run_iasi_compress.m

function run_iasi_compress()
addpath(genpath('~/git/rtp_prod2'));
addpath('~/git/iasi_pcc');

% grab the slurm array index for this process
slurmindex = str2num(getenv('SLURM_ARRAY_TASK_ID'));
fprintf(1, 'Processing start %s\n', datetime)

chunk = 8;
for i = 1:chunk
    dayindex = (slurmindex*chunk) + i;
    fprintf(1, '> chunk %d  dayindex %d\n', i, dayindex);

    % File iasi_file_list is a list of filepaths to the input
    % files or this processing. For the initial runs, this was
    % generated by a call to 'ls' while sitting in the directory
    % /asl/iasi/iasi1/l1c/2020/164
    %      ls $PWD/IASI_xxx_1C_M02_* > ~/git/iasi_pcc/iasi_file_list
    %
    % iasi_file_list, then, contains lines like:
    %      /asl/iasi/iasi1/l1c/2020/164/IASI_xxx_1C_M02_20200612130854Z_20200612131157Z
    [status, infile] = system(sprintf('sed -n "%dp" %s | tr -d "\n"', ...
                                      dayindex, '~/git/iasi_pcc/iasi_file_list'));

    % granule file name base will remain the same. path will change
    % from l1c -> pcc
    [pathstr, name, ext] = fileparts(infile);
    IASI_PCC_DIR = strrep(pathstr, 'l1c', 'pcc');
    outfile = fullfile(IASI_PCC_DIR, [name, '.pcc']);
    % if output file already exists, jump to next
    if exist(outfile) ~= 0
        fprintf(1, '>>> Output file %s exists. Next granule.\n', outfile)
        continue
    end
    
    if exist(IASI_PCC_DIR) == 0
        fprintf(1, '>>>> %s does not exist. Creating\n', IASI_PCC_DIR);
        mkdir(IASI_PCC_DIR);
    end

    fprintf(1, '>> Writing compressed granule to %s\n', outfile)

    % call the processing function
    fprintf(1, '>> Compressing granule %s\n', infile)
    iasi_pcc_compress_granule(infile, outfile);

end
fprintf(1, 'Processing complete %s\n', datetime)