def test_export_wsp(self): wsp_path = "examples/data/8_color_data_set/8_color_ICS.wsp" sample_grp = 'DEN' # use a leaf gate to test if the new WSP session is created correctly gate_name = 'TNFa+' gate_path = ('root', 'Time', 'Singlets', 'aAmine-', 'CD3+', 'CD4+') fks = Session(copy.deepcopy(test_samples_8c_full_set)) fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True) out_file = BytesIO() fks.export_wsp(out_file, sample_grp) out_file.seek(0) fks_out = Session(copy.deepcopy(test_samples_8c_full_set)) fks_out.import_flowjo_workspace(out_file, ignore_missing_files=True) self.assertIsInstance(fks_out, Session) fks_gate = fks.get_gate(sample_grp, gate_name, gate_path) fks_out_gate = fks_out.get_gate(sample_grp, gate_name, gate_path) self.assertIsInstance(fks_gate, gates.RectangleGate) self.assertIsInstance(fks_out_gate, gates.RectangleGate) self.assertEqual(fks_gate.gate_name, gate_name) self.assertEqual(fks_out_gate.gate_name, gate_name)
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_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_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_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_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_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_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_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)