Increase test coverage (#10)

* update docstring. test leakcorrect

* Output QC values as array. Add tests and fix get_onbard_QC_df

* remove unused import

* add line to test

* Increase test coverage. Fix get_onboard_QC_df

* Lint code

* Update tests/test_trace_class.py

Co-authored-by: Matt J Owen <matt.owen@nottingham.ac.uk>

* Update test_trace_class.py

* Fix whitespace

* fix imports

* test output of voltage protocol

* fix whitespace

* fix imports

---------

Co-authored-by: Joseph Shuttleworth <joseph.shuttleworth@nottingham.ac.uk>
Co-authored-by: Matt J Owen <matt.owen@nottingham.ac.uk>

Author: 3 people

.gitignore

@@ -3,3 +3,4 @@
 *.DS_Store
 *__pycache__*
 *.egg_info
+*__pycache__*

syncropatch_export/trace.py

@@ -41,9 +41,9 @@ def __init__(self, filepath, json_file: str):
         self.MeasurementLayout = TraceHeader['MeasurementLayout']
         self.FileInformation = TraceHeader['FileInformation']
 
-        self.WELL_ID = [
+        self.WELL_ID = np.array([
             [lab + str(i).zfill(2) for lab in string.ascii_uppercase[:16]]
-            for i in range(1, 25)]
+            for i in range(1, 25)])
 
         self.NofSweeps = self.MeasurementLayout['NofSweeps']
         self.WP_nRows = TraceHeader['Chiplayout']['WP_nRows']
@@ -73,6 +73,12 @@ def get_voltage_protocol(self, holding_potential=-80.0):
 
         return voltage_protocol
 
+    def get_voltage_protocol_json(self):
+        """
+        Returns the voltage protocol as a JSON object
+        """
+        return self.meta['ExperimentConditions']['VoltageProtocol'][0]
+
     def get_protocol_description(self, holding_potential=-80.0):
         """Get the protocol as a numpy array describing the voltages and
         durations for each section
@@ -100,11 +106,10 @@ def get_all_traces(self, leakcorrect=False):
         '''
 
         Params:
-        leakcorrect: Bool. Set to true if onboard leak correction was used
+        leakcorrect: Bool. Set to true if using onboard leak correction
 
         Returns: all raw current traces from .dat files
 
-        TODO: Rename. Detect 'leakcorrect' flag automatically
         '''
         return self.get_trace_sweeps(leakcorrect=leakcorrect)
 
@@ -245,6 +250,15 @@ def get_onboard_QC_values(self, sweeps=None):
                                                          Capacitance[k, i, j],
                                                          Rseries[k, i, j]))
 
+        # Convert values to np arrays taking care to remove handle None values
+        for well in out_dict:
+            vals = out_dict[well]
+            if vals:
+                shape = (len(vals), len(vals[0]))
+                vals = [x if x is not None else np.nan for x in vals]
+                vals = np.vstack(vals).reshape(shape).astype(np.float64)
+                out_dict[well] = vals
+
         return out_dict
 
     def get_onboard_QC_df(self, sweeps=None):
@@ -263,9 +277,7 @@ def get_onboard_QC_df(self, sweeps=None):
 
         df_rows = []
         for sweep in sweeps:
-            for well in self.WELL_ID.values():
-                if well <= len(QC_dict[well]):
-                    continue
+            for well in self.WELL_ID.flatten():
                 Rseal, Capacitance, Rseries = QC_dict[well][sweep]
                 df_row = {'Rseal': Rseal,
                           'Cm': Capacitance,
@@ -275,4 +287,4 @@ def get_onboard_QC_df(self, sweeps=None):
                           }
                 df_rows.append(df_row)
 
-        return pd.from_records(df_rows)
+        return pd.DataFrame.from_records(df_rows)

tests/test_trace_class.py

@@ -1,8 +1,10 @@
+import json
 import os
 import unittest
 
 import matplotlib.pyplot as plt
 import numpy as np
+import pandas as pd
 
 from syncropatch_export.trace import Trace as tr
 from syncropatch_export.voltage_protocols import VoltageProtocol
@@ -40,6 +42,14 @@ def test_protocol_descriptions(self):
         self.assertLess(t_error, 1e-2)
         self.assertLess(v_error, 1e-4)
 
+    def test_protocol_export(self):
+        protocol = self.test_trace.get_voltage_protocol()
+        protocol.export_txt(os.path.join(self.output_dir, 'protocol.txt'))
+        json_protocol = self.test_trace.get_voltage_protocol_json()
+
+        with open(os.path.join(self.output_dir, 'protocol.json'), 'w') as fin:
+            json.dump(json_protocol, fin)
+
     def test_protocol_timeseries(self):
         voltages = self.test_trace.get_voltage()
         times = self.test_trace.get_times()
@@ -59,10 +69,20 @@ def voltage_func(t):
         for t, v in zip(times, voltages):
             self.assertLess(voltage_func(t) - v, 1e-3)
 
+    def test_get_QC(self):
+        tr = self.test_trace
+        QC_values = tr.get_onboard_QC_values()
+        self.assertGreater(len(QC_values), 0)
+        df = tr.get_onboard_QC_df()
+
+        self.assertGreater(df.shape[0], 0)
+        self.assertGreater(df.shape[1], 0)
+
     def test_get_traces(self):
         tr = self.test_trace
         v = tr.get_voltage()
         ts = tr.get_times()
+        all_traces = tr.get_all_traces(leakcorrect=True)
         all_traces = tr.get_all_traces()
 
         self.assertTrue(np.all(np.isfinite(v)))
@@ -88,3 +108,21 @@ def test_get_traces(self):
             plt.savefig(os.path.join(self.output_dir,
                                      'example_trace'))
             plt.close(fig)
+
+    def test_qc_df(self):
+        dfs = [self.test_trace.get_onboard_QC_df(sweeps=[0]),
+               self.test_trace.get_onboard_QC_df(sweeps=None)]
+        for res in dfs:
+            # Check res is a pd.DataFrame
+            self.assertIsInstance(res, pd.DataFrame)
+
+            # Check it contains data (number of rows>0)
+            self.assertGreater(res.shape[0], 0)
+
+            # Check it contains all quality control parameters
+            for qcParam in ['Rseal', 'Cm', 'Rseries', 'well', 'sweep']:
+                self.assertIn(qcParam, res)
+
+        # Check restricting number of sweeps returns less data
+        self.assertLess(dfs[0].shape[0], dfs[1].shape[0])
+