STIC-JPL 1.1.0__py3-none-any.whl → 1.2.1__py3-none-any.whl

STIC_JPL/FVC_from_NDVI.py

@@ -0,0 +1,26 @@
+from typing import Union
+import numpy as np
+import rasters as rt
+from rasters import Raster
+
+KPAR = 0.5
+MIN_FIPAR = 0.0
+MAX_FIPAR = 1.0
+MIN_LAI = 0.0
+MAX_LAI = 10.0
+
+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

STIC_JPL/{vegetation_conversion/vegetation_conversion.py → LAI_from_NDVI.py}

@@ -9,22 +9,6 @@ MAX_FIPAR = 1.0
 MIN_LAI = 0.0
 MAX_LAI = 10.0
 
-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
-
 def LAI_from_NDVI(
         NDVI: Union[Raster, np.ndarray],
         min_fIPAR: float = MIN_FIPAR,

STIC_JPL/STIC_JPL.py

@@ -1,370 +1,3 @@
-from typing import Union, Callable
-import logging
-from datetime import datetime, timedelta
-from os.path import join, abspath, expanduser
-from typing import Dict, List
-import numpy as np
-import warnings
-from .diagnostic import diagnostic
-import colored_logging as cl
-from .meteorology_conversion import calculate_air_density, calculate_specific_heat, calculate_specific_humidity, calculate_surface_pressure, celcius_to_kelvin
-import rasters as rt
-from GEOS5FP import GEOS5FP
-from solar_apparent_time import solar_day_of_year_for_area, solar_hour_of_day_for_area
-
-from .timer import Timer
-
-from rasters import Raster, RasterGeometry
-
-from .vegetation_conversion.vegetation_conversion import FVC_from_NDVI, LAI_from_NDVI
-
-from .constants import *
-from .closure import STIC_closure
-from .soil_moisture_initialization import initialize_soil_moisture
-from .soil_moisture_iteration import iterate_soil_moisture
-from .net_radiation import calculate_net_longwave_radiation
-from .initialize_with_solar import initialize_with_solar
-from .canopy_air_stream import calculate_canopy_air_stream_vapor_pressure
-from .initialize_without_solar import initialize_without_solar
-from .iterate_with_solar import iterate_with_solar
-from .iterate_without_solar import iterate_without_solar
-from .root_zone_initialization import calculate_root_zone_moisture
-
-from .soil_heat_flux import calculate_SEBAL_soil_heat_flux
-
-__author__ = 'Kaniska Mallick, Madeleine Pascolini-Campbell, Gregory Halverson'
-
-logger = logging.getLogger(__name__)
-
-def STIC_JPL(
-        ST_C: Union[Raster, np.ndarray],
-        emissivity: Union[Raster, np.ndarray],
-        NDVI: Union[Raster, np.ndarray],
-        albedo: Union[Raster, np.ndarray],
-        Rn_Wm2: Union[Raster, np.ndarray],
-        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,
-        RH: Union[Raster, np.ndarray] = None,
-        G: Union[Raster, np.ndarray] = None,
-        G_method: str = DEFAULT_G_METHOD,
-        SM: Union[Raster, np.ndarray] = None,
-        Rg_Wm2: Union[Raster, np.ndarray] = None,
-        FVC: Union[Raster, np.ndarray] = None,
-        LAI: Union[Raster, np.ndarray] = None,
-        elevation_m: Union[Raster, np.ndarray] = None,
-        delta_hPa: Union[Raster, np.ndarray] = None,
-        gamma_hPa: Union[Raster, np.ndarray, float] = GAMMA_HPA,
-        rho_kgm3: Union[Raster, np.ndarray] = RHO_KGM3,
-        Cp_Jkg: Union[Raster, np.ndarray] = CP_JKG,
-        alpha: float = PT_ALPHA,
-        LE_convergence_target: float = LE_CONVERGENCE_TARGET_WM2,
-        max_iterations: int = MAX_ITERATIONS,
-        diagnostic_directory: str = None,
-        show_distributions: bool = SHOW_DISTRIBUTIONS,
-        use_variable_alpha: bool = USE_VARIABLE_ALPHA) -> Dict[str, Union[Raster, np.ndarray]]:
-    results = {}
-
-    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")
-
-    diag_kwargs = {
-        "show_distributions": show_distributions, 
-        "output_directory": diagnostic_directory
-    }
-
-    seconds_of_day = hour_of_day * 3600.0
-
-    # 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)
-
-    # calculate fraction of vegetation cover if it's not given
-    if FVC is None:
-        FVC = FVC_from_NDVI(NDVI)
-    
-    # calculate leaf area index if it's not given
-    if LAI is None:
-        LAI = LAI_from_NDVI(NDVI)
-
-    # saturation air pressure in hPa
-    SVP_hPa = 6.13753 * (np.exp((17.27 * Ta_C) / (Ta_C + 237.3)))
-
-    # calculate delta term if it's not given
-    if delta_hPa is None:
-        # slope of saturation vapor pressure to air temperature (hpa/K)
-        delta_hPa = 4098 * SVP_hPa / (Ta_C + 237.3) ** 2
-
-    Ta_K = celcius_to_kelvin(Ta_C)
-
-    # actual vapor pressure at TA (hpa/K)
-    Ea_hPa = SVP_hPa * (RH)
-    Ea_Pa = Ea_hPa * 100.0
-
-    # vapor pressure deficit (hPa)
-    VPD_hPa = SVP_hPa - Ea_hPa
-
-    # swapping in the dew-point calculation from PT-JPL
-    Td_C = Ta_C - ((100 - RH * 100) / 5.0)
-
-    # difference between surface and air temperature (Celsius)
-    dTS_C = ST_C - Ta_C
-
-    # saturation vapor pressure at surface temperature (hPa/K)
-    Estar_hPa = 6.13753 * np.exp((17.27 * ST_C) / (ST_C + 237.3))
-
-    if Rg_Wm2 is None:
-        # if G is None and SM is None:
-        #     raise ValueError("soil heat flux or soil moisture prior required if solar radiation is not given")
-
-        if G is None:
-            G = calculate_SEBAL_soil_heat_flux(
-                ST_C=ST_C,
-                NDVI=NDVI,
-                albedo=albedo,
-                Rn=Rn_Wm2,
-            )
-        
-        phi_Wm2 = Rn_Wm2 - G
-
-        # initialize without solar radiation
-        SM, SMrz, s1, s3, s33, s44, Ms, Tsd_C, Es_hPa, Ds = initialize_without_solar(
-            ST_C = ST_C,  # Surface temperature in Celsius
-            Ta_C = Ta_C,  # Air temperature in Celsius
-            dTS = dTS_C,  # Temperature difference between surface and air in Celsius
-            Td_C = Td_C,  # Dewpoint temperature in Celsius
-            Ea_hPa = Ea_hPa,  # Actual vapor pressure in hPa
-            Estar_hPa = Estar_hPa,  # Saturation vapor pressure at surface temperature (hPa/K)
-            SVP_hPa = SVP_hPa,  # Saturation vapor pressure at the surface in hPa
-            delta_hPa = delta_hPa,  # Slope of the saturation vapor pressure-temperature curve in hPa/K
-            phi_Wm2 = phi_Wm2,  # Available energy in W/m2
-            gamma_hPa = gamma_hPa,  # Psychrometric constant in hPa/°C
-            alpha = alpha  # Priestley-Taylor alpha
-        )
-    else:
-        SM, SMrz, Ms, s1, s3, Ep_PT, Rnsoil, LWnet_Wm2, G, Tsd_C, Ds, Es_hPa, phi_Wm2 = initialize_with_solar(
-            seconds_of_day = seconds_of_day,  # time of day in seconds since midnight
-            Rg_Wm2 = Rg_Wm2,  # solar radiation (W/m^2)
-            Rn_Wm2 = Rn_Wm2,  # net radiation (W/m^2)
-            ST_C = ST_C,  # surface temperature (Celsius)
-            emissivity = emissivity,  # emissivity of the surface
-            Ta_C = Ta_C,  # air temperature (Celsius)
-            dTS_C = dTS_C,  # surface air temperature difference (Celsius)
-            Td_C = Td_C,  # dew point temperature (Celsius)
-            VPD_hPa = VPD_hPa,  # vapor pressure deficit (hPa)
-            SVP_hPa = SVP_hPa,  # saturation vapor pressure at given air temperature (hPa)
-            Ea_hPa = Ea_hPa,  # actual vapor pressure at air temperature (hPa)
-            Estar_hPa = Estar_hPa,  # saturation vapor pressure at surface temperature (hPa)
-            delta_hPa = delta_hPa,  # slope of saturation vapor pressure to air temperature (hpa/K)
-            NDVI=NDVI,  # normalized difference vegetation index
-            FVC = FVC,  # fractional vegetation cover
-            LAI = LAI,  # leaf area index
-            albedo = albedo,  # albedo of the surface
-            gamma_hPa=gamma_hPa,  # psychrometric constant (hPa/°C)
-            G_method = DEFAULT_G_METHOD,  # method for calculating soil heat flux
-        )
-    
-    diagnostic(Ms, "Ms", **diag_kwargs)
-
-    # STIC analytical equations (convergence on LE)
-    gB_ms, gS_ms, dT_C, EF = STIC_closure(
-        delta_hPa=delta_hPa, 
-        phi_Wm2=phi_Wm2, 
-        Es_hPa=Es_hPa, 
-        Ea_hPa=Ea_hPa, 
-        Estar_hPa=Estar_hPa, 
-        SM=SM,
-        gamma_hPa=gamma_hPa,
-        rho_kgm3=rho_kgm3,
-        Cp_Jkg=Cp_Jkg,
-        alpha=alpha
-    )
-    
-    gBB = gB_ms
-    gSS = gS_ms
-    gBB_by_gSS = rt.where(gSS == 0, 0, gBB / gSS)
-    gB_by_gS = rt.where(gS_ms == 0, 0, gB_ms / gS_ms)
-    dT_C = dT_C
-    T0_C = dT_C + Ta_C
-    
-    PET_Wm2 = ((delta_hPa * phi_Wm2 + rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa))  # Penman potential evaporation
-    
-    gR = (4 * SB_SIGMA * (Ta_C + 273) ** 3 * emissivity) / (rho_kgm3 * Cp_Jkg)
-    omega = ((delta_hPa / gamma_hPa) + 1) / ((delta_hPa / gamma_hPa) + 1 + gB_by_gS)
-    LE_eq = (phi_Wm2 * (delta_hPa / gamma_hPa)) / ((delta_hPa / gamma_hPa) + 1)
-    LE_imp = (Cp_Jkg * 0.0289644 / gamma_hPa) * gS_ms * 40 * VPD_hPa
-    LE_init = omega * LE_eq + (1 - omega) * LE_imp
-    dry = (Ds > VPD_hPa) & (PET_Wm2 > phi_Wm2) & (dTS_C > 0) & (Td_C <= 0)
-    omega = rt.where(dry,
-                        ((delta_hPa / gamma_hPa) + 1 + gR / gB_ms) / ((delta_hPa / gamma_hPa) + 1 + gB_ms / gS_ms + gR / gS_ms + gR / gB_ms),
-                        omega)
-    LE_eq = rt.where(dry, (phi_Wm2 * (delta_hPa / gamma_hPa)) / ((delta_hPa / gamma_hPa) + 1 + gR / gB_ms), LE_eq)
-    LE_init = rt.where(dry, omega * LE_eq + (1 - omega * LE_imp), LE_init)
-    
-    # sensible heat flux
-    H_Wm2 = ((gamma_hPa * phi_Wm2 * (1 + gB_by_gS) - rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa * (1 + (gB_by_gS))))
-    
-    LE_Wm2_new = LE_init
-    LE_Wm2_change = LE_convergence_target
-    LE_Wm2_old = LE_Wm2_new
-    LE_transpiration_Wm2 = None
-    PT_Wm2 = None
-    iteration = 1
-    LE_Wm2_max_change = 0
-    t = Timer()
-
-    while (np.nanmax(LE_Wm2_change) >= LE_convergence_target and iteration <= max_iterations):
-        logger.info(f"running STIC iteration {cl.val(iteration)} / {cl.val(max_iterations)}")
-
-        if Rg_Wm2 is None:
-            SM, SMrz, Ms, s1, e0, e0star, Tsd_C, D0, alphaN = iterate_without_solar(
-                LE = LE_Wm2_new,  # Latent heat flux (W/m^2)
-                PET = PET_Wm2,  # Potential evapotranspiration (W/m^2)
-                SM = SM,
-                ST_C = ST_C,  # Surface temperature (°C)
-                Ta_C = Ta_C,  # Air temperature (°C)
-                dTS = dTS_C,  # Surface-air temperature difference (°C)
-                T0 = T0_C,  # Reference temperature (°C)
-                gB = gB_ms,  # Boundary layer conductance (m/s)
-                gS = gS_ms,  # Stomatal conductance (m/s)
-                Ea_hPa = Ea_hPa,  # Actual vapor pressure (hPa)
-                Td_C = Td_C,  # Dew point temperature (°C)
-                VPD_hPa = VPD_hPa,  # Vapor pressure deficit (hPa)
-                Estar = Estar_hPa,  # Saturation vapor pressure at surface temperature (hPa)
-                delta = delta_hPa,  # Slope of the saturation vapor pressure-temperature curve (hPa/°C)
-                phi = phi_Wm2,  # available energy (W/m^2)
-                Ds = Ds,  # Vapor pressure deficit at source (hPa)
-                Es = Es_hPa,  # Saturation vapor pressure (hPa)
-                s3 = s3,  # Slope of the saturation vapor pressure and temperature 
-                s4 = s44,  # Slope of the saturation vapor pressure and temperature 
-                gB_by_gS = gB_by_gS,  # Ratio of boundary layer conductance to stomatal conductance
-                gamma_hPa = gamma_hPa,  # Psychrometric constant (hPa/°C)
-                rho_kgm3 = rho_kgm3,  # Air density (kg/m^3)
-                Cp_Jkg = Cp_Jkg  # Specific heat at constant pressure (J/kg/K)
-            )
-        else:
-            SM, G, e0, e0star, D0, alphaN = iterate_with_solar(
-                seconds_of_day = seconds_of_day,  # Seconds of the day
-                ST_C = ST_C,  # Soil temperature (°C)
-                NDVI = NDVI,  # Normalized Difference Vegetation Index
-                albedo = albedo,  # Albedo
-                gB_ms = gB_ms,  # boundary layer conductance (m/s)
-                gS_ms = gS_ms,  # stomatal conductance (m/s)
-                LE_Wm2 = LE_Wm2_new,  # latent heat flux (W/m^2)
-                Rg_Wm2 = Rg_Wm2,  # Incoming solar radiation (W/m^2)
-                Rn_Wm2 = Rn_Wm2,  # Net radiation (W/m^2)
-                LWnet_Wm2 = LWnet_Wm2,  # Net longwave radiation (W/m^2)
-                Ta_C = Ta_C,  # Air temperature (°C)
-                dTS_C = dTS_C,  # Change in soil temperature (°C)
-                Td_C = Td_C,  # Dew point temperature (°C)
-                Tsd_C = Tsd_C,  # Soil dew point temperature (°C)
-                Ea_hPa = Ea_hPa,  # actual vapor pressure (hPa)
-                Estar_hPa = Estar_hPa,  # saturation vapor pressure at surface temperature (hPa)
-                VPD_hPa = VPD_hPa,  # Vapor pressure deficit (hPa)
-                SVP_hPa = SVP_hPa,  # Saturation vapor pressure (hPa)
-                delta_hPa = delta_hPa,  # Slope of the saturation vapor pressure-temperature curve (hPa/°C)
-                phi_Wm2 = phi_Wm2,  # Net radiation minus soil heat flux (W/m^2)
-                Es_hPa = Es_hPa,  # Saturation vapor pressure (hPa)
-                s1 = s1,  # Soil moisture parameter
-                s3 = s3,  # Soil moisture parameter
-                FVC = FVC,  # Fractional canopy cover
-                T0_C = T0_C,  # Reference temperature (°C)
-                gB_by_gS = gB_by_gS,  # Ratio of boundary layer conductance to stomatal conductance
-                gamma_hPa = gamma_hPa,  # Psychrometric constant (hPa/°C)
-                rho_kgm3 = rho_kgm3,  # Air density (kg/m^3)
-                Cp_Jkg = Cp_Jkg,  # Specific heat at constant pressure (J/kg/K)
-                G_method = "santanello"  # Method for calculating soil heat flux
-            )
-
-        if use_variable_alpha:
-            alpha = alphaN
-            logger.info(f"using variable Priestley-Taylor alpha with mean: {cl.val(np.round(np.nanmean(alpha), 3))}")
-
-        # re-estimated conductances and states
-        gB_ms, gS_ms, dT_C, EF = STIC_closure(
-            delta_hPa=delta_hPa,  # Slope of the saturation vapor pressure-temperature curve (hPa/°C)
-            phi_Wm2=phi_Wm2,  # available energy (W/m^2)
-            Es_hPa=Es_hPa,  # Vapor pressure at the reference height (hPa)
-            Ea_hPa=Ea_hPa,  # Actual vapor pressure (hPa)
-            Estar_hPa=Estar_hPa,  # Saturation vapor pressure at the reference height (hPa)
-            SM=SM,  # Soil moisture (m³/m³)
-            gamma_hPa=gamma_hPa,  # Psychrometric constant (hPa/°C)
-            rho_kgm3=rho_kgm3,  # Air density (kg/m³)
-            Cp_Jkg=Cp_Jkg,  # Specific heat capacity of air (J/kg/°C)
-            alpha=alpha  # Stability correction factor for conductance 
-        )
-
-        gB_by_gS = rt.where(gS_ms == 0, 0, gB_ms / gS_ms)
-        T0_C = dT_C + Ta_C
-        # latent heat flux
-        LE_Wm2_new = ((delta_hPa * phi_Wm2 + rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa * (1 + gB_by_gS)))
-        LE_Wm2_new = rt.where(LE_Wm2_new > phi_Wm2, phi_Wm2, LE_Wm2_new)
-        # Sensible Heat Flux
-        H_Wm2 = ((gamma_hPa * phi_Wm2 * (1 + gB_by_gS) - rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa * (1 + (gB_by_gS))))
-        # potential evaporation (Penman)
-        PET_Wm2 = ((delta_hPa * phi_Wm2 + rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa))
-        # Potential Transpiration
-        PT_Wm2 = (delta_hPa * phi_Wm2 + rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa * (1 + SM * gB_by_gS))  # potential transpiration
-        # ET PARTITIONING
-        LE_soil_Wm2 = rt.clip(SM * PET_Wm2, 0, None)
-        LE_transpiration_Wm2 = rt.clip(LE_Wm2_new - LE_soil_Wm2, 0, None)
-        # change in latent heat flux estimate
-        LE_Wm2_change = np.abs(LE_Wm2_old - LE_Wm2_new)
-        LE_Wm2_new = rt.where(np.isnan(LE_Wm2_new), LE_Wm2_old, LE_Wm2_new)
-        LE_Wm2_old = LE_Wm2_new
-        LE_Wm2_max_change = np.nanmax(LE_Wm2_change)
-        logger.info(
-            f"completed STIC iteration {cl.val(iteration)} / {cl.val(max_iterations)} with max LE change: {cl.val(np.round(LE_Wm2_max_change, 3))} ({t} seconds)")
-        
-        diagnostic(SM, f"SM_{iteration}", **diag_kwargs)
-        diagnostic(G, f"G_{iteration}", **diag_kwargs)
-        diagnostic(LE_Wm2_new, f"LE_{iteration}", **diag_kwargs)
-
-        if LE_Wm2_max_change <= LE_convergence_target:
-            logger.info(f"max LE change {cl.val(np.round(LE_Wm2_max_change, 3))} within convergence target {cl.val(np.round(LE_convergence_target, 3))} with {cl.val(iteration)} iteration{'s' if iteration > 1 else ''}")
-
-        iteration += 1
-
-    iteration -= 1
-    results["LE_max_change"] = LE_Wm2_max_change
-    results["iteration"] = iteration
-
-    LE = LE_Wm2_new
-
-    results["LE"] = LE
-    results["LE_change"] = LE_Wm2_change
-    results["LEt"] = LE_transpiration_Wm2
-    results["PT"] = PT_Wm2
-    results["PET"] = PET_Wm2
-    results["G"] = G
-
-    if isinstance(geometry, RasterGeometry):
-        for name, array in results.items():
-            try:
-                results[name] = Raster(array.reshape(geometry.shape), geometry=geometry)
-            except Exception as e:
-                pass
-        
-        results["LE"].cmap = ET_COLORMAP
-        results["PET"].cmap = ET_COLORMAP
-
-    warnings.resetwarnings()
-
-    return results
+from .model import *
+from .generate_STIC_inputs import generate_STIC_inputs
+from .process_STIC_table import process_STIC_table

STIC_JPL/celcius_to_kelvin.py

@@ -0,0 +1,11 @@
+from typing import Union
+import numpy as np
+from rasters import Raster
+
+def celcius_to_kelvin(T_C: Union[Raster, np.ndarray]) -> Union[Raster, np.ndarray]:
+    """
+    convert temperature in celsius to kelvin.
+    :param T_C: temperature in celsius
+    :return: temperature in kelvin
+    """
+    return T_C + 273.15

STIC_JPL/generate_STIC_inputs.py

@@ -0,0 +1,65 @@
+import logging
+
+import numpy as np
+from dateutil import parser
+from pandas import DataFrame
+from rasters import Point
+from sentinel_tiles import sentinel_tiles
+from solar_apparent_time import UTC_to_solar
+from SEBAL_soil_heat_flux import calculate_SEBAL_soil_heat_flux
+
+from .model import STIC_JPL, MAX_ITERATIONS, USE_VARIABLE_ALPHA
+
+logger = logging.getLogger(__name__)
+
+def generate_STIC_inputs(STIC_inputs_from_calval_df: DataFrame) -> DataFrame:
+    """
+    STIC_inputs_from_claval_df:
+        Pandas DataFrame containing the columns: tower, lat, lon, time_UTC, albedo, elevation_km
+    return:
+        Pandas DataFrame containing the columns: tower, lat, lon, time_UTC, doy, albedo, elevation_km, AOT, COT, vapor_gccm, ozone_cm, SZA, KG
+    """
+    # output_rows = []
+    STIC_inputs_df = STIC_inputs_from_calval_df.copy()
+
+    hour_of_day = []
+    doy = []
+    Topt = []
+    fAPARmax = []
+
+    for i, input_row in STIC_inputs_from_calval_df.iterrows():
+        tower = input_row.tower
+        lat = input_row.lat
+        lon = input_row.lon
+        time_UTC = input_row.time_UTC
+        albedo = input_row.albedo
+        elevation_km = input_row.elevation_km
+        logger.info(f"collecting STIC inputs for tower {tower} lat {lat} lon {lon} time {time_UTC} UTC")
+        time_UTC = parser.parse(str(time_UTC))
+        time_solar = UTC_to_solar(time_UTC, lon)
+        hour_of_day.append(time_solar.hour)
+        doy.append(time_UTC.timetuple().tm_yday)
+        date_UTC = time_UTC.date()
+        tile = sentinel_tiles.toMGRS(lat, lon)[:5]
+        tile_grid = sentinel_tiles.grid(tile=tile, cell_size=70)
+        rows, cols = tile_grid.shape
+        row, col = tile_grid.index_point(Point(lon, lat))
+        geometry = tile_grid[max(0, row - 1):min(row + 2, rows - 1),
+                             max(0, col - 1):min(col + 2, cols - 1)]
+    
+    if not "hour_of_day" in STIC_inputs_df.columns:
+        STIC_inputs_df["hour_of_day"] = hour_of_day
+
+    if not "doy" in STIC_inputs_df.columns:
+        STIC_inputs_df["doy"] = doy
+    
+    if not "Topt" in STIC_inputs_df.columns:
+        STIC_inputs_df["Topt"] = Topt
+    
+    if not "fAPARmax" in STIC_inputs_df.columns:
+        STIC_inputs_df["fAPARmax"] = fAPARmax
+    
+    if "Ta" in STIC_inputs_df and "Ta_C" not in STIC_inputs_df:
+        STIC_inputs_df.rename({"Ta": "Ta_C"}, inplace=True)
+    
+    return STIC_inputs_df

STIC_JPL/initialize_with_solar.py

@@ -5,8 +5,7 @@ import rasters as rt
 
 from rasters import Raster
 
-from .vegetation_conversion.vegetation_conversion import FVC_from_NDVI
-from .soil_heat_flux import calculate_SEBAL_soil_heat_flux
+from SEBAL_soil_heat_flux import calculate_SEBAL_soil_heat_flux
 
 from .constants import *
 from .soil_moisture_initialization import initialize_soil_moisture

STIC_JPL/iterate_with_solar.py

@@ -5,7 +5,7 @@ import rasters as rt
 
 from rasters import Raster
 
-from .soil_heat_flux import calculate_SEBAL_soil_heat_flux
+from SEBAL_soil_heat_flux import calculate_SEBAL_soil_heat_flux
 
 from .constants import *
 from .canopy_air_stream import calculate_canopy_air_stream_vapor_pressure

STIC_JPL/model.py

@@ -0,0 +1,369 @@
+from typing import Union, Callable
+import logging
+from datetime import datetime, timedelta
+from os.path import join, abspath, expanduser
+from typing import Dict, List
+import numpy as np
+import warnings
+from .diagnostic import diagnostic
+import colored_logging as cl
+import rasters as rt
+from GEOS5FP import GEOS5FP
+from solar_apparent_time import solar_day_of_year_for_area, solar_hour_of_day_for_area
+from SEBAL_soil_heat_flux import calculate_SEBAL_soil_heat_flux
+
+from rasters import Raster, RasterGeometry
+
+from .constants import *
+from .closure import STIC_closure
+from .soil_moisture_initialization import initialize_soil_moisture
+from .soil_moisture_iteration import iterate_soil_moisture
+from .net_radiation import calculate_net_longwave_radiation
+from .initialize_with_solar import initialize_with_solar
+from .canopy_air_stream import calculate_canopy_air_stream_vapor_pressure
+from .initialize_without_solar import initialize_without_solar
+from .iterate_with_solar import iterate_with_solar
+from .iterate_without_solar import iterate_without_solar
+from .root_zone_initialization import calculate_root_zone_moisture
+from .FVC_from_NDVI import FVC_from_NDVI
+from .LAI_from_NDVI import LAI_from_NDVI
+from .celcius_to_kelvin import celcius_to_kelvin
+
+from .timer import Timer
+
+__author__ = 'Kaniska Mallick, Madeleine Pascolini-Campbell, Gregory Halverson'
+
+logger = logging.getLogger(__name__)
+
+def STIC_JPL(
+        ST_C: Union[Raster, np.ndarray],
+        emissivity: Union[Raster, np.ndarray],
+        NDVI: Union[Raster, np.ndarray],
+        albedo: Union[Raster, np.ndarray],
+        Rn_Wm2: Union[Raster, np.ndarray],
+        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,
+        RH: Union[Raster, np.ndarray] = None,
+        G: Union[Raster, np.ndarray] = None,
+        G_method: str = DEFAULT_G_METHOD,
+        SM: Union[Raster, np.ndarray] = None,
+        Rg_Wm2: Union[Raster, np.ndarray] = None,
+        FVC: Union[Raster, np.ndarray] = None,
+        LAI: Union[Raster, np.ndarray] = None,
+        elevation_m: Union[Raster, np.ndarray] = None,
+        delta_hPa: Union[Raster, np.ndarray] = None,
+        gamma_hPa: Union[Raster, np.ndarray, float] = GAMMA_HPA,
+        rho_kgm3: Union[Raster, np.ndarray] = RHO_KGM3,
+        Cp_Jkg: Union[Raster, np.ndarray] = CP_JKG,
+        alpha: float = PT_ALPHA,
+        LE_convergence_target: float = LE_CONVERGENCE_TARGET_WM2,
+        max_iterations: int = MAX_ITERATIONS,
+        diagnostic_directory: str = None,
+        show_distributions: bool = SHOW_DISTRIBUTIONS,
+        use_variable_alpha: bool = USE_VARIABLE_ALPHA) -> Dict[str, Union[Raster, np.ndarray]]:
+    results = {}
+
+    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")
+
+    diag_kwargs = {
+        "show_distributions": show_distributions, 
+        "output_directory": diagnostic_directory
+    }
+
+    seconds_of_day = hour_of_day * 3600.0
+
+    # 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)
+
+    # calculate fraction of vegetation cover if it's not given
+    if FVC is None:
+        FVC = FVC_from_NDVI(NDVI)
+    
+    # calculate leaf area index if it's not given
+    if LAI is None:
+        LAI = LAI_from_NDVI(NDVI)
+
+    # saturation air pressure in hPa
+    SVP_hPa = 6.13753 * (np.exp((17.27 * Ta_C) / (Ta_C + 237.3)))
+
+    # calculate delta term if it's not given
+    if delta_hPa is None:
+        # slope of saturation vapor pressure to air temperature (hpa/K)
+        delta_hPa = 4098 * SVP_hPa / (Ta_C + 237.3) ** 2
+
+    Ta_K = celcius_to_kelvin(Ta_C)
+
+    # actual vapor pressure at TA (hpa/K)
+    Ea_hPa = SVP_hPa * (RH)
+    Ea_Pa = Ea_hPa * 100.0
+
+    # vapor pressure deficit (hPa)
+    VPD_hPa = SVP_hPa - Ea_hPa
+
+    # swapping in the dew-point calculation from PT-JPL
+    Td_C = Ta_C - ((100 - RH * 100) / 5.0)
+
+    # difference between surface and air temperature (Celsius)
+    dTS_C = ST_C - Ta_C
+
+    # saturation vapor pressure at surface temperature (hPa/K)
+    Estar_hPa = 6.13753 * np.exp((17.27 * ST_C) / (ST_C + 237.3))
+
+    if Rg_Wm2 is None:
+        # if G is None and SM is None:
+        #     raise ValueError("soil heat flux or soil moisture prior required if solar radiation is not given")
+
+        if G is None:
+            G = calculate_SEBAL_soil_heat_flux(
+                ST_C=ST_C,
+                NDVI=NDVI,
+                albedo=albedo,
+                Rn=Rn_Wm2,
+            )
+        
+        phi_Wm2 = Rn_Wm2 - G
+
+        # initialize without solar radiation
+        SM, SMrz, s1, s3, s33, s44, Ms, Tsd_C, Es_hPa, Ds = initialize_without_solar(
+            ST_C = ST_C,  # Surface temperature in Celsius
+            Ta_C = Ta_C,  # Air temperature in Celsius
+            dTS = dTS_C,  # Temperature difference between surface and air in Celsius
+            Td_C = Td_C,  # Dewpoint temperature in Celsius
+            Ea_hPa = Ea_hPa,  # Actual vapor pressure in hPa
+            Estar_hPa = Estar_hPa,  # Saturation vapor pressure at surface temperature (hPa/K)
+            SVP_hPa = SVP_hPa,  # Saturation vapor pressure at the surface in hPa
+            delta_hPa = delta_hPa,  # Slope of the saturation vapor pressure-temperature curve in hPa/K
+            phi_Wm2 = phi_Wm2,  # Available energy in W/m2
+            gamma_hPa = gamma_hPa,  # Psychrometric constant in hPa/°C
+            alpha = alpha  # Priestley-Taylor alpha
+        )
+    else:
+        SM, SMrz, Ms, s1, s3, Ep_PT, Rnsoil, LWnet_Wm2, G, Tsd_C, Ds, Es_hPa, phi_Wm2 = initialize_with_solar(
+            seconds_of_day = seconds_of_day,  # time of day in seconds since midnight
+            Rg_Wm2 = Rg_Wm2,  # solar radiation (W/m^2)
+            Rn_Wm2 = Rn_Wm2,  # net radiation (W/m^2)
+            ST_C = ST_C,  # surface temperature (Celsius)
+            emissivity = emissivity,  # emissivity of the surface
+            Ta_C = Ta_C,  # air temperature (Celsius)
+            dTS_C = dTS_C,  # surface air temperature difference (Celsius)
+            Td_C = Td_C,  # dew point temperature (Celsius)
+            VPD_hPa = VPD_hPa,  # vapor pressure deficit (hPa)
+            SVP_hPa = SVP_hPa,  # saturation vapor pressure at given air temperature (hPa)
+            Ea_hPa = Ea_hPa,  # actual vapor pressure at air temperature (hPa)
+            Estar_hPa = Estar_hPa,  # saturation vapor pressure at surface temperature (hPa)
+            delta_hPa = delta_hPa,  # slope of saturation vapor pressure to air temperature (hpa/K)
+            NDVI=NDVI,  # normalized difference vegetation index
+            FVC = FVC,  # fractional vegetation cover
+            LAI = LAI,  # leaf area index
+            albedo = albedo,  # albedo of the surface
+            gamma_hPa=gamma_hPa,  # psychrometric constant (hPa/°C)
+            G_method = DEFAULT_G_METHOD,  # method for calculating soil heat flux
+        )
+    
+    diagnostic(Ms, "Ms", **diag_kwargs)
+
+    # STIC analytical equations (convergence on LE)
+    gB_ms, gS_ms, dT_C, EF = STIC_closure(
+        delta_hPa=delta_hPa, 
+        phi_Wm2=phi_Wm2, 
+        Es_hPa=Es_hPa, 
+        Ea_hPa=Ea_hPa, 
+        Estar_hPa=Estar_hPa, 
+        SM=SM,
+        gamma_hPa=gamma_hPa,
+        rho_kgm3=rho_kgm3,
+        Cp_Jkg=Cp_Jkg,
+        alpha=alpha
+    )
+    
+    gBB = gB_ms
+    gSS = gS_ms
+    gBB_by_gSS = rt.where(gSS == 0, 0, gBB / gSS)
+    gB_by_gS = rt.where(gS_ms == 0, 0, gB_ms / gS_ms)
+    dT_C = dT_C
+    T0_C = dT_C + Ta_C
+    
+    PET_Wm2 = ((delta_hPa * phi_Wm2 + rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa))  # Penman potential evaporation
+    
+    gR = (4 * SB_SIGMA * (Ta_C + 273) ** 3 * emissivity) / (rho_kgm3 * Cp_Jkg)
+    omega = ((delta_hPa / gamma_hPa) + 1) / ((delta_hPa / gamma_hPa) + 1 + gB_by_gS)
+    LE_eq = (phi_Wm2 * (delta_hPa / gamma_hPa)) / ((delta_hPa / gamma_hPa) + 1)
+    LE_imp = (Cp_Jkg * 0.0289644 / gamma_hPa) * gS_ms * 40 * VPD_hPa
+    LE_init = omega * LE_eq + (1 - omega) * LE_imp
+    dry = (Ds > VPD_hPa) & (PET_Wm2 > phi_Wm2) & (dTS_C > 0) & (Td_C <= 0)
+    omega = rt.where(dry,
+                        ((delta_hPa / gamma_hPa) + 1 + gR / gB_ms) / ((delta_hPa / gamma_hPa) + 1 + gB_ms / gS_ms + gR / gS_ms + gR / gB_ms),
+                        omega)
+    LE_eq = rt.where(dry, (phi_Wm2 * (delta_hPa / gamma_hPa)) / ((delta_hPa / gamma_hPa) + 1 + gR / gB_ms), LE_eq)
+    LE_init = rt.where(dry, omega * LE_eq + (1 - omega * LE_imp), LE_init)
+    
+    # sensible heat flux
+    H_Wm2 = ((gamma_hPa * phi_Wm2 * (1 + gB_by_gS) - rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa * (1 + (gB_by_gS))))
+    
+    LE_Wm2_new = LE_init
+    LE_Wm2_change = LE_convergence_target
+    LE_Wm2_old = LE_Wm2_new
+    LE_transpiration_Wm2 = None
+    PT_Wm2 = None
+    iteration = 1
+    LE_Wm2_max_change = 0
+    t = Timer()
+
+    while (np.nanmax(LE_Wm2_change) >= LE_convergence_target and iteration <= max_iterations):
+        logger.info(f"running STIC iteration {cl.val(iteration)} / {cl.val(max_iterations)}")
+
+        if Rg_Wm2 is None:
+            SM, SMrz, Ms, s1, e0, e0star, Tsd_C, D0, alphaN = iterate_without_solar(
+                LE = LE_Wm2_new,  # Latent heat flux (W/m^2)
+                PET = PET_Wm2,  # Potential evapotranspiration (W/m^2)
+                SM = SM,
+                ST_C = ST_C,  # Surface temperature (°C)
+                Ta_C = Ta_C,  # Air temperature (°C)
+                dTS = dTS_C,  # Surface-air temperature difference (°C)
+                T0 = T0_C,  # Reference temperature (°C)
+                gB = gB_ms,  # Boundary layer conductance (m/s)
+                gS = gS_ms,  # Stomatal conductance (m/s)
+                Ea_hPa = Ea_hPa,  # Actual vapor pressure (hPa)
+                Td_C = Td_C,  # Dew point temperature (°C)
+                VPD_hPa = VPD_hPa,  # Vapor pressure deficit (hPa)
+                Estar = Estar_hPa,  # Saturation vapor pressure at surface temperature (hPa)
+                delta = delta_hPa,  # Slope of the saturation vapor pressure-temperature curve (hPa/°C)
+                phi = phi_Wm2,  # available energy (W/m^2)
+                Ds = Ds,  # Vapor pressure deficit at source (hPa)
+                Es = Es_hPa,  # Saturation vapor pressure (hPa)
+                s3 = s3,  # Slope of the saturation vapor pressure and temperature 
+                s4 = s44,  # Slope of the saturation vapor pressure and temperature 
+                gB_by_gS = gB_by_gS,  # Ratio of boundary layer conductance to stomatal conductance
+                gamma_hPa = gamma_hPa,  # Psychrometric constant (hPa/°C)
+                rho_kgm3 = rho_kgm3,  # Air density (kg/m^3)
+                Cp_Jkg = Cp_Jkg  # Specific heat at constant pressure (J/kg/K)
+            )
+        else:
+            SM, G, e0, e0star, D0, alphaN = iterate_with_solar(
+                seconds_of_day = seconds_of_day,  # Seconds of the day
+                ST_C = ST_C,  # Soil temperature (°C)
+                NDVI = NDVI,  # Normalized Difference Vegetation Index
+                albedo = albedo,  # Albedo
+                gB_ms = gB_ms,  # boundary layer conductance (m/s)
+                gS_ms = gS_ms,  # stomatal conductance (m/s)
+                LE_Wm2 = LE_Wm2_new,  # latent heat flux (W/m^2)
+                Rg_Wm2 = Rg_Wm2,  # Incoming solar radiation (W/m^2)
+                Rn_Wm2 = Rn_Wm2,  # Net radiation (W/m^2)
+                LWnet_Wm2 = LWnet_Wm2,  # Net longwave radiation (W/m^2)
+                Ta_C = Ta_C,  # Air temperature (°C)
+                dTS_C = dTS_C,  # Change in soil temperature (°C)
+                Td_C = Td_C,  # Dew point temperature (°C)
+                Tsd_C = Tsd_C,  # Soil dew point temperature (°C)
+                Ea_hPa = Ea_hPa,  # actual vapor pressure (hPa)
+                Estar_hPa = Estar_hPa,  # saturation vapor pressure at surface temperature (hPa)
+                VPD_hPa = VPD_hPa,  # Vapor pressure deficit (hPa)
+                SVP_hPa = SVP_hPa,  # Saturation vapor pressure (hPa)
+                delta_hPa = delta_hPa,  # Slope of the saturation vapor pressure-temperature curve (hPa/°C)
+                phi_Wm2 = phi_Wm2,  # Net radiation minus soil heat flux (W/m^2)
+                Es_hPa = Es_hPa,  # Saturation vapor pressure (hPa)
+                s1 = s1,  # Soil moisture parameter
+                s3 = s3,  # Soil moisture parameter
+                FVC = FVC,  # Fractional canopy cover
+                T0_C = T0_C,  # Reference temperature (°C)
+                gB_by_gS = gB_by_gS,  # Ratio of boundary layer conductance to stomatal conductance
+                gamma_hPa = gamma_hPa,  # Psychrometric constant (hPa/°C)
+                rho_kgm3 = rho_kgm3,  # Air density (kg/m^3)
+                Cp_Jkg = Cp_Jkg,  # Specific heat at constant pressure (J/kg/K)
+                G_method = "santanello"  # Method for calculating soil heat flux
+            )
+
+        if use_variable_alpha:
+            alpha = alphaN
+            logger.info(f"using variable Priestley-Taylor alpha with mean: {cl.val(np.round(np.nanmean(alpha), 3))}")
+
+        # re-estimated conductances and states
+        gB_ms, gS_ms, dT_C, EF = STIC_closure(
+            delta_hPa=delta_hPa,  # Slope of the saturation vapor pressure-temperature curve (hPa/°C)
+            phi_Wm2=phi_Wm2,  # available energy (W/m^2)
+            Es_hPa=Es_hPa,  # Vapor pressure at the reference height (hPa)
+            Ea_hPa=Ea_hPa,  # Actual vapor pressure (hPa)
+            Estar_hPa=Estar_hPa,  # Saturation vapor pressure at the reference height (hPa)
+            SM=SM,  # Soil moisture (m³/m³)
+            gamma_hPa=gamma_hPa,  # Psychrometric constant (hPa/°C)
+            rho_kgm3=rho_kgm3,  # Air density (kg/m³)
+            Cp_Jkg=Cp_Jkg,  # Specific heat capacity of air (J/kg/°C)
+            alpha=alpha  # Stability correction factor for conductance 
+        )
+
+        gB_by_gS = rt.where(gS_ms == 0, 0, gB_ms / gS_ms)
+        T0_C = dT_C + Ta_C
+        # latent heat flux
+        LE_Wm2_new = ((delta_hPa * phi_Wm2 + rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa * (1 + gB_by_gS)))
+        LE_Wm2_new = rt.where(LE_Wm2_new > phi_Wm2, phi_Wm2, LE_Wm2_new)
+        # Sensible Heat Flux
+        H_Wm2 = ((gamma_hPa * phi_Wm2 * (1 + gB_by_gS) - rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa * (1 + (gB_by_gS))))
+        # potential evaporation (Penman)
+        PET_Wm2 = ((delta_hPa * phi_Wm2 + rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa))
+        # Potential Transpiration
+        PT_Wm2 = (delta_hPa * phi_Wm2 + rho_kgm3 * Cp_Jkg * gB_ms * VPD_hPa) / (delta_hPa + gamma_hPa * (1 + SM * gB_by_gS))  # potential transpiration
+        # ET PARTITIONING
+        LE_soil_Wm2 = rt.clip(SM * PET_Wm2, 0, None)
+        LE_transpiration_Wm2 = rt.clip(LE_Wm2_new - LE_soil_Wm2, 0, None)
+        # change in latent heat flux estimate
+        LE_Wm2_change = np.abs(LE_Wm2_old - LE_Wm2_new)
+        LE_Wm2_new = rt.where(np.isnan(LE_Wm2_new), LE_Wm2_old, LE_Wm2_new)
+        LE_Wm2_old = LE_Wm2_new
+        LE_Wm2_max_change = np.nanmax(LE_Wm2_change)
+        logger.info(
+            f"completed STIC iteration {cl.val(iteration)} / {cl.val(max_iterations)} with max LE change: {cl.val(np.round(LE_Wm2_max_change, 3))} ({t} seconds)")
+        
+        diagnostic(SM, f"SM_{iteration}", **diag_kwargs)
+        diagnostic(G, f"G_{iteration}", **diag_kwargs)
+        diagnostic(LE_Wm2_new, f"LE_{iteration}", **diag_kwargs)
+
+        if LE_Wm2_max_change <= LE_convergence_target:
+            logger.info(f"max LE change {cl.val(np.round(LE_Wm2_max_change, 3))} within convergence target {cl.val(np.round(LE_convergence_target, 3))} with {cl.val(iteration)} iteration{'s' if iteration > 1 else ''}")
+
+        iteration += 1
+
+    iteration -= 1
+    results["LE_max_change"] = LE_Wm2_max_change
+    results["iteration"] = iteration
+
+    LE = LE_Wm2_new
+
+    results["LE"] = LE
+    results["LE_change"] = LE_Wm2_change
+    results["LEt"] = LE_transpiration_Wm2
+    results["PT"] = PT_Wm2
+    results["PET"] = PET_Wm2
+    results["G"] = G
+
+    if isinstance(geometry, RasterGeometry):
+        for name, array in results.items():
+            try:
+                results[name] = Raster(array.reshape(geometry.shape), geometry=geometry)
+            except Exception as e:
+                pass
+        
+        results["LE"].cmap = ET_COLORMAP
+        results["PET"].cmap = ET_COLORMAP
+
+    warnings.resetwarnings()
+
+    return results

STIC_JPL/process_STIC_table.py

@@ -0,0 +1,61 @@
+import logging
+
+import numpy as np
+from dateutil import parser
+from pandas import DataFrame
+from rasters import Point
+from sentinel_tiles import sentinel_tiles
+from solar_apparent_time import UTC_to_solar
+from SEBAL_soil_heat_flux import calculate_SEBAL_soil_heat_flux
+
+from .model import STIC_JPL, MAX_ITERATIONS, USE_VARIABLE_ALPHA
+
+logger = logging.getLogger(__name__)
+
+def process_STIC_table(
+        input_df: DataFrame, 
+        max_iterations = MAX_ITERATIONS, 
+        use_variable_alpha = USE_VARIABLE_ALPHA) -> DataFrame:
+    hour_of_day = np.float64(np.array(input_df.hour_of_day))
+    lon = np.float64(np.array(input_df.lon))
+    ST_C = np.float64(np.array(input_df.ST_C))
+    emissivity = np.float64(np.array(input_df.EmisWB))
+    NDVI = np.float64(np.array(input_df.NDVI))
+    albedo = np.float64(np.array(input_df.albedo))
+    Ta_C = np.float64(np.array(input_df.Ta_C))
+    RH = np.float64(np.array(input_df.RH))
+    Rn = np.float64(np.array(input_df.Rn))
+    Rg = np.float64(np.array(input_df.Rg))
+
+    if "G" in input_df:
+        G = np.array(input_df.G)
+    else:
+        G = calculate_SEBAL_soil_heat_flux(
+            Rn=Rn,
+            ST_C=ST_C,
+            NDVI=NDVI,
+            albedo=albedo
+        )
+    
+    results = STIC_JPL(
+        hour_of_day=hour_of_day,
+        # longitude=lon,
+        ST_C = ST_C,
+        emissivity=emissivity,
+        NDVI=NDVI,
+        albedo=albedo,
+        Ta_C=Ta_C,
+        RH=RH,
+        Rn_Wm2=Rn,
+        G=G,
+        # Rg_Wm2=Rg,
+        max_iterations=max_iterations,
+        use_variable_alpha=use_variable_alpha
+    )
+
+    output_df = input_df.copy()
+
+    for key, value in results.items():
+        output_df[key] = value
+
+    return output_df

STIC_JPL/soil_moisture_initialization.py

@@ -4,7 +4,8 @@ import numpy as np
 import rasters as rt
 from rasters import Raster
 
-from .vegetation_conversion.vegetation_conversion import FVC_from_NDVI
+from .FVC_from_NDVI import FVC_from_NDVI
+from .LAI_from_NDVI import LAI_from_NDVI
 
 from .constants import GAMMA_HPA
 from .root_zone_initialization import calculate_root_zone_moisture

STIC_JPL/version.txt

@@ -1 +1 @@
-1.0.4
+1.2.1

{stic_jpl-1.1.0.dist-info → stic_jpl-1.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: STIC-JPL
-Version: 1.1.0
+Version: 1.2.1
 Summary: Surface Temperature Initiated Closure (STIC) Evapotranspiration Model Python Implementation
 Author-email: Gregory Halverson <gregory.h.halverson@jpl.nasa.gov>, Kaniska Mallick <kaniska.mallick@list.lu>, Madeleine Pascolini-Campbell <madeleine.a.pascolini-campbell@jpl.nasa.gov>, "Claire S. Villanueva-Weeks" <claire.s.villanueva-weeks@jpl.gov>
 Project-URL: Homepage, https://github.com/JPL-Evapotranspiration-Algorithms/STIC-JPL
@@ -9,13 +9,18 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 Requires-Dist: colored-logging
-Requires-Dist: ECOv002-CMR
-Requires-Dist: ECOv002-granules
+Requires-Dist: ECOv002-CMR>=1.0.5
+Requires-Dist: ECOv002-granules>=1.0.3
+Requires-Dist: ECOv003-granules
 Requires-Dist: GEOS5FP>=1.1.1
+Requires-Dist: monte-carlo-sensitivity
 Requires-Dist: numpy
 Requires-Dist: pandas
-Requires-Dist: rasters
+Requires-Dist: rasters>=1.4.6
+Requires-Dist: seaborn
+Requires-Dist: SEBAL-soil-heat-flux
 Requires-Dist: solar-apparent-time
+Requires-Dist: verma-net-radiation>=1.1.0
 Provides-Extra: dev
 Requires-Dist: build; extra == "dev"
 Requires-Dist: pytest>=6.0; extra == "dev"
@@ -24,7 +29,8 @@ Requires-Dist: jupyter; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: twine; extra == "dev"
 
-# Surface Temperature Initiated Closure (STIC) Evapotranspiration Model Python Implementation
+# `STIC-JPL` 
+## Surface Temperature Initiated Closure (STIC) Evapotranspiration Model Python Implementation
 
 [![CI](https://github.com/JPL-Evapotranspiration-Algorithms/STIC/actions/workflows/ci.yml/badge.svg)](https://github.com/JPL-Evapotranspiration-Algorithms/STIC/actions/workflows/ci.yml)
 
@@ -63,21 +69,23 @@ NASA Jet Propulsion Laboratory 329G
 
 ## Installation
 
-Use the pip package manager to install the `STIC` PyPi package.
+Use the pip package manager to install the `STIC-JPL` PyPi package with dashes in the name.
 
 ```
-pip install STIC
+pip install STIC-JPL
 ```
 
 ## Usage
 
-Import the `STIC` function from the `STIC` package.
+Import the `STIC_JPL` function from the `STIC_JPL` package with underscores in the name.
 
 ```
-from STIC import STIC
+from STIC_JPL import STIC_JPL
 ```
 
-See the [ECOSTRESS example](ECOSTRESS%20Example.ipynb) for usage.
+See the [ECOSTRESS example](ECOSTRESS%20Example.ipynb) notebook for usage.
+
+See the [STIC sensitivity](STIC%20Sensitivity.ipynb) notebook for sensitivity analysis.
 
 ## References
  

stic_jpl-1.2.1.dist-info/RECORD

@@ -0,0 +1,27 @@
+STIC_JPL/FVC_from_NDVI.py,sha256=NCGMu4-XzvYqg7UOqKqNkfqwmV73zipoc09Q1IubNm0,638
+STIC_JPL/LAI_from_NDVI.py,sha256=iqlCkuH53iDrAz_VbMs4y4EwHcNuGGo5nJfJtnmsO70,833
+STIC_JPL/STIC_JPL.py,sha256=qqxz7JOEHgmP_hoz1ZT_66v0WNs9R0SITRt-60rYb3I,127
+STIC_JPL/__init__.py,sha256=FmTp-Ir0Wbae0SbZgxlNIxq48TDrWCev17Gv1hWskxU,216
+STIC_JPL/canopy_air_stream.py,sha256=UYp3l7mt0XH4SqvCGZhRzCIL-v7-Rvxxfm-C81lheSU,1637
+STIC_JPL/celcius_to_kelvin.py,sha256=QZ1gA8BHBHbdlgn1v8tEMG17yY2r-SCBnaHrGXySItg,316
+STIC_JPL/closure.py,sha256=AzWoLnpoZ1MlQAKq0CgpmCMfDGVsp8-hYZ50ry33cic,4031
+STIC_JPL/constants.py,sha256=xIVTsdc3_Rf3EPSgSk1QPjWiojFGn4lf1Swffov3oTM,595
+STIC_JPL/diagnostic.py,sha256=RXjtZbCEJMiTyRuiMGUvekDgO_GcrhXVXvorR0WlAsk,2613
+STIC_JPL/generate_STIC_inputs.py,sha256=Vwuqq-PLiH2IBd1v0Vt2TVbdIRK8D1zU_uMgReCefmQ,2382
+STIC_JPL/initialize_with_solar.py,sha256=P-22Wn8-sdvh2o4LGb9XfbCdXGWcOxdWwMzEYfx2Nfo,3759
+STIC_JPL/initialize_without_solar.py,sha256=M_7QfP2pr2w5sQO7UOW1GPqxpmQkjmsQ526BgYVVALk,4675
+STIC_JPL/iterate_with_solar.py,sha256=T9DezL59xaV63o6f7_ouCGcQwPi1dIvhlJB26TMGuDo,6373
+STIC_JPL/iterate_without_solar.py,sha256=09RERpN6tdZr6ORDhMwEFXwx8941vyn1HMJQ-Q_bY6s,6140
+STIC_JPL/model.py,sha256=PwN4T7Ic-TMz6c0Br39H0QGX4yK4IdEo2Ww0VP-nD0w,17323
+STIC_JPL/net_radiation.py,sha256=Uwudsazul8V-x5t8KQLi3wpYi-wjMwT__eqZCRV2bIw,1187
+STIC_JPL/process_STIC_table.py,sha256=5s-fxbchyVnPCzUG5KZX-RrHZDpN4JVcwu42s821Kdw,1712
+STIC_JPL/root_zone_initialization.py,sha256=3JVKNDt3ebIiGVfuhBawjKs-BicNwkbfMprkzSxd4Cg,1581
+STIC_JPL/root_zone_iteration.py,sha256=1XOMFE3-TdJZzUU5vouflUO4NKaZwAW6s1KJrNez3Es,3787
+STIC_JPL/soil_moisture_initialization.py,sha256=wWhAmvNT8tAIm_Sul8mEj6VdNuj7K14TBGUjKfqJrso,5610
+STIC_JPL/soil_moisture_iteration.py,sha256=QJXOPMxxwIIskpx9zLkXUPfuhWgFPUBcRnGhZo2UjAw,6493
+STIC_JPL/timer.py,sha256=tn5e3NQmsh55Jp9Fstjf-8KJW4F8UIJs-d_ZLooFYE8,1610
+STIC_JPL/version.txt,sha256=IGYgplfxzMivcrhm_c7yDmQcSPOc4n8zjOgxOUnGPlM,5
+stic_jpl-1.2.1.dist-info/METADATA,sha256=jKGqTkUD0wSUa1LCmVP3fBSC7XMiLJbPYOAgnBw8C7o,5731
+stic_jpl-1.2.1.dist-info/WHEEL,sha256=wXxTzcEDnjrTwFYjLPcsW_7_XihufBwmpiBeiXNBGEA,91
+stic_jpl-1.2.1.dist-info/top_level.txt,sha256=9NkchxttzACJcGcAaWzMaZarzX40OXQ216hERNA9LIo,9
+stic_jpl-1.2.1.dist-info/RECORD,,

{stic_jpl-1.1.0.dist-info → stic_jpl-1.2.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

STIC_JPL/meteorology_conversion/__init__.py

@@ -1 +0,0 @@
-from .meteorology_conversion import *

STIC_JPL/meteorology_conversion/meteorology_conversion.py

@@ -1,123 +0,0 @@
-from typing import Union
-import numpy as np
-import rasters as rt
-from rasters import Raster
-
-# gas constant for dry air in joules per kilogram per kelvin
-RD = 286.9
-
-# gas constant for moist air in joules per kilogram per kelvin
-RW = 461.5
-
-# specific heat of water vapor in joules per kilogram per kelvin
-CPW = 1846.0
-
-# specific heat of dry air in joules per kilogram per kelvin
-CPD = 1005.0
-
-def kelvin_to_celsius(T_K: Union[Raster, np.ndarray]) -> Union[Raster, np.ndarray]:
-    """
-    convert temperature in kelvin to celsius.
-    :param T_K: temperature in kelvin
-    :return: temperature in celsius
-    """
-    return T_K - 273.15
-
-def celcius_to_kelvin(T_C: Union[Raster, np.ndarray]) -> Union[Raster, np.ndarray]:
-    """
-    convert temperature in celsius to kelvin.
-    :param T_C: temperature in celsius
-    :return: temperature in kelvin
-    """
-    return T_C + 273.15
-
-def calculate_specific_humidity(
-        Ea_Pa: Union[Raster, np.ndarray], 
-        Ps_Pa: Union[Raster, np.ndarray]) -> Union[Raster, np.ndarray]:
-    """
-    Calculate the specific humidity of air as a ratio of kilograms of water to kilograms of air.
-    
-    Args:
-        Ea_Pa (Union[Raster, np.ndarray]): Actual water vapor pressure in Pascal.
-        surface_pressure_Pa (Union[Raster, np.ndarray]): Surface pressure in Pascal.
-    
-    Returns:
-        Union[Raster, np.ndarray]: Specific humidity in kilograms of water per kilograms of air.
-    """
-    return ((0.622 * Ea_Pa) / (Ps_Pa - (0.387 * Ea_Pa)))
-
-def calculate_specific_heat(specific_humidity: Union[Raster, np.ndarray]):
-    # calculate specific heat capacity of the air (Cp)
-    # in joules per kilogram per kelvin
-    # from specific heat of water vapor (CPW)
-    # and specific heat of dry air (CPD)
-    Cp_Jkg = specific_humidity * CPW + (1 - specific_humidity) * CPD
-
-    return Cp_Jkg
-
-def calculate_air_density(
-        surface_pressure_Pa: Union[Raster, np.ndarray], 
-        Ta_K: Union[Raster, np.ndarray], 
-        specific_humidity: Union[Raster, np.ndarray]) -> Union[Raster, np.ndarray]:
-    """
-    Calculate air density.
-
-    Parameters:
-    surface_pressure_Pa (Union[Raster, np.ndarray]): Surface pressure in Pascal.
-    Ta_K (Union[Raster, np.ndarray]): Air temperature in Kelvin.
-    specific_humidity (Union[Raster, np.ndarray]): Specific humidity.
-
-    Returns:
-    Union[Raster, np.ndarray]: Air density in kilograms per cubic meter.
-    """
-    # numerator: Pa(N / m ^ 2 = kg * m / s ^ 2); denominator: J / kg / K * K)
-    rhoD = surface_pressure_Pa / (RD * Ta_K)
-
-    # calculate air density (rho) in kilograms per cubic meter
-    rho = rhoD * ((1.0 + specific_humidity) / (1.0 + specific_humidity * (RW / RD)))
-
-    return rho
-
-def SVP_kPa_from_Ta_C(Ta_C: Union[Raster, np.ndarray]) -> Union[Raster, np.ndarray]:
-    """
-    Calculate the saturation vapor pressure in kiloPascal (kPa) from air temperature in Celsius.
-
-    Parameters:
-    Ta_C (Union[Raster, np.ndarray]): Air temperature in Celsius.
-
-    Returns:
-    Union[Raster, np.ndarray]: Saturation vapor pressure in kPa.
-
-    """
-    SVP_kPa = np.clip(0.611 * np.exp((Ta_C * 17.27) / (Ta_C + 237.7)), 1, None)
-
-    return SVP_kPa
-
-def SVP_Pa_from_Ta_C(Ta_C: Union[Raster, np.ndarray]) -> Union[Raster, np.ndarray]:
-    """
-    Calculate the saturation vapor pressure in Pascal (Pa) from the air temperature in Celsius (Ta_C).
-
-    Parameters:
-        Ta_C (Union[Raster, np.ndarray]): Air temperature in Celsius.
-
-    Returns:
-        Union[Raster, np.ndarray]: Saturation vapor pressure in Pascal (Pa).
-    """
-    return SVP_kPa_from_Ta_C(Ta_C) * 1000
-
-def calculate_surface_pressure(elevation_m: Union[Raster, np.ndarray], Ta_C: Union[Raster, np.ndarray]) -> Union[Raster, np.ndarray]:
-    """
-    Calculate surface pressure using elevation and air temperature.
-
-    Parameters:
-        elevation_m (Union[Raster, np.ndarray]): Elevation in meters.
-        Ta_K (Union[Raster, np.ndarray]): Air temperature in Kelvin.
-
-    Returns:
-        Union[Raster, np.ndarray]: Surface pressure in Pascal (Pa).
-    """
-    Ta_K = kelvin_to_celsius(Ta_C)
-    Ps_Pa = 101325.0 * (1.0 - 0.0065 * elevation_m / Ta_K) ** (9.807 / (0.0065 * 287.0))  # [Pa]
-
-    return Ps_Pa
-

STIC_JPL/soil_heat_flux/__init__.py

@@ -1 +0,0 @@
-from .calculate_SEBAL_soil_heat_flux import calculate_SEBAL_soil_heat_flux

STIC_JPL/soil_heat_flux/calculate_SEBAL_soil_heat_flux.py

@@ -1,40 +0,0 @@
-from typing import Union
-
-import numpy as np
-import rasters as rt
-from rasters import Raster
-
-def calculate_SEBAL_soil_heat_flux(
-        Rn: Union[Raster, np.ndarray], 
-        ST_C: Union[Raster, np.ndarray], 
-        NDVI: Union[Raster, np.ndarray], 
-        albedo: Union[Raster, np.ndarray]) -> Union[Raster, np.ndarray]:
-    """
-    This function calculates the soil heat flux (G) in the Surface Energy Balance Algorithm for Land (SEBAL) model.
-    The formula used in the function is a simplification of the more complex relationship between these variables in the energy balance at the surface.
-    
-    Parameters:
-    Rn (np.ndarray): Net radiation at the surface.
-    ST_C (np.ndarray): Surface temperature in Celsius.
-    NDVI (np.ndarray): Normalized Difference Vegetation Index, indicating the presence and condition of vegetation.
-    albedo (np.ndarray): Measure of the diffuse reflection of solar radiation.
-    
-    Returns:
-    np.ndarray: The soil heat flux (G), a key component in the energy balance.
-    
-    Reference:
-    "Evapotranspiration Estimation Based on Remote Sensing and the SEBAL Model in the Bosten Lake Basin of China" [^1^][1]
-    """
-    # Empirical coefficients used in the calculation
-    coeff1 = 0.0038
-    coeff2 = 0.0074
-    
-    # Vegetation cover correction factor
-    NDVI_correction = 1 - 0.98 * NDVI ** 4
-    
-    # Calculation of the soil heat flux (G)
-    G = Rn * ST_C * (coeff1 + coeff2 * albedo) * NDVI_correction
-    
-    G = rt.clip(G, 0, None)
-
-    return G

STIC_JPL/timer/__init__.py

@@ -1 +0,0 @@
-from .timer import *

STIC_JPL/vegetation_conversion/__init__.py

@@ -1 +0,0 @@
-from .vegetation_conversion import *

stic_jpl-1.1.0.dist-info/RECORD

@@ -1,28 +0,0 @@
-STIC_JPL/STIC_JPL.py,sha256=a0EpRTX6Sd75RPIqAzWckIuj9-KwbCE8T1aSEDpLM-c,17434
-STIC_JPL/__init__.py,sha256=FmTp-Ir0Wbae0SbZgxlNIxq48TDrWCev17Gv1hWskxU,216
-STIC_JPL/canopy_air_stream.py,sha256=UYp3l7mt0XH4SqvCGZhRzCIL-v7-Rvxxfm-C81lheSU,1637
-STIC_JPL/closure.py,sha256=AzWoLnpoZ1MlQAKq0CgpmCMfDGVsp8-hYZ50ry33cic,4031
-STIC_JPL/constants.py,sha256=xIVTsdc3_Rf3EPSgSk1QPjWiojFGn4lf1Swffov3oTM,595
-STIC_JPL/diagnostic.py,sha256=RXjtZbCEJMiTyRuiMGUvekDgO_GcrhXVXvorR0WlAsk,2613
-STIC_JPL/initialize_with_solar.py,sha256=6DUUHdVfeKvDk1pf_bOteSW8qd-n9pU4dowO1sMYOpw,3825
-STIC_JPL/initialize_without_solar.py,sha256=M_7QfP2pr2w5sQO7UOW1GPqxpmQkjmsQ526BgYVVALk,4675
-STIC_JPL/iterate_with_solar.py,sha256=WKySvuIJ4HzcDni0UYafmk5lXex2lJfde82kGnGUDI8,6368
-STIC_JPL/iterate_without_solar.py,sha256=09RERpN6tdZr6ORDhMwEFXwx8941vyn1HMJQ-Q_bY6s,6140
-STIC_JPL/net_radiation.py,sha256=Uwudsazul8V-x5t8KQLi3wpYi-wjMwT__eqZCRV2bIw,1187
-STIC_JPL/root_zone_initialization.py,sha256=3JVKNDt3ebIiGVfuhBawjKs-BicNwkbfMprkzSxd4Cg,1581
-STIC_JPL/root_zone_iteration.py,sha256=1XOMFE3-TdJZzUU5vouflUO4NKaZwAW6s1KJrNez3Es,3787
-STIC_JPL/soil_moisture_initialization.py,sha256=YF0GcHkpH5amABNPpxD8f1lLPRyIAkG2dYJTfEuIX4g,5599
-STIC_JPL/soil_moisture_iteration.py,sha256=QJXOPMxxwIIskpx9zLkXUPfuhWgFPUBcRnGhZo2UjAw,6493
-STIC_JPL/version.txt,sha256=rqWtvvV0eFJzxPOcG3aHz4AZk-DLa_Z4GkFonk7bsgw,5
-STIC_JPL/meteorology_conversion/__init__.py,sha256=dLF40imqJCC_l8_QMetbsj1YzkXZuFt9tQ2fsd7Wcdw,38
-STIC_JPL/meteorology_conversion/meteorology_conversion.py,sha256=8vzx71FLLNhR5v6EQBL8OSgAmupQcgdLX2c9tL9TPxA,4202
-STIC_JPL/soil_heat_flux/__init__.py,sha256=bN0dHUfqR9ob68M1TqdjQTK3kmaL5S4P08yK0Thub6k,74
-STIC_JPL/soil_heat_flux/calculate_SEBAL_soil_heat_flux.py,sha256=PZylUGET5-Uj6BGfhOeqS4tp2pGE__gdc5X1nidLjxw,1516
-STIC_JPL/timer/__init__.py,sha256=I_MQKp_aamBLUzZv0psEbRgs6GZLOJd4mmJ7bli0Ikc,21
-STIC_JPL/timer/timer.py,sha256=tn5e3NQmsh55Jp9Fstjf-8KJW4F8UIJs-d_ZLooFYE8,1610
-STIC_JPL/vegetation_conversion/__init__.py,sha256=8gnz0yK_euCV0TtVGDrSGaVfx4g0EJCG2J68ppuA5oc,37
-STIC_JPL/vegetation_conversion/vegetation_conversion.py,sha256=-K3FLV6pXkpxtRxQvimqqkXAgkn9mUUlHQ8FIscq1Zg,1306
-stic_jpl-1.1.0.dist-info/METADATA,sha256=sDO9vRDdU6d-qTxHfk-0ZoCLX5ZyT1o1F086M0hbqWA,5348
-stic_jpl-1.1.0.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-stic_jpl-1.1.0.dist-info/top_level.txt,sha256=9NkchxttzACJcGcAaWzMaZarzX40OXQ216hERNA9LIo,9
-stic_jpl-1.1.0.dist-info/RECORD,,