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Retrieval

The following functions are methods from the class ProfilesData

Aerosol Extinction

This module is used to calculate extinction profiles from single attenuated backscatter profiles using an a priori.

backward_inversion(data, iref, apriori, rayleigh)

Backward (Klett [Klett1985]_ ) inversion method.

.. [Klett1985] Klett, J. D. (1985). Lidar inversion with variable backscatter/extinction ratios. Applied optics, 24(11), 1638-1643.

Parameters:

Name Type Description Default
data array_like

1D array of a single profile of the attenuated backscatter coefficient.

 required
iref float

Index of the reference altitude returned by :func:aprofiles.retrieval.ref_altitude.get_iref().

 required
apriori dict

A priori values used to constrain the inversion. Valid keys include: - lr (float): Lidar Ratio (in sr). - aod (float): AOD (unitless).

 required
rayleigh

class:aprofiles.rayleigh.RayleighData): Instance of the RayleighData class.

 required

Raises:

Type Description
NotImplementedError

AOD apriori is not implemented yet.

Returns:

Type Description
array_like

Extinction coefficient (in m⁻¹).
Source code in aprofiles/retrieval/extinction.py 
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def backward_inversion(data, iref, apriori, rayleigh):
    """
    Backward (Klett [Klett1985]_ ) inversion method.

    .. [Klett1985] Klett, J. D. (1985). Lidar inversion with variable backscatter/extinction ratios. Applied optics, 24(11), 1638-1643.

    Args:
        data (array_like): 1D array of a single profile of the attenuated backscatter coefficient.
        iref (float): Index of the reference altitude returned by :func:`aprofiles.retrieval.ref_altitude.get_iref()`.
        apriori (dict): A priori values used to constrain the inversion. Valid keys include:
            - **lr** (float): Lidar Ratio (in sr).
            - **aod** (float): AOD (unitless).
        rayleigh (:class:`aprofiles.rayleigh.RayleighData`): Instance of the `RayleighData` class.

    Raises:
        NotImplementedError: AOD apriori is not implemented yet.

    Returns:
        (array_like): Extinction coefficient (in m⁻¹).
    """


    if "aod" in apriori:
        # search by dichotomy the LR that matches the apriori aod
        raise NotImplementedError("AOD apriori is not implemented yet")
        lr_aer = 50
    else:
        # if we assume the LR, no need to minimize for matching aod
        lr_aer = apriori["lr"]
    lr_mol = 8.0 * np.pi / 3.0

    # vertical resolution
    dz = min(np.diff(rayleigh.altitude))

    int1_a = np.cumsum((lr_aer - lr_mol) * rayleigh.backscatter[:iref] * dz)
    int1_b = [2 * int1_a[-1] - 2 * int1_a[i] for i in range(iref)]
    phi = [np.log(abs(data[i] / data[iref])) + int1_b[i] for i in range(iref)]

    int2_a = 2 * np.nancumsum(lr_aer * np.exp(phi) * dz)
    int2_b = [int2_a[-1] - int2_a[i] for i in range(iref)]

    # initialize total backscatter
    back_aer_iref = 0  # m-1
    beta_tot_iref = rayleigh.backscatter[iref] + back_aer_iref

    # total backscatter
    beta_tot = [np.exp(phi[i]) / ((1 / beta_tot_iref) + int2_b[i]) for i in range(iref)]
    # aerosol backsatter (m-1.sr-1)
    beta_aer = beta_tot - rayleigh.backscatter[:iref]
    # aerosol extinction (m-1)
    sigma_aer = lr_aer * beta_aer
    # returns extinction in m-1 when valid, and np.nan elsewhere
    ext = [sigma_aer[i] if i < len(sigma_aer) else np.nan for i in range(len(data))]
    return ext

forward_inversion(data, iref, apriori, rayleigh)

Forward iterative inversion method [#]_.

.. [#] Li, D., Wu, Y., Gross, B., & Moshary, F. (2021). Capabilities of an Automatic Lidar Ceilometer to Retrieve Aerosol Characteristics within the Planetary Boundary Layer. Remote Sensing, 13(18), 3626.

Method principle:

At z0, the aerosol transmission is assumed as being close to 1. We evaluate the aerosol extinction based on this assumption. This evaluation gives a refined aerosol extinction that is used to calculate a second time the aerosol transmission. The aerosol extinction retrieval will converge after a certain number iterations. After the convergence, the aerosol extinction is retrieved in the next upper layer.

Parameters:

Name Type Description Default
data array_like

1D Array of single profile of attenuated backscatter coefficient, in m-1.sr-1.

 required
iref float

index of the reference altitude returned by :func:aprofiles.retrieval.ref_altitude.get_iref().

 required
apriori dict

A priori value to be used to constrain the inversion. Valid keys: ‘lr’ (Lidar Ratio, in sr) and ‘aod’ (unitless).

 required
rayleigh aprofiles.rayleigh.RayleighData). Instance of the

class:aprofiles.rayleigh.RayleighData class.

 required

Raises:

Type Description
NotImplementedError

AOD apriori is not implemented yet.

Returns:

Type Description
array_like

Extinction coefficient (in m⁻¹).
Source code in aprofiles/retrieval/extinction.py 
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def forward_inversion(data, iref, apriori, rayleigh):
    """Forward iterative inversion method [#]_.

    .. [#] Li, D., Wu, Y., Gross, B., & Moshary, F. (2021). Capabilities of an Automatic Lidar Ceilometer to Retrieve Aerosol Characteristics within the Planetary Boundary Layer. Remote Sensing, 13(18), 3626.

    Method principle:

    At z0, the aerosol transmission is assumed as being close to 1. We evaluate the aerosol extinction based on this assumption.
    This evaluation gives a refined aerosol extinction that is used to calculate a second time the aerosol transmission.
    The aerosol extinction retrieval will converge after a certain number iterations.
    After the convergence, the aerosol extinction is retrieved in the next upper layer.

    Args:
        data (array_like): 1D Array of single profile of attenuated backscatter coefficient, in m-1.sr-1.
        iref (float): index of the reference altitude returned by :func:`aprofiles.retrieval.ref_altitude.get_iref()`.
        apriori (dict): A priori value to be used to constrain the inversion. Valid keys: ‘lr’ (Lidar Ratio, in sr) and ‘aod’ (unitless).
        rayleigh (aprofiles.rayleigh.RayleighData). Instance of the :class:`aprofiles.rayleigh.RayleighData` class.

    Raises:
        NotImplementedError: AOD apriori is not implemented yet.

    Returns:
        (array_like): Extinction coefficient (in m⁻¹).
    """

    if "aod" in apriori:
        # search by dichotomy the LR that matches the apriori aod
        raise NotImplementedError("AOD apriori is not implemented yet")
        lr_aer = 50
    elif "lr" in apriori:
        # if we assume the LR, no need to minimize for matching aod
        lr_aer = apriori["lr"]
    lr_mol = 8.0 * np.pi / 3.0

    def _get_aer_at_i(data, i, Tm, Bm, Ta, Ba, Ea, dz, nloop_max=30, diff_ext=0.01):
        # suppress warnings
        warnings.filterwarnings('ignore')

        for _ in range(nloop_max):
            if np.isnan(Ea[i]):
                Ta[i] = 1
            else:
                Ta[i] = np.exp(-np.nancumsum(Ea * dz))[i]
            if (Tm[i] ** 2 * Ta[i] ** 2) != 0:
                Ba[i] = data[i] / (Tm[i] ** 2 * Ta[i] ** 2) - Bm[i]
            else:
                Ba[i] = np.nan
            # test extinction
            if 1 - (lr_aer * Ba[i] / Ea[i]) < diff_ext:
                Ea[i] = lr_aer * Ba[i]
                break
            Ea[i] = lr_aer * Ba[i]

        return Ba[i], Ea[i], Ta[i]

    # vertical resolution
    dz = min(np.diff(rayleigh.altitude))

    Bm = rayleigh.backscatter
    Em = rayleigh.extinction
    Tm = np.exp(-np.cumsum(Em * dz))

    # Initialize aer profiles
    Ta = np.asarray([np.nan for _ in range(len(data))])
    Ba = np.asarray([np.nan for _ in range(len(data))])
    Ea = np.asarray([np.nan for _ in range(len(data))])

    for i in range(iref):
        Ba[i], Ea[i], Ta[i] = _get_aer_at_i(data, i, Tm, Bm, Ta, Ba, Ea, dz)
        if np.isnan(Ba[i]):
            continue
    # returns extinction in m-1
    ext = Ea
    return ext

inversion(profiles, time_avg=1, zmin=4000.0, zmax=6000.0, min_snr=0.0, under_clouds=False, method='forward', apriori={'lr': 50.0}, remove_outliers=False, verbose=False)

Aerosol inversion of the attenuated backscatter profiles using an apriori.

Parameters:

Name Type Description Default
profiles ProfilesData

ProfilesData instance.

 required
time_avg int

in minutes, the time during which we aggregate the profiles before inverting the profiles.

 1
zmin float

minimum altitude AGL, in m, for looking for the initialization altitude.

 4000.0
zmax float

maximum altitude AGL, in m, for looking for the initialization altitude.

 6000.0
min_snr float

Minimum SNR required at the reference altitude to be valid.

 0.0
under_clouds bool

If True, and if the ProfilesData has a cloud_base variable (returned by the clouds method), forces the initialization altitude to be found below the first cloud detected in the profile.

 False
method str

must be in [‘backward’, ‘forward’].

 'forward'
apriori dict

A priori value to be used to constrain the inversion. Valid keys: ‘lr’ (Lidar Ratio, in sr), ‘aod’ (unitless), 'cfg' (path of config file).

 {'lr': 50.0}
remove_outliers bool

Remove profiles considered as outliers based on aod calculation (AOD<0, or AOD>2).

 False
verbose bool

verbose mode.

 False

Raises:

Type Description
NotImplementedError

AOD apriori is not implemented yet.

Returns:

Type Description
ProfilesData

object with additional (xarray.DataArray):

  • 'extinction' (time, altitude): 2D array corresponding to the aerosol extinction, in km-1.
  • 'aod' (time): 1D array corresponding to the aerosol optical depth associated to the extinction profiles.
  • 'lidar_ratio' (time): 1D array corresponding to the lidar ratio associated to the extinction profiles.
Example

Profiles preparation 

import aprofiles as apro
#read example file
path = "examples/data/L2_0-20000-001492_A20210909.nc"
reader = apro.reader.ReadProfiles(path)
profiles = reader.read()
#extrapolate lowest layers
profiles.extrapolate_below(z=150, inplace=True)

Backward inversion 

#aerosol inversion
profiles.inversion(zmin=4000, zmax=6000, remove_outliers=False, method='backward')
#plot extinction profiles
profiles.plot(var='extinction', zmax=6000, vmin=0, vmax=5e-2)

Extinction profiles retrieved with the backward method

Forward inversion 

#aerosol inversion
profiles.inversion(zmin=4000, zmax=6000, remove_outliers=False, method='forward')
#plot extinction profiles
profiles.plot(var='extinction', zmax=6000, vmin=0, vmax=5e-2)

Extinction profiles retrieved with the forward method

Source code in aprofiles/retrieval/extinction.py 
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def inversion(
    profiles,
    time_avg=1,
    zmin=4000.0,
    zmax=6000.0,
    min_snr=0.0,
    under_clouds=False,
    method="forward",
    apriori={"lr": 50.0},
    remove_outliers=False,
    verbose=False,
):
    """Aerosol inversion of the attenuated backscatter profiles using an apriori.

    Args:
        profiles (aprofiles.profiles.ProfilesData): `ProfilesData` instance.
        time_avg (int, optional): in minutes, the time during which we aggregate the profiles before inverting the profiles.
        zmin (float, optional): minimum altitude AGL, in m, for looking for the initialization altitude.
        zmax (float, optional): maximum altitude AGL, in m, for looking for the initialization altitude.
        min_snr (float, optional): Minimum SNR required at the reference altitude to be valid.
        under_clouds (bool, optional): If True, and if the `ProfilesData` has a `cloud_base` variable (returned by the `clouds` method), forces the initialization altitude to be found below the first cloud detected in the profile.
        method (str, optional): must be in [‘backward’, ‘forward’].
        apriori (dict, optional): A priori value to be used to constrain the inversion. Valid keys: ‘lr’ (Lidar Ratio, in sr), ‘aod’ (unitless), 'cfg' (path of config file).
        remove_outliers (bool, optional): Remove profiles considered as outliers based on aod calculation (AOD<0, or AOD>2).
        verbose (bool, optional): verbose mode.

    Raises:
        NotImplementedError: AOD apriori is not implemented yet.

    Returns:
        (aprofiles.profiles.ProfilesData):
            object with additional (xarray.DataArray):

            - `'extinction' (time, altitude)`: 2D array corresponding to the aerosol extinction, in km-1.
            - `'aod' (time)`: 1D array corresponding to the aerosol optical depth associated to the extinction profiles.
            - `'lidar_ratio' (time)`: 1D array corresponding to the lidar ratio associated to the extinction profiles.

    Example:
        Profiles preparation
        ```python
        import aprofiles as apro
        #read example file
        path = "examples/data/L2_0-20000-001492_A20210909.nc"
        reader = apro.reader.ReadProfiles(path)
        profiles = reader.read()
        #extrapolate lowest layers
        profiles.extrapolate_below(z=150, inplace=True)
        ```

        Backward inversion
        ```python
        #aerosol inversion
        profiles.inversion(zmin=4000, zmax=6000, remove_outliers=False, method='backward')
        #plot extinction profiles
        profiles.plot(var='extinction', zmax=6000, vmin=0, vmax=5e-2)
        ```

        ![Extinction profiles retrieved with the backward method](../../assets/images/backward.png)

        Forward inversion
        ```python
        #aerosol inversion
        profiles.inversion(zmin=4000, zmax=6000, remove_outliers=False, method='forward')
        #plot extinction profiles
        profiles.plot(var='extinction', zmax=6000, vmin=0, vmax=5e-2)
        ```

        ![Extinction profiles retrieved with the forward method](../../assets/images/forward.png)
    """

    # we work on profiles averaged in time to reduce the noise
    rcs = profiles.time_avg(
        time_avg, var="attenuated_backscatter_0", inplace=False
    ).data.attenuated_backscatter_0

    """
    #if clouds detected, set to nan profiles where cloud is found below 4000m
    lowest_clouds = profiles._get_lowest_clouds()
    for i in range(len(profiles.data.time.data)):
        if lowest_clouds[i]<=4000:
            rcs.data[i,:] = [np.nan for _ in rcs.data[i,:]]
    """

    # if under_clouds, check if clouds_bases is available
    if under_clouds and "clouds_bases" in list(profiles.data.data_vars):
        lowest_clouds = profiles._get_lowest_clouds()
    elif under_clouds and "clouds_bases" not in list(profiles.data.data_vars):
        warnings.warn(
            "under_clouds parameter sets to True (defaults value) when the clouds detection has not been applied to ProfileData object."
        )
        lowest_clouds = [np.nan for i in np.arange(len(profiles.data.time))]
    else:
        lowest_clouds = [np.nan for i in np.arange(len(profiles.data.time))]

    # aerosol retrieval requires a molecular profile
    altitude = np.asarray(profiles.data.altitude.data)
    wavelength = float(profiles.data.l0_wavelength.data)
    rayleigh = apro.rayleigh.RayleighData(
        altitude, T0=298, P0=1013, wavelength=wavelength
    )

    # apriori definition
    if 'cfg' in apriori:
        cfg_path = apriori['cfg']
        # open config 
        f = open(Path(Path(__file__).parent, '..', cfg_path))
        cfg = json.load(f)
        f.close()
        station_id = f'{profiles._data.attrs["wigos_station_id"]}-{profiles._data.attrs["instrument_id"]}'
        if station_id in cfg:
            apriori = cfg[station_id]["apriori"]
        else:
            apriori = cfg["attributes"]["default"]["apriori"]
    else:
        cfg = None

    # aerosol inversion
    ext, lr, aod, z_ref = [], [], [], []
    aod_min, aod_max = 0, 2
    vertical_resolution = profiles._get_resolution("altitude")
    for i in (track(range(len(profiles.data.time.data)), description="klett ",disable=not verbose)):
        # for this inversion, it is important to use the right units
        if "Mm" in profiles.data.attenuated_backscatter_0.units:
            calibrated_data = rcs.data[i, :] * 1e-6 # conversion from Mm-1.sr-1 to m-1.sr-1
        else:
            calibrated_data = rcs.data[i, :]

        # reference altitude
        lowest_cloud_agl = lowest_clouds[i] - profiles.data.station_altitude.data
        imin = profiles._get_index_from_altitude_AGL(zmin)
        imax = profiles._get_index_from_altitude_AGL(np.nanmin([zmax, lowest_cloud_agl]))
        if method == "backward":
            iref = get_iref(rcs.data[i, :], imin, imax, min_snr)
        elif method == "forward":
            iref = imax
        z_ref.append(altitude[iref])

        if iref is not None:
            # aerosol inversion
            if method == "backward":
                _ext = backward_inversion(calibrated_data, iref, apriori, rayleigh)
            elif method == "forward":
                _ext = forward_inversion(calibrated_data, iref, apriori, rayleigh)
        else:
            _ext = [np.nan for _ in range(len(calibrated_data))]

        # add aod and lr
        if "aod" in apriori:
            # search by dichotomy the LR that matches the apriori aod
            raise NotImplementedError("AOD apriori is not implemented yet")
        else:
            # if we assume the LR, no need to minimize for matching aod
            _lr = apriori["lr"]
            _aod = np.nancumsum(np.asarray(_ext) * vertical_resolution)[-1]
            if remove_outliers and _aod < aod_min or remove_outliers and _aod > aod_max:
                lr.append(np.nan)
                aod.append(np.nan)
                ext.append([np.nan for x in _ext])
            else:
                lr.append(_lr)
                aod.append(_aod)
                ext.append(_ext)

    # creates dataarrays
    profiles.data["extinction"] = (("time","altitude"), np.asarray(ext) * 1e3)
    profiles.data["extinction"] = profiles.data.extinction.assign_attrs({
        'long_name': f"Extinction Coefficient @ {int(wavelength)} nm",
        'method': f"{method.capitalize()} Klett",
        'units': "km-1",
        'time_avg': time_avg,
        'zmin': zmin,
        'zmax': zmax,
        'apriori_variable': list(apriori.keys())[0],
        'apriori_value': apriori[list(apriori.keys())[0]],
        })

    profiles.data["aod"] = ("time", aod)
    profiles.data["aod"] = profiles.data.aod.assign_attrs({
        'long_name': f"Aerosol Optical Depth @ {int(wavelength)} nm",
        'unit': ''
    })

    profiles.data["lidar_ratio"] = ('time', lr)
    profiles.data["lidar_ratio"] = profiles.data.lidar_ratio.assign_attrs({
        'long_name': f"Lidar Ratio @ {int(wavelength)} nm",
        'units': 'sr'
    })
    if cfg is not None:
        profiles.data["lidar_ratio"] = profiles.data.lidar_ratio.assign_attrs({
            'use_cfg': 'True',
            'cfg_file': cfg_path,
            'use_default': str(not station_id in cfg),
            'cfg_attributes': str(cfg.get('attributes'))
        })
        if cfg.get(station_id):
            profiles.data["lidar_ratio"] = profiles.data.lidar_ratio.assign_attrs({
                f'cfg_{station_id}': str(cfg.get(station_id)),
            })
    else:
        profiles.data["lidar_ratio"] = profiles.data.lidar_ratio.assign_attrs({
            'use_cfg': 'False'
        })

    profiles.data["z_ref"] = ('time', z_ref)
    profiles.data["z_ref"] = profiles.data.z_ref.assign_attrs({
        'long_name': f"Reference altitude ASL",
        'units': 'm'
    })

    return profiles

Mass Concentration

This module is used to calculate mass concentration profiles from extinction profiles for given aerosol types.

concentration_profiles(profiles, method)

Calculates Mass concentration profiles for different aerosol types

Parameters:

Name Type Description Default
profiles ProfilesData

ProfilesData instance.

 required
method str

Method for calculating EMC. Must be one of {"mortier_2013", "literature"}.

 required

Returns:

Type Description
ProfilesData

object with additional (xarray.Dataset):

  • 'mass_concentration:<aer_type>'
Example

Profiles preparation 

import aprofiles as apro
# read example file
path = "examples/data/L2_0-20000-001492_A20210909.nc"
reader = apro.reader.ReadProfiles(path)
profiles = reader.read()
# extrapolate lowest layers
profiles.extrapolate_below(z=150, inplace=True)

Forward inversion 

# aerosol inversion
profiles.inversion(
    zmin=4000, zmax=6000, remove_outliers=False, method='forward', 
    method_mass_conc='mortier_2013'
)
# plot mass concentration profiles for urban particles
profiles.plot(var='mass_concentration:urban', zmax=6000, vmin=0, vmax=100)

Mass concentration profiles in the case of urban particles

Source code in aprofiles/retrieval/mass_conc.py 
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def concentration_profiles(profiles, method):
    """Calculates Mass concentration profiles for different aerosol types

    Args:
        profiles (aprofiles.profiles.ProfilesData): `ProfilesData` instance.
        method (str): Method for calculating EMC. Must be one of {"mortier_2013", "literature"}.

    Returns:
        (aprofiles.profiles.ProfilesData):
            object with additional (xarray.Dataset):

            - `'mass_concentration:<aer_type>'`

    Example:
        Profiles preparation
        ```python
        import aprofiles as apro
        # read example file
        path = "examples/data/L2_0-20000-001492_A20210909.nc"
        reader = apro.reader.ReadProfiles(path)
        profiles = reader.read()
        # extrapolate lowest layers
        profiles.extrapolate_below(z=150, inplace=True)
        ```

        Forward inversion
        ```python
        # aerosol inversion
        profiles.inversion(
            zmin=4000, zmax=6000, remove_outliers=False, method='forward', 
            method_mass_conc='mortier_2013'
        )
        # plot mass concentration profiles for urban particles
        profiles.plot(var='mass_concentration:urban', zmax=6000, vmin=0, vmax=100)
        ```

        ![Mass concentration profiles in the case of urban particles](../../assets/images/mass_conc-urban.png)
    """

    # read aer_properties.json files
    f = open(Path(Path(__file__).parent,'..','config','aer_properties.json'))
    aer_properties = json.load(f)
    f.close()
    # check if the aer_type exist in the json file
    aer_types = aer_properties.keys()

    # get wavelength
    wavelength = float(profiles.data.l0_wavelength.data)
    if profiles.data.l0_wavelength.units != "nm":
        raise ValueError("wavelength units is not `nm`.")

    for aer_type in aer_types:
        # calculates emc
        emc = apro.emc.EMCData(aer_type, wavelength, method)

        # compute mass_concentration profile. Use extinction as base.
        mass_concentration = profiles.data.extinction*1e-3 #conversion from km-1 to m-1
        # mass_concentration = copy.deepcopy(profiles.data.extinction)
        mass_concentration.data = np.divide(mass_concentration, emc.emc)
        # # conversion from g.m-3 to µg.m-3
        mass_concentration.data = mass_concentration.data*1e6

        # creates dataset with a dataarray for each aer_type
        profiles.data[f"mass_concentration:{aer_type}"] = (('time', 'altitude'), mass_concentration.data)
        profiles.data[f"mass_concentration:{aer_type}"] = profiles.data[f"mass_concentration:{aer_type}"].assign_attrs({
            'long_name': f"Mass concentration [{aer_type.replace('_', ' ')} particles]",
            'units': 'µg.m-3',
            'emc': emc.emc,
        })
    return profiles