GH AllenInstitute#533 - Add tests for sweep with autobias_v = None

Setup a test sweep with autobias_v = None and added assert statements to
functions to verify outputs for sweeps with autobias_v = None. Removed
test_none_autobias_v function as no longer returning delta = None if
autobias_v = None, but returning delta between mean pre and post-
stimulus baselines.

tests/test_pre_and_post_vm_delta.py

@@ -16,23 +16,29 @@
 dt = 1./sampling_rate
 t = np.arange(0,len(i))*dt  
 
-passing_sweep = Sweep(t, passing_v, i, sampling_rate=sampling_rate, autobias_v=autobias_v, clamp_mode="CurrentClamp")
-failing_sweep = Sweep(t, failing_v, i, sampling_rate=sampling_rate, autobias_v=autobias_v, clamp_mode="CurrentClamp")  
+passing_sweep = Sweep(t, passing_v, i, "CurrentClamp", sampling_rate, sweep_number=1, autobias_v=autobias_v)
+failing_sweep = Sweep(t, failing_v, i, "CurrentClamp", sampling_rate, sweep_number=1, autobias_v=autobias_v)  
+no_autobias_sweep = Sweep(t, passing_v, i, "CurrentClamp", sampling_rate, sweep_number=1, autobias_v=None)
 
-passing_mean_first_stability_epoch, _ = qcf.measure_vm(passing_v[4:7])
-passing_mean_last_stability_epoch, _ = qcf.measure_vm(passing_v[12:16])
+passing_mean_first_stability_epoch, _ = qcf.measure_vm(passing_sweep.v[4:7])
+passing_mean_last_stability_epoch, _ = qcf.measure_vm(passing_sweep.v[12:16])
 
-failing_mean_first_stability_epoch, _ = qcf.measure_vm(failing_v[4:7])
-failing_mean_last_stability_epoch, _ = qcf.measure_vm(failing_v[12:16])
+failing_mean_first_stability_epoch, _ = qcf.measure_vm(failing_sweep.v[4:7])
+failing_mean_last_stability_epoch, _ = qcf.measure_vm(failing_sweep.v[12:16])
+
+no_autobias_mean_first_stability_epoch, _ = qcf.measure_vm(no_autobias_sweep.v[4:7])
+no_autobias_mean_last_stability_epoch, _ = qcf.measure_vm(no_autobias_sweep.v[12:16])
 
 passing_qc_features = qfex.current_clamp_sweep_qc_features(passing_sweep, False)
 failing_qc_features = qfex.current_clamp_sweep_qc_features(failing_sweep, False)
+no_autobias_qc_features = qfex.current_clamp_sweep_qc_features(no_autobias_sweep, False)
 
 
 def test_sweep_autobias_v():
 
     assert passing_sweep.autobias_v == autobias_v
     assert failing_sweep.autobias_v == autobias_v
+    assert no_autobias_sweep.autobias_v == None
 
 
 def test_measure_vm_delta():
@@ -43,32 +49,44 @@ def test_measure_vm_delta():
     assert round(qcf.measure_vm_delta(failing_mean_first_stability_epoch, failing_sweep.autobias_v), 2) == 1.01
     assert round(qcf.measure_vm_delta(failing_mean_last_stability_epoch, failing_sweep.autobias_v), 2) == 1.01
 
+    assert round(qcf.measure_vm_delta(no_autobias_mean_first_stability_epoch, no_autobias_mean_last_stability_epoch), 2) == 1.98   
+
 
 def test_current_clamp_qc_features():
 
     assert passing_qc_features["pre_vm_delta_mv"] < vm_delta_mv_max
     assert passing_qc_features["post_vm_delta_mv"] < vm_delta_mv_max
+    assert passing_qc_features["vm_delta_mv"] == None
 
     assert failing_qc_features["pre_vm_delta_mv"] > vm_delta_mv_max
     assert failing_qc_features["post_vm_delta_mv"] > vm_delta_mv_max
+    assert failing_qc_features["vm_delta_mv"] == None
+
+    assert no_autobias_qc_features["vm_delta_mv"] > vm_delta_mv_max
+    assert no_autobias_qc_features["pre_vm_delta_mv"] == None
+    assert no_autobias_qc_features["post_vm_delta_mv"] == None
 
 
 def test_qc_current_clamp_sweep():
 
-    failing_qc_features["sweep_number"] = 1
-    failing_qc_features["stimulus_name"] = "test_stimulus"
+    sweep_num = 1
+    stim_name = "test_stimulus"
 
-    fail_tags = qfev.qc_current_clamp_sweep(failing_qc_features, False)
-
-    assert fail_tags[0] == "pre Vm delta: 1.010 above threshold:1.000"
-    assert fail_tags[1] == "post Vm delta: 1.010 above threshold:1.000"
+    passing_qc_features["sweep_number"] = sweep_num
+    failing_qc_features["sweep_number"] = sweep_num
+    no_autobias_qc_features["sweep_number"] = sweep_num
+    passing_qc_features["stimulus_name"] = stim_name
+    failing_qc_features["stimulus_name"] = stim_name
+    no_autobias_qc_features["stimulus_name"] = stim_name
 
+    passing_fail_tags = qfev.qc_current_clamp_sweep(passing_qc_features, False)
+    failing_fail_tags = qfev.qc_current_clamp_sweep(failing_qc_features, False)
+    no_autobias_fail_tags = qfev.qc_current_clamp_sweep(no_autobias_qc_features, False)
+
+    assert passing_fail_tags == []
 
-def test_none_autobias_v():
+    assert failing_fail_tags[0] == "pre Vm delta: 1.010 above threshold: 1.000"
+    assert failing_fail_tags[1] == "post Vm delta: 1.010 above threshold: 1.000"
 
-    none_autobias_v = None
-    sweep = Sweep(t, passing_v, i, sampling_rate=sampling_rate, autobias_v=none_autobias_v, clamp_mode="CurrentClamp")
-    delta = qcf.measure_vm_delta(passing_mean_first_stability_epoch, sweep.autobias_v)
-
-    assert delta is None
+    assert no_autobias_fail_tags == ["Vm delta: 1.980 above threshold: 1.000"]