def test_stog_plot_df(self, mock_show):
df = pd.DataFrame(np.random.randn(10, 2),
index=np.arange(10),
columns=list('XY'))
stog = StoG()
stog._plot_df(df, 'x', 'y', 'title', None)
mock_show.assert_called_with()
def test_stog_real_space_function_setter(self):
stog = StoG()
stog.real_space_function = "GK(r)"
self.assertEqual(stog.real_space_function, "GK(r)")
self.assertEqual(stog.gr_title, "GK(r) Merged")
self.assertEqual(stog.real_space_function, "GK(r)")
self.assertEqual(stog.gr_ft_title, "GK(r) FT")
self.assertEqual(stog.gr_lorch_title, "GK(r) FT Lorched")
def test_stog_read_all_data_for_files_length(self):
# Load S(Q) for Argon from test data
stog = StoG()
stog.files = self.kwargs_for_files['Files']
stog.read_all_data()
# Check S(Q) data against targets
self.assertEqual(len(stog.files), len(self.kwargs_for_files['Files']))
def test_stog_add_dataset_default_reciprocal_space_function(self):
# Checks the default reciprocal space function is S(Q) and the index is
# set
stog = StoG()
index = 300
info = {'data': pd.DataFrame({'x': self.q, 'y': self.sq})}
stog.add_dataset(info, index=index)
self.assertEqual(list(stog.df_individuals.columns.values),
['S(Q)_%d' % index])
def test_stog_plotting_kwargs_setter(self):
stog = StoG()
new_kwargs = {
'figsize': (4, 4),
'style': 'o',
'ms': 2,
'lw': 2,
}
stog.plotting_kwargs = new_kwargs
self.assertEqual(stog.plotting_kwargs, new_kwargs)
def setUp(self):
super(TestStogPlottingDataFrameMethods, self).setUp()
stog = StoG(**self.kwargs_for_stog_input)
stog.files = self.kwargs_for_files['Files']
stog.read_all_data()
stog.merge_data()
stog.transform_merged()
self.stog = stog
def test_stog_transform_merged_for_nan_after_filter(self):
# Load S(Q) for Argon from test data
stog = StoG(**self.kwargs_for_stog_input)
stog.files = self.kwargs_for_files['Files']
stog.real_space_function = "GK(r)"
stog.read_all_data()
stog.merge_data()
stog.transform_merged()
self.assertFalse(
np.isnan(stog.df_sq_master[stog.sq_title].values).any())
self.assertFalse(
np.isnan(stog.df_gr_master[stog.gr_title].values).any())
def test_stog_add_dataset_wrong_reciprocal_space_function_exception(self):
# Check qmin and qmax apply cropping
stog = StoG()
index = 0
info = {
'data': pd.DataFrame({
'x': self.q,
'y': self.sq
}),
'ReciprocalFunction': 'ABCDEFG(Q)'
}
with self.assertRaises(ValueError):
stog.add_dataset(info, index=index)
def test_stog_add_dataset_xoffset(self):
# Offset Q from 1.96 -> 2.14
stog = StoG()
index = 0
info = {
'data': pd.DataFrame({
'x': self.q,
'y': self.sq
}),
'ReciprocalFunction': 'S(Q)',
'X': {
'Offset': 0.2
}
}
stog.add_dataset(info, index=index)
self.assertEqual(stog.df_individuals.iloc[self.first].name, 2.14)
def test_stog_read_all_data_assertion(self):
stog = StoG()
with self.assertRaises(AssertionError):
stog.read_all_data()
stog.files = list()
with self.assertRaises(AssertionError):
stog.read_all_data()
def test_stog_fourier_filter_before_transform_merged_call(self):
# Number of decimal places for precision
places = 1
# Load S(Q) for Argon from test data
stog = StoG(**self.kwargs_for_stog_input)
stog.files = self.kwargs_for_files['Files']
stog.plot_flag = False
stog.read_all_data()
stog.merge_data()
stog.fourier_filter()
# Check g(r) data against targets
self.assertAlmostEqual(
stog.df_gr_master.iloc[self.real_space_first].name,
self.real_xtarget,
places=places)
self.assertAlmostEqual(
stog.df_gr_master.iloc[self.real_space_first][stog.gr_ft_title],
self.gofr_ff_target[0],
places=places)
def test_stog_add_dataset_yoffset(self):
# Offset S(Q) and make sure it does not equal original target values
stog = StoG()
index = 0
info = {
'data': pd.DataFrame({
'x': self.q,
'y': self.sq
}),
'ReciprocalFunction': 'S(Q)',
'Y': {
'Offset': 2.0
}
}
stog.add_dataset(info, index=index)
self.assertNotEqual(
stog.df_individuals.iloc[self.first]['S(Q)_%d' % index],
self.sq_target[0])
self.assertNotEqual(
stog.df_sq_individuals.iloc[self.first]['S(Q)_%d' % index],
self.sq_target[0])
def test_stog_transform_merged_GKofR(self):
# Number of decimal places for precision
places = 2
# Load S(Q) for Argon from test data
stog = StoG(**self.kwargs_for_stog_input)
stog.files = self.kwargs_for_files['Files']
stog.real_space_function = "GK(r)"
stog.read_all_data()
stog.merge_data()
stog.transform_merged()
# Check GK(r) data against targets
self.assertAlmostEqual(
stog.df_gr_master.iloc[self.real_space_first].name,
self.real_xtarget,
places=places)
self.assertAlmostEqual(
stog.df_gr_master.iloc[self.real_space_first][stog.gr_title],
self.GKofR_target[0],
places=places)
def test_stog_read_all_data(self):
# Number of decimal places for precision
places = 5
# Load S(Q) for Argon from test data
stog = StoG()
stog.files = self.kwargs_for_files['Files']
stog.read_all_data()
# Check S(Q) data against targets
self.assertEqual(stog.df_individuals.iloc[self.first].name,
self.reciprocal_xtarget)
for index in range(len(stog.files)):
self.assertAlmostEqual(
stog.df_individuals.iloc[self.first]['S(Q)_%d' % index],
self.sq_target[0],
places=places)
self.assertAlmostEqual(
stog.df_sq_individuals.iloc[self.first]['S(Q)_%d' % index],
self.sq_target[0],
places=places)
def test_stog_read_dataset(self):
# Number of decimal places for precision
places = 5
# Load S(Q) for Argon from test data
stog = StoG(
**{
'<b_coh>^2': self.kwargs['<b_coh>^2'],
'<b_tot^2>': self.kwargs['<b_tot^2>']
})
info = {
'Filename': get_data_path(self.material.reciprocal_space_filename),
'ReciprocalFunction': 'S(Q)',
'Qmin': 0.02,
'Qmax': 35.2,
'Y': {
'Offset': 0.0,
'Scale': 1.0
},
'X': {
'Offset': 0.0
}
}
info['index'] = 0
stog.read_dataset(info)
# Check S(Q) data against targets
self.assertEqual(stog.df_individuals.iloc[self.first].name,
self.reciprocal_xtarget)
self.assertAlmostEqual(
stog.df_individuals.iloc[self.first]['S(Q)_%d' % info['index']],
self.sq_target[0],
places=places)
self.assertAlmostEqual(
stog.df_sq_individuals.iloc[self.first]['S(Q)_%d' % info['index']],
self.sq_target[0],
places=places)
def test_stog_merge_data_qsq_opts_offset(self):
# Number of decimal places for precision
places = 5
# Load S(Q) for Argon from test data
stog = StoG()
stog.files = self.kwargs_for_files['Files']
stog.read_all_data()
qsq_opts = {'Y': {'Offset': 1.0}}
# Test Q[S(Q)-1] scale
stog.merged_opts['Q[S(Q)-1]'] = qsq_opts
stog.merge_data()
self.assertAlmostEqual(
stog.df_sq_master.iloc[self.first][stog.qsq_minus_one_title],
qsq_opts['Y']['Offset'] + self.fq_target[0],
places=places)
def test_stog_merge_data(self):
# Number of decimal places for precision
places = 5
# Load S(Q) for Argon from test data
stog = StoG()
stog.files = self.kwargs_for_files['Files']
stog.read_all_data()
stog.merge_data()
# Check S(Q) data against targets
self.assertEqual(stog.df_sq_master.iloc[self.first].name,
self.reciprocal_xtarget)
self.assertAlmostEqual(
stog.df_sq_master.iloc[self.first][stog.sq_title],
self.sq_target[0],
places=places)
def test_stog_init(self):
stog = StoG()
self.assertEqual(stog.xmin, 100)
self.assertEqual(stog.xmax, 0)
self.assertEqual(stog.qmin, None)
self.assertEqual(stog.qmax, None)
self.assertEqual(stog.files, None)
self.assertEqual(stog.sq_title, "S(Q) Merged")
self.assertEqual(stog.qsq_minus_one_title, "Q[S(Q)-1] Merged")
self.assertEqual(stog.sq_ft_title, "S(Q) FT")
self.assertEqual(stog.fq_title, "F(Q) Merged")
self.assertEqual(stog.real_space_function, "g(r)")
self.assertEqual(stog.gr_title, "g(r) Merged")
self.assertEqual(stog.gr_ft_title, "g(r) FT")
self.assertEqual(stog.gr_lorch_title, "g(r) FT Lorched")
self.assertEqual(stog.GKofR_title, "G(r) (Keen Version)")
self.assertEqual(stog.rmin, 0.0)
self.assertEqual(stog.rmax, 50.0)
self.assertEqual(stog.rdelta, 0.01)
self.assertEqual(stog.density, 1.0)
self.assertEqual(stog.bcoh_sqrd, 1.0)
self.assertEqual(stog.btot_sqrd, 1.0)
self.assertEqual(stog.low_q_correction, False)
self.assertEqual(stog.lorch_flag, False)
self.assertEqual(stog.fourier_filter_cutoff, None)
self.assertEqual(stog.plot_flag, True)
self.assertEqual(stog.plotting_kwargs, {
'figsize': (16, 8),
'style': '-',
'ms': 1,
'lw': 1,
})
self.assertEqual(stog.merged_opts,
{"Y": {
"Offset": 0.0,
"Scale": 1.0
}})
self.assertEqual(stog.stem_name, "out")
self.assertTrue(stog.df_individuals.empty)
self.assertTrue(stog.df_sq_master.empty)
self.assertTrue(stog.df_sq_individuals.empty)
self.assertTrue(stog.df_gr_master.empty)
def test_stog_add_dataset_qmin_qmax_crop(self):
# Check qmin and qmax apply cropping
stog = StoG()
index = 0
info = {
'data': pd.DataFrame({
'x': self.q,
'y': self.sq
}),
'ReciprocalFunction': 'S(Q)'
}
stog.qmin = 1.5
stog.qmax = 12.0
stog.add_dataset(info, index=index)
self.assertEqual(stog.df_individuals.iloc[0].name, stog.qmin)
self.assertEqual(stog.df_individuals.iloc[-1].name, stog.qmax)
def test_stog_fourier_filter_for_nan_after_filter(self):
# Load S(Q) for Argon from test data
stog = StoG(**self.kwargs_for_stog_input)
stog.files = self.kwargs_for_files['Files']
stog.plot_flag = False
stog.read_all_data()
stog.merge_data()
stog.transform_merged()
stog.fourier_filter()
self.assertFalse(
np.isnan(stog.df_gr_master[stog.gr_title].values).any())
self.assertFalse(
np.isnan(stog.df_sq_master[stog.sq_title].values).any())
self.assertFalse(
np.isnan(stog.df_sq_master[stog._ft_title].values).any())
self.assertFalse(
np.isnan(stog.df_sq_master[stog.sq_ft_title].values).any())
def test_stog_apply_lorch_GofR(self):
# Number of decimal places for precision
places = 5
# Load S(Q) for Argon from test data
stog = StoG(**self.kwargs_for_stog_input)
stog.files = self.kwargs_for_files['Files']
stog.plot_flag = False
stog.real_space_function = "G(r)"
stog.read_all_data()
stog.merge_data()
stog.transform_merged()
q, sq, r, gr = stog.fourier_filter()
stog.apply_lorch(q, sq, r)
self.assertAlmostEqual(
stog.df_gr_master.iloc[self.real_space_first][stog.gr_lorch_title],
self.GofR_lorch_target[0],
places=places)
def test_stog_low_q_correction_exception(self):
stog = StoG()
with self.assertRaises(TypeError):
stog.low_q_correction = 1.0
def test_stog_fourier_filter_with_plot_flag(self, mock_show):
# Load S(Q) for Argon from test data
stog = StoG(**self.kwargs_for_stog_input)
stog.files = self.kwargs_for_files['Files']
stog.plot_flag = True
stog.read_all_data()
stog.merge_data()
stog.transform_merged()
stog.fourier_filter()
mock_show.assert_called_with()
def test_stog_real_space_function_exception(self):
stog = StoG()
with self.assertRaises(ValueError):
stog.real_space_function = "Dog"
def test_stog_plot_flag_exception(self):
stog = StoG()
with self.assertRaises(TypeError):
stog.plot_flag = 1.0
def test_stog_df_sq_individuals_setter(self):
stog = StoG()
stog.df_sq_individuals = self.df_target
self.assertTrue(stog.df_sq_individuals.equals(self.df_target))
def test_stog_df_gr_master_setter(self):
stog = StoG()
stog.df_gr_master = self.df_target
self.assertTrue(stog.df_gr_master.equals(self.df_target))
def test_stog_append_file(self):
stog = StoG(**{'Files': ['file1.txt', 'file2.txt']})
stog.append_file('file3.txt')
self.assertEqual(stog.files, ['file1.txt', 'file2.txt', 'file3.txt'])
def test_stog_extend_file_list(self):
stog = StoG(**{'Files': ['file1.txt', 'file2.txt']})
stog.extend_file_list(['file3.txt', 'file4.txt'])
self.assertEqual(stog.files,
['file1.txt', 'file2.txt', 'file3.txt', 'file4.txt'])
def test_stog_add_dataset(self):
# Number of decimal places for precision
places = 5
# Initialize with material info for Argon
stog = StoG(
**{
'<b_coh>^2': self.kwargs['<b_coh>^2'],
'<b_tot^2>': self.kwargs['<b_tot^2>']
})
# Add the S(Q) data set and check values against targets
index = 0
info = {
'data': pd.DataFrame({
'x': self.q,
'y': self.sq
}),
'ReciprocalFunction': 'S(Q)'
}
stog.add_dataset(info, index=index)
self.assertEqual(stog.df_individuals.iloc[self.first].name,
self.reciprocal_xtarget)
self.assertAlmostEqual(stog.df_individuals.iloc[self.first]['S(Q)_%d' %
index],
self.sq_target[0],
places=places)
self.assertAlmostEqual(
stog.df_sq_individuals.iloc[self.first]['S(Q)_%d' % index],
self.sq_target[0],
places=places)
# Add the Q[S(Q)-1] data set and check values for it and S(Q) against
# targets
index = 1
info = {
'data': pd.DataFrame({
'x': self.q,
'y': self.fq
}),
'ReciprocalFunction': 'Q[S(Q)-1]'
}
stog.add_dataset(info, index=index)
self.assertAlmostEqual(
stog.df_individuals.iloc[self.first]['Q[S(Q)-1]_%d' % index],
self.fq_target[0],
places=places)
self.assertAlmostEqual(
stog.df_sq_individuals.iloc[self.first]['S(Q)_%d' % index],
self.sq_target[0],
places=places)
# Add the FK(Q) data set and check values for it and S(Q) against
# targets
index = 2
info = {
'data': pd.DataFrame({
'x': self.q,
'y': self.fq_keen
}),
'ReciprocalFunction': 'FK(Q)'
}
stog.add_dataset(info, index=index)
self.assertAlmostEqual(
stog.df_individuals.iloc[self.first]['FK(Q)_%d' % index],
self.fq_keen_target[0],
places=places)
self.assertAlmostEqual(
stog.df_sq_individuals.iloc[self.first]['S(Q)_%d' % index],
self.sq_target[0],
places=places)
# Add the DCS(Q) data set and check values for it and S(Q) against
# targets
index = 3
info = {
'data': pd.DataFrame({
'x': self.q,
'y': self.dcs
}),
'ReciprocalFunction': 'DCS(Q)'
}
stog.add_dataset(info, index=index)
self.assertAlmostEqual(
stog.df_individuals.iloc[self.first]['DCS(Q)_%d' % index],
self.dcs_target[0],
places=places)
self.assertAlmostEqual(
stog.df_sq_individuals.iloc[self.first]['S(Q)_%d' % index],
self.sq_target[0],
places=places)