def test_get_gate_from_template(self): fks = Session(fcs_samples=data1_sample) fks.add_gate(poly1_gate) template_gate = fks.get_gate('default', 'Polygon1') self.assertEqual(template_gate.gate_name, 'Polygon1')
def test_load_samples_from_list_of_paths(self): fks = Session(fcs_samples=fcs_file_paths) self.assertEqual(len(fks.sample_lut.keys()), 3) self.assertIsInstance(fks.get_sample('100715.fcs'), Sample) sample_ids = ["100715.fcs", "109567.fcs", "113548.fcs"] self.assertListEqual(fks.get_sample_ids(), sample_ids)
def test_get_group_transforms(self): wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp" sample_grp = 'DEN' fks = Session(copy.deepcopy(test_samples_8c_full_set)) fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True) xforms = fks.get_group_transforms(sample_grp) self.assertEqual(len(xforms), 23) for cm in xforms: self.assertIsInstance(cm, Transform)
def test_get_sample_comp_matrices(self): wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp" sample_grp = 'DEN' sample_id = '101_DEN084Y5_15_E01_008_clean.fcs' fks = Session(copy.deepcopy(test_samples_8c_full_set)) fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True) comp_matrices = fks.get_sample_comp_matrices(sample_grp, sample_id) self.assertEqual(len(comp_matrices), 1) for cm in comp_matrices: self.assertIsInstance(cm, Matrix)
def test_load_wsp_single_quad(self): wsp_path = "examples/data/simple_diamond_example/simple_diamond_example_quad_gate.wsp" fcs_path = "examples/data/simple_diamond_example/test_data_diamond_01.fcs" fks = Session(fcs_samples=fcs_path) fks.import_flowjo_workspace(wsp_path) # FlowJo quadrant gates are not true quadrant gates, rather a collection of rectangle gates self.assertIsInstance( fks.get_gate('All Samples', 'Q1: channel_A- , channel_B+', sample_id='test_data_diamond_01.fcs'), gates.RectangleGate) fks.analyze_samples(group_name='All Samples') results = fks.get_gating_results('All Samples', 'test_data_diamond_01.fcs') gate_count_q1 = results.get_gate_count('Q1: channel_A- , channel_B+') gate_count_q2 = results.get_gate_count('Q2: channel_A+ , channel_B+') gate_count_q3 = results.get_gate_count('Q3: channel_A+ , channel_B-') gate_count_q4 = results.get_gate_count('Q4: channel_A- , channel_B-') self.assertEqual(gate_count_q1, 49671) self.assertEqual(gate_count_q2, 50596) self.assertEqual(gate_count_q3, 50330) self.assertEqual(gate_count_q4, 49403)
def test_get_sample_gate_events(self): wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp" sample_grp = 'DEN' sample_id = '101_DEN084Y5_15_E01_008_clean.fcs' gate_name = 'CD3+' fks = Session(copy.deepcopy(test_samples_8c_full_set)) fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True) fks.analyze_samples(sample_grp, sample_id) sample_comp = fks.get_sample_comp_matrices(sample_grp, sample_id)[0] sample_xform = transforms.LogicleTransform('my_logicle', param_t=262144.0, param_w=1.0, param_m=4.418539922, param_a=0.0) df_gated_events = fks.get_gate_events(sample_grp, sample_id, gate_name, matrix=sample_comp, transform=sample_xform) self.assertIsInstance(df_gated_events, pd.DataFrame) self.assertEqual(len(df_gated_events), 133670)
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_parse_wsp_reused_gate_with_child(self): wsp_path = "examples/data/8_color_data_set/reused_quad_gate_with_child.wsp" fks = Session(copy.deepcopy(test_samples_8c_full_set)) fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True) group_name = 'All Samples' gate_name = 'some_child_gate' gate_ids = fks.get_gate_ids(group_name) gate_id_1 = (gate_name, ('root', 'good cells', 'cd4+', 'Q2: CD107a+, IL2+')) gate_id_2 = (gate_name, ('root', 'good cells', 'cd8+', 'Q2: CD107a+, IL2+')) self.assertIn(gate_id_1, gate_ids) self.assertIn(gate_id_2, gate_ids)
def test_analyze_single_sample(self): wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp" sample_id = '101_DEN084Y5_15_E01_008_clean.fcs' sample_grp = 'DEN' fks = Session(copy.deepcopy(test_samples_8c_full_set)) fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True) sample_ids = fks.get_group_sample_ids(sample_grp) self.assertEqual(len(sample_ids), 3) fks.analyze_samples(sample_grp, sample_id=sample_id) report = fks.get_group_report(sample_grp) self.assertEqual(report['sample'].nunique(), 1)
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_analyze_single_sample(self): wsp_path = "examples/8_color_data_set/8_color_ICS_simple.wsp" fcs_path = "examples/8_color_data_set/fcs_files" sample_id = '101_DEN084Y5_15_E01_008_clean.fcs' sample_grp = 'DEN' fks = Session(fcs_samples=fcs_path) fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True) sample_ids = fks.get_group_sample_ids(sample_grp) self.assertEqual(len(sample_ids), 3) fks.analyze_samples(sample_grp, sample_id=sample_id) report = fks.get_group_report(sample_grp) self.assertEqual(report.index.get_level_values('sample').nunique(), 1)
def test_load_wsp_single_ellipse(self): wsp_path = "examples/simple_line_example/single_ellipse_51_events.wsp" fcs_path = "examples/simple_line_example/data_set_simple_line_100.fcs" fks = Session(fcs_samples=fcs_path) fks.import_flowjo_workspace(wsp_path) self.assertIsInstance( fks.get_gate('All Samples', 'data_set_simple_line_100.fcs', 'ellipse1'), gates.EllipsoidGate) fks.analyze_samples(sample_group='All Samples') results = fks.get_gating_results('All Samples', 'data_set_simple_line_100.fcs') gate_count = results.get_gate_count('ellipse1') self.assertEqual(gate_count, 48)
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_add_poly1_gate(): fks = Session(fcs_samples=data1_sample) fks.add_gate(poly1_gate) fks.analyze_samples() result = fks.get_gating_results('default', data1_sample.original_filename) res_path = 'examples/gate_ref/truth/Results_Polygon1.txt' truth = pd.read_csv(res_path, header=None, squeeze=True, dtype='bool').values np.testing.assert_array_equal(truth, result.get_gate_indices('Polygon1'))
def test_get_sample_groups(self): wsp_path = "examples/simple_line_example/simple_poly_and_rect.wsp" fcs_path = "examples/simple_line_example/data_set_simple_line_100.fcs" fks = Session(fcs_samples=fcs_path) fks.import_flowjo_workspace(wsp_path) groups = fks.get_sample_groups() groups_truth = ['default', 'my_group'] self.assertListEqual(groups, groups_truth) fks.add_sample_group('group2') groups_truth.append('group2') groups = fks.get_sample_groups() self.assertListEqual(groups, groups_truth)
def test_wsp_fasinh_transform(self): wsp_path = "examples/data/simple_diamond_example/test_data_diamond_asinh_rect.wsp" fcs_path = "examples/data/simple_diamond_example/test_data_diamond_01.fcs" fks = Session(fcs_samples=fcs_path) fks.import_flowjo_workspace(wsp_path) self.assertIsInstance( fks.get_gate('All Samples', 'upper_right', sample_id='test_data_diamond_01.fcs'), gates.RectangleGate) fks.analyze_samples(group_name='All Samples') results = fks.get_gating_results('All Samples', 'test_data_diamond_01.fcs') gate_count = results.get_gate_count('upper_right') self.assertEqual(gate_count, 50559)
def test_add_matrix_poly4_gate(): fks = Session(fcs_samples=data1_sample) fks.add_comp_matrix(comp_matrix_01) dim1 = Dimension('PE', compensation_ref='MySpill') dim2 = Dimension('PerCP', compensation_ref='MySpill') dims = [dim1, dim2] poly_gate = gates.PolygonGate('Polygon4', None, dims, poly1_vertices) fks.add_gate(poly_gate) res_path = 'examples/gate_ref/truth/Results_Polygon4.txt' truth = pd.read_csv(res_path, header=None, squeeze=True, dtype='bool').values fks.analyze_samples() result = fks.get_gating_results('default', data1_sample.original_filename) np.testing.assert_array_equal(truth, result.get_gate_indices('Polygon4'))
def test_analyze_samples_multiproc(self): wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp" sample_grp = 'DEN' sample_id = '101_DEN084Y5_15_E01_008_clean.fcs' gate_name = 'CD3+' fks = Session(copy.deepcopy(test_samples_8c_full_set)) fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True) fks.analyze_samples(sample_grp) gate_membership = fks.get_gate_membership(sample_grp, sample_id, gate_name) self.assertEqual(gate_membership.sum(), 133670)
def test_get_wsp_gated_events(self): wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp" sample_grp = 'DEN' sample_id = '101_DEN084Y5_15_E01_008_clean.fcs' gate_name = 'CD3+' fks = Session(copy.deepcopy(test_samples_8c_full_set)) fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True) fks.analyze_samples(sample_grp, sample_id) df_gated_events = fks.get_wsp_gated_events(sample_grp, [sample_id], gate_name) self.assertIsInstance(df_gated_events, list) self.assertEqual(len(df_gated_events[0]), 133670)
def test_load_wsp_single_poly(self): wsp_path = "examples/simple_line_example/simple_poly_and_rect.wsp" fcs_path = "examples/simple_line_example/data_set_simple_line_100.fcs" fks = Session(fcs_samples=fcs_path) fks.import_flowjo_workspace(wsp_path) self.assertIsInstance( fks.get_gate('my_group', 'data_set_simple_line_100.fcs', 'poly1'), gates.PolygonGate) gate_ids = {'rect1', 'poly1'} self.assertSetEqual(set(fks.get_gate_ids('my_group')), gate_ids)
def test_add_transform_asinh_range1_gate(): fks = Session(fcs_samples=data1_sample) fks.add_transform(asinh_xform1) dim1 = Dimension('FL1-H', 'uncompensated', 'AsinH_10000_4_1', range_min=0.37, range_max=0.63) dims = [dim1] rect_gate = gates.RectangleGate('ScaleRange1', None, dims) fks.add_gate(rect_gate) res_path = 'examples/gate_ref/truth/Results_ScaleRange1.txt' truth = pd.read_csv(res_path, header=None, squeeze=True, dtype='bool').values fks.analyze_samples() result = fks.get_gating_results('default', data1_sample.original_filename) np.testing.assert_array_equal(truth, result.get_gate_indices('ScaleRange1'))
def test_get_ambiguous_gate_objects(self): wsp_path = "examples/8_color_data_set/8_color_ICS.wsp" fcs_path = "examples/8_color_data_set/fcs_files/101_DEN084Y5_15_E01_008_clean.fcs" sample_id = '101_DEN084Y5_15_E01_008_clean.fcs' sample_grp = 'DEN' gate_id = 'TNFa+' gate_path = ['root', 'Time', 'Singlets', 'aAmine-', 'CD3+', 'CD4+'] fks = Session(fcs_samples=fcs_path) fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True) fks.analyze_samples(sample_grp) gate_indices = fks.get_gate_indices(sample_grp, sample_id, gate_id, gate_path=gate_path) self.assertIsInstance(gate_indices, np.ndarray) self.assertEqual(np.sum(gate_indices), 21)
def test_parse_wsp_with_ellipse(self): wsp_path = "examples/data/8_color_data_set/8_color_ICS_with_ellipse.wsp" fcs_path = "examples/data/8_color_data_set/fcs_files/101_DEN084Y5_15_E01_008_clean.fcs" sample_id = '101_DEN084Y5_15_E01_008_clean.fcs' sample_grp = 'DEN' gate_name = 'ellipse1' gate_path = ('root', 'Time', 'Singlets', 'aAmine-', 'CD3+') fks = Session(fcs_samples=fcs_path) fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True) fks.analyze_samples(sample_grp, sample_id=sample_id) gate_indices = fks.get_gate_membership(sample_grp, sample_id, gate_name, gate_path=gate_path) self.assertIsInstance(gate_indices, np.ndarray) self.assertEqual(np.sum(gate_indices), 7018)
def test_load_wsp_single_poly(self): wsp_path = "examples/data/simple_line_example/simple_poly_and_rect.wsp" fcs_path = "examples/data/simple_line_example/data_set_simple_line_100.fcs" fks = Session(fcs_samples=fcs_path) fks.import_flowjo_workspace(wsp_path) self.assertIsInstance( fks.get_gate('my_group', 'poly1', sample_id='data_set_simple_line_100.fcs'), gates.PolygonGate) gate_names = {'rect1', 'poly1'} wsp_gates_tuple = fks.get_gate_ids('my_group') wsp_gate_names = set([g[0] for g in wsp_gates_tuple]) self.assertSetEqual(wsp_gate_names, gate_names)
def test_parent_quadrant_rect_gate(): gml_path = 'examples/data/gate_ref/gml/gml_parent_quadrant_rect_gate.xml' res_path = 'examples/data/gate_ref/truth/Results_ParQuadRect.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, 'ParRectangle1') np.testing.assert_array_equal(truth, result)
def test_matrix_transform_logicle_range8c_gate(): gml_path = 'examples/data/gate_ref/gml/gml_matrix_transform_logicle_range8c_gate.xml' res_path = 'examples/data/gate_ref/truth/Results_ScaleRange8c.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, 'ScaleRange8c') np.testing.assert_array_equal(truth, result)
def test_quadrant2_gate(): gml_path = 'examples/data/gate_ref/gml/gml_quadrant2_gate.xml' res1_path = 'examples/data/gate_ref/truth/Results_FSCN-SSCN.txt' res2_path = 'examples/data/gate_ref/truth/Results_FSCD-SSCN-FL1N.txt' res3_path = 'examples/data/gate_ref/truth/Results_FSCP-SSCN-FL1N.txt' res4_path = 'examples/data/gate_ref/truth/Results_FSCD-FL1P.txt' res5_path = 'examples/data/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_samples(data1_sample.original_filename, group_name) s.analyze_samples(group_name=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_membership('FSCN-SSCN')) np.testing.assert_array_equal( truth2, result.get_gate_membership('FSCD-SSCN-FL1N')) np.testing.assert_array_equal( truth3, result.get_gate_membership('FSCP-SSCN-FL1N')) np.testing.assert_array_equal(truth4, result.get_gate_membership('FSCD-FL1P')) np.testing.assert_array_equal( truth5, result.get_gate_membership('FSCN-SSCP-FL1P'))
def test_quadrant_gate_relative_percent(self): gml_path = 'examples/data/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_samples(data1_sample.original_filename, group_name) s.analyze_samples(group_name=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)
def test_quadrant1_gate(): gml_path = 'examples/data/gate_ref/gml/gml_quadrant1_gate.xml' res1_path = 'examples/data/gate_ref/truth/Results_FL2N-FL4N.txt' res2_path = 'examples/data/gate_ref/truth/Results_FL2N-FL4P.txt' res3_path = 'examples/data/gate_ref/truth/Results_FL2P-FL4N.txt' res4_path = 'examples/data/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_samples(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_membership('FL2N-FL4N') result2 = results.get_gate_membership('FL2N-FL4P') result3 = results.get_gate_membership('FL2P-FL4N') result4 = results.get_gate_membership('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)