"""Script to encode layers into a Matrix."""
import argparse
import os
from lmpy.data_preparation.layer_encoder import LayerEncoder
from lmpy.tools._config_parser import _process_arguments
DESCRIPTION = 'Encode raster and / or vector layers into a site by layer matrix.'
# .....................................................................................
[docs]def cli():
"""Command line interface for layer encoding.
Raises:
ValueError: Raised if an unknown encoding method is provided or too many layer
arguments.
"""
parser = argparse.ArgumentParser(description=DESCRIPTION)
parser.add_argument('--config_file', type=str, help='Path to configuration file.')
parser.add_argument(
'--encode_method',
'-m',
type=str,
choices=['biogeo', 'presence_absence', 'largest_class', 'mean_value'],
default='mean_value',
help='The method to use to encode each layer.',
)
parser.add_argument(
'--min_coverage',
type=float,
default=25,
help='Minimum percentage of a cell that has to be covered to encode it.',
)
parser.add_argument(
'--min_presence',
type=float,
default=10,
help='Minimum value to be considered present when encoding presence absence.',
)
parser.add_argument(
'--max_presence',
type=float,
default=127,
help='The maximum value that should be considered present.',
)
parser.add_argument(
'shapegrid_filename',
type=str,
help='File location of shapegrid to use for site geometries.',
)
parser.add_argument(
'out_matrix_filename',
type=str,
help='File location to write the encoded matrix.',
)
# Layers to encode
parser.add_argument(
'--layer',
'-l',
nargs='*',
action='append',
help='File location of layer [ LABEL [ ATTRIBUTE FIELD ]].',
)
args = _process_arguments(parser, config_arg='config_file')
encoder = LayerEncoder(args.shapegrid_filename)
for layer_args in args.layer:
# if there are too many layer arguments, fail
if len(layer_args) > 3:
raise ValueError(
'Too many layer arguments {}.'
'Hint: Specify layer args last in command.'.format(layer_args)
)
# Process layer arguments, get filename for sure, try label and attribute field
lyr_fn = layer_args[0]
layer_attribute = None
# Label
if len(layer_args) > 1:
lyr_label = layer_args[1]
if len(layer_args) > 2:
layer_attribute = layer_args[2]
else:
lyr_label = os.path.splitext(os.path.basename(lyr_fn))[0]
if args.encode_method == 'biogeo':
encoder.encode_biogeographic_hypothesis(
lyr_fn, lyr_label, args.min_coverage, attribute_field=layer_attribute
)
elif args.encode_method == 'presence_absence':
encoder.encode_presence_absence(
lyr_fn,
lyr_label,
args.min_presence,
args.max_presence,
args.min_coverage,
attribute_name=layer_attribute,
)
elif args.encode_method == 'largest_class':
encoder.encode_largest_class(
lyr_fn,
lyr_label,
args.min_coverage,
attribute_name=layer_attribute,
)
elif args.encode_method == 'mean_value':
encoder.encode_mean_value(
lyr_fn, lyr_label, attribute_name=layer_attribute
)
else:
raise ValueError('Unknown encoding method: {}'.format(args.encode_method))
enc_mtx = encoder.get_encoded_matrix()
enc_mtx.write(args.out_matrix_filename)
# .....................................................................................
__all__ = ['cli']
# .....................................................................................
if __name__ == '__main__': # pragma: no cover
cli()