def standalone_main():
parser = ArgumentParser()
parser.add_argument("l2_filename",
help="L2 file from which to plot soundings")
parser.add_argument("-i", "--sounding_id", metavar="SOUNDING_ID", action="append",
help="Plot the single specified sounding id")
parser.add_argument("-l", "--sounding_id_list", metavar="FILE",
help="A file with a list of sounding ids to plot")
parser.add_argument("-o", "--output_file", metavar="FILE",
help="Name of output file to be used instead of default")
parser.add_argument("-v", "--verbose", action="store_true",
help="Output additional verbose information")
# Parse command line arguments
args = parser.parse_args()
if (args.verbose):
init_logging(logging.DEBUG)
else:
init_logging(logging.INFO)
if not os.path.exists(args.l2_filename):
raise IOError("L2 filename specified does not exist: %s" % args.l2_filename)
analysis = l2_analysis.AnalysisEnvironment([args.l2_filename])
analysis.add_routines(l2_analysis.FrankenburgPlotRoutines(analysis_env=analysis))
plot_sounding_ids = []
if args.sounding_id or args.sounding_id_list:
id_type = analysis.comparison_ids[0].dtype.type
if args.sounding_id:
plot_sounding_ids += [ id_type(snd_id) for snd_id in args.sounding_id ]
if args.sounding_id_list:
with open(args.sounding_id_list) as id_file:
plot_sounding_ids += [ id_type(line.strip()) for line in id_file ]
else:
plot_sounding_ids = analysis.comparison_ids
if args.output_file:
output_file = args.output_file
else:
if len(plot_sounding_ids) > 1:
output_file = "spectral_fit_%s-%s.pdf" % (plot_sounding_ids[0], plot_sounding_ids[-1])
else:
output_file = "spectral_fit_%s.pdf" % (plot_sounding_ids[0])
logging.info("Writing plots to: %s" % output_file)
pdf = PdfPages(output_file)
num_soundings = len(plot_sounding_ids)
for idx, (snd_id, figs) in enumerate(zip(plot_sounding_ids, analysis.call_analysis_routine("plot_spectral_fits", ids=(plot_sounding_ids,), all_soundings=True))):
logging.info("[%d / %d] %s" % (idx+1, num_soundings, snd_id))
for band_fig in figs:
pdf.savefig(band_fig)
pdf.close()
def standalone_main():
parser = ArgumentParser(description="Splices together input HDF5 products for a given set of sounding ids")
parser.add_argument( "filenames", metavar="FILE", nargs='*',
help="files to splice, may be left blank if using the -i --input-files-list option" )
parser.add_argument( "-i", "--input-files-list", dest="input_files_list",
metavar="FILE",
help="text file with input filenames to splice")
parser.add_argument( "-s", "--sounding-id-file", dest="sounding_id_file",
metavar="FILE",
help="file containing list of soundings for destination file")
parser.add_argument( "-o", "--output-file", dest="output_filename",
metavar="FILE", default=DEFAULT_OUTPUT_FILENAME,
help="output filename of splice data, default: %s" % DEFAULT_OUTPUT_FILENAME)
parser.add_argument( "-d", "--datasets-list-file", dest="datasets_list_file",
metavar="FILE",
help="file containing list of only datasets to consider for copying. If rename_mapping is enabled then the names are matched on their destination dataset name")
parser.add_argument( "-r", "--rename-mapping", dest="rename_mapping",
action="store_true",
default=False,
help="rename datasets into output file according to internal mapping table as they would appear in the L2Agg PGE")
parser.add_argument( "-w", "--workers", dest="workers", type=int, default=1,
help="Number of workers to use when parallelizing splicing" )
parser.add_argument( "--temp", dest="temp_dir", default=os.curdir,
help="Directory where temporary files are saved when number of parallel workers is greater than 1" )
parser.add_argument( "-l", "--log_file", dest="log_file",
help="Save verbose information to log file" )
parser.add_argument( "--agg-names-filter", dest="agg_names_filter",
action="store_true",
default=False,
help="include only dataset names that would appear in the L2Agg PGE. Its only makes sense to use this option with --rename_mapping")
parser.add_argument( "--splice-all", dest="splice_all",
action="store_true",
default=False,
help="splice all datasets, including those which do not have a sounding dimension. Note that datasets without an explicit handler and no sounding dimension are simply copied from the first file.")
parser.add_argument( "--multiple-file-types", dest="multi_source_types", action="store_true", default=None,
help="indicates that multiple file type sources are being spliced. Speeds up multiple source type determination stage by being specified." )
parser.add_argument( "--single-file-type", dest="multi_source_types", action="store_false", default=None,
help="indicates that a single type of file is being spliced. Speeds up multiple source type determination stage by being specified." )
parser.add_argument( "-v", "--verbose", dest="verbose",
action="store_true",
default=False,
help="enable verbose informational reporting")
# Parse command line arguments
args = parser.parse_args()
if len(args.filenames) == 0 and args.input_files_list == None:
parser.error("Input list file must be specified")
# Set up logging
if args.verbose:
# Include HDF5 errors in output
h5py._errors.unsilence_errors()
log_level = logging.DEBUG
else:
log_level = logging.INFO
main_logger = log_util.init_logging(log_level=log_level, format="%(message)s")
# Initialize logging
if args.log_file:
log_file = log_util.open_log_file(args.log_file, logger=main_logger)
log_file.setFormatter( logging.Formatter("%(asctime)s: %(name)8s - %(levelname)7s - %(message)s") )
else:
log_file = None
source_files = load_source_files(args.filenames, args.input_files_list)
if args.sounding_id_file != None:
sounding_ids = [ sid.strip() for sid in open(args.sounding_id_file).readlines() ]
else:
main_logger.debug("No sounding ids file supplied, aggregating all ids from all files")
sounding_ids = None
copy_datasets_list = None
if args.datasets_list_file != None:
copy_datasets_list = [ ds.strip() for ds in open(args.datasets_list_file).readlines() ]
if args.agg_names_filter:
if copy_datasets_list == None:
copy_datasets_list = aggregator_dataset_dest_names
else:
copy_datasets_list += aggregator_dataset_dest_names
process_files(source_files, args.output_filename, sounding_ids, splice_all=args.splice_all, desired_datasets_list=copy_datasets_list, rename_mapping=args.rename_mapping, multi_source_types=args.multi_source_types, workers=args.workers, temp_dir=args.temp_dir, main_logger=main_logger, log_file=log_file)
-q, --quiet
Do not output details of program operation to console
-l, --log_file=FILE
Log file where populator operations are stored instead of printed
to stdout
'''
args = docopt_simple(usage, version=version)
# Logger for file operations
logger = logging.getLogger(os.path.basename(__file__))
if args.quiet:
log_util.init_logging(logging.ERROR)
else:
log_util.init_logging(logging.INFO)
# Initialize logging
if args.log_file:
log_obj = log_util.open_log_file(args.log_file)
log_obj.setFormatter(
logging.Formatter(
"%(asctime)s: %(name)25s - %(levelname)7s - %(message)s"))
else:
log_obj = None
populate_options = {}
if (args.binary):
populate_options["l2_binary_filename"] = args.binary
if (args.l2_config):
sounding_id = create_sounding_id(obs_id, l1b_fts)
logger.debug('Obs ID = %s, Sounding ID = %s' % (obs_id, sounding_id))
logger.debug('Spectrum A = %s' % spec_a)
logger.debug('Spectrum B = %s' % spec_b)
store_l1b_data(sounding_id, idx, l1b_fts, output_file, l1b_file)
if __name__ == "__main__":
parser = ArgumentParser(description='Converts FTS data into ')
parser.add_argument('fts_dir', metavar='FILENAME')
parser.add_argument('--output_file', '-o', metavar='FILENAME', required=True,
help='File to write convolved FTS data in OCO format')
parser.add_argument('--l1b_file', '-l', metavar='FILENAME', default=REFERENCE_L1B_FILE,
help='L1B file to get ILS information from')
parser.add_argument('--verbose', '-v', default=False, action='store_true',
help='Output verbose debugging information')
args = parser.parse_args()
if args.verbose:
log_util.init_logging(logging.DEBUG)
else:
log_util.init_logging(logging.INFO)
convert_fts_data(args.fts_dir, args.output_file, args.l1b_file)
def standalone_main():
parser = ArgumentParser(
description=
"Splices together input HDF5 products for a given set of sounding ids")
parser.add_argument(
"filenames",
metavar="FILE",
nargs='*',
help=
"files to splice, may be left blank if using the -i --input-files-list option"
)
parser.add_argument("-i",
"--input-files-list",
dest="input_files_list",
metavar="FILE",
help="text file with input filenames to splice")
parser.add_argument(
"-s",
"--sounding-id-file",
dest="sounding_id_file",
metavar="FILE",
help="file containing list of soundings for destination file")
parser.add_argument("-o",
"--output-file",
dest="output_filename",
metavar="FILE",
default=DEFAULT_OUTPUT_FILENAME,
help="output filename of splice data, default: %s" %
DEFAULT_OUTPUT_FILENAME)
parser.add_argument(
"-d",
"--datasets-list-file",
dest="datasets_list_file",
metavar="FILE",
help=
"file containing list of only datasets to consider for copying. If rename_mapping is enabled then the names are matched on their destination dataset name"
)
parser.add_argument(
"-r",
"--rename-mapping",
dest="rename_mapping",
action="store_true",
default=False,
help=
"rename datasets into output file according to internal mapping table as they would appear in the L2Agg PGE"
)
parser.add_argument(
"-w",
"--workers",
dest="workers",
type=int,
default=1,
help="Number of workers to use when parallelizing splicing")
parser.add_argument(
"--temp",
dest="temp_dir",
default=os.curdir,
help=
"Directory where temporary files are saved when number of parallel workers is greater than 1"
)
parser.add_argument("-l",
"--log_file",
dest="log_file",
help="Save verbose information to log file")
parser.add_argument(
"--agg-names-filter",
dest="agg_names_filter",
action="store_true",
default=False,
help=
"include only dataset names that would appear in the L2Agg PGE. Its only makes sense to use this option with --rename_mapping"
)
parser.add_argument(
"--splice-all",
dest="splice_all",
action="store_true",
default=False,
help=
"splice all datasets, including those which do not have a sounding dimension. Note that datasets without an explicit handler and no sounding dimension are simply copied from the first file."
)
parser.add_argument(
"--multiple-file-types",
dest="multi_source_types",
action="store_true",
default=None,
help=
"indicates that multiple file type sources are being spliced. Speeds up multiple source type determination stage by being specified."
)
parser.add_argument(
"--single-file-type",
dest="multi_source_types",
action="store_false",
default=None,
help=
"indicates that a single type of file is being spliced. Speeds up multiple source type determination stage by being specified."
)
parser.add_argument("-v",
"--verbose",
dest="verbose",
action="store_true",
default=False,
help="enable verbose informational reporting")
# Parse command line arguments
args = parser.parse_args()
if len(args.filenames) == 0 and args.input_files_list == None:
parser.error("Input list file must be specified")
# Set up logging
if args.verbose:
# Include HDF5 errors in output
h5py._errors.unsilence_errors()
log_level = logging.DEBUG
else:
log_level = logging.INFO
main_logger = log_util.init_logging(log_level=log_level,
format="%(message)s")
# Initialize logging
if args.log_file:
log_file = log_util.open_log_file(args.log_file, logger=main_logger)
log_file.setFormatter(
logging.Formatter(
"%(asctime)s: %(name)8s - %(levelname)7s - %(message)s"))
else:
log_file = None
source_files = load_source_files(args.filenames, args.input_files_list)
if args.sounding_id_file != None:
sounding_ids = [
sid.strip() for sid in open(args.sounding_id_file).readlines()
]
else:
main_logger.debug(
"No sounding ids file supplied, aggregating all ids from all files"
)
sounding_ids = None
copy_datasets_list = None
if args.datasets_list_file != None:
copy_datasets_list = [
ds.strip() for ds in open(args.datasets_list_file).readlines()
]
if args.agg_names_filter:
if copy_datasets_list == None:
copy_datasets_list = aggregator_dataset_dest_names
else:
copy_datasets_list += aggregator_dataset_dest_names
process_files(source_files,
args.output_filename,
sounding_ids,
splice_all=args.splice_all,
desired_datasets_list=copy_datasets_list,
rename_mapping=args.rename_mapping,
multi_source_types=args.multi_source_types,
workers=args.workers,
temp_dir=args.temp_dir,
main_logger=main_logger,
log_file=log_file)
help='static input file to get window information from')
parser.add_argument(
'--sounding_pos',
'-s',
metavar='INT',
default=DEFAULT_SOUNDING,
type=int,
choices=range(8),
help='specify which footprint ils to use (zero-based index)')
parser.add_argument('--verbose',
'-v',
default=False,
action='store_true',
help='Output verbose debugging information')
args = parser.parse_args()
if args.verbose:
log_util.init_logging(logging.DEBUG)
else:
log_util.init_logging(logging.INFO)
convert_fts_data(args.fts_dir,
args.output_file,
args.l1b_file,
args.config_file,
args.window_file,
sounding_pos=args.sounding_pos)
def standalone_main():
parser = ArgumentParser()
parser.add_argument("l2_filename",
help="L2 file from which to plot soundings")
parser.add_argument("-i",
"--sounding_id",
metavar="SOUNDING_ID",
action="append",
help="Plot the single specified sounding id")
parser.add_argument("-l",
"--sounding_id_list",
metavar="FILE",
help="A file with a list of sounding ids to plot")
parser.add_argument(
"-o",
"--output_file",
metavar="FILE",
help="Name of output file to be used instead of default")
parser.add_argument("-v",
"--verbose",
action="store_true",
help="Output additional verbose information")
# Parse command line arguments
args = parser.parse_args()
if (args.verbose):
init_logging(logging.DEBUG)
else:
init_logging(logging.INFO)
if not os.path.exists(args.l2_filename):
raise IOError("L2 filename specified does not exist: %s" %
args.l2_filename)
analysis = l2_analysis.AnalysisEnvironment([args.l2_filename])
analysis.add_routines(
l2_analysis.FrankenburgPlotRoutines(analysis_env=analysis))
plot_sounding_ids = []
if args.sounding_id or args.sounding_id_list:
id_type = analysis.comparison_ids[0].dtype.type
if args.sounding_id:
plot_sounding_ids += [
id_type(snd_id) for snd_id in args.sounding_id
]
if args.sounding_id_list:
with open(args.sounding_id_list) as id_file:
plot_sounding_ids += [
id_type(line.strip()) for line in id_file
]
else:
plot_sounding_ids = analysis.comparison_ids
if args.output_file:
output_file = args.output_file
else:
if len(plot_sounding_ids) > 1:
output_file = "spectral_fit_%s-%s.pdf" % (plot_sounding_ids[0],
plot_sounding_ids[-1])
else:
output_file = "spectral_fit_%s.pdf" % (plot_sounding_ids[0])
logging.info("Writing plots to: %s" % output_file)
pdf = PdfPages(output_file)
num_soundings = len(plot_sounding_ids)
for idx, (snd_id, figs) in enumerate(
zip(
plot_sounding_ids,
analysis.call_analysis_routine("plot_spectral_fits",
ids=(plot_sounding_ids, ),
all_soundings=True))):
logging.info("[%d / %d] %s" % (idx + 1, num_soundings, snd_id))
for band_fig in figs:
pdf.savefig(band_fig)
pdf.close()
-q, --quiet
Do not output details of program operation to console
-l, --log_file=FILE
Log file where populator operations are stored instead of printed
to stdout
"""
args = docopt_simple(usage, version=version)
# Logger for file operations
logger = logging.getLogger(os.path.basename(__file__))
if args.quiet:
log_util.init_logging(logging.ERROR)
else:
log_util.init_logging(logging.INFO)
# Initialize logging
if args.log_file:
log_obj = log_util.open_log_file(args.log_file)
log_obj.setFormatter(logging.Formatter("%(asctime)s: %(name)25s - %(levelname)7s - %(message)s"))
else:
log_obj = None
populate_options = {}
if args.binary:
populate_options["l2_binary_filename"] = args.binary
if args.l2_config:
populate_options["l2_config_filename"] = args.l2_config
populate_options["aggregate"] = args.aggregate