srs_preprocess_s2: prosail-master/R/Lib

annotate prosail-master/R/Lib_PROSAIL.R @ 0:33a1e15f7252 draft default tip

planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7

author	ecology
date	Mon, 09 Jan 2023 13:37:05 +0000
parents
children

rev	line source
0 33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1 # ============================================================================= =
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	2 # prosail
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	3 # Lib_PROSAIL.R
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	4 # ============================================================================= =
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	5 # PROGRAMMERS:
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	6 # Jean-Baptiste FERET <jb.feret@teledetection.fr >
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	7 # Florian de BOISSIEU <fdeboiss@gmail.com >
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	8 # copyright 2019 / 11 Jean-Baptiste FERET
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	9 # ============================================================================= =
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	10 # This Library includes functions dedicated to PROSAIL simulation
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	11 # SAIL versions available are 4SAIL and 4SAIL2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	12 # ============================================================================= =
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	13
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	14 #" computes bidirectional reflectance factor based on outputs from PROSAIL and sun position
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	15 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	16 #" The direct and diffuse light are taken into account as proposed by:
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	17 #" Francois et al. (2002) conversion of 400-1100 nm vegetation albedo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	18 #" measurements into total shortwave broadband albedo using a canopy
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	19 #" radiative transfer model, Agronomie
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	20 #" Es = direct
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	21 #" Ed = diffuse
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	22 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	23 #" @param rdot numeric. Hemispherical-directional reflectance factor in viewing direction
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	24 #" @param rsot numeric. Bi-directional reflectance factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	25 #" @param tts numeric. Solar zenith angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	26 #" @param specatm_sensor list. direct and diffuse radiation for clear conditions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	27 #" @return brf numeric. Bidirectional reflectance factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	28 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	29 compute_brf <- function(rdot, rsot, tts, specatm_sensor) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	30
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	31 ############################## #
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	32 ## direct / diffuse light ##
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	33 ############################## #
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	34 es <- specatm_sensor$Direct_Light
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	35 ed <- specatm_sensor$Diffuse_Light
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	36 rd <- pi / 180
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	37 skyl <- 0.847 - 1.61 * sin((90 - tts) * rd) + 1.04 * sin((90 - tts) * rd) * sin((90 - tts) * rd) # diffuse radiation (Francois et al., 2002)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	38 pardiro <- (1 - skyl) * es
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	39 pardifo <- skyl * ed
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	40 brf <- (rdot * pardifo + rsot * pardiro) / (pardiro + pardifo)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	41 return(brf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	42 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	43
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	44 #" Performs PROSAIL simulation based on a set of combinations of input parameters
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	45 #" @param spec_sensor list. Includes optical constants required for PROSPECT
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	46 #" refractive index, specific absorption coefficients and corresponding spectral bands
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	47 #" @param input_prospect list. PROSPECT input variables
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	48 #" @param n numeric. Leaf structure parameter
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	49 #" @param chl numeric. chlorophyll content (microg.cm-2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	50 #" @param car numeric. carotenoid content (microg.cm-2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	51 #" @param ant numeric. anthocyain content (microg.cm-2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	52 #" @param brown numeric. brown pigment content (Arbitrary units)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	53 #" @param ewt numeric. Equivalent Water Thickness (g.cm-2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	54 #" @param lma numeric. Leaf Mass per Area (g.cm-2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	55 #" @param prot numeric. protein content (g.cm-2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	56 #" @param cbc numeric. nonprotcarbon-based constituent content (g.cm-2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	57 #" @param alpha numeric. Solid angle for incident light at surface of leaf (simulation of roughness)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	58 #" @param typelidf numeric. Type of leaf inclination distribution function
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	59 #" @param lidfa numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	60 #" if typelidf == 1, controls the average leaf slope
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	61 #" if typelidf == 2, corresponds to average leaf angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	62 #" @param lidfb numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	63 #" if typelidf == 1, unused
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	64 #" if typelidf == 2, controls the distribution"s bimodality
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	65 #" @param lai numeric. Leaf Area Index
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	66 #" @param q numeric. Hot Spot parameter
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	67 #" @param tts numeric. Sun zeith angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	68 #" @param tto numeric. Observer zeith angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	69 #" @param psi numeric. Azimuth Sun / Observer
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	70 #" @param rsoil numeric. Soil reflectance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	71 #" @param fraction_brown numeric. Fraction of brown leaf area
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	72 #" @param diss numeric. Layer dissociation factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	73 #" @param cv numeric. vertical crown cover percentage
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	74 #" = % ground area covered with crowns as seen from nadir direction
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	75 #" @param zeta numeric. Tree shape factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	76 #" = ratio of crown diameter to crown height
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	77 #" @param sailversion character. choose between 4SAIL and 4SAIL2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	78 #" @param brownvegetation list. Defines optical properties for brown vegetation, if not nULL
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	79 #" - WVL, reflectance, Transmittance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	80 #" - Set to nULL if use PROSPECT to generate it
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	81 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	82 #" @return list. rdot, rsot, rddt, rsdt
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	83 #" rdot: hemispherical-directional reflectance factor in viewing direction
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	84 #" rsot: bi-directional reflectance factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	85 #" rsdt: directional-hemispherical reflectance factor for solar incident flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	86 #" rddt: bi-hemispherical reflectance factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	87 #" @import prospect
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	88 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	89 pro4sail <- function(spec_sensor, input_prospect = nULL, n = 1.5, chl = 40.0,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	90 car = 8.0, ant = 0.0, brown = 0.0, ewt = 0.01,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	91 lma = 0.008, prot = 0.0, cbc = 0.0, alpha = 40.0,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	92 typelidf = 2, lidfa = nULL, lidfb = nULL, lai = nULL,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	93 q = nULL, tts = nULL, tto = nULL, psi = nULL, rsoil = nULL,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	94 fraction_brown = 0.0, diss = 0.0, cv = 1, zeta = 1,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	95 sailversion = "4SAIL", brownvegetation = nULL) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	96
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	97 ############################ #
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	98 # LEAF OPTICAL PROPERTIES ##
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	99 ############################ #
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	100 if (is.null(input_prospect)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	101 input_prospect <- data.frame("chl" = chl, "car" = car, "ant" = ant, "brown" = brown, "ewt" = ewt,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	102 "lma" = lma, "prot" = prot, "cbc" = cbc, "n" = n, "alpha" = alpha)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	103 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	104 greenvegetation <- prospect::PROSPECT(SpecPROSPECT = spec_sensor,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	105 n = input_prospect$n[1],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	106 chl = input_prospect$chl[1],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	107 car = input_prospect$car[1],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	108 ant = input_prospect$ant[1],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	109 brown = input_prospect$brown[1],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	110 ewt = input_prospect$ewt[1],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	111 lma = input_prospect$lma[1],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	112 prot = input_prospect$prot[1],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	113 cbc = input_prospect$cbc[1],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	114 alpha = input_prospect$alpha[1])
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	115
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	116 if (sailversion == "4SAIL2") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	117 # 4SAIL2 requires one of the following combination of input parameters
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	118 # Case #1: valid optical properties for brown vegetation
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	119 if (!is.null(brownvegetation)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	120 # need to define reflectance and Transmittance for brownvegetation
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	121 if (length(grep("reflectance", names(brownvegetation))) == 0 \|\| length(grep("Transmittance", names(brownvegetation))) == 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	122 message("Please define brownvegetation as a list including reflectance and Transmittance")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	123 stop()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	124 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	125 # check if spectral domain for optical properties of brown vegetation match
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	126 # with spectral domain for optical properties of green vegetation
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	127 if (length(setdiff(spec_sensor$lambda, brownvegetation$wvl)) > 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	128 message("Please define same spectral domain for brownvegetation and SpecPROSPECT")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	129 stop()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	130 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	131 if (length(unique(lengths(input_prospect))) == 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	132 if (!unique(lengths(input_prospect)) == 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	133 message("brownvegetation defined along with multiple leaf chemical properties")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	134 message("Only first set of leaf chemical properties will be used to simulate green vegetation")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	135 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	136 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	137 # if no leaf optical properties brown vegetation defined
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	138 } else if (is.null(brownvegetation)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	139 # if all PROSPECT input parameters have the same length
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	140 if (length(unique(lengths(input_prospect))) == 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	141 # if all PROSPECT input parameters are unique (no possibility to simulate 2 types of leaf optics)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	142 if (unique(lengths(input_prospect)) == 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	143 # if fraction_brown set to 0, then assign green vegetation optics to brown vegetation optics
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	144 if (fraction_brown == 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	145 brownvegetation <- greenvegetation
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	146 # else run 4SAIL
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	147 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	148 message("4SAIL2 needs two sets of optical properties for green and brown vegetation")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	149 message("Currently one set is defined. will run 4SAIL instead of 4SAIL2")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	150 sailversion <- "4SAIL"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	151 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	152 # if all PROSPECT parameters have at least 2 elements
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	153 } else if (unique(lengths(input_prospect)) >= 2) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	154 # compute leaf optical properties
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	155 brownvegetation <- prospect::PROSPECT(SpecPROSPECT = spec_sensor,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	156 n = input_prospect$n[2],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	157 chl = input_prospect$chl[2],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	158 car = input_prospect$car[2],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	159 ant = input_prospect$ant[2],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	160 brown = input_prospect$brown[2],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	161 ewt = input_prospect$ewt[2],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	162 lma = input_prospect$lma[2],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	163 prot = input_prospect$prot[2],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	164 cbc = input_prospect$cbc[2],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	165 alpha = input_prospect$alpha[2])
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	166 if (unique(lengths(input_prospect)) > 2) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	167 message("4SAIL2 needs two sets of optical properties for green and brown vegetation")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	168 message("Currently more than 2 sets are defined. will only use the first 2")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	169 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	170 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	171 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	172 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	173 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	174 if (sailversion == "4SAIL") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	175 if (length(unique(lengths(input_prospect))) == 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	176 if (unique(lengths(input_prospect)) > 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	177 message("4SAIL needs only one set of optical properties")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	178 message("Currently more than one set of leaf chemical constituents is defined.")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	179 message("Will run 4SAIL with the first set of leaf chemical constituents")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	180 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	181 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	182 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	183
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	184 if (sailversion == "4SAIL") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	185 # run 4SAIL
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	186 ref <- foursail(leafoptics = greenvegetation,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	187 typelidf, lidfa, lidfb, lai, q, tts, tto, psi, rsoil)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	188 } else if (sailversion == "4SAIL2") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	189 # run 4SAIL2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	190 ref <- foursail2(leafgreen = greenvegetation, leafbrown = brownvegetation,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	191 typelidf, lidfa, lidfb, lai, q, tts, tto, psi, rsoil,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	192 fraction_brown, diss, cv, zeta)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	193 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	194 return(ref)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	195 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	196
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	197 #" Performs PROSAIL simulation based on a set of combinations of input parameters
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	198 #" @param leafoptics list. Includes leaf optical properties (reflectance and transmittance)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	199 #" and corresponding spectral bands
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	200 #" @param typelidf numeric. Type of leaf inclination distribution function
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	201 #" @param lidfa numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	202 #" if typelidf == 1, controls the average leaf slope
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	203 #" if typelidf == 2, corresponds to average leaf angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	204 #" @param lidfb numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	205 #" if typelidf == 1, unused
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	206 #" if typelidf == 2, controls the distribution"s bimodality
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	207 #" @param lai numeric. Leaf Area Index
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	208 #" @param q numeric. Hot Spot parameter
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	209 #" @param tts numeric. Sun zeith angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	210 #" @param tto numeric. Observer zeith angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	211 #" @param psi numeric. Azimuth Sun / Observer
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	212 #" @param rsoil numeric. Soil reflectance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	213 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	214 #" @return list. rdot, rsot, rddt, rsdt
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	215 #" rdot: hemispherical-directional reflectance factor in viewing direction
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	216 #" rsot: bi-directional reflectance factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	217 #" rsdt: directional-hemispherical reflectance factor for solar incident flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	218 #" rddt: bi-hemispherical reflectance factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	219 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	220
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	221 foursail <- function(leafoptics, typelidf = 2, lidfa = nULL, lidfb = nULL, lai = nULL,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	222 q = nULL, tts = nULL, tto = nULL, psi = nULL, rsoil = nULL) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	223
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	224 ############################## #
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	225 # LEAF OPTICAL PROPERTIES ##
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	226 ############################## #
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	227 rho <- leafoptics$Reflectance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	228 tau <- leafoptics$Transmittance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	229
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	230 # Geometric quantities
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	231 rd <- pi / 180
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	232 cts <- cos(rd * tts)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	233 cto <- cos(rd * tto)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	234 ctscto <- cts * cto
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	235 tants <- tan(rd * tts)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	236 tanto <- tan(rd * tto)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	237 cospsi <- cos(rd * psi)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	238 dso <- sqrt(tants * tants + tanto * tanto - 2. * tants * tanto * cospsi)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	239
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	240 # Generate leaf angle distribution from average leaf angle (ellipsoidal) or (a, b) parameters
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	241 if (typelidf == 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	242 foliar_distrib <- dladgen(lidfa, lidfb)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	243 lidf <- foliar_distrib$lidf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	244 litab <- foliar_distrib$litab
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	245
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	246 } else if (typelidf == 2) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	247 foliar_distrib <- campbell(lidfa)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	248 lidf <- foliar_distrib$lidf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	249 litab <- foliar_distrib$litab
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	250 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	251
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	252 # angular distance, compensation of shadow length
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	253 # Calculate geometric factors associated with extinction and scattering
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	254 # Initialise sums
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	255 ks <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	256 ko <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	257 bf <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	258 sob <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	259 sof <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	260
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	261 # Weighted sums over LIDF
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	262 na <- length(litab)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	263 for (i in 1:na) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	264 ttl <- litab[i] # leaf inclination discrete values
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	265 ctl <- cos(rd * ttl)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	266 # SAIL volume scattering phase function gives interception and portions to be
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	267 # multiplied by rho and tau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	268 resvolscatt <- volscatt(tts, tto, psi, ttl)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	269 chi_s <- resvolscatt$chi_s
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	270 chi_o <- resvolscatt$chi_o
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	271 frho <- resvolscatt$frho
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	272 ftau <- resvolscatt$ftau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	273
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	274 #********************************************************************************
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	275 #* SUITS SYSTEM coEFFICIEnTS
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	276 #*
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	277 #* ks : Extinction coefficient for direct solar flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	278 #* ko : Extinction coefficient for direct observed flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	279 #* att : Attenuation coefficient for diffuse flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	280 #* sigb : Backscattering coefficient of the diffuse downward flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	281 #* sigf : Forwardscattering coefficient of the diffuse upward flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	282 #* sf : Scattering coefficient of the direct solar flux for downward diffuse flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	283 #* sb : Scattering coefficient of the direct solar flux for upward diffuse flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	284 #* vf : Scattering coefficient of upward diffuse flux in the observed direction
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	285 #* vb : Scattering coefficient of downward diffuse flux in the observed direction
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	286 #* w : Bidirectional scattering coefficient
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	287 #********************************************************************************
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	288
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	289 # Extinction coefficients
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	290 ksli <- chi_s / cts
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	291 koli <- chi_o / cto
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	292
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	293 # Area scattering coefficient fractions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	294 sobli <- frho * pi / ctscto
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	295 sofli <- ftau * pi / ctscto
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	296 bfli <- ctl * ctl
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	297 ks <- ks + ksli * lidf[i]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	298 ko <- ko + koli * lidf[i]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	299 bf <- bf + bfli * lidf[i]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	300 sob <- sob + sobli * lidf[i]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	301 sof <- sof + sofli * lidf[i]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	302 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	303
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	304 # Geometric factors to be used later with rho and tau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	305 sdb <- 0.5 * (ks + bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	306 sdf <- 0.5 * (ks - bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	307 dob <- 0.5 * (ko + bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	308 dof <- 0.5 * (ko - bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	309 ddb <- 0.5 * (1. + bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	310 ddf <- 0.5 * (1. - bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	311
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	312 # Here rho and tau come in
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	313 sigb <- ddb * rho + ddf * tau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	314 sigf <- ddf * rho + ddb * tau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	315 att <- 1 - sigf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	316 m2 <- (att + sigb) * (att - sigb)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	317 m2[which(m2 <= 0)] <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	318 m <- sqrt(m2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	319
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	320 sb <- sdb * rho + sdf * tau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	321 sf <- sdf * rho + sdb * tau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	322 vb <- dob * rho + dof * tau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	323 vf <- dof * rho + dob * tau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	324 w <- sob * rho + sof * tau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	325
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	326 # Here the LAI comes in
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	327 # Outputs for the case LAI = 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	328 if (lai < 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	329 tss <- 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	330 too <- 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	331 tsstoo <- 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	332 rdd <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	333 tdd <- 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	334 rsd <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	335 tsd <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	336 rdo <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	337 tdo <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	338 rso <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	339 rsos <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	340 rsod <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	341
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	342 rddt <- rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	343 rsdt <- rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	344 rdot <- rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	345 rsodt <- 0 * rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	346 rsost <- rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	347 rsot <- rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	348 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	349 # Other cases (LAI > 0)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	350 e1 <- exp(-m * lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	351 e2 <- e1 * e1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	352 rinf <- (att - m) / sigb
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	353 rinf2 <- rinf * rinf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	354 re <- rinf * e1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	355 denom <- 1. - rinf2 * e2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	356
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	357 j1ks <- jfunc1(ks, m, lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	358 j2ks <- jfunc2(ks, m, lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	359 j1ko <- jfunc1(ko, m, lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	360 j2ko <- jfunc2(ko, m, lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	361
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	362 ps <- (sf + sb * rinf) * j1ks
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	363 qs <- (sf * rinf + sb) * j2ks
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	364 pv <- (vf + vb * rinf) * j1ko
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	365 qv <- (vf * rinf + vb) * j2ko
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	366
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	367 rdd <- rinf * (1. - e2) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	368 tdd <- (1. - rinf2) * e1 / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	369 tsd <- (ps - re * qs) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	370 rsd <- (qs - re * ps) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	371 tdo <- (pv - re * qv) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	372 rdo <- (qv - re * pv) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	373
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	374 tss <- exp(-ks * lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	375 too <- exp(-ko * lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	376 z <- jfunc3(ks, ko, lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	377 g1 <- (z - j1ks * too) / (ko + m)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	378 g2 <- (z - j1ko * tss) / (ks + m)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	379
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	380 tv1 <- (vf * rinf + vb) * g1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	381 tv2 <- (vf + vb * rinf) * g2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	382 t1 <- tv1 * (sf + sb * rinf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	383 t2 <- tv2 * (sf * rinf + sb)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	384 t3 <- (rdo * qs + tdo * ps) * rinf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	385
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	386 # Multiple scattering contribution to bidirectional canopy reflectance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	387 rsod <- (t1 + t2 - t3) / (1. - rinf2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	388
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	389 # Treatment of the hotspot-effect
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	390 alf <- 1e6
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	391 # Apply correction 2 / (K + k) suggested by F.-M. Breon
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	392 if (q > 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	393 alf <- (dso / q) * 2. / (ks + ko)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	394 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	395 if (alf > 200) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	396 # inserted H. Bach 1 / 3 / 04
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	397 alf <- 200
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	398 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	399 if (alf == 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	400 # The pure hotspot - no shadow
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	401 tsstoo <- tss
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	402 sumint <- (1 - tss) / (ks * lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	403 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	404 # Outside the hotspot
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	405 fhot <- lai * sqrt(ko * ks)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	406 # Integrate by exponential Simpson method in 20 steps
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	407 # the steps are arranged according to equal partitioning
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	408 # of the slope of the joint probability function
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	409 x1 <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	410 y1 <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	411 f1 <- 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	412 fint <- (1. - exp(-alf)) * 0.05
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	413 sumint <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	414 for (i in 1:20) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	415 if (i < 20) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	416 x2 <- -log(1. - i * fint) / alf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	417 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	418 x2 <- 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	419 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	420 y2 <- -(ko + ks) * lai * x2 + fhot * (1. - exp(-alf * x2)) / alf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	421 f2 <- exp(y2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	422 sumint <- sumint + (f2 - f1) * (x2 - x1) / (y2 - y1)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	423 x1 <- x2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	424 y1 <- y2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	425 f1 <- f2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	426 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	427 tsstoo <- f1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	428 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	429 # Bidirectional reflectance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	430 # Single scattering contribution
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	431 rsos <- w * lai * sumint
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	432 # Total canopy contribution
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	433 rso <- rsos + rsod
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	434 # Interaction with the soil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	435 dn <- 1. - rsoil * rdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	436 # rddt: bi-hemispherical reflectance factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	437 rddt <- rdd + tdd * rsoil * tdd / dn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	438 # rsdt: directional-hemispherical reflectance factor for solar incident flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	439 rsdt <- rsd + (tsd + tss) * rsoil * tdd / dn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	440 # rdot: hemispherical-directional reflectance factor in viewing direction
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	441 rdot <- rdo + tdd * rsoil * (tdo + too) / dn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	442 # rsot: bi-directional reflectance factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	443 rsodt <- rsod + ((tss + tsd) * tdo + (tsd + tss * rsoil * rdd) * too) * rsoil / dn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	444 rsost <- rsos + tsstoo * rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	445 rsot <- rsost + rsodt
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	446 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	447 my_list <- list("rdot" = rdot, "rsot" = rsot, "rddt" = rddt, "rsdt" = rsdt)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	448 return(my_list)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	449 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	450
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	451 #" Performs pro4sail2 simulation based on a set of combinations of input parameters
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	452 #" @param leafgreen list. includes relfectance and transmittance for vegetation #1 (e.g. green vegetation)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	453 #" @param leafbrown list. includes relfectance and transmittance for vegetation #2 (e.g. brown vegetation)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	454 #" @param typelidf numeric. Type of leaf inclination distribution function
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	455 #" @param lidfa numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	456 #" if typelidf == 1, controls the average leaf slope
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	457 #" if typelidf == 2, corresponds to average leaf angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	458 #" @param lidfb numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	459 #" if typelidf == 1, unused
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	460 #" if typelidf == 2, controls the distribution"s bimodality
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	461 #" @param lai numeric. Leaf Area Index
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	462 #" @param hot numeric. Hot Spot parameter = ratio of the correlation length of leaf projections in the horizontal plane and the canopy height (doi:10.1016 / j.rse.2006.12.013)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	463 #" @param tts numeric. Sun zeith angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	464 #" @param tto numeric. Observer zeith angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	465 #" @param psi numeric. Azimuth Sun / Observer
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	466 #" @param rsoil numeric. Soil reflectance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	467 #" @param fraction_brown numeric. Fraction of brown leaf area
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	468 #" @param diss numeric. Layer dissociation factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	469 #" @param cv numeric. vertical crown cover percentage
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	470 #" = % ground area covered with crowns as seen from nadir direction
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	471 #" @param zeta numeric. Tree shape factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	472 #" = ratio of crown diameter to crown height
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	473 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	474 #" @return list. rdot, rsot, rddt, rsdt
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	475 #" rdot: hemispherical-directional reflectance factor in viewing direction
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	476 #" rsot: bi-directional reflectance factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	477 #" rsdt: directional-hemispherical reflectance factor for solar incident flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	478 #" rddt: bi-hemispherical reflectance factor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	479 #" alfast: canopy absorptance for direct solar incident flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	480 #" alfadt: canopy absorptance for hemispherical diffuse incident flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	481 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	482
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	483 foursail2 <- function(leafgreen, leafbrown,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	484 typelidf = 2, lidfa = nULL, lidfb = nULL,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	485 lai = nULL, hot = nULL, tts = nULL, tto = nULL, psi = nULL, rsoil = nULL,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	486 fraction_brown = 0.5, diss = 0.5, cv = 1, zeta = 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	487
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	488 # This version does not include non-Lambertian soil properties.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	489 # original codes do, and only need to add the following variables as input
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	490 rddsoil <- rdosoil <- rsdsoil <- rsosoil <- rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	491
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	492 # Geometric quantities
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	493 rd <- pi / 180
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	494
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	495 # Generate leaf angle distribution from average leaf angle (ellipsoidal) or (a, b) parameters
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	496 if (typelidf == 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	497 foliar_distrib <- dladgen(lidfa, lidfb)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	498 lidf <- foliar_distrib$lidf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	499 litab <- foliar_distrib$litab
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	500
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	501 } else if (typelidf == 2) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	502 foliar_distrib <- campbell(lidfa)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	503 lidf <- foliar_distrib$lidf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	504 litab <- foliar_distrib$litab
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	505 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	506
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	507 if (lai < 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	508 message("Please define positive LAI value")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	509 rddt <- rsdt <- rdot <- rsost <- rsot <- rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	510 alfast <- alfadt <- 0 * rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	511 } else if (lai == 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	512 tss <- too <- tsstoo <- tdd <- 1.0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	513 rdd <- rsd <- tsd <- rdo <- tdo <- 0.0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	514 rso <- rsos <- rsod <- rsodt <- 0.0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	515 rddt <- rsdt <- rdot <- rsost <- rsot <- rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	516 alfast <- alfadt <- 0 * rsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	517 } else if (lai > 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	518 cts <- cos(rd * tts)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	519 cto <- cos(rd * tto)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	520 ctscto <- cts * cto
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	521 tants <- tan(rd * tts)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	522 tanto <- tan(rd * tto)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	523 cospsi <- cos(rd * psi)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	524 dso <- sqrt(tants * tants + tanto * tanto - 2.0 * tants * tanto * cospsi)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	525
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	526 # Clumping effects
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	527 cs <- co <- 1.0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	528 if (cv <= 1.0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	529 cs <- 1.0 - (1.0 - cv)^(1.0 / cts)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	530 co <- 1.0 - (1.0 - cv)^(1.0 / cto)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	531 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	532 overlap <- 0.0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	533 if (zeta > 0.0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	534 overlap <- min(cs * (1.0 - co), co * (1.0 - cs)) * exp(-dso / zeta)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	535 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	536 fcd <- cs * co + overlap
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	537 fcs <- (1.0 - cs) * co - overlap
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	538 fod <- cs * (1.0 - co) - overlap
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	539 fos <- (1.0 - cs) * (1.0 - co) + overlap
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	540 fcdc <- 1.0 - (1.0 - fcd)^(0.5 / cts + 0.5 / cto)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	541
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	542 # Part depending on diss, fraction_brown, and leaf optical properties
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	543 # First save the input fraction_brown as the old fraction_brown, as the following change is only artificial
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	544 # Better define an fraction_brown that is actually used: fb, so that the input is not modified!
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	545
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	546 fb <- fraction_brown
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	547 # if only green leaves
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	548 if (fraction_brown == 0.0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	549 fb <- 0.5
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	550 leafbrown$Reflectance <- leafgreen$Reflectance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	551 leafbrown$Transmittance <- leafgreen$Transmittance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	552 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	553 if (fraction_brown == 1.0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	554 fb <- 0.5
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	555 leafgreen$Reflectance <- leafbrown$Reflectance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	556 leafgreen$Transmittance <- leafbrown$Transmittance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	557 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	558 s <- (1.0 - diss) * fb * (1.0 - fb)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	559 # rho1 && tau1 : green foliage
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	560 # rho2 && tau2 : brown foliage (bottom layer)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	561 rho1 <- ((1 - fb - s) * leafgreen$Reflectance + s * leafbrown$Reflectance) / (1 - fb)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	562 tau1 <- ((1 - fb - s) * leafgreen$Transmittance + s * leafbrown$Transmittance) / (1 - fb)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	563 rho2 <- (s * leafgreen$Reflectance + (fb - s) * leafbrown$Reflectance) / fb
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	564 tau2 <- (s * leafgreen$Transmittance + (fb - s) * leafbrown$Transmittance) / fb
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	565
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	566 # angular distance, compensation of shadow length
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	567 # Calculate geometric factors associated with extinction and scattering
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	568 # Initialise sums
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	569 ks <- ko <- bf <- sob <- sof <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	570
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	571 # Weighted sums over LIDF
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	572
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	573 for (i in 1:seq_along(litab)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	574 ttl <- litab[i]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	575 ctl <- cos(rd * ttl)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	576 # SAIL volscatt function gives interception coefficients
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	577 # and two portions of the volume scattering phase function to be
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	578 # multiplied by rho and tau, respectively
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	579 resvolscatt <- volscatt(tts, tto, psi, ttl)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	580 chi_s <- resvolscatt$chi_s
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	581 chi_o <- resvolscatt$chi_o
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	582 frho <- resvolscatt$frho
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	583 ftau <- resvolscatt$ftau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	584 # Extinction coefficients
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	585 ksli <- chi_s / cts
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	586 koli <- chi_o / cto
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	587 # Area scattering coefficient fractions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	588 sobli <- frho * pi / ctscto
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	589 sofli <- ftau * pi / ctscto
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	590 bfli <- ctl * ctl
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	591 ks <- ks + ksli * lidf[i]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	592 ko <- ko + koli * lidf[i]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	593 bf <- bf + bfli * lidf[i]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	594 sob <- sob + sobli * lidf[i]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	595 sof <- sof + sofli * lidf[i]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	596 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	597 # Geometric factors to be used later in combination with rho and tau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	598 sdb <- 0.5 * (ks + bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	599 sdf <- 0.5 * (ks - bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	600 dob <- 0.5 * (ko + bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	601 dof <- 0.5 * (ko - bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	602 ddb <- 0.5 * (1. + bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	603 ddf <- 0.5 * (1. - bf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	604
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	605 # LAIs in two layers
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	606 lai1 <- (1 - fb) * lai
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	607 lai2 <- fb * lai
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	608
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	609 tss <- exp(-ks * lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	610 ck <- exp(-ks * lai1)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	611 alf <- 1e6
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	612 if (hot > 0.0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	613 alf <- (dso / hot) * 2.0 / (ks + ko)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	614 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	615 if (alf > 200.0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	616 alf <- 200.0 # inserted H. Bach 1 / 3 / 04
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	617 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	618 if (alf == 0.0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	619 # The pure hotspot
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	620 tsstoo <- tss
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	621 s1 <- (1 - ck) / (ks * lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	622 s2 <- (ck - tss) / (ks * lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	623 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	624 # Outside the hotspot
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	625 fhot <- lai * sqrt(ko * ks)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	626 # Integrate 2 layers by exponential simpson method in 20 steps
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	627 # the steps are arranged according to equal partitioning
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	628 # of the derivative of the joint probability function
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	629 x1 <- y1 <- 0.0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	630 f1 <- 1.0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	631 ca <- exp(alf * (fb - 1.0))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	632 fint <- (1.0 - ca) * .05
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	633 s1 <- 0.0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	634 for (istep in 1:20) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	635 if (istep < 20) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	636 x2 <- -log(1. - istep * fint) / alf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	637 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	638 x2 <- 1. - fb
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	639 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	640 y2 <- -(ko + ks) * lai * x2 + fhot * (1.0 - exp(-alf * x2)) / alf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	641 f2 <- exp(y2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	642 s1 <- s1 + (f2 - f1) * (x2 - x1) / (y2 - y1)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	643 x1 <- x2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	644 y1 <- y2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	645 f1 <- f2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	646 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	647 fint <- (ca - exp(-alf)) * .05
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	648 s2 <- 0.0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	649 for (istep in 1:20) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	650 if (istep < 20) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	651 x2 <- -log(ca - istep * fint) / alf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	652 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	653 x2 <- 1.0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	654 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	655 y2 <- -(ko + ks) * lai * x2 + fhot * (1.0 - exp(-alf * x2)) / alf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	656 f2 <- exp(y2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	657 s2 <- s2 + (f2 - f1) * (x2 - x1) / (y2 - y1)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	658 x1 <- x2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	659 y1 <- y2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	660 f1 <- f2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	661 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	662 tsstoo <- f1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	663 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	664
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	665 # Calculate reflectances and transmittances
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	666 # Bottom layer
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	667 tss <- exp(-ks * lai2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	668 too <- exp(-ko * lai2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	669 sb <- sdb * rho2 + sdf * tau2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	670 sf <- sdf * rho2 + sdb * tau2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	671
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	672 vb <- dob * rho2 + dof * tau2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	673 vf <- dof * rho2 + dob * tau2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	674
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	675 w2 <- sob * rho2 + sof * tau2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	676
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	677 sigb <- ddb * rho2 + ddf * tau2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	678 sigf <- ddf * rho2 + ddb * tau2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	679 att <- 1.0 - sigf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	680 m2 <- (att + sigb) * (att - sigb)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	681 m2[m2 < 0] <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	682 m <- sqrt(m2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	683 which_ncs <- which(m > 0.01)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	684 which_cs <- which(m <= 0.01)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	685
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	686 tdd <- rdd <- tsd <- rsd <- tdo <- rdo <- 0 * m
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	687 rsod <- 0 * m
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	688 if (length(which_ncs) > 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	689 resncs <- nonconservativescattering(m[which_ncs], lai2, att[which_ncs], sigb[which_ncs],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	690 ks, ko, sf[which_ncs], sb[which_ncs], vf[which_ncs], vb[which_ncs], tss, too)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	691 tdd[which_ncs] <- resncs$tdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	692 rdd[which_ncs] <- resncs$rdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	693 tsd[which_ncs] <- resncs$tsd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	694 rsd[which_ncs] <- resncs$rsd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	695 tdo[which_ncs] <- resncs$tdo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	696 rdo[which_ncs] <- resncs$rdo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	697 rsod[which_ncs] <- resncs$rsod
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	698 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	699 if (length(which_cs) > 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	700 rescs <- conservativescattering(m[which_cs], lai2, att[which_cs], sigb[which_cs],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	701 ks, ko, sf[which_cs], sb[which_cs], vf[which_cs], vb[which_cs], tss, too)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	702 tdd[which_cs] <- rescs$tdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	703 rdd[which_cs] <- rescs$rdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	704 tsd[which_cs] <- rescs$tsd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	705 rsd[which_cs] <- rescs$rsd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	706 tdo[which_cs] <- rescs$tdo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	707 rdo[which_cs] <- rescs$rdo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	708 rsod[which_cs] <- rescs$rsod
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	709 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	710
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	711 # Set background properties equal to those of the bottom layer on a black soil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	712 rddb <- rdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	713 rsdb <- rsd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	714 rdob <- rdo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	715 rsodb <- rsod
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	716 tddb <- tdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	717 tsdb <- tsd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	718 tdob <- tdo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	719 toob <- too
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	720 tssb <- tss
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	721 # Top layer
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	722 tss <- exp(-ks * lai1)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	723 too <- exp(-ko * lai1)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	724
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	725 sb <- sdb * rho1 + sdf * tau1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	726 sf <- sdf * rho1 + sdb * tau1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	727
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	728 vb <- dob * rho1 + dof * tau1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	729 vf <- dof * rho1 + dob * tau1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	730
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	731 w1 <- sob * rho1 + sof * tau1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	732
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	733 sigb <- ddb * rho1 + ddf * tau1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	734 sigf <- ddf * rho1 + ddb * tau1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	735 att <- 1.0 - sigf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	736
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	737 m2 <- (att + sigb) * (att - sigb)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	738 m2[m2 < 0] <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	739 m <- sqrt(m2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	740 which_ncs <- which(m > 0.01)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	741 which_cs <- which(m <= 0.01)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	742
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	743 tdd <- rdd <- tsd <- rsd <- tdo <- rdo <- 0 * m
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	744 rsod <- 0 * m
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	745 if (length(which_ncs) > 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	746 resncs <- nonconservativescattering(m[which_ncs], lai1, att[which_ncs], sigb[which_ncs],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	747 ks, ko, sf[which_ncs], sb[which_ncs], vf[which_ncs], vb[which_ncs], tss, too)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	748 tdd[which_ncs] <- resncs$tdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	749 rdd[which_ncs] <- resncs$rdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	750 tsd[which_ncs] <- resncs$tsd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	751 rsd[which_ncs] <- resncs$rsd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	752 tdo[which_ncs] <- resncs$tdo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	753 rdo[which_ncs] <- resncs$rdo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	754 rsod[which_ncs] <- resncs$rsod
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	755 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	756 if (length(which_cs) > 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	757 rescs <- conservativescattering(m[which_cs], lai1, att[which_cs], sigb[which_cs],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	758 ks, ko, sf[which_cs], sb[which_cs], vf[which_cs], vb[which_cs], tss, too)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	759 tdd[which_cs] <- rescs$tdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	760 rdd[which_cs] <- rescs$rdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	761 tsd[which_cs] <- rescs$tsd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	762 rsd[which_cs] <- rescs$rsd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	763 tdo[which_cs] <- rescs$tdo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	764 rdo[which_cs] <- rescs$rdo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	765 rsod[which_cs] <- rescs$rsod
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	766 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	767
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	768 # combine with bottom layer reflectances and transmittances (adding method)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	769 rn <- 1.0 - rdd * rddb
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	770 tup <- (tss * rsdb + tsd * rddb) / rn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	771 tdn <- (tsd + tss * rsdb * rdd) / rn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	772 rsdt <- rsd + tup * tdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	773 rdot <- rdo + tdd * (rddb * tdo + rdob * too) / rn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	774 rsodt <- rsod + (tss * rsodb + tdn * rdob) * too + tup * tdo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	775
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	776 rsost <- (w1 * s1 + w2 * s2) * lai
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	777
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	778 rsot <- rsost + rsodt
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	779
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	780 # Diffuse reflectances at the top and the bottom are now different
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	781 rddt_t <- rdd + tdd * rddb * tdd / rn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	782 rddt_b <- rddb + tddb * rdd * tddb / rn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	783
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	784 # Transmittances of the combined canopy layers
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	785 tsst <- tss * tssb
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	786 toot <- too * toob
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	787 tsdt <- tss * tsdb + tdn * tddb
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	788 tdot <- tdob * too + tddb * (tdo + rdd * rdob * too) / rn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	789 tddt <- tdd * tddb / rn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	790
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	791 # Apply clumping effects to vegetation layer
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	792 rddcb <- cv * rddt_b
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	793 rddct <- cv * rddt_t
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	794 tddc <- 1 - cv + cv * tddt
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	795 rsdc <- cs * rsdt
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	796 tsdc <- cs * tsdt
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	797 rdoc <- co * rdot
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	798 tdoc <- co * tdot
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	799 tssc <- 1 - cs + cs * tsst
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	800 tooc <- 1 - co + co * toot
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	801
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	802 # new weight function fcdc for crown contribution (W. Verhoef, 22-05-08)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	803 rsoc <- fcdc * rsot
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	804 tssooc <- fcd * tsstoo + fcs * toot + fod * tsst + fos
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	805 # Canopy absorptance for black background (W. Verhoef, 02-03-04)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	806 alfas <- 1. - tssc - tsdc - rsdc
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	807 alfad <- 1. - tddc - rddct
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	808 # Add the soil background
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	809 rn <- 1 - rddcb * rddsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	810 tup <- (tssc * rsdsoil + tsdc * rddsoil) / rn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	811 tdn <- (tsdc + tssc * rsdsoil * rddcb) / rn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	812
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	813 rddt <- rddct + tddc * rddsoil * tddc / rn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	814 rsdt <- rsdc + tup * tddc
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	815 rdot <- rdoc + tddc * (rddsoil * tdoc + rdosoil * tooc) / rn
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	816 rsot <- rsoc + tssooc * rsosoil + tdn * rdosoil * tooc + tup * tdoc
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	817
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	818 # Effect of soil background on canopy absorptances (W. Verhoef, 02-03-04)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	819 alfast <- alfas + tup * alfad
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	820 alfadt <- alfad * (1. + tddc * rddsoil / rn)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	821 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	822 my_list <- list("rdot" = rdot, "rsot" = rsot, "rddt" = rddt, "rsdt" = rsdt,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	823 "alfast" = alfast, "alfadt" = alfadt)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	824 return(my_list)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	825 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	826
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	827
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	828
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	829 #" computes non conservative scattering conditions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	830 #" @param m numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	831 #" @param lai numeric. Leaf Area Index
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	832 #" @param att numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	833 #" @param sigb numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	834 #" @param ks numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	835 #" @param ko numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	836 #" @param sf numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	837 #" @param sb numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	838 #" @param vf numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	839 #" @param vb numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	840 #" @param tss numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	841 #" @param too numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	842 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	843 #" @return list. tdd, rdd, tsd, rsd, tdo, rdo, rsod
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	844 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	845 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	846 nonconservativescattering <- function(m, lai, att, sigb, ks, ko, sf, sb, vf, vb, tss, too) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	847
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	848 e1 <- exp(-m * lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	849 e2 <- e1 * e1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	850 rinf <- (att - m) / sigb
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	851 rinf2 <- rinf * rinf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	852 re <- rinf * e1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	853 denom <- 1. - rinf2 * e2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	854
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	855 j1ks <- jfunc1(ks, m, lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	856 j2ks <- jfunc2(ks, m, lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	857 j1ko <- jfunc1(ko, m, lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	858 j2ko <- jfunc2(ko, m, lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	859
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	860 ps <- (sf + sb * rinf) * j1ks
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	861 qs <- (sf * rinf + sb) * j2ks
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	862 pv <- (vf + vb * rinf) * j1ko
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	863 qv <- (vf * rinf + vb) * j2ko
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	864
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	865 tdd <- (1. - rinf2) * e1 / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	866 rdd <- rinf * (1. - e2) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	867 tsd <- (ps - re * qs) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	868 rsd <- (qs - re * ps) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	869 tdo <- (pv - re * qv) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	870 rdo <- (qv - re * pv) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	871
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	872 z <- jfunc2(ks, ko, lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	873 g1 <- (z - j1ks * too) / (ko + m)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	874 g2 <- (z - j1ko * tss) / (ks + m)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	875
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	876 tv1 <- (vf * rinf + vb) * g1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	877 tv2 <- (vf + vb * rinf) * g2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	878
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	879 t1 <- tv1 * (sf + sb * rinf)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	880 t2 <- tv2 * (sf * rinf + sb)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	881 t3 <- (rdo * qs + tdo * ps) * rinf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	882
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	883 # Multiple scattering contribution to bidirectional canopy reflectance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	884 rsod <- (t1 + t2 - t3) / (1. - rinf2)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	885 my_list <- list("tdd" = tdd, "rdd" = rdd, "tsd" = tsd,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	886 "rsd" = rsd, "tdo" = tdo, "rdo" = rdo,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	887 "rsod" = rsod)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	888 return(my_list)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	889 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	890
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	891 #" computes conservative scattering conditions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	892 #" @param m numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	893 #" @param lai numeric. Leaf Area Index
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	894 #" @param att numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	895 #" @param sigb numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	896 #" @param ks numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	897 #" @param ko numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	898 #" @param sf numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	899 #" @param sb numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	900 #" @param vf numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	901 #" @param vb numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	902 #" @param tss numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	903 #" @param too numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	904 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	905 #" @return list. tdd, rdd, tsd, rsd, tdo, rdo, rsod
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	906 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	907 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	908 conservativescattering <- function(m, lai, att, sigb, ks, ko, sf, sb, vf, vb, tss, too) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	909
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	910 # near or complete conservative scattering
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	911 j4 <- jfunc4(m, lai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	912 amsig <- att - sigb
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	913 apsig <- att + sigb
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	914 rtp <- (1 - amsig * j4) / (1 + amsig * j4)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	915 rtm <- (-1 + apsig * j4) / (1 + apsig * j4)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	916 rdd <- 0.5 * (rtp + rtm)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	917 tdd <- 0.5 * (rtp - rtm)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	918
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	919 dns <- ks * ks - m * m
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	920 dno <- ko * ko - m * m
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	921 cks <- (sb * (ks - att) - sf * sigb) / dns
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	922 cko <- (vb * (ko - att) - vf * sigb) / dno
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	923 dks <- (-sf * (ks + att) - sb * sigb) / dns
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	924 dko <- (-vf * (ko + att) - vb * sigb) / dno
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	925 ho <- (sf * cko + sb * dko) / (ko + ks)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	926
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	927 rsd <- cks * (1 - tss * tdd) - dks * rdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	928 rdo <- cko * (1 - too * tdd) - dko * rdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	929 tsd <- dks * (tss - tdd) - cks * tss * rdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	930 tdo <- dko * (too - tdd) - cko * too * rdd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	931 # Multiple scattering contribution to bidirectional canopy reflectance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	932 rsod <- ho * (1 - tss * too) - cko * tsd * too - dko * rsd
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	933
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	934 my_list <- list("tdd" = tdd, "rdd" = rdd, "tsd" = tsd,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	935 "rsd" = rsd, "tdo" = tdo, "rdo" = rdo,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	936 "rsod" = rsod)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	937 return(my_list)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	938 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	939
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	940
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	941
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	942
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	943
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	944
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	945 #" computes the leaf angle distribution function value (freq)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	946 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	947 #" Ellipsoidal distribution function characterised by the average leaf
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	948 #" inclination angle in degree (ala)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	949 #" Campbell 1986
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	950 #" @param ala average leaf angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	951 #" @return foliar_distrib list. lidf and litab
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	952 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	953 campbell <- function(ala) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	954
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	955 tx1 <- c(10., 20., 30., 40., 50., 60., 70., 80., 82., 84., 86., 88., 90.)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	956 tx2 <- c(0., 10., 20., 30., 40., 50., 60., 70., 80., 82., 84., 86., 88.)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	957 litab <- (tx2 + tx1) / 2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	958 n <- length(litab)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	959 tl1 <- tx1 * (pi / 180)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	960 tl2 <- tx2 * (pi / 180)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	961 excent <- exp(-1.6184e-5 * ala*3 + 2.1145e-3 ala*2 - 1.2390e-1 ala + 3.2491)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	962 sum0 <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	963
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	964 freq <- c()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	965 for (i in 1:n) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	966 x1 <- excent / (sqrt(1. + excent*2. tan(tl1[i])**2))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	967 x2 <- excent / (sqrt(1. + excent*2. tan(tl2[i])**2))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	968 if (excent == 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	969 freq[i] <- abs(cos(tl1[i]) - cos(tl2[i]))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	970 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	971 alpha <- excent / sqrt(abs(1 - excent**2))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	972 alpha2 <- alpha**2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	973 x12 <- x1**2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	974 x22 <- x2**2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	975 alpx1 <- 0 * alpha2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	976 alpx2 <- 0 * alpha2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	977 almx1 <- 0 * alpha2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	978 almx2 <- 0 * alpha2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	979 if (excent > 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	980 alpx1 <- sqrt(alpha2[excent > 1] + x12[excent > 1])
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	981 alpx2[excent > 1] <- sqrt(alpha2[excent > 1] + x22[excent > 1])
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	982 dum <- x1 * alpx1 + alpha2 * log(x1 + alpx1)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	983 freq[i] <- abs(dum - (x2 * alpx2 + alpha2 * log(x2 + alpx2)))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	984 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	985 almx1 <- sqrt(alpha2 - x12)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	986 almx2 <- sqrt(alpha2 - x22)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	987 dum <- x1 * almx1 + alpha2 * asin(x1 / alpha)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	988 freq[i] <- abs(dum - (x2 * almx2 + alpha2 * asin(x2 / alpha)))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	989 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	990 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	991 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	992 sum0 <- sum(freq)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	993 freq0 <- freq / sum0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	994 foliar_distrib <- list("lidf" = freq0, "litab" = litab)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	995 return(foliar_distrib)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	996 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	997
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	998 #" computes the leaf angle distribution function value (freq)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	999 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1000 #" Using the original bimodal distribution function initially proposed in SAIL
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1001 #" references
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1002 #" ----------
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1003 #" (Verhoef1998) Verhoef, Wout. Theory of radiative transfer models applied
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1004 #" in optical remote sensing of vegetation canopies.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1005 #" nationaal Lucht en Ruimtevaartlaboratorium, 1998.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1006 #" http: / / library.wur.nl / WebQuery / clc / 945481.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1007 #" @param a controls the average leaf slope
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1008 #" @param b controls the distribution"s bimodality
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1009 #" LIDF type a b
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1010 #" Planophile 1 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1011 #" Erectophile -1 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1012 #" Plagiophile 0 -1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1013 #" Extremophile 0 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1014 #" Spherical -0.35 -0.15
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1015 #" Uniform 0 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1016 #" requirement: \|\|lidfa\|\| + \|\|lidfb\|\| < 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1017 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1018 #" @return foliar_distrib list. lidf and litab
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1019 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1020 dladgen <- function(a, b) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1021 litab <- c(5., 15., 25., 35., 45., 55., 65., 75., 81., 83., 85., 87., 89.)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1022 freq <- c()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1023 for (i1 in 1:8) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1024 t <- i1 * 10
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1025 freq[i1] <- dcum(a, b, t)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1026 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1027 for (i2 in 9:12) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1028 t <- 80. + (i2 - 8) * 2.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1029 freq[i2] <- dcum(a, b, t)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1030 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1031 freq[13] <- 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1032 for (i in 13:2) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1033 freq[i] <- freq[i] - freq[i - 1]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1034 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1035 foliar_distrib <- list("lidf" = freq, "litab" = litab)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1036 return(foliar_distrib)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1037 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1038
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1039 #" dcum function
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1040 #" @param a numeric. controls the average leaf slope
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1041 #" @param b numeric. controls the distribution"s bimodality
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1042 #" @param t numeric. angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1043 #" @return f
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1044 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1045 dcum <- function(a, b, t) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1046 rd <- pi / 180
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1047 if (a >= 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1048 f <- 1 - cos(rd * t)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1049 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1050 eps <- 1e-8
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1051 delx <- 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1052 x <- 2 * rd * t
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1053 p <- x
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1054 while (delx >= eps) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1055 y <- a * sin(x) + .5 * b * sin(2. * x)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1056 dx <- .5 * (y - x + p)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1057 x <- x + dx
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1058 delx <- abs(dx)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1059 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1060 f <- (2. * y + p) / pi
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1061 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1062 return(f)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1063 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1064
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1065 #" J1 function with avoidance of singularity problem
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1066 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1067 #" @param k numeric. Extinction coefficient for direct (solar or observer) flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1068 #" @param l numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1069 #" @param t numeric. Leaf Area Index
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1070 #" @return jout numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1071 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1072 jfunc1 <- function(k, l, t) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1073 # J1 function with avoidance of singularity problem
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1074 del <- (k - l) * t
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1075 jout <- 0 * l
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1076 jout[which(abs(del) > 1e-3)] <- (exp(-l[which(abs(del) > 1e-3)] * t) - exp(-k * t)) / (k - l[which(abs(del) > 1e-3)])
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1077 jout[which(abs(del) <= 1e-3)] <- 0.5 * t * (exp(-k * t) + exp(-l[which(abs(del) <= 1e-3)] * t)) * (1 - del[which(abs(del) <= 1e-3)] * del[which(abs(del) <= 1e-3)] / 12)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1078 return(jout)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1079 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1080
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1081 #" J2 function with avoidance of singularity problem
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1082 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1083 #" @param k numeric. Extinction coefficient for direct (solar or observer) flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1084 #" @param l numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1085 #" @param t numeric. Leaf Area Index
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1086 #" @return jout numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1087 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1088 jfunc2 <- function(k, l, t) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1089 # J2 function
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1090 jout <- (1. - exp(-(k + l) * t)) / (k + l)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1091 return(jout)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1092 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1093
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1094 #" J3 function with avoidance of singularity problem
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1095 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1096 #" @param k numeric. Extinction coefficient for direct (solar or observer) flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1097 #" @param l numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1098 #" @param t numeric. Leaf Area Index
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1099 #" @return jout numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1100 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1101 jfunc3 <- function(k, l, t) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1102 out <- (1. - exp(-(k + l) * t)) / (k + l)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1103 return(out)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1104 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1105
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1106
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1107 #" j4 function for treating (near) conservative scattering
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1108 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1109 #" @param m numeric. Extinction coefficient for direct (solar or observer) flux
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1110 #" @param t numeric. Leaf Area Index
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1111 #" @return jout numeric.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1112 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1113 jfunc4 <- function(m, t) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1114
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1115 del <- m * t
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1116 out <- 0 * del
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1117 out[del > 1e-3] <- (1 - exp(-del)) / (m * (1 + exp(-del)))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1118 out[del <= 1e-3] <- 0.5 * t * (1. - del * del / 12.)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1119 return(out)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1120 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1121
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1122
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1123 #" compute volume scattering functions and interception coefficients
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1124 #" for given solar zenith, viewing zenith, azimuth and leaf inclination angle.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1125 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1126 #" @param tts numeric. solar zenith
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1127 #" @param tto numeric. viewing zenith
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1128 #" @param psi numeric. azimuth
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1129 #" @param ttl numeric. leaf inclination angle
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1130 #" @return res list. includes chi_s, chi_o, frho, ftau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1131 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1132 volscatt <- function(tts, tto, psi, ttl) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1133 #********************************************************************************
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1134 #* chi_s = interception functions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1135 #* chi_o = interception functions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1136 #* frho = function to be multiplied by leaf reflectance rho
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1137 #* ftau = functions to be multiplied by leaf transmittance tau
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1138 #********************************************************************************
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1139 # Wout Verhoef, april 2001, for CROMA
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1140
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1141 rd <- pi / 180
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1142 costs <- cos(rd * tts)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1143 costo <- cos(rd * tto)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1144 sints <- sin(rd * tts)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1145 sinto <- sin(rd * tto)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1146 cospsi <- cos(rd * psi)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1147 psir <- rd * psi
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1148 costl <- cos(rd * ttl)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1149 sintl <- sin(rd * ttl)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1150 cs <- costl * costs
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1151 co <- costl * costo
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1152 ss <- sintl * sints
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1153 so <- sintl * sinto
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1154
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1155 #c ..............................................................................
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1156 #c betas -bts- and betao -bto- computation
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1157 #c Transition angles (beta) for solar (betas) and view (betao) directions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1158 #c if thetav + thetal > pi / 2, bottom side of the leaves is observed for leaf azimut
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1159 #c interval betao + phi<leaf azimut<2pi-betao + phi.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1160 #c if thetav + thetal<pi / 2, top side of the leaves is always observed, betao=pi
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1161 #c same consideration for solar direction to compute betas
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1162 #c ..............................................................................
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1163
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1164 cosbts <- 5
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1165 if (abs(ss) > 1e-6) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1166 cosbts <- -cs / ss
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1167 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1168 cosbto <- 5
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1169 if (abs(so) > 1e-6) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1170 cosbto <- -co / so
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1171 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1172
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1173 if (abs(cosbts) < 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1174 bts <- acos(cosbts)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1175 ds <- ss
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1176 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1177 bts <- pi
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1178 ds <- cs
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1179 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1180 chi_s <- 2. / pi * ((bts - pi * .5) * cs + sin(bts) * ss)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1181 if (abs(cosbto) < 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1182 bto <- acos(cosbto)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1183 doo <- so
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1184 } else if (tto < 90) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1185 bto <- pi
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1186 doo <- co
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1187 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1188 bto <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1189 doo <- -co
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1190 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1191 chi_o <- 2. / pi * ((bto - pi * .5) * co + sin(bto) * so)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1192
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1193 #c ..............................................................................
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1194 #c computation of auxiliary azimut angles bt1, bt2, bt3 used
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1195 #c for the computation of the bidirectional scattering coefficient w
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1196 #c .............................................................................
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1197
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1198 btran1 <- abs(bts - bto)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1199 btran2 <- pi - abs(bts + bto - pi)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1200
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1201 if (psir <= btran1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1202 bt1 <- psir
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1203 bt2 <- btran1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1204 bt3 <- btran2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1205 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1206 bt1 <- btran1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1207 if (psir <= btran2) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1208 bt2 <- psir
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1209 bt3 <- btran2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1210 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1211 bt2 <- btran2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1212 bt3 <- psir
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1213 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1214 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1215 t1 <- 2. * cs * co + ss * so * cospsi
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1216 t2 <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1217 if (bt2 > 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1218 t2 <- sin(bt2) * (2. * ds * doo + ss * so * cos(bt1) * cos(bt3))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1219 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1220
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1221 denom <- 2. * pi * pi
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1222 frho <- ((pi - bt2) * t1 + t2) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1223 ftau <- (-bt2 * t1 + t2) / denom
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1224
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1225 if (frho < 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1226 frho <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1227 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1228 if (ftau < 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1229 ftau <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1230 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1231 res <- list("chi_s" = chi_s, "chi_o" = chi_o, "frho" = frho, "ftau" = ftau)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1232 return(res)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7 ecology parents: diff changeset	1233 }

Mercurial > repos > ecology > srs_preprocess_s2

annotate prosail-master/R/Lib_PROSAIL.R @ 0:33a1e15f7252 draft default tip