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)
