def _make_partially_collapsed_coord(self, coord, grid, guessed_axis):
"""
Make a new DimCoord which represents a partially collapsed (aggregated into bins) coordinate.
This dimcoord will have a grid
:type coord: data_io.Coord.Coord
:param coord: Coordinate to partially collapse
:type grid: aggregation.aggregation_grid.AggregationGrid
:param grid: grid on which this coordinate will aggregate
:type guessed_axis: str
:param guessed_axis: String identifier of the axis to which this coordinate belongs (e.g. 'T', 'X')
:return: DimCoord
"""
if grid.is_time or guessed_axis == 'T':
# Ensure that the limits are date/times.
dt = parse_datetime.convert_datetime_components_to_datetime(grid.start, True)
grid_start = Subset._convert_datetime_to_coord_unit(coord, dt)
dt = parse_datetime.convert_datetime_components_to_datetime(grid.end, False)
grid_end = Subset._convert_datetime_to_coord_unit(coord, dt)
grid_delta = grid.delta
else:
# Assume to be a non-time axis
(grid_start, grid_end) = Subset._fix_non_circular_limits(float(grid.start), float(grid.end))
grid_delta = float(grid.delta)
new_coordinate_grid = aggregation_grid_array(grid_start, grid_end, grid_delta, grid.is_time, coord)
new_coord = DimCoord(new_coordinate_grid, var_name=coord.name(), standard_name=coord.standard_name,
units=coord.units)
if len(new_coord.points) == 1:
new_coord.bounds = [[grid_start, grid_end]]
else:
new_coord.guess_bounds()
return new_coord
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 subset_cmd(main_arguments):
"""
Main routine for handling calls to the subset command.
:param main_arguments: The command line arguments (minus the subset command)
"""
from cis.subsetting.subset import Subset
if len(main_arguments.datagroups) > 1:
__error_occurred("Subsetting can only be performed on one data group")
input_group = main_arguments.datagroups[0]
variables = input_group['variables']
filenames = input_group['filenames']
product = input_group["product"] if input_group["product"] is not None else None
subset = Subset(main_arguments.limits, main_arguments.output)
subset.subset(variables, filenames, product)
def aggregation_grid_array(start, end, delta, is_time, coordinate):
if is_time:
start_dt = Subset._convert_coord_unit_to_datetime(coordinate, start)
end_dt = Subset._convert_coord_unit_to_datetime(coordinate, end)
# Some logic to find the mid point to start on
if delta.year > 0:
start_dt = add_year_midpoint(start_dt, delta.year)
# We make an assumption here that half a month is always 15 days.
if delta.month > 0:
start_dt = add_month_midpoint(start_dt, delta.month)
dt = datetime.timedelta(days=delta.day, seconds=delta.second, microseconds=0, milliseconds=0,
minutes=delta.minute, hours=delta.hour, weeks=0)
start_dt += dt / 2
new_time_grid = []
new_time = start_dt
while new_time < end_dt:
new_time_grid.append(Subset._convert_datetime_to_coord_unit(coordinate, new_time))
new_year = new_time.year + delta.year
new_month = new_time.month + delta.month
if new_month > 12:
new_month, new_year = month_past_end_of_year(new_month, new_year)
# TODO this is a slightly inelegant fix for the problem of something like 30th Jan +1 month
# Need to work out what correct behaviour should be in this case.
try:
new_time = new_time.replace(year=new_year, month=new_month)
except ValueError:
new_time += datetime.timedelta(days=28)
new_time += datetime.timedelta(days=delta.day, seconds=delta.second, microseconds=0, milliseconds=0,
minutes=delta.minute, hours=delta.hour, weeks=0)
new_time_grid = numpy.array(new_time_grid)
return new_time_grid
else:
new_grid = numpy.arange(start + delta / 2, end + delta / 2, delta)
return new_grid
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_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)