def test_all_gates():
gml_path = 'examples/gate_ref/gml/gml_all_gates.xml'
truth_pattern = 'examples/gate_ref/truth/Results*.txt'
res_files = glob.glob(truth_pattern)
truth_dict = {}
for res_path in res_files:
match = re.search("Results_(.+)\\.txt$", res_path)
if match is not None:
g_id = match.group(1)
truth = pd.read_csv(res_path,
header=None,
squeeze=True,
dtype='bool').values
truth_dict[g_id] = truth
gs = GatingStrategy(gml_path)
gs_results = gs.gate_sample(data1_sample)
for row in gs_results.report.itertuples():
np.testing.assert_array_equal(
truth_dict[row[0][1]], gs_results.get_gate_indices(row[0][1]))
def test_quadrant1_gate():
gml_path = 'examples/gate_ref/gml/gml_quadrant1_gate.xml'
res1_path = 'examples/gate_ref/truth/Results_FL2N-FL4N.txt'
res2_path = 'examples/gate_ref/truth/Results_FL2N-FL4P.txt'
res3_path = 'examples/gate_ref/truth/Results_FL2P-FL4N.txt'
res4_path = 'examples/gate_ref/truth/Results_FL2P-FL4P.txt'
gs = GatingStrategy(gml_path)
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_indices('FL2N-FL4N'))
np.testing.assert_array_equal(truth2,
result.get_gate_indices('FL2N-FL4P'))
np.testing.assert_array_equal(truth3,
result.get_gate_indices('FL2P-FL4N'))
np.testing.assert_array_equal(truth4,
result.get_gate_indices('FL2P-FL4P'))
def __init__(self,
fcs_samples=None,
comp_bead_samples=None,
gating_strategy=None):
self.samples = []
self.bead_samples = []
self.bead_lut = {}
self.report = None
self._results = None
if comp_bead_samples == fcs_samples and isinstance(fcs_samples, str):
# there's a mix of regular FCS files with bead files in the same directory,
# which isn't supported at this time. Raise error
raise ValueError(
"Specify bead samples as a list of paths if in the same directory as other samples"
)
self.samples = load_samples(fcs_samples)
self.bead_samples = load_samples(comp_bead_samples)
self.process_bead_samples()
if isinstance(gating_strategy, GatingStrategy):
self.gating_strategy = gating_strategy
elif isinstance(gating_strategy, str):
# assume a path to a GatingML XML file
self.gating_strategy = GatingStrategy(gating_strategy)
elif gating_strategy is None:
self.gating_strategy = GatingStrategy()
else:
raise ValueError(
"'gating_strategy' must be either a GatingStrategy instance or a path to a GatingML document"
)
def test_boolean_or2_not_gate():
gml_path = 'examples/gate_ref/gml/gml_boolean_or2_gate.xml'
res_path = 'examples/gate_ref/truth/Results_Or2.txt'
gs = GatingStrategy(gml_path)
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample, 'Or2')
np.testing.assert_array_equal(truth, result.get_gate_indices('Or2'))
def test_poly3_non_solid_gate():
gml_path = 'examples/gate_ref/gml/gml_poly3ns_gate.xml'
res_path = 'examples/gate_ref/truth/Results_Polygon3NS.txt'
gs = GatingStrategy(gml_path)
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample, 'Polygon3NS')
np.testing.assert_array_equal(truth,
result.get_gate_indices('Polygon3NS'))
def test_parent_quadrant_rect_gate():
gml_path = 'examples/gate_ref/gml/gml_parent_quadrant_rect_gate.xml'
res_path = 'examples/gate_ref/truth/Results_ParQuadRect.txt'
gs = GatingStrategy(gml_path)
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample, 'ParRectangle1')
np.testing.assert_array_equal(truth,
result.get_gate_indices('ParRectangle1'))
def test_matrix_transform_logicle_rect1_gate():
gml_path = 'examples/gate_ref/gml/gml_matrix_transform_logicle_rect1_gate.xml'
res_path = 'examples/gate_ref/truth/Results_ScaleRect1.txt'
gs = GatingStrategy(gml_path)
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample, 'ScaleRect1')
np.testing.assert_array_equal(truth,
result.get_gate_indices('ScaleRect1'))
def test_log_ratio_range1_gate():
gml_path = 'examples/gate_ref/gml/gml_log_ratio_range1_gate.xml'
res_path = 'examples/gate_ref/truth/Results_RatRange1a.txt'
gs = GatingStrategy(gml_path)
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = gs.gate_sample(data1_sample, 'RatRange1a')
np.testing.assert_array_equal(truth,
result.get_gate_indices('RatRange1a'))
def test_quadrant_gate_relative_percent(self):
gml_path = 'examples/gate_ref/gml/gml_quadrant1_gate.xml'
gs = GatingStrategy(gml_path)
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)