#21 Implement QCDict with UserDict

pcpostprocess/hergQC.py

@@ -1,6 +1,6 @@
 import logging
 import os
-from collections import OrderedDict
+from collections import OrderedDict, UserDict
 
 import matplotlib.pyplot as plt
 import numpy as np
@@ -9,7 +9,7 @@
 NOISE_LEN = 200
 
 
-class QCDict:
+class QCDict(UserDict):
     """
     Stores the results from QC checks.
 
@@ -40,36 +40,16 @@ class QCDict:
     ]
 
     def __init__(self):
-        self._dict = OrderedDict(
-            [(label, [(False, None)]) for label in QCDict.labels]
-        )
-
-    def __str__(self):
-        return self._dict.__str__()
-
-    def __repr__(self):
-        return self._dict.__repr__()
-
-    def __getitem__(self, key):
-        return self._dict.__getitem__(key)
+        super().__init__([(label, [(False, None)]) for label in QCDict.labels])
 
     def __setitem__(self, key, value):
         if key not in QCDict.labels:
             raise KeyError(f"Invalid QC key: {key}")
-        self._dict.__setitem__(key, value)
-
-    def keys(self):
-        return self._dict.keys()
-
-    def items(self):
-        return self._dict.items()
-
-    def values(self):
-        return self._dict.values()
+        super().__setitem__(key, value)
 
     def qc_passed(self, label):
         """Return whether a single QC passed."""
-        return all([x for x, _ in self._dict[label]])
+        return all([x for x, _ in self[label]])
 
     def passed_list(self):
         """Return a list of booleans indicating whether each QC passed."""
@@ -250,9 +230,12 @@ def run_qc(self, voltage_steps, times,
         QC['qc6.1.subtracted'] = []
         QC['qc6.2.subtracted'] = []
         for i in range(before.shape[0]):
-            qc6 = self.qc6((before[i, :] - after[i, :]), self.qc6_win, label="0")
-            qc6_1 = self.qc6((before[i, :] - after[i, :]), self.qc6_1_win, label="1")
-            qc6_2 = self.qc6((before[i, :] - after[i, :]), self.qc6_2_win, label="2")
+            qc6 = self.qc6((before[i, :] - after[i, :]),
+                           self.qc6_win, label="0")
+            qc6_1 = self.qc6((before[i, :] - after[i, :]),
+                             self.qc6_1_win, label="1")
+            qc6_2 = self.qc6((before[i, :] - after[i, :]),
+                             self.qc6_2_win, label="2")
 
             QC['qc6.subtracted'].append(qc6)
             QC['qc6.1.subtracted'].append(qc6_1)
@@ -463,7 +446,8 @@ def qc5_1(self, recording1, recording2, win=None, label=''):
 
         if (rmsd0_diff < rmsd0_diffc) or not (np.isfinite(rmsd0_diff)
                                               and np.isfinite(rmsd0_diffc)):
-            self.logger.debug(f"rmsd0_diff: {rmsd0_diff}, rmsd0c: {rmsd0_diffc}")
+            self.logger.debug(
+                f"rmsd0_diff: {rmsd0_diff}, rmsd0c: {rmsd0_diffc}")
             result = False
         else:
             result = True

tests/test_herg_qc.py

@@ -64,7 +64,7 @@ def setUp(self):
         )
         self.hergqc._debug = False  # Turn this on to output plots
 
-    def clone_herg_qc(self, plot_dir):
+    def clone_hergqc(self, plot_dir):
         hergqc = copy.deepcopy(self.hergqc)
         plot_dir = os.path.join(hergqc.plot_dir, plot_dir)
         os.makedirs(plot_dir, exist_ok=True)
@@ -81,15 +81,15 @@ def test_qc_inputs(self):
         self.assertTrue(np.all(np.isfinite(times)))
         self.assertTrue(np.all(np.isfinite(voltage)))
 
-        # Ensure thats the windows are correct by checking the voltage trace
+        # Ensures that the windows are correct by checking the voltage trace
         assert np.all(np.abs(voltage[qc6_win[0]: qc6_win[1]] - 40.0)) < 1e-8
         assert np.all(np.abs(voltage[qc6_1_win[0]: qc6_1_win[1]] - 40.0)) < 1e-8
         assert np.all(np.abs(voltage[qc6_2_win[0]: qc6_2_win[1]] - 40.0)) < 1e-8
 
     def test_qc1(self):
-        hergqc = self.clone_herg_qc("test_qc1")
-
         # qc1 checks that rseal, cm, rseries are within range
+        hergqc = self.clone_hergqc("test_qc1")
+
         rseal_lo, rseal_hi = 1e8, 1e12
         rseal_mid = (rseal_lo + rseal_hi) / 2
         rseal_tol = 0.1
@@ -295,9 +295,9 @@ def test_qc1(self):
             )
 
     def test_qc2(self):
-        hergqc = self.clone_herg_qc("test_qc2")
-
         # qc2 checks that raw and subtracted SNR are above a minimum threshold
+        hergqc = self.clone_hergqc("test_qc2")
+
         test_matrix = [
             (10, True, 8082.1),
             (1, True, 74.0),
@@ -347,9 +347,8 @@ def test_qc2(self):
             )
 
     def test_qc3(self):
-        hergqc = self.clone_herg_qc("test_qc3")
-
         # qc3 checks that rmsd of two sweeps are similar
+        hergqc = self.clone_hergqc("test_qc3")
 
         # Test with same noise, different signal
         test_matrix = [
@@ -455,9 +454,9 @@ def test_qc3(self):
             )
 
     def test_qc4(self):
-        hergqc = self.clone_herg_qc("test_qc4")
-
         # qc4 checks that rseal, cm, rseries are similar before/after E-4031 change
+        hergqc = self.clone_hergqc("test_qc4")
+
         r_lo, r_hi = 1e6, 3e7
         c_lo, c_hi = 1e-12, 1e-10
 
@@ -615,10 +614,10 @@ def test_qc4(self):
             )
 
     def test_qc5(self):
-        hergqc = self.clone_herg_qc("test_qc5")
-
         # qc5 checks that the maximum current during the second half of the
         # staircase changes by at least 75% of the raw trace after E-4031 addition
+        hergqc = self.clone_hergqc("test_qc5")
+
         test_matrix = [
             (-1.0, True, -12.5),
             (0.1, True, -1.5),
@@ -687,10 +686,10 @@ def test_qc5(self):
             )
 
     def test_qc5_1(self):
-        hergqc = self.clone_herg_qc("test_qc5_1")
-
         # qc5_1 checks that the RMSD to zero of staircase protocol changes
         # by at least 50% of the raw trace after E-4031 addition.
+        hergqc = self.clone_hergqc("test_qc5_1")
+
         test_matrix = [
             (-1.0, False, 4.22),
             (-0.5, False, 0),
@@ -763,10 +762,10 @@ def test_qc5_1(self):
             )
 
     def test_qc6(self):
-        hergqc = self.clone_herg_qc("test_qc6")
-
         # qc6 checks that the first step up to +40 mV, before the staircase, in
         # the subtracted trace is bigger than -2 x estimated noise level.
+        hergqc = self.clone_hergqc("test_qc6")
+
         test_matrix = [
             (-100, False, 9.9),
             (-10, False, 0.9),
@@ -888,7 +887,7 @@ def test_qc6(self):
 
     def test_run_qc(self):
         # Test all wells
-        hergqc = self.clone_herg_qc("test_run_qc")
+        hergqc = self.clone_hergqc("test_run_qc")
 
         failed_wells = [
             'A04', 'A05', 'A06', 'A07', 'A08', 'A10', 'A11', 'A12', 'A13', 'A15',