def main(argv=None):
"""Load in the arguments and ensure they are set correctly. Then run
the time-lagged ensembles on the input cubes.
"""
parser = ArgParser(
description='This combines the realizations from different forecast '
'cycles into one cube. It does this by taking an input '
'CubeList containing forecasts from different cycles and '
'merges them into a single cube, removing any metadata '
'that does not match.')
parser.add_argument('input_filenames',
metavar='INPUT_FILENAMES',
nargs="+",
type=str,
help='Paths to input NetCDF files for the time-lagged '
'ensemble to combine the realizations.')
parser.add_argument('output_file',
metavar='OUTPUT_FILE',
help='The output file for the processed NetCDF.')
args = parser.parse_args(args=argv)
# Load the cubes
cubes = iris.cube.CubeList([])
for filename in args.input_filenames:
new_cube = load_cube(filename)
cubes.append(new_cube)
# Process Cube
result = process(cubes)
# Save Cube
save_netcdf(result, args.output_file)
def main(argv=None):
""" Load in the arguments for feels like temperature and ensure they are
set correctly. Then calculate the feels like temperature using the data
in the input cubes."""
parser = ArgParser(
description="This calculates the feels like temperature using a "
"combination of the wind chill index and Steadman's "
"apparent temperature equation.")
parser.add_argument("temperature", metavar="TEMPERATURE",
help="Path to a NetCDF file of air temperatures at "
"screen level.")
parser.add_argument("wind_speed", metavar="WIND_SPEED",
help="Path to the NetCDF file of wind speed at 10m.")
parser.add_argument("relative_humidity", metavar="RELATIVE_HUMIDITY",
help="Path to the NetCDF file of relative humidity "
"at screen level.")
parser.add_argument("pressure", metavar="PRESSURE",
help="Path to a NetCDF file of mean sea level "
"pressure.")
parser.add_argument("output_filepath", metavar="OUTPUT_FILE",
help="The output path for the processed NetCDF")
args = parser.parse_args(args=argv)
# Load Cubes
temperature = load_cube(args.temperature)
wind_speed = load_cube(args.wind_speed)
relative_humidity = load_cube(args.relative_humidity)
pressure = load_cube(args.pressure)
# Process Cube
result = process(temperature, wind_speed, relative_humidity, pressure)
# Save Cube
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in arguments for wind-gust diagnostic.
Wind-gust and Wind-speed data should be supplied along with the required
percentile value. The wind-gust diagnostic will be the Max of the specified
percentile data.
Currently:
* Typical gusts is
MAX(wind-gust(50th percentile),wind-speed(95th percentile))
* Extreme gust is
MAX(wind-gust(95th percentile),wind-speed(100th percentile))
If no percentile values are supplied the code defaults
to values for Typical gusts.
"""
parser = ArgParser(
description="Calculate revised wind-gust data using a specified "
"percentile of wind-gust data and a specified percentile "
"of wind-speed data through the WindGustDiagnostic plugin. "
"The wind-gust diagnostic will be the Max of the specified "
"percentile data."
"Currently Typical gusts is "
"MAX(wind-gust(50th percentile),wind-speed(95th percentile))"
"and Extreme gust is "
"MAX(wind-gust(95th percentile),wind-speed(100th percentile)). "
"If no percentile values are supplied the code defaults "
"to values for Typical gusts.")
parser.add_argument("input_filegust",
metavar="INPUT_FILE_GUST",
help="A path to an input Wind Gust Percentile"
" NetCDF file")
parser.add_argument("input_filews",
metavar="INPUT_FILE_WINDSPEED",
help="A path to an input Wind Speed Percentile"
" NetCDF file")
parser.add_argument("output_filepath",
metavar="OUTPUT_FILE",
help="The output path for the processed NetCDF")
parser.add_argument("--percentile_gust",
metavar="PERCENTILE_GUST",
default="50.0",
help="Percentile of wind-gust required."
" Default=50.0",
type=float)
parser.add_argument("--percentile_ws",
metavar="PERCENTILE_WIND_SPEED",
default="95.0",
help="Percentile of wind-speed required."
" Default=95.0",
type=float)
args = parser.parse_args(args=argv)
# Load Cube
gust_cube = load_cube(args.input_filegust)
speed_cube = load_cube(args.input_filews)
# Process Cube
result = process(gust_cube, speed_cube, args.percentile_gust,
args.percentile_ws)
# Save Cube
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Invoke data extraction."""
parser = ArgParser(description='Extracts subset of data from a single '
'input file, subject to equality-based constraints.')
parser.add_argument('input_file',
metavar='INPUT_FILE',
help="File containing a dataset to extract from.")
parser.add_argument('output_file',
metavar='OUTPUT_FILE',
help="File to write the extracted dataset to.")
parser.add_argument('constraints',
metavar='CONSTRAINTS',
nargs='+',
help='The constraint(s) to be applied. These must be'
' of the form "key=value", eg "threshold=1". Scalars'
', boolean and string values are supported. Comma-'
'separated lists (eg "key=[value1,value2]") are '
'supported. These comma-separated lists can either '
'extract all values specified in the list or '
'all values specified within a range e.g. '
'key=[value1:value2]. When a range is specified, '
'this is inclusive of the endpoints of the range.')
parser.add_argument('--units',
metavar='UNITS',
nargs='+',
default=None,
help='Optional: units of coordinate constraint(s) to '
'be applied, for use when the input coordinate '
'units are not ideal (eg for float equality). If '
'used, this list must match the CONSTRAINTS list in '
'order and length (with null values set to None).')
parser.add_argument('--ignore-failure',
action='store_true',
default=False,
help='Option to ignore constraint match failure and '
'return the input cube.')
args = parser.parse_args(args=argv)
# Load Cube
cube = load_cube(args.input_file)
# Process Cube
output_cube = process(cube, args.constraints, args.units)
# Save Cube
if output_cube is None and args.ignore_failure:
save_netcdf(cube, args.output_file)
elif output_cube is None:
msg = "Constraint(s) could not be matched in input cube"
raise ValueError(msg)
else:
save_netcdf(output_cube, args.output_file)
def main(argv=None):
"""Load arguments"""
parser = ArgParser(description='Calculates probabilities of occurrence '
'between thresholds')
parser.add_argument('input_file',
metavar='INPUT_FILE',
help='Path to NetCDF file containing probabilities '
'above or below thresholds')
parser.add_argument('output_file',
metavar='OUTPUT_FILE',
help='Path to NetCDF file to write probabilities of '
'occurrence between thresholds')
parser.add_argument('threshold_ranges',
metavar='THRESHOLD_RANGES',
help='Path to json file specifying threshold ranges')
parser.add_argument('--threshold_units',
metavar='THRESHOLD_UNITS',
type=str,
default=None,
help='Units in which thresholds are specified')
args = parser.parse_args(args=argv)
# Load Cube and json
cube = load_cube(args.input_file)
with open(args.threshold_ranges) as input_file:
# read list of thresholds from json file
threshold_ranges = json.load(input_file)
# Process Cube
result = process(cube,
threshold_ranges,
threshold_units=args.threshold_units)
# Save Cube
save_netcdf(result, args.output_file)
def main(argv=None):
r"""
Load arguments and run ProbabilitiesFromPercentiles plugin.
Plugin generates probabilities at a fixed threshold (height) from a set of
(height) percentiles.
Example:
Snow-fall level::
Reference field: Percentiled snow fall level (m ASL)
Other field: Orography (m ASL)
300m ----------------- 30th Percentile snow fall level
200m ----_------------ 20th Percentile snow fall level
100m ---/-\----------- 10th Percentile snow fall level
000m --/---\---------- 0th Percentile snow fall level
______/ \_________ Orogaphy
The orography heights are compared against the heights that correspond
with percentile values to find the band in which they fall, then
interpolated linearly to obtain a probability of snow level at / below
the ground surface.
"""
parser = ArgParser(
description="Calculate probability from a percentiled field at a "
"2D threshold level. Eg for 2D percentile levels at different "
"heights, calculate probability that height is at ground level, where"
" the threshold file contains a 2D topography field.")
parser.add_argument("percentiles_filepath",
metavar="PERCENTILES_FILE",
help="A path to an input NetCDF file containing a "
"percentiled field")
parser.add_argument("threshold_filepath",
metavar="THRESHOLD_FILE",
help="A path to an input NetCDF file containing a "
"threshold value at which probabilities should be "
"calculated.")
parser.add_argument("output_filepath",
metavar="OUTPUT_FILE",
help="The output path for the processed NetCDF")
parser.add_argument("output_diagnostic_name",
metavar="OUTPUT_DIAGNOSTIC_NAME",
type=str,
help="Name for data in output file e.g. "
"probability_of_snow_falling_level_below_ground_level")
args = parser.parse_args(args=argv)
# Load Cubes
threshold_cube = load_cube(args.threshold_filepath)
percentiles_cube = load_cube(args.percentiles_filepath)
# Process Cubes
probability_cube = process(percentiles_cube, threshold_cube,
args.output_diagnostic_name)
# Save Cubes
save_netcdf(probability_cube, args.output_filepath)
def main(argv=None):
"""Parser to accept input data and an output destination before invoking
the wet bulb temperature plugin. Also accepted is an optional
convergence_condition argument that can be used to specify the tolerance of
the Newton iterator used to calculate the wet bulb temperatures."""
parser = ArgParser(
description='Calculate a field of wet bulb temperatures.')
parser.add_argument('temperature',
metavar='TEMPERATURE',
help='Path to a NetCDF file of air temperatures at '
'the points for which the wet bulb temperatures are '
'being calculated.')
parser.add_argument('relative_humidity',
metavar='RELATIVE_HUMIDITY',
help='Path to a NetCDF file of relative humidities at '
'the points for for which the wet bulb temperatures '
'are being calculated.')
parser.add_argument('pressure',
metavar='PRESSURE',
help='Path to a NetCDF file of air pressures at the '
'points for which the wet bulb temperatures are being'
' calculated.')
parser.add_argument('output_filepath',
metavar='OUTPUT_FILE',
help='The output path for the processed NetCDF.')
parser.add_argument('--convergence_condition',
metavar='CONVERGENCE_CONDITION',
type=float,
default=0.05,
help='The convergence condition for the Newton '
'iterator in K. When the wet bulb temperature '
'stops changing by more than this amount between'
' iterations, the solution is accepted.')
args = parser.parse_args(args=argv)
# Load Cubes
temperature = load_cube(args.temperature)
relative_humidity = load_cube(args.relative_humidity)
pressure = load_cube(args.pressure)
# Process Cube
result = process(temperature, relative_humidity, pressure,
args.convergence_condition)
# Save Cube
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in arguments and get going."""
parser = ArgParser(description=('Read the input landmask, and correct '
'to boolean values.'))
parser.add_argument('--force',
dest='force',
default=False,
action='store_true',
help=('If True, ancillaries will be generated '
'even if doing so will overwrite existing '
'files.'))
parser.add_argument('input_filepath_standard',
metavar='INPUT_FILE_STANDARD',
help='A path to an input NetCDF file to be processed')
parser.add_argument('output_filepath',
metavar='OUTPUT_FILE',
help='The output path for the processed NetCDF')
args = parser.parse_args(args=argv)
# Check if improver ancillary already exists.
if not os.path.exists(args.output_filepath) or args.force:
landmask = load_cube(args.input_filepath_standard)
land_binary_mask = CorrectLandSeaMask().process(landmask)
save_netcdf(land_binary_mask, args.output_filepath)
else:
print('File already exists here: ', args.output_filepath)
def main(argv=None):
""" Calculate the UV index using the data
in the input cubes."""
parser = ArgParser(
description="Calculates the UV index.")
parser.add_argument("radiation_flux_upward",
metavar="RADIATION_FLUX_UPWARD",
help="Path to a NetCDF file of radiation flux "
"in uv upward at surface.")
parser.add_argument("radiation_flux_downward",
metavar="RADIATION_FLUX_DOWNWARD",
help="Path to a NetCDF file of radiation flux "
"in uv downward at surface.")
parser.add_argument("output_filepath", metavar="OUTPUT_FILE",
help="The output path for the processed NetCDF")
args = parser.parse_args(args=argv)
# Load Cube
rad_uv_up = load_cube(args.radiation_flux_upward)
rad_uv_down = load_cube(args.radiation_flux_downward)
# Process Cube
result = process(rad_uv_up, rad_uv_down)
# Save Cube
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in the arguments and ensure they are set correctly. Then run
the time-lagged ensembles on the input cubes."""
parser = ArgParser(
description='This combines the realizations from different forecast '
'cycles into one cube. It does this by taking an input '
'CubeList containing forecasts from different cycles and '
'merges them into a single cube, removing any metadata '
'that does not match.')
parser.add_argument('input_filenames', metavar='INPUT_FILENAMES',
nargs="+", type=str,
help='Paths to input NetCDF files for the time-lagged '
'ensemble to combine the realizations.')
parser.add_argument('output_file', metavar='OUTPUT_FILE',
help='The output file for the processed NetCDF.')
args = parser.parse_args(args=argv)
# Load the cubes
cubes = iris.cube.CubeList([])
for filename in args.input_filenames:
new_cube = load_cube(filename)
cubes.append(new_cube)
# Warns if a single file is input
if len(cubes) == 1:
warnings.warn('Only a single cube input, so time lagging will have '
'no effect.')
save_netcdf(cubes[0], args.output_file)
# Raises an error if the validity times do not match
else:
for i, this_cube in enumerate(cubes):
for later_cube in cubes[i+1:]:
if this_cube.coord('time') == later_cube.coord('time'):
continue
else:
msg = ("Cubes with mismatched validity times are not "
"compatible.")
raise ValueError(msg)
result = GenerateTimeLaggedEnsemble().process(cubes)
save_netcdf(result, args.output_file)
def main(argv=None):
"""Generate target grid with a halo around the source file grid."""
parser = ArgParser(description='Generate grid with halo from a source '
'domain input file. The grid is populated with zeroes.')
parser.add_argument('input_file',
metavar='INPUT_FILE',
help="NetCDF file "
"containing data on a source grid.")
parser.add_argument('output_file',
metavar='OUTPUT_FILE',
help="NetCDF "
"file defining the target grid with additional halo.")
parser.add_argument('--halo_radius',
metavar='HALO_RADIUS',
default=162000,
type=float,
help="Size of halo (in m) with which to "
"pad the input grid. Default is 162 000 m.")
args = parser.parse_args(args=argv)
# Load Cube
cube = load_cube(args.input_file)
# Process Cube
result = process(cube, args.halo_radius)
# Save Cube
save_netcdf(result, args.output_file)
def main(argv=None):
"""Apply lapse rates to temperature data."""
parser = ArgParser(description='Apply downscaling temperature adjustment '
'using calculated lapse rate.')
parser.add_argument('temperature_filepath',
metavar='TEMPERATURE_FILEPATH',
help='Full path to input temperature NetCDF file')
parser.add_argument('lapse_rate_filepath',
metavar='LAPSE_RATE_FILEPATH',
help='Full path to input lapse rate NetCDF file')
parser.add_argument('source_orography',
metavar='SOURCE_OROG_FILE',
help='Full path to NetCDF file containing the source '
'model orography')
parser.add_argument('target_orography',
metavar='TARGET_OROG_FILE',
help='Full path to target orography NetCDF file '
'(to which temperature will be downscaled)')
parser.add_argument('output_file',
metavar='OUTPUT_FILE',
help='File name '
'to write lapse rate adjusted temperature data')
args = parser.parse_args(args=argv)
# read cubes
temperature = load_cube(args.temperature_filepath)
lapse_rate = load_cube(args.lapse_rate_filepath)
source_orog = load_cube(args.source_orography)
target_orog = load_cube(args.target_orography)
# apply lapse rate to temperature data
adjusted_temperature = apply_gridded_lapse_rate(temperature, lapse_rate,
source_orog, target_orog)
# save to output file
save_netcdf(adjusted_temperature, args.output_file)
def main(argv=None):
"""Parser to accept input data and an output destination before invoking
the weather symbols plugin.
"""
diagnostics = interrogate_decision_tree('high_resolution')
n_files = len(diagnostics)
dlist = (' - {}\n' * n_files)
diagnostics_global = interrogate_decision_tree('global')
n_files_global = len(diagnostics_global)
dlist_global = (' - {}\n' * n_files_global)
parser = ArgParser(
description='Calculate gridded weather symbol codes.\nThis plugin '
'requires a specific set of input diagnostics, where data\nmay be in '
'any units to which the thresholds given below can\nbe converted:\n' +
dlist.format(*diagnostics) + '\n\n or for global data\n\n' +
dlist_global.format(*diagnostics_global),
formatter_class=RawTextHelpFormatter)
parser.add_argument(
'input_filepaths',
metavar='INPUT_FILES',
nargs="+",
help='Paths to files containing the required input diagnostics.')
parser.add_argument('output_filepath',
metavar='OUTPUT_FILE',
help='The output path for the processed NetCDF.')
parser.add_argument("--wxtree",
metavar="WXTREE",
default="high_resolution",
choices=["high_resolution", "global"],
help="Weather Code tree.\n"
"Choices are high_resolution or global.\n"
"Default=high_resolution.",
type=str)
args = parser.parse_args(args=argv)
# Load Cube
cubes = load_cubelist(args.input_filepaths, no_lazy_load=True)
required_number_of_inputs = n_files
if args.wxtree == 'global':
required_number_of_inputs = n_files_global
if len(cubes) != required_number_of_inputs:
msg = ('Incorrect number of inputs: files {} gave {} cubes' +
', {} required').format(args.input_filepaths, len(cubes),
required_number_of_inputs)
raise argparse.ArgumentTypeError(msg)
# Process Cube
result = process(cubes, args.wxtree)
# Save Cube
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Extend radar mask based on coverage data."""
parser = ArgParser(description="Extend radar mask based on coverage "
"data.")
parser.add_argument("radar_data_filepath",
metavar="RADAR_DATA_FILEPATH",
type=str,
help="Full path to input NetCDF file "
"containing the radar variable to remask.")
parser.add_argument("coverage_filepath",
metavar="COVERAGE_FILEPATH",
type=str,
help="Full path to input NetCDF file "
"containing radar coverage data.")
parser.add_argument("output_filepath",
metavar="OUTPUT_FILEPATH",
type=str,
help="Full path to save remasked radar data "
"NetCDF file.")
parser.add_argument("--fix_float64",
action='store_true',
default=False,
help="Check and fix cube for float64 data. Without "
"this option an exception will be raised if "
"float64 data is found but no fix applied.")
args = parser.parse_args(args=argv)
# load data
radar_data = load_cube(args.radar_data_filepath)
coverage = load_cube(args.coverage_filepath)
# extend mask
remasked_data = ExtendRadarMask().process(radar_data, coverage)
# Check and fix for float64 data only option:
check_cube_not_float64(remasked_data, fix=args.fix_float64)
# save output file
save_netcdf(remasked_data, args.output_filepath)
def main(argv=None):
"""Calculate orographic enhancement of precipitation from model pressure,
temperature, relative humidity and wind input files"""
parser = ArgParser(description='Calculate orographic enhancement using the'
' ResolveWindComponents() and OrographicEnhancement() '
'plugins. Outputs data on the high resolution orography'
' grid and regridded to the coarser resolution of the '
'input diagnostic variables.')
parser.add_argument('temperature_filepath',
metavar='TEMPERATURE_FILEPATH',
help='Full path to input NetCDF file of temperature on'
' height levels')
parser.add_argument('humidity_filepath',
metavar='HUMIDITY_FILEPATH',
help='Full path to input NetCDF file of relative '
'humidity on height levels')
parser.add_argument('pressure_filepath',
metavar='PRESSURE_FILEPATH',
help='Full path to input NetCDF file of pressure on '
'height levels')
parser.add_argument('windspeed_filepath',
metavar='WINDSPEED_FILEPATH',
help='Full path to input NetCDF file of wind speed on '
'height levels')
parser.add_argument('winddir_filepath',
metavar='WINDDIR_FILEPATH',
help='Full path to input NetCDF file of wind direction'
' on height levels')
parser.add_argument('orography_filepath',
metavar='OROGRAPHY_FILEPATH',
help='Full path to input NetCDF high resolution '
'orography ancillary. This should be on the same or a '
'finer resolution grid than the input variables, and '
'defines the grid on which the orographic enhancement '
'will be calculated.')
parser.add_argument('output_dir',
metavar='OUTPUT_DIR',
help='Directory '
'to write output orographic enhancement files')
parser.add_argument('--boundary_height',
type=float,
default=1000.,
help='Model height level to extract variables for '
'calculating orographic enhancement, as proxy for '
'the boundary layer.')
parser.add_argument('--boundary_height_units',
type=str,
default='m',
help='Units of the boundary height specified for '
'extracting model levels.')
args = parser.parse_args(args=argv)
constraint_info = (args.boundary_height, args.boundary_height_units)
temperature = load_and_extract(args.temperature_filepath, *constraint_info)
humidity = load_and_extract(args.humidity_filepath, *constraint_info)
pressure = load_and_extract(args.pressure_filepath, *constraint_info)
wind_speed = load_and_extract(args.windspeed_filepath, *constraint_info)
wind_dir = load_and_extract(args.winddir_filepath, *constraint_info)
# load high resolution orography
orography = load_cube(args.orography_filepath)
orogenh_high_res, orogenh_standard = process(temperature, humidity,
pressure, wind_speed,
wind_dir, orography)
# generate file names
fname_standard = os.path.join(args.output_dir,
generate_file_name(orogenh_standard))
fname_high_res = os.path.join(
args.output_dir,
generate_file_name(orogenh_high_res,
parameter="orographic_enhancement_high_resolution"))
# save output files
save_netcdf(orogenh_standard, fname_standard)
save_netcdf(orogenh_high_res, fname_high_res)
def main(argv=None):
"""Load in arguments and get going."""
parser = ArgParser(
description="Calculate the continuous falling snow level ")
parser.add_argument("temperature",
metavar="TEMPERATURE",
help="Path to a NetCDF file of air temperatures at"
" heights (m) at the points for which the continuous "
"falling snow level is being calculated.")
parser.add_argument("relative_humidity",
metavar="RELATIVE_HUMIDITY",
help="Path to a NetCDF file of relative_humidities at"
" heights (m) at the points for which the continuous "
"falling snow level is being calculated.")
parser.add_argument("pressure",
metavar="PRESSURE",
help="Path to a NetCDF file of air pressures at"
" heights (m) at the points for which the continuous "
"falling snow level is being calculated.")
parser.add_argument("orography",
metavar="OROGRAPHY",
help="Path to a NetCDF file containing "
"the orography height in m of the terrain "
"over which the continuous falling snow level is "
"being calculated.")
parser.add_argument("land_sea_mask",
metavar="LAND_SEA_MASK",
help="Path to a NetCDF file containing "
"the binary land-sea mask for the points "
"for which the continuous falling snow level is "
"being calculated. Land points are set to 1, sea "
"points are set to 0.")
parser.add_argument("output_filepath",
metavar="OUTPUT_FILE",
help="The output path for the processed NetCDF")
parser.add_argument("--precision",
metavar="NEWTON_PRECISION",
default=0.005,
type=float,
help="Precision to which the wet bulb temperature "
"is required: This is used by the Newton iteration "
"default value is 0.005")
parser.add_argument("--falling_level_threshold",
metavar="FALLING_LEVEL_THRESHOLD",
default=90.0,
type=float,
help=("Cutoff threshold for the wet-bulb integral used"
" to calculate the falling snow level. This "
"threshold indicates the level at which falling "
"snow is deemed to have melted to become rain. "
"The default value is 90.0, an empirically "
"derived value."))
args = parser.parse_args(args=argv)
# Load Cubes
temperature = load_cube(args.temperature, no_lazy_load=True)
relative_humidity = load_cube(args.relative_humidity, no_lazy_load=True)
pressure = load_cube(args.pressure, no_lazy_load=True)
orog = load_cube(args.orography, no_lazy_load=True)
land_sea = load_cube(args.land_sea_mask, no_lazy_load=True)
# Process Cube
result = process(temperature, relative_humidity, pressure, orog, land_sea,
args.precision, args.falling_level_threshold)
# Save Cube
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in arguments and get going."""
parser = ArgParser(
description="Calculate percentiled data over a given coordinate by "
"collapsing that coordinate. Typically used to convert realization "
"data into percentiled data, but may calculate over any "
"dimension coordinate. Alternatively, calling this CLI with a dataset"
" containing probabilities will convert those to percentiles using "
"the ensemble copula coupling plugin. If no particular percentiles "
"are given at which to calculate values and no 'number of percentiles'"
" to calculate are specified, the following defaults will be used: "
"[0, 5, 10, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 95, 100]")
parser.add_argument("input_filepath",
metavar="INPUT_FILE",
help="A path to an input NetCDF file to be processed")
parser.add_argument("output_filepath",
metavar="OUTPUT_FILE",
help="The output path for the processed NetCDF")
parser.add_argument("--coordinates",
metavar="COORDINATES_TO_COLLAPSE",
nargs="+",
help="Coordinate or coordinates over which to collapse"
" data and calculate percentiles; e.g. "
"'realization' or 'latitude longitude'. This argument "
"must be provided when collapsing a coordinate or "
"coordinates to create percentiles, but is redundant "
"when converting probabilities to percentiles and may "
"be omitted. This coordinate(s) will be removed "
"and replaced by a percentile coordinate.")
parser.add_argument('--ecc_bounds_warning',
default=False,
action='store_true',
help='If True, where calculated percentiles are '
'outside the ECC bounds range, raise a warning '
'rather than an exception.')
group = parser.add_mutually_exclusive_group(required=False)
group.add_argument("--percentiles",
metavar="PERCENTILES",
nargs="+",
default=None,
type=float,
help="Optional definition of percentiles at which to "
"calculate data, e.g. --percentiles 0 33.3 66.6 100")
group.add_argument('--no-of-percentiles',
default=None,
type=int,
metavar='NUMBER_OF_PERCENTILES',
help="Optional definition of the number of percentiles "
"to be generated, these distributed regularly with the "
"aim of dividing into blocks of equal probability.")
args = parser.parse_args(args=argv)
# Load Cube
cube = load_cube(args.input_filepath)
# Process Cube
result = process(cube, args.coordinates, args.ecc_bounds_warning,
args.percentiles, args.no_of_percentiles)
# Save Cube
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in arguments for estimating coefficients for Ensemble Model Output
Statistics (EMOS), otherwise known as Non-homogeneous Gaussian
Regression (NGR). 2 sources of input data must be provided: historical
forecasts and historical truth data (to use in calibration). The
estimated coefficients are written to a netCDF file.
"""
parser = ArgParser(
description='Estimate coefficients for Ensemble Model Output '
'Statistics (EMOS), otherwise known as Non-homogeneous '
'Gaussian Regression (NGR). There are two methods for '
'inputting data into this CLI, either by providing the '
'historic forecasts and truth separately, or by providing '
'a combined list of historic forecasts and truths along '
'with historic_forecast_identifier and truth_identifier '
'arguments to provide metadata that distinguishes between '
'them.')
parser.add_argument('distribution', metavar='DISTRIBUTION',
choices=['gaussian', 'truncated_gaussian'],
help='The distribution that will be used for '
'calibration. This will be dependent upon the '
'input phenomenon. This has to be supported by '
'the minimisation functions in '
'ContinuousRankedProbabilityScoreMinimisers.')
parser.add_argument('cycletime', metavar='CYCLETIME', type=str,
help='This denotes the cycle at which forecasts '
'will be calibrated using the calculated '
'EMOS coefficients. The validity time in the '
'output coefficients cube will be calculated '
'relative to this cycletime. '
'This cycletime is in the format '
'YYYYMMDDTHHMMZ.')
# Historic forecast and truth filepaths
parser.add_argument(
'--historic_filepath', metavar='HISTORIC_FILEPATH', nargs='+',
help='Paths to the input NetCDF files containing the '
'historic forecast(s) used for calibration. '
'This must be supplied with an associated truth filepath. '
'Specification of either the combined_filepath, '
'historic_forecast_identifier or the truth_identifier is '
'invalid with this argument.')
parser.add_argument(
'--truth_filepath', metavar='TRUTH_FILEPATH', nargs='+',
help='Paths to the input NetCDF files containing the '
'historic truth analyses used for calibration. '
'This must be supplied with an associated historic filepath. '
'Specification of either the combined_filepath, '
'historic_forecast_identifier or the truth_identifier is '
'invalid with this argument.')
# Input filepaths
parser.add_argument(
'--combined_filepath', metavar='COMBINED_FILEPATH', nargs='+',
help='Paths to the input NetCDF files containing '
'both the historic forecast(s) and truth '
'analyses used for calibration. '
'This must be supplied with both the '
'historic_forecast_identifier and the truth_identifier. '
'Specification of either the historic_filepath or the '
'truth_filepath is invalid with this argument.')
parser.add_argument(
"--historic_forecast_identifier",
metavar='HISTORIC_FORECAST_IDENTIFIER',
help='The path to a json file containing metadata '
'information that defines the historic forecast. '
'This must be supplied with both the combined_filepath and the '
'truth_identifier. Specification of either the historic_filepath'
'or the truth_filepath is invalid with this argument. '
'The intended contents is described in improver.'
'ensemble_calibration.ensemble_calibration_utilities.'
'SplitHistoricForecastAndTruth.')
parser.add_argument(
"--truth_identifier", metavar='TRUTH_IDENTIFIER',
help='The path to a json file containing metadata '
'information that defines the truth.'
'This must be supplied with both the combined_filepath and the '
'historic_forecast_identifier. Specification of either the '
'historic_filepath or the truth_filepath is invalid with this '
'argument. The intended contents is described in improver.'
'ensemble_calibration.ensemble_calibration_utilities.'
'SplitHistoricForecastAndTruth.')
# Output filepath
parser.add_argument('output_filepath', metavar='OUTPUT_FILEPATH',
help='The output path for the processed NetCDF')
# Optional arguments.
parser.add_argument('--units', metavar='UNITS',
help='The units that calibration should be undertaken '
'in. The historical forecast and truth will be '
'converted as required.')
parser.add_argument('--predictor_of_mean', metavar='PREDICTOR_OF_MEAN',
choices=['mean', 'realizations'], default='mean',
help='String to specify the predictor used to '
'calibrate the forecast mean. Currently the '
'ensemble mean ("mean") and the ensemble '
'realizations ("realizations") are supported as '
'options. Default: "mean".')
parser.add_argument('--max_iterations', metavar='MAX_ITERATIONS',
type=np.int32, default=1000,
help='The maximum number of iterations allowed '
'until the minimisation has converged to a '
'stable solution. If the maximum number '
'of iterations is reached, but the '
'minimisation has not yet converged to a '
'stable solution, then the available solution '
'is used anyway, and a warning is raised.'
'This may be modified for testing purposes '
'but otherwise kept fixed. If the '
'predictor_of_mean is "realizations", '
'then the number of iterations may require '
'increasing, as there will be more coefficients '
'to solve for.')
args = parser.parse_args(args=argv)
# Load Cubes
historic_forecast = load_cube(args.historic_filepath, allow_none=True)
truth = load_cube(args.truth_filepath, allow_none=True)
combined = (load_cubelist(args.combined_filepath)
if args.combined_filepath else None)
historic_forecast_dict = (
load_json_or_none(args.historic_forecast_identifier))
truth_dict = load_json_or_none(args.truth_identifier)
# Process Cube
coefficients = process(historic_forecast, truth, combined,
historic_forecast_dict, truth_dict,
args.distribution, args.cycletime, args.units,
args.predictor_of_mean, args.max_iterations)
# Save Cube
# Check whether a coefficients cube has been created. If the historic
# forecasts and truths provided did not match in validity time, then
# no coefficients would have been calculated.
if coefficients:
save_netcdf(coefficients, args.output_filepath)
def main(argv=None):
"""Load in arguments for applying neighbourhood processing when using a
mask."""
parser = ArgParser(
description='Neighbourhood the input dataset over two distinct regions'
' of land and sea. If performed as a single level neighbourhood, a '
'land-sea mask should be provided. If instead topographic_zone '
'neighbourhooding is being employed, the mask should be one of '
'topographic zones. In the latter case a weights array is also needed'
' to collapse the topographic_zone coordinate. These weights are '
'created with the improver generate-topography-bands-weights CLI and '
'should be made using a land-sea mask, which will then be employed '
'within this code to draw the distinction between the two surface '
'types.')
parser.add_argument('input_filepath',
metavar='INPUT_FILE',
help='A path to an input NetCDF file to be processed.')
parser.add_argument('input_mask_filepath',
metavar='INPUT_MASK',
help=('A path to an input NetCDF file containing '
'either a mask of topographic zones over land '
'or a land-sea mask.'))
parser.add_argument('output_filepath',
metavar='OUTPUT_FILE',
help='The output path for the processed NetCDF.')
mask_group = parser.add_argument_group(
'Collapse weights - required if using a topographic zones mask')
mask_group.add_argument('--weights_for_collapsing_dim',
metavar='WEIGHTS',
default=None,
help='A path to an weights NetCDF file containing '
'the weights which are used for collapsing the '
'dimension gained through masking. These weights '
'must have been created using a land-sea mask.')
radius_group = parser.add_argument_group(
'Neighbourhooding Radius - Set only one of the options')
group = radius_group.add_mutually_exclusive_group()
group.add_argument('--radius',
metavar='RADIUS',
type=float,
help='The radius (in m) for neighbourhood processing.')
group.add_argument('--radii-by-lead-time',
metavar=('RADII_BY_LEAD_TIME', 'LEAD_TIME_IN_HOURS'),
nargs=2,
help='The radii for neighbourhood processing '
'and the associated lead times at which the radii are '
'valid. The radii are in metres whilst the lead time '
'has units of hours. The radii and lead times are '
'expected as individual comma-separated lists with '
'the list of radii given first followed by a list of '
'lead times to indicate at what lead time each radii '
'should be used. For example: 10000,12000,14000 1,2,3 '
'where a lead time of 1 hour uses a radius of 10000m, '
'a lead time of 2 hours uses a radius of 12000m, etc.')
parser.add_argument('--sum_or_fraction',
default="fraction",
choices=["sum", "fraction"],
help='The neighbourhood output can either be in the '
'form of a sum of the neighbourhood, or a '
'fraction calculated by dividing the sum of the '
'neighbourhood by the neighbourhood area. '
'"fraction" is the default option.')
parser.add_argument('--intermediate_filepath',
default=None,
help='Intermediate filepath for results following '
'topographic masked neighbourhood processing of '
'land points and prior to collapsing the '
'topographic_zone coordinate. Intermediate files '
'will not be produced if no topographic masked '
'neighbourhood processing occurs.')
args = parser.parse_args(args=argv)
cube = load_cube(args.input_filepath)
mask = load_cube(args.input_mask_filepath, no_lazy_load=True)
weights = None
if any([
'topographic_zone' in coord.name()
for coord in mask.coords(dim_coords=True)
]):
if mask.attributes['topographic_zones_include_seapoints'] == 'True':
raise ValueError('The topographic zones mask cube must have been '
'masked to exclude sea points, but '
'topographic_zones_include_seapoints = True')
if not args.weights_for_collapsing_dim:
raise IOError('A weights cube must be provided if using a mask '
'of topographic zones to collapse the resulting '
'vertical dimension.')
weights = load_cube(args.weights_for_collapsing_dim, no_lazy_load=True)
result, intermediate_cube = process(cube, mask, args.radius,
args.radii_by_lead_time, weights,
args.sum_or_fraction,
args.intermediate_filepath)
save_netcdf(result, args.output_filepath)
if args.intermediate_filepath:
save_netcdf(intermediate_cube, args.intermediate_filepath)
def main(argv=None):
"""Load in arguments and get going."""
parser = ArgParser(
description="Run a recursive filter to convert a square neighbourhood "
"into a Gaussian-like kernel or smooth over short "
"distances. The filter uses an alpha parameter (0 < alpha < 1) to "
"control what proportion of the probability is passed onto the next "
"grid-square in the x and y directions. The alpha parameter can be "
"set on a grid-square by grid-square basis for the x and y directions "
"separately (using two arrays of alpha parameters of the same "
"dimensionality as the domain). Alternatively a single alpha value "
"can be set for each of the x and y directions. These methods can be "
"mixed, e.g. an array for the x direction and a float for the y "
"direction and vice versa.")
parser.add_argument("input_filepath",
metavar="INPUT_FILE",
help="A path to an input NetCDF file to be processed")
parser.add_argument("output_filepath",
metavar="OUTPUT_FILE",
help="The output path for the processed NetCDF")
parser.add_argument("--input_filepath_alphas_x",
metavar="ALPHAS_X_FILE",
help="A path to a NetCDF file describing the alpha "
"factors to be used for smoothing in the x "
"direction")
parser.add_argument("--input_filepath_alphas_y",
metavar="ALPHAS_Y_FILE",
help="A path to a NetCDF file describing the alpha "
"factors to be used for smoothing in the y "
"direction")
parser.add_argument("--alpha_x",
metavar="ALPHA_X",
default=None,
type=float,
help="A single alpha factor (0 < alpha_x < 1) to be "
"applied to every grid square in the x "
"direction.")
parser.add_argument("--alpha_y",
metavar="ALPHA_Y",
default=None,
type=float,
help="A single alpha factor (0 < alpha_y < 1) to be "
"applied to every grid square in the y "
"direction.")
parser.add_argument("--iterations",
metavar="ITERATIONS",
default=1,
type=int,
help="Number of times to apply the filter, default=1 "
"(typically < 5)")
parser.add_argument('--input_mask_filepath',
metavar='INPUT_MASK_FILE',
help='A path to an input mask NetCDF file to be '
'used to mask the input file.')
parser.add_argument("--re_mask",
action='store_true',
default=False,
help="Re-apply mask to recursively filtered output.")
args = parser.parse_args(args=argv)
# Load Cubes.
cube = load_cube(args.input_filepath)
mask_cube = load_cube(args.input_mask_filepath, allow_none=True)
alphas_x_cube = load_cube(args.input_filepath_alphas_x, allow_none=True)
alphas_y_cube = load_cube(args.input_filepath_alphas_y, allow_none=True)
# Process Cube
result = process(cube, mask_cube, alphas_x_cube, alphas_y_cube,
args.alpha_x, args.alpha_y, args.iterations, args.re_mask)
# Save Cube
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in arguments and ensure they are set correctly.
Then load in the data to blend and calculate default weights
using the method chosen before carrying out the blending."""
parser = ArgParser(
description='Calculate the default weights to apply in weighted '
'blending plugins using the ChooseDefaultWeightsLinear or '
'ChooseDefaultWeightsNonLinear plugins. Then apply these '
'weights to the dataset using the BasicWeightedAverage plugin.'
' Required for ChooseDefaultWeightsLinear: y0val and ynval.'
' Required for ChooseDefaultWeightsNonLinear: cval.'
' Required for ChooseWeightsLinear with dict: wts_dict.')
parser.add_argument('--wts_calc_method',
metavar='WEIGHTS_CALCULATION_METHOD',
choices=['linear', 'nonlinear', 'dict'],
default='linear',
help='Method to use to calculate '
'weights used in blending. "linear" (default): '
'calculate linearly varying blending weights. '
'"nonlinear": calculate blending weights that decrease'
' exponentially with increasing blending coordinate. '
'"dict": calculate weights using a dictionary passed '
'in as a command line argument.')
parser.add_argument('coordinate',
type=str,
metavar='COORDINATE_TO_AVERAGE_OVER',
help='The coordinate over which the blending '
'will be applied.')
parser.add_argument('--coordinate_unit',
metavar='UNIT_STRING',
default='hours since 1970-01-01 00:00:00',
help='Units for blending coordinate. Default= '
'hours since 1970-01-01 00:00:00')
parser.add_argument('--calendar',
metavar='CALENDAR',
help='Calendar for time coordinate. Default=gregorian')
parser.add_argument('--cycletime',
metavar='CYCLETIME',
type=str,
help='The forecast reference time to be used after '
'blending has been applied, in the format '
'YYYYMMDDTHHMMZ. If not provided, the blended file '
'will take the latest available forecast reference '
'time from the input cubes supplied.')
parser.add_argument('--model_id_attr',
metavar='MODEL_ID_ATTR',
type=str,
default="mosg__model_configuration",
help='The name of the netCDF file attribute to be '
'used to identify the source model for '
'multi-model blends. Default assumes Met Office '
'model metadata. Must be present on all input '
'files if blending over models.')
parser.add_argument('--spatial_weights_from_mask',
action='store_true',
default=False,
help='If set this option will result in the generation'
' of spatially varying weights based on the'
' masks of the data we are blending. The'
' one dimensional weights are first calculated '
' using the chosen weights calculation method,'
' but the weights will then be adjusted spatially'
' based on where there is masked data in the data'
' we are blending. The spatial weights are'
' calculated using the'
' SpatiallyVaryingWeightsFromMask plugin.')
parser.add_argument('weighting_mode',
metavar='WEIGHTED_BLEND_MODE',
choices=['weighted_mean', 'weighted_maximum'],
help='The method used in the weighted blend. '
'"weighted_mean": calculate a normal weighted'
' mean across the coordinate. '
'"weighted_maximum": multiplies the values in the'
' coordinate by the weights, and then takes the'
' maximum.')
parser.add_argument('input_filepaths',
metavar='INPUT_FILES',
nargs="+",
help='Paths to input files to be blended.')
parser.add_argument('output_filepath',
metavar='OUTPUT_FILE',
help='The output path for the processed NetCDF.')
spatial = parser.add_argument_group(
'Spatial weights from mask options',
'Options for calculating the spatial weights using the '
'SpatiallyVaryingWeightsFromMask plugin.')
spatial.add_argument('--fuzzy_length',
metavar='FUZZY_LENGTH',
type=float,
default=20000,
help='When calculating spatially varying weights we'
' can smooth the weights so that areas close to'
' areas that are masked have lower weights than'
' those further away. This fuzzy length controls'
' the scale over which the weights are smoothed.'
' The fuzzy length is in terms of m, the'
' default is 20km. This distance is then'
' converted into a number of grid squares,'
' which does not have to be an integer. Assumes'
' the grid spacing is the same in the x and y'
' directions, and raises an error if this is not'
' true. See SpatiallyVaryingWeightsFromMask for'
' more detail.')
linear = parser.add_argument_group(
'linear weights options', 'Options for the linear weights '
'calculation in '
'ChooseDefaultWeightsLinear')
linear.add_argument('--y0val',
metavar='LINEAR_STARTING_POINT',
type=float,
help='The relative value of the weighting start point '
'(lowest value of blend coord) for choosing default '
'linear weights. This must be a positive float or 0.')
linear.add_argument('--ynval',
metavar='LINEAR_END_POINT',
type=float,
help='The relative value of the weighting '
'end point (highest value of blend coord) for choosing'
' default linear weights. This must be a positive '
'float or 0. Note that if blending over forecast '
'reference time, ynval >= y0val would normally be '
'expected (to give greater weight to the more recent '
'forecast).')
nonlinear = parser.add_argument_group(
'nonlinear weights options', 'Options for the non-linear '
'weights calculation in '
'ChooseDefaultWeightsNonLinear')
nonlinear.add_argument('--cval',
metavar='NON_LINEAR_FACTOR',
type=float,
help='Factor used to determine how skewed the '
'non linear weights will be. '
'A value of 1 implies equal weighting. If not '
'set, a default value of cval=0.85 is set.')
wts_dict = parser.add_argument_group(
'dict weights options', 'Options for linear weights to be '
'calculated based on parameters '
'read from a json file dict')
wts_dict.add_argument('--wts_dict',
metavar='WEIGHTS_DICTIONARY',
help='Path to json file containing dictionary from '
'which to calculate blending weights. Dictionary '
'format is as specified in the improver.blending.'
'weights.ChooseWeightsLinear plugin.')
wts_dict.add_argument('--weighting_coord',
metavar='WEIGHTING_COORD',
default='forecast_period',
help='Name of '
'coordinate over which linear weights should be '
'scaled. This coordinate must be avilable in the '
'weights dictionary.')
args = parser.parse_args(args=argv)
# if the linear weights method is called with non-linear args or vice
# versa, exit with error
if (args.wts_calc_method == "linear") and args.cval:
parser.wrong_args_error('cval', 'linear')
if ((args.wts_calc_method == "nonlinear")
and np.any([args.y0val, args.ynval])):
parser.wrong_args_error('y0val, ynval', 'non-linear')
if (args.wts_calc_method == "dict") and not args.wts_dict:
parser.error('Dictionary is required if --wts_calc_method="dict"')
# set blending coordinate units
if "time" in args.coordinate:
coord_unit = Unit(args.coordinate_unit, args.calendar)
elif args.coordinate_unit != 'hours since 1970-01-01 00:00:00.':
coord_unit = args.coordinate_unit
else:
coord_unit = 'no_unit'
# For blending across models, only blending across "model_id" is directly
# supported. This is because the blending coordinate must be sortable, in
# order to ensure that the data cube and the weights cube have coordinates
# in the same order for blending. Whilst the model_configuration is
# sortable itself, as it is associated with model_id, which is the
# dimension coordinate, sorting the model_configuration coordinate can
# result in the model_id coordinate becoming non-monotonic. As dimension
# coordinates must be monotonic, this leads to the model_id coordinate
# being demoted to an auxiliary coordinate. Therefore, for simplicity
# model_id is used as the blending coordinate, instead of
# model_configuration.
# TODO: Support model_configuration as a blending coordinate directly.
if args.coordinate == "model_configuration":
blend_coord = "model_id"
dict_coord = "model_configuration"
else:
blend_coord = args.coordinate
dict_coord = args.coordinate
# load cubes to be blended
cubelist = load_cubelist(args.input_filepaths)
# determine whether or not to equalise forecast periods for model
# blending weights calculation
weighting_coord = (args.weighting_coord
if args.weighting_coord else "forecast_period")
# prepare cubes for weighted blending
merger = MergeCubesForWeightedBlending(blend_coord,
weighting_coord=weighting_coord,
model_id_attr=args.model_id_attr)
cube = merger.process(cubelist, cycletime=args.cycletime)
# if the coord for blending does not exist or has only one value,
# update metadata only
coord_names = [coord.name() for coord in cube.coords()]
if (blend_coord not in coord_names) or (len(
cube.coord(blend_coord).points) == 1):
result = cube.copy()
conform_metadata(result, cube, blend_coord, cycletime=args.cycletime)
# raise a warning if this happened because the blend coordinate
# doesn't exist
if blend_coord not in coord_names:
warnings.warn('Blend coordinate {} is not present on input '
'data'.format(blend_coord))
# otherwise, calculate weights and blend across specified dimension
else:
weights = calculate_blending_weights(
cube,
blend_coord,
args.wts_calc_method,
wts_dict=args.wts_dict,
weighting_coord=args.weighting_coord,
coord_unit=coord_unit,
y0val=args.y0val,
ynval=args.ynval,
cval=args.cval,
dict_coord=dict_coord)
if args.spatial_weights_from_mask:
check_if_grid_is_equal_area(cube)
grid_cells_x, _ = convert_distance_into_number_of_grid_cells(
cube, args.fuzzy_length, int_grid_cells=False)
SpatialWeightsPlugin = SpatiallyVaryingWeightsFromMask(
grid_cells_x)
weights = SpatialWeightsPlugin.process(cube, weights, blend_coord)
# blend across specified dimension
BlendingPlugin = WeightedBlendAcrossWholeDimension(
blend_coord, args.weighting_mode, cycletime=args.cycletime)
result = BlendingPlugin.process(cube, weights=weights)
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in arguments and get going."""
parser = ArgParser(
description="Calculate percentiled data over a given coordinate by "
"collapsing that coordinate. Typically used to convert realization "
"data into percentiled data, but may calculate over any "
"dimension coordinate. Alternatively, calling this CLI with a dataset"
" containing probabilities will convert those to percentiles using "
"the ensemble copula coupling plugin. If no particular percentiles "
"are given at which to calculate values and no 'number of percentiles'"
" to calculate are specified, the following defaults will be used: "
"[0, 5, 10, 20, 25, 30, 40, 50, 60, 70, 75, 80, 90, 95, 100]")
parser.add_argument("input_filepath",
metavar="INPUT_FILE",
help="A path to an input NetCDF file to be processed")
parser.add_argument("output_filepath",
metavar="OUTPUT_FILE",
help="The output path for the processed NetCDF")
parser.add_argument("--coordinates",
metavar="COORDINATES_TO_COLLAPSE",
nargs="+",
help="Coordinate or coordinates over which to collapse"
" data and calculate percentiles; e.g. "
"'realization' or 'latitude longitude'. This argument "
"must be provided when collapsing a coordinate or "
"coordinates to create percentiles, but is redundant "
"when converting probabilities to percentiles and may "
"be omitted. This coordinate(s) will be removed "
"and replaced by a percentile coordinate.")
parser.add_argument('--ecc_bounds_warning',
default=False,
action='store_true',
help='If True, where calculated percentiles are '
'outside the ECC bounds range, raise a warning '
'rather than an exception.')
group = parser.add_mutually_exclusive_group(required=False)
group.add_argument("--percentiles",
metavar="PERCENTILES",
nargs="+",
default=None,
type=float,
help="Optional definition of percentiles at which to "
"calculate data, e.g. --percentiles 0 33.3 66.6 100")
group.add_argument('--no-of-percentiles',
default=None,
type=int,
metavar='NUMBER_OF_PERCENTILES',
help="Optional definition of the number of percentiles "
"to be generated, these distributed regularly with the "
"aim of dividing into blocks of equal probability.")
args = parser.parse_args(args=argv)
cube = load_cube(args.input_filepath)
percentiles = args.percentiles
if args.no_of_percentiles is not None:
percentiles = choose_set_of_percentiles(args.no_of_percentiles,
sampling="quantile")
# TODO: Correct when formal cf-standards exists
if 'probability_of_' in cube.name():
if args.coordinates:
warnings.warn("Converting probabilities to percentiles. The "
"provided COORDINATES_TO_COLLAPSE variable will "
"not be used.")
result = GeneratePercentilesFromProbabilities(
ecc_bounds_warning=args.ecc_bounds_warning).process(
cube, percentiles=percentiles)
else:
if not args.coordinates:
raise ValueError("To collapse a coordinate to calculate "
"percentiles, a coordinate or list of "
"coordinates must be provided.")
# Switch back to use the slow scipy method if the cube contains masked
# data which the numpy method cannot handle.
fast_percentile_method = True
if np.ma.is_masked(cube.data):
# Check for masked points:
fast_percentile_method = False
elif np.ma.isMaskedArray(cube.data):
# Check if we have a masked array with an empty mask. If so,
# replace it with a non-masked array:
cube.data = cube.data.data
result = PercentileConverter(
args.coordinates,
percentiles=percentiles,
fast_percentile_method=fast_percentile_method).process(cube)
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Calculate temperature lapse rates."""
parser = ArgParser(
description='Calculate temperature lapse rates in units of K m-1 '
'over a given orography grid. ')
parser.add_argument('temperature_filepath',
metavar='INPUT_TEMPERATURE_FILE',
help='A path to an input NetCDF temperature file to'
'be processed. ')
parser.add_argument('--orography_filepath',
metavar='INPUT_OROGRAPHY_FILE',
help='A path to an input NetCDF orography file. ')
parser.add_argument('--land_sea_mask_filepath',
metavar='LAND_SEA_MASK_FILE',
help='A path to an input NetCDF land/sea mask file. ')
parser.add_argument('output_filepath',
metavar='OUTPUT_FILE',
help='The output path for the processed temperature '
'lapse rates NetCDF. ')
parser.add_argument('--max_height_diff',
metavar='MAX_HEIGHT_DIFF',
type=float,
default=35,
help='Maximum allowable height difference between the '
'central point and points in the neighbourhood '
'over which the lapse rate will be calculated '
'(metres).')
parser.add_argument('--nbhood_radius',
metavar='NBHOOD_RADIUS',
type=int,
default=7,
help='Radius of neighbourhood around each point. '
'The neighbourhood will be a square array with '
'side length 2*nbhood_radius + 1.')
parser.add_argument('--max_lapse_rate',
metavar='MAX_LAPSE_RATE',
type=float,
default=-3 * DALR,
help='Maximum lapse rate allowed which must be '
'provided in units of K m-1. Default is -3*DALR')
parser.add_argument('--min_lapse_rate',
metavar='MIN_LAPSE_RATE',
type=float,
default=DALR,
help='Minimum lapse rate allowed which must be '
'provided in units of K m-1. Default is the DALR')
parser.add_argument('--return_dalr',
action='store_true',
default=False,
help='Flag to return a cube containing the dry '
'adiabatic lapse rate rather than calculating '
'the true lapse rate.')
args = parser.parse_args(args=argv)
# Load Cubes
temperature_cube = load_cube(args.temperature_filepath)
orography_cube = None
land_sea_mask_cube = None
if not args.return_dalr:
orography_cube = load_cube(args.orography_filepath)
land_sea_mask_cube = load_cube(args.land_sea_mask_filepath)
# Process Cube
result = process(temperature_cube, orography_cube, land_sea_mask_cube,
args.max_height_diff, args.nbhood_radius,
args.max_lapse_rate, args.min_lapse_rate,
args.return_dalr)
# Save Cube
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in arguments and get going."""
parser = ArgParser(
description='Apply the requested neighbourhood method via '
'the NeighbourhoodProcessing plugin to a file '
'whose data can be loaded as a single iris.cube.Cube.')
parser.add_argument(
'neighbourhood_output',
metavar='NEIGHBOURHOOD_OUTPUT',
help='The form of the results generated using neighbourhood '
'processing. If "probabilities" is selected, the mean '
'probability within a neighbourhood is calculated. If '
'"percentiles" is selected, then the percentiles are calculated '
'within a neighbourhood. Calculating percentiles from a '
'neighbourhood is only supported for a circular neighbourhood. '
'Options: "probabilities", "percentiles".')
parser.add_argument('neighbourhood_shape',
metavar='NEIGHBOURHOOD_SHAPE',
choices=["circular", "square"],
help='The shape of the neighbourhood to apply in '
'neighbourhood processing. Only a "circular" '
'neighbourhood shape is applicable for '
'calculating "percentiles" output. '
'Options: "circular", "square".')
group = parser.add_mutually_exclusive_group()
group.add_argument('--radius',
metavar='RADIUS',
type=float,
help='The radius (in m) for neighbourhood processing.')
group.add_argument('--radii-by-lead-time',
metavar=('RADII_BY_LEAD_TIME', 'LEAD_TIME_IN_HOURS'),
nargs=2,
help='The radii for neighbourhood processing '
'and the associated lead times at which the radii are '
'valid. The radii are in metres whilst the lead time '
'has units of hours. The radii and lead times are '
'expected as individual comma-separated lists with '
'the list of radii given first followed by a list of '
'lead times to indicate at what lead time each radii '
'should be used. For example: 10000,12000,14000 1,2,3 '
'where a lead time of 1 hour uses a radius of 10000m, '
'a lead time of 2 hours uses a radius of 12000m, etc.')
parser.add_argument('--degrees_as_complex',
action='store_true',
default=False,
help='Set this flag to process angles,'
' eg wind directions, as complex numbers. Not '
'compatible with circular kernel, percentiles or '
'recursive filter.')
parser.add_argument('--weighted_mode',
action='store_true',
default=False,
help='For neighbourhood processing using a circular '
'kernel, setting the weighted_mode indicates the '
'weighting decreases with radius. '
'If weighted_mode is not set, a constant '
'weighting is assumed. weighted_mode is only '
'applicable for calculating "probability" '
'neighbourhood output.')
parser.add_argument('--sum_or_fraction',
default="fraction",
choices=["sum", "fraction"],
help='The neighbourhood output can either be in the '
'form of a sum of the neighbourhood, or a '
'fraction calculated by dividing the sum of the '
'neighbourhood by the neighbourhood area. '
'"fraction" is the default option.')
parser.add_argument('--re_mask',
action='store_true',
help='If re_mask is set (i.e. True), the original '
'un-neighbourhood processed mask is applied to '
'mask out the neighbourhood processed dataset. '
'If not set, re_mask defaults to False and the '
'original un-neighbourhood processed mask is '
'not applied. Therefore, the neighbourhood '
'processing may result in values being present '
'in areas that were originally masked. ')
parser.add_argument('--percentiles',
metavar='PERCENTILES',
default=DEFAULT_PERCENTILES,
nargs='+',
type=float,
help='Calculate values at the specified percentiles '
'from the neighbourhood surrounding each grid '
'point.')
parser.add_argument('input_filepath',
metavar='INPUT_FILE',
help='A path to an input NetCDF file to be processed.')
parser.add_argument('output_filepath',
metavar='OUTPUT_FILE',
help='The output path for the processed NetCDF.')
parser.add_argument('--input_mask_filepath',
metavar='INPUT_MASK_FILE',
help='A path to an input mask NetCDF file to be '
'used to mask the input file. '
'This is currently only supported for square '
'neighbourhoods. The data should contain 1 for '
'usable points and 0 for discarded points, e.g. '
'a land-mask.')
parser.add_argument('--halo_radius',
metavar='HALO_RADIUS',
default=None,
type=float,
help='radius in metres of excess halo to clip.'
' Used where a larger'
' grid was defined than the standard grid'
' and we want to clip the grid back to the'
' standard grid e.g. for global data'
' regridded to UK area. Default=None')
parser.add_argument('--apply-recursive-filter',
action='store_true',
default=False,
help='Option to apply the recursive filter to a '
'square neighbourhooded output dataset, '
'converting it into a Gaussian-like kernel or '
'smoothing over short distances. '
'The filter uses an alpha '
'parameter (0 < alpha < 1) to control what '
'proportion of the probability is passed onto '
'the next grid-square in the x and y directions. '
'The alpha parameter can be set on a grid-square '
'by grid-square basis for the x and y directions '
'separately (using two arrays of alpha '
'parameters of the same dimensionality as the '
'domain). Alternatively a single alpha value can '
'be set for each of the x and y directions. These'
' methods can be mixed, e.g. an array for the x '
'direction and a float for the y direction and '
'vice versa. The recursive filter cannot be '
'applied to a circular kernel')
parser.add_argument('--input_filepath_alphas_x_cube',
metavar='ALPHAS_X_FILE',
help='A path to a NetCDF file describing the alpha '
'factors to be used for smoothing in the x '
'direction when applying the recursive filter')
parser.add_argument('--input_filepath_alphas_y_cube',
metavar='ALPHAS_Y_FILE',
help='A path to a NetCDF file describing the alpha '
'factors to be used for smoothing in the y '
'direction when applying the recursive filter')
parser.add_argument('--alpha_x',
metavar='ALPHA_X',
default=None,
type=float,
help='A single alpha factor (0 < alpha_x < 1) to be '
'applied to every grid square in the x '
'direction when applying the recursive filter')
parser.add_argument('--alpha_y',
metavar='ALPHA_Y',
default=None,
type=float,
help='A single alpha factor (0 < alpha_y < 1) to be '
'applied to every grid square in the y '
'direction when applying the recursive filter.')
parser.add_argument('--iterations',
metavar='ITERATIONS',
default=1,
type=int,
help='Number of times to apply the filter, default=1 '
'(typically < 5)')
args = parser.parse_args(args=argv)
if (args.neighbourhood_output == "percentiles"
and args.neighbourhood_shape == "square"):
parser.wrong_args_error('square', 'neighbourhood_shape')
if (args.neighbourhood_output == "percentiles" and args.weighted_mode):
parser.wrong_args_error('weighted_mode',
'neighbourhood_shape=percentiles')
if (args.neighbourhood_output == "probabilities"
and args.percentiles != DEFAULT_PERCENTILES):
parser.wrong_args_error('percentiles',
'neighbourhood_shape=probabilities')
if (args.input_mask_filepath and args.neighbourhood_shape == "circular"):
parser.wrong_args_error('neighbourhood_shape=circular',
'input_mask_filepath')
if args.degrees_as_complex:
if args.neighbourhood_output == "percentiles":
parser.error('Cannot generate percentiles from complex numbers')
if args.neighbourhood_shape == "circular":
parser.error('Cannot process complex numbers with circular '
'neighbourhoods')
if args.apply_recursive_filter:
parser.error('Cannot process complex numbers with recursive '
'filter')
cube = load_cube(args.input_filepath)
if args.degrees_as_complex:
# convert cube data into complex numbers
cube.data = WindDirection.deg_to_complex(cube.data)
if args.radius:
radius_or_radii = args.radius
lead_times = None
elif args.radii_by_lead_time:
radius_or_radii = args.radii_by_lead_time[0].split(",")
lead_times = args.radii_by_lead_time[1].split(",")
if args.input_mask_filepath:
mask_cube = load_cube(args.input_mask_filepath)
else:
mask_cube = None
if args.neighbourhood_output == "probabilities":
result = (NeighbourhoodProcessing(args.neighbourhood_shape,
radius_or_radii,
lead_times=lead_times,
weighted_mode=args.weighted_mode,
sum_or_fraction=args.sum_or_fraction,
re_mask=args.re_mask).process(
cube, mask_cube=mask_cube))
elif args.neighbourhood_output == "percentiles":
result = (GeneratePercentilesFromANeighbourhood(
args.neighbourhood_shape,
radius_or_radii,
lead_times=lead_times,
percentiles=args.percentiles).process(cube))
# If the '--apply-recursive-filter' option has been specified in the
# input command, pass the neighbourhooded 'result' cube obtained above
# through the recursive-filter plugin before saving the output.
# The recursive filter is only applicable to square neighbourhoods.
if args.neighbourhood_shape == 'square' and args.apply_recursive_filter:
alphas_x_cube = None
alphas_y_cube = None
if args.input_filepath_alphas_x_cube is not None:
alphas_x_cube = load_cube(args.input_filepath_alphas_x_cube)
if args.input_filepath_alphas_y_cube is not None:
alphas_y_cube = load_cube(args.input_filepath_alphas_y_cube)
result = RecursiveFilter(alpha_x=args.alpha_x,
alpha_y=args.alpha_y,
iterations=args.iterations,
re_mask=args.re_mask).process(
result,
alphas_x=alphas_x_cube,
alphas_y=alphas_y_cube,
mask_cube=mask_cube)
elif args.neighbourhood_shape == 'circular' and \
args.apply_recursive_filter:
raise ValueError('Recursive filter option is not applicable to '
'circular neighbourhoods. ')
if args.degrees_as_complex:
# convert neighbourhooded cube back to degrees
result.data = WindDirection.complex_to_deg(result.data)
if args.halo_radius is not None:
result = remove_cube_halo(result, args.halo_radius)
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in arguments for applying neighbourhood processing when using a
mask."""
from improver.argparser import ArgParser
parser = ArgParser(
description='Apply the requested neighbourhood method via the '
'ApplyNeighbourhoodProcessingWithAMask plugin to a file '
'with one diagnostic dataset in combination with a file '
'containing one or more masks. The mask dataset may have '
'an extra dimension compared to the input diagnostic. '
'In this case, the user specifies the name of '
'the extra coordinate and this coordinate is iterated '
'over so each mask is applied to separate slices over the'
' input data. These intermediate masked datasets are then'
' concatenated, resulting in a dataset that has been '
' processed using multiple masks and has gained an extra '
'dimension from the masking. There is also an option to '
're-mask the output dataset, so that after '
'neighbourhood processing, non-zero values are only '
'present for unmasked grid points. '
'There is an alternative option of collapsing the '
'dimension that we gain using this processing using a '
'weighted average.')
parser.add_argument('coord_for_masking', metavar='COORD_FOR_MASKING',
help='Coordinate to iterate over when applying a mask '
'to the neighbourhood processing. ')
parser.add_argument('input_filepath', metavar='INPUT_FILE',
help='A path to an input NetCDF file to be processed.')
parser.add_argument('input_mask_filepath', metavar='INPUT_MASK_FILE',
help='A path to an input mask NetCDF file to be '
'used to mask the input file.')
parser.add_argument('output_filepath', metavar='OUTPUT_FILE',
help='The output path for the processed NetCDF.')
group = parser.add_mutually_exclusive_group()
group.add_argument('--radius', metavar='RADIUS', type=float,
help='The radius (in m) for neighbourhood processing.')
group.add_argument('--radii-by-lead-time',
metavar=('RADII_BY_LEAD_TIME', 'LEAD_TIME_IN_HOURS'),
nargs=2,
help='The radii for neighbourhood processing '
'and the associated lead times at which the radii are '
'valid. The radii are in metres whilst the lead time '
'has units of hours. The radii and lead times are '
'expected as individual comma-separated lists with '
'the list of radii given first followed by a list of '
'lead times to indicate at what lead time each radii '
'should be used. For example: 10000,12000,14000 1,2,3 '
'where a lead time of 1 hour uses a radius of 10000m, '
'a lead time of 2 hours uses a radius of 12000m, etc.')
parser.add_argument('--sum_or_fraction', default="fraction",
choices=["sum", "fraction"],
help='The neighbourhood output can either be in the '
'form of a sum of the neighbourhood, or a '
'fraction calculated by dividing the sum of the '
'neighbourhood by the neighbourhood area. '
'"fraction" is the default option.')
group2 = parser.add_mutually_exclusive_group()
group2.add_argument('--re_mask', action='store_true',
help='If re_mask is set (i.e. True), the output data '
'following neighbourhood processing is '
're-masked. This re-masking removes any values '
'that have been generated by neighbourhood '
'processing at grid points that were '
'originally masked. '
'If not set, re_mask defaults to False and no '
're-masking is applied to the neighbourhood '
'processed output. Therefore, the neighbourhood '
'processing may result in values being present '
'in areas that were originally masked. This '
'allows the the values in adjacent bands to be'
'weighted together if the additional dimension'
'from the masking process is collapsed.')
group2.add_argument('--collapse_dimension', action='store_true',
help='Collapse the dimension from the mask, by doing '
'a weighted mean using the weights provided. '
'This is only suitable when the result is is '
'left unmasked, so there is data to weight '
'between the points in coordinate we are '
'collapsing.')
parser.add_argument('--weights_for_collapsing_dim', metavar='WEIGHTS',
default=None,
help='A path to an weights NetCDF file containing the '
'weights which are used for collapsing the '
'dimension gained through masking.')
parser.add_argument('--intermediate_filepath', default=None,
help='If provided the result after neighbourhooding, '
'before collapsing the extra dimension is saved '
'in the given filepath.')
args = parser.parse_args(args=argv)
# Load Cubes
cube = cli.inputcube(args.input_filepath)
mask_cube = cli.inputcube(args.input_mask_filepath)
weights = cli.inputcube(args.weights_for_collapsing_dim) if \
args.collapse_dimension else None
# Process Cube
# pylint: disable=E1123
process(cube, mask_cube, weights, coord_for_masking=args.coord_for_masking,
radius=args.radius, radii_by_lead_time=args.radii_by_lead_time,
sum_or_fraction=args.sum_or_fraction, remask=args.re_mask,
collapse_dimension=args.collapse_dimension,
output=args.output_filepath,
intermediate_output=args.intermediate_filepath)
def main(argv=None):
"""Load in arguments and ensure they are set correctly.
Then load in the data to blend and calculate default weights
using the method chosen before carrying out the blending."""
parser = ArgParser(
description='Calculate the default weights to apply in weighted '
'blending plugins using the ChooseDefaultWeightsLinear or '
'ChooseDefaultWeightsNonLinear plugins. Then apply these '
'weights to the dataset using the BasicWeightedAverage plugin.'
' Required for ChooseDefaultWeightsLinear: y0val and ynval.'
' Required for ChooseDefaultWeightsNonLinear: cval.'
' Required for ChooseWeightsLinear with dict: wts_dict.')
parser.add_argument('--wts_calc_method',
metavar='WEIGHTS_CALCULATION_METHOD',
choices=['linear', 'nonlinear', 'dict'],
default='linear',
help='Method to use to calculate '
'weights used in blending. "linear" (default): '
'calculate linearly varying blending weights. '
'"nonlinear": calculate blending weights that decrease'
' exponentially with increasing blending coordinate. '
'"dict": calculate weights using a dictionary passed '
'in as a command line argument.')
parser.add_argument('coordinate',
type=str,
metavar='COORDINATE_TO_AVERAGE_OVER',
help='The coordinate over which the blending '
'will be applied.')
parser.add_argument('--cycletime',
metavar='CYCLETIME',
type=str,
help='The forecast reference time to be used after '
'blending has been applied, in the format '
'YYYYMMDDTHHMMZ. If not provided, the blended file '
'will take the latest available forecast reference '
'time from the input cubes supplied.')
parser.add_argument('--model_id_attr',
metavar='MODEL_ID_ATTR',
type=str,
default=None,
help='The name of the netCDF file attribute to be '
'used to identify the source model for '
'multi-model blends. Default is None. '
'Must be present on all input '
'files if blending over models.')
parser.add_argument('--spatial_weights_from_mask',
action='store_true',
default=False,
help='If set this option will result in the generation'
' of spatially varying weights based on the'
' masks of the data we are blending. The'
' one dimensional weights are first calculated '
' using the chosen weights calculation method,'
' but the weights will then be adjusted spatially'
' based on where there is masked data in the data'
' we are blending. The spatial weights are'
' calculated using the'
' SpatiallyVaryingWeightsFromMask plugin.')
parser.add_argument('input_filepaths',
metavar='INPUT_FILES',
nargs="+",
help='Paths to input files to be blended.')
parser.add_argument('output_filepath',
metavar='OUTPUT_FILE',
help='The output path for the processed NetCDF.')
spatial = parser.add_argument_group(
'Spatial weights from mask options',
'Options for calculating the spatial weights using the '
'SpatiallyVaryingWeightsFromMask plugin.')
spatial.add_argument('--fuzzy_length',
metavar='FUZZY_LENGTH',
type=float,
default=20000,
help='When calculating spatially varying weights we'
' can smooth the weights so that areas close to'
' areas that are masked have lower weights than'
' those further away. This fuzzy length controls'
' the scale over which the weights are smoothed.'
' The fuzzy length is in terms of m, the'
' default is 20km. This distance is then'
' converted into a number of grid squares,'
' which does not have to be an integer. Assumes'
' the grid spacing is the same in the x and y'
' directions, and raises an error if this is not'
' true. See SpatiallyVaryingWeightsFromMask for'
' more detail.')
linear = parser.add_argument_group(
'linear weights options', 'Options for the linear weights '
'calculation in '
'ChooseDefaultWeightsLinear')
linear.add_argument('--y0val',
metavar='LINEAR_STARTING_POINT',
type=float,
help='The relative value of the weighting start point '
'(lowest value of blend coord) for choosing default '
'linear weights. This must be a positive float or 0.')
linear.add_argument('--ynval',
metavar='LINEAR_END_POINT',
type=float,
help='The relative value of the weighting '
'end point (highest value of blend coord) for choosing'
' default linear weights. This must be a positive '
'float or 0. Note that if blending over forecast '
'reference time, ynval >= y0val would normally be '
'expected (to give greater weight to the more recent '
'forecast).')
nonlinear = parser.add_argument_group(
'nonlinear weights options', 'Options for the non-linear '
'weights calculation in '
'ChooseDefaultWeightsNonLinear')
nonlinear.add_argument('--cval',
metavar='NON_LINEAR_FACTOR',
type=float,
help='Factor used to determine how skewed the '
'non linear weights will be. A value of 1 '
'implies equal weighting.')
wts_dict = parser.add_argument_group(
'dict weights options', 'Options for linear weights to be '
'calculated based on parameters '
'read from a json file dict')
wts_dict.add_argument('--wts_dict',
metavar='WEIGHTS_DICTIONARY',
help='Path to json file containing dictionary from '
'which to calculate blending weights. Dictionary '
'format is as specified in the improver.blending.'
'weights.ChooseWeightsLinear plugin.')
wts_dict.add_argument('--weighting_coord',
metavar='WEIGHTING_COORD',
default='forecast_period',
help='Name of '
'coordinate over which linear weights should be '
'scaled. This coordinate must be available in the '
'weights dictionary.')
args = parser.parse_args(args=argv)
# reject incorrect argument combinations
if (args.wts_calc_method == "linear") and args.cval:
parser.wrong_args_error('cval', 'linear')
if ((args.wts_calc_method == "nonlinear")
and np.any([args.y0val, args.ynval])):
parser.wrong_args_error('y0val, ynval', 'non-linear')
if (args.wts_calc_method == "dict") and not args.wts_dict:
parser.error('Dictionary is required if --wts_calc_method="dict"')
weights_dict = load_json_or_none(args.wts_dict)
# Load cubes to be blended.
cubelist = load_cubelist(args.input_filepaths)
result = process(cubelist, args.wts_calc_method, args.coordinate,
args.cycletime, args.weighting_coord, weights_dict,
args.y0val, args.ynval, args.cval, args.model_id_attr,
args.spatial_weights_from_mask, args.fuzzy_length)
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in arguments for applying neighbourhood processing when using a
mask."""
parser = ArgParser(
description='Neighbourhood the input dataset over two distinct regions'
' of land and sea. If performed as a single level neighbourhood, a '
'land-sea mask should be provided. If instead topographic_zone '
'neighbourhooding is being employed, the mask should be one of '
'topographic zones. In the latter case a weights array is also needed'
' to collapse the topographic_zone coordinate. These weights are '
'created with the improver generate-topography-bands-weights CLI and '
'should be made using a land-sea mask, which will then be employed '
'within this code to draw the distinction between the two surface '
'types.')
parser.add_argument('input_filepath',
metavar='INPUT_FILE',
help='A path to an input NetCDF file to be processed.')
parser.add_argument('input_mask_filepath',
metavar='INPUT_MASK',
help=('A path to an input NetCDF file containing '
'either a mask of topographic zones over land '
'or a land-sea mask.'))
parser.add_argument('output_filepath',
metavar='OUTPUT_FILE',
help='The output path for the processed NetCDF.')
mask_group = parser.add_argument_group(
'Collapse weights - required if using a topographic zones mask')
mask_group.add_argument('--weights_for_collapsing_dim',
metavar='WEIGHTS',
default=None,
help='A path to an weights NetCDF file containing '
'the weights which are used for collapsing the '
'dimension gained through masking. These weights '
'must have been created using a land-sea mask.')
radius_group = parser.add_argument_group(
'Neighbourhooding Radius - Set only one of the options')
group = radius_group.add_mutually_exclusive_group()
group.add_argument('--radius',
metavar='RADIUS',
type=float,
help='The radius (in m) for neighbourhood processing.')
group.add_argument('--radii-by-lead-time',
metavar=('RADII_BY_LEAD_TIME', 'LEAD_TIME_IN_HOURS'),
nargs=2,
help='The radii for neighbourhood processing '
'and the associated lead times at which the radii are '
'valid. The radii are in metres whilst the lead time '
'has units of hours. The radii and lead times are '
'expected as individual comma-separated lists with '
'the list of radii given first followed by a list of '
'lead times to indicate at what lead time each radii '
'should be used. For example: 10000,12000,14000 1,2,3 '
'where a lead time of 1 hour uses a radius of 10000m, '
'a lead time of 2 hours uses a radius of 12000m, etc.')
parser.add_argument('--sum_or_fraction',
default="fraction",
choices=["sum", "fraction"],
help='The neighbourhood output can either be in the '
'form of a sum of the neighbourhood, or a '
'fraction calculated by dividing the sum of the '
'neighbourhood by the neighbourhood area. '
'"fraction" is the default option.')
parser.add_argument('--intermediate_filepath',
default=None,
help='Intermediate filepath for results following '
'topographic masked neighbourhood processing of '
'land points and prior to collapsing the '
'topographic_zone coordinate. Intermediate files '
'will not be produced if no topographic masked '
'neighbourhood processing occurs.')
args = parser.parse_args(args=argv)
cube = load_cube(args.input_filepath)
mask = load_cube(args.input_mask_filepath, no_lazy_load=True)
masking_coordinate = None
if any([
'topographic_zone' in coord.name()
for coord in mask.coords(dim_coords=True)
]):
if mask.attributes['topographic_zones_include_seapoints'] == 'True':
raise ValueError('The topographic zones mask cube must have been '
'masked to exclude sea points, but '
'topographic_zones_include_seapoints = True')
if not args.weights_for_collapsing_dim:
raise IOError('A weights cube must be provided if using a mask '
'of topographic zones to collapse the resulting '
'vertical dimension.')
weights = load_cube(args.weights_for_collapsing_dim, no_lazy_load=True)
if weights.attributes['topographic_zones_include_seapoints'] == 'True':
raise ValueError('The weights cube must be masked to exclude sea '
'points, but topographic_zones_include_seapoints '
'= True')
masking_coordinate = 'topographic_zone'
landmask = weights[0].copy(data=weights[0].data.mask)
landmask.rename('land_binary_mask')
landmask.remove_coord(masking_coordinate)
# Create land and sea masks in IMPROVER format (inverse of
# numpy standard) 1 - include this region, 0 - exclude this region.
land_only = landmask.copy(
data=np.logical_not(landmask.data).astype(int))
sea_only = landmask.copy(data=landmask.data.astype(int))
else:
if args.weights_for_collapsing_dim:
warnings.warn('A weights cube has been provided but will not be '
'used as there is no topographic zone coordinate '
'to collapse.')
landmask = mask
# In this case the land is set to 1 and the sea is set to 0 in the
# input mask.
sea_only = landmask.copy(
data=np.logical_not(landmask.data).astype(int))
land_only = landmask.copy(data=landmask.data.astype(int))
if args.radius:
radius_or_radii = args.radius
lead_times = None
elif args.radii_by_lead_time:
radius_or_radii = args.radii_by_lead_time[0].split(",")
lead_times = args.radii_by_lead_time[1].split(",")
if args.intermediate_filepath is not None and masking_coordinate is None:
msg = ('No topographic_zone coordinate found, so no intermediate file '
'will be saved.')
warnings.warn(msg)
# Section for neighbourhood processing land points.
if land_only.data.max() > 0.0:
if masking_coordinate is not None:
result_land = ApplyNeighbourhoodProcessingWithAMask(
masking_coordinate,
radius_or_radii,
lead_times=lead_times,
sum_or_fraction=args.sum_or_fraction,
re_mask=False).process(cube, mask)
else:
result_land = NeighbourhoodProcessing(
'square',
radius_or_radii,
lead_times=lead_times,
sum_or_fraction=args.sum_or_fraction,
re_mask=True).process(cube, land_only)
if masking_coordinate is not None:
if args.intermediate_filepath is not None:
save_netcdf(result_land, args.intermediate_filepath)
# Collapse the masking coordinate.
result_land = CollapseMaskedNeighbourhoodCoordinate(
masking_coordinate, weights=weights).process(result_land)
result = result_land
# Section for neighbourhood processing sea points.
if sea_only.data.max() > 0.0:
result_sea = NeighbourhoodProcessing(
'square',
radius_or_radii,
lead_times=lead_times,
sum_or_fraction=args.sum_or_fraction,
re_mask=True).process(cube, sea_only)
result = result_sea
# Section for combining land and sea points following land and sea points
# being neighbourhood processed individually.
if sea_only.data.max() > 0.0 and land_only.data.max() > 0.0:
# Recombine cubes to be a single output.
combined_data = result_land.data.filled(0) + result_sea.data.filled(0)
result = result_land.copy(data=combined_data)
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in arguments and get going."""
parser = ArgParser(
description=('Reads input orography and landmask fields. Creates '
'a series of topographic zone weights to indicate '
'where an orography point sits within the defined '
'topographic bands. If the orography point is in the '
'centre of a topographic band, then a single band will '
'have a weight of 1.0. If the orography point is at the '
'edge of a topographic band, then the upper band will '
'have a 0.5 weight whilst the lower band will also have '
'a 0.5 weight. Otherwise, the weight will vary linearly '
'between the centre of a topographic band and the edge.'))
parser.add_argument('input_filepath_standard_orography',
metavar='INPUT_FILE_STANDARD_OROGRAPHY',
help=('A path to an input NetCDF orography file to '
'be processed'))
parser.add_argument('output_filepath', metavar='OUTPUT_FILE',
help='The output path for the processed NetCDF.')
parser.add_argument('--input_filepath_landmask', metavar='INPUT_FILE_LAND',
help=('A path to an input NetCDF land mask file to be '
'processed. If provided, sea points will be '
'masked and set to the default fill value. If '
'no land mask is provided, weights will be '
'generated for sea points as well as land, '
'included in the appropriate topographic band.'))
parser.add_argument('--force', dest='force', default=False,
action='store_true',
help=('If keyword is set (i.e. True), ancillaries '
'will be generated even if doing so will '
'overwrite existing files'))
parser.add_argument('--thresholds_filepath',
metavar='THRESHOLDS_FILEPATH',
default=None,
help=("The path to a json file which can be used "
"to set the number and size of topographic "
"bounds. If unset a default bounds dictionary"
" will be used:"
"{'bounds': [[-500., 50.], [50., 100.], "
"[100., 150.],[150., 200.], [200., 250.], "
"[250., 300.], [300., 400.], [400., 500.], "
"[500., 650.],[650., 800.], [800., 950.], "
"[950., 6000.]], 'units': 'm'}"))
args = parser.parse_args(args=argv)
thresholds_dict = load_json_or_none(args.thresholds_filepath)
if not os.path.exists(args.output_filepath) or args.force:
orography = load_cube(args.input_filepath_standard_orography)
landmask = None
if args.input_filepath_landmask:
try:
landmask = load_cube(args.input_filepath_landmask)
except IOError as err:
msg = ("Loading land mask has been unsuccessful: {}. "
"This may be because the land mask could not be "
"located in {}; run "
'improver-generate-landmask-ancillary first.').format(
err, args.input_filepath_landmask)
raise IOError(msg)
result = process(landmask, orography, thresholds_dict)
# Save Cube
save_netcdf(result, args.output_filepath)
else:
print('File already exists here: ', args.output_filepath)
def main(argv=None):
"""Load in arguments for the cube combiner plugin.
"""
parser = ArgParser(
description="Combine the input files into a single file using "
"the requested operation e.g. + - min max etc.")
parser.add_argument("input_filenames", metavar="INPUT_FILENAMES",
nargs="+", type=str,
help="Paths to the input NetCDF files. Each input"
" file should be able to be loaded as a single "
" iris.cube.Cube instance. The resulting file"
" metadata will be based on the first file but"
" its metadata can be overwritten via"
" the metadata_jsonfile option.")
parser.add_argument("output_filepath", metavar="OUTPUT_FILE",
help="The output path for the processed NetCDF.")
parser.add_argument("--operation", metavar="OPERATION",
default="+",
choices=["+", "-", "*",
"add", "subtract", "multiply",
"min", "max", "mean"],
help="Operation to use in combining NetCDF datasets"
" Default=+ i.e. add ", type=str)
parser.add_argument("--new-name", metavar="NEW_NAME",
default=None,
help="New name for the resulting dataset. Will"
" default to the name of the first dataset if "
"not set.", type=str)
parser.add_argument("--metadata_jsonfile", metavar="METADATA_JSONFILE",
default=None,
help="Filename for the json file containing "
"required changes to the metadata. "
" default=None", type=str)
parser.add_argument('--warnings_on', action='store_true',
help="If warnings_on is set (i.e. True), "
"Warning messages where metadata do not match "
"will be given. Default=False", default=False)
args = parser.parse_args(args=argv)
new_metadata = load_json_or_none(args.metadata_jsonfile)
# Load cubes
cubelist = iris.cube.CubeList([])
new_cube_name = args.new_name
for filename in args.input_filenames:
new_cube = load_cube(filename)
cubelist.append(new_cube)
if new_cube_name is None:
new_cube_name = new_cube.name()
if args.warnings_on:
if (args.new_name is None and
new_cube_name != new_cube.name()):
msg = ("Defaulting to first cube name, {} but combining with"
"a cube with name, {}.".format(
new_cube_name, new_cube.name()))
warnings.warn(msg)
# Process Cube
result = process(cubelist, args.operation, new_cube_name,
new_metadata, args.warnings_on)
# Save Cube
save_netcdf(result, args.output_filepath)
def main(argv=None):
"""Load in arguments for applying coefficients for Ensemble Model Output
Statistics (EMOS), otherwise known as Non-homogeneous Gaussian
Regression (NGR). The coefficients are applied to the forecast
that is supplied, so as to calibrate the forecast. The calibrated
forecast is written to a netCDF file.
"""
parser = ArgParser(
description='Apply coefficients for Ensemble Model Output '
'Statistics (EMOS), otherwise known as Non-homogeneous '
'Gaussian Regression (NGR). The supported input formats '
'are realizations, probabilities and percentiles. '
'The forecast will be converted to realizations before '
'applying the coefficients and then converted back to '
'match the input format.')
# Filepaths for the forecast, EMOS coefficients and the output.
parser.add_argument(
'forecast_filepath',
metavar='FORECAST_FILEPATH',
help='A path to an input NetCDF file containing the forecast to be '
'calibrated. The input format could be either realizations, '
'probabilities or percentiles.')
parser.add_argument('coefficients_filepath',
metavar='COEFFICIENTS_FILEPATH',
help='A path to an input NetCDF file containing the '
'coefficients used for calibration.')
parser.add_argument('output_filepath',
metavar='OUTPUT_FILEPATH',
help='The output path for the processed NetCDF')
# Optional arguments.
parser.add_argument(
'--num_realizations',
metavar='NUMBER_OF_REALIZATIONS',
default=None,
type=np.int32,
help='Optional argument to specify the number of '
'ensemble realizations to produce. '
'If the current forecast is input as probabilities or '
'percentiles then this argument is used to create the requested '
'number of realizations. In addition, this argument is used to '
'construct the requested number of realizations from the mean '
'and variance output after applying the EMOS coefficients.'
'Default will be the number of realizations in the raw input '
'file, if realizations are provided as input, otherwise if the '
'input format is probabilities or percentiles, then an error '
'will be raised if no value is provided.')
parser.add_argument(
'--random_ordering',
default=False,
action='store_true',
help='Option to reorder the post-processed forecasts randomly. If not '
'set, the ordering of the raw ensemble is used. This option is '
'only valid when the input format is realizations.')
parser.add_argument(
'--random_seed',
metavar='RANDOM_SEED',
default=None,
help='Option to specify a value for the random seed for testing '
'purposes, otherwise, the default random seed behaviour is '
'utilised. The random seed is used in the generation of the '
'random numbers used for either the random_ordering option to '
'order the input percentiles randomly, rather than use the '
'ordering from the raw ensemble, or for splitting tied values '
'within the raw ensemble, so that the values from the input '
'percentiles can be ordered to match the raw ensemble.')
parser.add_argument(
'--ecc_bounds_warning',
default=False,
action='store_true',
help='If True, where the percentiles exceed the ECC bounds range, '
'raise a warning rather than an exception. This occurs when the '
'current forecast is in the form of probabilities and is '
'converted to percentiles, as part of converting the input '
'probabilities into realizations.')
parser.add_argument(
'--predictor_of_mean',
metavar='PREDICTOR_OF_MEAN',
choices=['mean', 'realizations'],
default='mean',
help='String to specify the predictor used to calibrate the forecast '
'mean. Currently the ensemble mean ("mean") and the ensemble '
'realizations ("realizations") are supported as options. '
'Default: "mean".')
args = parser.parse_args(args=argv)
current_forecast = load_cube(args.forecast_filepath)
coeffs = load_cube(args.coefficients_filepath)
original_current_forecast = current_forecast.copy()
msg = ("The current forecast has been provided as {0}. "
"These {0} need to be converted to realizations "
"for ensemble calibration. The args.num_realizations "
"argument is used to define the number of realizations "
"to construct from the input {0}, so if the "
"current forecast is provided as {0} then "
"args.num_realizations must be defined.")
try:
find_percentile_coordinate(current_forecast)
input_forecast_type = "percentiles"
except CoordinateNotFoundError:
input_forecast_type = "realizations"
if current_forecast.name().startswith("probability_of"):
input_forecast_type = "probabilities"
# If probabilities, convert to percentiles.
conversion_plugin = GeneratePercentilesFromProbabilities(
ecc_bounds_warning=args.ecc_bounds_warning)
elif input_forecast_type == "percentiles":
# If percentiles, resample percentiles so that the percentiles are
# evenly spaced.
conversion_plugin = ResamplePercentiles(
ecc_bounds_warning=args.ecc_bounds_warning)
# If percentiles, resample percentiles and then rebadge.
# If probabilities, generate percentiles and then rebadge.
if input_forecast_type in ["percentiles", "probabilities"]:
if not args.num_realizations:
raise ValueError(msg.format(input_forecast_type))
current_forecast = conversion_plugin.process(
current_forecast, no_of_percentiles=args.num_realizations)
current_forecast = (
RebadgePercentilesAsRealizations().process(current_forecast))
# Default number of ensemble realizations is the number in
# the raw forecast.
if not args.num_realizations:
args.num_realizations = len(
current_forecast.coord('realization').points)
# Apply coefficients as part of Ensemble Model Output Statistics (EMOS).
ac = ApplyCoefficientsFromEnsembleCalibration(
current_forecast,
coeffs,
predictor_of_mean_flag=args.predictor_of_mean)
calibrated_predictor, calibrated_variance = ac.process()
# If input forecast is probabilities, convert output into probabilities.
# If input forecast is percentiles, convert output into percentiles.
# If input forecast is realizations, convert output into realizations.
if input_forecast_type == "probabilities":
result = GenerateProbabilitiesFromMeanAndVariance().process(
calibrated_predictor, calibrated_variance,
original_current_forecast)
elif input_forecast_type == "percentiles":
perc_coord = find_percentile_coordinate(original_current_forecast)
result = GeneratePercentilesFromMeanAndVariance().process(
calibrated_predictor,
calibrated_variance,
percentiles=perc_coord.points)
elif input_forecast_type == "realizations":
# Ensemble Copula Coupling to generate realizations
# from mean and variance.
percentiles = GeneratePercentilesFromMeanAndVariance().process(
calibrated_predictor,
calibrated_variance,
no_of_percentiles=args.num_realizations)
result = EnsembleReordering().process(
percentiles,
current_forecast,
random_ordering=args.random_ordering,
random_seed=args.random_seed)
save_netcdf(result, args.output_filepath)
