def col_cmd(main_arguments):
"""
Main routine for handling calls to the collocate ('col') command.
:param main_arguments: The command line arguments (minus the col command)
"""
from cis.exceptions import ClassNotFoundError, CISError
from cis.collocation.col import Collocate
output_file = main_arguments.output
data_reader = DataReader()
missing_data_for_missing_samples = False
if main_arguments.samplevariable is not None:
sample_data = data_reader.read_data_list(main_arguments.samplefiles, main_arguments.samplevariable,
main_arguments.sampleproduct)[0]
else:
sample_data = data_reader.read_coordinates(main_arguments.samplefiles, main_arguments.sampleproduct)
missing_data_for_missing_samples = True
try:
col = Collocate(sample_data, missing_data_for_missing_samples)
except IOError as e:
__error_occurred("There was an error reading one of the files: \n" + str(e))
col_name = main_arguments.samplegroup['collocator'][0] if main_arguments.samplegroup[
'collocator'] is not None else None
col_options = main_arguments.samplegroup['collocator'][1] if main_arguments.samplegroup[
'collocator'] is not None else {}
kern_name = main_arguments.samplegroup['kernel'][0] if main_arguments.samplegroup['kernel'] is not None else None
kern_options = main_arguments.samplegroup['kernel'][1] if main_arguments.samplegroup['kernel'] is not None else None
for input_group in main_arguments.datagroups:
variables = input_group['variables']
filenames = input_group['filenames']
product = input_group["product"] if input_group["product"] is not None else None
data = data_reader.read_data_list(filenames, variables, product)
data_writer = DataWriter()
try:
output = col.collocate(data, col_name, col_options, kern_name, kern_options)
data_writer.write_data(output, output_file)
except ClassNotFoundError as e:
__error_occurred(str(e) + "\nInvalid collocation option.")
except (CISError, IOError) as e:
__error_occurred(e)
def test_GIVEN_GriddedData_WHEN_collocate_THEN_collocator_called_correctly(self):
sample = gridded_data.make_from_cube(mock.make_square_5x3_2d_cube())
out_name = "output-name"
col_name = "dummy"
col_options = {}
mock_collocator = MagicMock()
mock_collocator.collocate = MagicMock(return_value=GriddedDataList([sample]))
mock_constraint = MagicMock()
mock_kernel = MagicMock()
mock_collocator_factory = CollocatorFactory()
mock_collocator_factory.get_collocator_instances_for_method = MagicMock(
return_value=(mock_collocator, mock_constraint, mock_kernel)
)
col = Collocate(sample, out_name, collocator_factory=mock_collocator_factory)
data = gridded_data.make_from_cube(mock.make_square_5x3_2d_cube())
output = col.collocate(data, col_name, col_options)
assert_that(mock_collocator_factory.get_collocator_instances_for_method.call_count, is_(1))
factory_call_args = mock_collocator_factory.get_collocator_instances_for_method.call_args_list[0][0]
assert_that(factory_call_args[0], is_(col_name))
assert_that(factory_call_args[1], is_(None))
col_options["missing_data_for_missing_sample"] = False
assert_that(factory_call_args[2], is_(col_options))
assert_that(factory_call_args[3], is_(None))
assert_that(factory_call_args[4], is_(True))
assert_that(factory_call_args[5], is_(True))
assert_that(mock_collocator.collocate.call_count, is_(1))
collocator_args = mock_collocator.collocate.call_args_list[0][0]
assert_that(collocator_args[0], is_(sample))
assert_that(collocator_args[1], is_(data))
assert_that(collocator_args[2], is_(mock_constraint))
assert_that(collocator_args[3], is_(mock_kernel))
assert_that(isinstance(output, GriddedDataList))
assert_that(len(output), is_(1))
assert_that(output[0].data.flatten().tolist(), is_(sample.data.flatten().tolist()))