NASA Ocean Color

ocssw V2022

 #! /usr/bin/env python3
  
 # Extractor for L1C files
  
 import argparse
 import datetime
 from dateutil import tz
 import netCDF4
 import numpy as np
 from os.path import basename
 import pathlib
 from shutil import copyfile as cp
 import sys
  
 from seadasutils.setupenv import env
 from seadasutils.netcdf_utils import ncsubset_vars
  
 versionStr = "1.0_2024-11-06"
  
 class extract:
  
     def __init__(self, ifile, ofile=None,
                  spixl=None, epixl=None, sline=None, eline=None,
                  verbose=False):
         # inputs
         self.ifile = pathlib.Path(ifile)
         self.ofile = pathlib.Path(ofile)
         self.spixl = spixl
         self.epixl = epixl
         self.sline = sline
         self.eline = eline
         self.verbose = verbose
  
         # defaults
         self.runtime = None
         self.attrs = None
  
         # unused, but needed by setupenv.py
         self.dirs = {}
         self.ancdir = None
         self.curdir = False
         self.sensor = None
         env(self)  # run setupenv
  
     def runextract(self, subset):
  
         srcfile = self.ifile
         if srcfile.exists():
             dstfile = self.ofile
             if self.verbose:
                 print('Extracting', srcfile)
  
             ncsubset_vars(srcfile, dstfile, subset, timestamp=self.runtime, verbose=self.verbose)
  
             # Read infile as netCDF dataset
             infile = netCDF4.Dataset(srcfile, 'r')
             # Read and write outfile as netCDF4 dataset
             outfile = netCDF4.Dataset(dstfile, 'r+')
  
             #_____________________________________________________________________________________________________________________________________
             #                                                                                 |
             # Add extract_pixel/line_start/stop:                                              |
             #_________________________________________________________________________________|
             
             if 'extract_pixel_start' in infile.ncattrs():
                 outfile.extract_pixel_start = np.dtype('int32').type(infile.extract_pixel_start + self.spixl + 1)
                 outfile.extract_pixel_stop  =  np.dtype('int32').type(infile.extract_pixel_stop + self.epixl + 1)
                 outfile.extract_line_start  =  np.dtype('int32').type(infile.extract_line_start + self.sline + 1)
                 outfile.extract_line_stop   =  np.dtype('int32').type(infile.extract_line_stop + self.eline + 1)
             else:
                 outfile.extract_pixel_start = np.dtype('int32').type(self.spixl + 1)
                 outfile.extract_pixel_stop  =  np.dtype('int32').type(self.epixl + 1)
                 
                 outfile.extract_line_start  =  np.dtype('int32').type(self.sline + 1)
                 outfile.extract_line_stop   =  np.dtype('int32').type(self.eline + 1)
             
             #_____________________________________________________________________________________________________________________________________
             #                                                                                 |
             # Modify time_coverage_start/end of output file:                                  |
             #_________________________________________________________________________________|
  
             # Read infile as netCDF dataset
             infile = netCDF4.Dataset(srcfile, 'r')
             # Read and write outfile as netCDF4 dataset
             outfile = netCDF4.Dataset(dstfile, 'r+')
             utc = tz.tzutc()
             scantime = outfile.variables['time'][:]
             stime = datetime.datetime.fromtimestamp(scantime[0],tz=utc)
             etime = datetime.datetime.fromtimestamp(scantime[-1],tz=utc)
             # Change outfile time_coverage_start/end
             outfile.time_coverage_start = str(stime.strftime('%Y-%m-%dT%H:%M:%S') + 'Z')
             outfile.time_coverage_end = str(etime.strftime('%Y-%m-%dT%H:%M:%S') + 'Z')
  
     def run(self):
         # convert to zero-based index
         self.spixl, self.epixl, self.sline, self.eline = \
         (v-1 for v in (self.spixl, self.epixl, self.sline, self.eline))
  
         # extract file
         subset = {'pixels':[self.spixl, self.epixl],
                   'scans':   [self.sline, self.eline]}
         infile = netCDF4.Dataset(self.ifile, 'r')
         dims = list(infile.dimensions.keys())
         infile.close()
         if 'nsamp' in dims:
             subset = {'nsamp':[self.spixl, self.epixl],
                       'lines':[self.sline, self.eline]}
  
         self.runextract(subset)
  
 def chk_pixl(args, infile):
     if args.epixl == -1:
         args.epixl = infile.dimensions['pixels'].size
     if args.eline == -1:
         args.eline = infile.dimensions['scans'].size
     return args.spixl, args.epixl, args.sline, args.eline
         
 if __name__ == "__main__":
     print("l1aextract_netcdf", versionStr)
  
     # parse command line
     parser = argparse.ArgumentParser(
         description='Extract specified area from an L1A netCDF file')
     parser.add_argument('-v', '--verbose', help='print status messages',
                         action='store_true')
     parser.add_argument('ifile',
                         help='SeaWiFS Level 1A input file')
     parser.add_argument('ofile',
                         help='output file')
  
     group2 = parser.add_argument_group('pixel/line ranges (1-based)')
     group2.add_argument('--spixl', type=int, help='start pixel', default = 1)
     group2.add_argument('--epixl', type=int, help='end pixel', default = -1)
  
     group2.add_argument('--sline', type=int, help='start line', default = 1)
     group2.add_argument('--eline', type=int, help='end line', default = -1)
  
     if len(sys.argv) == 1:
         parser.print_help()
         sys.exit(1) 
     args = parser.parse_args()
     
     # Read infile as netCDF dataset
     infile = netCDF4.Dataset(args.ifile, 'r')
     
     args.spixl, args.epixl, args.sline, args.in_eline = chk_pixl(args, infile)
              
     # initialize
     this = extract(ifile=args.ifile,
                    ofile=args.ofile,
                    spixl=args.spixl,
                    epixl=args.epixl,
                    sline=args.sline,
                    eline=args.eline,
                    verbose=args.verbose)
  
     this.run()