BESS-JPL 1.6.0__py3-none-any.whl

BESS_JPL/BESS.py

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+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 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 .constants import *
+from .vegetation_conversion import LAI_from_NDVI
+from .canopy_shortwave_radiation import canopy_shortwave_radiation
+from .carbon_water_fluxes import carbon_water_fluxes
+from .meteorology import meteorology, SVP_Pa_from_Ta_K
+from .interpolate_C3_C4 import interpolate_C3_C4
+from .calculate_VCmax import calculate_VCmax
+from .load_NDVI_minimum import load_NDVI_minimum
+from .load_NDVI_maximum import load_NDVI_maximum
+from .load_C4_fraction import load_C4_fraction
+from .load_carbon_uptake_efficiency import load_carbon_uptake_efficiency
+from .load_kn import load_kn
+from .load_peakVCmax_C3 import load_peakVCmax_C3
+from .load_peakVCmax_C4 import load_peakVCmax_C4
+from .load_ball_berry_intercept_C3 import load_ball_berry_intercept_C3
+from .load_ball_berry_slope_C3 import load_ball_berry_slope_C3
+from .load_ball_berry_slope_C4 import load_ball_berry_slope_C4
+
+logger = logging.getLogger(__name__)
+
+def BESS(
+        ST_C: Union[Raster, np.ndarray],  # surface temperature in Celsius
+        NDVI: Union[Raster, np.ndarray],  # NDVI
+        albedo: Union[Raster, np.ndarray],  # surface albedo
+        elevation_km: Union[Raster, np.ndarray],  # elevation in kilometers
+        geometry: RasterGeometry = None,
+        time_UTC: datetime = None,
+        hour_of_day: np.ndarray = None,
+        day_of_year: np.ndarray = None,
+        GEOS5FP_connection: GEOS5FP = None,
+        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 (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")
+
+    # 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)
+
+    # 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(
+            day_of_year=day_of_year,
+            hour_of_day=hour_of_day,
+            albedo=albedo,
+            COT=COT,
+            AOT=AOT,
+            vapor_gccm=vapor_gccm,
+            ozone_cm=ozone_cm,
+            elevation_km=elevation_km,
+            SZA=SZA,
+            KG_climate=KG_climate,
+            geometry=geometry,
+            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"]
+
+    # 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(lat, 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)
+
+    # 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/BESS_JPL.py

@@ -0,0 +1,23 @@
+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 FVC_from_NDVI
+from .interpolate_C3_C4 import interpolate_C3_C4
+from .LAI_from_NDVI import LAI_from_NDVI
+from .load_C4_fraction import load_C4_fraction
+from .load_carbon_uptake_efficiency import load_carbon_uptake_efficiency
+from .load_kn import load_kn
+from .load_NDVI_minimum import load_NDVI_minimum
+from .load_NDVI_maximum import load_NDVI_maximum
+from .load_peakVCmax_C3 import load_peakVCmax_C3
+from .load_peakVCmax_C4 import load_peakVCmax_C4
+from .load_ball_berry_intercept_C3 import load_ball_berry_intercept_C3
+from .load_ball_berry_slope_C3 import load_ball_berry_slope_C3
+from .load_ball_berry_slope_C4 import load_ball_berry_slope_C4
+from .meteorology import *
+from .BESS import BESS
+from .soil_energy_balance import *

BESS_JPL/C3_photosynthesis.py

@@ -0,0 +1,72 @@
+import numpy as np
+
+
+def calculate_C3_photosynthesis(
+        Tf_K: np.ndarray,  # leaf temperature in Kelvin
+        Ci: np.ndarray,  # intercellular CO2 concentration [umol mol-1]
+        APAR: np.ndarray,  # leaf absorptance to photosynthetically active radiation [umol m-2 s-1]
+        Vcmax25: np.ndarray,  # maximum carboxylation rate at 25C [umol m-2 s-1]
+        Ps_Pa: np.ndarray,  # surface pressure in Pascal
+        carbon_uptake_efficiency: np.ndarray) -> np.ndarray:  # intrinsic quantum efficiency for carbon uptake
+    """
+    photosynthesis for C3 plants
+    Collatz et al., 1991
+    https://www.sciencedirect.com/science/article/abs/pii/0168192391900028
+    Adapted from Youngryel Ryu's code by Gregory Halverson and Robert Freepartner
+    :param Tf_K: leaf temperature in Kelvin
+    :param Ci: intercellular CO2 concentration [umol mol-1]
+    :param APAR: leaf absorptance to photosynthetically active radiation [umol m-2 s-1]
+    :param Vcmax25: maximum carboxylation rate at 25C [umol m-2 s-1]
+    :param Ps_Pa: surface pressure in Pascal
+    :param carbon_uptake_efficiency: intrinsic quantum efficiency for carbon uptake
+    :return: net assimilation [umol m-2 s-1]
+    """
+    # gas constant
+    R = 8.314e-3  # [kJ K-1 mol-1]
+
+    # calculate oxygen concentration
+    O2 = Ps_Pa * 0.21  # [Pa]
+
+    # convert intercellular CO2 concentration to Pascal
+    Pi = Ci * 1e-6 * Ps_Pa  # [umol mol-1] -> [Pa]
+
+    # Temperature correction
+    item = (Tf_K - 298.15) / 10
+    KC25 = 30  # [Pa]
+    KCQ10 = 2.1  # [-]
+    KO25 = 30000  # [Pa]
+    KOQ10 = 1.2  # [-]
+    tao25 = 2600  # [Pa]
+    taoQ10 = 0.57  # [-]
+    KC = KC25 * KCQ10 ** item  # [Pa]
+    KO = KO25 * KOQ10 ** item  # [Pa]
+    K = KC * (1.0 + O2 / KO)  # [Pa]
+    tao = tao25 * taoQ10 ** item  # [Pa]
+    GammaS = O2 / (2.0 * tao)  # [Pa]
+    VcmaxQ10 = 2.4  # [-]
+    Vcmax_o = Vcmax25 * VcmaxQ10 ** item  # [umol m-2 s-1]
+    Vcmax = Vcmax_o / (1.0 + np.exp((-220.0 + 0.703 * Tf_K) / (R * Tf_K)))  # [umol m-2 s-1]
+    Rd_o = 0.015 * Vcmax  # [umol m-2 s-1]
+    Rd = Rd_o * 1.0 / (1.0 + np.exp(1.3 * (Tf_K - 273.15 - 55.0)))  # [umol m-2 s-1]
+
+    # Three limiting states
+    JC = Vcmax * (Pi - GammaS) / (Pi + K)
+    JE = carbon_uptake_efficiency * APAR * (Pi - GammaS) / (Pi + 2.0 * GammaS)
+    JS = Vcmax / 2.0
+
+    # Colimitation (not the case at canopy level according to DePury and Farquhar)
+    a = 0.98
+    b = -(JC + JE)
+    c = JC * JE
+    JCE = (-b + np.sign(b) * np.sqrt(b * b - 4.0 * a * c)) / (2.0 * a)
+    JCE = np.real(JCE)
+    a = 0.95
+    b = -(JCE + JS)
+    c = JCE * JS
+    JCES = (-b + np.sign(b) * np.sqrt(b * b - 4.0 * a * c)) / (2.0 * a)
+    JCES = np.real(JCES)
+
+    # calculate net assimilation
+    An = np.clip(JCES - Rd, 0, None)
+
+    return An

BESS_JPL/C4_photosynthesis.py

@@ -0,0 +1,56 @@
+import numpy as np
+
+
+def calculate_C4_photosynthesis(Tf_K: np.ndarray, Ci: np.ndarray, APAR: np.ndarray, Vcmax25: np.ndarray) -> np.ndarray:
+    """
+    =============================================================================
+    Collatz et al., 1992
+
+    Module     : Photosynthesis for C4 plant
+    Input      : leaf temperature (Tf) [K],
+               : intercellular CO2 concentration (Ci) [umol mol-1],
+               : absorbed photosynthetically active radiation (APAR) [umol m-2 s-1],
+               : maximum carboxylation rate at 25C (Vcmax25) [umol m-2 s-1].
+    Output     : net assimilation (An) [umol m-2 s-1].
+
+
+    Conversion from MatLab by Robert Freepartner, JPL/Raytheon/JaDa Systems
+    March 2020
+
+    =============================================================================
+    """
+    # Temperature correction
+    item = (Tf_K - 298.15) / 10.0
+    Q10 = 2.0
+    k = 0.7 * pow(Q10, item)  # [mol m-2 s-1]
+    Vcmax_o = Vcmax25 * pow(Q10, item)  # [umol m-2 s-1]
+    Vcmax = Vcmax_o / (
+            (1.0 + np.exp(0.3 * (286.15 - Tf_K))) * (1.0 + np.exp(0.3 * (Tf_K - 309.15))))  # [umol m-2 s-1]
+    Rd_o = 0.8 * pow(Q10, item)  # [umol m-2 s-1]
+    Rd = Rd_o / (1.0 + np.exp(1.3 * (Tf_K - 328.15)))  # [umol m-2 s-1]
+
+    # Three limiting states
+    Je = Vcmax  # [umol m-2 s-1]
+    alf = 0.067  # [mol CO2 mol photons-1]
+    Ji = alf * APAR  # [umol m-2 s-1]
+    ci = Ci * 1e-6  # [umol mol-1] -> [mol CO2 mol CO2-1]
+    Jc = ci * k * 1e6  # [umol m-2 s-1]
+
+    # Colimitation (not the case at canopy level according to DePury and Farquhar)
+    a = 0.83
+    b = -(Je + Ji)
+    c = Je * Ji
+    Jei = (-b + np.sign(b) * np.sqrt(b * b - 4.0 * a * c)) / (2.0 * a)
+    Jei = np.real(Jei)
+    a = 0.93
+    b = -(Jei + Jc)
+    c = Jei * Jc
+    Jeic = (-b + np.sign(b) * np.sqrt(b * b - 4.0 * a * c)) / (2.0 * a)
+    Jeic = np.real(Jeic)
+
+    # Net assimilation
+    # An = nanmin(cat(3,Je,Ji,Jc),[],3) - Rd;    % [umol m-2 s-1]
+    An = np.clip(Jeic - Rd, 0, None)
+    # An[An<0.0] = 0.0
+
+    return An

BESS_JPL/FVC_from_NDVI.py

@@ -0,0 +1,22 @@
+from typing import Union
+
+import numpy as np
+import rasters as rt
+from rasters import Raster
+
+
+def FVC_from_NDVI(NDVI: Union[Raster, np.ndarray]) -> Union[Raster, np.ndarray]:
+    """
+    Convert Normalized Difference Vegetation Index (NDVI) to Fractional Vegetation Cover (FVC).
+
+    Parameters:
+        NDVI (Union[Raster, np.ndarray]): Input NDVI data.
+
+    Returns:
+        Union[Raster, np.ndarray]: Converted FVC data.
+    """
+    NDVIv = 0.52  # +- 0.03
+    NDVIs = 0.04  # +- 0.03
+    FVC = rt.clip((NDVI - NDVIs) / (NDVIv - NDVIs), 0.0, 1.0)
+
+    return FVC

BESS_JPL/LAI_from_NDVI.py

@@ -0,0 +1,29 @@
+from typing import Union
+
+import numpy as np
+import rasters as rt
+from rasters import Raster
+
+from .constants import KPAR, MIN_FIPAR, MAX_FIPAR, MIN_LAI, MAX_LAI
+
+
+def LAI_from_NDVI(
+        NDVI: Union[Raster, np.ndarray],
+        min_fIPAR: float = MIN_FIPAR,
+        max_fIPAR: float = MAX_FIPAR,
+        min_LAI: float = MIN_LAI,
+        max_LAI: float = MAX_LAI) -> Union[Raster, np.ndarray]:
+    """
+    Convert Normalized Difference Vegetation Index (NDVI) to Leaf Area Index (LAI).
+
+    Parameters:
+        NDVI (Union[Raster, np.ndarray]): Input NDVI data.
+
+    Returns:
+        Union[Raster, np.ndarray]: Converted LAI data.
+    """
+    fIPAR = rt.clip(NDVI - 0.05, min_fIPAR, max_fIPAR)
+    fIPAR = np.where(fIPAR == 0, np.nan, fIPAR)
+    LAI = rt.clip(-np.log(1 - fIPAR) * (1 / KPAR), min_LAI, max_LAI)
+
+    return LAI