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Flake8 improvements
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@hilaryh
hilaryh committed Dec 11, 2024
1 parent e2e4f28 commit 7acc743
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Showing 2 changed files with 22 additions and 16 deletions.
2 changes: 1 addition & 1 deletion pcpostprocess/scripts/run_herg_qc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,7 @@ def main():
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
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])}
export_config.savedir = args.output_dir

Expand Down
36 changes: 21 additions & 15 deletions pcpostprocess/subtraction_plots.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
from syncropatch_export.trace import Trace
from scipy.stats import pearsonr


def setup_subtraction_grid(fig, nsweeps):
# Use 5 x 2 grid when there are 2 sweeps
gs = GridSpec(6, nsweeps, figure=fig)
Expand Down Expand Up @@ -176,7 +177,7 @@ def do_subtraction_plot(fig, times, sweeps, before_currents, after_currents,
long_protocol_ax.set_ylabel(r'$V_\mathrm{cmd}$ (mV)')
long_protocol_ax.tick_params(axis='y', rotation=90)

corr_dict = {'sweeps': sweeps,'pcs': pcs}
corr_dict = {'sweeps': sweeps, 'pcs': pcs}
return corr_dict


Expand All @@ -200,18 +201,19 @@ def linear_reg(V, I_obs):
return b_0, b_1


def regenerate_subtraction_plots(data_path='.', save_dir='.', processed_path=None, protocols_in=None, passed_only=False):
def regenerate_subtraction_plots(data_path='.', save_dir='.', processed_path=None,
protocols_in=None, passed_only=False):
'''
Generate subtraction plots of all sweeps of all experiments in a directory
'''
data_dir = os.listdir(data_path)
passed_wells=None
passed=''
passed_wells = None
passed = ''
if 'passed_wells.txt' in data_dir:
return None
else:
data_dir = [x for x in data_dir if os.path.isdir(os.path.join(data_path,x))]
fig = plt.figure(figsize=[15,24], layout='constrained')
data_dir = [x for x in data_dir if os.path.isdir(os.path.join(data_path, x))]
fig = plt.figure(figsize=[15, 24], layout='constrained')
exp_list = []
protocol_list = []
well_list = []
Expand Down Expand Up @@ -246,14 +248,16 @@ def regenerate_subtraction_plots(data_path='.', save_dir='.', processed_path=Non
time_strs = [[time_strs[0], time_strs[2]],[time_strs[1], time_strs[3]]]
for it, time_str in enumerate(time_strs):
filepath_before = os.path.join(data_path, exp,
f"{prot}_{time_str[0]}")
f"{prot}_{time_str[0]}")
json_file_before = f"{prot}_{time_str[0]}"
before_trace = Trace(filepath_before, json_file_before)
filepath_after = os.path.join(data_path, exp,
f"{prot}_{time_str[1]}")
f"{prot}_{time_str[1]}")
json_file_after = f"{prot}_{time_str[1]}"
after_trace = Trace(filepath_after, json_file_after)
# traces = {z:[x for x in os.listdir(data_path+'/'+exp+'/traces') if x.endswith('.csv') and all([y in x for y in [z+'-','subtracted']])] for z in protocols}
# traces = {z:[x for x in os.listdir(data_path+'/'+exp+'/traces')
# if x.endswith('.csv') and all([y in x for y in [z+'-','subtracted']])]
# for z in protocols}
times = before_trace.get_times()
voltages = before_trace.get_voltage()
voltage_protocol = before_trace.get_voltage_protocol()
Expand All @@ -270,7 +274,7 @@ def regenerate_subtraction_plots(data_path='.', save_dir='.', processed_path=Non
before_current = before_current_all[well]
after_current = after_current_all[well]
sweep_dict = do_subtraction_plot(fig, times, sweeps, before_current, after_current,
voltages, ramp_bounds, well=None, protocol=None)
voltages, ramp_bounds, well=None, protocol=None)
exp_list += [exp]*len(sweep_dict['sweeps'])
protocol_list += [prot]*len(sweep_dict['sweeps'])
well_list += [well]*len(sweep_dict['sweeps'])
Expand All @@ -283,13 +287,15 @@ def regenerate_subtraction_plots(data_path='.', save_dir='.', processed_path=Non
passed = 'failed'
passed_list += [passed]*len(sweep_dict['sweeps'])
# fig.savefig(os.path.join(save_dir,
# f"{exp}-{prot}-{well}-sweep{it}-subtraction-{passed}"))
# f"{exp}-{prot}-{well}-sweep{it}-subtraction-{passed}"))
fig.clf()
if passed_wells:
outdf = pd.DataFrame.from_dict({'exp': exp_list, 'protocol': protocol_list, 'well': well_list, 'sweep': sweep_list, 'pc': corr_list, 'passed': passed_list})
outdf = pd.DataFrame.from_dict({'exp': exp_list, 'protocol': protocol_list,
'well': well_list, 'sweep': sweep_list, 'pc': corr_list, 'passed': passed_list})
else:
outdf = pd.DataFrame.from_dict({'exp': exp_list, 'protocol': protocol_list, 'well': well_list, 'sweep': sweep_list, 'pc': corr_list})
outdf.to_csv(os.path.join(save_dir,'subtraction_results.csv'))
outdf = pd.DataFrame.from_dict({'exp': exp_list, 'protocol': protocol_list,
'well': well_list, 'sweep': sweep_list, 'pc': corr_list})
outdf.to_csv(os.path.join(save_dir, 'subtraction_results.csv'))


def detect_ramp_bounds(times, voltage_sections, ramp_no=0):
Expand All @@ -314,4 +320,4 @@ def detect_ramp_bounds(times, voltage_sections, ramp_no=0):
tstart, tend = ramp[:2]

ramp_bounds = [np.argmax(times > tstart), np.argmax(times > tend)]
return ramp_bounds
return ramp_bounds

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