README -- Updated MODIS BNU product 29 Jun 2021 Jenny Fisher jennyf@uow.edu.au Overview: =============================================================================== This directory contains MODIS LAI data from the BNU product developed by Yuan et al. (2011). Reference: ---------- Yuan, H., Dai, Y., Li, S., 2020. Reprocessed MODIS Version 6 Leaf Area Index Data Sets for Land Surface and Climate Modelling. Sun Yat-sen University. Yuan, H., Dai, Y., Xiao, Z., Ji, D., Shangguan, W., 2011. Reprocessing the MODIS Leaf Area Index Products for Land Surface and Climate Modelling. Remote Sensing of Environment, 115(5), 1171-1187. doi:10.1016/j.rse.2011.01.001 URL: ---- http://globalchange.bnu.edu.cn/research/laiv6 Files: =============================================================================== Yuan_proc_MODIS_XLAI.025x025.YYYY.nc -- 8-day Yuan processed MODIS LAI data for a given year (2000-2020). The "XLAI" denotes that the LAI data has been separated into 73 netCDF variables, one per Olson land type. This is necessary for regridding via HEMCO (for backwards compatibility with the existing dry deposition module in GEOS-Chem). Source : Yuan et al. (2011), http://globalchange.bnu.edu.cn/research/lai Resolution: : Generic 0.25 x 0.25 grid (3600 x 1800 boxes) Units : cm2/cm2 Timestamps: : Every 8 days, starting from YYYY/01/02, where YYYY is the year listed in the file name Compression : Level 1 (e.g. nccopy -d1) Chunking : nccopy -c lon/1440,lat/720,time/1 NOTE: The HEMCO philosophy is to use the data at the highest resolution possible; however, the native files are at an extremely high resolution of 30sec. We have regridded here to 0.25 degree to not only to save space, but also to match the resolution of the Olson land map (which is necessary for regridding by land type via HEMCO to work). MODIS.LAI.BNUv6.generic.01x01.YYYY.nc -- 8-day MODIS LAI data for a given year Source : Yuan et al. (2011), http://globalchange.bnu.edu.cn/research/laiv6 Resolution: : Generic 0.1 x 0.1 grid (3600 x 1800 boxes) Units : m2/m2 Timestamps : 8-day based on day of year Compression : Level 1 (e.g. nccopy -d1) NOTE: The HEMCO philosophy is to use the data at the highest resolution possible; however, the native files are at an extremely high resolution of 15sec. For this version of the product, we have directly downloaded the 0.1 degree resolution files to save space and match other high resolution emission inventories. Higher resolution files are available for download from the website linked above. How the netCDF files were created: =============================================================================== The above files were created as follows: 1) Download the original 0.1 degree resolution netcdf files using wget "http://globalchange.bnu.edu.cn/data/global_lai_0.1/lai_8-day_0.1_YYYY.nc" (with YYYY replaced by a year of interest). This results in a set of yearly files: lai_8-day_0.1_YYYY.nc 2) Fix variable names, attributes, add compression. All steps are done using the included bash script: ./fix_LAIv6.bash YYYY Note YYYY in the above command should be replaced by the year in question. This results in a set of 0.1x0.1 resolution yearly HEMCO-ready files: MODIS.LAI.BNUv6.generic.01x01.YYYY.nc 3) Repeat steps 1-2 for all years. Currently 2000-2020 data are available. Further steps for regridding the data to 0.25 x 0.25 for use with HEMCO: =============================================================================== All scripts are stored in the scripts/ folder NOTE: Originally data was stored in for_HEMCO and scripts were stored in for_HEMCO/scripts Step 1: ------- Run the Python script regrid_BNU_LAI_to_025x025.py. This regrids the 0.1 x 0.1 degree data files MODIS.LAI.BNUv6.generic.01x01.YYYY.nc, to 0.25 x 0.25 degree resolution. The new files are saved in with filenames MODIS.LAI.BNUv6.generic.025x025.YYYY.nc. YYYY = {2000..2020} Step 2: ------- Edit the NCL script make_XMODIS_for_HEMCO.ncl: infile_modis should be the path that points to the 0.25 x 0.25 degree data files MODIS.LAI.BNUv6.generic.025x025.YYYY.nc Step 3: ------- Run the script make_XMODIS.run. This will call the script make_XMODIS_for_HEMCO.ncl, which produces a single netCDF file for each day of output. Output files will be: YYYY/MODIS_XLAI_BNUv6.025x025.YYYY_002.nc Step 4: ------- Run the script combine_files.sh. This will use the NCO ncrcat operator to combine all of the 46 files (1 per each MODIS BNU time slice) into a single file: MODIS_XLAI_BNUv6.025x025.YYYY.nc Step 5: ------- Run the script fix_attrs.sh. This will use the NCO ncatted operator to fix variable attributes for lon, lat, and time for COARDS compliance. To create the Condensed*.nc files, follow these additional steps: ============================================================================== Step 6: ------- Clone the CsGrid repository if you do not already have it: git clone https://github.com/geoschem/CsGrid.git Step 7: ------- Edit the Matlab script condense_data.m as follows: (a) Add the full pathname to your local clone of the CsGrid. (b) Add the full pathname to the folder where the MODIS_XLAI_BNUv6.025x025.YYYY.nc files are found. (c) Change the start and end years of the data (default is 2000 to 2020). Step 8: ------- Open Matlab (ask your IT staff if you have to first load it via a module or other system command). Then once the Matlab prompt appears, type: condense_data Step 9: ------- Compress and chunk the Condensed*.nc data files. We recommend that you use our nc_chunk.pl script. See: http://wiki.geos-chem.org/Working_with_netCDF_data_files#Chunking_and_deflating_a_netCDF_file_to_improve_I.2FO Further notes: ============================================================================== The GCSC has requested that we call this product "Yuan processed MODIS LAI". Therefore, we have to run two additional scripts: rename.sh : Renames data files to reflect that these are now Yuan processed MODIS LAI data. change_titles.sh : Changes the title string in the netCDF global attributes