## 2 Materials and Methods
### Radiative Transfer Modelling  
The radiative transfer modelling was split into two components: (1) a three-dimensional canopy model designed to evaluate optical properties just above the canopy or above individual coral structures (Figure 1d) [18; 21], and (2) a plane-parallel water column model (Figure 1c), HydroLight [19]. All modelling was conducted hyperspectrally in 168 bands of 2 nm step, from 400 to 736 nm. The 3D model has been described and used in a number of previous publications [21; 22; 23; 18]. The solution method involves breaking down all surfaces and volumes into discrete elements, triangular surface polygons (as already provided by the 3D digital models), and cubic voxels, for scattering and attenuating media (the water). In this application, the coral shapes were placed on a flat underlying substrate that was decomposed into 100 \(\times\) 100 squares (each being two triangles) over an area of approximately 20 cm \(\times\) 20 cm. The model domain can either have light incident from above with horizontally periodic boundaries (i.e., the model set-up repeats in all horizontal directions), or be embedded into a \"far-field\" radiance distribution characterized from all directions (appropriate for modelling an isolated structure). The model is solved by calculating light transfer between all pairs of elements and propagating the incident light through the system by iteration, \begin{table}
\begin{tabular}{l l r r r r r} \hline \hline \multirow{2}{*}{**ID**} & \multirow{2}{*}{**Species**} & \multicolumn{3}{c}{**Polygon Count**} & \multicolumn{1}{c}{**Ruggosity**} & \multicolumn{1}{c}{**Max \(L_{\text{u}}/E_{\text{d}}\) Difference**} \\ \cline{3-6}  & & **Group** & **Low Res.** & **High Res.** & & **Low vs. High** \\ \hline
03 & _Montipora capitata_ & n/a & 2306 & 152,185 & 1.98 & 0.36 \\
08 & _Porites evermanni_ & D & 1712 & 69,945 & 2.74 & 0.51 \\
10 & _Porites evermanni_ & D & 1832 & 75,524 & 2.16 & 0.28 \\
11 & _Montipora capitata_ & D & 1830 & 103,394 & 1.77 & 0.29 \\
12 & _Porites evermanni_ & D & 2150 & 51,954 & 2.16 & 0.24 \\
16 & _Porites compressa_ & D & 1454 & 89,703 & 5.43 & 1.33 \\
17 & _Porites evermanni_ & S & 2079 & 124,092 & 2.05 & 0.27 \\
18 & _Porites compressa_ & D & 1898 & 103,430 & 5.82 & 0.47 \\
19 & _Porites evermanni_ & S & 1804 & 183,283 & 1.61 & 0.22 \\
31 & _Porites compressa_ & D & 1226 & 56,726 & 2.96 & 0.43 \\
32 & _Montipora capitata_ & S & 2461 & 100,886 & 2.01 & 0.31 \\
33 & _Porites compressa_ & S & 2160 & 98,502 & 2.90 & 0.47 \\
35 & _Pocillopora sp._ & S & 2966 & 240,353 & 3.06 & 0.21 \\
38 & _Porites evermanni or lutea_ & S & 1908 & 95,265 & 1.72 & 0.17 \\
39 & _Montipora patula_ & S & 2264 & 133,594 & 1.81 & 0.39 \\
40 & _Porites evermanni or lutea_ & S & 1403 & 56,696 & 1.45 & 0.17 \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Coral shapes used in this study. “Group” indicates grouping based on depth of collection, shallow (S, <8 m) or deep (D, 10–20 m). Coral 03 was from a site subjected to terrestrial run-off and was not placed in either group. Polygon counts for the high- and low-resolution models are given. The final column is discussed in the results and is the maximum percentage difference that choice of resolution leads to in reflectance averaged over the coral area in any band. for a predetermined number of passes or until convergence is detected. Surfaces are treated as locally Lambertian, but volumetric elements embody full directional scattering, according to a scattering coefficient combined with a phase function [18]. As an update to previous work, this model is now implemented on modern Graphics Processing Units (GPUs), which facilitates improved performance on computationally demanding applications with many bands and elements. Since the coral structures were small (\(\sim\)20 cm max. height), it would be inefficient to use the 3D model for the full water column, since depths up to 10 m were of interest. More efficiently, the 3D model was coupled to HydroLight in two ways:  
1.