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Run QC1 and QC4 on multiple sweeps #108

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63e1350
Run QC1 and QC4 on multiple sweeps
Nov 4, 2025
766b83a
Run QC1 & QC4 on mu,tiple sweeps
Nov 4, 2025
7f9b23b
Use correct protocol names (D2SQC.values)
Nov 4, 2025
0e78290
Add extra logging message
Nov 4, 2025
c1ba157
Update test case
Nov 4, 2025
9125cc3
Fix whitespace, logging
Nov 4, 2025
6c43022
Update test cases
Nov 4, 2025
3015405
Merge branch 'main' into js_multiple_qc1_4
MichaelClerx Nov 11, 2025
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34 changes: 25 additions & 9 deletions pcpostprocess/hergQC.py
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Original file line number Diff line number Diff line change
Expand Up @@ -172,8 +172,19 @@ def run_qc(self, voltage_steps, times,
if (None in qc_vals_before) or (None in qc_vals_after):
return QC

qc1_1 = self.qc1(*qc_vals_before)
qc1_2 = self.qc1(*qc_vals_after)
qc1_1 = True
for i in range(n_sweeps):
_qc1_1 = self.qc1(*qc_vals_before[i, :])
qc1_1 = qc1_1 and _qc1_1
if not qc1_1:
break

qc1_2 = True
for i in range(n_sweeps):
_qc1_2 = self.qc1(*qc_vals_after[i, :])
if not qc1_2:
break
qc1_2 = qc1_2 and _qc1_2

QC['qc1.rseal'] = [qc1_1[0], qc1_2[0]]
QC['qc1.cm'] = [qc1_1[1], qc1_2[1]]
Expand All @@ -197,14 +208,19 @@ def run_qc(self, voltage_steps, times,
QC['qc3.E4031'] = [qc3_2]
QC['qc3.subtracted'] = [qc3_3]

rseals = [qc_vals_before[0], qc_vals_after[0]]
cms = [qc_vals_before[1], qc_vals_after[1]]
rseriess = [qc_vals_before[2], qc_vals_after[2]]
qc4 = self.qc4(rseals, cms, rseriess)
qc4 = []
for i in range(n_sweeps):
rseals = [qc_vals_before[i, 0], qc_vals_after[i, 0]]
cms = [qc_vals_before[i, 1], qc_vals_after[i, 1]]
rseriess = [qc_vals_before[i, 2], qc_vals_after[i, 2]]
qc4.append(self.qc4(rseals, cms, rseriess))

# Combine sweepwise QC4 results
qc4 = np.array(qc4)

QC['qc4.rseal'] = [qc4[0]]
QC['qc4.cm'] = [qc4[1]]
QC['qc4.rseries'] = [qc4[2]]
QC['qc4.rseal'] = [(bool(row[0]), row[1]) for row in qc4[:, 0, :]]
QC['qc4.cm'] = [(bool(row[0]), row[1]) for row in qc4[:, 1, :]]
QC['qc4.rseries'] = [(bool(row[0]), row[1]) for row in qc4[:, 2, :]]

# indices where hERG peaks
qc5 = self.qc5(before[0, :], after[0, :],
Expand Down
15 changes: 8 additions & 7 deletions pcpostprocess/scripts/run_herg_qc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,7 @@ def main():

# this error is raised if the user has not specified the dictionary of protocols in the export_config.py file
if not readnames:
logging.error("No compatible protocols found in export config file.")
logging.error("No compatible protocols found in export config file")
return

with multiprocessing.Pool(min(args.no_cpus, len(readnames)),
Expand Down Expand Up @@ -266,7 +266,8 @@ def main():

wells_to_export = wells if args.export_failed else overall_selection

logging.info(f"exporting wells {wells}")
logging.info(f"Wells passing QC so far: {overall_selection}")
logging.info(f"exporting wells {wells_to_export}")

no_protocols = len(res_dict)

Expand All @@ -281,6 +282,7 @@ def main():

if dfs:
extract_df = pd.concat(dfs, ignore_index=True)

extract_df['selected'] = extract_df['well'].isin(overall_selection)
else:
logging.error("Didn't export any data")
Expand Down Expand Up @@ -424,8 +426,6 @@ def agg_func(x):
qc_df['protocol'] = ['staircaseramp1_2' if p == 'staircaseramp2' else p
for p in qc_df.protocol]

print(qc_df.protocol.unique())

fails_dict = {}
no_wells = 384

Expand Down Expand Up @@ -855,6 +855,8 @@ def run_qc_for_protocol(readname, savename, time_strs, args, output_dir):
raw_before_all = before_trace.get_trace_sweeps(sweeps)
raw_after_all = after_trace.get_trace_sweeps(sweeps)

logging.info(f"sampling_rate is {sampling_rate}")

selected_wells = []
for well in args.wells:

Expand Down Expand Up @@ -929,7 +931,6 @@ def run_qc_for_protocol(readname, savename, time_strs, args, output_dir):
after_currents[sweep, :] = after_raw

logging.info(f"{well} {savename}\n----------")
logging.info(f"sampling_rate is {sampling_rate}")

voltage_steps = [tend
for tstart, tend, vstart, vend in
Expand All @@ -941,8 +942,8 @@ def run_qc_for_protocol(readname, savename, time_strs, args, output_dir):
times,
before_currents_corrected,
after_currents_corrected,
np.array(qc_before[well])[0, :],
np.array(qc_after[well])[0, :],
np.array(qc_before[well]),
np.array(qc_after[well]),
nsweeps,
)

Expand Down
68 changes: 34 additions & 34 deletions tests/test_herg_qc.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -891,46 +891,46 @@ def test_run_qc(self):
hergqc = self.clone_hergqc("test_run_qc")

failed_wells = [
'A04', 'A05', 'A06', 'A07', 'A08', 'A10', 'A11', 'A12', 'A13', 'A15',
'A16', 'A19', 'A20', 'A21', 'A22', 'A23', 'A24', 'B02', 'B04', 'B05',
'B07', 'B09', 'B10', 'B11', 'B12', 'B13', 'B14', 'B15', 'B16', 'B18',
'B19', 'B21', 'B23', 'C01', 'C02', 'C04', 'C05', 'C07', 'C08', 'C09',
'C10', 'C11', 'C12', 'C14', 'C17', 'C18', 'C19', 'C20', 'C21', 'C22',
'C23', 'C24', 'D01', 'D02', 'D03', 'D04', 'D05', 'D09', 'D10', 'D11',
'D12', 'D13', 'D14', 'D15', 'D16', 'D17', 'D18', 'D19', 'D21', 'D23',
'E01', 'E02', 'E03', 'E04', 'E06', 'E07', 'E09', 'E10', 'E11', 'E13',
'E14', 'E15', 'E16', 'E17', 'E18', 'E19', 'E20', 'E21', 'E22', 'E23',
'E24', 'F01', 'F02', 'F03', 'F04', 'F05', 'F06', 'F07', 'F09', 'F10',
'F11', 'F12', 'F13', 'F14', 'F15', 'F16', 'F18', 'F19', 'F20', 'F21',
'F22', 'F23', 'F24', 'G03', 'G06', 'G08', 'G09', 'G10', 'G12', 'G13',
'G14', 'G15', 'G16', 'G17', 'G18', 'G19', 'G20', 'G21', 'G23', 'G24',
'H01', 'H02', 'H03', 'H04', 'H06', 'H07', 'H08', 'H09', 'H10', 'H11',
'H13', 'H14', 'H15', 'H16', 'H17', 'H18', 'H19', 'H20', 'H21', 'H23',
'H24', 'I01', 'I03', 'I04', 'I05', 'I06', 'I07', 'I08', 'I10', 'I11',
'I12', 'I13', 'I14', 'I15', 'I16', 'I17', 'I18', 'I19', 'I20', 'I21',
'J03', 'J06', 'J07', 'J08', 'J09', 'J10', 'J11', 'J12', 'J14', 'J15',
'J16', 'J17', 'J18', 'J19', 'J20', 'J21', 'J23', 'J24', 'K01', 'K02',
'K03', 'K05', 'K06', 'K07', 'K09', 'K10', 'K11', 'K12', 'K13', 'K14',
'K16', 'K17', 'K18', 'K20', 'K22', 'K23', 'K24', 'L01', 'L02', 'L03',
'L04', 'L05', 'L06', 'L07', 'L08', 'L10', 'L11', 'L12', 'L13', 'L16',
'L17', 'L18', 'L20', 'L21', 'L23', 'L24', 'M01', 'M02', 'M03', 'M04',
'M05', 'M06', 'M07', 'M08', 'M09', 'M10', 'M11', 'M12', 'M13', 'M14',
'M15', 'M16', 'M17', 'M18', 'M19', 'M20', 'M21', 'N01', 'N02', 'N03',
'N04', 'N06', 'N07', 'N08', 'N09', 'N11', 'N13', 'N14', 'N16', 'N17',
'N18', 'N19', 'N20', 'N21', 'N22', 'N23', 'N24', 'O01', 'O02', 'O03',
'O04', 'O05', 'O06', 'O07', 'O08', 'O10', 'O11', 'O12', 'O13', 'O14',
'O15', 'O16', 'O17', 'O18', 'O19', 'O20', 'O21', 'O22', 'O24', 'P01',
'P03', 'P05', 'P06', 'P07', 'P08', 'P09', 'P10', 'P11', 'P12', 'P13',
'P14', 'P15', 'P16', 'P17', 'P18', 'P19', 'P20', 'P21', 'P22', 'P24'
'A01', 'A04', 'A05', 'A06', 'A07', 'A08', 'A10', 'A11', 'A12', 'A13',
'A15', 'A16', 'A19', 'A20', 'A21', 'A22', 'A23', 'A24', 'B01', 'B02',
'B04', 'B05', 'B06', 'B07', 'B09', 'B10', 'B11', 'B12', 'B13', 'B14',
'B15', 'B16', 'B18', 'B19', 'B21', 'B22', 'B23', 'C01', 'C02', 'C04',
'C05', 'C07', 'C08', 'C09', 'C10', 'C11', 'C12', 'C14', 'C15', 'C17',
'C18', 'C19', 'C20', 'C21', 'C22', 'C23', 'C24', 'D01', 'D02', 'D03',
'D04', 'D05', 'D08', 'D09', 'D10', 'D11', 'D12', 'D13', 'D14', 'D15',
'D16', 'D17', 'D18', 'D19', 'D21', 'D23', 'E01', 'E02', 'E03', 'E04',
'E06', 'E07', 'E09', 'E10', 'E11', 'E12', 'E13', 'E14', 'E15', 'E16',
'E17', 'E18', 'E19', 'E20', 'E21', 'E22', 'E23', 'E24', 'F01', 'F02',
'F03', 'F04', 'F05', 'F06', 'F07', 'F08', 'F09', 'F10', 'F11', 'F12',
'F13', 'F14', 'F15', 'F16', 'F18', 'F19', 'F20', 'F21', 'F22', 'F23',
'F24', 'G03', 'G06', 'G08', 'G09', 'G10', 'G12', 'G13', 'G14', 'G15',
'G16', 'G17', 'G18', 'G19', 'G20', 'G21', 'G23', 'G24', 'H01', 'H02',
'H03', 'H04', 'H06', 'H07', 'H08', 'H09', 'H10', 'H11', 'H13', 'H14',
'H15', 'H16', 'H17', 'H18', 'H19', 'H20', 'H21', 'H23', 'H24', 'I01',
'I03', 'I04', 'I05', 'I06', 'I07', 'I08', 'I10', 'I11', 'I12', 'I13',
'I14', 'I15', 'I16', 'I17', 'I18', 'I19', 'I20', 'I21', 'I24', 'J03',
'J06', 'J07', 'J08', 'J09', 'J10', 'J11', 'J12', 'J14', 'J15', 'J16',
'J17', 'J18', 'J19', 'J20', 'J21', 'J23', 'J24', 'K01', 'K02', 'K03',
'K05', 'K06', 'K07', 'K09', 'K10', 'K11', 'K12', 'K13', 'K14', 'K16',
'K17', 'K18', 'K20', 'K22', 'K23', 'K24', 'L01', 'L02', 'L03', 'L04',
'L05', 'L06', 'L07', 'L08', 'L10', 'L11', 'L12', 'L13', 'L16', 'L17',
'L18', 'L20', 'L21', 'L23', 'L24', 'M01', 'M02', 'M03', 'M04', 'M05',
'M06', 'M07', 'M08', 'M09', 'M10', 'M11', 'M12', 'M13', 'M14', 'M15',
'M16', 'M17', 'M18', 'M19', 'M20', 'M21', 'N01', 'N02', 'N03', 'N04',
'N06', 'N07', 'N08', 'N09', 'N11', 'N13', 'N14', 'N16', 'N17', 'N18',
'N19', 'N20', 'N21', 'N22', 'N23', 'N24', 'O01', 'O02', 'O03', 'O04',
'O05', 'O06', 'O07', 'O08', 'O10', 'O11', 'O12', 'O13', 'O14', 'O15',
'O16', 'O17', 'O18', 'O19', 'O20', 'O21', 'O22', 'O24', 'P01', 'P03',
'P05', 'P06', 'P07', 'P08', 'P09', 'P10', 'P11', 'P12', 'P13', 'P14',
'P15', 'P16', 'P17', 'P18', 'P19', 'P20', 'P21', 'P22', 'P24'
]

for well in self.all_wells:
before = np.array(self.trace_sweeps_before[well])
after = np.array(self.trace_sweeps_after[well])

# Take values from the first sweep only
qc_vals_before = np.array(self.qc_vals_before[well])[0, :]
qc_vals_after = np.array(self.qc_vals_after[well])[0, :]
qc_vals_before = np.array(self.qc_vals_before[well])
qc_vals_after = np.array(self.qc_vals_after[well])

QC = hergqc.run_qc(
voltage_steps=self.voltage_steps,
Expand Down