def test_collocated_NetCDF_Gridded_onto_GASSP(self):
# First do a collocation of ECHAMHAM onto GASSP
vars = valid_echamham_variable_1, valid_echamham_variable_2
filename = escape_colons(valid_echamham_filename)
sample_file = escape_colons(valid_GASSP_aeroplane_filename)
sample_var = valid_GASSP_aeroplane_variable
collocator_and_opts = 'nn[missing_data_for_missing_sample=True],variable=%s' % sample_var
arguments = [
'col', ",".join(vars) + ':' + filename,
sample_file + ':collocator=' + collocator_and_opts, '-o',
'collocated_gassp'
]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
# Check collocation is the same
self.ds = netCDF4.Dataset('collocated_gassp.nc')
col_var1 = self.ds.variables[valid_echamham_variable_1][:]
col_var2 = self.ds.variables[valid_echamham_variable_2][:]
# A hand calculated selection of values
expected_col1 = numpy.ma.masked_invalid([
float('Nan'),
float('Nan'),
float('Nan'), 0.0814601778984, 0.0814601778984
])
compare_masked_arrays(expected_col1, col_var1[:][0:5])
expected_col2 = numpy.ma.masked_invalid([
float('Nan'),
float('Nan'),
float('Nan'), 0.0741240680218, 0.0741240680218
])
compare_masked_arrays(expected_col2, col_var2[:][0:5])
# Then do an evaluation using the collocated data:
args = [
'eval',
"%s,%s:%s" % (valid_echamham_variable_1, valid_echamham_variable_2,
'collocated_gassp.nc'),
"%s=gassp_alias:%s" %
(valid_GASSP_aeroplane_variable,
escape_colons(valid_GASSP_aeroplane_filename)),
"(%s + %s) / gassp_alias " %
(valid_echamham_variable_1, valid_echamham_variable_2), '1', '-o',
self.OUTPUT_FILENAME
]
arguments = parse_args(args)
evaluate_cmd(arguments)
self.ds.close()
# Check correct
self.ds = netCDF4.Dataset(self.OUTPUT_FILENAME)
calculated_result = self.ds.variables['calculated_variable'][:]
# A hand calculated selection of values
expected_result = numpy.ma.masked_invalid(
[0.00196121983491, 0.00197255626472, 0.00120850731992])
assert_that(calculated_result.shape, is_((311, )))
# Check the first 3 vald values
compare_masked_arrays(expected_result, calculated_result[:][10:13])
os.remove('collocated_gassp.nc')
def test_collocated_NetCDF_Gridded_onto_GASSP(self):
# Takes 2s
# First do a collocation of ECHAMHAM onto GASSP
sample_file = valid_GASSP_aeroplane_filename
sample_var = valid_GASSP_aeroplane_variable
collocator_and_opts = 'nn,variable=%s' % sample_var
arguments = [
'col',
'%s:%s' % (valid_echamham_variable_1,
escape_colons(valid_echamham_filename)),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', 'collocated_gassp'
]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
# Then do a statistics calculation using the collocated data:
args = [
'stats',
"%s:%s" % (valid_echamham_variable_1, 'collocated_gassp.nc'),
"%s:%s" % (valid_GASSP_aeroplane_variable,
escape_colons(valid_GASSP_aeroplane_filename)), '-o',
self.OUTPUT_FILENAME
]
arguments = parse_args(args)
stats_cmd(arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME,
self.output_vars)
os.remove('collocated_gassp.nc')
def test_GASSP_onto_CALIOP_L2(self):
variable = valid_GASSP_aeroplane_variable
filename = valid_GASSP_aeroplane_filename
sample_file = valid_caliop_l2_filename
collocator_and_opts = 'box[h_sep=10km],kernel=mean'
arguments = ['col', variable + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
def test_GASSP_onto_CALIOP_L1(self):
# Ran for 14hr, not finished. (with no h_sep)
variable = valid_GASSP_aeroplane_variable
filename = valid_GASSP_aeroplane_filename
sample_file = valid_caliop_l1_filename
collocator_and_opts = 'box[h_sep=10km],kernel=mean'
arguments = ['col', variable + ':' + filename,
sample_file + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
def test_GIVEN_single_variable_WHEN_collocate_THEN_successful_collocation(self):
variable = cis_test_files["NCAR_NetCDF_RAF"].data_variable_name
filename = cis_test_files["NCAR_NetCDF_RAF"].master_filename
sample_file = valid_hadgem_filename
collocator_and_opts = 'bin,kernel=mean'
arguments = ['col', variable + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, ['ATX'])
def test_GIVEN_multiple_variables_on_same_coords_plus_dim_vars_WHEN_collocate_THEN_successful_collocation(self):
variables = valid_aerosol_cci_variable, valid_aerosol_cci_variable_2, 'time'
filename = valid_aerosol_cci_filename
sample_file = valid_echamham_filename
collocator_and_opts = 'bin,kernel=mean'
arguments = ['col', ','.join(variables) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, variables)
def test_GASSP_onto_Aeronet(self):
# Takes 73s
variable = valid_GASSP_aeroplane_variable
filename = valid_GASSP_aeroplane_filename
sample_file = valid_aeronet_filename
collocator_and_opts = 'box[h_sep=10km],kernel=mean'
arguments = ['col', variable + ':' + filename,
sample_file + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, variable.split(","))
def test_GIVEN_single_variable_WHEN_collocate_box_THEN_successful_collocation(self):
# Takes 13 s
variable = cis_test_files["NCAR_NetCDF_RAF"].data_variable_name
filename = cis_test_files["NCAR_NetCDF_RAF"].master_filename
sample_file = valid_echamham_filename
collocator_and_opts = 'box[h_sep=10],kernel=mean'
arguments = ['col', variable + ':' + filename,
sample_file + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, ['ATX'])
def test_GASSP_onto_GASSP(self):
# Takes 6.5mins
vars = valid_GASSP_station_vars[:2]
filename = valid_GASSP_station_filename
sample_file = valid_GASSP_aeroplane_filename
collocator_and_opts = 'box[h_sep=10km],kernel=mean'
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
def test_Aeronet_onto_CloudSat(self):
# Takes 5hrs
variable = "AOT_440,AOT_870"
filename = valid_aeronet_filename
sample_file = valid_cloudsat_PRECIP_file
collocator_and_opts = 'box[h_sep=700km],kernel=mean'
arguments = ['col', variable + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, variable.split(","))
def test_GASSP_aux_coord_onto_Aeronet(self):
# Takes 73s
filename = cis_test_files['GASSP_aux_coord'].master_filename
variable = cis_test_files['GASSP_aux_coord'].data_variable_name
sample_file = valid_aeronet_filename
collocator_and_opts = 'box[h_sep=10km],kernel=mean'
arguments = ['col', variable + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, variable.split(","))
def test_CALIOP_L1_onto_NetCDF_Gridded(self):
vars = [valid_caliop_l1_variable]
filename = valid_caliop_l1_filename
sample_file = valid_hadgem_filename
sample_var = valid_hadgem_variable
collocator_and_opts = 'bin,kernel=mean,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_Aeronet_onto_GASSP(self):
# Takes 81 s
# Two vars takes 160s - shouldn't?
variable = "AOT_440,AOT_870"
filename = valid_aeronet_filename
sample_file = valid_GASSP_aeroplane_filename
collocator_and_opts = 'box[h_sep=10m],kernel=mean'
arguments = ['col', variable + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, variable.split(","))
def test_GASSP_aux_onto_NetCDF_Gridded(self):
filename = cis_test_files['GASSP_aux_coord'].master_filename
var = cis_test_files['GASSP_aux_coord'].data_variable_name
sample_file = valid_echamham_filename
sample_var = valid_echamham_variable_1
collocator_and_opts = 'bin,kernel=mean'
arguments = ['col', var + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, [var])
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, [var])
def test_NetCDF_Gridded_onto_CALIOP_L2(self):
vars = valid_echamham_variable_1, valid_echamham_variable_2
filename = valid_echamham_filename
sample_file = valid_caliop_l2_filename
sample_var = valid_caliop_l2_variable
collocator_and_opts = 'nn,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_hybrid_pressure_onto_GASSP_li(self):
# Takes 1s
vars = [valid_hybrid_pressure_variable]
filename = valid_hybrid_pressure_filename
sample_file = valid_GASSP_aircraft_files_with_different_timestamps[0]
sample_var = valid_GASSP_aircraft_var_with_different_timestamps
collocator_and_opts = 'lin,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, ['mmrbc'])
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, ['mmrbc'])
def test_hybrid_height_onto_GASSP_li(self):
# Takes 1s
vars = [valid_hybrid_height_flat_variable]
filename = valid_hybrid_height_flat_filename
sample_file = valid_GASSP_aeroplane_filename
sample_var = valid_GASSP_aeroplane_variable
collocator_and_opts = 'lin,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_HadGem_onto_cis_gridded_output_lin(self):
# Takes 1s
vars = [valid_hadgem_variable]
filename = valid_hadgem_filename
sample_file = valid_cis_gridded_output_filename
sample_var = valid_cis_gridded_output_variable
collocator_and_opts = 'lin,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + filename,
sample_file + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_NetCDF_Gridded_onto_ASCII_no_variable(self):
# Takes 4s
vars = valid_echamham_variable_1, valid_echamham_variable_2
filename = valid_echamham_filename
sample_file = cis_test_files["ascii"].master_filename
sample_var = cis_test_files["ascii"].data_variable_name
collocator_and_opts = 'nn'
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_ASCII_onto_NetCDF_Gridded(self):
# Takes 5s
vars = ["values"]
filename = valid_ascii_filename
sample_file = valid_hadgem_filename
sample_var = valid_hadgem_variable
collocator_and_opts = 'bin,kernel=mean'
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, ["value"])
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, ["value"])
def test_cloudsat_RVOD_onto_NetCDF_Gridded(self):
# Takes 290s
vars = [valid_cloudsat_RVOD_sdata_variable, valid_cloudsat_RVOD_vdata_variable]
filename = valid_cloudsat_RVOD_file
sample_file = valid_hadgem_filename
sample_var = valid_hadgem_variable
collocator_and_opts = 'bin,kernel=mean'
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_GASSP_onto_Aeronet_using_moments_kernel(self):
# Takes 73s
variable = valid_GASSP_aeroplane_variable
filename = valid_GASSP_aeroplane_filename
sample_file = valid_aeronet_filename
collocator_and_opts = 'box[h_sep=10km],kernel=moments'
arguments = ['col', variable + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
out_vars = [variable, variable + '_std_dev', variable + '_num_points']
self.check_output_contains_variables(self.OUTPUT_FILENAME, out_vars)
self.check_output_col_grid(sample_file, valid_aeronet_variable, self.OUTPUT_FILENAME, out_vars)
def test_GASSP_plane_onto_NetCDF_Gridded(self):
# Takes 15s
vars = valid_GASSP_aeroplane_vars
filename = valid_GASSP_aeroplane_filename
sample_file = valid_echamham_filename
sample_var = valid_echamham_variable_1
collocator_and_opts = 'bin,kernel=mean,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + filename,
sample_file + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_MODIS_L3_onto_NetCDF_Gridded(self):
# Takes 27s
vars = [valid_modis_l3_variable]
filename = valid_modis_l3_filename
sample_file = valid_hadgem_filename
sample_var = valid_hadgem_variable
collocator_and_opts = 'bin,kernel=mean,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + filename,
sample_file + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_hybrid_pressure_onto_GASSP_nn(self):
# Takes 1s
vars = [valid_hybrid_pressure_variable]
filename = valid_hybrid_pressure_filename
sample_file = valid_GASSP_aeroplane_filename
sample_var = valid_GASSP_aeroplane_variable
collocator_and_opts = 'nn,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + filename,
sample_file + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, ['mmrbc'])
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, ['mmrbc'])
def test_MODIS_L2_onto_NetCDF_Gridded(self):
# Takes 20s
vars = ['Solar_Zenith', 'Optical_Depth_Ratio_Small_Land_And_Ocean']
filename = valid_modis_l2_filename
sample_file = valid_hadgem_filename
sample_var = valid_hadgem_variable
collocator_and_opts = 'bin,kernel=mean,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_NetCDF_Gridded_onto_MODIS_L3(self):
# Takes 47s
vars = valid_hadgem_variable,
filename = valid_hadgem_filename
sample_file = valid_modis_l3_filename
sample_var = valid_modis_l3_variable
collocator_and_opts = 'nn,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_NetCDF_Gridded_onto_cis_output_data(self):
# Takes 3s
vars = valid_echamham_variable_1, valid_echamham_variable_2
filename = valid_echamham_filename
sample_file = valid_cis_ungridded_output_filename
sample_var = valid_cis_ungridded_output_variable
collocator_and_opts = 'nn,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + filename,
sample_file + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_NetCDF_Gridded_onto_NCAR_RAF(self):
# Takes 30s
vars = valid_echamham_variable_1, valid_echamham_variable_2
filename = valid_echamham_filename
sample_file = valid_NCAR_NetCDF_RAF_filename
sample_var = valid_NCAR_NetCDF_RAF_variable
collocator_and_opts = 'nn'
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_GASSP_ship_onto_NetCDF_Gridded(self):
# Takes 10mins
vars = valid_GASSP_ship_vars
filename = valid_GASSP_ship_filename
sample_file = valid_echamham_filename
sample_var = valid_echamham_variable_1
collocator_and_opts = 'bin,kernel=mean'
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_Aeronet_onto_NetCDF_Gridded(self):
# JASCIS-120
# Takes 6s
vars = ["AOT_440", "AOT_870"]
filename = valid_aeronet_filename
sample_file = valid_echamham_filename
sample_var = valid_echamham_variable_1
collocator_and_opts = 'bin,kernel=mean'
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
def test_NetCDF_Gridded_onto_GASSP_aux_coord_li(self):
# Takes 1s
vars = valid_echamham_variable_1, valid_echamham_variable_2
filename = valid_echamham_filename
sample_file = cis_test_files['GASSP_aux_coord'].master_filename
sample_var = cis_test_files['GASSP_aux_coord'].data_variable_name
collocator_and_opts = 'lin,variable=%s' % sample_var
arguments = ['col', ",".join(vars) + ':' + escape_colons(filename),
escape_colons(sample_file) + ':collocator=' + collocator_and_opts,
'-o', self.OUTPUT_FILENAME]
main_arguments = parse_args(arguments)
col_cmd(main_arguments)
self.check_output_contains_variables(self.OUTPUT_FILENAME, vars)
self.check_output_col_grid(sample_file, sample_var, self.OUTPUT_FILENAME, vars)
self.check_output_vars_are_different(self.OUTPUT_FILENAME, vars)