def setUp(self):
self.cwd = os.path.dirname(
os.path.abspath(__file__)) + "/data/Plate01/"
tube1 = flow.Tube(file=self.cwd + 'RFP_Well_A3.fcs',
conditions={"Dox": 10.0})
tube2 = flow.Tube(file=self.cwd + 'CFP_Well_A4.fcs',
conditions={"Dox": 1.0})
import_op = flow.ImportOp(conditions={"Dox": "float"},
tubes=[tube1, tube2])
ex = import_op.apply()
# this works so much better on transformed data
logicle = flow.LogicleTransformOp()
logicle.name = "Logicle transformation"
logicle.channels = ['V2-A', 'Y2-A', 'B1-A']
logicle.estimate(ex)
self.ex = logicle.apply(ex)
self.gate = flow.Range2DOp(name="Range2D",
xchannel="V2-A",
ychannel="Y2-A",
xlow=0.0,
xhigh=0.4,
ylow=0.4,
yhigh=0.8)
def test_logicle_apply(self):
"""
Make sure the function applies without segfaulting
"""
el = flow.LogicleTransformOp()
el.name = "Logicle"
el.channels = ['Y2-A']
el.estimate(self.ex)
el.apply(self.ex)
def test_logicle_estimate(self):
"""
Test the parameter estimator against the R implementation
"""
el = flow.LogicleTransformOp()
el.name = "Logicle"
el.channels = ["Y2-A"]
el.estimate(self.ex)
# these are the values the R implementation gives
self.assertAlmostEqual(el.A['Y2-A'], 0.0)
self.assertAlmostEqual(el.W['Y2-A'], 0.533191950161284)