def test_add_matrix_transform_logicle_rect1_gate():
gs = fk.GatingStrategy()
gs.add_comp_matrix(comp_matrix_01)
gs.add_transform(logicle_xform1)
dim1 = fk.Dimension('PE',
'MySpill',
'Logicle_10000_0.5_4.5_0',
range_min=0.31,
range_max=0.69)
dim2 = fk.Dimension('PerCP',
'MySpill',
'Logicle_10000_0.5_4.5_0',
range_min=0.27,
range_max=0.73)
dims = [dim1, dim2]
rect_gate = fk.gates.RectangleGate('ScaleRect1', None, dims)
gs.add_gate(rect_gate)
res_path = 'examples/data/gate_ref/truth/Results_ScaleRect1.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth,
result.get_gate_membership('ScaleRect1'))
def test_gating_strategy_repr(self):
gs = fk.GatingStrategy()
gs.add_comp_matrix(prog_test_data.comp_matrix_01)
gs.add_transform(prog_test_data.logicle_xform1)
gs.add_transform(prog_test_data.hyperlog_xform1)
gs.add_gate(prog_test_data.poly1_gate)
dim1 = fk.Dimension('PE', 'MySpill', 'Logicle_10000_0.5_4.5_0', range_min=0.31, range_max=0.69)
dim2 = fk.Dimension('PerCP', 'MySpill', 'Logicle_10000_0.5_4.5_0', range_min=0.27, range_max=0.73)
dims1 = [dim1, dim2]
rect_gate1 = fk.gates.RectangleGate('ScaleRect1', None, dims1)
gs.add_gate(rect_gate1)
dim3 = fk.Dimension('FITC', 'MySpill', 'Hyperlog_10000_1_4.5_0', range_min=0.12, range_max=0.43)
dims2 = [dim3]
rect_gate2 = fk.gates.RectangleGate('ScalePar1', 'ScaleRect1', dims2)
gs.add_gate(rect_gate2)
gs_string = "GatingStrategy(3 gates, 2 transforms, 1 compensations)"
self.assertEqual(repr(gs), gs_string)
def test_add_transform_log_range6_gate():
gs = fk.GatingStrategy()
xform = fk.transforms.LogTransform('Logarithmic_10000_5',
param_t=10000,
param_m=5)
gs.add_transform(xform)
dim1 = fk.Dimension('FL1-H',
'uncompensated',
'Logarithmic_10000_5',
range_min=0.37,
range_max=0.63)
dims = [dim1]
rect_gate = fk.gates.RectangleGate('ScaleRange6', None, dims)
gs.add_gate(rect_gate)
res_path = 'examples/data/gate_ref/truth/Results_ScaleRange6.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(
truth, result.get_gate_membership('ScaleRange6'))
def test_add_parent_quadrant_rect_gate():
gs = fk.GatingStrategy()
gs.add_gate(quad1_gate)
dim1 = fk.Dimension('FL2-H',
'uncompensated',
None,
range_min=6,
range_max=14.4)
dim2 = fk.Dimension('FL4-H',
'uncompensated',
None,
range_min=7,
range_max=16)
dims1 = [dim1, dim2]
rect_gate1 = fk.gates.RectangleGate('ParRectangle1', 'FL2P-FL4P',
dims1)
gs.add_gate(rect_gate1)
res_path = 'examples/data/gate_ref/truth/Results_ParQuadRect.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(
truth, result.get_gate_membership('ParRectangle1'))
def test_add_matrix_rect5_gate():
gs = fk.GatingStrategy()
gs.add_comp_matrix(comp_matrix_01)
dim1 = fk.Dimension('PerCP',
compensation_ref='MySpill',
range_min=7,
range_max=90)
dim2 = fk.Dimension('FSC-H',
compensation_ref='uncompensated',
range_min=10)
dims = [dim1, dim2]
rect_gate = fk.gates.RectangleGate('Rectangle5', None, dims)
gs.add_gate(rect_gate)
res_path = 'examples/data/gate_ref/truth/Results_Rectangle5.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth,
result.get_gate_membership('Rectangle5'))
def test_add_boolean_and3_complement_gate():
gs = fk.GatingStrategy()
gs.add_gate(range1_gate)
gs.add_gate(poly1_gate)
gs.add_gate(ellipse1_gate)
gate_refs = [{
'ref': 'Range1',
'path': ('root', ),
'complement': False
}, {
'ref': 'Ellipse1',
'path': ('root', ),
'complement': True
}, {
'ref': 'Polygon1',
'path': ('root', ),
'complement': False
}]
bool_gate = fk.gates.BooleanGate('And3', None, 'and', gate_refs)
gs.add_gate(bool_gate)
res_path = 'examples/data/gate_ref/truth/Results_And3.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth,
result.get_gate_membership('And3'))
def test_add_matrix_transform_hyperlog_range7c_gate():
gs = fk.GatingStrategy()
gs.add_comp_matrix(comp_matrix_01)
gs.add_transform(hyperlog_xform1)
dim1 = fk.Dimension('PE',
'MySpill',
'Hyperlog_10000_1_4.5_0',
range_min=0.09,
range_max=0.36)
dims = [dim1]
rect_gate = fk.gates.RectangleGate('ScaleRange7c', None, dims)
gs.add_gate(rect_gate)
res_path = 'examples/data/gate_ref/truth/Results_ScaleRange7c.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(
truth, result.get_gate_membership('ScaleRange7c'))
def test_add_ratio_range2_gate():
gs = fk.GatingStrategy()
rat_xform = fk.transforms.RatioTransform('FL2Rat2', ['FL2-H', 'FL2-A'],
param_a=2.7,
param_b=-100,
param_c=-300)
gs.add_transform(rat_xform)
dim_rat2 = fk.RatioDimension('FL2Rat2',
compensation_ref='uncompensated',
range_min=0.95,
range_max=1.05)
dims = [dim_rat2]
rect_gate = fk.gates.RectangleGate('RatRange2', None, dims)
gs.add_gate(rect_gate)
res_path = 'examples/data/gate_ref/truth/Results_RatRange2.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth,
result.get_gate_membership('RatRange2'))
def test_add_log_ratio_range1_gate():
gs = fk.GatingStrategy()
rat_xform = fk.transforms.RatioTransform('FL2Rat1', ['FL2-H', 'FL2-A'],
param_a=1,
param_b=0,
param_c=-1)
gs.add_transform(rat_xform)
log_rat_xform = fk.transforms.LogTransform('MyRatLog',
param_t=100,
param_m=2)
gs.add_transform(log_rat_xform)
dim_rat1 = fk.RatioDimension('FL2Rat1',
compensation_ref='uncompensated',
transformation_ref='MyRatLog',
range_min=0.40625,
range_max=0.6601562)
dims = [dim_rat1]
rect_gate = fk.gates.RectangleGate('RatRange1a', None, dims)
gs.add_gate(rect_gate)
res_path = 'examples/data/gate_ref/truth/Results_RatRange1a.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth,
result.get_gate_membership('RatRange1a'))
def test_cache_preprocessed_events(self):
gs = fk.GatingStrategy()
gs.add_comp_matrix(comp_matrix_01)
gs.add_transform(logicle_xform1)
gs.add_transform(hyperlog_xform1)
gs.add_gate(poly1_gate)
dim1 = fk.Dimension('PE', 'MySpill', 'Logicle_10000_0.5_4.5_0', range_min=0.31, range_max=0.69)
dim2 = fk.Dimension('PerCP', 'MySpill', 'Logicle_10000_0.5_4.5_0', range_min=0.27, range_max=0.73)
dims1 = [dim1, dim2]
rect_gate1 = fk.gates.RectangleGate('ScaleRect1', None, dims1)
gs.add_gate(rect_gate1)
dim3 = fk.Dimension('FITC', 'MySpill', 'Hyperlog_10000_1_4.5_0', range_min=0.12, range_max=0.43)
dims2 = [dim3]
rect_gate2 = fk.gates.RectangleGate('ScalePar1', 'ScaleRect1', dims2)
gs.add_gate(rect_gate2)
_ = gs.gate_sample(data1_sample, cache_events=True)
pre_proc_events = gs._cached_preprocessed_events
truth_key_set = {
('MySpill', None, None),
('MySpill', 'Logicle_10000_0.5_4.5_0', 3),
('MySpill', 'Logicle_10000_0.5_4.5_0', 4),
('MySpill', 'Hyperlog_10000_1_4.5_0', 2)
}
self.assertSetEqual(set(pre_proc_events['B07'].keys()), truth_key_set)
def test_add_poly3_non_solid_gate():
gs = fk.GatingStrategy()
dim1 = fk.Dimension('SSC-H', compensation_ref='uncompensated')
dim2 = fk.Dimension('FL3-H', compensation_ref='FCS')
dims = [dim1, dim2]
vertices = [
fk.Vertex([10, 10]),
fk.Vertex([500, 10]),
fk.Vertex([500, 390]),
fk.Vertex([100, 390]),
fk.Vertex([100, 180]),
fk.Vertex([200, 180]),
fk.Vertex([200, 300]),
fk.Vertex([10, 300])
]
poly_gate = fk.gates.PolygonGate('Polygon3NS', None, dims, vertices)
gs.add_gate(poly_gate)
res_path = 'examples/data/gate_ref/truth/Results_Polygon3NS.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth,
result.get_gate_membership('Polygon3NS'))
def test_get_parent_gate_is_none(self):
gs = fk.GatingStrategy()
gs.add_gate(poly1_gate)
parent_gate = gs.get_parent_gate('Polygon1')
self.assertIsNone(parent_gate)
def test_add_quadrant_gate_relative_percent(self):
gs = fk.GatingStrategy()
gs.add_gate(quad1_gate)
result = gs.gate_sample(data1_sample)
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_add_ellipse1_gate():
gs = fk.GatingStrategy()
gs.add_gate(ellipse1_gate)
res_path = 'examples/data/gate_ref/truth/Results_Ellipse1.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth,
result.get_gate_membership('Ellipse1'))
def test_add_time_range_gate():
res_path = 'examples/data/gate_ref/truth/Results_Range2.txt'
gs = fk.GatingStrategy()
gs.add_gate(range2_gate)
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth,
result.get_gate_membership('Range2'))
def test_add_matrix_poly4_gate():
gs = fk.GatingStrategy()
gs.add_comp_matrix(comp_matrix_01)
dim1 = fk.Dimension('PE', compensation_ref='MySpill')
dim2 = fk.Dimension('PerCP', compensation_ref='MySpill')
dims = [dim1, dim2]
poly_gate = fk.gates.PolygonGate('Polygon4', None, dims,
poly1_vertices)
gs.add_gate(poly_gate)
res_path = 'examples/data/gate_ref/truth/Results_Polygon4.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth,
result.get_gate_membership('Polygon4'))
def test_add_transform_logicle_range5_gate():
gs = fk.GatingStrategy()
gs.add_transform(logicle_xform3)
dim1 = fk.Dimension('FL1-H',
'uncompensated',
'Logicle_10000_1_4_0.5',
range_min=0.37,
range_max=0.63)
dims = [dim1]
rect_gate = fk.gates.RectangleGate('ScaleRange5', None, dims)
gs.add_gate(rect_gate)
res_path = 'examples/data/gate_ref/truth/Results_ScaleRange5.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(
truth, result.get_gate_membership('ScaleRange5'))
def test_add_quadrant1_gate():
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'
gs = fk.GatingStrategy()
gs.add_gate(quad1_gate)
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
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth1,
result.get_gate_membership('FL2N-FL4N'))
np.testing.assert_array_equal(truth2,
result.get_gate_membership('FL2N-FL4P'))
np.testing.assert_array_equal(truth3,
result.get_gate_membership('FL2P-FL4N'))
np.testing.assert_array_equal(truth4,
result.get_gate_membership('FL2P-FL4P'))
def test_add_boolean_or2_complement_gate():
gs = fk.GatingStrategy()
dim1 = fk.Dimension('SSC-H',
compensation_ref='FCS',
range_min=20,
range_max=80)
dim2 = fk.Dimension('FL1-H',
compensation_ref='FCS',
range_min=70,
range_max=200)
rect_dims = [dim1, dim2]
rect_gate = fk.gates.RectangleGate('Rectangle2', None, rect_dims)
gs.add_gate(rect_gate)
gs.add_gate(quad1_gate)
gate1_refs = [{
'ref': 'Rectangle2',
'path': ('root', ),
'complement': False
}, {
'ref': 'FL2N-FL4N',
'path': ('root', 'Quadrant1'),
'complement': True
}]
bool1_gate = fk.gates.BooleanGate('Or2', None, 'or', gate1_refs)
gs.add_gate(bool1_gate)
res_path = 'examples/data/gate_ref/truth/Results_Or2.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth, result.get_gate_membership('Or2'))
def test_absolute_percent(self):
gs = fk.GatingStrategy()
gs.add_comp_matrix(comp_matrix_01)
gs.add_transform(logicle_xform1)
gs.add_transform(hyperlog_xform1)
gs.add_gate(poly1_gate)
dim1 = fk.Dimension('PE', 'MySpill', 'Logicle_10000_0.5_4.5_0', range_min=0.31, range_max=0.69)
dim2 = fk.Dimension('PerCP', 'MySpill', 'Logicle_10000_0.5_4.5_0', range_min=0.27, range_max=0.73)
dims1 = [dim1, dim2]
rect_gate1 = fk.gates.RectangleGate('ScaleRect1', None, dims1)
gs.add_gate(rect_gate1)
dim3 = fk.Dimension('FITC', 'MySpill', 'Hyperlog_10000_1_4.5_0', range_min=0.12, range_max=0.43)
dims2 = [dim3]
rect_gate2 = fk.gates.RectangleGate('ScalePar1', 'ScaleRect1', dims2)
gs.add_gate(rect_gate2)
result = gs.gate_sample(data1_sample)
parent_gate = gs.get_parent_gate(rect_gate2.gate_name)
parent_gate_count = result.get_gate_count(parent_gate.gate_name)
gate_count = result.get_gate_count(rect_gate2.gate_name)
gate_abs_pct = result.get_gate_absolute_percent(rect_gate2.gate_name)
gate_rel_pct = result.get_gate_relative_percent(rect_gate2.gate_name)
true_count = 558
true_abs_pct = (558 / data1_sample.event_count) * 100
true_rel_pct = (558 / float(parent_gate_count)) * 100
self.assertEqual(true_count, gate_count)
self.assertEqual(true_abs_pct, gate_abs_pct)
self.assertEqual(true_rel_pct, gate_rel_pct)
def test_add_parent_poly1_boolean_and2_gate():
gs = fk.GatingStrategy()
gs.add_gate(poly1_gate)
dim3 = fk.Dimension('FL3-H', compensation_ref='FCS')
dim4 = fk.Dimension('FL4-H', compensation_ref='FCS')
dims2 = [dim3, dim4]
ellipse_gate = fk.gates.EllipsoidGate('Ellipse1', None, dims2,
ell1_coords, ell1_cov_mat,
ell1_dist_square)
gs.add_gate(ellipse_gate)
gs.add_gate(range1_gate)
gate_refs = [{
'ref': 'Range1',
'path': ('root', ),
'complement': False
}, {
'ref': 'Ellipse1',
'path': ('root', ),
'complement': False
}]
bool_gate = fk.gates.BooleanGate('ParAnd2', 'Polygon1', 'and',
gate_refs)
gs.add_gate(bool_gate)
res_path = 'examples/data/gate_ref/truth/Results_ParAnd2.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth,
result.get_gate_membership('ParAnd2'))
def test_add_rect2_gate():
gs = fk.GatingStrategy()
dim1 = fk.Dimension('SSC-H',
compensation_ref='FCS',
range_min=20,
range_max=80)
dim2 = fk.Dimension('FL1-H',
compensation_ref='FCS',
range_min=70,
range_max=200)
dims = [dim1, dim2]
rect_gate = fk.gates.RectangleGate('Rectangle2', None, dims)
gs.add_gate(rect_gate)
res_path = 'examples/data/gate_ref/truth/Results_Rectangle2.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(truth,
result.get_gate_membership('Rectangle2'))
def test_add_ellipsoid_3d_gate():
gs = fk.GatingStrategy()
dim1 = fk.Dimension('FL3-H', compensation_ref='FCS')
dim2 = fk.Dimension('FL4-H', compensation_ref='FCS')
dim3 = fk.Dimension('FL1-H', compensation_ref='FCS')
dims = [dim1, dim2, dim3]
coords = [40.3, 30.6, 20.8]
cov_mat = [[2.5, 7.5, 17.5], [7.5, 7.0, 13.5], [15.5, 13.5, 4.3]]
dist_square = 1
poly_gate = fk.gates.EllipsoidGate('Ellipsoid3D', None, dims, coords,
cov_mat, dist_square)
gs.add_gate(poly_gate)
res_path = 'examples/data/gate_ref/truth/Results_Ellipsoid3D.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample)
np.testing.assert_array_equal(
truth, result.get_gate_membership('Ellipsoid3D'))
def test_add_duplicate_matrix_id(self):
gs = fk.GatingStrategy()
gs.add_comp_matrix(comp_matrix_01)
self.assertRaises(KeyError, gs.add_comp_matrix, comp_matrix_01)
def test_add_matrix_non_matrix_class(self):
gs = fk.GatingStrategy()
self.assertRaises(ValueError, gs.add_comp_matrix, "not a matrix class")
def test_add_duplicate_transform_id(self):
gs = fk.GatingStrategy()
gs.add_transform(logicle_xform1)
self.assertRaises(KeyError, gs.add_transform, logicle_xform1)
def test_add_transform_non_transform_class(self):
gs = fk.GatingStrategy()
self.assertRaises(ValueError, gs.add_transform, "not a transform class")
def test_get_gate_raises_ValueError(self):
gs = fk.GatingStrategy()
gs.add_gate(poly1_gate)
self.assertRaises(ValueError, gs.get_gate, 'nonexistent-gate')
def test_add_duplicate_gate_id(self):
gs = fk.GatingStrategy()
gs.add_gate(poly1_gate)
self.assertRaises(KeyError, gs.add_gate, poly1_gate)
def test_add_gate_non_gate_class(self):
gs = fk.GatingStrategy()
self.assertRaises(ValueError, gs.add_gate, "not a gate class")
