BESS-JPL 1.9.2__py3-none-any.whl → 1.10.0__py3-none-any.whl

BESS_JPL/BESS_JPL.py

@@ -41,496 +41,4 @@ from .load_ball_berry_slope_C4 import *
 from .calculate_VCmax import *
 from .meteorology import *
 from .soil_energy_balance import *
-
-logger = logging.getLogger(__name__)
-
-def BESS_JPL(
-        ST_C: Union[Raster, np.ndarray],  # surface temperature in Celsius
-        NDVI: Union[Raster, np.ndarray],  # NDVI
-        albedo: Union[Raster, np.ndarray],  # surface albedo
-        geometry: RasterGeometry = None,
-        time_UTC: datetime = None,
-        hour_of_day: np.ndarray = None,
-        day_of_year: np.ndarray = None,
-        GEOS5FP_connection: GEOS5FP = None,
-        elevation_km: Union[Raster, np.ndarray] = None,  # elevation in kilometers
-        Ta_C: Union[Raster, np.ndarray] = None,  # air temperature in Celsius
-        RH: Union[Raster, np.ndarray] = None,  # relative humidity as a proportion
-        NDVI_minimum: Union[Raster, np.ndarray] = None,  # minimum NDVI
-        NDVI_maximum: Union[Raster, np.ndarray] = None,  # maximum NDVI
-        Rg: Union[Raster, np.ndarray] = None,  # incoming shortwave radiation in W/m^2
-        VISdiff: Union[Raster, np.ndarray] = None,  # diffuse visible radiation in W/m^2
-        VISdir: Union[Raster, np.ndarray] = None,  # direct visible radiation in W/m^2
-        NIRdiff: Union[Raster, np.ndarray] = None,  # diffuse near-infrared radiation in W/m^2
-        NIRdir: Union[Raster, np.ndarray] = None,  # direct near-infrared radiation in W/m^2
-        UV: Union[Raster, np.ndarray] = None,  # incoming ultraviolet radiation in W/m^2
-        albedo_visible: Union[Raster, np.ndarray] = None, # surface albedo in visible wavelengths (initialized to surface albedo if left as None)
-        albedo_NIR: Union[Raster, np.ndarray] = None, # surface albedo in near-infrared wavelengths (initialized to surface albedo if left as None)
-        COT: Union[Raster, np.ndarray] = None,  # cloud optical thickness
-        AOT: Union[Raster, np.ndarray] = None,  # aerosol optical thickness
-        vapor_gccm: Union[Raster, np.ndarray] = None,  # water vapor in g/ccm
-        ozone_cm: Union[Raster, np.ndarray] = None,  # ozone in cm
-        KG_climate: Union[Raster, np.ndarray] = None,  # KG climate
-        canopy_height_meters: Union[Raster, np.ndarray] = None,  # canopy height in meters
-        Ca: Union[Raster, np.ndarray] = None,  # atmospheric CO2 concentration in ppm
-        wind_speed_mps: Union[Raster, np.ndarray] = None,  # wind speed in meters per second
-        SZA: Union[Raster, np.ndarray] = None,  # solar zenith angle in degrees
-        canopy_temperature_C: Union[Raster, np.ndarray] = None, # canopy temperature in Celsius (initialized to surface temperature if left as None)
-        soil_temperature_C: Union[Raster, np.ndarray] = None, # soil temperature in Celsius (initialized to surface temperature if left as None)
-        C4_fraction: Union[Raster, np.ndarray] = None,  # fraction of C4 plants
-        carbon_uptake_efficiency: Union[Raster, np.ndarray] = None,  # intrinsic quantum efficiency for carbon uptake
-        kn: np.ndarray = None,
-        ball_berry_intercept_C3: np.ndarray = None,  # Ball-Berry intercept for C3 plants
-        ball_berry_intercept_C4: Union[np.ndarray, float] = BALL_BERRY_INTERCEPT_C4, # Ball-Berry intercept for C4 plants
-        ball_berry_slope_C3: np.ndarray = None,  # Ball-Berry slope for C3 plants
-        ball_berry_slope_C4: np.ndarray = None,  # Ball-Berry slope for C4 plants
-        peakVCmax_C3: np.ndarray = None,  # peak maximum carboxylation rate for C3 plants
-        peakVCmax_C4: np.ndarray = None,  # peak maximum carboxylation rate for C4 plants
-        CI: Union[Raster, np.ndarray] = None,
-        resampling: str = RESAMPLING):  # clumping index
-    if geometry is None and isinstance(ST_C, Raster):
-        geometry = ST_C.geometry
-
-    if GEOS5FP_connection is None:
-        GEOS5FP_connection = GEOS5FP()
-
-    if (day_of_year is None or hour_of_day is None) and time_UTC is not None and geometry is not None:
-        day_of_year = solar_day_of_year_for_area(time_UTC=time_UTC, geometry=geometry)
-        hour_of_day = solar_hour_of_day_for_area(time_UTC=time_UTC, geometry=geometry)
-
-    if time_UTC is None and day_of_year is None and hour_of_day is None:
-        raise ValueError("no time given between time_UTC, day_of_year, and hour_of_day")
-
-    if elevation_km is None and geometry is not None:
-        elevation_km = NASADEM.elevation_km(geometry=geometry)
-
-    # load air temperature in Celsius if not provided
-    if Ta_C is None:
-        Ta_C = GEOS5FP_connection.Ta_C(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
-
-    # load relative humidity if not provided
-    if RH is None:
-        RH = GEOS5FP_connection.RH(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
-
-    # load minimum NDVI if not provided
-    if NDVI_minimum is None and geometry is not None:
-        NDVI_minimum = load_NDVI_minimum(geometry=geometry, resampling=resampling)
-
-    # load maximum NDVI if not provided
-    if NDVI_maximum is None and geometry is not None:
-        NDVI_maximum = load_NDVI_maximum(geometry=geometry, resampling=resampling)
-
-    # load C4 fraction if not provided
-    if C4_fraction is None:
-        C4_fraction = load_C4_fraction(geometry=geometry, resampling=resampling)
-
-    # load carbon uptake efficiency if not provided
-    if carbon_uptake_efficiency is None:
-        carbon_uptake_efficiency = load_carbon_uptake_efficiency(geometry=geometry, resampling=resampling)
-    
-    # load kn if not provided
-    if kn is None:
-        kn = load_kn(geometry=geometry, resampling=resampling)
-
-    # load peak VC max for C3 plants if not provided
-    if peakVCmax_C3 is None:
-        peakVCmax_C3 = load_peakVCmax_C3(geometry=geometry, resampling=resampling)
-
-    # load peak VC max for C4 plants if not provided
-    if peakVCmax_C4 is None:
-        peakVCmax_C4 = load_peakVCmax_C4(geometry=geometry, resampling=resampling)
-
-    # load Ball-Berry slope for C3 plants if not provided
-    if ball_berry_slope_C3 is None:
-        ball_berry_slope_C3 = load_ball_berry_slope_C3(geometry=geometry, resampling=resampling)
-    
-    # load Ball-Berry slope for C4 plants if not provided
-    if ball_berry_slope_C4 is None:
-        ball_berry_slope_C4 = load_ball_berry_slope_C4(geometry=geometry, resampling=resampling)
-
-    # load Ball-Berry intercept for C3 plants if not provided
-    if ball_berry_intercept_C3 is None:
-        ball_berry_intercept_C3 = load_ball_berry_intercept_C3(geometry=geometry, resampling=resampling)
-
-    # Create a dictionary of variables to check
-    variables_to_check = {
-        "Rg": Rg,
-        "VISdiff": VISdiff,
-        "VISdir": VISdir,
-        "NIRdiff": NIRdiff,
-        "NIRdir": NIRdir,
-        "UV": UV,
-        "albedo_visible": albedo_visible,
-        "albedo_NIR": albedo_NIR
-    }
-
-    # Check for None values and size mismatches
-    reference_size = None
-    missing_radiative_transfer_variables = []
-    need_radiative_transfer = False
-
-    for name, var in variables_to_check.items():
-        if var is None:
-            logger.info(f"{name}: None")
-        else:
-            logger.info(f"{name}: {var.shape}")
-
-        if var is None:
-            logger.warning(f"Variable '{name}' is None.")
-            missing_radiative_transfer_variables = missing_radiative_transfer_variables.append(name)
-        else:
-            # Get the size of the variable if it's a numpy array
-            size = var.shape if isinstance(var, np.ndarray) else None
-
-            if reference_size is None:
-                reference_size = size  # Set the first non-None size as the reference
-            elif size != reference_size:
-                logger.warning(f"Variable '{name}' has a different size: {size} (expected: {reference_size}).")
-                missing_radiative_transfer_variables = missing_radiative_transfer_variables.append(name)
-
-    if len(missing_radiative_transfer_variables) > 0:
-        need_radiative_transfer = True
-
-    # check if any of the FLiES outputs are not given
-    if need_radiative_transfer:
-        logger.info(f"running FLiES for missing variables: {', '.join(missing_radiative_transfer_variables)}")
-        # load cloud optical thickness if not provided
-        if COT is None:
-            COT = GEOS5FP_connection.COT(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
-
-        # load aerosol optical thickness if not provided
-        if AOT is None:
-            AOT = GEOS5FP_connection.AOT(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
-
-        ## FIXME fix FLiES interface
-
-        # run FLiES radiative transfer model
-        FLiES_results = FLiESANN(
-            time_UTC=time_UTC,
-            day_of_year=day_of_year,
-            hour_of_day=hour_of_day,
-            geometry=geometry,
-            albedo=albedo,
-            COT=COT,
-            AOT=AOT,
-            vapor_gccm=vapor_gccm,
-            ozone_cm=ozone_cm,
-            elevation_km=elevation_km,
-            SZA=SZA,
-            KG_climate=KG_climate,
-            GEOS5FP_connection=GEOS5FP_connection
-        )
-
-        # extract FLiES outputs
-        Rg = FLiES_results["Rg"]
-        VISdiff = FLiES_results["VISdiff"]
-        VISdir = FLiES_results["VISdir"]
-        NIRdiff = FLiES_results["NIRdiff"]
-        NIRdir = FLiES_results["NIRdir"]
-        UV = FLiES_results["UV"]
-        # albedo_visible = FLiES_results["VIS"]
-        # albedo_NIR = FLiES_results["NIR"]
-        albedo_NWP = GEOS5FP_connection.ALBEDO(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
-        RVIS_NWP = GEOS5FP_connection.ALBVISDR(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
-        albedo_visible = rt.clip(albedo * (RVIS_NWP / albedo_NWP), 0, 1)
-        check_distribution(albedo_visible, "RVIS")
-        RNIR_NWP = GEOS5FP_connection.ALBNIRDR(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
-        albedo_NIR = rt.clip(albedo * (RNIR_NWP / albedo_NWP), 0, 1)
-        check_distribution(albedo_NIR, "RNIR")
-        PARDir = VISdir
-        check_distribution(PARDir, "PARDir")
-    else:
-        logger.info("using given FLiES output as BESS parameters")
-
-    # load koppen geiger climate classification if not provided
-    if KG_climate is None:
-        KG_climate = load_koppen_geiger(geometry=geometry)
-
-    # load canopy height in meters if not provided
-    if canopy_height_meters is None:
-        canopy_height_meters = load_canopy_height(geometry=geometry, resampling=resampling)
-
-    # load CO2 concentration in ppm if not provided
-    if Ca is None:
-        Ca = GEOS5FP_connection.CO2SC(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
-
-    # load wind speed in meters per second if not provided
-    if wind_speed_mps is None:
-        wind_speed_mps = GEOS5FP_connection.wind_speed(time_UTC=time_UTC, geometry=geometry, resampling=resampling)    
-
-    # canopy temperature defaults to surface temperature
-    if canopy_temperature_C is None:
-        canopy_temperature_C = ST_C
-
-    # soil temperature defaults to surface temperature
-    if soil_temperature_C is None:
-        soil_temperature_C = ST_C
-
-    # visible albedo defaults to surface albedo
-    if albedo_visible is None:
-        albedo_visible = albedo
-
-    # near-infrared albedo defaults to surface albedo
-    if albedo_NIR is None:
-        albedo_NIR = albedo
-
-    # calculate solar zenith angle if not provided
-    if SZA is None:
-        SZA = calculate_SZA_from_DOY_and_hour(geometry.lat, geometry.lon, day_of_year, hour_of_day)
-
-    if CI is None and geometry is not None:
-        modisci = MODISCI()
-        CI = modisci.CI(geometry=geometry, resampling=resampling)
-
-    # canopy height defaults to zero
-    canopy_height_meters = np.where(np.isnan(canopy_height_meters), 0, canopy_height_meters)
-
-    # calculate saturation vapor pressure in Pascal from air temperature in Kelvin
-    Ta_K = Ta_C + 273.15
-    SVP_Pa = SVP_Pa_from_Ta_K(Ta_K)
-
-    # calculate actual vapor pressure in Pascal from relative humidity and saturation vapor pressure
-    Ea_Pa = RH * SVP_Pa
-
-    # convert elevation to meters
-    elevation_m = elevation_km * 1000
-
-    latitude = geometry.lat
-
-    Ps_Pa, VPD_Pa, RH, desTa, ddesTa, gamma, Cp, rhoa, epsa, R, Rc, Rs, SFd, SFd2, DL, Ra, fStress = meteorology(
-        day_of_year=day_of_year,
-        hour_of_day=hour_of_day,
-        latitude=latitude,
-        elevation_m=elevation_m,
-        SZA=SZA,
-        Ta_K=Ta_K,
-        Ea_Pa=Ea_Pa,
-        Rg=Rg,
-        wind_speed_mps=wind_speed_mps,
-        canopy_height_meters=canopy_height_meters
-    )
-
-    meteorology_outputs = {
-        "Ps_Pa": Ps_Pa,
-        "VPD_Pa": VPD_Pa,
-        "RH": RH,
-        "desTa": desTa,
-        "ddesTa": ddesTa,
-        "gamma": gamma,
-        "Cp": Cp,
-        "rhoa": rhoa,
-        "epsa": epsa,
-        "R": R,
-        "Rc": Rc,
-        "Rs": Rs,
-        "SFd": SFd,
-        "SFd2": SFd2,
-        "DL": DL,
-        "Ra": Ra,
-        "fStress": fStress
-    }
-
-    # Check the distribution for each variable
-    for var_name, var_value in meteorology_outputs.items():
-        check_distribution(var_value, var_name, time_UTC)
-
-    # convert NDVI to LAI
-    LAI = LAI_from_NDVI(NDVI)
-    LAI_minimum = LAI_from_NDVI(NDVI_minimum)
-    LAI_maximum = LAI_from_NDVI(NDVI_maximum)
-
-    VCmax_C3_sunlit, VCmax_C4_sunlit, VCmax_C3_shaded, VCmax_C4_shaded = calculate_VCmax(
-        LAI=LAI,
-        LAI_minimum=LAI_minimum,
-        LAI_maximum=LAI_maximum,
-        peakVCmax_C3=peakVCmax_C3,
-        peakVCmax_C4=peakVCmax_C4,
-        SZA=SZA,
-        kn=kn
-    )
-
-    # List of variable names and their corresponding values
-    VCmax_outputs = {
-        "VCmax_C3_sunlit": VCmax_C3_sunlit,
-        "VCmax_C4_sunlit": VCmax_C4_sunlit,
-        "VCmax_C3_shaded": VCmax_C3_shaded,
-        "VCmax_C4_shaded": VCmax_C4_shaded
-    }
-
-    # Check the distribution for each variable
-    for var_name, var_value in VCmax_outputs.items():
-        check_distribution(var_value, var_name, time_UTC)
-
-    sunlit_fraction, APAR_sunlit, APAR_shaded, ASW_sunlit, ASW_shaded, ASW_soil, G = canopy_shortwave_radiation(
-        PARDiff=VISdiff,  # diffuse photosynthetically active radiation in W/m^2
-        PARDir=VISdir,  # direct photosynthetically active radiation in W/m^2
-        NIRDiff=NIRdiff,  # diffuse near-infrared radiation in W/m^2
-        NIRDir=NIRdir,  # direct near-infrared radiation in W/m^2
-        UV=UV,  # incoming ultraviolet radiation in W/m^2
-        SZA=SZA,  # solar zenith angle in degrees
-        LAI=LAI,  # leaf area index
-        CI=CI,  # clumping index
-        albedo_visible=albedo_visible,  # surface albedo in visible wavelengths
-        albedo_NIR=albedo_NIR  # surface albedo in near-infrared wavelengths
-    )
-
-    # List of variable names and their corresponding values
-    canopy_radiation_outputs = {
-        "sunlit_fraction": sunlit_fraction,
-        "APAR_sunlit": APAR_sunlit,
-        "APAR_shaded": APAR_shaded,
-        "ASW_sunlit": ASW_sunlit,
-        "ASW_shaded": ASW_shaded,
-        "ASW_soil": ASW_soil,
-        "G": G
-    }
-
-    # Check the distribution for each variable
-    for var_name, var_value in canopy_radiation_outputs.items():
-        check_distribution(var_value, var_name, time_UTC)
-
-    canopy_temperature_K = canopy_temperature_C + 273.15
-    soil_temperature_K = soil_temperature_C + 273.15
-
-    GPP_C3, LE_C3, LE_soil_C3, LE_canopy_C3, Rn_C3, Rn_soil_C3, Rn_canopy_C3 = carbon_water_fluxes(
-        canopy_temperature_K=canopy_temperature_K,  # canopy temperature in Kelvin
-        soil_temperature_K=soil_temperature_K,  # soil temperature in Kelvin
-        LAI=LAI,  # leaf area index
-        Ta_K=Ta_K,  # air temperature in Kelvin
-        APAR_sunlit=APAR_sunlit,  # sunlit leaf absorptance of photosynthetically active radiation
-        APAR_shaded=APAR_shaded,  # shaded leaf absorptance of photosynthetically active radiation
-        ASW_sunlit=ASW_sunlit,  # sunlit absorbed shortwave radiation
-        ASW_shaded=ASW_shaded,  # shaded absorbed shortwave radiation
-        ASW_soil=ASW_soil,  # absorbed shortwave radiation of soil
-        Vcmax25_sunlit=VCmax_C3_sunlit,  # sunlit maximum carboxylation rate at 25 degrees C
-        Vcmax25_shaded=VCmax_C3_shaded,  # shaded maximum carboxylation rate at 25 degrees C
-        ball_berry_slope=ball_berry_slope_C3,  # Ball-Berry slope for C3 photosynthesis
-        ball_berry_intercept=ball_berry_intercept_C3,  # Ball-Berry intercept for C3 photosynthesis
-        sunlit_fraction=sunlit_fraction,  # fraction of sunlit leaves
-        G=G,  # soil heat flux
-        SZA=SZA,  # solar zenith angle
-        Ca=Ca,  # atmospheric CO2 concentration
-        Ps_Pa=Ps_Pa,  # surface pressure in Pascal
-        gamma=gamma,  # psychrometric constant
-        Cp=Cp,  # specific heat of air in J/kg/K
-        rhoa=rhoa,  # density of air in kg/m3
-        VPD_Pa=VPD_Pa,  # vapor pressure deficit in Pascal
-        RH=RH,  # relative humidity as a fraction
-        desTa=desTa,
-        ddesTa=ddesTa,
-        epsa=epsa,
-        Rc=Rc,
-        Rs=Rs,
-        carbon_uptake_efficiency=carbon_uptake_efficiency,  # intrinsic quantum efficiency for carbon uptake
-        fStress=fStress,
-        C4_photosynthesis=False  # C3 or C4 photosynthesis
-    )
-
-    # List of variable names and their corresponding values
-    carbon_water_fluxes_outputs = {
-        "GPP_C3": GPP_C3,
-        "LE_C3": LE_C3,
-        "LE_soil_C3": LE_soil_C3,
-        "LE_canopy_C3": LE_canopy_C3,
-        "Rn_C3": Rn_C3,
-        "Rn_soil_C3": Rn_soil_C3,
-        "Rn_canopy_C3": Rn_canopy_C3
-    }
-
-    # Check the distribution for each variable
-    for var_name, var_value in carbon_water_fluxes_outputs.items():
-        check_distribution(var_value, var_name, time_UTC)
-
-    GPP_C4, LE_C4, LE_soil_C4, LE_canopy_C4, Rn_C4, Rn_soil_C4, Rn_canopy_C4 = carbon_water_fluxes(
-        canopy_temperature_K=canopy_temperature_K,  # canopy temperature in Kelvin
-        soil_temperature_K=soil_temperature_K,  # soil temperature in Kelvin
-        LAI=LAI,  # leaf area index
-        Ta_K=Ta_K,  # air temperature in Kelvin
-        APAR_sunlit=APAR_sunlit,  # sunlit leaf absorptance of photosynthetically active radiation
-        APAR_shaded=APAR_shaded,  # shaded leaf absorptance of photosynthetically active radiation
-        ASW_sunlit=ASW_sunlit,  # sunlit absorbed shortwave radiation
-        ASW_shaded=ASW_shaded,  # shaded absorbed shortwave radiation
-        ASW_soil=ASW_soil,  # absorbed shortwave radiation of soil
-        Vcmax25_sunlit=VCmax_C4_sunlit,  # sunlit maximum carboxylation rate at 25 degrees C
-        Vcmax25_shaded=VCmax_C4_shaded,  # shaded maximum carboxylation rate at 25 degrees C
-        ball_berry_slope=ball_berry_slope_C4,  # Ball-Berry slope for C4 photosynthesis
-        ball_berry_intercept=ball_berry_intercept_C4,  # Ball-Berry intercept for C4 photosynthesis
-        sunlit_fraction=sunlit_fraction,  # fraction of sunlit leaves
-        G=G,  # soil heat flux
-        SZA=SZA,  # solar zenith angle
-        Ca=Ca,  # atmospheric CO2 concentration
-        Ps_Pa=Ps_Pa,  # surface pressure in Pascal
-        gamma=gamma,  # psychrometric constant
-        Cp=Cp,  # specific heat of air in J/kg/K
-        rhoa=rhoa,  # density of air in kg/m3
-        VPD_Pa=VPD_Pa,  # vapor pressure deficit in Pascal
-        RH=RH,  # relative humidity as a fraction
-        desTa=desTa,
-        ddesTa=ddesTa,
-        epsa=epsa,
-        Rc=Rc,
-        Rs=Rs,
-        carbon_uptake_efficiency=carbon_uptake_efficiency,  # intrinsic quantum efficiency for carbon uptake
-        fStress=fStress,
-        C4_photosynthesis=True  # C3 or C4 photosynthesis
-    )
-
-    # List of variable names and their corresponding values
-    carbon_water_fluxes_C4_outputs = {
-        "GPP_C4": GPP_C4,
-        "LE_C4": LE_C4,
-        "LE_soil_C4": LE_soil_C4,
-        "LE_canopy_C4": LE_canopy_C4,
-        "Rn_C4": Rn_C4,
-        "Rn_soil_C4": Rn_soil_C4,
-        "Rn_canopy_C4": Rn_canopy_C4
-    }
-
-    # Check the distribution for each variable
-    for var_name, var_value in carbon_water_fluxes_C4_outputs.items():
-        check_distribution(var_value, var_name, time_UTC)
-
-    # interpolate C3 and C4 GPP
-    ST_K = ST_C + 273.15
-    GPP = np.clip(interpolate_C3_C4(GPP_C3, GPP_C4, C4_fraction), 0, 50)
-    GPP = np.where(np.isnan(ST_K), np.nan, GPP)
-
-    if isinstance(geometry, RasterGeometry):
-        GPP = Raster(GPP, geometry=geometry)
-
-    # upscale from instantaneous to daily
-
-    # upscale GPP to daily
-    GPP_daily = 1800 * GPP / SFd * 1e-6 * 12  # Eq. (3) in Ryu et al 2008
-    GPP_daily = np.where(SFd < 0.01, 0, GPP_daily)
-    GPP_daily = np.where(SZA >= 90, 0, GPP_daily)
-
-    # interpolate C3 and C4 net radiation
-    Rn = np.clip(interpolate_C3_C4(Rn_C3, Rn_C4, C4_fraction), 0, 1000)
-
-    # interpolate C3 and C4 soil net radiation
-    Rn_soil = np.clip(interpolate_C3_C4(Rn_soil_C3, Rn_soil_C4, C4_fraction), 0, 1000)
-
-    # interpolate C3 and C4 canopy net radiation
-    Rn_canopy = np.clip(interpolate_C3_C4(Rn_canopy_C3, Rn_canopy_C4, C4_fraction), 0, 1000)
-
-    # interpolate C3 and C4 latent heat flux
-    LE = np.clip(interpolate_C3_C4(LE_C3, LE_C4, C4_fraction), 0, 1000)
-
-    # interpolate C3 and C4 soil latent heat flux
-    LE_soil = np.clip(interpolate_C3_C4(LE_soil_C3, LE_soil_C4, C4_fraction), 0, 1000)
-
-    # interpolate C3 and C4 canopy latent heat flux
-    LE_canopy = np.clip(interpolate_C3_C4(LE_canopy_C3, LE_canopy_C4, C4_fraction), 0, 1000)
-
-    return {
-        "GPP": GPP,
-        "GPP_daily": GPP_daily,
-        "Rn": Rn,
-        "Rn_soil": Rn_soil,
-        "Rn_canopy": Rn_canopy,
-        "G": G,
-        "LE": LE,
-        "LE_soil": LE_soil,
-        "LE_canopy": LE_canopy
-    }
+from .model import *

BESS_JPL/model.py

@@ -0,0 +1,520 @@
+from typing import Union
+from datetime import datetime
+import logging
+import numpy as np
+
+import rasters as rt
+from rasters import Raster, RasterGeometry
+
+from check_distribution import check_distribution
+
+from sun_angles import calculate_SZA_from_DOY_and_hour
+from solar_apparent_time import solar_day_of_year_for_area, solar_hour_of_day_for_area
+
+from koppengeiger import load_koppen_geiger
+from gedi_canopy_height import load_canopy_height
+from FLiESANN import FLiESANN
+from GEOS5FP import GEOS5FP
+from MODISCI import MODISCI
+from NASADEM import NASADEM
+
+from .constants import *
+from .C3_photosynthesis import *
+from .C4_photosynthesis import *
+from .canopy_energy_balance import *
+from .canopy_longwave_radiation import *
+from .canopy_shortwave_radiation import *
+from .carbon_water_fluxes import *
+from .FVC_from_NDVI import *
+from .interpolate_C3_C4 import *
+from .LAI_from_NDVI import *
+from .load_C4_fraction import *
+from .load_carbon_uptake_efficiency import *
+from .load_kn import *
+from .load_NDVI_minimum import *
+from .load_NDVI_maximum import *
+from .load_peakVCmax_C3 import *
+from .load_peakVCmax_C4 import *
+from .load_ball_berry_intercept_C3 import *
+from .load_ball_berry_slope_C3 import *
+from .load_ball_berry_slope_C4 import *
+from .calculate_VCmax import *
+from .meteorology import *
+from .soil_energy_balance import *
+
+logger = logging.getLogger(__name__)
+
+def BESS_JPL(
+        ST_C: Union[Raster, np.ndarray],  # surface temperature in Celsius
+        NDVI: Union[Raster, np.ndarray],  # NDVI
+        albedo: Union[Raster, np.ndarray],  # surface albedo
+        geometry: RasterGeometry = None,
+        time_UTC: datetime = None,
+        hour_of_day: np.ndarray = None,
+        day_of_year: np.ndarray = None,
+        GEOS5FP_connection: GEOS5FP = None,
+        elevation_km: Union[Raster, np.ndarray] = None,  # elevation in kilometers
+        Ta_C: Union[Raster, np.ndarray] = None,  # air temperature in Celsius
+        RH: Union[Raster, np.ndarray] = None,  # relative humidity as a proportion
+        NDVI_minimum: Union[Raster, np.ndarray] = None,  # minimum NDVI
+        NDVI_maximum: Union[Raster, np.ndarray] = None,  # maximum NDVI
+        Rg: Union[Raster, np.ndarray] = None,  # incoming shortwave radiation in W/m^2
+        VISdiff: Union[Raster, np.ndarray] = None,  # diffuse visible radiation in W/m^2
+        VISdir: Union[Raster, np.ndarray] = None,  # direct visible radiation in W/m^2
+        NIRdiff: Union[Raster, np.ndarray] = None,  # diffuse near-infrared radiation in W/m^2
+        NIRdir: Union[Raster, np.ndarray] = None,  # direct near-infrared radiation in W/m^2
+        UV: Union[Raster, np.ndarray] = None,  # incoming ultraviolet radiation in W/m^2
+        albedo_visible: Union[Raster, np.ndarray] = None, # surface albedo in visible wavelengths (initialized to surface albedo if left as None)
+        albedo_NIR: Union[Raster, np.ndarray] = None, # surface albedo in near-infrared wavelengths (initialized to surface albedo if left as None)
+        COT: Union[Raster, np.ndarray] = None,  # cloud optical thickness
+        AOT: Union[Raster, np.ndarray] = None,  # aerosol optical thickness
+        vapor_gccm: Union[Raster, np.ndarray] = None,  # water vapor in g/ccm
+        ozone_cm: Union[Raster, np.ndarray] = None,  # ozone in cm
+        KG_climate: Union[Raster, np.ndarray] = None,  # KG climate
+        canopy_height_meters: Union[Raster, np.ndarray] = None,  # canopy height in meters
+        Ca: Union[Raster, np.ndarray] = None,  # atmospheric CO2 concentration in ppm
+        wind_speed_mps: Union[Raster, np.ndarray] = None,  # wind speed in meters per second
+        SZA: Union[Raster, np.ndarray] = None,  # solar zenith angle in degrees
+        canopy_temperature_C: Union[Raster, np.ndarray] = None, # canopy temperature in Celsius (initialized to surface temperature if left as None)
+        soil_temperature_C: Union[Raster, np.ndarray] = None, # soil temperature in Celsius (initialized to surface temperature if left as None)
+        C4_fraction: Union[Raster, np.ndarray] = None,  # fraction of C4 plants
+        carbon_uptake_efficiency: Union[Raster, np.ndarray] = None,  # intrinsic quantum efficiency for carbon uptake
+        kn: np.ndarray = None,
+        ball_berry_intercept_C3: np.ndarray = None,  # Ball-Berry intercept for C3 plants
+        ball_berry_intercept_C4: Union[np.ndarray, float] = BALL_BERRY_INTERCEPT_C4, # Ball-Berry intercept for C4 plants
+        ball_berry_slope_C3: np.ndarray = None,  # Ball-Berry slope for C3 plants
+        ball_berry_slope_C4: np.ndarray = None,  # Ball-Berry slope for C4 plants
+        peakVCmax_C3: np.ndarray = None,  # peak maximum carboxylation rate for C3 plants
+        peakVCmax_C4: np.ndarray = None,  # peak maximum carboxylation rate for C4 plants
+        CI: Union[Raster, np.ndarray] = None,
+        resampling: str = RESAMPLING):  # clumping index
+    if geometry is None and isinstance(ST_C, Raster):
+        geometry = ST_C.geometry
+
+    if GEOS5FP_connection is None:
+        GEOS5FP_connection = GEOS5FP()
+
+    if (day_of_year is None or hour_of_day is None) and time_UTC is not None and geometry is not None:
+        day_of_year = solar_day_of_year_for_area(time_UTC=time_UTC, geometry=geometry)
+        hour_of_day = solar_hour_of_day_for_area(time_UTC=time_UTC, geometry=geometry)
+
+    if time_UTC is None and day_of_year is None and hour_of_day is None:
+        raise ValueError("no time given between time_UTC, day_of_year, and hour_of_day")
+
+    if elevation_km is None and geometry is not None:
+        elevation_km = NASADEM.elevation_km(geometry=geometry)
+
+    # load air temperature in Celsius if not provided
+    if Ta_C is None:
+        Ta_C = GEOS5FP_connection.Ta_C(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
+
+    # load relative humidity if not provided
+    if RH is None:
+        RH = GEOS5FP_connection.RH(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
+
+    # load minimum NDVI if not provided
+    if NDVI_minimum is None and geometry is not None:
+        NDVI_minimum = load_NDVI_minimum(geometry=geometry, resampling=resampling)
+
+    # load maximum NDVI if not provided
+    if NDVI_maximum is None and geometry is not None:
+        NDVI_maximum = load_NDVI_maximum(geometry=geometry, resampling=resampling)
+
+    # load C4 fraction if not provided
+    if C4_fraction is None:
+        C4_fraction = load_C4_fraction(geometry=geometry, resampling=resampling)
+
+    # load carbon uptake efficiency if not provided
+    if carbon_uptake_efficiency is None:
+        carbon_uptake_efficiency = load_carbon_uptake_efficiency(geometry=geometry, resampling=resampling)
+    
+    # load kn if not provided
+    if kn is None:
+        kn = load_kn(geometry=geometry, resampling=resampling)
+
+    # load peak VC max for C3 plants if not provided
+    if peakVCmax_C3 is None:
+        peakVCmax_C3 = load_peakVCmax_C3(geometry=geometry, resampling=resampling)
+
+    # load peak VC max for C4 plants if not provided
+    if peakVCmax_C4 is None:
+        peakVCmax_C4 = load_peakVCmax_C4(geometry=geometry, resampling=resampling)
+
+    # load Ball-Berry slope for C3 plants if not provided
+    if ball_berry_slope_C3 is None:
+        ball_berry_slope_C3 = load_ball_berry_slope_C3(geometry=geometry, resampling=resampling)
+    
+    # load Ball-Berry slope for C4 plants if not provided
+    if ball_berry_slope_C4 is None:
+        ball_berry_slope_C4 = load_ball_berry_slope_C4(geometry=geometry, resampling=resampling)
+
+    # load Ball-Berry intercept for C3 plants if not provided
+    if ball_berry_intercept_C3 is None:
+        ball_berry_intercept_C3 = load_ball_berry_intercept_C3(geometry=geometry, resampling=resampling)
+
+    # Create a dictionary of variables to check
+    variables_to_check = {
+        "Rg": Rg,
+        "VISdiff": VISdiff,
+        "VISdir": VISdir,
+        "NIRdiff": NIRdiff,
+        "NIRdir": NIRdir,
+        "UV": UV,
+        "albedo_visible": albedo_visible,
+        "albedo_NIR": albedo_NIR
+    }
+
+    # Check for None values and size mismatches
+    reference_size = None
+    for name, var in variables_to_check.items():
+        if var is None:
+            logger.warning(f"Variable '{name}' is None.")
+        else:
+            # Get the size of the variable if it's a numpy array
+            size = var.shape if isinstance(var, np.ndarray) else None
+            if reference_size is None:
+                reference_size = size  # Set the first non-None size as the reference
+            elif size != reference_size:
+                logger.warning(f"Variable '{name}' has a different size: {size} (expected: {reference_size}).")
+
+    # check if any of the FLiES outputs are not given
+    if None in (Rg, VISdiff, VISdir, NIRdiff, NIRdir, UV, albedo_visible, albedo_NIR):
+        # load cloud optical thickness if not provided
+        if COT is None:
+            COT = GEOS5FP_connection.COT(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
+
+        # load aerosol optical thickness if not provided
+        if AOT is None:
+            AOT = GEOS5FP_connection.AOT(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
+
+        ## FIXME fix FLiES interface
+
+        # run FLiES radiative transfer model
+        FLiES_results = FLiESANN(
+            time_UTC=time_UTC,
+            day_of_year=day_of_year,
+            hour_of_day=hour_of_day,
+            geometry=geometry,
+            albedo=albedo,
+            COT=COT,
+            AOT=AOT,
+            vapor_gccm=vapor_gccm,
+            ozone_cm=ozone_cm,
+            elevation_km=elevation_km,
+            SZA=SZA,
+            KG_climate=KG_climate,
+            GEOS5FP_connection=GEOS5FP_connection
+        )
+
+        # extract FLiES outputs
+        Rg = FLiES_results["Rg"]
+        VISdiff = FLiES_results["VISdiff"]
+        VISdir = FLiES_results["VISdir"]
+        NIRdiff = FLiES_results["NIRdiff"]
+        NIRdir = FLiES_results["NIRdir"]
+        UV = FLiES_results["UV"]
+        # albedo_visible = FLiES_results["VIS"]
+        # albedo_NIR = FLiES_results["NIR"]
+        albedo_NWP = GEOS5FP_connection.ALBEDO(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
+        RVIS_NWP = GEOS5FP_connection.ALBVISDR(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
+        albedo_visible = rt.clip(albedo * (RVIS_NWP / albedo_NWP), 0, 1)
+        check_distribution(albedo_visible, "RVIS")
+        RNIR_NWP = GEOS5FP_connection.ALBNIRDR(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
+        albedo_NIR = rt.clip(albedo * (RNIR_NWP / albedo_NWP), 0, 1)
+        check_distribution(albedo_NIR, "RNIR")
+        PARDir = VISdir
+        check_distribution(PARDir, "PARDir")
+    else:
+        logger.info("using given FLiES output as BESS parameters")
+
+    # load koppen geiger climate classification if not provided
+    if KG_climate is None:
+        KG_climate = load_koppen_geiger(geometry=geometry)
+
+    # load canopy height in meters if not provided
+    if canopy_height_meters is None:
+        canopy_height_meters = load_canopy_height(geometry=geometry, resampling=resampling)
+
+    # load CO2 concentration in ppm if not provided
+    if Ca is None:
+        Ca = GEOS5FP_connection.CO2SC(time_UTC=time_UTC, geometry=geometry, resampling=resampling)
+
+    # load wind speed in meters per second if not provided
+    if wind_speed_mps is None:
+        wind_speed_mps = GEOS5FP_connection.wind_speed(time_UTC=time_UTC, geometry=geometry, resampling=resampling)    
+
+    # canopy temperature defaults to surface temperature
+    if canopy_temperature_C is None:
+        canopy_temperature_C = ST_C
+
+    # soil temperature defaults to surface temperature
+    if soil_temperature_C is None:
+        soil_temperature_C = ST_C
+
+    # visible albedo defaults to surface albedo
+    if albedo_visible is None:
+        albedo_visible = albedo
+
+    # near-infrared albedo defaults to surface albedo
+    if albedo_NIR is None:
+        albedo_NIR = albedo
+
+    # calculate solar zenith angle if not provided
+    if SZA is None:
+        SZA = calculate_SZA_from_DOY_and_hour(geometry.lat, geometry.lon, day_of_year, hour_of_day)
+
+    if CI is None and geometry is not None:
+        modisci = MODISCI()
+        CI = modisci.CI(geometry=geometry, resampling=resampling)
+
+    # canopy height defaults to zero
+    canopy_height_meters = np.where(np.isnan(canopy_height_meters), 0, canopy_height_meters)
+
+    # calculate saturation vapor pressure in Pascal from air temperature in Kelvin
+    Ta_K = Ta_C + 273.15
+    SVP_Pa = SVP_Pa_from_Ta_K(Ta_K)
+
+    # calculate actual vapor pressure in Pascal from relative humidity and saturation vapor pressure
+    Ea_Pa = RH * SVP_Pa
+
+    # convert elevation to meters
+    elevation_m = elevation_km * 1000
+
+    latitude = geometry.lat
+
+    Ps_Pa, VPD_Pa, RH, desTa, ddesTa, gamma, Cp, rhoa, epsa, R, Rc, Rs, SFd, SFd2, DL, Ra, fStress = meteorology(
+        day_of_year=day_of_year,
+        hour_of_day=hour_of_day,
+        latitude=latitude,
+        elevation_m=elevation_m,
+        SZA=SZA,
+        Ta_K=Ta_K,
+        Ea_Pa=Ea_Pa,
+        Rg=Rg,
+        wind_speed_mps=wind_speed_mps,
+        canopy_height_meters=canopy_height_meters
+    )
+
+    meteorology_outputs = {
+        "Ps_Pa": Ps_Pa,
+        "VPD_Pa": VPD_Pa,
+        "RH": RH,
+        "desTa": desTa,
+        "ddesTa": ddesTa,
+        "gamma": gamma,
+        "Cp": Cp,
+        "rhoa": rhoa,
+        "epsa": epsa,
+        "R": R,
+        "Rc": Rc,
+        "Rs": Rs,
+        "SFd": SFd,
+        "SFd2": SFd2,
+        "DL": DL,
+        "Ra": Ra,
+        "fStress": fStress
+    }
+
+    # Check the distribution for each variable
+    for var_name, var_value in meteorology_outputs.items():
+        check_distribution(var_value, var_name, time_UTC)
+
+    # convert NDVI to LAI
+    LAI = LAI_from_NDVI(NDVI)
+    LAI_minimum = LAI_from_NDVI(NDVI_minimum)
+    LAI_maximum = LAI_from_NDVI(NDVI_maximum)
+
+    VCmax_C3_sunlit, VCmax_C4_sunlit, VCmax_C3_shaded, VCmax_C4_shaded = calculate_VCmax(
+        LAI=LAI,
+        LAI_minimum=LAI_minimum,
+        LAI_maximum=LAI_maximum,
+        peakVCmax_C3=peakVCmax_C3,
+        peakVCmax_C4=peakVCmax_C4,
+        SZA=SZA,
+        kn=kn
+    )
+
+    # List of variable names and their corresponding values
+    VCmax_outputs = {
+        "VCmax_C3_sunlit": VCmax_C3_sunlit,
+        "VCmax_C4_sunlit": VCmax_C4_sunlit,
+        "VCmax_C3_shaded": VCmax_C3_shaded,
+        "VCmax_C4_shaded": VCmax_C4_shaded
+    }
+
+    # Check the distribution for each variable
+    for var_name, var_value in VCmax_outputs.items():
+        check_distribution(var_value, var_name, time_UTC)
+
+    sunlit_fraction, APAR_sunlit, APAR_shaded, ASW_sunlit, ASW_shaded, ASW_soil, G = canopy_shortwave_radiation(
+        PARDiff=VISdiff,  # diffuse photosynthetically active radiation in W/m^2
+        PARDir=VISdir,  # direct photosynthetically active radiation in W/m^2
+        NIRDiff=NIRdiff,  # diffuse near-infrared radiation in W/m^2
+        NIRDir=NIRdir,  # direct near-infrared radiation in W/m^2
+        UV=UV,  # incoming ultraviolet radiation in W/m^2
+        SZA=SZA,  # solar zenith angle in degrees
+        LAI=LAI,  # leaf area index
+        CI=CI,  # clumping index
+        albedo_visible=albedo_visible,  # surface albedo in visible wavelengths
+        albedo_NIR=albedo_NIR  # surface albedo in near-infrared wavelengths
+    )
+
+    # List of variable names and their corresponding values
+    canopy_radiation_outputs = {
+        "sunlit_fraction": sunlit_fraction,
+        "APAR_sunlit": APAR_sunlit,
+        "APAR_shaded": APAR_shaded,
+        "ASW_sunlit": ASW_sunlit,
+        "ASW_shaded": ASW_shaded,
+        "ASW_soil": ASW_soil,
+        "G": G
+    }
+
+    # Check the distribution for each variable
+    for var_name, var_value in canopy_radiation_outputs.items():
+        check_distribution(var_value, var_name, time_UTC)
+
+    canopy_temperature_K = canopy_temperature_C + 273.15
+    soil_temperature_K = soil_temperature_C + 273.15
+
+    GPP_C3, LE_C3, LE_soil_C3, LE_canopy_C3, Rn_C3, Rn_soil_C3, Rn_canopy_C3 = carbon_water_fluxes(
+        canopy_temperature_K=canopy_temperature_K,  # canopy temperature in Kelvin
+        soil_temperature_K=soil_temperature_K,  # soil temperature in Kelvin
+        LAI=LAI,  # leaf area index
+        Ta_K=Ta_K,  # air temperature in Kelvin
+        APAR_sunlit=APAR_sunlit,  # sunlit leaf absorptance of photosynthetically active radiation
+        APAR_shaded=APAR_shaded,  # shaded leaf absorptance of photosynthetically active radiation
+        ASW_sunlit=ASW_sunlit,  # sunlit absorbed shortwave radiation
+        ASW_shaded=ASW_shaded,  # shaded absorbed shortwave radiation
+        ASW_soil=ASW_soil,  # absorbed shortwave radiation of soil
+        Vcmax25_sunlit=VCmax_C3_sunlit,  # sunlit maximum carboxylation rate at 25 degrees C
+        Vcmax25_shaded=VCmax_C3_shaded,  # shaded maximum carboxylation rate at 25 degrees C
+        ball_berry_slope=ball_berry_slope_C3,  # Ball-Berry slope for C3 photosynthesis
+        ball_berry_intercept=ball_berry_intercept_C3,  # Ball-Berry intercept for C3 photosynthesis
+        sunlit_fraction=sunlit_fraction,  # fraction of sunlit leaves
+        G=G,  # soil heat flux
+        SZA=SZA,  # solar zenith angle
+        Ca=Ca,  # atmospheric CO2 concentration
+        Ps_Pa=Ps_Pa,  # surface pressure in Pascal
+        gamma=gamma,  # psychrometric constant
+        Cp=Cp,  # specific heat of air in J/kg/K
+        rhoa=rhoa,  # density of air in kg/m3
+        VPD_Pa=VPD_Pa,  # vapor pressure deficit in Pascal
+        RH=RH,  # relative humidity as a fraction
+        desTa=desTa,
+        ddesTa=ddesTa,
+        epsa=epsa,
+        Rc=Rc,
+        Rs=Rs,
+        carbon_uptake_efficiency=carbon_uptake_efficiency,  # intrinsic quantum efficiency for carbon uptake
+        fStress=fStress,
+        C4_photosynthesis=False  # C3 or C4 photosynthesis
+    )
+
+    # List of variable names and their corresponding values
+    carbon_water_fluxes_outputs = {
+        "GPP_C3": GPP_C3,
+        "LE_C3": LE_C3,
+        "LE_soil_C3": LE_soil_C3,
+        "LE_canopy_C3": LE_canopy_C3,
+        "Rn_C3": Rn_C3,
+        "Rn_soil_C3": Rn_soil_C3,
+        "Rn_canopy_C3": Rn_canopy_C3
+    }
+
+    # Check the distribution for each variable
+    for var_name, var_value in carbon_water_fluxes_outputs.items():
+        check_distribution(var_value, var_name, time_UTC)
+
+    GPP_C4, LE_C4, LE_soil_C4, LE_canopy_C4, Rn_C4, Rn_soil_C4, Rn_canopy_C4 = carbon_water_fluxes(
+        canopy_temperature_K=canopy_temperature_K,  # canopy temperature in Kelvin
+        soil_temperature_K=soil_temperature_K,  # soil temperature in Kelvin
+        LAI=LAI,  # leaf area index
+        Ta_K=Ta_K,  # air temperature in Kelvin
+        APAR_sunlit=APAR_sunlit,  # sunlit leaf absorptance of photosynthetically active radiation
+        APAR_shaded=APAR_shaded,  # shaded leaf absorptance of photosynthetically active radiation
+        ASW_sunlit=ASW_sunlit,  # sunlit absorbed shortwave radiation
+        ASW_shaded=ASW_shaded,  # shaded absorbed shortwave radiation
+        ASW_soil=ASW_soil,  # absorbed shortwave radiation of soil
+        Vcmax25_sunlit=VCmax_C4_sunlit,  # sunlit maximum carboxylation rate at 25 degrees C
+        Vcmax25_shaded=VCmax_C4_shaded,  # shaded maximum carboxylation rate at 25 degrees C
+        ball_berry_slope=ball_berry_slope_C4,  # Ball-Berry slope for C4 photosynthesis
+        ball_berry_intercept=ball_berry_intercept_C4,  # Ball-Berry intercept for C4 photosynthesis
+        sunlit_fraction=sunlit_fraction,  # fraction of sunlit leaves
+        G=G,  # soil heat flux
+        SZA=SZA,  # solar zenith angle
+        Ca=Ca,  # atmospheric CO2 concentration
+        Ps_Pa=Ps_Pa,  # surface pressure in Pascal
+        gamma=gamma,  # psychrometric constant
+        Cp=Cp,  # specific heat of air in J/kg/K
+        rhoa=rhoa,  # density of air in kg/m3
+        VPD_Pa=VPD_Pa,  # vapor pressure deficit in Pascal
+        RH=RH,  # relative humidity as a fraction
+        desTa=desTa,
+        ddesTa=ddesTa,
+        epsa=epsa,
+        Rc=Rc,
+        Rs=Rs,
+        carbon_uptake_efficiency=carbon_uptake_efficiency,  # intrinsic quantum efficiency for carbon uptake
+        fStress=fStress,
+        C4_photosynthesis=True  # C3 or C4 photosynthesis
+    )
+
+    # List of variable names and their corresponding values
+    carbon_water_fluxes_C4_outputs = {
+        "GPP_C4": GPP_C4,
+        "LE_C4": LE_C4,
+        "LE_soil_C4": LE_soil_C4,
+        "LE_canopy_C4": LE_canopy_C4,
+        "Rn_C4": Rn_C4,
+        "Rn_soil_C4": Rn_soil_C4,
+        "Rn_canopy_C4": Rn_canopy_C4
+    }
+
+    # Check the distribution for each variable
+    for var_name, var_value in carbon_water_fluxes_C4_outputs.items():
+        check_distribution(var_value, var_name, time_UTC)
+
+    # interpolate C3 and C4 GPP
+    ST_K = ST_C + 273.15
+    GPP = np.clip(interpolate_C3_C4(GPP_C3, GPP_C4, C4_fraction), 0, 50)
+    GPP = np.where(np.isnan(ST_K), np.nan, GPP)
+
+    if isinstance(geometry, RasterGeometry):
+        GPP = Raster(GPP, geometry=geometry)
+
+    # upscale from instantaneous to daily
+
+    # upscale GPP to daily
+    GPP_daily = 1800 * GPP / SFd * 1e-6 * 12  # Eq. (3) in Ryu et al 2008
+    GPP_daily = np.where(SFd < 0.01, 0, GPP_daily)
+    GPP_daily = np.where(SZA >= 90, 0, GPP_daily)
+
+    # interpolate C3 and C4 net radiation
+    Rn = np.clip(interpolate_C3_C4(Rn_C3, Rn_C4, C4_fraction), 0, 1000)
+
+    # interpolate C3 and C4 soil net radiation
+    Rn_soil = np.clip(interpolate_C3_C4(Rn_soil_C3, Rn_soil_C4, C4_fraction), 0, 1000)
+
+    # interpolate C3 and C4 canopy net radiation
+    Rn_canopy = np.clip(interpolate_C3_C4(Rn_canopy_C3, Rn_canopy_C4, C4_fraction), 0, 1000)
+
+    # interpolate C3 and C4 latent heat flux
+    LE = np.clip(interpolate_C3_C4(LE_C3, LE_C4, C4_fraction), 0, 1000)
+
+    # interpolate C3 and C4 soil latent heat flux
+    LE_soil = np.clip(interpolate_C3_C4(LE_soil_C3, LE_soil_C4, C4_fraction), 0, 1000)
+
+    # interpolate C3 and C4 canopy latent heat flux
+    LE_canopy = np.clip(interpolate_C3_C4(LE_canopy_C3, LE_canopy_C4, C4_fraction), 0, 1000)
+
+    return {
+        "GPP": GPP,
+        "GPP_daily": GPP_daily,
+        "Rn": Rn,
+        "Rn_soil": Rn_soil,
+        "Rn_canopy": Rn_canopy,
+        "LE": LE,
+        "LE_soil": LE_soil,
+        "LE_canopy": LE_canopy
+    }

BESS_JPL/process_BESS_table.py

@@ -0,0 +1,55 @@
+import logging
+
+import numpy as np
+import rasters as rt
+from dateutil import parser
+from pandas import DataFrame
+
+from .model import BESS_JPL
+
+logger = logging.getLogger(__name__)
+
+def process_BESS_table(input_df: DataFrame) -> DataFrame:
+    ST_C = np.array(input_df.ST_C).astype(np.float64)
+    NDVI = np.array(input_df.NDVI).astype(np.float64)
+
+    NDVI = np.where(NDVI > 0.06, NDVI, np.nan).astype(np.float64)
+
+    albedo = np.array(input_df.albedo).astype(np.float64)
+    
+    if "Ta_C" in input_df:
+        Ta_C = np.array(input_df.Ta_C).astype(np.float64)
+    elif "Ta" in input_df:
+        Ta_C = np.array(input_df.Ta).astype(np.float64)
+
+    RH = np.array(input_df.RH).astype(np.float64)
+    # Rn = np.array(input_df.Rn).astype(np.float64)
+    # Topt = np.array(input_df.Topt).astype(np.float64)
+    # fAPARmax = np.array(input_df.fAPARmax).astype(np.float64)
+
+    # fAPARmax = np.where(fAPARmax == 0, np.nan, fAPARmax).astype(np.float64)
+
+    # if "G" in input_df:
+    #     G = np.array(input_df.G).astype(np.float64)
+    # else:
+    #     G = calculate_SEBAL_soil_heat_flux(
+    #         Rn=Rn,
+    #         ST_C=ST_C,
+    #         NDVI=NDVI,
+    #         albedo=albedo
+    #     ).astype(np.float64)
+    
+    results = BESS_JPL(
+        ST_C=ST_C,
+        albedo=albedo,
+        NDVI=NDVI,
+        Ta_C=Ta_C,
+        RH=RH
+    )
+
+    output_df = input_df.copy()
+
+    for key, value in results.items():
+        output_df[key] = value
+
+    return output_df

BESS_JPL/version.txt

@@ -1 +1 @@
-1.9.2
+1.10.0

{bess_jpl-1.9.2.dist-info → bess_jpl-1.10.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: BESS-JPL
-Version: 1.9.2
+Version: 1.10.0
 Summary: Breathing Earth System Simulator (BESS) Gross Primary Production (GPP) and Evapotranspiration (ET) Model Python
 Author-email: Gregory Halverson <gregory.h.halverson@jpl.nasa.gov>
 Project-URL: Homepage, https://github.com/JPL-Evapotranspiration-Algorithms/BESS-JPL

{bess_jpl-1.9.2.dist-info → bess_jpl-1.10.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-BESS_JPL/BESS_JPL.py,sha256=XZr-Y-pOs0aJXccb5VpgaDLKaKiFYshITs_6YZihsLM,22879
+BESS_JPL/BESS_JPL.py,sha256=CTby93_HwhONe2NOlt-8DuqDH7jL9mAc3euuzbouANg,1365
 BESS_JPL/C3_photosynthesis.py,sha256=-ormDycaWttCOoYJdOoOV_zlM6n0nxkgXxj7fyH_mIs,2760
 BESS_JPL/C4_fraction.jpeg,sha256=ECaEYWA8MnNd5z0Yq3beeUCR93KtTDxM8MrH-YYon3Y,2746
 BESS_JPL/C4_fraction.tif,sha256=DFS-J08JCjnf0hi_T_dFridAegVTiU3FGyMBjS9yc1w,25446
@@ -38,14 +38,16 @@ BESS_JPL/load_kn.py,sha256=_IE7w_VfahubfqjvgE6F6HCO0SizcpMu104_7ZXOiaw,345
 BESS_JPL/load_peakVCmax_C3.py,sha256=ISaCyaN81F3CyYbYwUqvUfQ_vjn4_jCpt1_x_b4fY5o,365
 BESS_JPL/load_peakVCmax_C4.py,sha256=8vtjEiJKCqSK04DfTs8Zgn-rWwGucmeeLMzblLT1U-Y,365
 BESS_JPL/meteorology.py,sha256=xIPQnIk9wGJPy8esJyxn35d6c_7UyiNuWTJXDnuSwf8,6995
+BESS_JPL/model.py,sha256=sJ_CkZ98h-5HDpAGUJnyTpUODDlTTgc_8s5Ib8Kz-90,22295
 BESS_JPL/peakVCmax_C3.jpeg,sha256=nVvwLx8JyRhtm5lWRW93HLz0mInshEdOCJ1tAdcFqa8,1006133
 BESS_JPL/peakVCmax_C3.tif,sha256=ax6wCOPc_ovgJJl9YRjPWNY13OCGlzs2djXqwob_U7A,1583598
 BESS_JPL/peakVCmax_C4.jpeg,sha256=s7dhpcD573KW9Se4mejDeSzbSHqPtQY2EL6KJKt7ZIo,961497
 BESS_JPL/peakVCmax_C4.tif,sha256=EST4_yy-HHYmazIv--RePL_bhLejMWql6hoV9EE38ok,1556928
+BESS_JPL/process_BESS_table.py,sha256=TYsDEZNELGdUc0xkB1MRQIDkVonNL5d49q7Zl1iaJvo,1472
 BESS_JPL/soil_energy_balance.py,sha256=5TKDVkKYJ8jhjuiwbRva_03fi_0gTM0IAKbSm4WhWnY,944
-BESS_JPL/version.txt,sha256=GF32WMesk-gMhlClaks8mbr0tl98nGPhAE7jrhiSBPo,5
-bess_jpl-1.9.2.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-bess_jpl-1.9.2.dist-info/METADATA,sha256=4z5GFhb7pdeL9z9JBNwKeBLu2mieeAkL2l1h5kYqaN0,6339
-bess_jpl-1.9.2.dist-info/WHEEL,sha256=DnLRTWE75wApRYVsjgc6wsVswC54sMSJhAEd4xhDpBk,91
-bess_jpl-1.9.2.dist-info/top_level.txt,sha256=GaKnzt-BBktYn1o-w4Qzh_jHxse4Y3ACOxZQrB2ufhc,9
-bess_jpl-1.9.2.dist-info/RECORD,,
+BESS_JPL/version.txt,sha256=6R3uO0EpIuVteI11fNMOqq6SsIRjI6vbme61i5z-MME,6
+bess_jpl-1.10.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+bess_jpl-1.10.0.dist-info/METADATA,sha256=PM7zyAhRude_y8P-nnEQTsPB_Y5WaOD8xKmT2oHr3wg,6340
+bess_jpl-1.10.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bess_jpl-1.10.0.dist-info/top_level.txt,sha256=GaKnzt-BBktYn1o-w4Qzh_jHxse4Y3ACOxZQrB2ufhc,9
+bess_jpl-1.10.0.dist-info/RECORD,,

{bess_jpl-1.9.2.dist-info → bess_jpl-1.10.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.4.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any