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MichaelClerxMichaelClerx
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Style fixes
1 parent 4eac863 commit fea8f50

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Lines changed: 39 additions & 55 deletions

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‎pcpostprocess/scripts/run_herg_qc.py‎

Lines changed: 39 additions & 55 deletions
Original file line numberDiff line numberDiff line change
@@ -632,26 +632,20 @@ def extract_protocol(readname, savename, time_strs, selected_wells, args):
632632
row_dict['Cm'] = qc_vals[1]
633633
row_dict['Rseries'] = qc_vals[2]
634634

635-
before_params, before_leak = fit_linear_leak(before_current[sweep, :],
636-
voltages, times,
637-
*ramp_bounds,
638-
output_dir=out_dir,
639-
save_fname=f"{well}_sweep{sweep}.png"
640-
)
635+
before_params, before_leak = fit_linear_leak(
636+
before_current[sweep, :], voltages, times, *ramp_bounds,
637+
output_dir=out_dir, save_fname=f"{well}_sweep{sweep}.png")
641638

642639
before_leak_currents.append(before_leak)
643640

644-
out_dir = os.path.join(savedir,
645-
f"{saveID}-{savename}-leak_fit-after")
641+
out_dir = os.path.join(savedir, f"{saveID}-{savename}-leak_fit-after")
646642
# Convert linear regression parameters into conductance and reversal
647643
row_dict['gleak_before'] = before_params[1]
648644
row_dict['E_leak_before'] = -before_params[0] / before_params[1]
649645

650-
after_params, after_leak = fit_linear_leak(after_current[sweep, :],
651-
voltages, times,
652-
*ramp_bounds,
653-
save_fname=f"{well}_sweep{sweep}.png",
654-
output_dir=out_dir)
646+
after_params, after_leak = fit_linear_leak(
647+
after_current[sweep, :], voltages, times, *ramp_bounds,
648+
save_fname=f"{well}_sweep{sweep}.png", output_dir=out_dir)
655649

656650
after_leak_currents.append(after_leak)
657651

@@ -664,24 +658,20 @@ def extract_protocol(readname, savename, time_strs, selected_wells, args):
664658
after_corrected = after_current[sweep, :] - after_leak
665659
before_corrected = before_current[sweep, :] - before_leak
666660

667-
E_rev_before = infer_reversal_potential(before_corrected, times,
668-
desc, voltages, plot=True,
669-
output_path=os.path.join(reversal_plot_dir,
670-
f"{well}_{savename}_sweep{sweep}_before.png"),
671-
known_Erev=args.Erev)
672-
673-
E_rev_after = infer_reversal_potential(after_corrected, times,
674-
desc, voltages,
675-
plot=True,
676-
output_path=os.path.join(reversal_plot_dir,
677-
f"{well}_{savename}_sweep{sweep}_after.png"),
678-
known_Erev=args.Erev)
679-
680-
E_rev = infer_reversal_potential(subtracted_trace, times, desc,
681-
voltages, plot=True,
682-
output_path=os.path.join(reversal_plot_dir,
683-
f"{well}_{savename}_sweep{sweep}_subtracted.png"),
684-
known_Erev=args.Erev)
661+
E_rev_before = infer_reversal_potential(
662+
before_corrected, times, desc, voltages, plot=True,
663+
output_path=os.path.join(reversal_plot_dir, f"{well}_{savename}_sweep{sweep}_before.png"),
664+
known_Erev=args.Erev)
665+
666+
E_rev_after = infer_reversal_potential(
667+
after_corrected, times, desc, voltages, plot=True,
668+
output_path=os.path.join(reversal_plot_dir, f"{well}_{savename}_sweep{sweep}_after.png"),
669+
known_Erev=args.Erev)
670+
671+
E_rev = infer_reversal_potential(
672+
subtracted_trace, times, desc, voltages, plot=True,
673+
output_path=os.path.join(reversal_plot_dir, f"{well}_{savename}_sweep{sweep}_subtracted.png"),
674+
known_Erev=args.Erev)
685675

686676
row_dict['R_leftover'] =\
687677
np.sqrt(np.sum((after_corrected)**2)/(np.sum(before_corrected**2)))
@@ -736,8 +726,8 @@ def extract_protocol(readname, savename, time_strs, selected_wells, args):
736726
row_dict['QC4'] = all([x for x, _ in qc4])
737727

738728
if args.output_traces:
739-
out_fname = os.path.join(traces_dir,
740-
f"{saveID}-{savename}-{well}-sweep{sweep}-subtracted.csv")
729+
out_fname = os.path.join(
730+
traces_dir, f"{saveID}-{savename}-{well}-sweep{sweep}-subtracted.csv")
741731

742732
np.savetxt(out_fname, subtracted_trace.flatten())
743733
rows.append(row_dict)
@@ -750,13 +740,11 @@ def extract_protocol(readname, savename, time_strs, selected_wells, args):
750740
t_step = times[1] - times[0]
751741
row_dict['total before-drug flux'] = np.sum(current) * (1.0 / t_step)
752742
res = \
753-
get_time_constant_of_first_decay(subtracted_trace, times, desc,
754-
args=args,
755-
output_path=os.path.join(args.output_dir,
756-
'debug',
757-
'-120mV time constant',
758-
f"{savename}-{well}-sweep"
759-
"{sweep}-time-constant-fit.pdf"))
743+
get_time_constant_of_first_decay(
744+
subtracted_trace, times, desc, args=args,
745+
output_path=os.path.join(
746+
args.output_dir, 'debug', '-120mV time constant',
747+
f"{savename}-{well}-sweep{sweep}-time-constant-fit.pdf"))
760748

761749
row_dict['-120mV decay time constant 1'] = res[0][0]
762750
row_dict['-120mV decay time constant 2'] = res[0][1]
@@ -793,8 +781,8 @@ def extract_protocol(readname, savename, time_strs, selected_wells, args):
793781
voltages, ramp_bounds, well=well,
794782
protocol=savename)
795783

796-
fig.savefig(os.path.join(subtraction_plots_dir,
797-
f"{saveID}-{savename}-{well}-sweep{sweep}-subtraction"))
784+
fig.savefig(os.path.join(
785+
subtraction_plots_dir, f"{saveID}-{savename}-{well}-sweep{sweep}-subtraction"))
798786
fig.clf()
799787

800788
plt.close(fig)
@@ -914,19 +902,15 @@ def run_qc_for_protocol(readname, savename, time_strs, args):
914902
before_raw = np.array(raw_before_all[well])[sweep, :]
915903
after_raw = np.array(raw_after_all[well])[sweep, :]
916904

917-
before_params1, before_leak = fit_linear_leak(before_raw,
918-
voltage,
919-
times,
920-
*ramp_bounds,
921-
save_fname=f"{well}-sweep{sweep}-before.png",
922-
output_dir=savedir)
923-
924-
after_params1, after_leak = fit_linear_leak(after_raw,
925-
voltage,
926-
times,
927-
*ramp_bounds,
928-
save_fname=f"{well}-sweep{sweep}-after.png",
929-
output_dir=savedir)
905+
before_params1, before_leak = fit_linear_leak(
906+
before_raw, voltage, times, *ramp_bounds,
907+
save_fname=f"{well}-sweep{sweep}-before.png",
908+
output_dir=savedir)
909+
910+
after_params1, after_leak = fit_linear_leak(
911+
after_raw, voltage, times, *ramp_bounds,
912+
save_fname=f"{well}-sweep{sweep}-after.png",
913+
output_dir=savedir)
930914

931915
before_currents_corrected[sweep, :] = before_raw - before_leak
932916
after_currents_corrected[sweep, :] = after_raw - after_leak

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