def setUp(self):
"""Setup files and base data for utility testing."""
self.data_path = example_data
self.data_path_full = example_data_full
data = [
[np.nan, 48.1, 48.3, 65.1, 47.1, 49.9, 49.5, 48.9, 35.5, 44.5],
[51.9, 44.3, 44.5, 58.7, 41.1, 43.9, 43.9, 44.5, 31.1, 40.5],
[48.5, 38.5, 37.1, 53.9, 27.1, 40.7, 34.5, 41.7, 28.7, 37.7],
[33.9, 21.5, 20.1, 48.7, 12.1, 38.5, 13.9, 33.7, 25.3, 28.1],
[19.1, 10.9, 9.9, 42.3, 4.3, 36.5, 6.1, 16.9, 13.9, 13.3],
[12.7, 4.7, 3.9, 31.3, 3.1, 29.1, 3.7, 4.9, 6.9, 4.7],
]
keys = ["V%s" % (i + 1) for i in range(6)]
self.expected_dict = {key: data[i] for i, key in enumerate(keys)}
self.expected_dict_nh = {i: row for i, row in enumerate(data)}
self.expected_dict_no_nan = deepcopy(self.expected_dict)
self.expected_dict_no_nan["V1"][0] = 56.5
self.expected_arr = np.array(data).T
self.expected_var_names = keys
self.const_data = deepcopy(self.expected_arr)
self.const_data[:, 0] = np.ones_like(self.expected_arr[:, 0])
self.stats_obj = ui.DVHAStats(self.data_path)
def test_control_chart_if_const_data(self):
"""Test that const data does not crash control chart"""
stats_obj = ui.DVHAStats(self.const_data)
ucc = stats_obj.univariate_control_charts(box_cox=True)
ucc[0].show()
self.assertEqual(
ucc[0].plot_title,
"Cannot calculate control chart with const data!",
)
def test_pca(self):
"""Test PCA initialization and plot"""
stats_obj = ui.DVHAStats(self.expected_dict_no_nan)
pca = stats_obj.pca()
fig = pca.show()
pca.close(fig)
# Test no transform
stats_obj.pca(transform=False)
def test_hotelling_t2_box_cox(self):
"""Test multivariate control chart creation and values"""
stats_obj = ui.DVHAStats(self.data_path_full)
ht2 = stats_obj.hotelling_t2(box_cox=True, const_policy="omit")
self.assertEqual(round(ht2.center_line, 3), 5.375)
lcl, ucl = ht2.control_limits
self.assertEqual(round(lcl, 3), 0)
self.assertEqual(round(ucl, 3), 13.555)
self.assertEqual(len(ht2.out_of_control), 2)
def test_del_const_var(self):
"""Test init deletes constant variables if del_const_vars is True"""
stats_obj = ui.DVHAStats(
self.const_data,
var_names=self.expected_var_names,
del_const_vars=True,
)
self.assertEqual(stats_obj.deleted_vars, ["V1"])
assert_array_equal(stats_obj.data, np.delete(self.const_data,
0,
axis=1))
def test_univariate_control_chart_box_cox(self):
"""Test univariate control chart creation and values with Box-Cox"""
stats_obj = ui.DVHAStats(self.data_path_full)
ucc = stats_obj.univariate_control_charts(box_cox=True,
const_policy="omit")
self.assertEqual(round(ucc[0].center_line, 3), 1835.702)
lcl, ucl = ucc[0].control_limits
self.assertEqual(round(lcl, 3), 136.258)
self.assertEqual(round(ucl, 3), 3535.147)
self.assertEqual(len(ucc[0].out_of_control), 3)
self.assertEqual(len(ucc[0].out_of_control_high), 1)
self.assertEqual(len(ucc[0].out_of_control_low), 2)
def test_multi_variable_regression(self):
"""Test Multi-Variable Linear Regression"""
y = np.linspace(1, 10, 10)
stats_obj = ui.DVHAStats(self.expected_dict_no_nan)
mvr = stats_obj.linear_reg(y)
mvr2 = stats_obj.linear_reg(y, saved_reg=mvr)
assert_array_equal(mvr.residuals, mvr2.residuals)
fig = mvr.show()
mvr.close(fig)
fig = mvr.show("prob")
mvr.close(fig)
self.assertIsNone(mvr.show("test"))
mvr3 = stats_obj.linear_reg("V1", reg_vars=["V1", "V2", "V3"])
self.assertEqual(mvr3.var_names, ["V2", "V3"])
assert_array_equal(stats_obj.data[:, 0], mvr3.y)
def test_show_calls(self):
"""Test matplotlib show calls"""
fig = self.stats_obj.show(0)
self.stats_obj.close(fig)
fig = self.stats_obj.show(0, plot_type="hist")
self.stats_obj.close(fig)
corr_mat = self.stats_obj.correlation_matrix(corr_type="Spearman")
fig = corr_mat.show()
corr_mat.close(fig)
ucc = self.stats_obj.univariate_control_charts()
fig = ucc[0].show()
ucc[0].close(fig)
ht2 = self.stats_obj.hotelling_t2()
fig = ht2.show()
ht2.close(fig)
y = list(range(10))
s = ui.DVHAStats(self.expected_dict_no_nan)
ra_cc = s.risk_adjusted_control_chart(y)
fig = ra_cc.show()
ra_cc.close(fig)
fig = self.stats_obj.show(plot_type="box")
self.stats_obj.close(fig)
# test if plot_type not accepted
with self.assertRaises(NotImplementedError):
self.stats_obj.show(plot_type="test")
# test if var_name = None and plot_type not "box"
with self.assertRaises(NotImplementedError):
self.stats_obj.show()
def test_invalid_data_import(self):
with self.assertRaises(NotImplementedError):
ui.DVHAStats("test")
def test_csv_import(self):
"""Test csv importing"""
stats_obj = ui.DVHAStats(self.data_path)
assert_array_equal(stats_obj.data, self.expected_arr)
self.assertEqual(stats_obj.var_names, self.expected_var_names)
def test_dict_import(self):
"""Test dict importing"""
stats_obj = ui.DVHAStats(self.expected_dict)
assert_array_equal(stats_obj.data, self.expected_arr)
self.assertEqual(stats_obj.var_names, self.expected_var_names)
def test_box_cox_const_policy_raise(self):
"""Test const_policy='raise' results in ValueError with const data"""
stats_obj = ui.DVHAStats(self.const_data)
with self.assertRaises(ValueError):
stats_obj.box_cox_by_index(0, const_policy="raise")