def test_GIVEN_no_matching_variables_found_overall_WHEN_read_data_THEN_raises_Error(self):
variables = ['test?.hdf', '*.nc']
file_vars = ['sample_file.hdf', 'aeronet.lev20']
filenames = 'filename1'
get_data_func = MagicMock()
get_var_func = MagicMock(return_value=file_vars)
reader = DataReader(get_data_func=get_data_func, get_variables_func=get_var_func)
with self.assertRaises(ValueError):
reader.read_data_list(filenames, variables)[0]
def test_GIVEN_no_matching_variables_for_wildcards_WHEN_read_data_THEN_no_Error(self):
variables = ['aeronet.lev20', '*.nc', 'test?.hdf']
file_vars = ['aeronet.lev20', 'var2.hdf']
filenames = 'filename1'
get_data_func = MagicMock(return_value=make_regular_2d_ungridded_data())
get_var_func = MagicMock(return_value=file_vars)
reader = DataReader(get_data_func=get_data_func, get_variables_func=get_var_func)
reader.read_data_list(filenames, variables)[0]
assert_that(reader._get_data_func.call_count, is_(1))
assert_that(reader._get_data_func.call_args_list[0][0][1], is_('aeronet.lev20'))
def test_GIVEN_no_matching_variables_found_overall_WHEN_read_data_THEN_raises_Error(
self):
variables = ['test?.hdf', '*.nc']
file_vars = ['sample_file.hdf', 'aeronet.lev20']
filenames = 'filename1'
get_data_func = MagicMock()
get_var_func = MagicMock(return_value=file_vars)
reader = DataReader(get_data_func=get_data_func,
get_variables_func=get_var_func)
with self.assertRaises(ValueError):
reader.read_data_list(filenames, variables)[0]
def test_GIVEN_wildcards_WHEN_read_data_THEN_matching_variables_identified(self):
variables = ['*.nc', 'test?.hdf']
file_vars = ['aeronet.lev20', 'var2.hdf', 'netcdf1.nc', 'netcdf3.nc', 'test.hdf', 'test1.hdf']
should_match = ['netcdf1.nc', 'netcdf3.nc', 'test1.hdf']
filenames = 'filename1'
get_data_func = MagicMock(return_value=make_regular_2d_ungridded_data())
get_var_func = MagicMock(return_value=file_vars)
reader = DataReader(get_data_func=get_data_func, get_variables_func=get_var_func)
reader.read_data_list(filenames, variables)[0]
assert_that(reader._get_data_func.call_count, is_(len(should_match)))
for i in range(len(should_match)):
assert_that(reader._get_data_func.call_args_list[i][0][1], is_(should_match[i]))
def test_GIVEN_no_matching_variables_for_wildcards_WHEN_read_data_THEN_no_Error(
self):
variables = ['aeronet.lev20', '*.nc', 'test?.hdf']
file_vars = ['aeronet.lev20', 'var2.hdf']
filenames = 'filename1'
get_data_func = MagicMock(
return_value=make_regular_2d_ungridded_data())
get_var_func = MagicMock(return_value=file_vars)
reader = DataReader(get_data_func=get_data_func,
get_variables_func=get_var_func)
reader.read_data_list(filenames, variables)[0]
assert_that(reader._get_data_func.call_count, is_(1))
assert_that(reader._get_data_func.call_args_list[0][0][1],
is_('aeronet.lev20'))
def test_GIVEN_single_variable_WHEN_aggregate_THEN_DataWriter_called_correctly(self):
variables = 'var_name'
filenames = 'filename'
output_file = 'output.hdf'
kernel = 'mean'
grid = None
input_data = GriddedDataList([make_from_cube(make_square_5x3_2d_cube())])
output_data = make_from_cube(make_square_5x3_2d_cube() + 1)
mock_data_reader = DataReader()
mock_data_reader.read_data_list = MagicMock(return_value=input_data)
mock_data_writer = DataWriter()
mock_data_writer.write_data = Mock()
mock_aggregator = Aggregator(None, None)
mock_aggregator.aggregate_gridded = MagicMock(return_value=output_data) # Return the modified data array
aggregate = Aggregate(grid, output_file, data_reader=mock_data_reader, data_writer=mock_data_writer)
aggregate._create_aggregator = MagicMock(return_value=mock_aggregator)
aggregate.aggregate(variables, filenames, None, kernel)
assert_that(mock_data_writer.write_data.call_count, is_(1))
written_data = mock_data_writer.write_data.call_args[0][0]
written_filename = mock_data_writer.write_data.call_args[0][1]
assert_that(written_data.data.tolist(), is_([[2, 3, 4], [5, 6, 7], [8, 9, 10], [11, 12, 13], [14, 15, 16]]))
assert_that(written_filename, is_(output_file))
def test_GIVEN_single_variable_WHEN_subset_THEN_DataWriter_called_correctly(self):
variable = 'var_name'
filename = 'filename'
xmin, xmax = -10, 10
ymin, ymax = 40, 60
limits = {'x': SubsetLimits(xmin, xmax, False),
'y': SubsetLimits(ymin, ymax, False)}
output_file = 'output.hdf'
def _mock_subset(data, constraint):
data.data += 1 # Modify the data slightly so we can be sure it's passed in correctly
return data
mock_subsetter = Subsetter()
mock_subsetter.subset = _mock_subset
mock_data_reader = DataReader()
mock_data_reader.read_data_list = MagicMock(return_value=make_regular_2d_ungridded_data())
mock_data_writer = DataWriter()
mock_data_writer.write_data = MagicMock()
subset = Subset(limits, output_file, subsetter=mock_subsetter,
data_reader=mock_data_reader, data_writer=mock_data_writer)
subset.subset(variable, filename, product=None)
assert_that(mock_data_writer.write_data.call_count, is_(1))
written_data = mock_data_writer.write_data.call_args[0][0]
written_filename = mock_data_writer.write_data.call_args[0][1]
assert_that(written_data.data_flattened.tolist(), is_([2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16]))
assert_that(written_filename, is_(output_file))
def test_GIVEN_single_variable_WHEN_subset_THEN_Subsetter_called_correctly(self):
variable = 'var_name'
filename = 'filename'
xmin, xmax = -10, 10
ymin, ymax = 40, 60
limits = {'x': SubsetLimits(xmin, xmax, False),
'y': SubsetLimits(ymin, ymax, False)}
output_file = 'output.hdf'
mock_data_reader = DataReader()
mock_data_reader.read_data_list = MagicMock(return_value=make_regular_2d_ungridded_data())
mock_data_writer = DataWriter()
mock_data_writer.write_data = Mock()
mock_subsetter = Subsetter()
mock_subsetter.subset = MagicMock(side_effect=lambda *args: args[0]) # Return the data array unmodified
subset = Subset(limits, output_file, subsetter=mock_subsetter,
data_reader=mock_data_reader, data_writer=mock_data_writer)
subset.subset(variable, filename, product=None)
assert_that(mock_subsetter.subset.call_count, is_(1))
called_data = mock_subsetter.subset.call_args[0][0]
called_constraint = mock_subsetter.subset.call_args[0][1]
assert_that(called_data.data_flattened.tolist(),
is_([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15]))
assert_that(called_constraint, instance_of(UngriddedSubsetConstraint))
assert_that(called_constraint._limits['lat'][1:3], is_((ymin, ymax)))
assert_that(called_constraint._limits['lon'][1:3], is_((xmin, xmax)))
def test_GIVEN_multiple_variables_WHEN_subset_THEN_DataWriter_called_correctly(self):
variables = ['var_name1', 'var_name2']
filename = 'filename'
xmin, xmax = 0, 5
ymin, ymax = -5, 5
limits = {'x': SubsetLimits(xmin, xmax, False),
'y': SubsetLimits(ymin, ymax, False)}
output_file = 'output.hdf'
def _mock_subset(data, constraint):
# Modify the data slightly so we can be sure it's passed in correctly
for var in data:
var.data += 1
return data
mock_subsetter = Subsetter()
mock_subsetter.subset = _mock_subset
mock_data_reader = DataReader()
mock_data_reader.read_data_list = MagicMock(return_value=GriddedDataList([make_square_5x3_2d_cube(),
make_square_5x3_2d_cube()]))
mock_data_writer = DataWriter()
mock_data_writer.write_data = MagicMock()
subset = Subset(limits, output_file, subsetter=mock_subsetter,
data_reader=mock_data_reader, data_writer=mock_data_writer)
subset.subset(variables, filename, product=None)
assert_that(mock_data_writer.write_data.call_count, is_(1))
written_data = mock_data_writer.write_data.call_args[0][0]
written_filename = mock_data_writer.write_data.call_args[0][1]
assert_that(written_data[0].data.tolist(), is_([[2, 3, 4], [5, 6, 7], [8, 9, 10], [11, 12, 13], [14, 15, 16]]))
assert_that(written_data[0].data.tolist(), written_data[1].data.tolist())
assert_that(written_filename, is_(output_file))
def test_GIVEN_multiple_variables_WHEN_subset_THEN_Subsetter_called_correctly(self):
variables = ['var_name1', 'var_name2']
filename = 'filename'
xmin, xmax = 0, 5
ymin, ymax = -5, 5
limits = {'x': SubsetLimits(xmin, xmax, False),
'y': SubsetLimits(ymin, ymax, False)}
output_file = 'output.hdf'
mock_data_reader = DataReader()
mock_data_reader.read_data_list = MagicMock(return_value=GriddedDataList(2 * [make_square_5x3_2d_cube()]))
mock_data_writer = DataWriter()
mock_data_writer.write_data = Mock()
mock_subsetter = Subsetter()
mock_subsetter.subset = MagicMock(side_effect=lambda *args: args[0]) # Return the data list unmodified
subset = Subset(limits, output_file, subsetter=mock_subsetter,
data_reader=mock_data_reader, data_writer=mock_data_writer)
subset.subset(variables, filename, product=None)
assert_that(mock_subsetter.subset.call_count, is_(1))
called_data = mock_subsetter.subset.call_args[0][0]
called_constraint = mock_subsetter.subset.call_args[0][1]
assert_that(called_data[0].data.tolist(), is_([[1, 2, 3], [4, 5, 6], [7, 8, 9], [10, 11, 12], [13, 14, 15]]))
assert_that(called_data[1].data.tolist(), is_(called_data[0].data.tolist()))
assert_that(called_constraint, instance_of(GriddedSubsetConstraint))
assert_that(called_constraint._limits['latitude'][1:3], is_((ymin, ymax)))
assert_that(called_constraint._limits['longitude'][1:3], is_((xmin, xmax)))
def test_GIVEN_multiple_variable_gridded_WHEN_read_data_THEN_GriddedDataList_returned(
self):
variables = ['var1', 'var2']
filenames = 'filename1'
product = None
gridded_data = make_square_5x3_2d_cube()
gridded_data.__class__ = GriddedData
get_data_func = MagicMock(return_value=gridded_data)
reader = DataReader(get_data_func=get_data_func)
data = reader.read_data_list(filenames, variables, product)
# Check the data read function is called correctly
assert_that(get_data_func.call_count, is_(2))
first_call_args = get_data_func.call_args_list[0][0]
second_call_args = get_data_func.call_args_list[1][0]
assert_that(first_call_args[0], is_([filenames]))
assert_that(first_call_args[1], is_(variables[0]))
assert_that(second_call_args[1], is_(variables[1]))
assert_that(first_call_args[2], is_(product))
# Check the data we got back is as expected
assert_that(data, instance_of(GriddedDataList))
assert_that(data[0].data.tolist(),
is_(make_square_5x3_2d_cube().data.tolist()))
assert_that(data[1].data.tolist(), is_(data[0].data.tolist()))
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_wildcards_WHEN_read_data_THEN_matching_variables_identified(
self):
variables = ['*.nc', 'test?.hdf']
file_vars = [
'aeronet.lev20', 'var2.hdf', 'netcdf1.nc', 'netcdf3.nc',
'test.hdf', 'test1.hdf'
]
should_match = ['netcdf1.nc', 'netcdf3.nc', 'test1.hdf']
filenames = 'filename1'
get_data_func = MagicMock(
return_value=make_regular_2d_ungridded_data())
get_var_func = MagicMock(return_value=file_vars)
reader = DataReader(get_data_func=get_data_func,
get_variables_func=get_var_func)
reader.read_data_list(filenames, variables)[0]
assert_that(reader._get_data_func.call_count, is_(len(should_match)))
for i in range(len(should_match)):
assert_that(reader._get_data_func.call_args_list[i][0][1],
is_(should_match[i]))
def test_GIVEN_multiple_variable_mix_of_gridded_ungridded_WHEN_read_data_THEN_raises_TypeError(self):
variables = ['var1', 'var2']
filenames = 'filename1'
product = None
gridded_data = make_square_5x3_2d_cube()
gridded_data.__class__ = GriddedData
ungridded_data = make_regular_2d_ungridded_data()
get_data_func = MagicMock(side_effect=[gridded_data, ungridded_data])
reader = DataReader(get_data_func=get_data_func)
with self.assertRaises(TypeError):
data = reader.read_data_list(filenames, variables, product)[0]
def test_GIVEN_multiple_variable_mix_of_gridded_ungridded_WHEN_read_data_THEN_raises_TypeError(
self):
variables = ['var1', 'var2']
filenames = 'filename1'
product = None
gridded_data = make_square_5x3_2d_cube()
gridded_data.__class__ = GriddedData
ungridded_data = make_regular_2d_ungridded_data()
get_data_func = MagicMock(side_effect=[gridded_data, ungridded_data])
reader = DataReader(get_data_func=get_data_func)
with self.assertRaises(TypeError):
data = reader.read_data_list(filenames, variables, product)[0]
def test_GIVEN_single_variable_ungridded_WHEN_read_data_THEN_GriddedData_returned(self):
variables = 'var1'
filenames = 'filename1'
product = None
get_data_func = MagicMock(return_value=make_regular_2d_ungridded_data())
reader = DataReader(get_data_func=get_data_func)
data = reader.read_data_list(filenames, variables, product)[0]
# Check the data read function is called correctly
assert_that(get_data_func.call_count, is_(1))
call_args = get_data_func.call_args_list[0][0]
assert_that(call_args[0], is_([filenames]))
assert_that(call_args[1], is_(variables))
assert_that(call_args[2], is_(product))
# Check the data we got back is as expected
assert_that(data, instance_of(UngriddedData))
assert_that(data.data.tolist(), is_(make_regular_2d_ungridded_data().data.tolist()))
def test_GIVEN_single_variable_ungridded_WHEN_read_data_THEN_GriddedData_returned(
self):
variables = 'var1'
filenames = 'filename1'
product = None
get_data_func = MagicMock(
return_value=make_regular_2d_ungridded_data())
reader = DataReader(get_data_func=get_data_func)
data = reader.read_data_list(filenames, variables, product)[0]
# Check the data read function is called correctly
assert_that(get_data_func.call_count, is_(1))
call_args = get_data_func.call_args_list[0][0]
assert_that(call_args[0], is_([filenames]))
assert_that(call_args[1], is_(variables))
assert_that(call_args[2], is_(product))
# Check the data we got back is as expected
assert_that(data, instance_of(UngriddedData))
assert_that(data.data.tolist(),
is_(make_regular_2d_ungridded_data().data.tolist()))
def test_GIVEN_multiple_variables_and_filenames_WHEN_subset_THEN_DataReader_called_correctly(self):
variables = ['var_name1', 'var_name2']
filenames = ['filename1', 'filename2']
output_file = 'output.hdf'
xmin, xmax = 0, 5
ymin, ymax = -5, 5
limits = {'x': SubsetLimits(xmin, xmax, False),
'y': SubsetLimits(ymin, ymax, False)}
mock_data_reader = DataReader()
mock_data_reader.read_data_list = MagicMock(return_value=GriddedDataList(2 * [make_square_5x3_2d_cube()]))
mock_data_writer = DataWriter()
mock_data_writer.write_data = Mock()
mock_subsetter = Subsetter()
mock_subsetter.subset = lambda *args: args[0] # Return the data array unmodified
subset = Subset(limits, output_file, subsetter=mock_subsetter,
data_reader=mock_data_reader, data_writer=mock_data_writer)
subset.subset(variables, filenames, product=None)
assert_that(mock_data_reader.read_data_list.call_count, is_(1))
assert_that(mock_data_reader.read_data_list.call_args[0][0], filenames)
assert_that(mock_data_reader.read_data_list.call_args[0][1], variables)
def test_GIVEN_multiple_variables_and_filenames_WHEN_aggregate_THEN_Aggregate_called_correctly(self):
variables = ['var_name1', 'var_name2']
filenames = ['filename1', 'filename2']
output_file = 'output.hdf'
kernel = 'mean'
grid = 'grid'
input_data = GriddedDataList(2 * [make_from_cube(make_square_5x3_2d_cube())])
output_data = input_data
mock_data_reader = DataReader()
mock_data_reader.read_data_list = MagicMock(return_value=input_data)
mock_data_writer = DataWriter()
mock_data_writer.write_data = Mock()
mock_aggregator = Aggregator(None, None)
mock_aggregator.aggregate_gridded = MagicMock(return_value=output_data) # Return the data array unmodified
aggregate = Aggregate(grid, output_file, data_reader=mock_data_reader, data_writer=mock_data_writer)
aggregate._create_aggregator = MagicMock(return_value=mock_aggregator)
aggregate.aggregate(variables, filenames, None, kernel)
assert_that(mock_aggregator.aggregate_gridded.call_count, is_(1))
assert_that(mock_aggregator.aggregate_gridded.call_args[0][0], kernel)
def test_GIVEN_single_variable_WHEN_subset_THEN_DataReader_called_correctly(self):
variable = 'var_name'
filename = 'filename'
output_file = 'output.hdf'
xmin, xmax = -10, 10
ymin, ymax = 40, 60
limits = {'x': SubsetLimits(xmin, xmax, False),
'y': SubsetLimits(ymin, ymax, False)}
mock_data_reader = DataReader()
mock_data_reader.read_data_list = MagicMock(return_value=make_regular_2d_ungridded_data())
mock_data_writer = DataWriter()
mock_data_writer.write_data = Mock()
mock_subsetter = Subsetter()
mock_subsetter.subset = lambda *args: args[0] # Return the data array unmodified
subset = Subset(limits, output_file, subsetter=mock_subsetter,
data_reader=mock_data_reader, data_writer=mock_data_writer)
subset.subset(variable, filename, product=None)
assert_that(mock_data_reader.read_data_list.call_count, is_(1))
assert_that(mock_data_reader.read_data_list.call_args[0][0], filename)
assert_that(mock_data_reader.read_data_list.call_args[0][1], variable)
def test_GIVEN_multiple_variable_gridded_WHEN_read_data_THEN_GriddedDataList_returned(self):
variables = ['var1', 'var2']
filenames = 'filename1'
product = None
gridded_data = make_square_5x3_2d_cube()
gridded_data.__class__ = GriddedData
get_data_func = MagicMock(return_value=gridded_data)
reader = DataReader(get_data_func=get_data_func)
data = reader.read_data_list(filenames, variables, product)
# Check the data read function is called correctly
assert_that(get_data_func.call_count, is_(2))
first_call_args = get_data_func.call_args_list[0][0]
second_call_args = get_data_func.call_args_list[1][0]
assert_that(first_call_args[0], is_([filenames]))
assert_that(first_call_args[1], is_(variables[0]))
assert_that(second_call_args[1], is_(variables[1]))
assert_that(first_call_args[2], is_(product))
# Check the data we got back is as expected
assert_that(data, instance_of(GriddedDataList))
assert_that(data[0].data.tolist(), is_(make_square_5x3_2d_cube().data.tolist()))
assert_that(data[1].data.tolist(), is_(data[0].data.tolist()))
