Full-resolution satellite time series of the California Current area

Mati Kahru, mkahru@ucsd.edu                                   Updated on:    10-Oct-2017




Global mapped datasets of various satellite products are available for downloading at the NASA Ocean Color website https://oceancolor.gsfc.nasa.gov/ and other data centers. For example, mapped SeaWiFS Level-3 products are available at 9 km resolution and MODIS-Aqua products at 4 and 9 km resolutions. Full-resolution data, i.e. approximately 1 km for SeaWiFS and MODISA ocean products, are available at Level-2, i.e. not mapped and not composited over time. This document describes a project that produces full-resolution, mapped and composited satellite time series of the California Current area. These data products are mapped to a common 1-km map and then merged from all available sensors: CZCS (1978-1986), OCTS (1996-1997), SeaWiFS (1997-2010), MODIS-Terra (MODIST, 2000-present), MODIS-Aqua (MODISA, 2002-present), MERIS (2003 to 7-April-2012), VIIRS-NPP (2-January-2012 to present) and OLCI on Sentinel3 (2017/01/1 to present). Corresponding sea-surface temperature (SST) products are merged from MODIST (2000-present) and MODISA (2002-present). For each dataset the temporal periods of compositing are 1 day, 5 days, 15 days, 1 month. Running averages of 5 days and any other periods can be generated and have been generated if requested by users. Current products include chlorophyll-a concentration (CHLA) and SST. Particulate organic varbon (POC) concentration merged from from SeaWiFS, MODISA and VIIRS has been added recently (see). For some periods other datasets such as diffuse attenuation coefficient at 490 nm (K490), natural fluorescence line height (NFLH), and remote sensing reflectance (Rrs) at different wavelengths have been generated. These and other products can be added upon request.

Software from Wimsoft (http://wimsoft.com), WIM Automation Module (WAM), is used to process Level-2 data files, map, composite and merge the various data products. A tutorial explaining the basic procedures is available here.

Processed data files are available at http://www.wimsoft.com/CAL/. Please note that the files are not available through FTP but through HTTP. For downloading multiple files at once you can use the widely available utility wget (e.g. http://www.gnu.org/software/wget/).


Related projects generate similar products for other regions, e.g. the Scotia Sea and surrounding areas in the Southern Ocean off Antarctica.



        CZCS, OCTS, SeaWiFS MLAC (Merged Local Area Coverage) and GAC, MODIST, MODISA and VIIRS-NPP Level-2 data are ordered and downloaded using the  Level 1 and 2 browser at http://oceancolor.gsfc.nasa.gov . MERIS reduced resolution (1 km, RR) data are downloaded from http://merci-srv.eo.esa.int/merci/. The sub-setting limits for the area were: 16-45 N; 140-100 W.

        Albers Conic Equal Area projection generated with the Terascan (SeaSpace Corp) utility master2 was chosen as the standard map. The advantage of using an equal area projection is that calculating areas, integrated masses and fluxes is very convenient. The selected map projection has 3840 columns and 3405 rows of pixels with an area of 1.0 km2. The latitude and longitude values of all pixels can be obtained from a HDF file named cal_aco_3840_Latitude_Longitude.hdf in http://wimsoft.com/CAL/files/.

        A mapped composite is generated for each calendar day using all available passes with a WAM utility wam_l2_map. The following L2 flags (if set) make a pixel invalid when using the default option:  ATMFAIL, LAND, PRODWARN, HIGLINT, HILT, HISATZEN, CLDICE, HISOLZEN, LOWLW, CHLFAIL, CHLWARN, SEAICE, NAVFAIL. In addition to eliminating the flagged pixels, the cloud image determined with the flag CLDICE is dilated (expanded) to eliminate affected pixels near cloud edges. Cloud edges are often associated with spiky and erroneous Chl-a values. This is obvious when looking at transects in low-chlorophyll areas in the open ocean where cloud edges produce elevated chlorophyll values. While this procedure eliminates a large fraction of the contaminated pixels near cloud edges, some erroneous pixels still slip through. In a typical day three SeaWiFS or MODISA passes contribute the area of interest. As pixels from the swath edges are eliminated (using flags as described above), the multiple daily passes never overlap. Therefore a daily composite of high-quality pixels has separate patches of pixels from individual passes. The resulting mapped daily composite is saved as HDF with the standard chlorophyll log-scaling. In addition, 4-times reduced and annotated HDF and PNG images are saved. The file names (e.g. S2003001_chl_mapped.hdf, S2003001_chl_mapped_annotated.hdf , S2003001_chl_mapped.png for SeaWiFS) show the year (2003), the Julian day of the year (001) and the variable (chl). For MODISA the first letter of the filename is A, for MODIST the first letter of the filename is T, for CZCS the first letter is C, for OCTS it is O, for MERIS  it is E (from the name of the satellite ENVISAT), for VIIRS the first letter is V. C is also typically used for the merged Chl-a. and N is also used for the merged Chl-a to separate the merged products from NASA sensors form the merged product including MERIS. Additional information is stored as HDF attributes.

        The following example is a SeaWiFS daily image for January 1, 2003 showing contributions from three separate passes (west, center and the south-east corner). The Chl-a concentration scale is logarithmic from 0.05 to 10 mg m-3.



        For years 1999 to present data from multiple sensors are available and the data from the individual sensors are combined into merged daily mapped images with the WAM utility wam_composite_2sensors. As orbits and the respective swaths of individual sensors are different, the merged data have better coverage. Also, because of the moving clouds between the satellite passes at different times (e.g. the SeaWiFS pass approximately at noon and the Aqua pass at 13:30 local time) the merged datasets have less area obscured by clouds. The following is a merged SeaWiFS-MODISA data from January 1, 2003. Note the increased coverage compared to SeaWiFS alone. Please also note that the 2003 Chl-a the product are actually merged from 4 sensors: SeaWiFS, MODIST, MODISA, MERIS.



        Daily mapped composite images were composited into 5-day and 15-day composites with a WAM utility wam_composite_2x.

        The following examples show 5-day and 15-day Chl-a composites using the merged SeaWiFS-MODISA. Note the improving coverage with increasing time length of compositing.




        The 1-km daily, 5-day, 15-day and monthly images are all available as HDF or PNG. The HDF files have the numerical values for each pixel and can be used to generate statistics for any selected area. The HDF files can be read with any HDF-aware software (e.g. Matlab, IDL, and WIM). When read with WIM the geo-location and scaling are automatically retrieved. When read with MATLAB or other software except WIM, the following equations have to be used to convert Pixel Value (PV) to geophysical values. Note that pixel value must be treated as unsigned 8-bit integer (uint8) that has possible value between 0 and 255. If your software retrieves pixel values as signed integers (int8) then you need to cast them into unsigned uint8 or add 256 to negative PV. Pixel values 0 and 255 represent invalid data.

        SST (deg C) = -3.0 + 0.15 * PV

                Chl ( mg m-3) =10^(0.015 * PV - 2.0)

        The mapped datasets cove a large area at equal area of 1 km2 pixel size. You may be interested in a smaller sub-area of the domain, may-be in a different projection. This can be easily accomplished by remapping the full-resolution 1-km data to another projection, and/or compositing into any time bin. In the example below the full-resolution Albers-projection images are remapped to a smaller Mercator projection.






        The annual mean for 2003 SeaWiFS data for a smaller domain is shown below-left and an animated GIF below right




        The process of merging datasets from different sensors depends on the availability of these different datasets. For SST the data merger is simple: between MODIST and MODISA using equal weight, i.e. valid values are averaged and if only one sensor has valid data, these pixel values are used in the merged dataset. For Chl-a the process is much more complex as a number of different sensors are used over the long time period. In some cases one sensor is deemed of lower quality compared to another sensor or dataset and in these cases the lower quality sensor is only used when valid data from the higher quality sensor are not available. These are referred as priority mergers and the * symbol behind the sensor name means higher priority compared to the other sensor. For example, in 2010 the merging process involved the following processes. The letter behind the sign shows the first letter of the merged filename.






In 2012 after the demise of SeaWiFS and addition of VIIRS the Chla merger became the following:




After 2012 the merger became the following:



POC  mergerfrom 2012 to present is the following:  (MODISA+VIIRS) C

From 2017 the Chla merger is:



For SST 2002-2011 the merger has been:




For SST 2012-present the merger is:





Processing is accomplished as a set of batch files. Copies of those batch files may be obtained upon request. They require keeping the same file structure.