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Hilary dev #53

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cdbc4ed
Update to subtraction_plots.py layout and function to generate separa…
hilaryh Dec 11, 2024
7b86e2e
Update run_herg_qc.py
hilaryh Dec 11, 2024
e2e4f28
Flake8 improvements
hilaryh Dec 11, 2024
7acc743
Flake8 improvements
hilaryh Dec 11, 2024
4ebde11
Flake8 improvements
hilaryh Dec 11, 2024
47e50e5
Flake8 improvements
hilaryh Dec 11, 2024
bc4c941
Flake8 improvements
hilaryh Dec 11, 2024
8b0b1b4
Flake8 improvements
hilaryh Dec 11, 2024
a2f11a7
Fixed bug that resulted in an error when there weren't two copies of …
hilaryh Jan 8, 2025
aea86c4
Fixed bug that resulted in an error when there weren't two copies of …
hilaryh Jan 8, 2025
312aefd
Added bash script to copy export_config.py into experiment data direc…
hilaryh Jan 14, 2025
4eac863
Merge branch 'main' into hilary_dev
MichaelClerx Jun 24, 2025
fea8f50
Style fixes
MichaelClerx Jun 24, 2025
d52f773
Updated formatting
MichaelClerx Jun 24, 2025
3b10476
Removed superfluous xticks, moved all legends outside of plot area, a…
hilaryh Jun 25, 2025
5314cb1
Fixed style issue
MichaelClerx Jun 25, 2025
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11 changes: 11 additions & 0 deletions copy_export_config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
#!/bin/bash

# If this is in a directory with a directory called "original_data" containing your data and an example export_config.py file called "export_config.py", it will copy export_config.py into each directory in original_data and change the EXPERIMENT_NAME to match the name of the directory.

for dir in original_data/*/
do
cp export_config.py $dir
dirname=${dir%*/}
strrep="s/EXPERIMENT_NAME/${dir#*/}"
sed -i $strrep "${dir}${exportfile}"
done
145 changes: 57 additions & 88 deletions pcpostprocess/scripts/run_herg_qc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -107,6 +107,9 @@ def main():
sys.modules['export_config'] = export_config
spec.loader.exec_module(export_config)

data_list = os.listdir(args.data_directory)
export_config.D2S_QC = {x: y for x, y in export_config.D2S_QC.items() if
any([x == '_'.join(z.split('_')[:-1]) for z in data_list])}
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@joeyshuttleworth joeyshuttleworth Jun 24, 2025

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I think this should work fine. But this could throw an error if the files aren't set out properly. Maybe we should just check that there is at least one "_" in all of these files. I think it's mostly safe to assume that the data folders will be formatted correctly, but there's nothing stopping someone from dragging any other sort of file in there!

export_config.savedir = args.output_dir

args.saveID = export_config.saveID
Expand Down Expand Up @@ -257,13 +260,13 @@ def main():
times = sorted(res_dict[protocol])
savename = combined_dict[protocol]

readnames.append(protocol)

if len(times) == 2:
readnames.append(protocol)
savenames.append(savename)
times_list.append(times)

elif len(times) == 4:
readnames.append(protocol)
savenames.append(savename)
times_list.append(times[::2])

Expand All @@ -277,6 +280,7 @@ def main():
wells_to_export = wells if args.export_failed else overall_selection

logging.info(f"exporting wells {wells}")
logging.info(f"overall selection {overall_selection}")

no_protocols = len(res_dict)

Expand Down Expand Up @@ -628,26 +632,20 @@ def extract_protocol(readname, savename, time_strs, selected_wells, args):
row_dict['Cm'] = qc_vals[1]
row_dict['Rseries'] = qc_vals[2]

before_params, before_leak = fit_linear_leak(before_current[sweep, :],
voltages, times,
*ramp_bounds,
output_dir=out_dir,
save_fname=f"{well}_sweep{sweep}.png"
)
before_params, before_leak = fit_linear_leak(
before_current[sweep, :], voltages, times, *ramp_bounds,
output_dir=out_dir, save_fname=f"{well}_sweep{sweep}.png")

before_leak_currents.append(before_leak)

out_dir = os.path.join(savedir,
f"{saveID}-{savename}-leak_fit-after")
out_dir = os.path.join(savedir, f"{saveID}-{savename}-leak_fit-after")
# Convert linear regression parameters into conductance and reversal
row_dict['gleak_before'] = before_params[1]
row_dict['E_leak_before'] = -before_params[0] / before_params[1]

after_params, after_leak = fit_linear_leak(after_current[sweep, :],
voltages, times,
*ramp_bounds,
save_fname=f"{well}_sweep{sweep}.png",
output_dir=out_dir)
after_params, after_leak = fit_linear_leak(
after_current[sweep, :], voltages, times, *ramp_bounds,
save_fname=f"{well}_sweep{sweep}.png", output_dir=out_dir)

after_leak_currents.append(after_leak)

Expand All @@ -660,24 +658,20 @@ def extract_protocol(readname, savename, time_strs, selected_wells, args):
after_corrected = after_current[sweep, :] - after_leak
before_corrected = before_current[sweep, :] - before_leak

E_rev_before = infer_reversal_potential(before_corrected, times,
desc, voltages, plot=True,
output_path=os.path.join(reversal_plot_dir,
f"{well}_{savename}_sweep{sweep}_before"),
known_Erev=args.Erev)

E_rev_after = infer_reversal_potential(after_corrected, times,
desc, voltages,
plot=True,
output_path=os.path.join(reversal_plot_dir,
f"{well}_{savename}_sweep{sweep}_after"),
known_Erev=args.Erev)

E_rev = infer_reversal_potential(subtracted_trace, times, desc,
voltages, plot=True,
output_path=os.path.join(reversal_plot_dir,
f"{well}_{savename}_sweep{sweep}_subtracted"),
known_Erev=args.Erev)
E_rev_before = infer_reversal_potential(
before_corrected, times, desc, voltages, plot=True,
output_path=os.path.join(reversal_plot_dir, f"{well}_{savename}_sweep{sweep}_before.png"),
known_Erev=args.Erev)

E_rev_after = infer_reversal_potential(
after_corrected, times, desc, voltages, plot=True,
output_path=os.path.join(reversal_plot_dir, f"{well}_{savename}_sweep{sweep}_after.png"),
known_Erev=args.Erev)

E_rev = infer_reversal_potential(
subtracted_trace, times, desc, voltages, plot=True,
output_path=os.path.join(reversal_plot_dir, f"{well}_{savename}_sweep{sweep}_subtracted.png"),
known_Erev=args.Erev)

row_dict['R_leftover'] =\
np.sqrt(np.sum((after_corrected)**2)/(np.sum(before_corrected**2)))
Expand Down Expand Up @@ -732,8 +726,8 @@ def extract_protocol(readname, savename, time_strs, selected_wells, args):
row_dict['QC4'] = all([x for x, _ in qc4])

if args.output_traces:
out_fname = os.path.join(traces_dir,
f"{saveID}-{savename}-{well}-sweep{sweep}-subtracted.csv")
out_fname = os.path.join(
traces_dir, f"{saveID}-{savename}-{well}-sweep{sweep}-subtracted.csv")

np.savetxt(out_fname, subtracted_trace.flatten())
rows.append(row_dict)
Expand All @@ -746,13 +740,11 @@ def extract_protocol(readname, savename, time_strs, selected_wells, args):
t_step = times[1] - times[0]
row_dict['total before-drug flux'] = np.sum(current) * (1.0 / t_step)
res = \
get_time_constant_of_first_decay(subtracted_trace, times, desc,
args=args,
output_path=os.path.join(args.output_dir,
'debug',
'-120mV time constant',
f"{savename}-{well}-sweep"
"{sweep}-time-constant-fit.pdf"))
get_time_constant_of_first_decay(
subtracted_trace, times, desc, args=args,
output_path=os.path.join(
args.output_dir, 'debug', '-120mV time constant',
f"{savename}-{well}-sweep{sweep}-time-constant-fit.pdf"))

row_dict['-120mV decay time constant 1'] = res[0][0]
row_dict['-120mV decay time constant 2'] = res[0][1]
Expand Down Expand Up @@ -789,8 +781,8 @@ def extract_protocol(readname, savename, time_strs, selected_wells, args):
voltages, ramp_bounds, well=well,
protocol=savename)

fig.savefig(os.path.join(subtraction_plots_dir,
f"{saveID}-{savename}-{well}-sweep{sweep}-subtraction"))
fig.savefig(os.path.join(
subtraction_plots_dir, f"{saveID}-{savename}-{well}-sweep{sweep}-subtraction"))
fig.clf()

plt.close(fig)
Expand Down Expand Up @@ -910,19 +902,15 @@ def run_qc_for_protocol(readname, savename, time_strs, args):
before_raw = np.array(raw_before_all[well])[sweep, :]
after_raw = np.array(raw_after_all[well])[sweep, :]

before_params1, before_leak = fit_linear_leak(before_raw,
voltage,
times,
*ramp_bounds,
save_fname=f"{well}-sweep{sweep}-before.png",
output_dir=savedir)
before_params1, before_leak = fit_linear_leak(
before_raw, voltage, times, *ramp_bounds,
save_fname=f"{well}-sweep{sweep}-before.png",
output_dir=savedir)

after_params1, after_leak = fit_linear_leak(after_raw,
voltage,
times,
*ramp_bounds,
save_fname=f"{well}-sweep{sweep}-after.png",
output_dir=savedir)
after_params1, after_leak = fit_linear_leak(
after_raw, voltage, times, *ramp_bounds,
save_fname=f"{well}-sweep{sweep}-after.png",
output_dir=savedir)

before_currents_corrected[sweep, :] = before_raw - before_leak
after_currents_corrected[sweep, :] = after_raw - after_leak
Expand Down Expand Up @@ -1062,26 +1050,15 @@ def qc3_bookend(readname, savename, time_strs, args):
save_fname = f"{well}_{savename}_before0.pdf"

#  Plot subtraction
get_leak_corrected(first_before_current,
voltage, times,
*ramp_bounds,
save_fname=save_fname,
output_dir=output_directory)

before_traces_first[well] = get_leak_corrected(first_before_current,
voltage, times,
*ramp_bounds)

before_traces_last[well] = get_leak_corrected(last_before_current,
voltage, times,
*ramp_bounds)

after_traces_first[well] = get_leak_corrected(first_after_current,
voltage, times,
*ramp_bounds)
after_traces_last[well] = get_leak_corrected(last_after_current,
voltage, times,
*ramp_bounds)
before_traces_first[well] = get_leak_corrected(
first_before_current, voltage, times, *ramp_bounds,
save_fname=save_fname, output_dir=output_directory)
before_traces_last[well] = get_leak_corrected(
last_before_current, voltage, times, *ramp_bounds)
after_traces_first[well] = get_leak_corrected(
first_after_current, voltage, times, *ramp_bounds)
after_traces_last[well] = get_leak_corrected(
last_after_current, voltage, times, *ramp_bounds)

# Store subtracted traces
first_processed[well] = before_traces_first[well] - after_traces_first[well]
Expand All @@ -1104,21 +1081,13 @@ def qc3_bookend(readname, savename, time_strs, args):
ax = fig.subplots()
for well in args.wells:
trace1 = hergqc.filter_capacitive_spikes(
first_processed[well], times, voltage_steps
).flatten()

first_processed[well], times, voltage_steps).flatten()
trace2 = hergqc.filter_capacitive_spikes(
last_processed[well], times, voltage_steps
).flatten()

last_processed[well], times, voltage_steps).flatten()
passed = hergqc.qc3(trace1, trace2)[0]

res_dict[well] = passed

save_fname = os.path.join(args.output_dir,
'debug',
f"debug_{well}_{savename}",
'qc3_bookend')
save_fname = os.path.join(
args.output_dir, 'debug', f"debug_{well}_{savename}", 'qc3_bookend')

ax.plot(times, trace1)
ax.plot(times, trace2)
Expand Down
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