#21 Update calls to hergQC methods

pcpostprocess/hergQC.py

@@ -1,6 +1,8 @@
 import logging
 import os
 
+from collections import OrderedDict
+
 import matplotlib.pyplot as plt
 import numpy as np
 import scipy.stats
@@ -123,7 +125,7 @@ def run_qc(self, voltage_steps, times,
         before = self.filter_capacitive_spikes(before, times, voltage_steps)
         after = self.filter_capacitive_spikes(after, times, voltage_steps)
 
-        QC = {label: [(False, None)] for label in self.qc_labels}
+        QC = OrderedDict([(label, [(False, None)]) for label in self.qc_labels])
 
         if len(before) == 0 or len(after) == 0:
             return QC
@@ -213,7 +215,7 @@ def run_qc(self, voltage_steps, times,
             plt.ylabel('Current [pA]')
 
             # https://stackoverflow.com/a/13589144
-            from collections import OrderedDict  # fix legend labels
+            # fix legend labels
             handles, labels = plt.gca().get_legend_handles_labels()
             by_label = OrderedDict(zip(labels, handles))
             fig.legend(by_label.values(), by_label.keys())

pcpostprocess/scripts/run_herg_qc.py

@@ -701,18 +701,22 @@ def extract_protocol(readname, savename, time_strs, selected_wells, args):
 
             row_dict['QC6'] = hergqc.qc6(current,
                                          win=hergqc.qc6_win,
-                                         label='0')
+                                         label='0')[0]
 
             #  Assume there is only one sweep for all non-QC protocols
             rseal_before, cm_before, rseries_before = qc_before[well][0]
             rseal_after, cm_after, rseries_after = qc_after[well][0]
 
-            row_dict['QC1'] = all(list(hergqc.qc1(rseal_before, cm_before, rseries_before)) +
-                                  list(hergqc.qc1(rseal_after, cm_after, rseries_after)))
+            qc1_1 = hergqc.qc1(rseal_before, cm_before, rseries_before)
+            qc1_2 = hergqc.qc1(rseal_after, cm_after, rseries_after)
 
-            row_dict['QC4'] = all(hergqc.qc4([rseal_before, rseal_after],
-                                             [cm_before, cm_after],
-                                             [rseries_before, rseries_after]))
+            row_dict['QC1'] = all([x for x, _ in qc1_1 + qc1_2])
+
+            qc4 = hergqc.qc4([rseal_before, rseal_after],
+                             [cm_before, cm_after],
+                             [rseries_before, rseries_after])
+
+            row_dict['QC4'] = all([x for x, _ in qc4])
 
             if args.output_traces:
                 out_fname = os.path.join(traces_dir,
@@ -935,7 +939,7 @@ def run_qc_for_protocol(readname, savename, time_strs, args):
                                      np.array(qc_before[well])[0, :],
                                      np.array(qc_after[well])[0, :], nsweeps)
 
-        df_rows.append([well] + list(QC))
+        df_rows.append([well] + [all([x for x, _ in qc]) for qc in QC.values()])
 
         if selected:
             selected_wells.append(well)
@@ -1086,7 +1090,7 @@ def qc3_bookend(readname, savename, time_strs, args):
             last_processed[well], times, voltage_steps
         ).flatten()
 
-        passed = hergqc.qc3(trace1, trace2)
+        passed = hergqc.qc3(trace1, trace2)[0]
 
         res_dict[well] = passed
 

tests/test_herg_qc.py

@@ -67,10 +67,10 @@ def test_run_qc(self):
 
         test_wells = ['A01', 'A02', 'A03', 'A04', 'A05', 'D01']
 
+        voltage_protocol = tr_before.get_voltage_protocol()
+
         for well in test_wells:
             with self.subTest(well):
-                voltage_protocol = tr_before.get_voltage_protocol()
-
                 # Take values from the first sweep only
                 qc_vals_before_well = np.array(qc_vals_before[well])[0, :]
                 qc_vals_after_well = np.array(qc_vals_after[well])[0, :]