def test_all_gates():
gml_path = 'examples/data/gate_ref/gml/gml_all_gates.xml'
truth_pattern = 'examples/data/gate_ref/truth/Results*.txt'
res_files = glob.glob(truth_pattern)
truth_dict = {}
for res_path in res_files:
match = re.search("Results_(.+)\\.txt$", res_path)
if match is not None:
g_id = match.group(1)
truth = pd.read_csv(res_path,
header=None,
squeeze=True,
dtype='bool').values
truth_dict[g_id] = truth
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_samples(data1_sample.original_filename, group_name)
s.analyze_samples(group_name=group_name)
results = s.get_gating_results(group_name,
data1_sample.original_filename)
for row in results.report.itertuples():
np.testing.assert_array_equal(
truth_dict[row.gate_name],
results.get_gate_membership(row.gate_name))
def test_quadrant2_gate():
gml_path = 'examples/gate_ref/gml/gml_quadrant2_gate.xml'
res1_path = 'examples/gate_ref/truth/Results_FSCN-SSCN.txt'
res2_path = 'examples/gate_ref/truth/Results_FSCD-SSCN-FL1N.txt'
res3_path = 'examples/gate_ref/truth/Results_FSCP-SSCN-FL1N.txt'
res4_path = 'examples/gate_ref/truth/Results_FSCD-FL1P.txt'
res5_path = 'examples/gate_ref/truth/Results_FSCN-SSCP-FL1P.txt'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_sample(data1_sample.original_filename, group_name)
s.analyze_samples(sample_group=group_name)
truth1 = pd.read_csv(res1_path, header=None, squeeze=True, dtype='bool').values
truth2 = pd.read_csv(res2_path, header=None, squeeze=True, dtype='bool').values
truth3 = pd.read_csv(res3_path, header=None, squeeze=True, dtype='bool').values
truth4 = pd.read_csv(res4_path, header=None, squeeze=True, dtype='bool').values
truth5 = pd.read_csv(res5_path, header=None, squeeze=True, dtype='bool').values
result = s.get_gating_results(group_name, data1_sample.original_filename)
np.testing.assert_array_equal(truth1, result.get_gate_indices('FSCN-SSCN'))
np.testing.assert_array_equal(truth2, result.get_gate_indices('FSCD-SSCN-FL1N'))
np.testing.assert_array_equal(truth3, result.get_gate_indices('FSCP-SSCN-FL1N'))
np.testing.assert_array_equal(truth4, result.get_gate_indices('FSCD-FL1P'))
np.testing.assert_array_equal(truth5, result.get_gate_indices('FSCN-SSCP-FL1P'))
def test_quadrant1_gate():
gml_path = 'examples/gate_ref/gml/gml_quadrant1_gate.xml'
res1_path = 'examples/gate_ref/truth/Results_FL2N-FL4N.txt'
res2_path = 'examples/gate_ref/truth/Results_FL2N-FL4P.txt'
res3_path = 'examples/gate_ref/truth/Results_FL2P-FL4N.txt'
res4_path = 'examples/gate_ref/truth/Results_FL2P-FL4P.txt'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_sample(data1_sample.original_filename, group_name)
truth1 = pd.read_csv(res1_path, header=None, squeeze=True, dtype='bool').values
truth2 = pd.read_csv(res2_path, header=None, squeeze=True, dtype='bool').values
truth3 = pd.read_csv(res3_path, header=None, squeeze=True, dtype='bool').values
truth4 = pd.read_csv(res4_path, header=None, squeeze=True, dtype='bool').values
s.analyze_samples(group_name)
results = s.get_gating_results(group_name, data1_sample.original_filename)
result1 = results.get_gate_indices('FL2N-FL4N')
result2 = results.get_gate_indices('FL2N-FL4P')
result3 = results.get_gate_indices('FL2P-FL4N')
result4 = results.get_gate_indices('FL2P-FL4P')
np.testing.assert_array_equal(truth1, result1)
np.testing.assert_array_equal(truth2, result2)
np.testing.assert_array_equal(truth3, result3)
np.testing.assert_array_equal(truth4, result4)
def test_new_group_membership_is_empty(self):
s = Session()
group_name = 'new_group'
s.add_sample_group(group_name)
s.add_samples(copy.deepcopy(
test_samples_base_set)) # load without assigning a group
s_sample_ids = sorted(s.get_group_sample_ids(group_name))
self.assertListEqual(s_sample_ids, [])
def test_add_samples_with_group(self):
sample_ids = ["100715.fcs", "109567.fcs", "113548.fcs"]
s = Session()
group_name = 'gml'
s.add_sample_group(group_name)
s.add_samples(copy.deepcopy(test_samples_base_set), group_name)
s_sample_ids = sorted(s.get_group_sample_ids(group_name))
self.assertListEqual(sample_ids, s_sample_ids)
def test_poly2_gate():
gml_path = 'examples/gate_ref/gml/gml_poly2_gate.xml'
res_path = 'examples/gate_ref/truth/Results_Polygon2.txt'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_sample(data1_sample.original_filename, group_name)
s.analyze_samples(sample_group=group_name)
truth = pd.read_csv(res_path, header=None, squeeze=True, dtype='bool').values
result = s.get_gate_indices(group_name, data1_sample.original_filename, 'Polygon2')
np.testing.assert_array_equal(truth, result)
def test_get_parent_quadrant_gate(self):
gml_path = 'examples/gate_ref/gml/gml_parent_quadrant_rect_gate.xml'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_sample(data1_sample.original_filename, group_name)
parent_id = s.get_parent_gate_id(group_name, 'ParRectangle1')
self.assertEqual(parent_id, 'FL2P-FL4P')
parent_gate = s.get_gate(group_name, data1_sample.original_filename, parent_id)
self.assertIsInstance(parent_gate, gates.Quadrant)
def test_get_parent_rect_gate(self):
gml_path = 'examples/data/gate_ref/gml/gml_parent_rect1_rect_par1_gate.xml'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_samples(data1_sample.original_filename, group_name)
parent_gate_name = s.get_parent_gate_name(group_name, 'ScalePar1')
self.assertEqual(parent_gate_name, 'ScaleRect1')
parent_gate = s.get_gate(group_name,
parent_gate_name,
sample_id=data1_sample.original_filename)
self.assertIsInstance(parent_gate, gates.RectangleGate)
def test_boolean_or2_complement_gate():
gml_path = 'examples/data/gate_ref/gml/gml_boolean_or2_gate.xml'
res_path = 'examples/data/gate_ref/truth/Results_Or2.txt'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_samples(data1_sample.original_filename, group_name)
s.analyze_samples(group_name=group_name)
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = s.get_gate_membership(group_name,
data1_sample.original_filename, 'Or2')
np.testing.assert_array_equal(truth, result)
def test_matrix_transform_logicle_rect1_gate():
gml_path = 'examples/data/gate_ref/gml/gml_matrix_transform_logicle_rect1_gate.xml'
res_path = 'examples/data/gate_ref/truth/Results_ScaleRect1.txt'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_samples(data1_sample.original_filename, group_name)
s.analyze_samples(group_name=group_name)
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = s.get_gate_membership(group_name,
data1_sample.original_filename,
'ScaleRect1')
np.testing.assert_array_equal(truth, result)
def test_quadrant_gate_relative_percent(self):
gml_path = 'examples/gate_ref/gml/gml_quadrant1_gate.xml'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_sample(data1_sample.original_filename, group_name)
s.analyze_samples(sample_group=group_name)
result = s.get_gating_results(group_name, data1_sample.original_filename)
total_percent = result.get_gate_relative_percent('FL2N-FL4N') + \
result.get_gate_relative_percent('FL2N-FL4P') + \
result.get_gate_relative_percent('FL2P-FL4N') + \
result.get_gate_relative_percent('FL2P-FL4P')
self.assertEqual(100.0, total_percent)
