -> "Optional[tzinfo]":
-        """ Get the time zone in which to output or display the data by providing a UTC offset
-        
-        Returns
-        -------
-        datetime.tzinfo
-            A timezone object
-        """
-        if self._output_utc_offset is None:
-            return None
-        else:
-            return self._output_utc_offset
-    
-    @output_utc_offset.setter
-    def output_utc_offset(self, offset:"Union[int,str]") -> None:
-        self.set_output_utc_offset(offset)
-
-    def set_output_utc_offset(self, offset:"Union[int,str]") -> None:
-        """ Set the time zone in which to display the output or data by providing a UTC offset
-        Parameters
-        ----------
-        offset : int, str
-            If int, the number of seconds. If str, a string in the format "+HH:MM" or "-HH:MM"
-        """
-        utc_offset = get_utc_offset(offset)
-        tz = timezone(timedelta(seconds = utc_offset))
-        self._output_utc_offset = tz
-        
-        TSP.wide.fget.cache_clear()
-        TSP.long.fget.cache_clear()
-
-    def reset_output_utc_offset(self) -> None:
-        """ Reset the time zone in which to output or display the data to the default (the one set by set_utc_offset)
-        
-        """
-        if self.utc_offset is None:
-            raise ValueError("You can't reset the output time zone if the time zone of the data hasn't yet been set with set_utc_offset.")
-        else:
-            self._output_utc_offset = self.utc_offset
-
-    def __nly(self, 
-              freq_fmt:str,
-              new_freq,
-              min_count:Optional[int],
-              max_gap:Optional[int],
-              min_span:Optional[int]) -> TSP:
-        """
-        Temporal aggregation by grouping according to a string-ified time
-
-        Parameters
-        ----------
-        freq_fmt : str
-            Python date format string  used to aggregate and recover time 
-        
-        Returns
-        -------
-        tuple[pd.DataFrame, pd.DataFrame]
-            A tuple of dataframes, the first containing the aggregated data, the second containing the number of observations
-        """
-        R = self.wide.drop("time", axis=1).resample(freq_fmt)
-        cumulative_obs = self.number_of_observations.drop("time", axis=1).resample(freq_fmt).sum()
-        total_obs = R.count()
-        values = R.mean()
-
-        # Calculate masks
-        mc_mask = Mg_mask = ms_mask = pd.DataFrame(index=values.index, columns=values.columns, data=False)
-
-        if min_count is not None:
-            mc_mask = (cumulative_obs < min_count)
-        if max_gap is not None:
-            Mg_mask = max_gap_mask(R, max_gap)
-        if min_span is not None:
-            ms_mask = min_span_mask(R, min_span)
-        
-        mask = (mc_mask | Mg_mask | ms_mask)
-        values[mask] = np.nan
-        
-        # Construct TSP
-        t = TSP.__from_tsp(self, times=values.index, 
-                           depths=values.columns, 
-                           values=values.values)
-        t.__number_of_observations = cumulative_obs
-        t.freq = new_freq
-
-        # Calculate data completeness
-        if self.freq is not None:
-            f1 = self.freq
-            f2 = new_freq
-            t._completeness = completeness(total_obs, f1, f2)
-
-        return t
-    
-    def monthly(self,
-                min_count:Optional[int]=24,
-                max_gap:Optional[int]=3600*24*8,
-                min_span:Optional[int]=3600*24*21) -> "TSP":
-        """ Monthly averages, possibly with some months unavailable (NaN) if there is insufficient data
-
-        Parameters
-        ----------
-        min_count : int
-            Minimum number of observations in a month to be considered a valid average,
-            defaults to None
-        max_gap : int
-            Maximum gap (in seconds) between data points to be considered a valid average,
-             defaults to None
-        min_span : int
-            Minimum total data range (in seconds) to be consiered a valid average,
-            defaults to None
-            
-        Returns
-        -------
-        TSP
-            A TSP object with data aggregated to monthly averages
-        """
-        t = self.__nly(freq_fmt="M", 
-                       new_freq=lbl.MONTHLY, 
-                       min_count=min_count, 
-                       max_gap=max_gap, 
-                       min_span=min_span)
-
-        return t
-
-    def daily(self, 
-              min_count:Optional[int]=None,
-              max_gap:Optional[int]=None,
-              min_span:Optional[int]=None) -> "TSP":
-        """ Daily averages, possibly with some days unavailable (NaN) if there is insufficient data
-
-        Parameters
-        ----------
-        min_count : int
-            Minimum number of observations in a day to be considered a valid average, 
-            defaults to None
-        max_gap : int
-            Maximum gap (in seconds) between data points to be considered a valid average, defaults to None
-        min_span : int
-            Minimum total data range (in seconds) to be consiered a valid average, defaults to None
-        
-        Returns
-        -------
-        TSP
-            A TSP object with data aggregated to daily averages
-        """
-        # if the data is already daily +/- 1min , just return it
-        t = self.__nly(freq_fmt="D", 
-                new_freq=lbl.DAILY, 
-                min_count=min_count, 
-                max_gap=max_gap, 
-                min_span=min_span)
-
-        return t
-
-    def yearly(self,
-               min_count:Optional[int]=None,
-               max_gap:Optional[int]=None,
-               min_span:Optional[int]=None) -> "TSP":
-        """ Yearly averages, possibly with some years unavailable (NaN) if there is insufficient data
-
-        Parameters
-        ----------
-        min_count : int
-            Minimum number of observations in a month to be considered a valid average, defaults to None
-        max_gap : int
-            Maximum gap (in seconds) between data points to be considered a valid average, defaults to None
-        min_span : int
-            Minimum total data range (in seconds) to be consiered a valid average, defaults to None
-        
-        Returns
-        -------
-        TSP
-            A TSP object with data aggregated to yearly averages
-        """
-        t = self.__nly(freq_fmt="Y", 
-                new_freq=lbl.YEARLY, 
-                min_count=min_count, 
-                max_gap=max_gap, 
-                min_span=min_span)
-
-        return t
-
-    @property
-    def depths(self) -> "np.ndarray":
-        """ Return the depth values in the profile 
-
-        Returns
-        -------
-        numpy.ndarray
-            The depths in the profile
-        """
-        return self._depths
-
-    @depths.setter
-    def depths(self, value):
-        depths = np.atleast_1d(value)
-        
-        if not len(depths) == len(self._depths):
-            raise ValueError(f"List of depths must have length of {len(self._depths)}.")
-
-        self._depths = depths
-
-        TSP.wide.fget.cache_clear()
-        TSP.long.fget.cache_clear()
-
-    @property
-    def times(self):
-        """ Return the timestamps in the time series 
-
-        Returns
-        -------
-        pandas.DatetimeIndex
-            The timestamps in the time series
-        """
-        if self.utc_offset is None:
-            return self._times
-        
-        elif self._output_utc_offset == self.utc_offset:
-            return self._times
-
-        else:
-            return self._times.tz_convert(self.output_utc_offset)
-
-    @property
-    def values(self):
-        return self._values
-
-    def to_gtnp(self, filename: str) -> None:
-        """ Write the data in GTN-P format
-        
-        Parameters
-        ----------
-        filename : str
-            Path to the file to write to
-        """
-        df = self.wide.rename(columns={'time': 'Date/Depth'})
-        df['Date/Depth'] = df['Date/Depth'].dt.strftime("%Y-%m-%d %H:%M:%S")
-
-        df.to_csv(filename, index=False, na_rep="-999")
-
-    def to_ntgs(self, filename:str, project_name:str="", site_id:"Optional[str]" = None, latitude:"Optional[float]"=None, longitude:"Optional[float]"=None) -> None:
-        """ Write the data in NTGS template format 
-
-        Parameters
-        ----------
-        filename : str
-            Path to the file to write to
-        project_name : str, optional
-            The project name, by default ""
-        site_id : str, optional
-            The name of the site , by default None
-        latitude : float, optional
-            WGS84 latitude at which the observations were recorded, by default None
-        longitude : float, optional
-            WGS84 longitude at which the observations were recorded, by default None
-        """
-        if latitude is None:
-            latitude = self.latitude if self.latitude is not None else ""
-
-        if longitude is None:
-            longitude = self.longitude if self.longitude is not None else ""
-
-        if site_id is None:
-                site_id = self.site_id if self.site_id is not None else ""
-        data = self.values
-
-        df = pd.DataFrame({'project_name': pd.Series(dtype='str'),
-                           'site_id': pd.Series(dtype='str'),
-                           'latitude': pd.Series(dtype='float'),
-                           'longitude': pd.Series(dtype='float')
-                           })
-
-        df["date_YYYY-MM-DD"] = pd.Series(self.times).dt.strftime(r"%Y-%m-%d")
-        df["time_HH:MM:SS"] = pd.Series(self.times).dt.strftime(r"%H:%M:%S")
-
-        df["project_name"] = project_name
-        df["site_id"] = site_id
-        df["latitude"] = latitude
-        df["longitude"] = longitude
-        
-        headers = [str(d) + "_m" for d in self.depths]
-        
-        for i, h in enumerate(headers):
-            df[h] = data[:, i]
-
-        df.to_csv(filename, index=False)
-
-    def to_netcdf(self, file: str) -> None:
-        """  Write the data as a netcdf"""
-        try:
-            ncf = make_temperature_base(file, len(self.depths))
-        except NameError:
-            warnings.warn("Missing required packages. Try installing with `pip install tsp[nc]`", stacklevel=2)
-            return
-        
-        with nc.Dataset(ncf, 'a') as ncd:
-            pytime = self.times.to_pydatetime()
-
-            ncd['depth_below_ground_surface'][:] = self.depths
-
-            
-            ncd['time'][:] = nc.date2num(pytime, ncd['time'].units, ncd['time'].calendar)
-            ncd['ground_temperature'][:] = self.values
-            
-            if self.latitude:
-                ncd['latitude'][:] = self.latitude
-            if self.longitude:
-                ncd['longitude'][:] = self.longitude
-            if self.site_id:
-                ncd['site_name'] = self.site_id
-            
-            for key, value in self.metadata:
-                try:
-                    ncd.setncattr(key, value)
-                except Exception:
-                    warnings.warn(f"Could not set metadata item: {key}", stacklevel=2)
-
-    def to_json(self, file: str) -> None:
-        """ Write the data to a serialized json file """
-        with open(file, 'w') as f:
-            f.write(self._to_json())
-
-    def _to_json(self) -> str:
-        return self.wide.to_json()
-
-    def plot_profiles(self, P:int=100, n:int=10) -> Figure:
-        """ Create a plot of the temperature profiles at different times
-        
-        Parameters
-        ----------
-        P : int
-            Percentage of time range to plot
-        n : int
-            Number of evenly-spaced profiles to plot
-        
-        Returns
-        -------
-        Figure
-            matplotlib `Figure` object
-        """
-        fig = profile_evolution(depths=self.depths, times=self.times, values=self._values, P=P, n=n)
-        fig.show()
-        return fig
-    
-    def plot_trumpet(self, 
-                     year: Optional[int]=None,
-                     begin: Optional[datetime]=None,
-                     end: Optional[datetime]=None,
-                     min_completeness: Optional[float]=None,
-                     **kwargs) -> Figure:
-        """ Create a trumpet plot from the data
-        
-        Parameters
-        ----------
-        year : int, optional
-            Which year to plot
-        begin : datetime, optional
-            If 'end' also provided, the earliest measurement to include in the averaging for the plot
-        end : datetime, optional
-            If 'begin' also provided, the latest measurement to include in the averaging for the plot
-        min_completeness : float, optional
-            If provided, the minimum completeness (fractional, 0 to 1) required to include
-            in temperature envelope, otherwise
-            the point is plotted as an unconnected, slightly transparent dot, by default None
-        **kwargs : dict, optional
-            Extra arguments to the plotting function: refer to the documentation for :func:`~tsp.plots.static.trumpet_curve` for a
-            list of all possible arguments.
-
-        Returns
-        -------
-        Figure
-            a matplotlib `Figure` object
-        """
-        df = self.long.dropna()
- 
-        if year is not None:
-            df = df[df['time'].dt.year == year]
-
-        elif begin is not None or end is not None:
-            raise NotImplementedError
-
-        else:
-            raise ValueError("One of 'year', 'begin', 'end' must be provided.")
-
-        grouped = df.groupby('depth')
-
-        max_t = grouped.max().get('temperature_in_ground').values
-        min_t = grouped.min().get('temperature_in_ground').values
-        mean_t = grouped.mean().get('temperature_in_ground').values
-        depth = np.array([d for d in grouped.groups.keys()])
-
-        # Calculate completeness
-        c = self.yearly(None, None, None).completeness
-        
-        if min_completeness is not None and c is not None:
-            C = c[c.index.year == year]
-            C = C[depth].iloc[0,:].values
-        
-        else:
-            C = None
-
-        fig = trumpet_curve(depth=depth, 
-                            t_max=max_t, 
-                            t_min=min_t, 
-                            t_mean=mean_t, 
-                            min_completeness=min_completeness,
-                            data_completeness=C,
-                            **kwargs)
-        fig.show()
-
-        return fig
-    
-    def plot_contour(self, **kwargs) -> Figure:
-        """ Create a contour plot
-        
-        Parameters
-        ----------
-        **kwargs : dict, optional
-            Extra arguments to the plotting function: refer to the documentation for :func:`~tsp.plots.static.colour_contour` for a
-            list of all possible arguments.
-
-        Returns
-        -------
-        Figure
-            matplotlib `Figure` object
-        """
-        fig = colour_contour(depths=self.depths, times=self.times, values=self._values, **kwargs)
-
-        if self.output_utc_offset is not None:
-            label = format_utc_offset(self.output_utc_offset)
-            if label != "UTC":
-                label = f"UTC{label}"         
-            fig.axes[0].set_xlabel(f"Time [{label}]")
-
-        fig.show()
-
-        return fig
-
-    def plot_timeseries(self, depths: list=[], **kwargs) -> Figure:
-        """Create a time series T(t) plot 
-
-        Parameters
-        ----------
-        depths : list, optional
-            If non-empty, restricts the depths to include in the plot, by default []
-        **kwargs : dict, optional
-            Extra arguments to the plotting function: refer to the documentation for :func:`~tsp.plots.static.time_series` for a
-            list of all possible arguments.
-
-        Returns
-        -------
-        Figure
-            matplotlib `Figure` object
-        """
-        if depths == []:
-            depths = self.depths
-        
-        d_mask = np.isin(self.depths, depths)
-        
-        fig = time_series(self.depths[d_mask], self.times, self.values[:, d_mask], **kwargs)
-  
-
-        if self.output_utc_offset is not None:
-            label = format_utc_offset(self.output_utc_offset)
-            if label != "UTC":
-                label = f"UTC{label}"         
-            fig.axes[0].set_xlabel(f"Time [{label}]")
-        fig.autofmt_xdate()
-        fig.show()
-        
-        return fig
-
-
-class AggregatedTSP(TSP):
-    """ A Time Series Profile that uses indices (1,2,3,...) instead of depth values. 
-    
-    Used in situations when depths are unknown (such as when reading datlogger exports
-    that don't have depth measurements.)
-    
-    Parameters
-    ----------
-    times : list-like
-        t-length array of datetime objects
-    values : numpy.ndarray
-        array with shape (t,d) containing values at (t)emperatures and (d)epths
-    **kwargs : dict
-        Extra arguments to parent class: refer to :py:class:`tsp.core.TSP` documentation for a
-        list of all possible arguments.
-    """
-
-
-class IndexedTSP(TSP):
-    """ A Time Series Profile that uses indices (1,2,3,...) instead of depth values. 
-    
-    Used in situations when depths are unknown (such as when reading datlogger exports
-    that don't have depth measurements.)
-    
-    Parameters
-    ----------
-    times : list-like
-        t-length array of datetime objects
-    values : numpy.ndarray
-        array with shape (t,d) containing values at (t)emperatures and (d)epths
-    **kwargs : dict
-        Extra arguments to parent class: refer to :py:class:`~tsp.core.TSP` documentation for a
-        list of all possible arguments.
-    """
-
-    def __init__(self, times, values, **kwargs):
-        depths = np.arange(0, values.shape[1]) + 1
-        super().__init__(times=times, depths=depths, values=values, **kwargs)
-
-    @property
-    def depths(self) -> np.ndarray:
-        """Depth indices 
-
-        Returns
-        -------
-        numpy.ndarray
-            An array of depth indices
-        """
-        warnings.warn("This TSP uses indices (1,2,3,...) instad of depths. Use set_depths() to use measured depths.", stacklevel=2)
-        return self._depths
-
-    @depths.setter
-    def depths(self, value):
-        TSP.depths.__set__(self, value)
-
-    def set_depths(self, depths: np.ndarray):
-        """Assign depth values to depth indices. Change the object to a :py:class:`~tsp.core.TSP`
-
-        Parameters
-        ----------
-        depths : np.ndarray
-            An array or list of depth values equal in lenth to the depth indices
-        """
-        self.depths = depths
-        self.__class__ = TSP
-
-
-
-def span(S: pd.Series) -> float:
-    first = S.first_valid_index()  # type: pd.Timestamp
-    last = S.last_valid_index()  # type: pd.Timestamp
-    if first is None or last is None:
-        return 0
-    
-    return (last - first).total_seconds()
-
-def min_span_mask(R: "pd.core.resample.DatetimeIndexResampler",
-             threshold: float) -> "pd.DataFrame":
-    s = R.apply(lambda x: span(x))
-    return s < threshold
-
-
-def gap(S: pd.Series) -> float:
-
-    d = np.diff(S.dropna().index)
-    if len(d) == 0:
-        return 0
-    elif len(d) == 1:
-        return 0
-    elif len(d) > 1:
-        gap = max(d).astype('timedelta64[s]').astype(float)
-    return gap
-
-
-def max_gap_mask(R: "pd.core.resample.DatetimeIndexResampler",
-            threshold: float) -> "pd.DataFrame":
-    g = R.apply(lambda x: gap(x))
-    return (g > threshold) | (g == 0)
-
-
-
-
-def _temporal_gap_mask(grouped: "pd.core.groupby.DataFrameGroupBy", max_gap: Optional[int], min_span: Optional[int]) -> np.ndarray:
-    """ Mask out observational groups in which there is more than a certain size temporal gap
-
-    Controls for gaps in the data within an aggregation group (using max_gap) and missing data at the beginning
-    or end of the aggregation group (using min_span).
-    
-    Parameters
-    ----------
-    grouped : pandas.core.groupby.DataFrameGroupBy
-        groupby  with 'time' and 'depth' columns
-    max_gap : int
-        maximum gap in seconds to tolerate between observations in a group
-    min_span : int
-        minimum data range (beginning to end) in seconds. 
-
-    Returns
-    -------
-    numpy.ndarray
-        boolean array with ``True`` where measurement spacing or range in group does not satisfy tolerances
-    """
-    if max_gap is not None:
-        max_diff = grouped.time.apply(np.diff).apply(lambda x: np.max(x, initial=np.timedelta64(0))).apply(lambda x: x.total_seconds())
-        max_diff = max_diff.unstack().to_numpy()
-        diff_mask = np.where((max_diff == 0) | (max_diff >= max_gap), True, False)
-    else:
-        diff_mask = np.zeros_like(grouped, dtype=bool)
-    
-    if min_span is not None:
-        total_span = grouped.time.apply(np.ptp).apply(lambda x: x.total_seconds()).unstack().to_numpy()
-        span_mask = np.where(total_span < min_span, True, False)
-    else:
-        span_mask = np.zeros_like(grouped, dtype=bool)
-
-    mask = diff_mask * span_mask
-
-    return mask
-
-
-def _observation_count_mask(number_of_observations: np.ndarray, min_count:int) -> np.ndarray:
-    """ Create a mask array for an
-    
-    Parameters
-    ----------
-    number_of_observations : numpy.ndarray
-        Array of how many data points are in aggregation
-    min_count : int
-        Minimum number of data points for aggregation to be 'valid'
-
-    Returns
-    -------
-    np.ndarray
-        a mask, True where data should be masked
-    """
-    valid = np.less(number_of_observations, min_count)  # type: np.ndarray
-    return valid
-
-
-def handle_incoming_times(times: "Union[np.ndarray, pd.DatetimeIndex, pd.Series, list]") -> "pd.DatetimeIndex":
-    """Convert a list of times to a pandas DatetimeIndex object"""
-    invalid_msg = "Times must be a list, numpy array, pandas DatetimeIndex, or pandas Series"
-
-    try:
-        if not len(times):
-            raise ValueError(invalid_msg)
-    except TypeError:
-        raise ValueError(invalid_msg)
-
-    if isinstance(times, pd.DatetimeIndex):
-        return times
-
-    if isinstance(times, pd.Series):
-        try:
-            times = pd.DatetimeIndex(times)
-        except Exception:
-            raise ValueError("Series must be convertible to DatetimeIndex")
-        times.name = 'time'
-
-        return times
-
-    elif isinstance(times, np.ndarray):
-        times = pd.to_datetime(times)
-        times.name = 'time'
-        return times
-    
-    elif isinstance(times, list):
-        return pd.to_datetime(times)
-
-    else:
-        raise ValueError(invalid_msg)
+from __future__ import annotations
+
+import pandas as pd
+import re
+import inspect
+import numpy as np
+import functools
+import warnings
+
+try:
+    import netCDF4 as nc
+
+    try:
+        from pfit.pfnet_standard import make_temperature_base, calculate_extent_metadata as calc_ext_meta
+    except ModuleNotFoundError:
+        warnings.warn("Missing pfit library. Some functionality will be limited.", stacklevel=2)
+
+except ModuleNotFoundError:
+    warnings.warn("Missing netCDF4 library. Some functionality will be limited.", stacklevel=2)
+
+from typing import Union, Optional
+from numpy.typing import NDArray
+from datetime import datetime, tzinfo, timezone, timedelta
+
+import tsp
+import tsp.labels as lbl
+import tsp.tspwarnings as tw
+
+from tsp.physics import analytical_fourier
+from tsp.plots.static import trumpet_curve, colour_contour, time_series, profile_evolution
+from tsp.time import format_utc_offset
+from tsp.time import get_utc_offset
+from tsp.misc import completeness
+from tsp.concatenation import _tsp_concat
+
+from matplotlib.figure import Figure
+
+
+class TSP:
+    """ A Time Series Profile (a collection of time series data at different depths)
+    
+    A TSP can also be:
+    Thermal State of Permafrost
+    Temperature du Sol en Profondeur
+    Temperatures, Secondes, Profondeurs
+
+    Parameters
+    ----------
+    times : pandas.DatetimeIndex
+        DatetimeIndex with optional UTC offset. List-like array of datetime objects can also be passed, 
+        but will be converted to a DatetimeIndex with no UTC offset.
+    depths : list-like
+        d-length array of depths
+    values : numpy.ndarray
+        array with shape (t,d) containing values at (t)emperatures and (d)epths
+    longitude : float, optional
+        Longitude at which data were collected
+    latitude : float, optional
+        Latitude at which data were collected
+    site_id : str, optional
+        Name of location at which data were collected
+    metadata : dict
+        Additional metadata
+
+    Attributes
+    ----------
+    values
+    latitude : float
+        Latitude at which data were collected
+    longitude : float  
+        Longitude at which data were collected
+    metadata : dict
+        Additional metadata provided at instantiation or by other methods
+    """
+
+    def __repr__(self) -> str:
+        return repr(self.wide)
+
+    def __str__(self) -> str:
+        return str(self.wide)
+    
+    def __add__(self, other: TSP) -> TSP:
+        """ Concatenate two TSP objects along the time axis. 
+        The two TSP objects must have the same depths and the same UTC offset.
+
+        Parameters
+        ----------
+        other : TSP
+            Another TSP object to concatenate with this one
+
+        Returns
+        -------
+        TSP
+            A new TSP object with the concatenated data
+        """
+        if not isinstance(other, TSP):
+            raise TypeError("Can only concatenate TSP objects.")
+        
+        if self.utc_offset != other.utc_offset:
+            raise ValueError("UTC offsets must be the same to concatenate.")
+        
+        return tsp_concat([self, other])
+
+    def __init__(self, times, depths, values, 
+                 latitude: Optional[float]=None, 
+                 longitude: Optional[float]=None,
+                 site_id: Optional[str]=None,
+                 metadata: dict={}):
+
+        self._times = handle_incoming_times(times)
+        if self._times.duplicated().any():
+            warnings.warn(tw.DuplicateTimesWarning(self._times), stacklevel=2)
+        
+        if self.utc_offset:
+            self._output_utc_offset = self.utc_offset
+        else:
+            self._output_utc_offset = None
+        
+        self._depths = np.atleast_1d(depths)
+        self._values = np.atleast_2d(values)
+        self.__number_of_observations = np.ones_like(values, dtype=int)
+        self.__number_of_observations[np.isnan(values)] = 0
+        self.metadata = metadata
+        self._latitude = latitude
+        self._longitude = longitude
+        self.site_id = site_id
+        self._freq = None
+        self._completeness = None
+
+        self._export_precision = 3
+
+    @property
+    def latitude(self):
+        """ Latitude at which data were collected """
+        return self._latitude
+    
+    @latitude.setter
+    def latitude(self, value: Optional[float]):
+        if value is not None:
+            try:
+                self._latitude = float(value)
+            except ValueError:
+                raise ValueError("Latitude must be a float or None.")
+        else:
+            self._latitude = None
+        self.metadata['_latitude'] = self._latitude
+
+    @property
+    def longitude(self):
+        """ Longitude at which data were collected """
+        return self._longitude
+
+    @longitude.setter
+    def longitude(self, value: Optional[float]):
+        if value is not None:
+            try:
+                self._longitude = float(value)
+            except ValueError:
+                raise ValueError("Longitude must be a float or None.")
+        else:
+            self._longitude = None
+        self.metadata['_longitude'] = self._longitude
+
+    @property
+    def freq(self) -> Optional[int]:
+        """ Measurement frequency [s] """
+        return self._freq
+    
+    @freq.setter
+    def freq(self, value: int):
+        if not isinstance(value, int):
+            raise TypeError("Must be string, e.g. '1D', '3600s'")
+        self._freq = value
+
+    @property
+    def completeness(self) -> Optional[pd.DataFrame]:
+        """ Data completeness """
+        return self._completeness
+    
+    @completeness.setter
+    def completeness(self, value):
+        raise ValueError("You can't assign this variable.")
+
+    @classmethod
+    def from_tidy_format(cls, times, depths, values,
+                        number_of_observations=None,
+                        latitude: Optional[float]=None, 
+                        longitude: Optional[float]=None,
+                        site_id: Optional[str]=None,
+                        metadata:dict={}):
+        """ Create a TSP from data in a 'tidy' or 'long' format 
+
+        Parameters
+        ----------
+        times : list-like
+            n-length array of datetime objects
+        depths : list-like
+            n-length array of depths
+        values : numpy.ndarray
+            n-length array of (temperaure) values at associated time and depth
+        number_of_observations : numpy.ndarray, optional
+            n-length array of number of observations at associated time and 
+            depth for aggregated values (default: 1)
+        longitude : float, optional
+            Longitude at which data were collected
+        latitude : float, optional
+            Latitude at which data were collected
+        site_id : str, optional
+            Name of location at which data were collected
+        metadata : dict
+            Additional metadata
+        """
+        times = np.atleast_1d(times)
+        depths = np.atleast_1d(depths)
+        values = np.atleast_1d(values)
+        
+        number_of_observations = number_of_observations if number_of_observations else np.ones_like(values)
+        df = pd.DataFrame({"times": times, "depths": depths, "temperature_in_ground": values, "number_of_observations": number_of_observations})
+        df.set_index(["times", "depths"], inplace=True)
+
+        try:
+            unstacked = df.unstack()
+        except ValueError as e:
+            if np.any(df.index.duplicated()):
+                print(f"Duplicate data found at {df.iloc[np.where(df.index.duplicated())[0], :].index.get_level_values(0).unique()}")
+            raise e
+
+        temps = unstacked.get('temperature_in_ground') 
+        
+        this = cls(times=temps.index.values,
+                   depths=temps.columns.values,
+                   values=temps.values,
+                   latitude=latitude, 
+                   longitude=longitude,
+                   site_id=site_id,
+                   metadata=metadata)
+        
+        number_of_observations = unstacked.get('number_of_observations').values
+
+        number_of_observations[np.isnan(number_of_observations)] = 0
+        this.__number_of_observations = number_of_observations
+        return this
+
+    @classmethod
+    def __from_tsp(cls, t:TSP, **kwargs) -> "TSP":
+        """ Use an existing TSP object as a template, """
+        kw = {}
+        for arg in inspect.getfullargspec(TSP).args[1:]:
+            if kwargs.get(arg) is not None:
+                kw[arg] = kwargs.get(arg)
+            else:
+                kw[arg] = getattr(t, arg)
+        
+        t = TSP(**kw)
+
+        return t
+
+    @classmethod
+    def from_json(cls, json_file) -> "TSP":
+        """ Read data from a json file 
+
+        Parameters
+        ----------
+        json_file : str
+            Path to a json file from which to read
+        """
+        df = pd.read_json(json_file)
+        depth_pattern = r"^(-?[0-9\.]+)$"
+
+        times = pd.to_datetime(df['time']).values
+        depths = [re.search(depth_pattern, c).group(1) for c in df.columns if tsp._is_depth_column(c, depth_pattern)]
+        values = df.loc[:, depths].to_numpy()
+        
+        t = cls(times=times, depths=depths, values=values)
+        
+        return t
+
+    @classmethod
+    def synthetic(cls, depths: NDArray[np.number], 
+                  start:str ="2000-01-01", 
+                  end:str ="2003-01-01",
+                  freq: "str"="D",
+                  Q:float=0.2, 
+                  c:float=1.6e6,
+                  k:float=2.5,
+                  A:float=6,
+                  MAGST:float=-0.5) -> "TSP":
+        """
+        Create a 'synthetic' temperature time series using the analytical solution to the heat conduction equation.
+        Suitable for testing 
+        
+        Parameters
+        ----------   
+        depths : np.ndarray
+            array of depths in metres
+        start : str
+            start date for the time series, in the format "YYYY-MM-DD"
+        end : str
+            end date for the time series, in the format "YYYY-MM-DD"
+        freq : str
+            pandas frequency string, e.g. "D" for daily, "H" for hourly, etc.
+        Q : Optional[float], optional
+            Ground heat flux [W m-2], by default 0.2
+        c : Optional[float], optional
+            heat capacity [J m-3 K-1], by default 1.6e6
+        k : Optional[float], optional
+            thermal conductivity [W m-1 K-1], by default 2.5
+        A : Optional[float], optional
+            Amplitude of temperature fluctuation [C], by default 6
+        MAGST : Optional[float], optional
+            Mean annual ground surface temperature [C], by default -0.5
+        
+        Returns 
+        -------
+        TSP 
+            A timeseries profile (TSP) object
+        """
+        times = pd.date_range(start=start, end=end, freq=freq).to_pydatetime()
+        t_sec = np.array([(t-times[0]).total_seconds() for t in times])
+        
+        values = analytical_fourier(depths=depths,
+                                    times=t_sec,
+                                    Q=Q,
+                                    c=c,
+                                    k=k,
+                                    A=A,
+                                    MAGST=MAGST)
+        
+        this = cls(depths=depths, times=times, values=values)
+        
+        return this
+
+    @property
+    @functools.lru_cache()
+    def long(self) -> "pd.DataFrame":
+        """ Return the data in a 'long' or 'tidy' format (one row per observation, one column per variable)
+
+        Returns
+        -------
+        pandas.DataFrame
+            Time series profile data with columns:
+                - **time**: time
+                - **depth**: depth 
+                - **temperature_in_ground**: temperature
+                - **number_of_observations**: If data are aggregated, how many observations are used in the aggregation
+        """
+        values = self.wide.melt(id_vars='time',
+                                var_name="depth",
+                                value_name="temperature_in_ground")
+
+        number_of_observations = self.number_of_observations.melt(id_vars='time',
+                                  var_name="depth",
+                                  value_name="number_of_observations")
+                              
+        values['number_of_observations'] = number_of_observations['number_of_observations']
+
+        return values
+
+    @property
+    @functools.lru_cache()
+    def wide(self) -> "pd.DataFrame":
+        """ Return the data in a 'wide' format (one column per depth)
+
+        Returns
+        -------
+        pandas.DataFrame
+            Time series profile data
+        """
+        tabular = pd.DataFrame(self._values)
+        tabular.columns = self._depths
+        tabular.index = self.times
+        tabular.insert(0, "time", self.times)
+
+        return tabular
+
+    @property
+    @functools.lru_cache()
+    def number_of_observations(self) -> "pd.DataFrame":
+        """ The number of observations for an average at a particular depth or time.
+
+        For pure observational data, the number of observations will always be '1'. When data are aggregated, 
+        (e.g. using :py:meth:`~tsp.core.TSP.monthly` or :py:meth:`~tsp.core.TSP.daily`) these numbers
+        will be greater than 1.
+
+        Returns
+        -------
+        DataFrame
+            Number of observations 
+        """
+        tabular = pd.DataFrame(self.__number_of_observations, dtype=int)
+        tabular.columns = self._depths
+        tabular.index = self._times
+        tabular.insert(0, "time", self._times)
+
+        return tabular
+
+    @number_of_observations.setter
+    def number_of_observations(self, value):
+        raise ValueError(f"You can't assign {value} to this variable (no assignment allowed).")
+
+    def reset_counts(self):
+        """ Set observation count to 1 if data exists, 0 otherwise """
+        self.__number_of_observations = (~self.wide.isna()).astype('boolean')
+
+    def set_utc_offset(self, offset:"Union[int,str]") -> None:
+        """ Set the time zone of the data by providing a UTC offset 
+
+        Parameters
+        ----------
+        offset : int, str
+            If int, the number of seconds. If str, a string in the format "+HH:MM" or "-HH:MM"
+        """
+        if self.utc_offset is not None:
+            raise ValueError("You can only set the UTC offset once.")
+
+        utc_offset = get_utc_offset(offset)
+
+        tz = timezone(timedelta(seconds = utc_offset)) 
+        self._times = self._times.tz_localize(tz)
+        self._output_utc_offset = timezone(timedelta(seconds = utc_offset)) 
+
+        TSP.wide.fget.cache_clear()
+        TSP.long.fget.cache_clear()
+
+    @property
+    def utc_offset(self) -> "Optional[tzinfo]":
+        """ Get the time zone of the data by providing a UTC offset
+
+        Returns
+        -------
+        datetime.tzinfo
+            A timezone object
+        """
+        if self._times.tz is None:
+            return None
+        else:
+            return self._times.tz
+    
+    @utc_offset.setter
+    def utc_offset(self, value):
+        self.set_utc_offset(value)
+    
+    @property
+    def output_utc_offset(self) -> "Optional[tzinfo]":
+        """ Get the time zone in which to output or display the data by providing a UTC offset
+        
+        Returns
+        -------
+        datetime.tzinfo
+            A timezone object
+        """
+        if self._output_utc_offset is None:
+            return None
+        else:
+            return self._output_utc_offset
+    
+    @output_utc_offset.setter
+    def output_utc_offset(self, offset:"Union[int,str]") -> None:
+        self.set_output_utc_offset(offset)
+
+    def set_output_utc_offset(self, offset:"Union[int,str]") -> None:
+        """ Set the time zone in which to display the output or data by providing a UTC offset
+        Parameters
+        ----------
+        offset : int, str
+            If int, the number of seconds. If str, a string in the format "+HH:MM" or "-HH:MM"
+        """
+        utc_offset = get_utc_offset(offset)
+        tz = timezone(timedelta(seconds = utc_offset))
+        self._output_utc_offset = tz
+        
+        TSP.wide.fget.cache_clear()
+        TSP.long.fget.cache_clear()
+
+    def reset_output_utc_offset(self) -> None:
+        """ Reset the time zone in which to output or display the data to the default (the one set by set_utc_offset)
+        
+        """
+        if self.utc_offset is None:
+            raise ValueError("You can't reset the output time zone if the time zone of the data hasn't yet been set with set_utc_offset.")
+        else:
+            self._output_utc_offset = self.utc_offset
+
+    def __nly(self, 
+              freq_fmt:str,
+              new_freq,
+              min_count:Optional[int],
+              max_gap:Optional[int],
+              min_span:Optional[int]) -> TSP:
+        """
+        Temporal aggregation by grouping according to a string-ified time
+
+        Parameters
+        ----------
+        freq_fmt : str
+            Python date format string  used to aggregate and recover time 
+        
+        Returns
+        -------
+        tuple[pd.DataFrame, pd.DataFrame]
+            A tuple of dataframes, the first containing the aggregated data, the second containing the number of observations
+        """
+        R = self.wide.drop("time", axis=1).resample(freq_fmt)
+        cumulative_obs = self.number_of_observations.drop("time", axis=1).resample(freq_fmt).sum()
+        total_obs = R.count()
+        values = R.mean()
+
+        # Calculate masks
+        mc_mask = Mg_mask = ms_mask = pd.DataFrame(index=values.index, columns=values.columns, data=False)
+
+        if min_count is not None:
+            mc_mask = (cumulative_obs < min_count)
+        if max_gap is not None:
+            Mg_mask = max_gap_mask(R, max_gap)
+        if min_span is not None:
+            ms_mask = min_span_mask(R, min_span)
+        
+        mask = (mc_mask | Mg_mask | ms_mask)
+        values[mask] = np.nan
+        
+        # Construct TSP
+        t = TSP.__from_tsp(self, times=values.index, 
+                           depths=values.columns, 
+                           values=values.values)
+        t.__number_of_observations = cumulative_obs
+        t.freq = new_freq
+
+        # Calculate data completeness
+        if self.freq is not None:
+            f1 = self.freq
+            f2 = new_freq
+            t._completeness = completeness(total_obs, f1, f2)
+
+        return t
+    
+    def monthly(self,
+                min_count:Optional[int]=24,
+                max_gap:Optional[int]=3600*24*8,
+                min_span:Optional[int]=3600*24*21) -> "TSP":
+        """ Monthly averages, possibly with some months unavailable (NaN) if there is insufficient data
+
+        Parameters
+        ----------
+        min_count : int
+            Minimum number of observations in a month to be considered a valid average,
+            defaults to None
+        max_gap : int
+            Maximum gap (in seconds) between data points to be considered a valid average,
+             defaults to None
+        min_span : int
+            Minimum total data range (in seconds) to be consiered a valid average,
+            defaults to None
+            
+        Returns
+        -------
+        TSP
+            A TSP object with data aggregated to monthly averages
+        """
+        t = self.__nly(freq_fmt="M", 
+                       new_freq=lbl.MONTHLY, 
+                       min_count=min_count, 
+                       max_gap=max_gap, 
+                       min_span=min_span)
+
+        return t
+
+    def daily(self, 
+              min_count:Optional[int]=None,
+              max_gap:Optional[int]=None,
+              min_span:Optional[int]=None) -> "TSP":
+        """ Daily averages, possibly with some days unavailable (NaN) if there is insufficient data
+
+        Parameters
+        ----------
+        min_count : int
+            Minimum number of observations in a day to be considered a valid average, 
+            defaults to None
+        max_gap : int
+            Maximum gap (in seconds) between data points to be considered a valid average, defaults to None
+        min_span : int
+            Minimum total data range (in seconds) to be consiered a valid average, defaults to None
+        
+        Returns
+        -------
+        TSP
+            A TSP object with data aggregated to daily averages
+        """
+        # if the data is already daily +/- 1min , just return it
+        t = self.__nly(freq_fmt="D", 
+                new_freq=lbl.DAILY, 
+                min_count=min_count, 
+                max_gap=max_gap, 
+                min_span=min_span)
+
+        return t
+
+    def yearly(self,
+               min_count:Optional[int]=None,
+               max_gap:Optional[int]=None,
+               min_span:Optional[int]=None) -> "TSP":
+        """ Yearly averages, possibly with some years unavailable (NaN) if there is insufficient data
+
+        Parameters
+        ----------
+        min_count : int
+            Minimum number of observations in a month to be considered a valid average, defaults to None
+        max_gap : int
+            Maximum gap (in seconds) between data points to be considered a valid average, defaults to None
+        min_span : int
+            Minimum total data range (in seconds) to be consiered a valid average, defaults to None
+        
+        Returns
+        -------
+        TSP
+            A TSP object with data aggregated to yearly averages
+        """
+        t = self.__nly(freq_fmt="Y", 
+                new_freq=lbl.YEARLY, 
+                min_count=min_count, 
+                max_gap=max_gap, 
+                min_span=min_span)
+
+        return t
+
+    @property
+    def depths(self) -> NDArray[np.number]:
+        """ Return the depth values in the profile 
+
+        Returns
+        -------
+        numpy.ndarray
+            The depths in the profile
+        """
+        return self._depths
+
+    @depths.setter
+    def depths(self, value):
+        depths = np.atleast_1d(value)
+        
+        if not len(depths) == len(self._depths):
+            raise ValueError(f"List of depths must have length of {len(self._depths)}.")
+
+        self._depths = depths
+
+        TSP.wide.fget.cache_clear()
+        TSP.long.fget.cache_clear()
+
+    @property
+    def times(self):
+        """ Return the timestamps in the time series 
+
+        Returns
+        -------
+        pandas.DatetimeIndex
+            The timestamps in the time series
+        """
+        if self.utc_offset is None:
+            return self._times
+        
+        elif self._output_utc_offset == self.utc_offset:
+            return self._times
+
+        else:
+            return self._times.tz_convert(self.output_utc_offset)
+
+    @property
+    def values(self):
+        return self._values
+
+    def to_gtnp(self, filename: str) -> None:
+        """ Write the data in GTN-P format
+        
+        Parameters
+        ----------
+        filename : str
+            Path to the file to write to
+        """
+        df = self.wide.round(self._export_precision).rename(columns={'time': 'Date/Depth'})
+        df['Date/Depth'] = df['Date/Depth'].dt.strftime("%Y-%m-%d %H:%M:%S")
+        
+        df.to_csv(filename, index=False, na_rep="-999")
+
+    def to_ntgs(self, filename:str, project_name:Optional[str]="", site_id:"Optional[str]" = None, latitude:"Optional[float]"=None, longitude:"Optional[float]"=None) -> None:
+        """ Write the data in NTGS template format 
+
+        Parameters
+        ----------
+        filename : str
+            Path to the file to write to
+        project_name : str, optional
+            The project name, by default ""
+        site_id : str, optional
+            The name of the site , by default None
+        latitude : float, optional
+            WGS84 latitude at which the observations were recorded, by default None
+        longitude : float, optional
+            WGS84 longitude at which the observations were recorded, by default None
+        """
+        if latitude is None:
+            latitude = self.latitude if self.latitude is not None else ""
+
+        if longitude is None:
+            longitude = self.longitude if self.longitude is not None else ""
+
+        if site_id is None:
+            site_id = self.site_id if self.site_id is not None else ""
+
+        if project_name is None:
+            project_name = self.metadata.get("project_name", "")
+
+        data = self.values
+
+        df = pd.DataFrame({'project_name': pd.Series(dtype='str'),
+                           'site_id': pd.Series(dtype='str'),
+                           'latitude': pd.Series(dtype='float'),
+                           'longitude': pd.Series(dtype='float')
+                           })
+
+        df["date_YYYY-MM-DD"] = pd.Series(self.times).dt.strftime(r"%Y-%m-%d")
+        df["time_HH:MM:SS"] = pd.Series(self.times).dt.strftime(r"%H:%M:%S")
+
+        df["project_name"] = project_name
+        df["site_id"] = site_id
+        df["latitude"] = latitude
+        df["longitude"] = longitude
+        
+        headers = [str(d) + "_m" for d in self.depths]
+        
+        for i, h in enumerate(headers):
+            df[h] = data[:, i].round(self._export_precision)
+
+        df.to_csv(filename, index=False)
+
+    def to_netcdf(self, file: str, only_use_cf_metadata=True, calculate_extent_metadata=True) -> None:
+        """  Write the data as a netcdf"""
+        try:
+            ncf = make_temperature_base(file, ndepth=len(self.depths), ntime=len(self.times), strings_as_strings=True)
+        except NameError:
+            warnings.warn("Missing required packages. Try installing with `pip install tsp[nc]`", stacklevel=2)
+            return
+        
+        with nc.Dataset(ncf, 'a') as ncd:
+            pytime = self.times.to_pydatetime()
+
+            ncd['depth_below_ground_surface'][:] = self.depths
+
+            
+            ncd['time'][:] = nc.date2num(pytime, ncd['time'].units, ncd['time'].calendar)
+            ncd['ground_temperature'][:] = self.values
+            
+            if self.latitude:
+                ncd['latitude'][:] = self.latitude
+            if self.longitude:
+                ncd['longitude'][:] = self.longitude
+            if self.site_id:
+                if ncd['site_name'].dtype == str:
+                    ncd['site_name'][0] = self.site_id
+                else:
+                    strlen = ncd['site_name'].shape[0]
+                    ncd['site_name'][:] = nc.stringtochar(np.array([self.site_id], f"S{strlen}"))
+
+            if "_elevation" in self.metadata:
+                ncd['surface_elevation'][:] = self.metadata.get("_elevation")
+            
+            if only_use_cf_metadata:
+                metadata = self.metadata.get('CF', {})
+            else:
+                metadata = self.metadata
+            
+            for key, value in metadata.items():
+                try:
+                    if isinstance(value, str):
+                        ncd.setncattr_string(key, value)
+                    else:
+                        ncd.setncattr(key, value)
+                except Exception:
+                    warnings.warn(f"Could not set metadata item: {key} : {value}", stacklevel=2)
+
+            if calculate_extent_metadata:
+                calc_ext_meta(ncd)
+                
+    def to_json(self, file: str) -> None:
+        """ Write the data to a serialized json file """
+        with open(file, 'w') as f:
+            f.write(self._to_json())
+
+    def _to_json(self) -> str:
+        return self.wide.round(self._export_precision).to_json()
+
+    def plot_profiles(self, P:int=100, n:int=10) -> Figure:
+        """ Create a plot of the temperature profiles at different times
+        
+        Parameters
+        ----------
+        P : int
+            Percentage of time range to plot
+        n : int
+            Number of evenly-spaced profiles to plot
+        
+        Returns
+        -------
+        Figure
+            matplotlib `Figure` object
+        """
+        fig = profile_evolution(depths=self.depths, times=self.times, values=self._values, P=P, n=n)
+        fig.show()
+        return fig
+    
+    def plot_trumpet(self, 
+                     year: Optional[int]=None,
+                     begin: Optional[datetime]=None,
+                     end: Optional[datetime]=None,
+                     min_completeness: Optional[float]=None,
+                     **kwargs) -> Figure:
+        """ Create a trumpet plot from the data
+        
+        Parameters
+        ----------
+        year : int, optional
+            Which year to plot
+        begin : datetime, optional
+            If 'end' also provided, the earliest measurement to include in the averaging for the plot
+        end : datetime, optional
+            If 'begin' also provided, the latest measurement to include in the averaging for the plot
+        min_completeness : float, optional
+            If provided, the minimum completeness (fractional, 0 to 1) required to include
+            in temperature envelope, otherwise
+            the point is plotted as an unconnected, slightly transparent dot, by default None
+        **kwargs : dict, optional
+            Extra arguments to the plotting function: refer to the documentation for :func:`~tsp.plots.static.trumpet_curve` for a
+            list of all possible arguments.
+
+        Returns
+        -------
+        Figure
+            a matplotlib `Figure` object
+        """
+        df = self.long.dropna()
+ 
+        if year is not None:
+            df = df[df['time'].dt.year == year]
+
+        elif begin is not None or end is not None:
+            raise NotImplementedError
+
+        else:
+            raise ValueError("One of 'year', 'begin', 'end' must be provided.")
+
+        grouped = df.groupby('depth')
+
+        max_t = grouped.max().get('temperature_in_ground').values
+        min_t = grouped.min().get('temperature_in_ground').values
+        mean_t = grouped.mean().get('temperature_in_ground').values
+        depth = np.array([d for d in grouped.groups.keys()])
+
+        # Calculate completeness
+        c = self.yearly(None, None, None).completeness
+        
+        if min_completeness is not None and c is not None:
+            C = c[c.index.year == year]
+            C = C[depth].iloc[0,:].values
+        
+        else:
+            C = None
+
+        fig = trumpet_curve(depth=depth, 
+                            t_max=max_t, 
+                            t_min=min_t, 
+                            t_mean=mean_t, 
+                            min_completeness=min_completeness,
+                            data_completeness=C,
+                            **kwargs)
+        fig.show()
+
+        return fig
+    
+    def plot_contour(self, **kwargs) -> Figure:
+        """ Create a contour plot
+        
+        Parameters
+        ----------
+        **kwargs : dict, optional
+            Extra arguments to the plotting function: refer to the documentation for :func:`~tsp.plots.static.colour_contour` for a
+            list of all possible arguments.
+
+        Returns
+        -------
+        Figure
+            matplotlib `Figure` object
+        """
+        fig = colour_contour(depths=self.depths, times=self.times, values=self._values, **kwargs)
+
+        if self.output_utc_offset is not None:
+            label = format_utc_offset(self.output_utc_offset)
+            if label != "UTC":
+                label = f"UTC{label}"         
+            fig.axes[0].set_xlabel(f"Time [{label}]")
+
+        fig.show()
+
+        return fig
+
+    def plot_timeseries(self, depths: list=[], **kwargs) -> Figure:
+        """Create a time series T(t) plot 
+
+        Parameters
+        ----------
+        depths : list, optional
+            If non-empty, restricts the depths to include in the plot, by default []
+        **kwargs : dict, optional
+            Extra arguments to the plotting function: refer to the documentation for :func:`~tsp.plots.static.time_series` for a
+            list of all possible arguments.
+
+        Returns
+        -------
+        Figure
+            matplotlib `Figure` object
+        """
+        if depths == []:
+            depths = self.depths
+        
+        d_mask = np.isin(self.depths, depths)
+        
+        fig = time_series(self.depths[d_mask], self.times, self.values[:, d_mask], **kwargs)
+  
+
+        if self.output_utc_offset is not None:
+            label = format_utc_offset(self.output_utc_offset)
+            if label != "UTC":
+                label = f"UTC{label}"         
+            fig.axes[0].set_xlabel(f"Time [{label}]")
+        fig.autofmt_xdate()
+        fig.show()
+        
+        return fig
+
+
+class AggregatedTSP(TSP):
+    """ A Time Series Profile that uses indices (1,2,3,...) instead of depth values. 
+    
+    Used in situations when depths are unknown (such as when reading datlogger exports
+    that don't have depth measurements.)
+    
+    Parameters
+    ----------
+    times : list-like
+        t-length array of datetime objects
+    values : numpy.ndarray
+        array with shape (t,d) containing values at (t)emperatures and (d)epths
+    **kwargs : dict
+        Extra arguments to parent class: refer to :py:class:`tsp.core.TSP` documentation for a
+        list of all possible arguments.
+    """
+
+
+class IndexedTSP(TSP):
+    """ A Time Series Profile that uses indices (1,2,3,...) instead of depth values. 
+    
+    Used in situations when depths are unknown (such as when reading datlogger exports
+    that don't have depth measurements.)
+    
+    Parameters
+    ----------
+    times : list-like
+        t-length array of datetime objects
+    values : numpy.ndarray
+        array with shape (t,d) containing values at (t)emperatures and (d)epths
+    **kwargs : dict
+        Extra arguments to parent class: refer to :py:class:`~tsp.core.TSP` documentation for a
+        list of all possible arguments.
+    """
+
+    def __init__(self, times, values, **kwargs):
+        depths = np.arange(0, values.shape[1]) + 1
+        super().__init__(times=times, depths=depths, values=values, **kwargs)
+
+    @property
+    def depths(self) -> np.ndarray:
+        """Depth indices 
+
+        Returns
+        -------
+        numpy.ndarray
+            An array of depth indices
+        """
+        warnings.warn("This TSP uses indices (1,2,3,...) instad of depths. Use set_depths() to use measured depths.", stacklevel=2)
+        return self._depths
+
+    @depths.setter
+    def depths(self, value):
+        TSP.depths.__set__(self, value)
+
+    def set_depths(self, depths: np.ndarray):
+        """Assign depth values to depth indices. Change the object to a :py:class:`~tsp.core.TSP`
+
+        Parameters
+        ----------
+        depths : np.ndarray
+            An array or list of depth values equal in lenth to the depth indices
+        """
+        self.depths = depths
+        self.__class__ = TSP
+
+
+
+def span(S: pd.Series) -> float:
+    first = S.first_valid_index()  # type: pd.Timestamp
+    last = S.last_valid_index()  # type: pd.Timestamp
+    if first is None or last is None:
+        return 0
+    
+    return (last - first).total_seconds()
+
+def min_span_mask(R: "pd.core.resample.DatetimeIndexResampler",
+             threshold: float) -> "pd.DataFrame":
+    s = R.apply(lambda x: span(x))
+    return s < threshold
+
+
+def gap(S: pd.Series) -> float:
+
+    d = np.diff(S.dropna().index)
+    if len(d) == 0:
+        return 0
+    elif len(d) == 1:
+        return 0
+    elif len(d) > 1:
+        gap = max(d).astype('timedelta64[s]').astype(float)
+    return gap
+
+
+def max_gap_mask(R: "pd.core.resample.DatetimeIndexResampler",
+            threshold: float) -> "pd.DataFrame":
+    g = R.apply(lambda x: gap(x))
+    return (g > threshold) | (g == 0)
+
+
+
+
+def _temporal_gap_mask(grouped: "pd.core.groupby.DataFrameGroupBy", max_gap: Optional[int], min_span: Optional[int]) -> np.ndarray:
+    """ Mask out observational groups in which there is more than a certain size temporal gap
+
+    Controls for gaps in the data within an aggregation group (using max_gap) and missing data at the beginning
+    or end of the aggregation group (using min_span).
+    
+    Parameters
+    ----------
+    grouped : pandas.core.groupby.DataFrameGroupBy
+        groupby  with 'time' and 'depth' columns
+    max_gap : int
+        maximum gap in seconds to tolerate between observations in a group
+    min_span : int
+        minimum data range (beginning to end) in seconds. 
+
+    Returns
+    -------
+    numpy.ndarray
+        boolean array with ``True`` where measurement spacing or range in group does not satisfy tolerances
+    """
+    if max_gap is not None:
+        max_diff = grouped.time.apply(np.diff).apply(lambda x: np.max(x, initial=np.timedelta64(0))).apply(lambda x: x.total_seconds())
+        max_diff = max_diff.unstack().to_numpy()
+        diff_mask = np.where((max_diff == 0) | (max_diff >= max_gap), True, False)
+    else:
+        diff_mask = np.zeros_like(grouped, dtype=bool)
+    
+    if min_span is not None:
+        total_span = grouped.time.apply(np.ptp).apply(lambda x: x.total_seconds()).unstack().to_numpy()
+        span_mask = np.where(total_span < min_span, True, False)
+    else:
+        span_mask = np.zeros_like(grouped, dtype=bool)
+
+    mask = diff_mask * span_mask
+
+    return mask
+
+
+def _observation_count_mask(number_of_observations: np.ndarray, min_count:int) -> np.ndarray:
+    """ Create a mask array for an
+    
+    Parameters
+    ----------
+    number_of_observations : numpy.ndarray
+        Array of how many data points are in aggregation
+    min_count : int
+        Minimum number of data points for aggregation to be 'valid'
+
+    Returns
+    -------
+    np.ndarray
+        a mask, True where data should be masked
+    """
+    valid = np.less(number_of_observations, min_count)  # type: np.ndarray
+    return valid
+
+
+def handle_incoming_times(times: "Union[np.ndarray, pd.DatetimeIndex, pd.Series, list]") -> "pd.DatetimeIndex":
+    """Convert a list of times to a pandas DatetimeIndex object"""
+    invalid_msg = "Times must be a list, numpy array, pandas DatetimeIndex, or pandas Series"
+
+    try:
+        if not len(times):
+            raise ValueError(invalid_msg)
+    except TypeError:
+        raise ValueError(invalid_msg)
+
+    if isinstance(times, pd.DatetimeIndex):
+        return times
+
+    if isinstance(times, pd.Series):
+        try:
+            times = pd.DatetimeIndex(times)
+        except Exception:
+            raise ValueError("Series must be convertible to DatetimeIndex")
+        times.name = 'time'
+
+        return times
+
+    elif isinstance(times, np.ndarray):
+        times = pd.to_datetime(times)
+        times.name = 'time'
+        return times
+    
+    elif isinstance(times, list):
+        return pd.to_datetime(times)
+
+    else:
+        raise ValueError(invalid_msg)
+
+def tsp_concat(tsp_list, on_conflict='error', metadata='first') -> TSP:
+    """Combine multiple TSPs into a single TSP.
+    
+    Parameters
+    ----------
+    tsp_list : list[TSP]
+        List of TSPs to combine. They must have the same depths
+    on_conflict : str, optional
+        Method to resolve duplicate times with different values. Chosen from "error", "keep", by default "error"
+        - "error": Raise an error if duplicate times with different values are found.
+        - "keep": Keep the first occurrence of the duplicate time.
+    metadata : str, optional
+        Method to select metadata from the TSPs. Chosen from "first", "identical", or "none", by default "first"
+        - "first": Use the metadata from the first TSP in the list.
+        - "identical": Only keep metadata records that are identical across TSPs.
+        - "none": Ignore metadata and set it to None.
+    Returns
+    -------
+    TSP
+        Combined TSP.
+        
+    Description
+    -----------
+    This function combines multiple TSPs into a single TSP. The TSPs must have the same depths.
+    """
+    tsp_dict = _tsp_concat(tsp_list=tsp_list, on_conflict=on_conflict, metadata=metadata)
+    times = tsp_dict.pop('times')
+    depths = tsp_dict.pop('depths')
+    values = tsp_dict.pop('values')
+
+    t = TSP(times, depths, values, **tsp_dict)
+    
+    return t