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_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_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_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_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_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_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_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_plot_gated_scatter(self):
fks = fk.Session(fcs_path)
fks.add_sample_group('my_group', gml_path)
group_name = 'my_group'
sample_name = 'B07'
fks.assign_sample(sample_name, group_name)
x_dim = fk.Dimension('FL2-H',
compensation_ref='MySpill',
transformation_ref='Logicle_10000_0.5_4.5_0')
y_dim = fk.Dimension('FL3-H',
compensation_ref='MySpill',
transformation_ref='Logicle_10000_0.5_4.5_0')
p = fks.plot_scatter(sample_name,
x_dim,
y_dim,
sample_group=group_name,
gate_id='ScaleRect1')
self.assertIsInstance(p, Figure)
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_plot_gated_scatter(self):
fks = fk.Session(copy.deepcopy(test_sample))
fks.add_sample_group('my_group', copy.deepcopy(test_gating_strategy))
group_name = 'my_group'
sample_name = 'B07'
fks.assign_samples(sample_name, group_name)
fks.analyze_samples(group_name, sample_id=sample_name)
x_dim = fk.Dimension('FL2-H', compensation_ref='MySpill', transformation_ref='Logicle_10000_0.5_4.5_0')
y_dim = fk.Dimension('FL3-H', compensation_ref='MySpill', transformation_ref='Logicle_10000_0.5_4.5_0')
p = fks.plot_scatter(
sample_name,
x_dim,
y_dim,
group_name=group_name,
gate_name='ScaleRect1',
subsample=True
)
self.assertIsInstance(p, bk_Figure)
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_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_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_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_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 setUp(self):
"""
This TestCase tests more complex GatingStrategy use cases, particularly
the re-use of a gate in 2 different branches where the parent of each
gate is also re-used. For example:
root
╰── Gate_A
├── Gate_B
│ ╰── ReusedParent
│ ╰── ReusedChild
╰── Gate_C
╰── ReusedParent
╰── ReusedChild
:return: None
"""
self.gs = fk.GatingStrategy()
time_dim = fk.Dimension('Gate_A', range_min=0.1, range_max=0.9)
dim_fsc_w = fk.Dimension('FSC-W')
dim_fsc_h = fk.Dimension('FSC-H')
dim_ssc_a = fk.Dimension('SSC-A')
dim_amine_a = fk.Dimension('Aqua Amine FLR-A')
dim_cd3_a = fk.Dimension('CD3 APC-H7 FLR-A')
gate_a = fk.gates.RectangleGate('Gate_A', None, [time_dim])
self.gs.add_gate(gate_a)
gate_b_vertices = [
fk.Vertex([0.328125, 0.1640625]),
fk.Vertex([0.296875, 0.1484375]),
fk.Vertex([0.30859375, 0.8515625]),
fk.Vertex([0.34765625, 0.3984375]),
fk.Vertex([0.3359375, 0.1875])
]
gate_b = fk.gates.PolygonGate(
'Gate_B', parent_gate_name=gate_a.gate_name, dimensions=[dim_fsc_w, dim_fsc_h], vertices=gate_b_vertices
)
self.gs.add_gate(gate_b)
gate_c_vertices = [
fk.Vertex([0.328125, 0.1640625]),
fk.Vertex([0.296875, 0.1484375]),
fk.Vertex([0.30859375, 0.8515625]),
fk.Vertex([0.34765625, 0.3984375]),
fk.Vertex([0.3359375, 0.1875])
]
gate_c = fk.gates.PolygonGate(
'Gate_C', parent_gate_name=gate_a.gate_name, dimensions=[dim_fsc_h, dim_fsc_w], vertices=gate_c_vertices
)
self.gs.add_gate(gate_c)
reused_parent_vertices = [
fk.Vertex([0.2629268137285685, 0.0625]),
fk.Vertex([0.24318837264468562, 0.03515625]),
fk.Vertex([0.21573453285608676, 0.0390625]),
fk.Vertex([0.29042797365869377, 0.24609375]),
fk.Vertex([0.29042797365869377, 0.1484375])
]
reused_parent_gate_1 = fk.gates.PolygonGate(
'ReusedParent', gate_b.gate_name, [dim_amine_a, dim_ssc_a], reused_parent_vertices
)
reused_parent_gate_2 = fk.gates.PolygonGate(
'ReusedParent', gate_c.gate_name, [dim_amine_a, dim_ssc_a], reused_parent_vertices
)
self.gs.add_gate(reused_parent_gate_1)
self.gs.add_gate(reused_parent_gate_2)
reused_child_vertices = [
fk.Vertex([0.28415161867527605, 0.11328125]),
fk.Vertex([0.3132637699981912, 0.203125]),
fk.Vertex([0.6896802981119161, 0.05078125]),
fk.Vertex([0.5692952580886116, 0.01953125]),
fk.Vertex([0.3192472844795108, 0.01953125])
]
reused_child_gate = fk.gates.PolygonGate(
'ReusedChild', 'ReusedParent', [dim_cd3_a, dim_ssc_a], reused_child_vertices
)
gate_path_1 = ('root', 'Gate_A', 'Gate_B', 'ReusedParent')
gate_path_2 = ('root', 'Gate_A', 'Gate_C', 'ReusedParent')
self.gs.add_gate(reused_child_gate, gate_path=gate_path_1)
self.gs.add_gate(reused_child_gate, gate_path=gate_path_2)
self.all_gate_ids = [
('Gate_A', ('root',)),
('Gate_B', ('root', 'Gate_A')),
('ReusedParent', ('root', 'Gate_A', 'Gate_B')),
('ReusedChild', ('root', 'Gate_A', 'Gate_B', 'ReusedParent')),
('Gate_C', ('root', 'Gate_A')),
('ReusedParent', ('root', 'Gate_A', 'Gate_C')),
('ReusedChild', ('root', 'Gate_A', 'Gate_C', 'ReusedParent'))
]
import unittest
import numpy as np
import flowkit as fk
data1_fcs_path = 'examples/data/gate_ref/data1.fcs'
data1_sample = fk.Sample(data1_fcs_path)
poly1_vertices = [
fk.Vertex([5, 5]),
fk.Vertex([500, 5]),
fk.Vertex([500, 500])
]
poly1_dim1 = fk.Dimension('FL2-H', compensation_ref='FCS')
poly1_dim2 = fk.Dimension('FL3-H', compensation_ref='FCS')
poly1_dims1 = [poly1_dim1, poly1_dim2]
poly1_gate = fk.gates.PolygonGate('Polygon1', None, poly1_dims1, poly1_vertices)
hyperlog_xform1 = fk.transforms.HyperlogTransform(
'Hyperlog_10000_1_4.5_0',
param_t=10000,
param_w=1,
param_m=4.5,
param_a=0
)
logicle_xform1 = fk.transforms.LogicleTransform(
'Logicle_10000_0.5_4.5_0',
param_t=10000,
param_w=0.5,
param_m=4.5,
def test_dim_repr(self):
poly1_dim1 = fk.Dimension('FL2-H', compensation_ref='FCS')
dim_string = "Dimension(id: FL2-H)"
self.assertEqual(repr(poly1_dim1), dim_string)
import numpy as np
import pandas as pd
sys.path.append(os.path.abspath('../..'))
import flowkit as fk
data1_fcs_path = 'examples/data/gate_ref/data1.fcs'
data1_sample = fk.Sample(data1_fcs_path)
poly1_vertices = [
fk.Vertex([5, 5]),
fk.Vertex([500, 5]),
fk.Vertex([500, 500])
]
poly1_dim1 = fk.Dimension('FL2-H', compensation_ref='FCS')
poly1_dim2 = fk.Dimension('FL3-H', compensation_ref='FCS')
poly1_dims1 = [poly1_dim1, poly1_dim2]
poly1_gate = fk.gates.PolygonGate('Polygon1', None, poly1_dims1,
poly1_vertices)
quad1_div1 = fk.QuadrantDivider('FL2', 'FL2-H', 'FCS', [12.14748])
quad1_div2 = fk.QuadrantDivider('FL4', 'FL4-H', 'FCS', [14.22417])
quad1_divs = [quad1_div1, quad1_div2]
quad_1 = fk.gates.Quadrant(quadrant_id='FL2P-FL4P',
divider_refs=['FL2', 'FL4'],
divider_ranges=[(12.14748, None), (14.22417, None)])
quad_2 = fk.gates.Quadrant(quadrant_id='FL2N-FL4P',
divider_refs=['FL2', 'FL4'],
divider_ranges=[(None, 12.14748), (14.22417, None)])
