2.1. Bi-hemispheric Reflectance Model
In the 1D turbid medium radiative transfer model SAIL [
3], an adding method [
4] is applied to calculate the bi-hemispherical reflectance of the combination soil and canopy, which is given by the simple expression below [
5]:
where
is the reflectance of the soil background and the right term describes the multiple reflections between canopy layer and soil background. To clearly express the downward and upward flows of diffuse radiation through the canopy required to account for the soil’s influence, the hemispheric canopy transmittance
appears twice in Equation (1). For a small LAI, this transmittance approaches unity, so it includes the direct transmission of light without any contact with leaves. The adding method is a simplified implementation of what has been termed by other investigators a combination of the so-called “black soil problem” and “S-problem” [
6,
7] in their explanations of numerical 3D radiative transfer as a particle transport problem, similar to approaches applied in the numerical modelling of neutron transport in nuclear reactor physics. In the much simpler analytical two-stream radiative transfer theory applied in SAIL, the bi-hemispheric reflectance and transmittance of the isolated canopy layer (the basic solutions of the black soil problem),
and
, are given by well-known expressions:
where
L is the leaf area index (LAI).
The quantities
m and
are known as the diffusion exponent and the so-called infinite reflectance, which is the BHR of a hypothetical canopy with an infinite LAI. Both quantities are functions of single leaf reflectance,
ρ, single leaf transmittance,
τ, and the leaf inclination distribution function, LIDF, which is symbolized as
f (
θl), where
θl is the zenith angle of the leaf’s normal. The leaf azimuth distribution is assumed to be uniform. Together, these quantities determine the diffuse backscattering coefficient
σ and the net attenuation coefficient
a as follows [
3,
7,
8]:
where
θl is in radians and
.
Table 1 shows some values of
γ for a few common LIDF types. They range from 0 to 1, but since in Equation (3) they are multiplied by half the difference of leaf reflectance and leaf transmittance, the effect of
γ on these quantities will never be large, since leaf reflectance and transmittance usually do not differ by more than 0.05. Note in column 2 of the table that
δ is the Dirac delta function.
The diffusion exponent
m is the eigenvalue of the coupled system of two-stream differential equations [
5,
7] and is given as follows:
where
and
denotes the single leaf absorptance. The infinite reflectance,
, finally is given by the following equation:
Figure 1 shows an example of the spectra of
and
m (unitless) as obtained from the leaf optical properties model Fluspect-B [
9], which, regarding leaf reflectance and transmittance, is very similar to PROSPECT-5 [
10], except that it still includes brown pigments, as in older versions of PROSPECT [
11]. In this typical case of a green leaf, the biochemical inputs are the ones listed in
Table 2.
The substitution of Equation (2) in Equation (1) gives an analytical expression for the canopy BHR in which the soil background, with reflectance
, is also incorporated. This yields the following quasi-linear combination of
and
:
where
.
Further elaboration of Equation (6) provides the BHR of the combination of the soil and canopy with a slightly simpler equation:
The quantity
. expresses the spectral soil/vegetation contrast. From Equation (7), it can be concluded that the sensitivity of
rdd tohe LAI will be most favourable for large values of
rs’, i.e., when there is a large contrast between
and
. Spectral regions in the red and the near-infrared (NIR) parts of the spectrum both allow a large soil/vegetation contrast, and therefore both are very sensitive to the LAI, since in the red, the
for green vegetation is very small (<0.05) and in the NIR it is high (>0.60,
Figure 1) when compared to the moderate reflectance of the soil in these spectral regions; however, the NIR has the advantage of featuring a much smaller value of the diffusion exponent
m, which means that saturation at high LAIs occurs much later than in the red band. It turns out that, in general, the reflectance in the red band is particularly sensitive to low LAIs, whereas the reflectance in the NIR band is relatively more sensitive to the LAI when it is high. Also, should the soil’s reflectance in either the red or the NIR band be close to the corresponding
, then the soil/vegetation contrast in the other band will be extra high, so both spectral regions will always complement each other. These cases may occur for either very dark or very bright soil backgrounds.
2.2. Red–NIR Feature Space Plots
Figure 2 shows how various combinations of soil brightness and canopy LAI appear in a red–NIR feature space plot. In this paper, the soil’s reflectance in the red is adopted as a measure of soil brightness. For reflectance values obtained from various crops observed in the field, the resulting quasi-triangular shape is also known under the name of “tasselled cap” [
12]. In the publication of Kauth and Thomas [
12], the tassels mark the various paths in the feature space that are followed by cereal crops during ripening. In
Figure 2, the tassels are actually missing in this simulated case of exclusively green vegetation. The plot also confirms why the NDVI is a fairly good indicator of the LAI, since lines of constant NDVI go through the origin, and the brown lines of constant LAI in the diagram show roughly the same behaviour, although for the low LAIs located just above the bare soil line this is clearly no longer the case [
13]. In
Figure 2, all green lines of constant soil brightness appear to join together in a single vertical line.
This means that in this region of the red–NIR feature space, only a very specific value of the reflectance (
) in the red band would allow possible solutions for model inversion. By allowing a much larger range of soil brightness values, the model’s “repertoire” can be extended, and it appears that the triangle then also fills the upper parts of the diagram, as shown in
Figure 3; however, the fact remains that solutions of model inversion are only possible for red reflectance values that exceed a certain minimum value, namely the canopy
in the red.
From Equation (7), we may obtain
, and therefore the LAI can in principle be solved by the following:
so that the LAI can be estimated analytically from the simple equation
.
This equation makes it clear that for the estimation of the LAI, knowledge about the soil’s reflectance is just as important as the measured reflectance of the soil and canopy combination and the optical properties of the vegetation, as expressed by
and
m; however, since the soil’s reflectance, in particular its brightness, is usually unknown, one still has to find a way to estimate
before one can estimate the LAI. Therefore, we will now try to exploit the relationship between the values of soil reflectance
at two wavelengths. This relationship is mostly very simple, since the ratio of the soil’s reflectance at two wavelengths for a given soil type is usually constant [
13,
14,
15]. One can derive
.
Since
, we find the following equation:
This indicates that, theoretically, with a known or assumed leaf area index L and given values of m, r, and , it is possible to derive the soil’s reflectance, provided of course that the LAI is not too high.
We may assume that for a given soil type, its reflectance
rs in the near-infrared band (
N) is a constant factor
S times its reflectance in the red band (
R). We express this by
Ns = SRs. Extending this notation for red and near-infrared reflectance (
R and
N) to the other quantities gives the following:
These expressions indicate that with an assumed leaf area index
L and given values of
m,
r, and
at both wavelengths, it should be possible to estimate the soil’s reflectance at these wavelengths, identified as
Rs and
Ns. In particular, the ratio
Ns/Rs can then be established, and if this ratio happens to be equal to
S, we can conclude that obviously the correct LAI was guessed. When
Rs and
Ns are plotted in a diagram as a series of points as a function of the assumed LAI, we obtain a graph like that shown in
Figure 4. Here, the red line is the locus of points of varying LAI that intersects the point of measured reflectance (the grey dot).
It is clear from this diagram that in this situation the matching LAI can be found from the intersection of one red line segment with the blue line. Next, the soil’s brightness follows from its position along the blue line relative to the origin. The grey dot corresponds to the point where the assumed
L equals 0. In that case, substitution in Equation (10) gives the red reflectance:
This makes sense, since, for an assumed L of zero, the soil’s reflectance must be equal to the measured reflectance. Note that L here does not indicate the actual LAI, but rather the one that would be needed to travel the path from the measured reflectance point at the position (R, N) to the soil line at (Rs, Ns).
2.3. Including Crown Clumping and Surface Heterogeneity (Linear Mixing) Effects
The BHR model discussed so far only simulates radiative transfer for homogeneous turbid medium-type vegetation canopies with infinite extension in the horizontal plane. In reality, vegetation canopies like forests may exhibit crown clumping and/or other forms of spatial heterogeneity, and satellite image pixels may also contain mixtures of bare soil and dense vegetation, certainly if the spatial resolution is moderate or low.
In the two-stream BHR model, a crown clumping effect as in forests can be introduced by modulating the canopy layer’s reflectance and transmittance as follows:
where
Cv is the vertically projected crown cover fraction. These expressions were taken from the SLC (soil–leaf-canopy) model [
16], which simulates crown clumping effects in one of the simplest possible ways. They are based on the concept of mixing the scattering properties of tree crowns with those of voids, which do not scatter light at all, but have a transmittance of unity.
For the modified canopy reflectance including the soil background, Equation (1) is employed again and then reads:
Note that for
Cv = 1 this is equivalent to the spatially uniform (turbid medium) model presented in
Section 2.2. Also, it turns out that according to Equation (13) this kind of 3D mixing is non-linear.
Estimating
rs from this equation however is still straightforward, since it can easily be derived from Equation (13) as follows:
As opposed to the above model of the 3D mixing of soil and vegetation, the simplest model of surface heterogeneity resulting into mixed pixels is linear and assumes that a fraction
fC of a pixel contains vegetation of a uniform composition and the complementary fraction 1 −
fC contains only bare soil, having the same reflectance as the one underneath the canopy,
rs. The final mixed-pixel reflectance then becomes the following:
This equation represents a new hybrid BHR canopy reflectance model in which vertical and lateral mixing with the bare soil are accommodated. In principle, estimating
rs from this model is still possible if it is the only unknown, but this then requires solving the following quadratic equation:
where the coefficients of the quadratic formula are the following:
It was found that the well-known formula for the pair of solutions
is less convenient for use in practice, as in the limit of
fC = 1, in which case
a = 0, only the root of the smallest magnitude can remain finite, which then must be estimated by means of L’Hôpital’s rule. Using the product of both roots, which equals
c/
a, it was found that the root of smallest magnitude can better be written in a less-known alternative form as follows:
where
a = 0 directly gives the correct solution −
c/b.
Note that Equation (18) can only yield a value of
rs if the LAI and both cover fractions are known. If this algorithm is applied to reflectance values in the red and the near-infrared bands, as shown in
Section 2.2 (
Figure 4), it turns out that the LAI and soil brightness can still be estimated from bi-spectral red–NIR reflectance values, provided again that both cover fractions
Cv and
fC are given.
The simulated effects of crown clumping and lateral linear mixing on the red–NIR diagram of
Figure 3 are shown in
Figure 5. Here, only the upper left panel, where both cover fractions are equal to unity, still represents a homogeneous turbid medium canopy corresponding to the original in
Figure 3. The other panels are modified versions of the upper left panel due to the effects of crown clumping (column direction) and incomplete linear fractional cover (row direction). From this figure, we may conclude that these non-linear and linear mixing effects definitely cannot be neglected. By these effects, all points in the red–NIR diagram are drawn into the direction of the bare soil line, especially the points in the upper left corner of the diagram. This also implies that points in the upper left of the diagram can only indicate pixels with dense homogeneous green vegetation. These points have the highest ratios
N/
R, and therefore also the highest NDVI. A high NDVI therefore not only indicates the presence of a large proportion of green vegetation in the target pixel, but also that the pixel was homogeneous (high
fC) and that the vegetation resembled a turbid medium (high
Cv), since otherwise the NDVI would have been smaller, as demonstrated in
Figure 5 by the panels for the lower values of
fC and
Cv. One can conclude that a high NDVI must indicate a combination of canopy parameters formed by a high leaf chlorophyll content, a high LAI, and high values of both vegetation coverage parameters
fC and
Cv; however, the downside is that a low NDVI may have a multitude of causes, namely low values of any of the parameters leaf chlorophyll, crown LAI, crown cover
Cv, or the pixel vegetation cover fraction
fC.
NDVI values are also slightly influenced by the brightness of the soil background, and to reduce this influence, several alternatives for the NDVI have been proposed, like the soil-adjusted vegetation index SAVI [
14], transformed SAVI (TSAVI) [
15], and modified SAVI (MSAVI) [
13]; however, from
Figure 5, we can conclude that these attempts to reduce soil brightness effects are most suitable for homogeneous turbid-medium type vegetation canopies, since for more open canopies, with
Cv and/or
fC less than unity, the slopes of the soil lines are again strongly influenced by the soil, in particular for high LAIs. The lower
fC and
Cv, the more we find that soil lines orient themselves parallel to the bare soil line, and in that respect the utility of indices (VIs) like the perpendicular VI (PVI) [
13] and weighted difference VI (WDVI) [
17,
18] increases in comparison to the NDVI, since these indices are constant along lines parallel to the bare soil line.
Due to the so-called saturation effect, in
Figure 5, the lines of varying soil brightness (shown in red) for an LAI of 8 must be very close to the similar lines corresponding to an infinite crown LAI (not shown) since the corresponding reflectance values are very close to each other, certainly in the red band. In other words, based on reflectance values alone, one can hardly discriminate between an infinite crown LAI and an LAI of 8. This factor alone already substantially complicates the estimation of the LAI from reflectance data when the LAI is high. However, there are more factors, such as the obvious ill-posedness of the model inversion from red–NIR reflectance data, which is manifested here by the fact that multiple combinations of LAI,
fC, and
Cv can produce exactly the same reflectance pairs of red–NIR reflectance. For instance, in one scenario, one might assume green vegetation with a high leaf chlorophyll content, a fixed crown LAI of 8, complete pixel coverage (
fC = 1), and then both vertical crown cover
Cv and soil brightness might be estimated from red–NIR reflectance data. In another scenario, one might neglect crown clumping by assuming
Cv = 1 and vary pixel heterogeneity by considering
fC as an unknown, as well as soil brightness. After model inversion in both of these scenarios, an effective LAI [
19] could be assigned to the pixel that is equal to the product of crown LAI and both cover fractions, i.e., LAI
eff = LAI ×
Cv ×
fC, but in principle these alternative scenarios are just as applicable as the scenario of a homogeneous turbid medium canopy, and the outcomes in terms of effective LAI would probably be different.
Another issue is that, even with assumed values of LAI and leaf chlorophyll, red and NIR reflectance data are not adequate to estimate both cover fractions if soil brightness is also left free, since the number of estimated parameters would still exceed the number of reflectance values by one. Therefore, the application of three extreme models (or scenarios) that are invertible based on different assumptions is proposed. The assumptions common to all three of them are the following:
The LIDF is spherical;
Single leaf reflectance and transmittance in the NIR band are 0.52 and 0.44, respectively (0.04 leaf absorptance). In the red band, we use 0.07 and 0.01, respectively, which is common for green leaves;
The maximum crown LAI is 8;
The bare soil’s spectral slope, defined by the ratio S = Ns/Rs, is given and equal to 1.2;
Soil brightness is always a free parameter that is to be estimated.
In the first model (I), both cover fractions are assumed to be equal to unity and the LAI is estimated. This model represents homogeneous surfaces covered with a uniform turbid-medium type of canopy.
In the second model (II), the crown LAI is assumed to be fixed at 8, the surface is homogeneous (fC = 1), and the crown cover fraction Cv is estimated. This model represents homogeneous forests with variable crown density.
In the third model (III), the vegetation LAI is also fixed at 8, the crown cover fraction Cv is unity, but the surface is heterogeneous. The fractional vegetation cover fC is estimated. This model represents green agricultural fields or grasslands interrupted by patches of bare soil within the pixel.
In all cases, soil brightness is estimated, as well as an effective pixel-level LAI, defined by LAI
eff = LAI ×
Cv ×
fC.
Figure 6 shows red–NIR feature space plots for the three models, in which soil brightness varies together with the other free parameter of the corresponding model, so LAI,
Cv, and
fC in models I, II, and III, respectively.
In all three panels, the red lines show the effect of soil brightness variations, and the green lines the effects of the other free parameter of the respective model. It appears that all three models occupy similar triangular shapes, and in the overlapping area we can conclude that the three models are equally acceptable as candidates for model inversion. For comparison,
Figure 7 shows a 2D histogram of the red and NIR bands obtained from the MODIS white-sky albedo product at the local moment of maximum NDVI, which reproduces the predicted triangular shapes very well.
The models clearly differ by their degrees of non-linearity. Model I is extremely non-linear in its response to LAI, the different responses in the red and the NIR, and in the soil lines, which show a large increase of slope with LAI. On the other hand, model III is almost perfectly linear, except in the upper left corner, where the soil line for unity
fC has a much higher slope, since this is the slope corresponding to a homogeneous turbid medium canopy with an LAI of 8. Model II is non-linear, like model I, but the response to
Cv is much more linear than the response to LAI in model I, and the soil lines of model II do have increasing slopes, but less so than in model I. In model I, the red reflectance hardly changes between LAIs of 4 and 8, so the soil lines for these cases are vertical and do virtually overlap. Here, the NDVI increases with soil brightness, unlike the situation for low LAIs and more open canopies. Model I is so close to linear that it allows the direct estimation of fractional cover
fC and soil brightness (
Rs) from red–NIR BHR reflectance data if
S is known:
where the estimated fractional cover
fC is obviously approximated by a linear combination of
R and
N, whereas the estimated soil brightness, represented by
Rs, is found as a ratio of two linear combinations of
R and
N. The linear combination of
R and
N that estimates
fC suggests that, with a proper choice of the weights, the WDVI [
17,
18] is a good predictor of the fractional vegetation cover, and in model III this is also a predictor of the effective LAI.
2.4. Estimation of fAPAR
Since the infinite reflectance in the red band is known from its assumed value
, and the soil’s reflectance follows one of the methods described in the previous section, one can derive all relevant quantities needed to estimate the fraction of absorbed photosynthetically active radiation, fAPAR, for diffuse incident radiation, while assuming that red light is representative for the whole visible or PAR region. In the homogeneous turbid medium model (I), the absorbed fraction of the incident hemispherical flux is given by the following equation:
This equation shows that canopy absorptance increases with soil reflectance, which is caused by light reflected upward by the soil into the canopy that for a black soil would be lost by absorption in the soil and now contributes to absorption in the canopy layer.
The absorptances by the canopy and by the soil, and the reflectance from the top, together must obey the law of radiant energy conservation. To demonstrate this, Equation (20) may be rewritten as follows:
where the last term is the effective absorptance of the soil, which is formed by the fraction of incident light at the canopy bottom that is not reflected by the soil and thus is given by the following equation:
By combining Equations (21) and (22), one may find that the sum is equal to unity, so the law of radiant energy conservation is thus obeyed.
The above derivations apply to model I, but they can easily be generalized to models II and III. To include the effects of crown clumping and lateral mixing, the canopy absorptance of Equation (20) must be modified into the following form:
In the literature, a linear relationship between fAPAR and the NDVI is often reported. These relationships are mostly based on experimental evidence, but model calculations [
6,
19,
20] also support this idea. Taking the canopy diffuse absorptance in the red band as a proxy for fAPAR, the relationship with the NDVI may be calculated with models I–III for varying soil brightness levels and the LAI or cover fractions. The result is presented in
Figure 8, which shows feature space plots of fAPAR vs. NDVI with varying soil brightness effects in red and the effects of the other free parameter in green. The near-linear relationships found earlier by other investigators are confirmed here for soils of moderate brightness (
Rs of approximately 0.25–0.40). For black soils, there is hardly any relationship, since in that case NDVIs are high regardless of the soil background, while fAPAR can still vary to a large extent. For dark soils, the relationships are strongly curved in all three models. Similar results have been reported by Myneni and Williams [
19]. When soil brightness is increased under a constant LAI or
Cv, fAPAR increases while NDVI decreases, especially at high soil brightnesses. In model III, we see horizontal red lines in this case, indicating that in this model fAPAR depends only on
fC. This is explained by the high fAPAR at a crown LAI of 8, but only for the fraction of the pixel that is covered with dense green vegetation, with minimum influence of the soil background on total fAPAR per pixel.
2.5. Retrieval of LAIeff, Soil Brightness and fAPAR from Red–NIR BHR Data
If no other information is available, the three scenarios of models I–III presented in the previous two sections are all equally likely to occur in reality for moderate-resolution satellite image pixels, although this may depend on the LAI. For instance, it is hard to imagine that a canopy can still resemble a turbid medium for LAIs < 1. It seems more likely that low LAIs are only possible in combination with clumping in plants or crop rows.
From
Figure 6, one can conclude that the repertoires of these models do largely overlap and it can be shown that, provided a sufficiently large range of soil brightness is accommodated, the triangular shape shown in panel (c) for model III corresponds to the minimum repertoire common to all three models, and this provides a simple criterion to decide whether a given combination of red and NIR reflectance values still belongs to the common repertoire or not. In practice, Equation (19) of
Section 2.3 can be applied to test whether the estimated values of
fC and
Rs are physically acceptable. If not, then one must decide to reject the input pixel for model inversion. Otherwise, inversion of models I–III should be possible, and the results would yield three solutions of soil brightness and separate solutions of LAI,
Cv and
fC, respectively. Since a crown LAI of 8 was assumed in models II and III, the effective LAI could be estimated by assuming equal weights:
For soil brightness, simply the average of the three outcomes can be taken. Regarding fAPAR, Equation (23) is universally applicable to all three models, so also in this case a simple average of the outcomes should suffice. For red–NIR pairs of measured reflectance values located below the bare soil line, none of the three models can provide a solution. In such cases we have to conclude that obviously the soil’s spectral slope is less than that assumed, and the pixel is vegetation-free. Here, the red reflectance
Rs is accepted as the soil brightness output. The equal-weight solution suggested in Equation (24) can be considered as a starting point for more refined solutions, e.g., by adapting the weights according to a biome classification, as is done in the MODIS LAI processing chain [
6]; however, to minimize possible spatial discontinuities, only the equal-weight solution is applied for the present paper, regardless of biomes.
For the application of the algorithm in practice, it has been proven to be beneficial to carry out the retrieval with a pre-computed direct look-up table (DLUT). Look-up table (LUT) solutions in radiative transfer model inversion problems are quite common and have been applied by numerous investigators [
6,
19]; however, these LUTs normally contain predicted reflectance values in a number of bands for a set of combinations of model input parameters, and the model inversion then consists of finding the vector of reflectance values that most closely resembles the measured reflectance data vector, possibly followed by some interpolation. Depending on the size of the LUT and its dimensionality, this may still take a considerable execution time. With a DLUT technique, however, the measured digital reflectance values are converted into an index, which is a direct pointer to the outputs stored in the DLUT. These outputs are the result of traditional model inversion techniques like numerical optimization. Once the DLUT has been generated, the application of this technique to images is nearly instantaneous regarding execution time, but it can only be applied in practice if the number of bands is limited to two or three. With the red and NIR MODIS bands as inputs, and a radiometric sampling interval of 0.001 reflectance units, a DLUT with about one million entries is sufficient to cover all possible combinations of red–NIR inputs. The generation of such a DLUT, which contains as outputs the effective LAI, average fAPAR, and average soil brightness (
Rs) calculated from the retrieval results obtained for models I–III, takes about 25 seconds in MATLAB on an average PC (Intel i5 processor) without any speed optimizations. Application of the DLUT to a single MODIS CMG global scene (3600 × 7200 pixels) may take only 0.18 seconds, which is nearly instantaneous indeed. The application of the DLUT to long time series of MODIS CMG data or other large datasets should therefore not be a problem. It should be mentioned that this DLUT technique can only be applied for a fixed assumed value of soil spectral slope
S and fixed green leaf optical properties. If
S and/or the leaf optical properties vary pixel by pixel, the DLUT technique can no longer be used and one should count on a processing time of about 25 microseconds per pixel, which for a global CMG image would be 650 seconds or approximately 11 minutes; however, by skipping all water pixels, that time could easily be reduced by one third or to about 4 minutes.