The VIRR method was applied to remove residual clouds in the MOD09A1 product and reconstruct time series of surface reflectance in the red, NIR and SWIR bands. The results were compared with the reconstructed surface reflectance from the TSCD algorithm.
3.1. Comparison in Space
An example of cloud detection and surface reflectance reconstruction is shown in
Figure 2 for tile h27v05 on day 273, 2003.
Figure 2a is an RGB image of surface reflectance from MOD09A1. RGB images of the reconstructed surface reflectance data using the VIRR and TSCD methods are shown in
Figure 2c,d respectively. The images were produced with an RGB color scheme that employs bands B6 (as red color), B2 (as green color), and B1 (as blue color), and the same color enhancement was used. In
Figure 2a, the surface reflectance from MOD09A1 is contaminated with residual clouds, and large clouds can be visually seen over the middle area of the image.
Figure 2b displays the cloud (grey) mask derived from the VIRR method. Generally, clouds in most areas can be identified by the VIRR algorithm. From the RGB image in
Figure 2c,d, the VIRR and TSCD methods removed the residual clouds in the surface reflectance from MOD09A1.
Figure 2.
Tile h27v05 for day 273, 2003. (a) RGB image for surface reflectance from MOD09A1; (b) cloud (grey) mask from the VIRR algorithm; (c) RGB image for reconstructed surface reflectance from the VIRR algorithm; (d) RGB image for reconstructed surface reflectance from the TSCD algorithm. The RGB images were produced with an RGB color scheme that employs bands B6 (as red color), B2 (as green color), and B1 (as blue color), and the same color enhancement was used.
Figure 2.
Tile h27v05 for day 273, 2003. (a) RGB image for surface reflectance from MOD09A1; (b) cloud (grey) mask from the VIRR algorithm; (c) RGB image for reconstructed surface reflectance from the VIRR algorithm; (d) RGB image for reconstructed surface reflectance from the TSCD algorithm. The RGB images were produced with an RGB color scheme that employs bands B6 (as red color), B2 (as green color), and B1 (as blue color), and the same color enhancement was used.
Figure 3.
Tile h12v09 for day 97, 2003. (a) RGB image for surface reflectance from MOD09A1; (b) cloud (grey) mask from the VIRR algorithm; (c) RGB image for reconstructed surface reflectance from the VIRR algorithm; (d) RGB image for reconstructed surface reflectance from the TSCD algorithm. The RGB images were produced with an RGB color scheme that employs bands B6 (as red color), B2 (as green color), and B1 (as blue color), and the same color enhancement was used.
Figure 3.
Tile h12v09 for day 97, 2003. (a) RGB image for surface reflectance from MOD09A1; (b) cloud (grey) mask from the VIRR algorithm; (c) RGB image for reconstructed surface reflectance from the VIRR algorithm; (d) RGB image for reconstructed surface reflectance from the TSCD algorithm. The RGB images were produced with an RGB color scheme that employs bands B6 (as red color), B2 (as green color), and B1 (as blue color), and the same color enhancement was used.
Figure 3 shows the cloud mask and reconstructed surface reflectance for tile h12v09 on day 97, 2003.
Figure 3a,c,d is the RGB images of surface reflectance from MOD09A1 and the reconstructed surface reflectance from the VIRR and TSCD methods, respectively. The images were produced with the same RGB color scheme and color enhancement as in
Figure 2. In
Figure 3a, most of the region was covered by thin clouds, except for several patches in the northwestern area of the image.
Figure 3b shows the cloud mask from the VIRR algorithm. The VIRR algorithm effectively identified the thin clouds over this tropical region based on the temporally continuous VIs. The RGB images of the reconstructed surface reflectance data from the VIRR and TSCD methods (
Figure 3c,d) show almost all contamination due to clouds was removed.
Density scatterplots of the reconstructed surface reflectance from the VIRR and TSCD algorithms versus the cloud-free surface reflectance from MYD09A1 over the BELMANIP sites in 2003 are shown in
Figure 4. Only the collocated surface reflectance values from MYD09A1 and the VIRR and TSCD algorithms are included in
Figure 4. The density scatterplots between the reconstructed surface reflectance from the TSCD algorithm and the cloud-free surface reflectance from MYD09A1 for the red and NIR bands (
Figure 4d,e) show outliers due to underestimation of the reconstructed surface reflectance from the TSCD algorithm. It is apparent that the reconstructed surface reflectance from the VIRR algorithm provides better agreement with the cloud-free surface reflectance from MYD09A1 for the red band (R
2 = 0.8606 and RMSE = 0.0366) and NIR band (R
2 = 0.6934 and RMSE = 0.0519) compared with the reconstructed surface reflectance from the TSCD algorithm (R
2 = 0.5811 and RMSE = 0.0649; and R
2 = 0.5005 and RMSE = 0.0675, respectively).
Figure 4.
Density scatterplots between the cloud-free surface reflectance from MYD09A1 and the reconstructed surface reflectance from the VIRR ((a)–(c)) and TSCD ((d)–(f)) algorithms over the BELMANIP sites in 2003.
Figure 4.
Density scatterplots between the cloud-free surface reflectance from MYD09A1 and the reconstructed surface reflectance from the VIRR ((a)–(c)) and TSCD ((d)–(f)) algorithms over the BELMANIP sites in 2003.
To further assess the consistency of the reconstructed surface reflectance in different bands, NDVI values calculated from the reconstructed surface reflectance were compared with NDVI values calculated from the cloud-free surface reflectance from MYD09A1.
Figure 5 shows the density scatterplots of the NDVI values calculated from the reconstructed surface reflectance from the VIRR and TSCD algorithms versus the NDVI values calculated from the cloud-free surface reflectance from MYD09A1 over the BELMANIP sites in 2003. As with
Figure 4, the NDVI values from the VIRR and TSCD algorithms are only compared to the collocated NDVI values from MYD09A1. Compared with the NDVI values calculated from the reconstructed surface reflectance from the TSCD algorithm, the NDVI values calculated from the reconstructed surface reflectance from the VIRR algorithm are distributed more closely around the 1:1 line with the NDVI values calculated from the cloud-free surface reflectance from MYD09A1 (with a higher correlation and slope). The NDVI values calculated from the reconstructed surface reflectance from the VIRR algorithm are in better agreement with the NDVI values calculated from the cloud-free surface reflectance from MYD09A1 (RMSE = 0.0854 and Bias = 0.0265) than those calculated from the reconstructed surface reflectance from the TSCD algorithm (RMSE = 0.1045 and Bias = 0.0351).
Figure 5.
Density scatterplots of the NDVI values calculated from the reconstructed surface reflectance from the VIRR (a) and TSCD (b) algorithms versus the NDVI values calculated from the cloud-free surface reflectance from MYD09A1 over the BELMANIP sites in 2003.
Figure 5.
Density scatterplots of the NDVI values calculated from the reconstructed surface reflectance from the VIRR (a) and TSCD (b) algorithms versus the NDVI values calculated from the cloud-free surface reflectance from MYD09A1 over the BELMANIP sites in 2003.
3.2. Temporal Analysis
In this section, the time series of surface reflectance from MOD09A1 and the reconstructed surface reflectance from the VIRR and TSCD algorithms over a sample of sites with different biome types were presented to further illustrate the performance of the VIRR algorithm. For a better comparison, the time series of NDVI calculated from these surface reflectances are also illustrated over these sites.
Figure 6 shows the time series of surface reflectance and NDVI for the center pixel of the Alpilles site for the year 2003. The biome type for this site is cropland according to MCD12Q1 product.
Figure 6a,c presents the time series of surface reflectance in the red and SWIR bands, respectively. It is observed that the time series of reconstructed surface reflectance from the VIRR method are in good agreement with those from the TSCD algorithm and residual clouds were removed in these reconstructed surface-reflectance data. The time series of surface reflectance in the NIR band are shown in
Figure 6b. Some discrepancies between the reconstructed surface reflectance in the NIR band from the VIRR and TSCD algorithm are observed for days 89–153, during which the reconstructed surface reflectance values from the VIRR algorithm were larger than those from the TSCD algorithm. Correspondingly, the NDVI values from the VIRR algorithm were also larger than those from the TSCD algorithm, but the time series of NDVI from the VIRR algorithm was more consistent with the upper envelope of NDVI calculated from MOD09A1 during these days (
Figure 6d), which demonstrates that the oscillations in surface reflectance from the VIRR algorithm are physical and related to seasonal variations.
Figure 6.
Time series of surface reflectance and NDVI from MOD09A1, the VIRR and TSCD algorithms for the center pixel of the Alpilles site in 2003. (a) surface reflectance in the red band; (b) surface reflectance in the NIR band; (c) surface reflectance in the SWIR band; (d) NDVI.
Figure 6.
Time series of surface reflectance and NDVI from MOD09A1, the VIRR and TSCD algorithms for the center pixel of the Alpilles site in 2003. (a) surface reflectance in the red band; (b) surface reflectance in the NIR band; (c) surface reflectance in the SWIR band; (d) NDVI.
Figure 7.
Time series of surface reflectance and NDVI from MOD09A1, the VIRR and TSCD algorithms for the center pixel of the Yucheng site in 2003. (a) surface reflectance in the red band; (b) surface reflectance in the NIR band; (c) surface reflectance in the SWIR band; (d) NDVI.
Figure 7.
Time series of surface reflectance and NDVI from MOD09A1, the VIRR and TSCD algorithms for the center pixel of the Yucheng site in 2003. (a) surface reflectance in the red band; (b) surface reflectance in the NIR band; (c) surface reflectance in the SWIR band; (d) NDVI.
Figure 7 shows the time series of surface reflectance and NDVI for the center pixel of the Yucheng site for the year 2003. The biome type for this site is also cropland, but with double annual vegetation seasons, and hence the time series of the surface reflectance and NDVI show seasonal fluctuation. The surface reflectance from MOD09A1, especially in the red band, has several abnormal values at this site (
Figure 7a). The VIRR and TSCD algorithms identified those observations with high reflectance values as clouds, and the residual clouds were removed in the reconstructed surface reflectance. However, some discrepancies are also observed. For example, the reconstructed surface reflectance values from the VIRR method are larger than those from the TSCD algorithm for days 33–73 (
Figure 7a–c). This is largely due to some clear-sky observations being labeled as clouds by the TSCD algorithm. The corresponding NDVI values calculated from the reconstructed surface reflectance from the TSCD algorithm (
Figure 7d) are also larger than those calculated from MOD09A1 and the reconstructed surface reflectance from the VIRR algorithm during those days.
Figure 8.
Time series of surface reflectance and NDVI from MOD09A1, the VIRR and TSCD algorithms for the center pixel of the Konza site in 2003. (a) surface reflectance in the red band; (b) surface reflectance in the NIR band; (c) surface reflectance in the SWIR band; (d) NDVI.
Figure 8.
Time series of surface reflectance and NDVI from MOD09A1, the VIRR and TSCD algorithms for the center pixel of the Konza site in 2003. (a) surface reflectance in the red band; (b) surface reflectance in the NIR band; (c) surface reflectance in the SWIR band; (d) NDVI.
The time series of surface reflectance and NDVI for the center pixel of the Konza site for the year 2003 are shown in
Figure 8. The biome type for this site is grassland according to MCD12Q1 product. On day 33, 2003, the surface reflectance from MOD09A1 in the red band is larger than 0.5, which is most likely cloud. Both the VIRR and TSCD algorithms remove residual clouds in the reconstructed surface reflectance data. However, the TSCD algorithm confirmed that the surface reflectances from MOD09A1 around this day were also contaminated by clouds, as a result of which the reconstructed surface reflectance data from the TSCD algorithm in the red, NIR, and SWIR bands were smaller than those from the VIRR algorithm and MOD09A1 for days 17–105 (
Figure 8a–c). Nevertheless, excellent agreement was achieved between the time series of NDVI from both the VIRR and TSCD algorithms for the entire year at this site (
Figure 8d).
Figure 9.
Time series of surface reflectance and NDVI from MOD09A1, the VIRR and TSCD algorithms for the center pixel of the Counami site in 2003. (a) surface reflectance in the red band; (b) surface reflectance in the NIR band; (c) surface reflectance in the SWIR band; (d) NDVI.
Figure 9.
Time series of surface reflectance and NDVI from MOD09A1, the VIRR and TSCD algorithms for the center pixel of the Counami site in 2003. (a) surface reflectance in the red band; (b) surface reflectance in the NIR band; (c) surface reflectance in the SWIR band; (d) NDVI.
Figure 9 shows the time series of surface reflectance and NDVI for the center pixel of the Counami site. The biome type for this site is evergreen broadleaf forests according to the MCD12Q1 product. Many residual clouds were observed in the surface reflectance from MOD09A1, and the time series of NDVI from MOD09A1 shows dramatic fluctuations over this site. The reconstructed surface reflectances from the TSCD algorithm are in good agreement with those from the VIRR algorithm after day 145. Large discrepancies are observed before Julian day 145 because of serious contamination due to residual clouds. The TSCD algorithm provides linear surface reflectance values, which cannot address seasonal changes of surface reflectance. However, the VIRR algorithm performed very well to eliminate the effects of clouds, and successfully reconstructed the continuous time series of surface reflectance.
Figure 10.
Time series of surface reflectance and NDVI from MOD09A1, the VIRR and TSCD algorithms for the center pixel of the Tapajos site in 2003. (a) surface reflectance in the red band; (b) surface reflectance in the NIR band; (c) surface reflectance in the SWIR band; (d) NDVI.
Figure 10.
Time series of surface reflectance and NDVI from MOD09A1, the VIRR and TSCD algorithms for the center pixel of the Tapajos site in 2003. (a) surface reflectance in the red band; (b) surface reflectance in the NIR band; (c) surface reflectance in the SWIR band; (d) NDVI.
Figure 10 shows the time series of surface reflectance and NDVI for the center pixel of the Tapajos site. The biome type for this site is also evergreen broadleaf forests. As with the Counami site, many residual clouds were observed in the MODIS surface reflectance and the time series of NDVI from MOD09A1 showed dramatic fluctuations for the entire year over this site (
Figure 10d). It is observed that most of the reconstructed surface reflectance data from the TSCD algorithm change linearly. In contrast, the reconstructed surface reflectance from the VIRR algorithm captures complete and reasonable time series (
Figure 10a–c). This, in turn, produces a time series of NDVI in good agreement with the upper envelope of the NDVI from MOD09A1 (
Figure 10d).